Featured publications

Lindblad-Toh, K., 2020. What animals can teach us about evolution, the human genome, and human disease. Ups J Med Sci 1–9. doi:10.1080/03009734.2020.1722298

2019

Megquier, K., Turner-Maier, J., Swofford, R., Kim, J.-H., Sarver, A.L., Wang, C., Sakthikumar, S., Johnson, J., Koltookian, M., Lewellen, M., Scott, M.C., Schulte, A.J., Borst, L., Tonomura, N., Alföldi, J., Painter, C., Thomas, R., Karlsson, E.K., Breen, M., Modiano, J.F., Elvers, I., Lindblad-Toh, K., 2019. Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma. Mol Cancer Res 17, 2410–2421. doi:10.1158/1541-7786.MCR-19-0221

Megquier, K., Genereux, D.P., Hekman, J., Swofford, R., Turner-Maier, J., Johnson, J., Alonso, J., Li, X., Morrill, K., Anguish, L.J., Koltookian, M., Logan, B., Sharp, C.R., Ferrer, L., Lindblad-Toh, K., Meyers-Wallen, V.N., Hoffman, A., Karlsson, E.K., 2019. BarkBase: Epigenomic Annotation of Canine Genomes. Genes (Basel) 10. doi:10.3390/genes10060433

Farias, F.H.G., Dahlqvist, J., Kozyrev, S.V., Leonard, D., Wilbe, M., Abramov, S.N., Alexsson, A., Pielberg, G.R., Hansson-Hamlin, H., Andersson, G., Tandre, K., Bengtsson, A.A., Sjowall, C., Svenungsson, E., Gunnarsson, I., Rantapaa-Dahlqvist, S., Syvänen, A.-C., Sandling, J.K., Eloranta, M.-L., Rönnblom, L., Lindblad-Toh, K., 2019. A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts. Eur J Hum Genet 27, 432–441. doi:10.1038/s41431-018-0297-x

2018

Chen, J., Swofford, R., Johnson, J., Cummings, B.B., Rogel, N., Lindblad-Toh, K., Haerty, W., Palma, F.D., Regev, A., 2019. A quantitative framework for characterizing the evolutionary history of mammalian gene expression. Genome Research 29, 53–63. doi:10.1101/gr.237636.118

Biasoli, D., Compston-Garnett, L., Ricketts, S.L., Birand, Z., Courtay-Cahen, C., Fineberg, E., Arendt, M., Boerkamp, K., Melin, M., Koltookian, M., Murphy, S., Rutteman, G., Lindblad-Toh, K., Starkey, M., 2019. A synonymous germline variant in a gene encoding a cell adhesion molecule is associated with cutaneous mast cell tumour development in Labrador and Golden Retrievers. PLoS Genet 15, e1007967.

Sakthikumar, S., Elvers, I., Kim, J., Arendt, M.L., Thomas, R., Turner-Maier, J., Swofford, R., Johnson, J., Schumacher, S.E., Alföldi, J., Axelsson, E., Couto, C.G., Kisseberth, W.C., Pettersson, M.E., Getz, G., Meadows, J.R.S., Modiano, J.F., Breen, M., Kierczak, M., Forsberg-Nilsson, K., Marinescu, V.D., Lindblad-Toh, K., 2018. SETD2 Is Recurrently Mutated in Whole-Exome Sequenced Canine Osteosarcoma. Cancer Res 78, 3421–3431. doi:10.1158/0008-5472.CAN-17-3558

Bremer, H.D., Landegren, N., Sjoberg, R., