Richard Durbin, FRS

Al Kindi Professor of Genetics, Department of Genetics

Richard Durbin's research interests include genetic variation, evolutionary and population genetics in humans and cichlid fishes, and algorithms and software for high-throughput sequencing and genome assembly. Learn more.

Research Areas

Genome sequences

Evolution

Cichlids

Ancient DNA

Techniques

Whole genome sequencing

High-throughput sequencing

Bioinformatics

Computational and population genetics

Research Theme

Publications

Journal articles

2022

Wang, Y., Pedersen, MW., Alsos, IG., De Sanctis, B., Racimo, F., Prohaska, A., Coissac, E., Owens, HL., Merkel, MKF., Fernandez-Guerra, A., Rouillard, A., Lammers, Y., Alberti, A., Denoeud, F., Money, D., Ruter, AH., McColl, H., Larsen, NK., Cherezova, AA., Edwards, ME., Fedorov, GB., Haile, J., Orlando, L., Vinner, L., Korneliussen, TS., Beilman, DW., Bjørk, AA., Cao, J., Dockter, C., Esdale, J., Gusarova, G., Kjeldsen, KK., Mangerud, J., Rasic, JT., Skadhauge, B., Svendsen, JI., Tikhonov, A., Wincker, P., Xing, Y., Zhang, Y., Froese, DG., Rahbek, C., Bravo, DN., Holden, PB., Edwards, NR., Durbin, R., Meltzer, DJ., Kjær, KH., Möller, P. and Willerslev, E., 2022. Author Correction: Late Quaternary dynamics of Arctic biota from ancient environmental genomics. Nature, v. 603
Doi: 10.1038/s41586-022-04628-x

Carruthers, M., Edgley, D., Saxon, A., Gabagambi, N., Shechonge, A., Miska, E., Durbin, R., Bridle, J., Turner, G. and Genner, M., 2022. Ecological speciation promoted by divergent regulation of functional genes within African cichlid fishes
Doi: 10.1101/2022.01.07.475335

Hawe, JS., Wilson, R., Schmid, KT., Zhou, L., Lakshmanan, LN., Lehne, BC., Kühnel, B., Scott, WR., Wielscher, M., Yew, YW., Baumbach, C., Lee, DP., Marouli, E., Bernard, M., Pfeiffer, L., Matías-García, PR., Autio, MI., Bourgeois, S., Herder, C., Karhunen, V., Meitinger, T., Prokisch, H., Rathmann, W., Roden, M., Sebert, S., Shin, J., Strauch, K., Zhang, W., Tan, WLW., Hauck, SM., Merl-Pham, J., Grallert, H., Barbosa, EGV., MuTHER Consortium, , Illig, T., Peters, A., Paus, T., Pausova, Z., Deloukas, P., Foo, RSY., Jarvelin, M-R., Kooner, JS., Loh, M., Heinig, M., Gieger, C., Waldenberger, M. and Chambers, JC., 2022. Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function. Nat Genet, v. 54
Doi: http://doi.org/10.1038/s41588-021-00969-x

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, AV., Mikheenko, A., Vollger, MR., Altemose, N., Uralsky, L., Gershman, A., Aganezov, S., Hoyt, SJ., Diekhans, M., Logsdon, GA., Alonge, M., Antonarakis, SE., Borchers, M., Bouffard, GG., Brooks, SY., Caldas, GV., Chen, N-C., Cheng, H., Chin, C-S., Chow, W., de Lima, LG., Dishuck, PC., Durbin, R., Dvorkina, T., Fiddes, IT., Formenti, G., Fulton, RS., Fungtammasan, A., Garrison, E., Grady, PGS., Graves-Lindsay, TA., Hall, IM., Hansen, NF., Hartley, GA., Haukness, M., Howe, K., Hunkapiller, MW., Jain, C., Jain, M., Jarvis, ED., Kerpedjiev, P., Kirsche, M., Kolmogorov, M., Korlach, J., Kremitzki, M., Li, H., Maduro, VV., Marschall, T., McCartney, AM., McDaniel, J., Miller, DE., Mullikin, JC., Myers, EW., Olson, ND., Paten, B., Peluso, P., Pevzner, PA., Porubsky, D., Potapova, T., Rogaev, EI., Rosenfeld, JA., Salzberg, SL., Schneider, VA., Sedlazeck, FJ., Shafin, K., Shew, CJ., Shumate, A., Sims, Y., Smit, AFA., Soto, DC., Sović, I., Storer, JM., Streets, A., Sullivan, BA., Thibaud-Nissen, F., Torrance, J., Wagner, J., Walenz, BP., Wenger, A., Wood, JMD., Xiao, C., Yan, SM., Young, AC., Zarate, S., Surti, U., McCoy, RC., Dennis, MY., Alexandrov, IA., Gerton, JL., O'Neill, RJ., Timp, W., Zook, JM., Schatz, MC., Eichler, EE., Miga, KH. and Phillippy, AM., 2022. The complete sequence of a human genome. Science, v. 376
Doi: http://doi.org/10.1126/science.abj6987

De Sanctis, B., Money, D., Pedersen, MW. and Durbin, R., 2022. A theoretical analysis of taxonomic binning accuracy. Mol Ecol Resour, v. 22
Doi: 10.1111/1755-0998.13608

Lawniczak, M., Durbin, R., Flicek, P., Lindlad-Toh, K., Wei, X., Archibald, J., Baker, W., Belov, K., Blaxter, M., Marques Bonet, T., Childers, A., Coddington, J., Crandall, K., Crarwford, A., Davey, R., Di Palma, F., Fang, Q., Haerty, W., Hall, N., Hoff, K., Howe, K., Jarvis, E., Johnson, W., Johnson, R., Kersey, P., Liu, X., Lopez, JV., Myers, E., Pettersson, O., Phillippy, A., Poelchau, M., Pruitt, K., Rhie, A., Castilla Rubio, JC., Kumar Sahu, S., Salmon, N., Solitis, P., Swarbreck, D., Thibaud-Nissen, F., Wang, S., Wegrzyn, J., Zhang, G., Zhang, H., Lewin, H. and Richards, S., 2022. Standards Recommendations for the Earth BioGenome Project Proceedings of the National Academy of Sciences of USA, v. 119
Doi: 10.1073/pnas.2115639118

Lewin, HA., Richards, S., Lieberman Aiden, E., Allende, ML., Archibald, JM., Bálint, M., Barker, KB., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, ML., Cai, J., Caperello, ND., Carlson, K., Castilla-Rubio, JC., Chaw, S-M., Chen, L., Childers, AK., Coddington, JA., Conde, DA., Corominas, M., Crandall, KA., Crawford, AJ., DiPalma, F., Durbin, R., Ebenezer, TE., Edwards, SV., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, RA., Gilbert, MTP., Goldstein, MM., Graves, JM., Greely, HT., Grigoriev, IV., Hackett, KJ., Hall, N., Haussler, D., Helgen, KM., Hogg, CJ., Isobe, S., Jakobsen, KS., Janke, A., Jarvis, ED., Johnson, WE., Jones, SJM., Karlsson, EK., Kersey, PJ., Kim, J-H., Kress, WJ., Kuraku, S., Lawniczak, MKN., Leebens-Mack, JH., Li, X., Lindblad-Toh, K., Liu, X., Lopez, JV., Marques-Bonet, T., Mazard, S., Mazet, JAK., Mazzoni, CJ., Myers, EW., O'Neill, RJ., Paez, S., Park, H., Robinson, GE., Roquet, C., Ryder, OA., Sabir, JSM., Shaffer, HB., Shank, TM., Sherkow, JS., Soltis, PS., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, JL., Xu, X., Yang, H., Yoder, AD. and Zhang, G., 2022. The Earth BioGenome Project 2020: Starting the clock. Proc Natl Acad Sci U S A, v. 119
Doi: http://doi.org/10.1073/pnas.2115635118

Blaxter, M., Archibald, JM., Childers, AK., Coddington, JA., Crandall, KA., Di Palma, F., Durbin, R., Edwards, SV., Graves, JAM., Hackett, KJ., Hall, N., Jarvis, ED., Johnson, RN., Karlsson, EK., Kress, WJ., Kuraku, S., Lawniczak, MKN., Lindblad-Toh, K., Lopez, JV., Moran, NA., Robinson, GE., Ryder, OA., Shapiro, B., Soltis, PS., Warnow, T., Zhang, G. and Lewin, HA., 2022. Why sequence all eukaryotes? Proc Natl Acad Sci U S A, v. 119
Doi: http://doi.org/10.1073/pnas.2115636118

Sherkow, JS., Barker, KB., Braverman, I., Cook-Deegan, R., Durbin, R., Easter, CL., Goldstein, MM., Hudson, M., Kress, WJ., Lewin, HA., Mathews, DJH., McCarthy, C., McCartney, AM., da Silva, M., Torrance, AW. and Greely, HT., 2022. Ethical, legal, and social issues in the Earth BioGenome Project. Proc Natl Acad Sci U S A, v. 119
Doi: http://doi.org/10.1073/pnas.2115859119

Martiniano, R., De Sanctis, B., Hallast, P. and Durbin, R., 2022. Placing ancient DNA sequences into reference phylogenies. Molecular Biology and Evolution,
Doi: http://doi.org/10.1093/molbev/msac017

2021

Durbin, R., 2021. Towards complete and error-free genome assemblies of all vertebrate species Nature,
Doi: http://doi.org/10.1038/s41586-021-03451-0

Generalovic, T., McCarthy, S., Warren, I., Wood, J., Torrance, J., Sims, Y., Quail, M., Howe, K., Pipan, M., Durbin, R. and Jiggins, C., 2021. A high-quality, chromosome-level genome assembly of the Black Soldier Fly (Hermetia illucens L.) G3: Genes, Genomes, Genetics,

Pedersen, MW., De Sanctis, B., Saremi, NF., Sikora, M., Puckett, EE., Gu, Z., Moon, KL., Kapp, JD., Vinner, L., Vardanyan, Z., Ardelean, CF., Arroyo-Cabrales, J., Cahill, JA., Heintzman, PD., Zazula, G., MacPhee, RDE., Shapiro, B., Durbin, R. and Willerslev, E., 2021. Environmental genomics of Late Pleistocene black bears and giant short-faced bears. Curr Biol, v. 31
Doi: 10.1016/j.cub.2021.04.027

Hansen, T., Fjelldal, PG., Lien, S., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Doulcan, J., Fedrigo, O., Mountcastle, J., Jarvis, E., McCarthy, SA., Chow, W., Howe, K., Torrance, J., Wood, J., Sims, Y., Haggerty, L., Challis, R., Threlfall, J., Mead, D., Durbin, R. and Blaxter, M., 2021. The genome sequence of the brown trout, Salmo trutta Linnaeus 1758. Wellcome Open Res, v. 6
Doi: http://doi.org/10.12688/wellcomeopenres.16838.1

Mead, D., Ogden, R., Meredith, A., Peniche, G., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Doulcan, J., Holmes, N., Wright, V., Loose, M., Quail, MA., McCarthy, SA., Howe, K., Chow, W., Torrance, J., Collins, J., Challis, R., Durbin, R. and Blaxter, M., 2021. The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758. Wellcome Open Res, v. 6
Doi: http://doi.org/10.12688/wellcomeopenres.16631.1

Formenti, G., Rhie, A., Balacco, J., Haase, B., Mountcastle, J., Fedrigo, O., Brown, S., Capodiferro, MR., Al-Ajli, FO., Ambrosini, R., Houde, P., Koren, S., Oliver, K., Smith, M., Skelton, J., Betteridge, E., Dolucan, J., Corton, C., Bista, I., Torrance, J., Tracey, A., Wood, J., Uliano-Silva, M., Howe, K., McCarthy, S., Winkler, S., Kwak, W., Korlach, J., Fungtammasan, A., Fordham, D., Costa, V., Mayes, S., Chiara, M., Horner, DS., Myers, E., Durbin, R., Achilli, A., Braun, EL., Phillippy, AM., Jarvis, ED. and Vertebrate Genomes Project Consortium, , 2021. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications. Genome Biol, v. 22
Doi: http://doi.org/10.1186/s13059-021-02336-9

Vernaz, G., Hudson, A., Emília Santos, M., Fischer, B., Carruthers, M., Shechonge, A., Gabagambi, N., Tyers, A., Ngatunga, B., Malinsky, M., Durbin, R., Turner, G., Genner, M. and Miska, E., 2021. Epigenetic Divergence during Early Stages of Speciation in an African Crater Lake Cichlid Fish
Doi: 10.1101/2021.07.30.435319

Hansen, T., Fjelldal, PG., Lien, S., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Doulcan, J., Fedrigo, O., Mountcastle, J., Jarvis, E., McCarthy, SA., Chow, W., Howe, K., Torrance, J., Wood, J., Sims, Y., Haggerty, L., Challis, R., Threlfall, J., Mead, D., Durbin, R. and Blaxter, M., 2021. The genome sequence of the brown trout, Salmo trutta Linnaeus 1758. Wellcome open research, v. 6
Doi: http://doi.org/10.12688/wellcomeopenres.16838.1

Mead, D., Ogden, R., Meredith, A., Peniche, G., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Doulcan, J., Holmes, N., Wright, V., Loose, M., Quail, MA., McCarthy, SA., Howe, K., Chow, W., Torrance, J., Collins, J., Challis, R., Durbin, R. and Blaxter, M., 2021. The genome sequence of the European golden eagle, Aquila chrysaetos chrysaetos Linnaeus 1758. Wellcome open research, v. 6
Doi: 10.12688/wellcomeopenres.16631.1

Wang, Y., Pedersen, MW., Alsos, IG., De Sanctis, B., Racimo, F., Prohaska, A., Coissac, E., Owens, HL., Merkel, MKF., Fernandez-Guerra, A., Rouillard, A., Lammers, Y., Alberti, A., Denoeud, F., Money, D., Ruter, AH., McColl, H., Larsen, NK., Cherezova, AA., Edwards, ME., Fedorov, GB., Haile, J., Orlando, L., Vinner, L., Korneliussen, TS., Beilman, DW., Bjørk, AA., Cao, J., Dockter, C., Esdale, J., Gusarova, G., Kjeldsen, KK., Mangerud, J., Rasic, JT., Skadhauge, B., Svendsen, JI., Tikhonov, A., Wincker, P., Xing, Y., Zhang, Y., Froese, DG., Rahbek, C., Bravo, DN., Holden, PB., Edwards, NR., Durbin, R., Meltzer, DJ., Kjær, KH., Möller, P. and Willerslev, E., 2021. Late Quaternary dynamics of Arctic biota from ancient environmental genomics. Nature, v. 600
Doi: 10.1038/s41586-021-04016-x

Yen, EC., McCarthy, SA., Galarza, JA., Generalovic, TN., Pelan, S., Nguyen, P., Meier, JI., Warren, IA., Mappes, J., Durbin, R. and Jiggins, CD., 2021. Correction to: A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning. Gigascience, v. 10
Doi: 10.1093/gigascience/giab073

Guan, D., McCarthy, SA., Ning, Z., Wang, G., Wang, Y. and Durbin, R., 2021. Efficient iterative Hi-C scaffolder based on N-best neighbors. BMC Bioinformatics, v. 22
Doi: http://doi.org/10.1186/s12859-021-04453-5

Guan, D., McCarthy, SA., Ning, Z., Wang, G., Wang, Y. and Durbin, R., 2021. Correction to: Efficient iterative Hi-C scaffolder based on N-best neighbors. BMC Bioinformatics, v. 22
Doi: http://doi.org/10.1186/s12859-021-04537-2

2020

Jiggins, C., Yen, E., McCarthy, S., Galarza, J., Generalovic, T., Pelan, S., Nguyen, P., Meier, J., warren, I., Mappes, J. and Durbin, R., 2020. A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning GigaScience,

Bista, I., McCarthy, SA., Wood, J., Ning, Z., Detrich Iii, HW., Desvignes, T., Postlethwait, J., Chow, W., Howe, K., Torrance, J., Smith, M., Oliver, K., Vertebrate Genomes Project Consortium, , Miska, EA. and Durbin, R., 2020. The genome sequence of the channel bull blenny, Cottoperca gobio (Günther, 1861). Wellcome Open Res, v. 5
Doi: 10.12688/wellcomeopenres.16012.1

Martiniano, R., Garrison, E., Jones, ER., Manica, A. and Durbin, R., 2020. Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph. Genome Biol, v. 21
Doi: 10.1186/s13059-020-02160-7

Mirauta, BA., Seaton, DD., Bensaddek, D., Brenes, A., Bonder, MJ., Kilpinen, H., HipSci Consortium, , Stegle, O. and Lamond, AI., 2020. Population-scale proteome variation in human induced pluripotent stem cells. Elife, v. 9
Doi: http://doi.org/10.7554/eLife.57390

Mead, D., Fingland, K., Cripps, R., Portela Miguez, R., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Doulcan, J., Quail, MA., McCarthy, SA., Howe, K., Sims, Y., Torrance, J., Tracey, A., Challis, R., Durbin, R. and Blaxter, M., 2020. The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788. Wellcome open research, v. 5
Doi: http://doi.org/10.12688/wellcomeopenres.15721.1

Kamm, J., Terhorst, J., Durbin, R. and Song, YS., 2020. Efficiently Inferring the Demographic History of Many Populations With Allele Count Data Journal of the American Statistical Association, v. 115
Doi: 10.1080/01621459.2019.1635482

Formenti, G., Rhie, A., Balacco, J., Haase, B., Mountcastle, J., Fedrigo, O., Brown, S., Capodiferro, M., Al-Ajli, FO., Ambrosini, R., Houde, P., Koren, S., Oliver, K., Smith, M., Skelton, J., Betteridge, E., Dolucan, J., Corton, C., Bista, I., Torrance, J., Tracey, A., Wood, J., Uliano-Silva, M., Howe, K., McCarthy, S., Winkler, S., Kwak, W., Korlach, J., Fungtammasan, A., Fordham, D., Costa, V., Mayes, S., Chiara, M., Horner, DS., Myers, E., Durbin, R., Achilli, A., Braun, EL., Phillippy, AM. and Jarvis, ED., 2020. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats
Doi: 10.1101/2020.06.30.177956

Mead, D., Fingland, K., Cripps, R., Portela Miguez, R., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Dolucan, J., Dudchenko, O., Omer, AD., Weisz, D., Lieberman Aiden, E., Fedrigo, O., Mountcastle, J., Jarvis, E., McCarthy, SA., Sims, Y., Torrance, J., Tracey, A., Howe, K., Challis, R., Durbin, R. and Blaxter, M., 2020. The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758. Wellcome Open Res, v. 5
Doi: http://doi.org/10.12688/wellcomeopenres.15679.1

Mead, D., Fingland, K., Cripps, R., Portela Miguez, R., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Doulcan, J., Quail, MA., McCarthy, SA., Howe, K., Sims, Y., Torrance, J., Tracey, A., Challis, R., Durbin, R. and Blaxter, M., 2020. The genome sequence of the eastern grey squirrel, Sciurus carolinensis Gmelin, 1788. Wellcome Open Res, v. 5
Doi: http://doi.org/10.12688/wellcomeopenres.15721.1

Cuomo, ASE., Seaton, DD., McCarthy, DJ., Martinez, I., Bonder, MJ., Garcia-Bernardo, J., Amatya, S., Madrigal, P., Isaacson, A., Buettner, F., Knights, A., Natarajan, KN., HipSci Consortium, , Vallier, L., Marioni, JC., Chhatriwala, M. and Stegle, O., 2020. Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression. Nat Commun, v. 11
Doi: http://doi.org/10.1038/s41467-020-14457-z

Cuomo, ASE., Seaton, DD., McCarthy, DJ., Martinez, I., Bonder, MJ., Garcia-Bernardo, J., Amatya, S., Madrigal, P., Isaacson, A., Buettner, F., Knights, A., Natarajan, KN., HipSci Consortium, , Vallier, L., Marioni, JC., Chhatriwala, M. and Stegle, O., 2020. Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression. Nat Commun, v. 11
Doi: http://doi.org/10.1038/s41467-020-15098-y

Svardal, H., Quah, FX., Malinsky, M., Ngatunga, BP., Miska, EA., Salzburger, W., Genner, MJ., Turner, GF. and Durbin, R., 2020. Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation. Molecular biology and evolution, v. 37
Doi: 10.1093/molbev/msz294

McCarthy, DJ., Rostom, R., Huang, Y., Kunz, DJ., Danecek, P., Bonder, MJ., Hagai, T., Lyu, R., HipSci Consortium, , Wang, W., Gaffney, DJ., Simons, BD., Stegle, O. and Teichmann, SA., 2020. Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes. Nat Methods, v. 17
Doi: 10.1038/s41592-020-0766-3

Mead, D., Hailer, F., Chadwick, E., Portela Miguez, R., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Doulcan, JD., Dudchenko, O., Omer, A., Weisz, D., Lieberman Aiden, E., McCarthy, S., Howe, K., Sims, Y., Torrance, J., Tracey, A., Challis, R., Durbin, R. and Blaxter, M., 2020. The genome sequence of the Eurasian river otter, Lutra lutra Linnaeus 1758. Wellcome Open Res, v. 5
Doi: http://doi.org/10.12688/wellcomeopenres.15722.1

Rhie, A., McCarthy, S., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Gedman, G., Cantin, L., Thibaud-Nissen, F., Haggerty, L., Lee, C., Ko, BJ., Kim, J., Bista, I., Smith, M., Haase, B., Mountcastle, J., Winkler, S., Paez, S., Howard, J., Vernes, S., Lama, T., Grutzner, F., Warren, W., Balakrishnan, C., Burt, D., George, J., Biegler, M., Iorns, D., Digby, A., Eason, D., Edwards, T., Wilkinson, M., Turner, G., Meyer, A., Kautt, A., Franchini, P., Detrich, W., Svardal, H., Wagner, M., Naylor, GJP., Pippel, M., Malinsky, M., Mooney, M., Simbirsky, M., Hannigan, B., Pesout, T., Houck, M., Misuraca, A., Kingan, S., Hall, R., Kronenberg, Z., Korlach, J., Sović, I., Dunn, C., Ning, Z., Hastie, A., Lee, J., Selvaraj, S., Green, R., Putnam, N., Ghurye, J., Garrison, E., Sims, Y., Collins, J., Pelan, S., Torrance, J., Tracey, A., Wood, J., Guan, D., London, S., Clayton, D., Mello, C., Friedrich, S., Lovell, P., Osipova, E., Al-Ajli, F., Secomandi, S., Kim, H., Theofanopoulou, C., Zhou, Y., Harris, R., Makova, K., Medvedev, P., Hoffman, J., Masterson, P., Clark, K., Martin, F., Howe, K., Flicek, P., Walenz, B., Kwak, W., Clawson, H., Diekhans, M., Nassar, L., Paten, B., Kraus, RHS., Lewin, H., Crawford, A., Gilbert, T., Zhang, G., Venkatesh, B., Murphy, R., Koepfli, K-P., Shapiro, B., Johnson, W., Di Palma, F., Margues-Bonet, T., Teeling, E., Warnow, T., Graves, JM., Ryder, O., Hausler, D., O’Brien, S., Howe, K., Myers, E., Durbin, R., Phillippy, A. and Jarvis, E., 2020. Towards complete and error-free genome assemblies of all vertebrate species
Doi: 10.1101/2020.05.22.110833

Mead, D., Fingland, K., Cripps, R., Portela Miguez, R., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Dolucan, J., Dudchenko, O., Omer, AD., Weisz, D., Lieberman Aiden, E., Fedrigo, O., Mountcastle, J., Jarvis, E., McCarthy, SA., Sims, Y., Torrance, J., Tracey, A., Howe, K., Challis, R., Durbin, R. and Blaxter, M., 2020. The genome sequence of the Eurasian red squirrel, Sciurus vulgaris Linnaeus 1758. Wellcome open research, v. 5
Doi: http://doi.org/10.12688/wellcomeopenres.15679.1

Svardal, H., Rusuwa, B., Linderoth, T., Kiran, A., Charmantier, A., Lattorff, HMG., Cagan, A., Ommeh, SC., Kamng'ona, A., Katongo, C., Santos, ME., Durbin, R., Kumwenda, B., Visscher, PM., von der Heyden, S. and Participants of SMBE Malawi, , 2020. Evolutionary Genomics at the Human-Environment Interface in Africa. Mol Biol Evol, v. 37
Doi: http://doi.org/10.1093/molbev/msaa132

2019

Bonfield, JK., McCarthy, SA. and Durbin, R., 2019. Crumble: reference free lossy compression of sequence quality values Bioinformatics, v. 35
Doi: http://doi.org/10.1093/bioinformatics/bty608

Kingan, SB., Heaton, H., Cudini, J., Lambert, CC., Baybayan, P., Galvin, BD., Durbin, R., Korlach, J. and Lawniczak, MKN., 2019. A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing. Genes (Basel), v. 10
Doi: http://doi.org/10.3390/genes10010062

Sikora, M., Pitulko, VV., Sousa, VC., Allentoft, ME., Vinner, L., Rasmussen, S., Margaryan, A., de Barros Damgaard, P., de la Fuente, C., Renaud, G., Yang, MA., Fu, Q., Dupanloup, I., Giampoudakis, K., Nogués-Bravo, D., Rahbek, C., Kroonen, G., Peyrot, M., McColl, H., Vasilyev, SV., Veselovskaya, E., Gerasimova, M., Pavlova, EY., Chasnyk, VG., Nikolskiy, PA., Gromov, AV., Khartanovich, VI., Moiseyev, V., Grebenyuk, PS., Fedorchenko, AY., Lebedintsev, AI., Slobodin, SB., Malyarchuk, BA., Martiniano, R., Meldgaard, M., Arppe, L., Palo, JU., Sundell, T., Mannermaa, K., Putkonen, M., Alexandersen, V., Primeau, C., Baimukhanov, N., Malhi, RS., Sjögren, K-G., Kristiansen, K., Wessman, A., Sajantila, A., Lahr, MM., Durbin, R., Nielsen, R., Meltzer, DJ., Excoffier, L. and Willerslev, E., 2019. The population history of northeastern Siberia since the Pleistocene. Nature, v. 570
Doi: 10.1038/s41586-019-1279-z

Heaton, H., Talman, A., Knights, A., Imaz, M., Gaffney, D., Gaffney, D., Durbin, R., Hemberg, M., Hemberg, M. and Lawniczak, M., 2019. souporcell: Robust clustering of single cell RNAseq by genotype and ambient RNA inference without reference genotypes
Doi: 10.1101/699637

Garg, S., Aach, J., Li, H., Durbin, R. and Church, G., 2019. A haplotype-aware de novo assembly of related individuals using pedigree graph
Doi: 10.1101/580159

Shchur, V., Ziganurova, L. and Durbin, R., 2019. Fast and scalable genome-wide inference of local tree topologies from large number of haplotypes based on tree consistent PBWT data structure
Doi: 10.1101/542035

Vigilante, A., Laddach, A., Moens, N., Meleckyte, R., Leha, A., Ghahramani, A., Culley, OJ., Kathuria, A., Hurling, C., Vickers, A., Wiseman, E., Tewary, M., Zandstra, PW., HipSci Consortium, , Durbin, R., Fraternali, F., Stegle, O., Birney, E., Luscombe, NM., Danovi, D. and Watt, FM., 2019. Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors. Cell Rep, v. 26
Doi: http://doi.org/10.1016/j.celrep.2019.01.094

2018

Skov, L., Hui, R., Shchur, V., Hobolth, A., Scally, A., Schierup, MH. and Durbin, R., 2018. Detecting archaic introgression using an unadmixed outgroup. PLoS Genet, v. 14
Doi: 10.1371/journal.pgen.1007641

Malinsky, M., Svardal, H., Tyers, AM., Miska, EA., Genner, MJ., Turner, GF. and Durbin, R., 2018. Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow. Nat Ecol Evol, v. 2
Doi: 10.1038/s41559-018-0717-x

Kingan, S., Heaton, H., Cudini, J., Lambert, C., Baybayan, P., Galvin, B., Durbin, R., Korlach, J. and Lawniczak, M., 2018. A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing
Doi: 10.1101/499954

Garrison, E., Sirén, J., Novak, AM., Hickey, G., Eizenga, JM., Dawson, ET., Jones, W., Garg, S., Markello, C., Lin, MF., Paten, B. and Durbin, R., 2018. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol, v. 36
Doi: http://doi.org/10.1038/nbt.4227

de Barros Damgaard, P., Martiniano, R., Kamm, J., Moreno-Mayar, JV., Kroonen, G., Peyrot, M., Barjamovic, G., Rasmussen, S., Zacho, C., Baimukhanov, N., Zaibert, V., Merz, V., Biddanda, A., Merz, I., Loman, V., Evdokimov, V., Usmanova, E., Hemphill, B., Seguin-Orlando, A., Yediay, FE., Ullah, I., Sjögren, K-G., Iversen, KH., Choin, J., de la Fuente, C., Ilardo, M., Schroeder, H., Moiseyev, V., Gromov, A., Polyakov, A., Omura, S., Senyurt, SY., Ahmad, H., McKenzie, C., Margaryan, A., Hameed, A., Samad, A., Gul, N., Khokhar, MH., Goriunova, OI., Bazaliiskii, VI., Novembre, J., Weber, AW., Orlando, L., Allentoft, ME., Nielsen, R., Kristiansen, K., Sikora, M., Outram, AK., Durbin, R. and Willerslev, E., 2018. The first horse herders and the impact of early Bronze Age steppe expansions into Asia. Science (New York, N.Y.), v. 360
Doi: 10.1126/science.aar7711

Durbin, RM. and Lewin, HA., 2018. Earth BioGenome Project: Sequencing life for the future of life Proceedings of the National Academy of Sciences of the United States of America,
Doi: http://doi.org/10.1073/pnas.1720115115

Scerri, EML., Thomas, MG., Manica, A., Gunz, P., Stock, JT., Stringer, C., Grove, M., Groucutt, HS., Timmermann, A., Rightmire, GP., d'Errico, F., Tryon, CA., Drake, NA., Brooks, AS., Dennell, RW., Durbin, R., Henn, BM., Lee-Thorp, J., deMenocal, P., Petraglia, MD., Thompson, JC., Scally, A. and Chikhi, L., 2018. Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter? Trends in Ecology & Evolution, v. 33
Doi: 10.1016/j.tree.2018.05.005

2017

Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, FP., Culley, OJ., Danecek, P., Faulconbridge, A., Harrison, PW., Kathuria, A., McCarthy, D., McCarthy, SA., Meleckyte, R., Memari, Y., Moens, N., Soares, F., Mann, A., Streeter, I., Agu, CA., Alderton, A., Nelson, R., Harper, S., Patel, M., White, A., Patel, SR., Clarke, L., Halai, R., Kirton, CM., Kolb-Kokocinski, A., Beales, P., Birney, E., Danovi, D., Lamond, AI., Ouwehand, WH., Vallier, L., Watt, FM., Durbin, R., Stegle, O. and Gaffney, DJ., 2017. Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs. Nature, v. 546
Doi: http://doi.org/10.1038/nature23012

Schneider, VA., Graves-Lindsay, T., Howe, K., Bouk, N., Chen, H-C., Kitts, PA., Murphy, TD., Pruitt, KD., Thibaud-Nissen, F., Albracht, D., Fulton, RS., Kremitzki, M., Magrini, V., Markovic, C., McGrath, S., Steinberg, KM., Auger, K., Chow, W., Collins, J., Harden, G., Hubbard, T., Pelan, S., Simpson, JT., Threadgold, G., Torrance, J., Wood, JM., Clarke, L., Koren, S., Boitano, M., Peluso, P., Li, H., Chin, C-S., Phillippy, AM., Durbin, R., Wilson, RK., Flicek, P., Eichler, EE. and Church, DM., 2017. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res, v. 27
Doi: http://doi.org/10.1101/gr.213611.116

Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, FP., Culley, OJ., Danecek, P., Faulconbridge, A., Harrison, PW., Kathuria, A., McCarthy, D., McCarthy, SA., Meleckyte, R., Memari, Y., Moens, N., Soares, F., Mann, A., Streeter, I., Agu, CA., Alderton, A., Nelson, R., Harper, S., Patel, M., White, A., Patel, SR., Clarke, L., Halai, R., Kirton, CM., Kolb-Kokocinski, A., Beales, P., Birney, E., Danovi, D., Lamond, AI., Ouwehand, WH., Vallier, L., Watt, FM., Durbin, R., Stegle, O. and Gaffney, DJ., 2017. Common genetic variation drives molecular heterogeneity in human iPSCs. Nature, v. 546
Doi: http://doi.org/10.1038/nature22403

Tachmazidou, I., Süveges, D., Min, JL., Ritchie, GRS., Steinberg, J., Walter, K., Iotchkova, V., Schwartzentruber, J., Huang, J., Memari, Y., McCarthy, S., Crawford, AA., Bombieri, C., Cocca, M., Farmaki, A-E., Gaunt, TR., Jousilahti, P., Kooijman, MN., Lehne, B., Malerba, G., Männistö, S., Matchan, A., Medina-Gomez, C., Metrustry, SJ., Nag, A., Ntalla, I., Paternoster, L., Rayner, NW., Sala, C., Scott, WR., Shihab, HA., Southam, L., St Pourcain, B., Traglia, M., Trajanoska, K., Zaza, G., Zhang, W., Artigas, MS., Bansal, N., Benn, M., Chen, Z., Danecek, P., Lin, W-Y., Locke, A., Luan, J., Manning, AK., Mulas, A., Sidore, C., Tybjaerg-Hansen, A., Varbo, A., Zoledziewska, M., Finan, C., Hatzikotoulas, K., Hendricks, AE., Kemp, JP., Moayyeri, A., Panoutsopoulou, K., Szpak, M., Wilson, SG., Boehnke, M., Cucca, F., Di Angelantonio, E., Langenberg, C., Lindgren, C., McCarthy, MI., Morris, AP., Nordestgaard, BG., Scott, RA., Tobin, MD., Wareham, NJ., SpiroMeta Consortium, , GoT2D Consortium, , Burton, P., Chambers, JC., Smith, GD., Dedoussis, G., Felix, JF., Franco, OH., Gambaro, G., Gasparini, P., Hammond, CJ., Hofman, A., Jaddoe, VWV., Kleber, M., Kooner, JS., Perola, M., Relton, C., Ring, SM., Rivadeneira, F., Salomaa, V., Spector, TD., Stegle, O., Toniolo, D., Uitterlinden, AG., arcOGEN Consortium, , Understanding Society Scientific Group, , UK10K Consortium, , Barroso, I., Greenwood, CMT., Perry, JRB., Walker, BR., Butterworth, AS., Xue, Y., Durbin, R., Small, KS., Soranzo, N., Timpson, NJ. and Zeggini, E., 2017. Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits American Journal of Human Genetics, v. 100
Doi: http://doi.org/10.1016/j.ajhg.2017.04.014

Giordano, F., Aigrain, L., Quail, MA., Coupland, P., Bonfield, JK., Davies, RM., Tischler, G., Jackson, DK., Keane, TM., Li, J., Yue, J-X., Liti, G., Durbin, R. and Ning, Z., 2017. De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms. Sci Rep, v. 7
Doi: http://doi.org/10.1038/s41598-017-03996-z

Xue, Y., Mezzavilla, M., Haber, M., McCarthy, S., Chen, Y., Narasimhan, V., Gilly, A., Ayub, Q., Colonna, V., Southam, L., Finan, C., Massaia, A., Chheda, H., Palta, P., Ritchie, G., Asimit, J., Dedoussis, G., Gasparini, P., Palotie, A., Ripatti, S., Soranzo, N., Toniolo, D., Wilson, JF., Durbin, R., Tyler-Smith, C. and Zeggini, E., 2017. Enrichment of low-frequency functional variants revealed by whole-genome sequencing of multiple isolated European populations. Nat Commun, v. 8
Doi: http://doi.org/10.1038/ncomms15927

Yue, J-X., Li, J., Aigrain, L., Hallin, J., Persson, K., Oliver, K., Bergström, A., Coupland, P., Warringer, J., Lagomarsino, MC., Fischer, G., Durbin, R. and Liti, G., 2017. Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nat Genet, v. 49
Doi: http://doi.org/10.1038/ng.3847

Chheda, H., Palta, P., Pirinen, M., McCarthy, S., Walter, K., Koskinen, S., Salomaa, V., Daly, M., Durbin, R., Palotie, A., Aittokallio, T. and Ripatti, S., 2017. Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom. Eur J Hum Genet, v. 25
Doi: http://doi.org/10.1038/ejhg.2016.205

Dolle, DD., Liu, Z., Cotten, M., Simpson, JT., Iqbal, Z., Durbin, R., McCarthy, SA. and Keane, TM., 2017. Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes Genome Research, v. 27
Doi: http://doi.org/10.1101/gr.211748.116

Sandor, C., Honti, F., Haerty, W., Szewczyk-Krolikowski, K., Tomlinson, P., Evetts, S., Millin, S., Keane, T., McCarthy, SA., Durbin, R., Talbot, K., Hu, M., Webber, C., Ponting, CP. and Wade-Martins, R., 2017. Whole-exome sequencing of 228 patients with sporadic Parkinson's disease. Sci Rep, v. 7
Doi: http://doi.org/10.1038/srep41188

2016

Malaspinas, A-S., Westaway, MC., Muller, C., Sousa, VC., Lao, O., Alves, I., Bergström, A., Athanasiadis, G., Cheng, JY., Crawford, JE., Heupink, TH., Macholdt, E., Peischl, S., Rasmussen, S., Schiffels, S., Subramanian, S., Wright, JL., Albrechtsen, A., Barbieri, C., Dupanloup, I., Eriksson, A., Margaryan, A., Moltke, I., Pugach, I., Korneliussen, TS., Levkivskyi, IP., Moreno-Mayar, JV., Ni, S., Racimo, F., Sikora, M., Xue, Y., Aghakhanian, FA., Brucato, N., Brunak, S., Campos, PF., Clark, W., Ellingvåg, S., Fourmile, G., Gerbault, P., Injie, D., Koki, G., Leavesley, M., Logan, B., Lynch, A., Matisoo-Smith, EA., McAllister, PJ., Mentzer, AJ., Metspalu, M., Migliano, AB., Murgha, L., Phipps, ME., Pomat, W., Reynolds, D., Ricaut, F-X., Siba, P., Thomas, MG., Wales, T., Wall, CM., Oppenheimer, SJ., Tyler-Smith, C., Durbin, R., Dortch, J., Manica, A., Schierup, MH., Foley, RA., Lahr, MM., Bowern, C., Wall, JD., Mailund, T., Stoneking, M., Nielsen, R., Sandhu, MS., Excoffier, L., Lambert, DM. and Willerslev, E., 2016. A genomic history of Aboriginal Australia. Nature, v. 538
Doi: 10.1038/nature18299

Dougherty, GW., Loges, NT., Klinkenbusch, JA., Olbrich, H., Pennekamp, P., Menchen, T., Raidt, J., Wallmeier, J., Werner, C., Westermann, C., Ruckert, C., Mirra, V., Hjeij, R., Memari, Y., Durbin, R., Kolb-Kokocinski, A., Praveen, K., Kashef, MA., Kashef, S., Eghtedari, F., Häffner, K., Valmari, P., Baktai, G., Aviram, M., Bentur, L., Amirav, I., Davis, EE., Katsanis, N., Brueckner, M., Shaposhnykov, A., Pigino, G., Dworniczak, B. and Omran, H., 2016. DNAH11 Localization in the Proximal Region of Respiratory Cilia Defines Distinct Outer Dynein Arm Complexes. Am J Respir Cell Mol Biol, v. 55
Doi: http://doi.org/10.1165/rcmb.2015-0353OC

Wallmeier, J., Shiratori, H., Dougherty, GW., Edelbusch, C., Hjeij, R., Loges, NT., Menchen, T., Olbrich, H., Pennekamp, P., Raidt, J., Werner, C., Minegishi, K., Shinohara, K., Asai, Y., Takaoka, K., Lee, C., Griese, M., Memari, Y., Durbin, R., Kolb-Kokocinski, A., Sauer, S., Wallingford, JB., Hamada, H. and Omran, H., 2016. TTC25 Deficiency Results in Defects of the Outer Dynein Arm Docking Machinery and Primary Ciliary Dyskinesia with Left-Right Body Asymmetry Randomization. Am J Hum Genet, v. 99
Doi: http://doi.org/10.1016/j.ajhg.2016.06.014

Loh, P-R., Danecek, P., Palamara, PF., Fuchsberger, C., A Reshef, Y., K Finucane, H., Schoenherr, S., Forer, L., McCarthy, S., Abecasis, GR., Durbin, R. and L Price, A., 2016. Reference-based phasing using the Haplotype Reference Consortium panel. Nature Genetics, v. 48
Doi: http://doi.org/10.1038/ng.3679

Schiffels, S., Haak, W., Paajanen, P., Llamas, B., Popescu, E., Loe, L., Clarke, R., Lyons, A., Mortimer, R., Sayer, D., Tyler-Smith, C., Cooper, A. and Durbin, R., 2016. Iron Age and Anglo-Saxon genomes from East England reveal British migration history. Nat Commun, v. 7
Doi: 10.1038/ncomms10408

Leha, A., Moens, N., Meleckyte, R., Culley, OJ., Gervasio, MK., Kerz, M., Reimer, A., Cain, SA., Streeter, I., Folarin, A., Stegle, O., Kielty, CM., HipSci Consortium, , Durbin, R., Watt, FM. and Danovi, D., 2016. A high-content platform to characterise human induced pluripotent stem cell lines. Methods, v. 96
Doi: 10.1016/j.ymeth.2015.11.012

Jeroncic, A., Memari, Y., Ritchie, GR., Hendricks, AE., Kolb-Kokocinski, A., Matchan, A., Vitart, V., Hayward, C., Kolcic, I., Glodzik, D., Wright, AF., Rudan, I., Campbell, H., Durbin, R., Polašek, O., Zeggini, E. and Boraska Perica, V., 2016. Whole-exome sequencing in an isolated population from the Dalmatian island of Vis. Eur J Hum Genet, v. 24
Doi: http://doi.org/10.1038/ejhg.2016.23

Danecek, P., McCarthy, SA., HipSci Consortium, and Durbin, R., 2016. A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data. PLoS One, v. 11
Doi: http://doi.org/10.1371/journal.pone.0155014

Narasimhan, V., Danecek, P., Scally, A., Xue, Y., Tyler-Smith, C. and Durbin, R., 2016. BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics, v. 32
Doi: 10.1093/bioinformatics/btw044

Narasimhan, VM., Hunt, KA., Mason, D., Baker, CL., Karczewski, KJ., Barnes, MR., Barnett, AH., Bates, C., Bellary, S., Bockett, NA., Giorda, K., Griffiths, CJ., Hemingway, H., Jia, Z., Kelly, MA., Khawaja, HA., Lek, M., McCarthy, S., McEachan, R., O'Donnell-Luria, A., Paigen, K., Parisinos, CA., Sheridan, E., Southgate, L., Tee, L., Thomas, M., Xue, Y., Schnall-Levin, M., Petkov, PM., Tyler-Smith, C., Maher, ER., Trembath, RC., MacArthur, DG., Wright, J., Durbin, R. and van Heel, DA., 2016. Health and population effects of rare gene knockouts in adult humans with related parents. Science, v. 352
Doi: http://doi.org/10.1126/science.aac8624

Van Haute, L., Dietmann, S., Kremer, L., Hussain, S., Pearce, SF., Powell, CA., Rorbach, J., Lantaff, R., Blanco, S., Sauer, S., Kotzaeridou, U., Hoffmann, GF., Memari, Y., Kolb-Kokocinski, A., Durbin, R., Mayr, JA., Frye, M., Prokisch, H. and Minczuk, M., 2016. Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3. Nat Commun, v. 7
Doi: http://doi.org/10.1038/ncomms12039

Boldt, K., van Reeuwijk, J., Lu, Q., Koutroumpas, K., Nguyen, T-MT., Texier, Y., van Beersum, SEC., Horn, N., Willer, JR., Mans, DA., Dougherty, G., Lamers, IJC., Coene, KLM., Arts, HH., Betts, MJ., Beyer, T., Bolat, E., Gloeckner, CJ., Haidari, K., Hetterschijt, L., Iaconis, D., Jenkins, D., Klose, F., Knapp, B., Latour, B., Letteboer, SJF., Marcelis, CL., Mitic, D., Morleo, M., Oud, MM., Riemersma, M., Rix, S., Terhal, PA., Toedt, G., van Dam, TJP., de Vrieze, E., Wissinger, Y., Wu, KM., Apic, G., Beales, PL., Blacque, OE., Gibson, TJ., Huynen, MA., Katsanis, N., Kremer, H., Omran, H., van Wijk, E., Wolfrum, U., Kepes, F., Davis, EE., Franco, B., Giles, RH., Ueffing, M., Russell, RB., Roepman, R. and UK10K Rare Diseases Group, , 2016. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nat Commun, v. 7
Doi: http://doi.org/10.1038/ncomms11491

McCarthy, S., Das, S., Kretzschmar, W., Delaneau, O., Wood, AR., Teumer, A., Kang, HM., Fuchsberger, C., Danecek, P., Sharp, K., Luo, Y., Sidore, C., Kwong, A., Timpson, N., Koskinen, S., Vrieze, S., Scott, LJ., Zhang, H., Mahajan, A., Veldink, J., Peters, U., Pato, C., van Duijn, CM., Gillies, CE., Gandin, I., Mezzavilla, M., Gilly, A., Cocca, M., Traglia, M., Angius, A., Barrett, JC., Boomsma, D., Branham, K., Breen, G., Brummett, CM., Busonero, F., Campbell, H., Chan, A., Chen, S., Chew, E., Collins, FS., Corbin, LJ., Smith, GD., Dedoussis, G., Dorr, M., Farmaki, A-E., Ferrucci, L., Forer, L., Fraser, RM., Gabriel, S., Levy, S., Groop, L., Harrison, T., Hattersley, A., Holmen, OL., Hveem, K., Kretzler, M., Lee, JC., McGue, M., Meitinger, T., Melzer, D., Min, JL., Mohlke, KL., Vincent, JB., Nauck, M., Nickerson, D., Palotie, A., Pato, M., Pirastu, N., McInnis, M., Richards, JB., Sala, C., Salomaa, V., Schlessinger, D., Schoenherr, S., Slagboom, PE., Small, K., Spector, T., Stambolian, D., Tuke, M., Tuomilehto, J., Van den Berg, LH., Van Rheenen, W., Volker, U., Wijmenga, C., Toniolo, D., Zeggini, E., Gasparini, P., Sampson, MG., Wilson, JF., Frayling, T., de Bakker, PIW., Swertz, MA., McCarroll, S., Kooperberg, C., Dekker, A., Altshuler, D., Willer, C., Iacono, W., Ripatti, S., Soranzo, N., Walter, K., Swaroop, A., Cucca, F., Anderson, CA., Myers, RM., Boehnke, M., McCarthy, MI., Durbin, R. and Haplotype Reference Consortium, , 2016. A reference panel of 64,976 haplotypes for genotype imputation. Nat Genet, v. 48
Doi: http://doi.org/10.1038/ng.3643

Kremer, LS., Distelmaier, F., Alhaddad, B., Hempel, M., Iuso, A., Küpper, C., Mühlhausen, C., Kovacs-Nagy, R., Satanovskij, R., Graf, E., Berutti, R., Eckstein, G., Durbin, R., Sauer, S., Hoffmann, GF., Strom, TM., Santer, R., Meitinger, T., Klopstock, T., Prokisch, H. and Haack, TB., 2016. Bi-allelic Truncating Mutations in TANGO2 Cause Infancy-Onset Recurrent Metabolic Crises with Encephalocardiomyopathy. Am J Hum Genet, v. 98
Doi: 10.1016/j.ajhg.2015.12.009

2015

Jeffares, DC., Rallis, C., Rieux, A., Speed, D., Převorovský, M., Mourier, T., Marsellach, FX., Iqbal, Z., Lau, W., Cheng, TMK., Pracana, R., Mülleder, M., Lawson, JLD., Chessel, A., Bala, S., Hellenthal, G., O'Fallon, B., Keane, T., Simpson, JT., Bischof, L., Tomiczek, B., Bitton, DA., Sideri, T., Codlin, S., Hellberg, JEEU., van Trigt, L., Jeffery, L., Li, J-J., Atkinson, S., Thodberg, M., Febrer, M., McLay, K., Drou, N., Brown, W., Hayles, J., Carazo Salas, RE., Ralser, M., Maniatis, N., Balding, DJ., Balloux, F., Durbin, R. and Bähler, J., 2015. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet, v. 47
Doi: 10.1038/ng.3215

Taylor, PN., Porcu, E., Chew, S., Campbell, PJ., Traglia, M., Brown, SJ., Mullin, BH., Shihab, HA., Min, J., Walter, K., Memari, Y., Huang, J., Barnes, MR., Beilby, JP., Charoen, P., Danecek, P., Dudbridge, F., Forgetta, V., Greenwood, C., Grundberg, E., Johnson, AD., Hui, J., Lim, EM., McCarthy, S., Muddyman, D., Panicker, V., Perry, JRB., Bell, JT., Yuan, W., Relton, C., Gaunt, T., Schlessinger, D., Abecasis, G., Cucca, F., Surdulescu, GL., Woltersdorf, W., Zeggini, E., Zheng, H-F., Toniolo, D., Dayan, CM., Naitza, S., Walsh, JP., Spector, T., Davey Smith, G., Durbin, R., Richards, JB., Sanna, S., Soranzo, N., Timpson, NJ., Wilson, SG. and UK0K Consortium, , 2015. Whole-genome sequence-based analysis of thyroid function. Nat Commun, v. 6
Doi: 10.1038/ncomms6681

Jeffares, DC., Rallis, C., Rieux, A., Speed, D., Převorovský, M., Mourier, T., Marsellach, FX., Iqbal, Z., Lau, W., Cheng, TMK., Pracana, R., Mülleder, M., Lawson, JLD., Chessel, A., Bala, S., Hellenthal, G., O'Fallon, B., Keane, T., Simpson, JT., Bischof, L., Tomiczek, B., Bitton, DA., Sideri, T., Codlin, S., Hellberg, JEEU., Van Trigt, L., Jeffery, L., Li, JJ., Atkinson, S., Thodberg, M., Febrer, M., McLay, K., Drou, N., Brown, W., Hayles, J., Salas, REC., Ralser, M., Maniatis, N., Balding, DJ., Balloux, F., Durbin, R. and Bähler, J., 2015. The genomic and phenotypic diversity of Schizosaccharomyces pombe Nature Genetics, v. 47
Doi: http://doi.org/10.1038/ng.3215

Pagani, L., Schiffels, S., Gurdasani, D., Danecek, P., Scally, A., Chen, Y., Xue, Y., Haber, M., Ekong, R., Oljira, T., Mekonnen, E., Luiselli, D., Bradman, N., Bekele, E., Zalloua, P., Durbin, R., Kivisild, T. and Tyler-Smith, C., 2015. Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians. Am J Hum Genet, v. 96
Doi: 10.1016/j.ajhg.2015.04.019

Schmidts, M., Hou, Y., Cortés, CR., Mans, DA., Huber, C., Boldt, K., Patel, M., van Reeuwijk, J., Plaza, J-M., van Beersum, SEC., Yap, ZM., Letteboer, SJF., Taylor, SP., Herridge, W., Johnson, CA., Scambler, PJ., Ueffing, M., Kayserili, H., Krakow, D., King, SM., UK10K, , Beales, PL., Al-Gazali, L., Wicking, C., Cormier-Daire, V., Roepman, R., Mitchison, HM. and Witman, GB., 2015. TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport. Nat Commun, v. 6
Doi: 10.1038/ncomms8074

Kaiser, VB., Svinti, V., Prendergast, JG., Chau, Y-Y., Campbell, A., Patarcic, I., Barroso, I., Joshi, PK., Hastie, ND., Miljkovic, A., Taylor, MS., Generation Scotland, , UK10K, , Enroth, S., Memari, Y., Kolb-Kokocinski, A., Wright, AF., Gyllensten, U., Durbin, R., Rudan, I., Campbell, H., Polašek, O., Johansson, Å., Sauer, S., Porteous, DJ., Fraser, RM., Drake, C., Vitart, V., Hayward, C., Semple, CA. and Wilson, JF., 2015. Homozygous loss-of-function variants in European cosmopolitan and isolate populations. Hum Mol Genet, v. 24
Doi: http://doi.org/10.1093/hmg/ddv272

Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera, C., Ávila-Arcos, MC., Malaspinas, A-S., Eriksson, A., Moltke, I., Metspalu, M., Homburger, JR., Wall, J., Cornejo, OE., Moreno-Mayar, JV., Korneliussen, TS., Pierre, T., Rasmussen, M., Campos, PF., de Barros Damgaard, P., Allentoft, ME., Lindo, J., Metspalu, E., Rodríguez-Varela, R., Mansilla, J., Henrickson, C., Seguin-Orlando, A., Malmström, H., Stafford, T., Shringarpure, SS., Moreno-Estrada, A., Karmin, M., Tambets, K., Bergström, A., Xue, Y., Warmuth, V., Friend, AD., Singarayer, J., Valdes, P., Balloux, F., Leboreiro, I., Vera, JL., Rangel-Villalobos, H., Pettener, D., Luiselli, D., Davis, LG., Heyer, E., Zollikofer, CPE., Ponce de León, MS., Smith, CI., Grimes, V., Pike, K-A., Deal, M., Fuller, BT., Arriaza, B., Standen, V., Luz, MF., Ricaut, F., Guidon, N., Osipova, L., Voevoda, MI., Posukh, OL., Balanovsky, O., Lavryashina, M., Bogunov, Y., Khusnutdinova, E., Gubina, M., Balanovska, E., Fedorova, S., Litvinov, S., Malyarchuk, B., Derenko, M., Mosher, MJ., Archer, D., Cybulski, J., Petzelt, B., Mitchell, J., Worl, R., Norman, PJ., Parham, P., Kemp, BM., Kivisild, T., Tyler-Smith, C., Sandhu, MS., Crawford, M., Villems, R., Smith, DG., Waters, MR., Goebel, T., Johnson, JR., Malhi, RS., Jakobsson, M., Meltzer, DJ., Manica, A., Durbin, R., Bustamante, CD., Song, YS., Nielsen, R. and Willerslev, E., 2015. POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science, v. 349
Doi: 10.1126/science.aab3884

Church, DM., Schneider, VA., Steinberg, KM., Schatz, MC., Quinlan, AR., Chin, C-S., Kitts, PA., Aken, B., Marth, GT., Hoffman, MM., Herrero, J., Mendoza, MLZ., Durbin, R. and Flicek, P., 2015. Extending reference assembly models. Genome Biol, v. 16
Doi: 10.1186/s13059-015-0587-3

Huang, J., Howie, B., McCarthy, S., Memari, Y., Walter, K., Min, JL., Danecek, P., Malerba, G., Trabetti, E., Zheng, H-F., UK10K Consortium, , Gambaro, G., Richards, JB., Durbin, R., Timpson, NJ., Marchini, J. and Soranzo, N., 2015. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel. Nat Commun, v. 6
Doi: 10.1038/ncomms9111

Chen, J-H., Segni, M., Payne, F., Huang-Doran, I., Sleigh, A., Adams, C., UK10K Consortium, , Savage, DB., O'Rahilly, S., Semple, RK. and Barroso, I., 2015. Truncation of POC1A associated with short stature and extreme insulin resistance. J Mol Endocrinol, v. 55
Doi: http://doi.org/10.1530/JME-15-0090

1000 Genomes Project Consortium, , Auton, A., Brooks, LD., Durbin, RM., Garrison, EP., Kang, HM., Korbel, JO., Marchini, JL., McCarthy, S., McVean, GA. and Abecasis, GR., 2015. A global reference for human genetic variation. Nature, v. 526
Doi: 10.1038/nature15393

UK10K Consortium, , Walter, K., Min, JL., Huang, J., Crooks, L., Memari, Y., McCarthy, S., Perry, JRB., Xu, C., Futema, M., Lawson, D., Iotchkova, V., Schiffels, S., Hendricks, AE., Danecek, P., Li, R., Floyd, J., Wain, LV., Barroso, I., Humphries, SE., Hurles, ME., Zeggini, E., Barrett, JC., Plagnol, V., Richards, JB., Greenwood, CMT., Timpson, NJ., Durbin, R. and Soranzo, N., 2015. The UK10K project identifies rare variants in health and disease. Nature, v. 526
Doi: 10.1038/nature14962

Zheng, H-F., Forgetta, V., Hsu, Y-H., Estrada, K., Rosello-Diez, A., Leo, PJ., Dahia, CL., Park-Min, KH., Tobias, JH., Kooperberg, C., Kleinman, A., Styrkarsdottir, U., Liu, C-T., Uggla, C., Evans, DS., Nielson, CM., Walter, K., Pettersson-Kymmer, U., McCarthy, S., Eriksson, J., Kwan, T., Jhamai, M., Trajanoska, K., Memari, Y., Min, J., Huang, J., Danecek, P., Wilmot, B., Li, R., Chou, W-C., Mokry, LE., Moayyeri, A., Claussnitzer, M., Cheng, C-H., Cheung, W., Medina-Gómez, C., Ge, B., Chen, S-H., Choi, K., Oei, L., Fraser, J., Kraaij, R., Hibbs, MA., Gregson, CL., Paquette, D., Hofman, A., Wibom, C., Tranah, GJ., Marshall, M., Gardiner, BB., Cremin, K., Auer, P., Hsu, L., Ring, S., Tung, JY., Thorleifsson, G., Enneman, AW., van Schoor, NM., de Groot, LCPGM., van der Velde, N., Melin, B., Kemp, JP., Christiansen, C., Sayers, A., Zhou, Y., Calderari, S., van Rooij, J., Carlson, C., Peters, U., Berlivet, S., Dostie, J., Uitterlinden, AG., Williams, SR., Farber, C., Grinberg, D., LaCroix, AZ., Haessler, J., Chasman, DI., Giulianini, F., Rose, LM., Ridker, PM., Eisman, JA., Nguyen, TV., Center, JR., Nogues, X., Garcia-Giralt, N., Launer, LL., Gudnason, V., Mellström, D., Vandenput, L., Amin, N., van Duijn, CM., Karlsson, MK., Ljunggren, Ö., Svensson, O., Hallmans, G., Rousseau, F., Giroux, S., Bussière, J., Arp, PP., Koromani, F., Prince, RL., Lewis, JR., Langdahl, BL., Hermann, AP., Jensen, J-EB., Kaptoge, S., Khaw, K-T., Reeve, J., Formosa, MM., Xuereb-Anastasi, A., Åkesson, K., McGuigan, FE., Garg, G., Olmos, JM., Zarrabeitia, MT., Riancho, JA., Ralston, SH., Alonso, N., Jiang, X., Goltzman, D., Pastinen, T., Grundberg, E., Gauguier, D., Orwoll, ES., Karasik, D., Davey-Smith, G., AOGC Consortium, , Smith, AV., Siggeirsdottir, K., Harris, TB., Zillikens, MC., van Meurs, JBJ., Thorsteinsdottir, U., Maurano, MT., Timpson, NJ., Soranzo, N., Durbin, R., Wilson, SG., Ntzani, EE., Brown, MA., Stefansson, K., Hinds, DA., Spector, T., Cupples, LA., Ohlsson, C., Greenwood, CMT., UK10K Consortium, , Jackson, RD., Rowe, DW., Loomis, CA., Evans, DM., Ackert-Bicknell, CL., Joyner, AL., Duncan, EL., Kiel, DP., Rivadeneira, F. and Richards, JB., 2015. Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture. Nature, v. 526
Doi: 10.1038/nature14878

Malinsky, M., Challis, RJ., Tyers, AM., Schiffels, S., Terai, Y., Ngatunga, BP., Miska, EA., Durbin, R., Genner, MJ. and Turner, GF., 2015. Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake. Science, v. 350
Doi: 10.1126/science.aac9927

Buil, A., Brown, AA., Lappalainen, T., Viñuela, A., Davies, MN., Zheng, H-F., Richards, JB., Glass, D., Small, KS., Durbin, R., Spector, TD. and Dermitzakis, ET., 2015. Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins. Nat Genet, v. 47
Doi: 10.1038/ng.3162

Frommer, A., Hjeij, R., Loges, NT., Edelbusch, C., Jahnke, C., Raidt, J., Werner, C., Wallmeier, J., Große-Onnebrink, J., Olbrich, H., Cindrić, S., Jaspers, M., Boon, M., Memari, Y., Durbin, R., Kolb-Kokocinski, A., Sauer, S., Marthin, JK., Nielsen, KG., Amirav, I., Elias, N., Kerem, E., Shoseyov, D., Haeffner, K. and Omran, H., 2015. Immunofluorescence Analysis and Diagnosis of Primary Ciliary Dyskinesia with Radial Spoke Defects. Am J Respir Cell Mol Biol, v. 53
Doi: http://doi.org/10.1165/rcmb.2014-0483OC

Anand Brown, A., Ding, Z., Viñuela, A., Glass, D., Parts, L., Spector, T., Winn, J. and Durbin, R., 2015. Pathway-based factor analysis of gene expression data produces highly heritable phenotypes that associate with age. G3 (Bethesda), v. 5
Doi: 10.1534/g3.114.011411

Haack, TB., Jackson, CB., Murayama, K., Kremer, LS., Schaller, A., Kotzaeridou, U., de Vries, MC., Schottmann, G., Santra, S., Büchner, B., Wieland, T., Graf, E., Freisinger, P., Eggimann, S., Ohtake, A., Okazaki, Y., Kohda, M., Kishita, Y., Tokuzawa, Y., Sauer, S., Memari, Y., Kolb-Kokocinski, A., Durbin, R., Hasselmann, O., Cremer, K., Albrecht, B., Wieczorek, D., Engels, H., Hahn, D., Zink, AM., Alston, CL., Taylor, RW., Rodenburg, RJ., Trollmann, R., Sperl, W., Strom, TM., Hoffmann, GF., Mayr, JA., Meitinger, T., Bolognini, R., Schuelke, M., Nuoffer, J-M., Kölker, S., Prokisch, H. and Klopstock, T., 2015. Deficiency of ECHS1 causes mitochondrial encephalopathy with cardiac involvement. Ann Clin Transl Neurol, v. 2
Doi: http://doi.org/10.1002/acn3.189

2014

Colonna, V., Ayub, Q., Chen, Y., Pagani, L., Luisi, P., Pybus, M., Garrison, E., Xue, Y., Tyler-Smith, C., 1000 Genomes Project Consortium, , Abecasis, GR., Auton, A., Brooks, LD., DePristo, MA., Durbin, RM., Handsaker, RE., Kang, HM., Marth, GT. and McVean, GA., 2014. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol, v. 15
Doi: http://doi.org/10.1186/gb-2014-15-6-r88

Delaneau, O., Marchini, J., 1000 Genomes Project Consortium, and 1000 Genomes Project Consortium, , 2014. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun, v. 5
Doi: http://doi.org/10.1038/ncomms4934

Young, AI. and Durbin, R., 2014. Estimation of epistatic variance components and heritability in founder populations and crosses. Genetics, v. 198
Doi: http://doi.org/10.1534/genetics.114.170795

Brown, AA., Buil, A., Viñuela, A., Lappalainen, T., Zheng, H-F., Richards, JB., Small, KS., Spector, TD., Dermitzakis, ET. and Durbin, R., 2014. Genetic interactions affecting human gene expression identified by variance association mapping. Elife, v. 3
Doi: 10.7554/eLife.01381

Ding, Z., Mangino, M., Aviv, A., Spector, T., Durbin, R. and UK10K Consortium, , 2014. Estimating telomere length from whole genome sequence data. Nucleic Acids Res, v. 42
Doi: 10.1093/nar/gku181

Timpson, NJ., Walter, K., Min, JL., Tachmazidou, I., Malerba, G., Shin, S-Y., Chen, L., Futema, M., Southam, L., Iotchkova, V., Cocca, M., Huang, J., Memari, Y., McCarthy, S., Danecek, P., Muddyman, D., Mangino, M., Menni, C., Perry, JRB., Ring, SM., Gaye, A., Dedoussis, G., Farmaki, A-E., Burton, P., Talmud, PJ., Gambaro, G., Spector, TD., Smith, GD., Durbin, R., Richards, JB., Humphries, SE., Zeggini, E., Soranzo, N., UK1OK Consortium Members, and UK1OK Consortium Members, , 2014. A rare variant in APOC3 is associated with plasma triglyceride and VLDL levels in Europeans. Nat Commun, v. 5
Doi: http://doi.org/10.1038/ncomms5871

Schiffels, S. and Durbin, R., 2014. Inferring human population size and separation history from multiple genome sequences. Nat Genet, v. 46
Doi: 10.1038/ng.3015

Bergström, A., Simpson, JT., Salinas, F., Barré, B., Parts, L., Zia, A., Nguyen Ba, AN., Moses, AM., Louis, EJ., Mustonen, V., Warringer, J., Durbin, R. and Liti, G., 2014. A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol, v. 31
Doi: 10.1093/molbev/msu037

Ding, Z., Ni, Y., Timmer, SW., Lee, B-K., Battenhouse, A., Louzada, S., Yang, F., Dunham, I., Crawford, GE., Lieb, JD., Durbin, R., Iyer, VR. and Birney, E., 2014. Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. PLoS Genet, v. 10
Doi: 10.1371/journal.pgen.1004798

Durbin, R., 2014. Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT). Bioinformatics, v. 30
Doi: http://doi.org/10.1093/bioinformatics/btu014

Young, AI. and Durbin, R., 2014. Estimation of Epistatic Variance Components and Heritability in Founder Populations and Crosses GENETICS, v. 198
Doi: 10.1534/genetics.114.170795

Kaye, J., Hurles, M., Griffin, H., Grewal, J., Bobrow, M., Timpson, N., Smee, C., Bolton, P., Durbin, R., Dyke, S., Fitzpatrick, D., Kennedy, K., Kent, A., Muddyman, D., Muntoni, F., Raymond, LF., Semple, R., Spector, T. and UK 10K, , 2014. Managing clinically significant findings in research: the UK10K example. Eur J Hum Genet, v. 22
Doi: 10.1038/ejhg.2013.290

2013

Altschul, S., Demchak, B., Durbin, R., Gentleman, R., Krzywinski, M., Li, H., Nekrutenko, A., Robinson, J., Rasband, W., Taylor, J. and Trapnell, C., 2013. The anatomy of successful computational biology software. Nat Biotechnol, v. 31
Doi: http://doi.org/10.1038/nbt.2721

Glass, D., Viñuela, A., Davies, MN., Ramasamy, A., Parts, L., Knowles, D., Brown, AA., Hedman, AK., Small, KS., Buil, A., Grundberg, E., Nica, AC., Di Meglio, P., Nestle, FO., Ryten, M., UK Brain Expression consortium, , MuTHER consortium, , Durbin, R., McCarthy, MI., Deloukas, P., Dermitzakis, ET., Weale, ME., Bataille, V. and Spector, TD., 2013. Gene expression changes with age in skin, adipose tissue, blood and brain. Genome Biol, v. 14
Doi: http://doi.org/10.1186/gb-2013-14-7-r75

Bradnam, KR., Fass, JN., Alexandrov, A., Baranay, P., Bechner, M., Birol, I., Boisvert, S., Chapman, JA., Chapuis, G., Chikhi, R., Chitsaz, H., Chou, W-C., Corbeil, J., Del Fabbro, C., Docking, TR., Durbin, R., Earl, D., Emrich, S., Fedotov, P., Fonseca, NA., Ganapathy, G., Gibbs, RA., Gnerre, S., Godzaridis, E., Goldstein, S., Haimel, M., Hall, G., Haussler, D., Hiatt, JB., Ho, IY., Howard, J., Hunt, M., Jackman, SD., Jaffe, DB., Jarvis, ED., Jiang, H., Kazakov, S., Kersey, PJ., Kitzman, JO., Knight, JR., Koren, S., Lam, T-W., Lavenier, D., Laviolette, F., Li, Y., Li, Z., Liu, B., Liu, Y., Luo, R., Maccallum, I., Macmanes, MD., Maillet, N., Melnikov, S., Naquin, D., Ning, Z., Otto, TD., Paten, B., Paulo, OS., Phillippy, AM., Pina-Martins, F., Place, M., Przybylski, D., Qin, X., Qu, C., Ribeiro, FJ., Richards, S., Rokhsar, DS., Ruby, JG., Scalabrin, S., Schatz, MC., Schwartz, DC., Sergushichev, A., Sharpe, T., Shaw, TI., Shendure, J., Shi, Y., Simpson, JT., Song, H., Tsarev, F., Vezzi, F., Vicedomini, R., Vieira, BM., Wang, J., Worley, KC., Yin, S., Yiu, S-M., Yuan, J., Zhang, G., Zhang, H., Zhou, S. and Korf, IF., 2013. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience, v. 2
Doi: http://doi.org/10.1186/2047-217X-2-10

Scally, A., Yngvadottir, B., Xue, Y., Ayub, Q., Durbin, R. and Tyler-Smith, C., 2013. A genome-wide survey of genetic variation in gorillas using reduced representation sequencing. PLoS One, v. 8
Doi: 10.1371/journal.pone.0065066

Khurana, E., Fu, Y., Colonna, V., Mu, XJ., Kang, HM., Lappalainen, T., Sboner, A., Lochovsky, L., Chen, J., Harmanci, A., Das, J., Abyzov, A., Balasubramanian, S., Beal, K., Chakravarty, D., Challis, D., Chen, Y., Clarke, D., Clarke, L., Cunningham, F., Evani, US., Flicek, P., Fragoza, R., Garrison, E., Gibbs, R., Gümüş, ZH., Herrero, J., Kitabayashi, N., Kong, Y., Lage, K., Liluashvili, V., Lipkin, SM., MacArthur, DG., Marth, G., Muzny, D., Pers, TH., Ritchie, GRS., Rosenfeld, JA., Sisu, C., Wei, X., Wilson, M., Xue, Y., Yu, F., 1000 Genomes Project Consortium, , Dermitzakis, ET., Yu, H., Rubin, MA., Tyler-Smith, C. and Gerstein, M., 2013. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science, v. 342
Doi: 10.1126/science.1235587

Cubillos, FA., Parts, L., Salinas, F., Bergström, A., Scovacricchi, E., Zia, A., Illingworth, CJR., Mustonen, V., Ibstedt, S., Warringer, J., Louis, EJ., Durbin, R. and Liti, G., 2013. High-resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics, v. 195
Doi: 10.1534/genetics.113.155515

2012

Danecek, P., Nellåker, C., McIntyre, RE., Buendia-Buendia, JE., Bumpstead, S., Ponting, CP., Flint, J., Durbin, R., Keane, TM. and Adams, DJ., 2012. High levels of RNA-editing site conservation amongst 15 laboratory mouse strains. Genome Biol, v. 13
Doi: http://doi.org/10.1186/gb-2012-13-4-r26

Howe, K., Davis, P., Paulini, M., Tuli, MA., Williams, G., Yook, K., Durbin, R., Kersey, P. and Sternberg, PW., 2012. WormBase: Annotating many nematode genomes. Worm, v. 1
Doi: 10.4161/worm.19574

Yook, K., Harris, TW., Bieri, T., Cabunoc, A., Chan, J., Chen, WJ., Davis, P., de la Cruz, N., Duong, A., Fang, R., Ganesan, U., Grove, C., Howe, K., Kadam, S., Kishore, R., Lee, R., Li, Y., Muller, H-M., Nakamura, C., Nash, B., Ozersky, P., Paulini, M., Raciti, D., Rangarajan, A., Schindelman, G., Shi, X., Schwarz, EM., Ann Tuli, M., Van Auken, K., Wang, D., Wang, X., Williams, G., Hodgkin, J., Berriman, M., Durbin, R., Kersey, P., Spieth, J., Stein, L. and Sternberg, PW., 2012. WormBase 2012: more genomes, more data, new website. Nucleic Acids Research, v. 40
Doi: http://doi.org/10.1093/nar/gkr954

Flicek, P., Amode, MR., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gil, L., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kähäri, AK., Keefe, D., Keenan, S., Kinsella, R., Komorowska, M., Koscielny, G., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Muffato, M., Overduin, B., Pignatelli, M., Pritchard, B., Riat, HS., Ritchie, GRS., Ruffier, M., Schuster, M., Sobral, D., Tang, YA., Taylor, K., Trevanion, S., Vandrovcova, J., White, S., Wilson, M., Wilder, SP., Aken, BL., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernández-Suarez, XM., Harrow, J., Herrero, J., Hubbard, TJP., Parker, A., Proctor, G., Spudich, G., Vogel, J., Yates, A., Zadissa, A. and Searle, SMJ., 2012. Ensembl 2012. Nucleic Acids Res, v. 40
Doi: http://doi.org/10.1093/nar/gkr991

Parts, L., Hedman, ÅK., Keildson, S., Knights, AJ., Abreu-Goodger, C., van de Bunt, M., Guerra-Assunção, JA., Bartonicek, N., van Dongen, S., Mägi, R., Nisbet, J., Barrett, A., Rantalainen, M., Nica, AC., Quail, MA., Small, KS., Glass, D., Enright, AJ., Winn, J., MuTHER Consortium, , Deloukas, P., Dermitzakis, ET., McCarthy, MI., Spector, TD., Durbin, R. and Lindgren, CM., 2012. Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PLoS Genet, v. 8
Doi: 10.1371/journal.pgen.1002704

Simpson, JT. and Durbin, R., 2012. Efficient de novo assembly of large genomes using compressed data structures. Genome Res, v. 22
Doi: http://doi.org/10.1101/gr.126953.111

Grundberg, E., Small, KS., Hedman, ÅK., Nica, AC., Buil, A., Keildson, S., Bell, JT., Yang, T-P., Meduri, E., Barrett, A., Nisbett, J., Sekowska, M., Wilk, A., Shin, S-Y., Glass, D., Travers, M., Min, JL., Ring, S., Ho, K., Thorleifsson, G., Kong, A., Thorsteindottir, U., Ainali, C., Dimas, AS., Hassanali, N., Ingle, C., Knowles, D., Krestyaninova, M., Lowe, CE., Di Meglio, P., Montgomery, SB., Parts, L., Potter, S., Surdulescu, G., Tsaprouni, L., Tsoka, S., Bataille, V., Durbin, R., Nestle, FO., O'Rahilly, S., Soranzo, N., Lindgren, CM., Zondervan, KT., Ahmadi, KR., Schadt, EE., Stefansson, K., Smith, GD., McCarthy, MI., Deloukas, P., Dermitzakis, ET., Spector, TD. and Multiple Tissue Human Expression Resource (MuTHER) Consortium, , 2012. Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet, v. 44
Doi: http://doi.org/10.1038/ng.2394

Scally, A., Dutheil, JY., Hillier, LW., Jordan, GE., Goodhead, I., Herrero, J., Hobolth, A., Lappalainen, T., Mailund, T., Marques-Bonet, T., McCarthy, S., Montgomery, SH., Schwalie, PC., Tang, YA., Ward, MC., Xue, Y., Yngvadottir, B., Alkan, C., Andersen, LN., Ayub, Q., Ball, EV., Beal, K., Bradley, BJ., Chen, Y., Clee, CM., Fitzgerald, S., Graves, TA., Gu, Y., Heath, P., Heger, A., Karakoc, E., Kolb-Kokocinski, A., Laird, GK., Lunter, G., Meader, S., Mort, M., Mullikin, JC., Munch, K., O'Connor, TD., Phillips, AD., Prado-Martinez, J., Rogers, AS., Sajjadian, S., Schmidt, D., Shaw, K., Simpson, JT., Stenson, PD., Turner, DJ., Vigilant, L., Vilella, AJ., Whitener, W., Zhu, B., Cooper, DN., de Jong, P., Dermitzakis, ET., Eichler, EE., Flicek, P., Goldman, N., Mundy, NI., Ning, Z., Odom, DT., Ponting, CP., Quail, MA., Ryder, OA., Searle, SM., Warren, WC., Wilson, RK., Schierup, MH., Rogers, J., Tyler-Smith, C. and Durbin, R., 2012. Insights into hominid evolution from the gorilla genome sequence. Nature, v. 483
Doi: 10.1038/nature10842

Grundberg, E., Small, KS., Hedman, AK., Nica, AC., Buil, A., Keildson, S., Bell, JT., Yang, TP., Meduri, E., Barrett, A., Nisbett, J., Sekowska, M., Wilk, A., Shin, SY., Glass, D., Travers, M., Min, JL., Ring, S., Ho, K., Thorleifsson, G., Kong, A., Thorsteindottir, U., Ainali, C., Dimas, AS., Hassanali, N., Ingle, C., Knowles, D., Krestyaninova, M., Lowe, CE., Di Meglio, P., Montgomery, SB., Parts, L., Potter, S., Surdulescu, G., Tsaprouni, L., Tsoka, S., Bataille, V., Durbin, R., Nestle, FO., O'Rahilly, S., Soranzo, N., Lindgren, CM., Zondervan, KT., Ahmadi, KR., Schadt, EE., Stefansson, K., Smith, GD., McCarthy, MI., Deloukas, P., Dermitzakis, ET. and Spector, TD., 2012. Mapping cis-and trans-regulatory effects across multiple tissues in twins Nature Genetics, v. 44
Doi: http://doi.org/10.1038/ng.2394

1000 Genomes Project Consortium, , Abecasis, GR., Auton, A., Brooks, LD., DePristo, MA., Durbin, RM., Handsaker, RE., Kang, HM., Marth, GT. and McVean, GA., 2012. An integrated map of genetic variation from 1,092 human genomes. Nature, v. 491
Doi: 10.1038/nature11632

Scally, A. and Durbin, R., 2012. Revising the human mutation rate: implications for understanding human evolution. Nat Rev Genet, v. 13
Doi: 10.1038/nrg3295

Stegle, O., Parts, L., Piipari, M., Winn, J. and Durbin, R., 2012. Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat Protoc, v. 7
Doi: http://doi.org/10.1038/nprot.2011.457

Stranger, BE., Montgomery, SB., Dimas, AS., Parts, L., Stegle, O., Ingle, CE., Sekowska, M., Smith, GD., Evans, D., Gutierrez-Arcelus, M., Price, A., Raj, T., Nisbett, J., Nica, AC., Beazley, C., Durbin, R., Deloukas, P. and Dermitzakis, ET., 2012. Patterns of cis regulatory variation in diverse human populations. PLoS Genet, v. 8
Doi: http://doi.org/10.1371/journal.pgen.1002639

2011

Parts, L., Stegle, O., Winn, J. and Durbin, R., 2011. Joint genetic analysis of gene expression data with inferred cellular phenotypes. PLoS Genet, v. 7
Doi: http://doi.org/10.1371/journal.pgen.1001276

Albers, CA., Lunter, G., MacArthur, DG., McVean, G., Ouwehand, WH. and Durbin, R., 2011. Dindel: accurate indel calls from short-read data. Genome Res, v. 21
Doi: http://doi.org/10.1101/gr.112326.110

Li, H. and Durbin, R., 2011. Inference of human population history from individual whole-genome sequences. Nature, v. 475
Doi: http://doi.org/10.1038/nature10231

Nica, AC., Parts, L., Glass, D., Nisbet, J., Barrett, A., Sekowska, M., Travers, M., Potter, S., Grundberg, E., Small, K., Hedman, AK., Bataille, V., Tzenova Bell, J., Surdulescu, G., Dimas, AS., Ingle, C., Nestle, FO., di Meglio, P., Min, JL., Wilk, A., Hammond, CJ., Hassanali, N., Yang, T-P., Montgomery, SB., O'Rahilly, S., Lindgren, CM., Zondervan, KT., Soranzo, N., Barroso, I., Durbin, R., Ahmadi, K., Deloukas, P., McCarthy, MI., Dermitzakis, ET., Spector, TD. and MuTHER Consortium, , 2011. The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet, v. 7
Doi: http://doi.org/10.1371/journal.pgen.1002003

Mills, RE., Walter, K., Stewart, C., Handsaker, RE., Chen, K., Alkan, C., Abyzov, A., Yoon, SC., Ye, K., Cheetham, RK., Chinwalla, A., Conrad, DF., Fu, Y., Grubert, F., Hajirasouliha, I., Hormozdiari, F., Iakoucheva, LM., Iqbal, Z., Kang, S., Kidd, JM., Konkel, MK., Korn, J., Khurana, E., Kural, D., Lam, HYK., Leng, J., Li, R., Li, Y., Lin, C-Y., Luo, R., Mu, XJ., Nemesh, J., Peckham, HE., Rausch, T., Scally, A., Shi, X., Stromberg, MP., Stütz, AM., Urban, AE., Walker, JA., Wu, J., Zhang, Y., Zhang, ZD., Batzer, MA., Ding, L., Marth, GT., McVean, G., Sebat, J., Snyder, M., Wang, J., Ye, K., Eichler, EE., Gerstein, MB., Hurles, ME., Lee, C., McCarroll, SA., Korbel, JO. and 1000 Genomes Project, , 2011. Mapping copy number variation by population-scale genome sequencing. Nature, v. 470
Doi: 10.1038/nature09708

Danecek, P., Auton, A., Abecasis, G., Albers, CA., Banks, E., DePristo, MA., Handsaker, RE., Lunter, G., Marth, GT., Sherry, ST., McVean, G., Durbin, R. and 1000 Genomes Project Analysis Group, , 2011. The variant call format and VCFtools. Bioinformatics, v. 27
Doi: http://doi.org/10.1093/bioinformatics/btr330

Le, SQ. and Durbin, R., 2011. SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples. Genome Res, v. 21
Doi: http://doi.org/10.1101/gr.113084.110

Flicek, P., Amode, MR., Barrell, D., Beal, K., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Gordon, L., Hendrix, M., Hourlier, T., Johnson, N., Kähäri, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Larsson, P., Longden, I., McLaren, W., Overduin, B., Pritchard, B., Riat, HS., Rios, D., Ritchie, GRS., Ruffier, M., Schuster, M., Sobral, D., Spudich, G., Tang, YA., Trevanion, S., Vandrovcova, J., Vilella, AJ., White, S., Wilder, SP., Zadissa, A., Zamora, J., Aken, BL., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernández-Suarez, XM., Herrero, J., Hubbard, TJP., Parker, A., Proctor, G., Vogel, J. and Searle, SMJ., 2011. Ensembl 2011. Nucleic Acids Res, v. 39
Doi: http://doi.org/10.1093/nar/gkq1064

Earl, D., Bradnam, K., St John, J., Darling, A., Lin, D., Fass, J., Yu, HOK., Buffalo, V., Zerbino, DR., Diekhans, M., Nguyen, N., Ariyaratne, PN., Sung, W-K., Ning, Z., Haimel, M., Simpson, JT., Fonseca, NA., Birol, İ., Docking, TR., Ho, IY., Rokhsar, DS., Chikhi, R., Lavenier, D., Chapuis, G., Naquin, D., Maillet, N., Schatz, MC., Kelley, DR., Phillippy, AM., Koren, S., Yang, S-P., Wu, W., Chou, W-C., Srivastava, A., Shaw, TI., Ruby, JG., Skewes-Cox, P., Betegon, M., Dimon, MT., Solovyev, V., Seledtsov, I., Kosarev, P., Vorobyev, D., Ramirez-Gonzalez, R., Leggett, R., MacLean, D., Xia, F., Luo, R., Li, Z., Xie, Y., Liu, B., Gnerre, S., MacCallum, I., Przybylski, D., Ribeiro, FJ., Yin, S., Sharpe, T., Hall, G., Kersey, PJ., Durbin, R., Jackman, SD., Chapman, JA., Huang, X., DeRisi, JL., Caccamo, M., Li, Y., Jaffe, DB., Green, RE., Haussler, D., Korf, I. and Paten, B., 2011. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res, v. 21
Doi: http://doi.org/10.1101/gr.126599.111

Keane, TM., Goodstadt, L., Danecek, P., White, MA., Wong, K., Yalcin, B., Heger, A., Agam, A., Slater, G., Goodson, M., Furlotte, NA., Eskin, E., Nellåker, C., Whitley, H., Cleak, J., Janowitz, D., Hernandez-Pliego, P., Edwards, A., Belgard, TG., Oliver, PL., McIntyre, RE., Bhomra, A., Nicod, J., Gan, X., Yuan, W., van der Weyden, L., Steward, CA., Bala, S., Stalker, J., Mott, R., Durbin, R., Jackson, IJ., Czechanski, A., Guerra-Assunção, JA., Donahue, LR., Reinholdt, LG., Payseur, BA., Ponting, CP., Birney, E., Flint, J. and Adams, DJ., 2011. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature, v. 477
Doi: http://doi.org/10.1038/nature10413

Warringer, J., Zörgö, E., Cubillos, FA., Zia, A., Gjuvsland, A., Simpson, JT., Forsmark, A., Durbin, R., Omholt, SW., Louis, EJ., Liti, G., Moses, A. and Blomberg, A., 2011. Trait variation in yeast is defined by population history. PLoS Genet, v. 7
Doi: http://doi.org/10.1371/journal.pgen.1002111

Parts, L., Cubillos, FA., Warringer, J., Jain, K., Salinas, F., Bumpstead, SJ., Molin, M., Zia, A., Simpson, JT., Quail, MA., Moses, A., Louis, EJ., Durbin, R. and Liti, G., 2011. Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res, v. 21
Doi: http://doi.org/10.1101/gr.116731.110

Palin, K., Campbell, H., Wright, AF., Wilson, JF. and Durbin, R., 2011. Identity-by-descent-based phasing and imputation in founder populations using graphical models. Genet Epidemiol, v. 35
Doi: http://doi.org/10.1002/gepi.20635

2010

Flicek, P., Aken, BL., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Fernandez-Banet, J., Gordon, L., Gräf, S., Haider, S., Hammond, M., Howe, K., Jenkinson, A., Johnson, N., Kähäri, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Koscielny, G., Kulesha, E., Lawson, D., Longden, I., Massingham, T., McLaren, W., Megy, K., Overduin, B., Pritchard, B., Rios, D., Ruffier, M., Schuster, M., Slater, G., Smedley, D., Spudich, G., Tang, YA., Trevanion, S., Vilella, A., Vogel, J., White, S., Wilder, SP., Zadissa, A., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernández-Suarez, XM., Herrero, J., Hubbard, TJP., Parker, A., Proctor, G., Smith, J. and Searle, SMJ., 2010. Ensembl's 10th year. Nucleic Acids Res, v. 38
Doi: http://doi.org/10.1093/nar/gkp972

Li, H. and Durbin, R., 2010. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, v. 26
Doi: http://doi.org/10.1093/bioinformatics/btp698

1000 Genomes Project Consortium, , Abecasis, GR., Altshuler, D., Auton, A., Brooks, LD., Durbin, RM., Gibbs, RA., Hurles, ME. and McVean, GA., 2010. A map of human genome variation from population-scale sequencing. Nature, v. 467
Doi: http://doi.org/10.1038/nature09534

Neumann, B., Walter, T., Hériché, J-K., Bulkescher, J., Erfle, H., Conrad, C., Rogers, P., Poser, I., Held, M., Liebel, U., Cetin, C., Sieckmann, F., Pau, G., Kabbe, R., Wünsche, A., Satagopam, V., Schmitz, MHA., Chapuis, C., Gerlich, DW., Schneider, R., Eils, R., Huber, W., Peters, J-M., Hyman, AA., Durbin, R., Pepperkok, R. and Ellenberg, J., 2010. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature, v. 464
Doi: http://doi.org/10.1038/nature08869

Sudmant, PH., Kitzman, JO., Antonacci, F., Alkan, C., Malig, M., Tsalenko, A., Sampas, N., Bruhn, L., Shendure, J., 1000 Genomes Project, and Eichler, EE., 2010. Diversity of human copy number variation and multicopy genes. Science, v. 330
Doi: http://doi.org/10.1126/science.1197005

Stegle, O., Parts, L., Durbin, R. and Winn, J., 2010. A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PLoS Comput Biol, v. 6
Doi: http://doi.org/10.1371/journal.pcbi.1000770

Hutchins, JRA., Toyoda, Y., Hegemann, B., Poser, I., Hériché, J-K., Sykora, MM., Augsburg, M., Hudecz, O., Buschhorn, BA., Bulkescher, J., Conrad, C., Comartin, D., Schleiffer, A., Sarov, M., Pozniakovsky, A., Slabicki, MM., Schloissnig, S., Steinmacher, I., Leuschner, M., Ssykor, A., Lawo, S., Pelletier, L., Stark, H., Nasmyth, K., Ellenberg, J., Durbin, R., Buchholz, F., Mechtler, K., Hyman, AA. and Peters, J-M., 2010. Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science, v. 328
Doi: http://doi.org/10.1126/science.1181348

Simpson, JT., McIntyre, RE., Adams, DJ. and Durbin, R., 2010. Copy number variant detection in inbred strains from short read sequence data. Bioinformatics, v. 26
Doi: 10.1093/bioinformatics/btp693

Harris, TW., Antoshechkin, I., Bieri, T., Blasiar, D., Chan, J., Chen, WJ., De La Cruz, N., Davis, P., Duesbury, M., Fang, R., Fernandes, J., Han, M., Kishore, R., Lee, R., Müller, H-M., Nakamura, C., Ozersky, P., Petcherski, A., Rangarajan, A., Rogers, A., Schindelman, G., Schwarz, EM., Tuli, MA., Van Auken, K., Wang, D., Wang, X., Williams, G., Yook, K., Durbin, R., Stein, LD., Spieth, J. and Sternberg, PW., 2010. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res, v. 38
Doi: http://doi.org/10.1093/nar/gkp952

2009

Toronto International Data Release Workshop Authors, , Birney, E., Hudson, TJ., Green, ED., Gunter, C., Eddy, S., Rogers, J., Harris, JR., Ehrlich, SD., Apweiler, R., Austin, CP., Berglund, L., Bobrow, M., Bountra, C., Brookes, AJ., Cambon-Thomsen, A., Carter, NP., Chisholm, RL., Contreras, JL., Cooke, RM., Crosby, WL., Dewar, K., Durbin, R., Dyke, SOM., Ecker, JR., El Emam, K., Feuk, L., Gabriel, SB., Gallacher, J., Gelbart, WM., Granell, A., Guarner, F., Hubbard, T., Jackson, SA., Jennings, JL., Joly, Y., Jones, SM., Kaye, J., Kennedy, KL., Knoppers, BM., Kyrpides, NC., Lowrance, WW., Luo, J., MacKay, JJ., Martín-Rivera, L., McCombie, WR., McPherson, JD., Miller, L., Miller, W., Moerman, D., Mooser, V., Morton, CC., Ostell, JM., Ouellette, BFF., Parkhill, J., Raina, PS., Rawlings, C., Scherer, SE., Scherer, SW., Schofield, PN., Sensen, CW., Stodden, VC., Sussman, MR., Tanaka, T., Thornton, J., Tsunoda, T., Valle, D., Vuorio, EI., Walker, NM., Wallace, S., Weinstock, G., Whitman, WB., Worley, KC., Wu, C., Wu, J. and Yu, J., 2009. Prepublication data sharing. Nature, v. 461
Doi: 10.1038/461168a

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R. and 1000 Genome Project Data Processing Subgroup, , 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics, v. 25
Doi: http://doi.org/10.1093/bioinformatics/btp352

Li, H. and Durbin, R., 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, v. 25
Doi: http://doi.org/10.1093/bioinformatics/btp324

Sudbery, I., Stalker, J., Simpson, JT., Keane, T., Rust, AG., Hurles, ME., Walter, K., Lynch, D., Teboul, L., Brown, SD., Li, H., Ning, Z., Nadeau, JH., Croniger, CM., Durbin, R. and Adams, DJ., 2009. Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels. Genome Biol, v. 10
Doi: http://doi.org/10.1186/gb-2009-10-10-r112

Liti, G., Carter, DM., Moses, AM., Warringer, J., Parts, L., James, SA., Davey, RP., Roberts, IN., Burt, A., Koufopanou, V., Tsai, IJ., Bergman, CM., Bensasson, D., O'Kelly, MJT., van Oudenaarden, A., Barton, DBH., Bailes, E., Nguyen, AN., Jones, M., Quail, MA., Goodhead, I., Sims, S., Smith, F., Blomberg, A., Durbin, R. and Louis, EJ., 2009. Population genomics of domestic and wild yeasts. Nature, v. 458
Doi: http://doi.org/10.1038/nature07743

Moses, AM. and Durbin, R., 2009. Inferring selection on amino acid preference in protein domains. Mol Biol Evol, v. 26
Doi: http://doi.org/10.1093/molbev/msn286

Pruitt, KD., Harrow, J., Harte, RA., Wallin, C., Diekhans, M., Maglott, DR., Searle, S., Farrell, CM., Loveland, JE., Ruef, BJ., Hart, E., Suner, M-M., Landrum, MJ., Aken, B., Ayling, S., Baertsch, R., Fernandez-Banet, J., Cherry, JL., Curwen, V., Dicuccio, M., Kellis, M., Lee, J., Lin, MF., Schuster, M., Shkeda, A., Amid, C., Brown, G., Dukhanina, O., Frankish, A., Hart, J., Maidak, BL., Mudge, J., Murphy, MR., Murphy, T., Rajan, J., Rajput, B., Riddick, LD., Snow, C., Steward, C., Webb, D., Weber, JA., Wilming, L., Wu, W., Birney, E., Haussler, D., Hubbard, T., Ostell, J., Durbin, R. and Lipman, D., 2009. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res, v. 19
Doi: http://doi.org/10.1101/gr.080531.108

Vilella, AJ., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R. and Birney, E., 2009. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res, v. 19
Doi: http://doi.org/10.1101/gr.073585.107

Hubbard, TJP., Aken, BL., Ayling, S., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L., Coates, G., Fairley, S., Fitzgerald, S., Fernandez-Banet, J., Gordon, L., Graf, S., Haider, S., Hammond, M., Holland, R., Howe, K., Jenkinson, A., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Rios, D., Schuster, M., Slater, G., Smedley, D., Spooner, W., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wilder, S., Zadissa, A., Birney, E., Cunningham, F., Curwen, V., Durbin, R., Fernandez-Suarez, XM., Herrero, J., Kasprzyk, A., Proctor, G., Smith, J., Searle, S. and Flicek, P., 2009. Ensembl 2009. Nucleic Acids Res, v. 37
Doi: http://doi.org/10.1093/nar/gkn828

2008

Poser, I., Sarov, M., Hutchins, JRA., Hériché, J-K., Toyoda, Y., Pozniakovsky, A., Weigl, D., Nitzsche, A., Hegemann, B., Bird, AW., Pelletier, L., Kittler, R., Hua, S., Naumann, R., Augsburg, M., Sykora, MM., Hofemeister, H., Zhang, Y., Nasmyth, K., White, KP., Dietzel, S., Mechtler, K., Durbin, R., Stewart, AF., Peters, J-M., Buchholz, F. and Hyman, AA., 2008. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods, v. 5
Doi: http://doi.org/10.1038/nmeth.1199

Down, TA., Rakyan, VK., Turner, DJ., Flicek, P., Li, H., Kulesha, E., Gräf, S., Johnson, N., Herrero, J., Tomazou, EM., Thorne, NP., Bäckdahl, L., Herberth, M., Howe, KL., Jackson, DK., Miretti, MM., Marioni, JC., Birney, E., Hubbard, TJP., Durbin, R., Tavaré, S. and Beck, S., 2008. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol, v. 26
Doi: http://doi.org/10.1038/nbt1414

Bentley, DR., Balasubramanian, S., Swerdlow, HP., Smith, GP., Milton, J., Brown, CG., Hall, KP., Evers, DJ., Barnes, CL., Bignell, HR., Boutell, JM., Bryant, J., Carter, RJ., Keira Cheetham, R., Cox, AJ., Ellis, DJ., Flatbush, MR., Gormley, NA., Humphray, SJ., Irving, LJ., Karbelashvili, MS., Kirk, SM., Li, H., Liu, X., Maisinger, KS., Murray, LJ., Obradovic, B., Ost, T., Parkinson, ML., Pratt, MR., Rasolonjatovo, IMJ., Reed, MT., Rigatti, R., Rodighiero, C., Ross, MT., Sabot, A., Sankar, SV., Scally, A., Schroth, GP., Smith, ME., Smith, VP., Spiridou, A., Torrance, PE., Tzonev, SS., Vermaas, EH., Walter, K., Wu, X., Zhang, L., Alam, MD., Anastasi, C., Aniebo, IC., Bailey, DMD., Bancarz, IR., Banerjee, S., Barbour, SG., Baybayan, PA., Benoit, VA., Benson, KF., Bevis, C., Black, PJ., Boodhun, A., Brennan, JS., Bridgham, JA., Brown, RC., Brown, AA., Buermann, DH., Bundu, AA., Burrows, JC., Carter, NP., Castillo, N., Chiara E Catenazzi, M., Chang, S., Neil Cooley, R., Crake, NR., Dada, OO., Diakoumakos, KD., Dominguez-Fernandez, B., Earnshaw, DJ., Egbujor, UC., Elmore, DW., Etchin, SS., Ewan, MR., Fedurco, M., Fraser, LJ., Fuentes Fajardo, KV., Scott Furey, W., George, D., Gietzen, KJ., Goddard, CP., Golda, GS., Granieri, PA., Green, DE., Gustafson, DL., Hansen, NF., Harnish, K., Haudenschild, CD., Heyer, NI., Hims, MM., Ho, JT., Horgan, AM., Hoschler, K., Hurwitz, S., Ivanov, DV., Johnson, MQ., James, T., Huw Jones, TA., Kang, G-D., Kerelska, TH., Kersey, AD., Khrebtukova, I., Kindwall, AP., Kingsbury, Z., Kokko-Gonzales, PI., Kumar, A., Laurent, MA., Lawley, CT., Lee, SE., Lee, X., Liao, AK., Loch, JA., Lok, M., Luo, S., Mammen, RM., Martin, JW., McCauley, PG., McNitt, P., Mehta, P., Moon, KW., Mullens, JW., Newington, T., Ning, Z., Ling Ng, B., Novo, SM., O'Neill, MJ., Osborne, MA., Osnowski, A., Ostadan, O., Paraschos, LL., Pickering, L., Pike, AC., Pike, AC., Chris Pinkard, D., Pliskin, DP., Podhasky, J., Quijano, VJ., Raczy, C., Rae, VH., Rawlings, SR., Chiva Rodriguez, A., Roe, PM., Rogers, J., Rogert Bacigalupo, MC., Romanov, N., Romieu, A., Roth, RK., Rourke, NJ., Ruediger, ST., Rusman, E., Sanches-Kuiper, RM., Schenker, MR., Seoane, JM., Shaw, RJ., Shiver, MK., Short, SW., Sizto, NL., Sluis, JP., Smith, MA., Ernest Sohna Sohna, J., Spence, EJ., Stevens, K., Sutton, N., Szajkowski, L., Tregidgo, CL., Turcatti, G., Vandevondele, S., Verhovsky, Y., Virk, SM., Wakelin, S., Walcott, GC., Wang, J., Worsley, GJ., Yan, J., Yau, L., Zuerlein, M., Rogers, J., Mullikin, JC., Hurles, ME., McCooke, NJ., West, JS., Oaks, FL., Lundberg, PL., Klenerman, D., Durbin, R. and Smith, AJ., 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature, v. 456
Doi: 10.1038/nature07517

Campbell, PJ., Stephens, PJ., Pleasance, ED., O'Meara, S., Li, H., Santarius, T., Stebbings, LA., Leroy, C., Edkins, S., Hardy, C., Teague, JW., Menzies, A., Goodhead, I., Turner, DJ., Clee, CM., Quail, MA., Cox, A., Brown, C., Durbin, R., Hurles, ME., Edwards, PAW., Bignell, GR., Stratton, MR. and Futreal, PA., 2008. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet, v. 40
Doi: http://doi.org/10.1038/ng.128

Ruan, J., Li, H., Chen, Z., Coghlan, A., Coin, LJM., Guo, Y., Hériché, J-K., Hu, Y., Kristiansen, K., Li, R., Liu, T., Moses, A., Qin, J., Vang, S., Vilella, AJ., Ureta-Vidal, A., Bolund, L., Wang, J. and Durbin, R., 2008. TreeFam: 2008 Update. Nucleic Acids Res, v. 36
Doi: http://doi.org/10.1093/nar/gkm1005

Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Zhang, J. and others, , 2008. The diploid genome sequence of an Asian individual Nature, v. 456

Li, H., Ruan, J. and Durbin, R., 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res, v. 18
Doi: http://doi.org/10.1101/gr.078212.108

Quail, MA., Kozarewa, I., Smith, F., Scally, A., Stephens, PJ., Durbin, R., Swerdlow, H. and Turner, DJ., 2008. A large genome center's improvements to the Illumina sequencing system. Nat Methods, v. 5
Doi: 10.1038/nmeth.1270

Rogers, A., Antoshechkin, I., Bieri, T., Blasiar, D., Bastiani, C., Canaran, P., Chan, J., Chen, WJ., Davis, P., Fernandes, J., Fiedler, TJ., Han, M., Harris, TW., Kishore, R., Lee, R., McKay, S., Müller, H-M., Nakamura, C., Ozersky, P., Petcherski, A., Schindelman, G., Schwarz, EM., Spooner, W., Tuli, MA., Van Auken, K., Wang, D., Wang, X., Williams, G., Yook, K., Durbin, R., Stein, LD., Spieth, J. and Sternberg, PW., 2008. WormBase 2007. Nucleic Acids Res, v. 36
Doi: http://doi.org/10.1093/nar/gkm975

Flicek, P., Aken, BL., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., Down, T., Dyer, SC., Eyre, T., Fitzgerald, S., Fernandez-Banet, J., Gräf, S., Haider, S., Hammond, M., Holland, R., Howe, KL., Howe, K., Johnson, N., Jenkinson, A., Kähäri, A., Keefe, D., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Megy, K., Meidl, P., Overduin, B., Parker, A., Pritchard, B., Prlic, A., Rice, S., Rios, D., Schuster, M., Sealy, I., Slater, G., Smedley, D., Spudich, G., Trevanion, S., Vilella, AJ., Vogel, J., White, S., Wood, M., Birney, E., Cox, T., Curwen, V., Durbin, R., Fernandez-Suarez, XM., Herrero, J., Hubbard, TJP., Kasprzyk, A., Proctor, G., Smith, J., Ureta-Vidal, A. and Searle, S., 2008. Ensembl 2008. Nucleic Acids Res, v. 36
Doi: http://doi.org/10.1093/nar/gkm988

2007

Hubbard, TJP., Aken, BL., Beal, K., Ballester, B., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cunningham, F., Cutts, T., Down, T., Dyer, SC., Fitzgerald, S., Fernandez-Banet, J., Graf, S., Haider, S., Hammond, M., Herrero, J., Holland, R., Howe, K., Howe, K., Johnson, N., Kahari, A., Keefe, D., Kokocinski, F., Kulesha, E., Lawson, D., Longden, I., Melsopp, C., Megy, K., Meidl, P., Ouverdin, B., Parker, A., Prlic, A., Rice, S., Rios, D., Schuster, M., Sealy, I., Severin, J., Slater, G., Smedley, D., Spudich, G., Trevanion, S., Vilella, A., Vogel, J., White, S., Wood, M., Cox, T., Curwen, V., Durbin, R., Fernandez-Suarez, XM., Flicek, P., Kasprzyk, A., Proctor, G., Searle, S., Smith, J., Ureta-Vidal, A. and Birney, E., 2007. Ensembl 2007. Nucleic Acids Res, v. 35
Doi: http://doi.org/10.1093/nar/gkl996

Moses, AM., Liku, ME., Li, JJ. and Durbin, R., 2007. Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites. Proc Natl Acad Sci U S A, v. 104
Doi: http://doi.org/10.1073/pnas.0700997104

Jiménez, JL., Hegemann, B., Hutchins, JRA., Peters, J-M. and Durbin, R., 2007. A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database. Genome Biol, v. 8
Doi: http://doi.org/10.1186/gb-2007-8-5-r90

Moses, AM., Hériché, J-K. and Durbin, R., 2007. Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase. Genome Biol, v. 8
Doi: http://doi.org/10.1186/gb-2007-8-2-r23

Coghlan, A. and Durbin, R., 2007. Genomix: a method for combining gene-finders' predictions, which uses evolutionary conservation of sequence and intron-exon structure. Bioinformatics, v. 23
Doi: http://doi.org/10.1093/bioinformatics/btm133

Bieri, T., Blasiar, D., Ozersky, P., Antoshechkin, I., Bastiani, C., Canaran, P., Chan, J., Chen, N., Chen, WJ., Davis, P., Fiedler, TJ., Girard, L., Han, M., Harris, TW., Kishore, R., Lee, R., McKay, S., Müller, H-M., Nakamura, C., Petcherski, A., Rangarajan, A., Rogers, A., Schindelman, G., Schwarz, EM., Spooner, W., Tuli, MA., Van Auken, K., Wang, D., Wang, X., Williams, G., Durbin, R., Stein, LD., Sternberg, PW. and Spieth, J., 2007. WormBase: new content and better access. Nucleic Acids Res, v. 35
Doi: http://doi.org/10.1093/nar/gkl818

2006

Carter, D. and Durbin, R., 2006. Vertebrate gene finding from multiple-species alignments using a two-level strategy. Genome Biol, v. 7 Suppl 1
Doi: http://doi.org/10.1186/gb-2006-7-s1-s6

Finn, RD., Mistry, J., Schuster-Böckler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R., Eddy, SR., Sonnhammer, ELL. and Bateman, A., 2006. Pfam: clans, web tools and services. Nucleic Acids Res, v. 34
Doi: http://doi.org/10.1093/nar/gkj149

Gregory, SG., Barlow, KF., Mclay, KE., Kaul, R., Swarbreck, D., Dunham, A., Scott, CE., Howe, KL., Woodfine, K., Spencer, CCA., Jones, MC., Gillson, C., Searle, S., Zhou, Y., Kokocinski, F., McDonald, L., Evans, R., Phillips, K., Atkinson, A., Cooper, R., Jones, C., Hall, RE., Andrews, TD., Lloyd, C., Ainscough, R., Almeida, JP., Ambrose, KD., Anderson, F., Andrew, RW., Ashwell, RIS., Aubin, K., Babbage, AK., Bagguley, CL., Bailey, J., Banerjee, R., Beasley, H., Bethel, G., Bird, CP., Bray-Allen, S., Brown, JY., Brown, AJ., Bryant, SP., Buckley, D., Burford, DC., Burrill, WDH., Burton, J., Bye, J., Carder, C., Chapman, JC., Clark, SY., Clarke, G., Clee, C., Clegg, SM., Cobley, V., Collier, RE., Corby, N., Coville, GJ., Davies, J., Deadman, R., Dhami, P., Dovey, O., Dunn, M., Earthrowl, M., Ellington, AG., Errington, H., Faulkner, LM., Frankish, A., Frankland, J., French, L., Garner, P., Garnett, J., Gay, L., Ghori, MRJ., Gibson, R., Gilby, LM., Gillett, W., Glithero, RJ., Grafham, DV., Gribble, SM., Griffiths, C., Griffiths-Jones, S., Grocock, R., Hammond, S., Harrison, ESI., Hart, E., Haugen, E., Heath, PD., Holmes, S., Holt, K., Howden, PJ., Hunt, AR., Hunt, SE., Hunter, G., Isherwood, J., James, R., Johnson, C., Johnson, D., Joy, A., Kay, M., Kershaw, JK., Kibukawa, M., Kimberley, AM., King, A., Knights, AJ., Lad, H., Laird, G., Langford, CF., Lawlor, S., Leongamornlert, DA., Lloyd, DM., Loveland, J., Lovell, J., Lush, MJ., Lyne, R., Martin, S., Mashreghi-Mohammadi, M., Matthews, L., Matthews, NSW., McLaren, S., Milne, S., Mistry, S., Moore, MJF., Nickerson, T., O'Dell, CN., Oliver, K., Palmeiri, A., Palmer, SA., Pandian, RD., Parker, A., Patel, D., Pearce, AV., Peck, AI., Pelan, S., Phelps, K., Phillimore, BJ., Plumb, R., Porter, KM., Prigmore, E., Rajan, J., Raymond, C., Rouse, G., Saenphimmachak, C., Sehra, HK., Sheridan, E., Shownkeen, R., Sims, S., Skuce, CD., Smith, M., Steward, C., Subramanian, S., Sycamore, N., Tracey, A., Tromans, A., Van Helmond, Z., Wallis, MWJM., White, S., Whitehead, SL., Wilkinson, JE., Willey, DL., Williams, H., Wilming, L., Wray, PW., Wu, Z., Coulson, A., Vaudin, M., Sulston, JE., Durbin, R., Hubbard, T., Wooster, R., Dunham, I., Carter, NP., McVean, G., Ross, MT., Harrow, J., Olson, MV., Beck, S., Rogers, J. and Bentley, DR., 2006. The DNA sequence and biological annotation of human chromosome 1 (vol 441, pg 315, 2006) NATURE, v. 443
Doi: http://doi.org/10.1038/nature05152

Birney, E., Andrews, D., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T., Down, T., Durbin, R., Fernandez-Suarez, XM., Flicek, P., Gräf, S., Hammond, M., Herrero, J., Howe, K., Iyer, V., Jekosch, K., Kähäri, A., Kasprzyk, A., Keefe, D., Kokocinski, F., Kulesha, E., London, D., Longden, I., Melsopp, C., Meidl, P., Overduin, B., Parker, A., Proctor, G., Prlic, A., Rae, M., Rios, D., Redmond, S., Schuster, M., Sealy, I., Searle, S., Severin, J., Slater, G., Smedley, D., Smith, J., Stabenau, A., Stalker, J., Trevanion, S., Ureta-Vidal, A., Vogel, J., White, S., Woodwark, C. and Hubbard, TJP., 2006. Ensembl 2006. Nucleic Acids Res, v. 34
Doi: http://doi.org/10.1093/nar/gkj133

Gregory, SG., Barlow, KF., McLay, KE., Kaul, R., Swarbreck, D., Dunham, A., Scott, CE., Howe, KL., Woodfine, K., Spencer, CCA., Jones, MC., Gillson, C., Searle, S., Zhou, Y., Kokocinski, F., McDonald, L., Evans, R., Phillips, K., Atkinson, A., Cooper, R., Jones, C., Hall, RE., Andrews, TD., Lloyd, C., Ainscough, R., Almeida, JP., Ambrose, KD., Anderson, F., Andrew, RW., Ashwell, RIS., Aubin, K., Babbage, AK., Bagguley, CL., Bailey, J., Beasley, H., Bethel, G., Bird, CP., Bray-Allen, S., Brown, JY., Brown, AJ., Buckley, D., Burton, J., Bye, J., Carder, C., Chapman, JC., Clark, SY., Clarke, G., Clee, C., Cobley, V., Collier, RE., Corby, N., Coville, GJ., Davies, J., Deadman, R., Dunn, M., Earthrowl, M., Ellington, AG., Errington, H., Frankish, A., Frankland, J., French, L., Garner, P., Garnett, J., Gay, L., Ghori, MRJ., Gibson, R., Gilby, LM., Gillett, W., Glithero, RJ., Grafham, DV., Griffiths, C., Griffiths-Jones, S., Grocock, R., Hammond, S., Harrison, ESI., Hart, E., Haugen, E., Heath, PD., Holmes, S., Holt, K., Howden, PJ., Hunt, AR., Hunt, SE., Hunter, G., Isherwood, J., James, R., Johnson, C., Johnson, D., Joy, A., Kay, M., Kershaw, JK., Kibukawa, M., Kimberley, AM., King, A., Knights, AJ., Lad, H., Laird, G., Lawlor, S., Leongamornlert, DA., Lloyd, DM., Loveland, J., Lovell, J., Lush, MJ., Lyne, R., Martin, S., Mashreghi-Mohammadi, M., Matthews, L., Matthews, NSW., McLaren, S., Milne, S., Mistry, S., Moore, MJF., Nickerson, T., O'Dell, CN., Oliver, K., Palmeiri, A., Palmer, SA., Parker, A., Patel, D., Pearce, AV., Peck, AI., Pelan, S., Phelps, K., Phillimore, BJ., Plumb, R., Rajan, J., Raymond, C., Rouse, G., Saenphimmachak, C., Sehra, HK., Sheridan, E., Shownkeen, R., Sims, S., Skuce, CD., Smith, M., Steward, C., Subramanian, S., Sycamore, N., Tracey, A., Tromans, A., Van Helmond, Z., Wall, M., Wallis, JM., White, S., Whitehead, SL., Wilkinson, JE., Willey, DL., Williams, H., Wilming, L., Wray, PW., Wu, Z., Coulson, A., Vaudin, M., Sulston, JE., Durbin, R., Hubbard, T., Wooster, R., Dunham, I., Carter, NP., McVean, G., Ross, MT., Harrow, J., Olson, MV., Beck, S., Rogers, J., Bentley, DR., Banerjee, R., Bryant, SP., Burford, DC., Burrill, WDH., Clegg, SM., Dhami, P., Dovey, O., Faulkner, LM., Gribble, SM., Langford, CF., Pandian, RD., Porter, KM. and Prigmore, E., 2006. The DNA sequence and biological annotation of human chromosome 1. Nature, v. 441
Doi: http://doi.org/10.1038/nature04727

Jiménez, JL. and Durbin, R., 2006. [X]uniqMAP: unique gene sequence regions in the human and mouse genomes. BMC Genomics, v. 7
Doi: http://doi.org/10.1186/1471-2164-7-249

Hajarnavis, A. and Durbin, R., 2006. A conserved sequence motif in 3' untranslated regions of ribosomal protein mRNAs in nematodes. RNA, v. 12
Doi: http://doi.org/10.1261/rna.51306

Minichiello, MJ. and Durbin, R., 2006. Mapping trait loci by use of inferred ancestral recombination graphs. Am J Hum Genet, v. 79
Doi: http://doi.org/10.1086/508901

Li, H., Coghlan, A., Ruan, J., Coin, LJ., Hériché, J-K., Osmotherly, L., Li, R., Liu, T., Zhang, Z., Bolund, L., Wong, GK-S., Zheng, W., Dehal, P., Wang, J. and Durbin, R., 2006. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res, v. 34
Doi: http://doi.org/10.1093/nar/gkj118

Schwarz, EM., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Canaran, P., Chan, J., Chen, N., Chen, WJ., Davis, P., Fiedler, TJ., Girard, L., Harris, TW., Kenny, EE., Kishore, R., Lawson, D., Lee, R., Müller, H-M., Nakamura, C., Ozersky, P., Petcherski, A., Rogers, A., Spooner, W., Tuli, MA., Van Auken, K., Wang, D., Durbin, R., Spieth, J., Stein, LD. and Sternberg, PW., 2006. WormBase: better software, richer content. Nucleic Acids Res, v. 34
Doi: http://doi.org/10.1093/nar/gkj061

2005

Mulder, NJ., Apweiler, R., Attwood, TK., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Nikolskaya, AN., Orchard, S., Pagni, M., Ponting, CP., Quevillon, E., Selengut, J., Sigrist, CJA., Silventoinen, V., Studholme, DJ., Vaughan, R. and Wu, CH., 2005. InterPro, progress and status in 2005. Nucleic Acids Res, v. 33
Doi: http://doi.org/10.1093/nar/gki106

Chen, N., Harris, TW., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Bradnam, K., Canaran, P., Chan, J., Chen, C-K., Chen, WJ., Cunningham, F., Davis, P., Kenny, E., Kishore, R., Lawson, D., Lee, R., Muller, H-M., Nakamura, C., Pai, S., Ozersky, P., Petcherski, A., Rogers, A., Sabo, A., Schwarz, EM., Van Auken, K., Wang, Q., Durbin, R., Spieth, J., Sternberg, PW. and Stein, LD., 2005. WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res, v. 33
Doi: http://doi.org/10.1093/nar/gki066

Eilbeck, K., Lewis, SE., Mungall, CJ., Yandell, M., Stein, L., Durbin, R. and Ashburner, M., 2005. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol, v. 6

Hubbard, T., Andrews, D., Caccamo, M., Cameron, G., Chen, Y., Clamp, M., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T., Down, T., Durbin, R., Fernandez-Suarez, XM., Gilbert, J., Hammond, M., Herrero, J., Hotz, H., Howe, K., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Kokocinsci, F., London, D., Longden, I., McVicker, G., Melsopp, C., Meidl, P., Potter, S., Proctor, G., Rae, M., Rios, D., Schuster, M., Searle, S., Severin, J., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Trevanion, S., Ureta-Vidal, A., Vogel, J., White, S., Woodwark, C. and Birney, E., 2005. Ensembl 2005. Nucleic Acids Res, v. 33
Doi: http://doi.org/10.1093/nar/gki138

Ross, MT., Grafham, DV., Coffey, AJ., Scherer, S., McLay, K., Muzny, D., Platzer, M., Howell, GR., Burrows, C., Bird, CP., Frankish, A., Lovell, FL., Howe, KL., Ashurst, JL., Fulton, RS., Sudbrak, R., Wen, G., Jones, MC., Hurles, ME., Andrews, TD., Scott, CE., Searle, S., Ramser, J., Whittaker, A., Deadman, R., Carter, NP., Hunt, SE., Chen, R., Cree, A., Gunaratne, P., Havlak, P., Hodgson, A., Metzker, ML., Richards, S., Scott, G., Steffen, D., Sodergren, E., Wheeler, DA., Worley, KC., Ainscough, R., Ambrose, KD., Ansari-Lari, MA., Aradhya, S., Ashwell, RIS., Babbage, AK., Bagguley, CL., Ballabio, A., Banerjee, R., Barker, GE., Barlow, KF., Barrett, IP., Bates, KN., Beare, DM., Beasley, H., Beasley, O., Beck, A., Bethel, G., Blechschmidt, K., Brady, N., Bray-Allen, S., Bridgeman, AM., Brown, AJ., Brown, MJ., Bonnin, D., Bruford, EA., Buhay, C., Burch, P., Burford, D., Burgess, J., Burrill, W., Burton, J., Bye, JM., Carder, C., Carrel, L., Chako, J., Chapman, JC., Chavez, D., Chen, E., Chen, G., Chen, Y., Chen, Z., Chinault, C., Ciccodicola, A., Clark, SY., Clarke, G., Clee, CM., Clegg, S., Clerc-Blankenburg, K., Clifford, K., Cobley, V., Cole, CG., Conquer, JS., Corby, N., Connor, RE., David, R., Davies, J., Davis, C., Davis, J., Delgado, O., Deshazo, D., Dhami, P., Ding, Y., Dinh, H., Dodsworth, S., Draper, H., Dugan-Rocha, S., Dunham, A., Dunn, M., Durbin, KJ., Dutta, I., Eades, T., Ellwood, M., Emery-Cohen, A., Errington, H., Evans, KL., Faulkner, L., Francis, F., Frankland, J., Fraser, AE., Galgoczy, P., Gilbert, J., Gill, R., Glöckner, G., Gregory, SG., Gribble, S., Griffiths, C., Grocock, R., Gu, Y., Gwilliam, R., Hamilton, C., Hart, EA., Hawes, A., Heath, PD., Heitmann, K., Hennig, S., Hernandez, J., Hinzmann, B., Ho, S., Hoffs, M., Howden, PJ., Huckle, EJ., Hume, J., Hunt, PJ., Hunt, AR., Isherwood, J., Jacob, L., Johnson, D., Jones, S., de Jong, PJ., Joseph, SS., Keenan, S., Kelly, S., Kershaw, JK., Khan, Z., Kioschis, P., Klages, S., Knights, AJ., Kosiura, A., Kovar-Smith, C., Laird, GK., Langford, C., Lawlor, S., Leversha, M., Lewis, L., Liu, W., Lloyd, C., Lloyd, DM., Loulseged, H., Loveland, JE., Lovell, JD., Lozado, R., Lu, J., Lyne, R., Ma, J., Maheshwari, M., Matthews, LH., McDowall, J., McLaren, S., McMurray, A., Meidl, P., Meitinger, T., Milne, S., Miner, G., Mistry, SL., Morgan, M., Morris, S., Müller, I., Mullikin, JC., Nguyen, N., Nordsiek, G., Nyakatura, G., O'Dell, CN., Okwuonu, G., Palmer, S., Pandian, R., Parker, D., Parrish, J., Pasternak, S., Patel, D., Pearce, AV., Pearson, DM., Pelan, SE., Perez, L., Porter, KM., Ramsey, Y., Reichwald, K., Rhodes, S., Ridler, KA., Schlessinger, D., Schueler, MG., Sehra, HK., Shaw-Smith, C., Shen, H., Sheridan, EM., Shownkeen, R., Skuce, CD., Smith, ML., Sotheran, EC., Steingruber, HE., Steward, CA., Storey, R., Swann, RM., Swarbreck, D., Tabor, PE., Taudien, S., Taylor, T., Teague, B., Thomas, K., Thorpe, A., Timms, K., Tracey, A., Trevanion, S., Tromans, AC., d'Urso, M., Verduzco, D., Villasana, D., Waldron, L., Wall, M., Wang, Q., Warren, J., Warry, GL., Wei, X., West, A., Whitehead, SL., Whiteley, MN., Wilkinson, JE., Willey, DL., Williams, G., Williams, L., Williamson, A., Williamson, H., Wilming, L., Woodmansey, RL., Wray, PW., Yen, J., Zhang, J., Zhou, J., Zoghbi, H., Zorilla, S., Buck, D., Reinhardt, R., Poustka, A., Rosenthal, A., Lehrach, H., Meindl, A., Minx, PJ., Hillier, LW., Willard, HF., Wilson, RK., Waterston, RH., Rice, CM., Vaudin, M., Coulson, A., Nelson, DL., Weinstock, G., Sulston, JE., Durbin, R., Hubbard, T., Gibbs, RA., Beck, S., Rogers, J. and Bentley, DR., 2005. The DNA sequence of the human X chromosome. Nature, v. 434
Doi: http://doi.org/10.1038/nature03440

2004

Birney, E., Clamp, M. and Durbin, R., 2004. GeneWise and Genomewise. Genome Res, v. 14
Doi: http://doi.org/10.1101/gr.1865504

Coin, L., Bateman, A. and Durbin, R., 2004. Enhanced protein domain discovery using taxonomy. BMC Bioinformatics, v. 5
Doi: http://doi.org/10.1186/1471-2105-5-56

Harris, TW., Chen, N., Cunningham, F., Tello-Ruiz, M., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Bradnam, K., Chan, J., Chen, C-K., Chen, WJ., Davis, P., Kenny, E., Kishore, R., Lawson, D., Lee, R., Muller, H-M., Nakamura, C., Ozersky, P., Petcherski, A., Rogers, A., Sabo, A., Schwarz, EM., Van Auken, K., Wang, Q., Durbin, R., Spieth, J., Sternberg, PW. and Stein, LD., 2004. WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res, v. 32
Doi: http://doi.org/10.1093/nar/gkh066

Birney, E., Andrews, D., Bevan, P., Caccamo, M., Cameron, G., Chen, Y., Clarke, L., Coates, G., Cox, T., Cuff, J., Curwen, V., Cutts, T., Down, T., Durbin, R., Eyras, E., Fernandez-Suarez, XM., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H., Iyer, V., Kahari, A., Jekosch, K., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, C., Clamp, M. and Hubbard, T., 2004. Ensembl 2004. Nucleic Acids Res, v. 32
Doi: http://doi.org/10.1093/nar/gkh038

Coin, L. and Durbin, R., 2004. Improved techniques for the identification of pseudogenes. Bioinformatics, v. 20 Suppl 1
Doi: http://doi.org/10.1093/bioinformatics/bth942

Humphray, SJ., Oliver, K., Hunt, AR., Plumb, RW., Loveland, JE., Howe, KL., Andrews, TD., Searle, S., Hunt, SE., Scott, CE., Jones, MC., Ainscough, R., Almeida, JP., Ambrose, KD., Ashwell, RIS., Babbage, AK., Babbage, S., Bagguley, CL., Bailey, J., Banerjee, R., Barker, DJ., Barlow, KF., Bates, K., Beasley, H., Beasley, O., Bird, CP., Bray-Allen, S., Brown, AJ., Brown, JY., Burford, D., Burrill, W., Burton, J., Carder, C., Carter, NP., Chapman, JC., Chen, Y., Clarke, G., Clark, SY., Clee, CM., Clegg, S., Collier, RE., Corby, N., Crosier, M., Cummings, AT., Davies, J., Dhami, P., Dunn, M., Dutta, I., Dyer, LW., Earthrowl, ME., Faulkner, L., Fleming, CJ., Frankish, A., Frankland, JA., French, L., Fricker, DG., Garner, P., Garnett, J., Ghori, J., Gilbert, JGR., Glison, C., Grafham, DV., Gribble, S., Griffiths, C., Griffiths-Jones, S., Grocock, R., Guy, J., Hall, RE., Hammond, S., Harley, JL., Harrison, ESI., Hart, EA., Heath, PD., Henderson, CD., Hopkins, BL., Howard, PJ., Howden, PJ., Huckle, E., Johnson, C., Johnson, D., Joy, AA., Kay, M., Keenan, S., Kershaw, JK., Kimberley, AM., King, A., Knights, A., Laird, GK., Langford, C., Lawlor, S., Leongamornlert, DA., Leversha, M., Lloyd, C., Lloyd, DM., Lovell, J., Martin, S., Mashreghi-Mohammadi, M., Matthews, L., McLaren, S., McLay, KE., McMurray, A., Milne, S., Nickerson, T., Nisbett, J., Nordsiek, G., Pearce, AV., Peck, AI., Porter, KM., Pandian, R., Pelan, S., Phillimore, B., Povey, S., Ramsey, Y., Rand, V., Scharfe, M., Sehra, HK., Shownkeen, R., Sims, SK., Skuce, CD., Smith, M., Steward, CA., Swarbreck, D., Sycamore, N., Tester, J., Thorpe, A., Tracey, A., Tromans, A., Thomas, DW., Wall, M., Wallis, JM., West, AP., Whitehead, SL., Willey, DL., Williams, SA., Wilming, L., Wray, PW., Young, L., Ashurst, JL., Coulson, A., Blöcker, H., Durbin, R., Sulston, JE., Hubbard, T., Jackson, MJ., Bentley, DR., Beck, S., Rogers, J. and Dunham, I., 2004. DNA sequence and analysis of human chromosome 9. Nature, v. 429
Doi: http://doi.org/10.1038/nature02465

Dunham, A., Matthews, LH., Burton, J., Ashurst, JL., Howe, KL., Ashcroft, KJ., Beare, DM., Burford, DC., Hunt, SE., Griffiths-Jones, S., Jones, MC., Keenan, SJ., Oliver, K., Scott, CE., Ainscough, R., Almeida, JP., Ambrose, KD., Andrews, DT., Ashwell, RIS., Babbage, AK., Bagguley, CL., Bailey, J., Bannerjee, R., Barlow, KF., Bates, K., Beasley, H., Bird, CP., Bray-Allen, S., Brown, AJ., Brown, JY., Burrill, W., Carder, C., Carter, NP., Chapman, JC., Clamp, ME., Clark, SY., Clarke, G., Clee, CM., Clegg, SCM., Cobley, V., Collins, JE., Corby, N., Coville, GJ., Deloukas, P., Dhami, P., Dunham, I., Dunn, M., Earthrowl, ME., Ellington, AG., Faulkner, L., Frankish, AG., Frankland, J., French, L., Garner, P., Garnett, J., Gilbert, JGR., Gilson, CJ., Ghori, J., Grafham, DV., Gribble, SM., Griffiths, C., Hall, RE., Hammond, S., Harley, JL., Hart, EA., Heath, PD., Howden, PJ., Huckle, EJ., Hunt, PJ., Hunt, AR., Johnson, C., Johnson, D., Kay, M., Kimberley, AM., King, A., Laird, GK., Langford, CJ., Lawlor, S., Leongamornlert, DA., Lloyd, DM., Lloyd, C., Loveland, JE., Lovell, J., Martin, S., Mashreghi-Mohammadi, M., McLaren, SJ., McMurray, A., Milne, S., Moore, MJF., Nickerson, T., Palmer, SA., Pearce, AV., Peck, AI., Pelan, S., Phillimore, B., Porter, KM., Rice, CM., Searle, S., Sehra, HK., Shownkeen, R., Skuce, CD., Smith, M., Steward, CA., Sycamore, N., Tester, J., Thomas, DW., Tracey, A., Tromans, A., Tubby, B., Wall, M., Wallis, JM., West, AP., Whitehead, SL., Willey, DL., Wilming, L., Wray, PW., Wright, MW., Young, L., Coulson, A., Durbin, R., Hubbard, T., Sulston, JE., Beck, S., Bentley, DR., Rogers, J. and Ross, MT., 2004. The DNA sequence and analysis of human chromosome 13. Nature, v. 428
Doi: http://doi.org/10.1038/nature02379

Birney, E., Andrews, TD., Bevan, P., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cuff, J., Curwen, V., Cutts, T., Down, T., Eyras, E., Fernandez-Suarez, XM., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H-R., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, KC., Cameron, G., Durbin, R., Cox, A., Hubbard, T. and Clamp, M., 2004. An overview of Ensembl. Genome Res, v. 14
Doi: http://doi.org/10.1101/gr.1860604

Bateman, A., Coin, L., Durbin, R., Finn, RD., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, ELL., Studholme, DJ., Yeats, C. and Eddy, SR., 2004. The Pfam protein families database. Nucleic Acids Res, v. 32
Doi: http://doi.org/10.1093/nar/gkh121

Deloukas, P., Earthrowl, ME., Grafham, DV., Rubenfield, M., French, L., Steward, CA., Sims, SK., Jones, MC., Searle, S., Scott, C., Howe, K., Hunt, SE., Andrews, TD., Gilbert, JGR., Swarbreck, D., Ashurst, JL., Taylor, A., Battles, J., Bird, CP., Ainscough, R., Almeida, JP., Ashwell, RIS., Ambrose, KD., Babbage, AK., Bagguley, CL., Bailey, J., Banerjee, R., Bates, K., Beasley, H., Bray-Allen, S., Brown, AJ., Brown, JY., Burford, DC., Burrill, W., Burton, J., Cahill, P., Camire, D., Carter, NP., Chapman, JC., Clark, SY., Clarke, G., Clee, CM., Clegg, S., Corby, N., Coulson, A., Dhami, P., Dutta, I., Dunn, M., Faulkner, L., Frankish, A., Frankland, JA., Garner, P., Garnett, J., Gribble, S., Griffiths, C., Grocock, R., Gustafson, E., Hammond, S., Harley, JL., Hart, E., Heath, PD., Ho, TP., Hopkins, B., Horne, J., Howden, PJ., Huckle, E., Hynds, C., Johnson, C., Johnson, D., Kana, A., Kay, M., Kimberley, AM., Kershaw, JK., Kokkinaki, M., Laird, GK., Lawlor, S., Lee, HM., Leongamornlert, DA., Laird, G., Lloyd, C., Lloyd, DM., Loveland, J., Lovell, J., McLaren, S., McLay, KE., McMurray, A., Mashreghi-Mohammadi, M., Matthews, L., Milne, S., Nickerson, T., Nguyen, M., Overton-Larty, E., Palmer, SA., Pearce, AV., Peck, AI., Pelan, S., Phillimore, B., Porter, K., Rice, CM., Rogosin, A., Ross, MT., Sarafidou, T., Sehra, HK., Shownkeen, R., Skuce, CD., Smith, M., Standring, L., Sycamore, N., Tester, J., Thorpe, A., Torcasso, W., Tracey, A., Tromans, A., Tsolas, J., Wall, M., Walsh, J., Wang, H., Weinstock, K., West, AP., Willey, DL., Whitehead, SL., Wilming, L., Wray, PW., Young, L., Chen, Y., Lovering, RC., Moschonas, NK., Siebert, R., Fechtel, K., Bentley, D., Durbin, R., Hubbard, T., Doucette-Stamm, L., Beck, S., Smith, DR. and Rogers, J., 2004. The DNA sequence and comparative analysis of human chromosome 10. Nature, v. 429
Doi: http://doi.org/10.1038/nature02462

Gibbs, RA., Weinstock, GM., Metzker, ML., Muzny, DM., Sodergren, EJ., Scherer, S., Scott, G., Steffen, D., Worley, KC., Burch, PE., Okwuonu, G., Hines, S., Lewis, L., DeRamo, C., Delgado, O., Dugan-Rocha, S., Miner, G., Morgan, M., Hawes, A., Gill, R., Celera, , Holt, RA., Adams, MD., Amanatides, PG., Baden-Tillson, H., Barnstead, M., Chin, S., Evans, CA., Ferriera, S., Fosler, C., Glodek, A., Gu, Z., Jennings, D., Kraft, CL., Nguyen, T., Pfannkoch, CM., Sitter, C., Sutton, GG., Venter, JC., Woodage, T., Smith, D., Lee, H-M., Gustafson, E., Cahill, P., Kana, A., Doucette-Stamm, L., Weinstock, K., Fechtel, K., Weiss, RB., Dunn, DM., Green, ED., Blakesley, RW., Bouffard, GG., De Jong, PJ., Osoegawa, K., Zhu, B., Marra, M., Schein, J., Bosdet, I., Fjell, C., Jones, S., Krzywinski, M., Mathewson, C., Siddiqui, A., Wye, N., McPherson, J., Zhao, S., Fraser, CM., Shetty, J., Shatsman, S., Geer, K., Chen, Y., Abramzon, S., Nierman, WC., Havlak, PH., Chen, R., Durbin, KJ., Egan, A., Ren, Y., Song, X-Z., Li, B., Liu, Y., Qin, X., Cawley, S., Worley, KC., Cooney, AJ., D'Souza, LM., Martin, K., Wu, JQ., Gonzalez-Garay, ML., Jackson, AR., Kalafus, KJ., McLeod, MP., Milosavljevic, A., Virk, D., Volkov, A., Wheeler, DA., Zhang, Z., Bailey, JA., Eichler, EE., Tuzun, E., Birney, E., Mongin, E., Ureta-Vidal, A., Woodwark, C., Zdobnov, E., Bork, P., Suyama, M., Torrents, D., Alexandersson, M., Trask, BJ., Young, JM., Huang, H., Wang, H., Xing, H., Daniels, S., Gietzen, D., Schmidt, J., Stevens, K., Vitt, U., Wingrove, J., Camara, F., Mar Albà, M., Abril, JF., Guigo, R., Smit, A., Dubchak, I., Rubin, EM., Couronne, O., Poliakov, A., Hübner, N., Ganten, D., Goesele, C., Hummel, O., Kreitler, T., Lee, Y-A., Monti, J., Schulz, H., Zimdahl, H., Himmelbauer, H., Lehrach, H., Jacob, HJ., Bromberg, S., Gullings-Handley, J., Jensen-Seaman, MI., Kwitek, AE., Lazar, J., Pasko, D., Tonellato, PJ., Twigger, S., Ponting, CP., Duarte, JM., Rice, S., Goodstadt, L., Beatson, SA., Emes, RD., Winter, EE., Webber, C., Brandt, P., Nyakatura, G., Adetobi, M., Chiaromonte, F., Elnitski, L., Eswara, P., Hardison, RC., Hou, M., Kolbe, D., Makova, K., Miller, W., Nekrutenko, A., Riemer, C., Schwartz, S., Taylor, J., Yang, S., Zhang, Y., Lindpaintner, K., Andrews, TD., Caccamo, M., Clamp, M., Clarke, L., Curwen, V., Durbin, R., Eyras, E., Searle, SM., Cooper, GM., Batzoglou, S., Brudno, M., Sidow, A., Stone, EA., Venter, JC., Payseur, BA., Bourque, G., López-Otín, C., Puente, XS., Chakrabarti, K., Chatterji, S., Dewey, C., Pachter, L., Bray, N., Yap, VB., Caspi, A., Tesler, G., Pevzner, PA., Haussler, D., Roskin, KM., Baertsch, R., Clawson, H., Furey, TS., Hinrichs, AS., Karolchik, D., Kent, WJ., Rosenbloom, KR., Trumbower, H., Weirauch, M., Cooper, DN., Stenson, PD., Ma, B., Brent, M., Arumugam, M., Shteynberg, D., Copley, RR., Taylor, MS., Riethman, H., Mudunuri, U., Peterson, J., Guyer, M., Felsenfeld, A., Old, S., Mockrin, S., Collins, F. and Rat Genome Sequencing Project Consortium, , 2004. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, v. 428
Doi: http://doi.org/10.1038/nature02426

Hajarnavis, A., Korf, I. and Durbin, R., 2004. A probabilistic model of 3' end formation in Caenorhabditis elegans. Nucleic Acids Res, v. 32
Doi: http://doi.org/10.1093/nar/gkh656

International Human Genome Sequencing Consortium., and Woodfine, K., 2004. Finishing the euchromatic sequence of the human genome Nature, v. 431

Meyer, IM. and Durbin, R., 2004. Gene structure conservation aids similarity based gene prediction. Nucleic Acids Res, v. 32
Doi: http://doi.org/10.1093/nar/gkh211

2003

Stein, LD., Bao, Z., Blasiar, D., Blumenthal, T., Brent, MR., Chen, N., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., Coulson, A., D'Eustachio, P., Fitch, DHA., Fulton, LA., Fulton, RE., Griffiths-Jones, S., Harris, TW., Hillier, LW., Kamath, R., Kuwabara, PE., Mardis, ER., Marra, MA., Miner, TL., Minx, P., Mullikin, JC., Plumb, RW., Rogers, J., Schein, JE., Sohrmann, M., Spieth, J., Stajich, JE., Wei, C., Willey, D., Wilson, RK., Durbin, R. and Waterston, RH., 2003. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol, v. 1
Doi: http://doi.org/10.1371/journal.pbio.0000045

Coin, L., Bateman, A. and Durbin, R., 2003. Enhanced protein domain discovery by using language modeling techniques from speech recognition. Proc Natl Acad Sci U S A, v. 100
Doi: http://doi.org/10.1073/pnas.0737502100

Kamath, RS., Fraser, AG., Dong, Y., Poulin, G., Durbin, R., Gotta, M., Kanapin, A., Le Bot, N., Moreno, S., Sohrmann, M., Welchman, DP., Zipperlen, P. and Ahringer, J., 2003. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature, v. 421
Doi: 10.1038/nature01278

Clamp, M., Andrews, D., Barker, D., Bevan, P., Cameron, G., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen, V., Down, T., Durbin, R., Eyras, E., Gilbert, J., Hammond, M., Hubbard, T., Kasprzyk, A., Keefe, D., Lehvaslaiho, H., Iyer, V., Melsopp, C., Mongin, E., Pettett, R., Potter, S., Rust, A., Schmidt, E., Searle, S., Slater, G., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Stupka, E., Ureta-Vidal, A., Vastrik, I. and Birney, E., 2003. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res, v. 31
Doi: http://doi.org/10.1093/nar/gkg083

Mungall, AJ., Palmer, SA., Sims, SK., Edwards, CA., Ashurst, JL., Wilming, L., Jones, MC., Horton, R., Hunt, SE., Scott, CE., Gilbert, JGR., Clamp, ME., Bethel, G., Milne, S., Ainscough, R., Almeida, JP., Ambrose, KD., Andrews, TD., Ashwell, RIS., Babbage, AK., Bagguley, CL., Bailey, J., Banerjee, R., Barker, DJ., Barlow, KF., Bates, K., Beare, DM., Beasley, H., Beasley, O., Bird, CP., Blakey, S., Bray-Allen, S., Brook, J., Brown, AJ., Brown, JY., Burford, DC., Burrill, W., Burton, J., Carder, C., Carter, NP., Chapman, JC., Clark, SY., Clark, G., Clee, CM., Clegg, S., Cobley, V., Collier, RE., Collins, JE., Colman, LK., Corby, NR., Coville, GJ., Culley, KM., Dhami, P., Davies, J., Dunn, M., Earthrowl, ME., Ellington, AE., Evans, KA., Faulkner, L., Francis, MD., Frankish, A., Frankland, J., French, L., Garner, P., Garnett, J., Ghori, MJR., Gilby, LM., Gillson, CJ., Glithero, RJ., Grafham, DV., Grant, M., Gribble, S., Griffiths, C., Griffiths, M., Hall, R., Halls, KS., Hammond, S., Harley, JL., Hart, EA., Heath, PD., Heathcott, R., Holmes, SJ., Howden, PJ., Howe, KL., Howell, GR., Huckle, E., Humphray, SJ., Humphries, MD., Hunt, AR., Johnson, CM., Joy, AA., Kay, M., Keenan, SJ., Kimberley, AM., King, A., Laird, GK., Langford, C., Lawlor, S., Leongamornlert, DA., Leversha, M., Lloyd, CR., Lloyd, DM., Loveland, JE., Lovell, J., Martin, S., Mashreghi-Mohammadi, M., Maslen, GL., Matthews, L., McCann, OT., McLaren, SJ., McLay, K., McMurray, A., Moore, MJF., Mullikin, JC., Niblett, D., Nickerson, T., Novik, KL., Oliver, K., Overton-Larty, EK., Parker, A., Patel, R., Pearce, AV., Peck, AI., Phillimore, B., Phillips, S., Plumb, RW., Porter, KM., Ramsey, Y., Ranby, SA., Rice, CM., Ross, MT., Searle, SM., Sehra, HK., Sheridan, E., Skuce, CD., Smith, S., Smith, M., Spraggon, L., Squares, SL., Steward, CA., Sycamore, N., Tamlyn-Hall, G., Tester, J., Theaker, AJ., Thomas, DW., Thorpe, A., Tracey, A., Tromans, A., Tubby, B., Wall, M., Wallis, JM., West, AP., White, SS., Whitehead, SL., Whittaker, H., Wild, A., Willey, DJ., Wilmer, TE., Wood, JM., Wray, PW., Wyatt, JC., Young, L., Younger, RM., Bentley, DR., Coulson, A., Durbin, R., Hubbard, T., Sulston, JE., Dunham, I., Rogers, J. and Beck, S., 2003. The DNA sequence and analysis of human chromosome 6. Nature, v. 425
Doi: http://doi.org/10.1038/nature02055

Mulder, NJ., Apweiler, R., Attwood, TK., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, RR., Courcelle, E., Das, U., Durbin, R., Falquet, L., Fleischmann, W., Griffiths-Jones, S., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Lonsdale, D., Silventoinen, V., Orchard, SE., Pagni, M., Peyruc, D., Ponting, CP., Selengut, JD., Servant, F., Sigrist, CJA., Vaughan, R. and Zdobnov, EM., 2003. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res, v. 31
Doi: http://doi.org/10.1093/nar/gkg046

Myers, G. and Durbin, R., 2003. A table-driven, full-sensitivity similarity search algorithm. J Comput Biol, v. 10
Doi: http://doi.org/10.1089/106652703321825919

Harris, TW., Lee, R., Schwarz, E., Bradnam, K., Lawson, D., Chen, W., Blasier, D., Kenny, E., Cunningham, F., Kishore, R., Chan, J., Muller, H-M., Petcherski, A., Thorisson, G., Day, A., Bieri, T., Rogers, A., Chen, C-K., Spieth, J., Sternberg, P., Durbin, R. and Stein, LD., 2003. WormBase: a cross-species database for comparative genomics. Nucleic Acids Res, v. 31
Doi: http://doi.org/10.1093/nar/gkg053

2002

Mulder, NJ., Apweiler, R., Attwood, TK., Bairoch, A., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R., Courcelle, E., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Griffith-Jones, S., Haft, D., Hermjakob, H., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Orchard, S., Pagni, M., Peyruc, D., Ponting, CP., Servant, F., Sigrist, CJA. and InterPro Consortium, , 2002. InterPro: an integrated documentation resource for protein families, domains and functional sites. Brief Bioinform, v. 3
Doi: http://doi.org/10.1093/bib/3.3.225

Howe, K., Bateman, A. and Durbin, R., 2002. QuickTree: building huge Neighbour-Joining trees of protein sequences. Bioinformatics, v. 18
Doi: http://doi.org/10.1093/bioinformatics/18.11.1546

Meyer, IM. and Durbin, R., 2002. Comparative ab initio prediction of gene structures using pair HMMs. Bioinformatics, v. 18
Doi: http://doi.org/10.1093/bioinformatics/18.10.1309

Hubbard, T., Barker, D., Birney, E., Cameron, G., Chen, Y., Clark, L., Cox, T., Cuff, J., Curwen, V., Down, T., Durbin, R., Eyras, E., Gilbert, J., Hammond, M., Huminiecki, L., Kasprzyk, A., Lehvaslaiho, H., Lijnzaad, P., Melsopp, C., Mongin, E., Pettett, R., Pocock, M., Potter, S., Rust, A., Schmidt, E., Searle, S., Slater, G., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Stupka, E., Ureta-Vidal, A., Vastrik, I. and Clamp, M., 2002. The Ensembl genome database project. Nucleic Acids Res, v. 30
Doi: http://doi.org/10.1093/nar/30.1.38

Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, SR., Griffiths-Jones, S., Howe, KL., Marshall, M. and Sonnhammer, ELL., 2002. The Pfam protein families database. Nucleic Acids Res, v. 30
Doi: http://doi.org/10.1093/nar/30.1.276

Howe, KL., Chothia, T. and Durbin, R., 2002. GAZE: a generic framework for the integration of gene-prediction data by dynamic programming. Genome Res, v. 12
Doi: http://doi.org/10.1101/gr.149502

2001

Levine, A. and Durbin, R., 2001. A computational scan for U12-dependent introns in the human genome sequence. Nucleic Acids Res, v. 29
Doi: http://doi.org/10.1093/nar/29.19.4006

Stein, L., Mangone, M., Schwarz, E., Durbin, R., Thierry-Mieg, J., Spieth, J. and Sternberg, P., 2001. WormBase: network access to the genome and biology of Caenorhabditis elegans (vol 29, pg 82, 2001) NUCLEIC ACIDS RESEARCH, v. 29

Apweiler, R., Attwood, TK., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, MD., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A., Karavidopoulou, Y., Lopez, R., Marx, B., Mulder, NJ., Oinn, TM., Pagni, M., Servant, F., Sigrist, CJ. and Zdobnov, EM., 2001. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res, v. 29
Doi: http://doi.org/10.1093/nar/29.1.37

Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J. and Spieth, J., 2001. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res, v. 29
Doi: http://doi.org/10.1093/nar/29.1.82

Deloukas, P., Matthews, LH., Ashurst, J., Burton, J., Gilbert, JG., Jones, M., Stavrides, G., Almeida, JP., Babbage, AK., Bagguley, CL., Bailey, J., Barlow, KF., Bates, KN., Beard, LM., Beare, DM., Beasley, OP., Bird, CP., Blakey, SE., Bridgeman, AM., Brown, AJ., Buck, D., Burrill, W., Butler, AP., Carder, C., Carter, NP., Chapman, JC., Clamp, M., Clark, G., Clark, LN., Clark, SY., Clee, CM., Clegg, S., Cobley, VE., Collier, RE., Connor, R., Corby, NR., Coulson, A., Coville, GJ., Deadman, R., Dhami, P., Dunn, M., Ellington, AG., Frankland, JA., Fraser, A., French, L., Garner, P., Grafham, DV., Griffiths, C., Griffiths, MN., Gwilliam, R., Hall, RE., Hammond, S., Harley, JL., Heath, PD., Ho, S., Holden, JL., Howden, PJ., Huckle, E., Hunt, AR., Hunt, SE., Jekosch, K., Johnson, CM., Johnson, D., Kay, MP., Kimberley, AM., King, A., Knights, A., Laird, GK., Lawlor, S., Lehvaslaiho, MH., Leversha, M., Lloyd, C., Lloyd, DM., Lovell, JD., Marsh, VL., Martin, SL., McConnachie, LJ., McLay, K., McMurray, AA., Milne, S., Mistry, D., Moore, MJ., Mullikin, JC., Nickerson, T., Oliver, K., Parker, A., Patel, R., Pearce, TA., Peck, AI., Phillimore, BJ., Prathalingam, SR., Plumb, RW., Ramsay, H., Rice, CM., Ross, MT., Scott, CE., Sehra, HK., Shownkeen, R., Sims, S., Skuce, CD., Smith, ML., Soderlund, C., Steward, CA., Sulston, JE., Swann, M., Sycamore, N., Taylor, R., Tee, L., Thomas, DW., Thorpe, A., Tracey, A., Tromans, AC., Vaudin, M., Wall, M., Wallis, JM., Whitehead, SL., Whittaker, P., Willey, DL., Williams, L., Williams, SA., Wilming, L., Wray, PW., Hubbard, T., Durbin, RM., Bentley, DR., Beck, S. and Rogers, J., 2001. The DNA sequence and comparative analysis of human chromosome 20. Nature, v. 414
Doi: http://doi.org/10.1038/414865a

Micklem, G. and The Genome Sequencing Consortium, , 2001. Initial sequencing and analysis of the human genome Nature, v. 409

Bentley, DR., Deloukas, P., Dunham, A., French, L., Gregory, SG., Humphray, SJ., Mungall, AJ., Ross, MT., Carter, NP., Dunham, I., Scott, CE., Ashcroft, KJ., Atkinson, AL., Aubin, K., Beare, DM., Bethel, G., Brady, N., Brook, JC., Burford, DC., Burrill, WD., Burrows, C., Butler, AP., Carder, C., Catanese, JJ., Clee, CM., Clegg, SM., Cobley, V., Coffey, AJ., Cole, CG., Collins, JE., Conquer, JS., Cooper, RA., Culley, KM., Dawson, E., Dearden, FL., Durbin, RM., de Jong, PJ., Dhami, PD., Earthrowl, ME., Edwards, CA., Evans, RS., Gillson, CJ., Ghori, J., Green, L., Gwilliam, R., Halls, KS., Hammond, S., Harper, GL., Heathcott, RW., Holden, JL., Holloway, E., Hopkins, BL., Howard, PJ., Howell, GR., Huckle, EJ., Hughes, J., Hunt, PJ., Hunt, SE., Izmajlowicz, M., Jones, CA., Joseph, SS., Laird, G., Langford, CF., Lehvaslaiho, MH., Leversha, MA., McCann, OT., McDonald, LM., McDowall, J., Maslen, GL., Mistry, D., Moschonas, NK., Neocleous, V., Pearson, DM., Phillips, KJ., Porter, KM., Prathalingam, SR., Ramsey, YH., Ranby, SA., Rice, CM., Rogers, J., Rogers, LJ., Sarafidou, T., Scott, DJ., Sharp, GJ., Shaw-Smith, CJ., Smink, LJ., Soderlund, C., Sotheran, EC., Steingruber, HE., Sulston, JE., Taylor, A., Taylor, RG., Thorpe, AA., Tinsley, E., Warry, GL., Whittaker, A., Whittaker, P., Williams, SH., Wilmer, TE., Wooster, R. and Wright, CL., 2001. The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X. Nature, v. 409
Doi: http://doi.org/10.1038/35057165

Lander, ES., Linton, LM., Birren, B., Nusbaum, C., Zody, MC., Baldwin, J., Devon, K., Dewar, K., Doyle, M., Fitzhugh, W., Funke, R., Gage, D., Harris, K., Heaford, A., Howland, J., Kann, L., Lehoczky, J., Levine, R., McEwan, P., McKernan, K., Meldrim, J., Mesirov, JP., Miranda, C., Morris, W., Naylor, J., Raymond, C., Rosetti, M., Santos, R., Sheridan, A., Sougnez, C., Stange-Thomann, N., Stojanovic, N., Subramanian, A., Wyman, D., Rogers, J., Sulston, J., Ainscough, R., Beck, S., Bentley, D., Burton, J., Clee, C., Carter, N., Coulson, A., Deadman, R., Deloukas, P., Dunham, A., Dunham, I., Durbin, R., French, L., Grafham, D., Gregory, S., Hubbard, T., Humphray, S., Hunt, A., Jones, M., Lloyd, C., McMurray, A., Matthews, L., Mercer, S., Milne, S., Mullikin, JC., Mungall, A., Plumb, R., Ross, M., Shownkeen, R., Sims, S., Waterston, RH., Wilson, RK., Hillier, LW., McPherson, JD., Marra, MA., Mardis, ER., Fulton, LA., Chinwalla, AT., Pepin, KH., Gish, WR., Chissoe, SL., Wendl, MC., Delehaunty, KD., Miner, TL., Delehaunty, A., Kramer, JB., Cook, LL., Fulton, RS., Johnson, DL., Minx, PJ., Clifton, SW., Hawkins, T., Branscomb, E., Predki, P., Richardson, P., Wenning, S., Slezak, T., Doggett, N., Cheng, JF., Olsen, A., Lucas, S., Elkin, C., Uberbacher, E. and Frazier, M., 2001. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature, v. 412
Doi: http://doi.org/10.1038/35087627

2000

Bateman, A., Birney, E., Durbin, R., Eddy, SR., Howe, KL. and Sonnhammer, EL., 2000. The Pfam protein families database. Nucleic Acids Res, v. 28
Doi: http://doi.org/10.1093/nar/28.1.263

Jareborg, N. and Durbin, R., 2000. Alfresco--a workbench for comparative genomic sequence analysis. Genome Res, v. 10
Doi: http://doi.org/10.1101/gr.10.8.1148

Apweiler, R., Attwood, TK., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, MD., Durbin, R., Falquet, L., Fleischmann, W., Gouzy, J., Hermjakob, H., Hulo, N., Jonassen, I., Kahn, D., Kanapin, A., Karavidopoulou, Y., Lopez, R., Marx, B., Mulder, NJ., Oinn, TM., Pagni, M., Servant, F., Sigrist, CJ., Zdobnov, EM. and InterPro Consortium, , 2000. InterPro--an integrated documentation resource for protein families, domains and functional sites. Bioinformatics, v. 16
Doi: http://doi.org/10.1093/bioinformatics/16.12.1145

Birney, E. and Durbin, R., 2000. Using GeneWise in the Drosophila annotation experiment. Genome Res, v. 10
Doi: http://doi.org/10.1101/gr.10.4.547

1999

Bateman, A., Birney, E., Durbin, R., Eddy, SR., Finn, RD. and Sonnhammer, EL., 1999. Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res, v. 27
Doi: http://doi.org/10.1093/nar/27.1.260

Jareborg, N., Birney, E. and Durbin, R., 1999. Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs (vol 9, pg 815, 1999) GENOME RESEARCH, v. 9

Dunham, I., Shimizu, N., Roe, BA., Chissoe, S., Hunt, AR., Collins, JE., Bruskiewich, R., Beare, DM., Clamp, M., Smink, LJ., Ainscough, R., Almeida, JP., Babbage, A., Bagguley, C., Bailey, J., Barlow, K., Bates, KN., Beasley, O., Bird, CP., Blakey, S., Bridgeman, AM., Buck, D., Burgess, J., Burrill, WD. and O'Brien, KP., 1999. The DNA sequence of human chromosome 22. Nature, v. 402
Doi: http://doi.org/10.1038/990031

Jareborg, N., Birney, E. and Durbin, R., 1999. Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res, v. 9
Doi: http://doi.org/10.1101/gr.9.9.815

1998

Dear, S., Durbin, R., Hillier, L., Marth, G., Thierry-Mieg, J. and Mott, R., 1998. Sequence assembly with CAFTOOLS. Genome Res, v. 8
Doi: http://doi.org/10.1101/gr.8.3.260

Sonnhammer, EL., Eddy, SR., Birney, E., Bateman, A. and Durbin, R., 1998. Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res, v. 26
Doi: http://doi.org/10.1093/nar/26.1.320

Durbin, R. and Dear, S., 1998. Base qualities help sequencing software. Genome Res, v. 8
Doi: http://doi.org/10.1101/gr.8.3.161

Holmes, I. and Durbin, R., 1998. Dynamic programming alignment accuracy. J Comput Biol, v. 5
Doi: http://doi.org/10.1089/cmb.1998.5.493

1997

Rezsohazy, R., van Luenen, HG., Durbin, RM. and Plasterk, RH., 1997. Tc7, a Tc1-hitch hiking transposon in Caenorhabditis elegans. Nucleic Acids Res, v. 25
Doi: http://doi.org/10.1093/nar/25.20.4048

Martinelli, SD., Brown, CG. and Durbin, R., 1997. Gene expression and development databases for C. elegans. Semin Cell Dev Biol, v. 8
Doi: 10.1006/scdb.1997.0171

Sonnhammer, EL. and Durbin, R., 1997. Analysis of protein domain families in Caenorhabditis elegans. Genomics, v. 46
Doi: http://doi.org/10.1006/geno.1997.4989

Sonnhammer, EL., Eddy, SR. and Durbin, R., 1997. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins, v. 28
Doi: http://doi.org/10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l

1996

Korswagen, HC., Durbin, RM., Smits, MT. and Plasterk, RH., 1996. Transposon Tc1-derived, sequence-tagged sites in Caenorhabditis elegans as markers for gene mapping. Proc Natl Acad Sci U S A, v. 93
Doi: http://doi.org/10.1073/pnas.93.25.14680

Hope, IA., Albertson, DG., Martinelli, SD., Lynch, AS., Sonnhammer, E. and Durbin, R., 1996. The C. elegans expression pattern database: a beginning. Trends Genet, v. 12

Hope, IA., Albertson, DG., Martinelli, SD., Lynch, AS., Sonnhammer, E. and Durbin, R., 1996. The C-elegans expression pattern database: A beginning TRENDS IN GENETICS, v. 12
Doi: 10.1016/0168-9525(96)60033-X

1995

Baxendale, S., Abdulla, S., Elgar, G., Buck, D., Berks, M., Micklem, G., Durbin, R., Bates, G., Brenner, S. and Beck, S., 1995. Comparative sequence analysis of the human and pufferfish Huntington's disease genes. Nat Genet, v. 10
Doi: 10.1038/ng0595-67

SONNHAMMER, ELL. and DURBIN, R., 1995. A DOT-MATRIX PROGRAM WITH DYNAMIC THRESHOLD CONTROL SUITED FOR GENOMIC DNA AND PROTEIN-SEQUENCE ANALYSIS GENE-COMBIS, v. 167

Sewell, RF. and Durbin, R., 1995. Method for calculation of probability of matching a bounded regular expression in a random data string. J Comput Biol, v. 2
Doi: http://doi.org/10.1089/cmb.1995.2.25

Eeckman, FH. and Durbin, R., 1995. ACeDB and macace. Methods Cell Biol, v. 48

Sonnhammer, EL. and Durbin, R., 1995. A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene, v. 167
Doi: http://doi.org/10.1016/0378-1119(95)00714-8

Eddy, SR., Mitchison, G. and Durbin, R., 1995. Maximum discrimination hidden Markov models of sequence consensus. J Comput Biol, v. 2
Doi: http://doi.org/10.1089/cmb.1995.2.9

Mitchison, G. and Durbin, R., 1995. Tree-based maximal likelihood substitution matrices and hidden Markov models Journal of Molecular Evolution, v. 41
Doi: http://doi.org/10.1007/BF00173195

1994

Ambrose, CM., Duyao, MP., Barnes, G., Bates, GP., Lin, CS., Srinidhi, J., Baxendale, S., Hummerich, H., Lehrach, H., Altherr, M., Wasmuth, J., Buckler, A., Church, D., Housman, D., Berks, M., Micklem, G., Durbin, R., Dodge, A., Read, A., Gusella, J. and MacDonald, ME., 1994. Structure and expression of the Huntington's disease gene: evidence against simple inactivation due to an expanded CAG repeat. Somat Cell Mol Genet, v. 20
Doi: 10.1007/BF02257483

Sonnhammer, EL. and Durbin, R., 1994. A workbench for large-scale sequence homology analysis. Comput Appl Biosci, v. 10
Doi: http://doi.org/10.1093/bioinformatics/10.3.301

Sonnhammer, EL. and Durbin, R., 1994. An expert system for processing sequence homology data. Proc Int Conf Intell Syst Mol Biol, v. 2

Eddy, SR. and Durbin, R., 1994. RNA sequence analysis using covariance models. Nucleic Acids Res, v. 22
Doi: http://doi.org/10.1093/nar/22.11.2079

Wilson, R., Ainscough, R., Anderson, K., Baynes, C., Berks, M., Bonfield, J., Burton, J., Connell, M., Copsey, T. and Cooper, J., 1994. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature, v. 368
Doi: http://doi.org/10.1038/368032a0

1992

Sulston, J., Du, Z., Thomas, K., Wilson, R., Hillier, L., Staden, R., Halloran, N., Green, P., Thierry-Mieg, J., Qiu, L., Dear, S., Coulson, A., Craxton, M., Durbin, R., Berks, M., Metzstein, M., Hawkins, T., Ainscough, R. and Waterston, R., 1992. The C. elegans genome sequencing project: A beginning Nature, v. 356
Doi: http://doi.org/10.1038/356037a0

Mitchison, G. and Durbin, R., 1992. Neural networks. Learning from your neighbour. Nature, v. 355
Doi: http://doi.org/10.1038/355112a0

Sulston, J., Du, Z., Thomas, K., Wilson, R., Hillier, L., Staden, R., Halloran, N., Green, P., Thierry-Mieg, J. and Qiu, L., 1992. The C. elegans genome sequencing project: a beginning. Nature, v. 356
Doi: http://doi.org/10.1038/356037a0

Mitchison, G. and Durbin, R., 1992. Learning from your neighbour Nature, v. 355
Doi: http://doi.org/10.1038/355112a0

Waterston, R., Martin, C., Craxton, M., Huynh, C., Coulson, A., Hillier, L., Durbin, R., Green, P., Shownkeen, R. and Halloran, N., 1992. A survey of expressed genes in Caenorhabditis elegans. Nat Genet, v. 1
Doi: http://doi.org/10.1038/ng0592-114

1990

Durbin, R. and Mitchison, G., 1990. A dimension reduction framework for understanding cortical maps. Nature, v. 343
Doi: http://doi.org/10.1038/343644a0

1989

Durbin, R. and Rumelhart, DE., 1989. Product Units: A Computationally Powerful and Biologically Plausible Extension to Backpropagation Networks NEURAL COMPUTATION, v. 1
Doi: http://doi.org/10.1162/neco.1989.1.1.133

Durbin, R., Szeliski, R. and Yuille, A., 1989. An Analysis of the Elastic Net Approach to the Traveling Salesman Problem NEURAL COMPUTATION, v. 1
Doi: http://doi.org/10.1162/neco.1989.1.3.348

Mitchison, GJ. and Durbin, RM., 1989. Bounds on the learning capacity of some multi-layer networks Biological Cybernetics, v. 60
Doi: http://doi.org/10.1007/BF00204772

Sulston, J., Mallett, F., Durbin, R. and Horsnell, T., 1989. Image analysis of restriction enzyme fingerprint autoradiograms. Comput Appl Biosci, v. 5
Doi: http://doi.org/10.1093/bioinformatics/5.2.101

1988

Sulston, J., Mallett, F., Staden, R., Durbin, R., Horsnell, T. and Coulson, A., 1988. Software for genome mapping by fingerprinting techniques. Comput Appl Biosci, v. 4
Doi: http://doi.org/10.1093/bioinformatics/4.1.125

Durbin, R. and Mitchison, G., 1988. Dimension reduction models for topographical maps in the cortex Neural Networks, v. 1
Doi: http://doi.org/10.1016/0893-6080(88)90513-8

Fine, A., Amos, WB., Durbin, RM. and McNaughton, PA., 1988. Confocal microscopy: applications in neurobiology. Trends Neurosci, v. 11
Doi: http://doi.org/10.1016/0166-2236(88)90056-2

1987

Durbin, R. and Willshaw, D., 1987. An analogue approach to the travelling salesman problem using an elastic net method. Nature, v. 326
Doi: http://doi.org/10.1038/326689a0

1986

Durbin, RM., Burns, R., Moulai, J., Metcalf, P., Freymann, D., Blum, M., Anderson, JE., Harrison, SC. and Wiley, DC., 1986. Protein, DNA, and virus crystallography with a focused imaging proportional counter. Science, v. 232
Doi: http://doi.org/10.1126/science.3704639

MITCHISON, G. and DURBIN, R., 1986. OPTIMAL NUMBERINGS OF AN NXN ARRAY SIAM JOURNAL ON ALGEBRAIC AND DISCRETE METHODS, v. 7
Doi: 10.1137/0607063

1985

Harrison, SC. and Durbin, R., 1985. Is there a single pathway for the folding of a polypeptide chain? Proc Natl Acad Sci U S A, v. 82
Doi: http://doi.org/10.1073/pnas.82.12.4028

Harrison, SC., Winkler, FK., Schutt, CE. and Durbin, RM., 1985. Diffraction methods for biological macromolecules. Oscillation method with large unit cells. Methods Enzymol, v. 114
Doi: http://doi.org/10.1016/0076-6879(85)14021-8

Davey, JW., Barker, SL., Rastas, PM., Pinharanda, A., Martin, SH., Durbin, R., McMillan, WO., Merrill, RM. and Jiggins, CD., No evidence for maintenance of a sympatric Heliconius species barrier by chromosomal inversions Evolution Letters,
Doi: 10.1002/evl3.12

Martiniano, R., Garrison, E., Jones, E., Manica, A. and Durbin, R., Removing reference bias in ancient DNA data analysis by mapping to a sequence variation graph Genome Biology,

Mead, D., Saccheri, I., Yung, CJ., Lohse, K., Lohse, C., Ashmole, P., Smith, M., Corton, C., Oliver, K., Skelton, J., Betteridge, E., Quail, MA., Dolucan, J., McCarthy, SA., Howe, K., Wood, J., Torrance, J., Tracey, A., Whiteford, S., Challis, R., Durbin, R. and Blaxter, M., The genome sequence of the ringlet, Aphantopus hyperantus Linnaeus 1758 Wellcome Open Research, v. 6
Doi: http://doi.org/10.12688/wellcomeopenres.16983.1

Ferguson-Smith, AC., Lilue, J., Doran, A., Fiddes, I., Abrudan, M., Armstrong, J., Bennett, R., Chow, W., Collins, J., Collins, S., Czechanski, A., Danecek, P., Diekhans, M., Dirk-Dominik, D., Dunn, M., Durbin, R., Earl, D., Flicek, P., Flint, J., Frankish, A., Fu, B., Gerstein, M., Gilbert, J., Goodstadt, L., Harrow, J., Howe, K., Ibarra-Soria, X., Kolmogorov, M., Lelliott, C., Logan, D., Loveland, J., Mathews, C., Mott, R., Muir, P., Nachtweide, S., Navarro, F., Odom, D., Park, N., Pelan, S., Pham, S., Quail, M., Reinholdt, L., Romoth, L., Shirley, L., Sisu, C., Sjoberg-Herrera, M., Stanke, M., Steward, C., Thomas, M., Threadgold, G., Thybert, D., Torrance, J., Wong, K., Wood, J., Yalcin, B., Yang, F., Adams, D., Paten, B. and Keane, T., Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci Nature Genetics,

Nik-Zainal, S., Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells Nature Genetics,
Doi: 10.1038/s41588-022-01147-3

Durbin, R., Dawson, E. and Garrison, E., Viral coinfection analysis using a MinHash toolkit BMC Bioinformatics,

Narasimhan, VM. and Maher, ER., Estimating the human mutation rate from autozygous segments reveals population differences in human mutational processes Nature Communications, v. 8
Doi: http://doi.org/10.1038/s41467-017-00323-y

Durbin, R., fruit fly BMC Biochemistry,

Garg, S., Aach, J., Li, H., Durbin, R. and Church, G., A haplotype-aware de novo assembly of related individuals using pedigree sequence graph. Bioinformatics,
Doi: http://doi.org/10.1093/bioinformatics/btz942

Vernaz, G., Malinsky, M., Svardal, H., Du, M., Tyers, A., Santos, E., Durbin, R., Genner, M., Turner, G. and Miska, E., Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes Nature Communications,

Sirén, J., Garrison, E., Novak, AM., Paten, B. and Durbin, R., Haplotype-aware graph indexes Bioinformatics,
Doi: http://doi.org/10.1093/bioinformatics/btz575

Bergstrom, A., McCarthy, S., Almarri, M., Hui, R., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., Blanche, H., Deleuze, J-F., Cann, H., Mallick, S., Reich, D., Sandhu, M., Skoglund, P., Scally, A., Xue, Y., Durbin, R. and Tyler-Smith, C., Insights into human genetic variation and population history from 929 diverse genomes Science,
Doi: 10.1126/science.aay5012

Guan, D., McCarthy, S., Wood, J., Howe, K., Wang, Y. and Durbin, R., Identifying and removing haplotypic duplication in primary genome assemblies Bioinformatics,
Doi: http://doi.org/10.1093/bioinformatics/btaa025

Heaton, W., Talman, A., Knights, A., Imaz, M., Gaffney, D., Durbin, R., Hemberg, M. and Lawniczak, M., souporcell: Robust clustering of single cell RNAseq by genotype without reference genotypes Nature Methods,

Dawson, E. and Durbin, R., GFAKluge: A C++ library and command line utilities for the Graphical Fragment Assembly formats Journal of Open Source Software, v. 4
Doi: http://doi.org/10.21105/joss.01083

Lim, AANDFTSISSP., Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population PLOS Genetics, v. 10
Doi: http://doi.org/10.1371/journal.pgen.1004494

Sherkow, JS., Barker, K., Braverman, I., Cook-Deegan, RM., Durbin, R., Easter, C., Goldstein, M., Hudson, M., Kress, WJ., Lewin, H., Mathews, DJH., McCarthy, C., McCartney, A., da Silva, M., Torrance, AW. and Greely, HHT., Ethical, Legal, and Social Issues in the Earth BioGenome Project SSRN Electronic Journal,
Doi: 10.2139/ssrn.3840280

Kwon, YM., Vranken, N., Hoge, C., Lichak, M., Francis, K., Camacho-Garcia, J., Bista, I., Wood, J., McCarthy, S., Chow, W., Tan, HH., Howe, K., Bandara, S., von Lintig, J., Rüber, L., Durbin, R., Svardal, H. and Bendesky, A., Genomic consequences of domestication of the Siamese fighting fish Science Advances,

Internet publications

2022

Guan, D., McCarthy, S., Wood, J., Sims, Y., Chow, W., Ning, Z., Howe, K., Wang, G., Wang, Y. and Durbin, R., 2022. Genome sequence assembly evaluation using long-range sequencing data
Doi: 10.1101/2022.05.10.491304

Zhou, C., McCarthy, S. and Durbin, R., 2022. YaHS: yet another Hi-C scaffolding tool
Doi: 10.1101/2022.06.09.495093

Bista, I., Wood, J., Desvignes, T., McCarthy, S., Matschiner, M., Ning, Z., Tracey, A., Torrance, J., Sims, Y., Chow, W., Smith, M., Oliver, K., Haggerty, L., Salzburger, W., Postlethwait, J., Howe, K., Clark, M., Detrich, W., Cheng, C-HC., Miska, E. and Durbin, R., 2022. Genomics of cold adaptations in the Antarctic notothenioid fish radiation
Doi: 10.1101/2022.06.08.494096

2021

Kwon, YM., Vranken, N., Hoge, C., Lichak, M., Francis, K., Camacho-Garcia, J., Bista, I., Wood, J., McCarthy, S., Chow, W., Tan, HH., Howe, K., Bandara, S., von Lintig, J., Rüber, L., Durbin, R., Svardal, H. and Bendesky, A., 2021. Genomic consequences of domestication of the Siamese fighting fish
Doi: 10.1101/2021.04.29.442030

2020

Vernaz, G., Malinsky, M., Svardal, H., Du, M., Tyers, A., Santos, E., Durbin, R., Genner, M., Turner, G. and Miska, E., 2020. Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes
Doi: 10.1101/2020.11.24.383034

2019

Bergström, A., McCarthy, S., Hui, R., Almarri, M., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., Blanché, H., Deleuze, J-F., Cann, H., Mallick, S., Reich, D., Sandhu, M., Skoglund, P., Scally, A., Xue, Y., Durbin, R. and Tyler-Smith, C., 2019. Insights into human genetic variation and population history from 929 diverse genomes
Doi: 10.1101/674986

Svardal, H., Quah, FX., Malinsky, M., Ngatunga, B., Miska, E., Salzburger, W., Genner, M., Turner, G. and Durbin, R., 2019. Ancestral hybridisation facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation
Doi: 10.1101/738633

Sirén, J., Garrison, E., Novak, A., Paten, B. and Durbin, R., 2019. Haplotype-aware graph indexes
Doi: 10.1101/559583

Guan, D., McCarthy, S., Wood, J., Howe, K., Wang, Y. and Durbin, R., 2019. Identifying and removing haplotypic duplication in primary genome assemblies
Doi: 10.1101/729962

2016

Malinsky, M., Simpson, J. and Durbin, R., 2016. trio-sga: facilitating de novo assembly of highly heterozygous genomes with parent-child trios
Doi: http://doi.org/10.1101/051516

Narasimhan, V., Rahbari, R., Scally, A., Wuster, A., Mason, D., Xue, Y., Wright, J., Trembath, R., Maher, E., van Heel, D., Auton, A., Hurles, M., Tyler-Smith, C. and Durbin, R., 2016. A direct multi-generational estimate of the human mutation rate from autozygous segments seen in thousands of parentally related individuals
Doi: 10.1101/059436

Book chapters

2015

Koepfli, K-P., Paten, B., Genome 10K Community of Scientists, and O'Brien, SJ., 2015. The Genome 10K Project: a way forward.
Doi: 10.1146/annurev-animal-090414-014900

2004

Durbin, R., 2004. Finding genes in the human genome with hidden Markov models
Doi: http://doi.org/10.1017/CBO9780511617010.015

1994

DURBIN, R. and THIERRYMIEG, J., 1994. THE ACEDB GENOME DATABASE

Books

1998

Durbin, R., Eddy, SR., Krogh, A. and Mitchison, G., 1998. Biological Sequence Analysis
Doi: 10.1017/cbo9780511790492

Conference proceedings

2018

Dawson, ET., Wagner, S., Roberson, D., Yeager, M., Boland, J., Garrison, E., Schiffman, M., Raine-Bennet, T., Lorey, T., Castle, P., Chanock, S., Mirabello, L. and Durbin, R., 2018. rkmh: A MinHash toolbox for analyzing HPV coinfections CANCER RESEARCH, v. 78
Doi: 10.1158/1538-7445.AM2018-3273

Sirén, J., Garrison, E., Novak, AM., Paten, B. and Durbin, R., 2018. Haplotype-aware graph indexes Leibniz International Proceedings in Informatics, LIPIcs, v. 113
Doi: http://doi.org/10.4230/LIPIcs.WABI.2018.4

Garg, S., Rautiainen, M., Novak, AM., Garrison, E., Durbin, R. and Marschall, T., 2018. A graph-based approach to diploid genome assembly. Bioinformatics, v. 34
Doi: 10.1093/bioinformatics/bty279

2014

Zheng, H-F., Forgetta, V., Hsu, Y-H., Estrada, K., Leo, P., Tobias, J., Kooperberg, C., Liu, C-T., Rosello-Diez, A., Evans, D., Nielson, C., Pettersson-Kymmer, U., Eriksson, J., Kwan, T., Walter, K., Memari, Y., McCarthy, S., Min, J., Huang, J., Danecek, P., Wilmot, B., Li, R., Chou, W-C., Mokry, L., Moayyeri, A., Claussnitzer, M., Cheng, C-H., Cheung, W., Medina-Gomez, C., Ge, B., Chen, S-H., Choi, K., Oei, L., Fraser, J., Kraaij, R., Hibbs, M., Gregson, C., Paquette, D., Hofman, A., Wibom, C., Marshall, M., Gardiner, B., Auer, P., Hsu, L., Ring, S., van der Velde, N., Melin, B., Kemp, J., Sayers, A., Zhou, Y., Calderari, S., Maurano, M., van Rooij, J., Carlson, C., Peters, U., Berlivet, S., Dostie, J., Ohlsson, C., Uitterlinden, A., Goltzman, D., Pastinen, T., Grundberg, E., Gauguier, D., Orwoll, E., Karasik, D., Dahia, C., Davey-Smith, G., Timpson, N., Soranzo, N., Durbin, R., Wilson, S., Brown, M., Spector, T., Cupples, LA., Greenwood, C., Loomis, C., Ackert-Bicknell, C., Joyner, A., Jackson, R., Duncan, E., Evans, D., Rivadeneira, F., Kiel, D. and Richards, B., 2014. A large-scale whole genome sequence-based analysis discovered novel genetic variants influencing bone mineral density: Results from the GEFOS and UK10K Consortia. JOURNAL OF BONE AND MINERAL RESEARCH, v. 29

Durbin, R., 2014. Human genetic diversity and functional variation FEBS JOURNAL, v. 281

2013

Liti, G., Bergstroem, A., Simpson, J., Salinas, F., Parts, L., Zia, A., Moses, A., Louis, E., Mustonen, V., Warringer, J. and Durbin, R., 2013. A high-definition view of functional variation from natural yeast genomes YEAST, v. 30

2012

Buil, A., Brown, A., Davies, M., Vinuela, A., Gallardo, M., Glass, D., Blasco, M., Durbin, R., Spector, TD. and Dermitzakis, ET., 2012. NGS Transcriptome Genomic Analysis in Three Tissues of a Twin Cohort GENETIC EPIDEMIOLOGY, v. 36

2011

Glass, D., Parts, L., Knowles, D., Nica, AC., Nisbet, J., Barrett, A., Sekowska, M., Travers, M., Potter, S., Grundberg, E., Small, K., Hedman, ASA., Bell, JT., Surdulescu, G., Nestle, FO., di Meglio, P., Durbin, R., Ahmadi, K., Winn, J., Bataille, V., Deloukas, P., McCarthy, MI., Spector, TD., Dermitzakis, ET. and For, M., 2011. Biomarkers of skin ageing using genome wide transcriptomics JOURNAL OF INVESTIGATIVE DERMATOLOGY, v. 131

2010

Durbin, R., 2010. Issues in interpreting and using genome-wide sequence data JOURNAL OF MEDICAL GENETICS, v. 47

Simpson, JT. and Durbin, R., 2010. Efficient construction of an assembly string graph using the FM-index. Bioinformatics, v. 26
Doi: http://doi.org/10.1093/bioinformatics/btq217

2008

Stegle, O., Kannan, A., Durbin, R. and Winn, J., 2008. Accounting for non-genetic factors improves the power of eQTL studies Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), v. 4955 LNBI
Doi: http://doi.org/10.1007/978-3-540-78839-3_35

1997

Birney, E. and Durbin, R., 1997. Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison. Proc Int Conf Intell Syst Mol Biol, v. 5

1994

COLLINS, JE., COLE, CR., SMINK, LJ., GARRETT, CL., COFFEY, AJ., GREGORY, SG., DAVIES, AF., HASSOCK, S., TODD, CM., DUMANSKI, JP., SCAMBLER, PJ., KIM, UJ., MASLEN, GL., SODERLUND, C., DURBIN, R., BENTLEY, DR. and DUNHAM, I., 1994. TOWARDS A FULLY INTEGRATED, HIGH-RESOLUTION PHYSICAL MAP OF CHROMOSOME-22 CYTOGENETICS AND CELL GENETICS, v. 67

MASLEN, GL., DUNHAM, I., BENTLEY, DR. and DURBIN, R., 1994. INTEGRATION OF X-CHROMOSOME CLONE MAPS WITH PHYSICAL AND GENETIC INFORMATION - THE XACE IMPLEMENTATION OF ACEDB CYTOGENETICS AND CELL GENETICS, v. 67

1993

Waterston, R., Ainscough, R., Anderson, K., Berks, M., Blair, D., Connell, M., Cooper, J., Coulson, A., Craxton, M. and Dear, S., 1993. The genome of the nematode Caenorhabditis elegans. Cold Spring Harb Symp Quant Biol, v. 58
Doi: http://doi.org/10.1101/sqb.1993.058.01.043

1984

DURBIN, RM., BURNS, R., MOULAI, J., METCALF, P., HARRISON, SC. and WILEY, DC., 1984. PROTEIN AND VIRUS X-RAY DATA-COLLECTION WITH A XENTRONICS AREA DETECTOR ACTA CRYSTALLOGRAPHICA SECTION A, v. 40
Doi: http://doi.org/10.1107/S0108767384088115

Theses / dissertations

Klarqvist, M., Efficient analysis and storage of large-scale genomic data

Heaton, W., Computational methods for single cell RNA and genome assembly resolution using genetic variation

Richard Durbin, FRS

Al Kindi Professor of Genetics, Department of Genetics

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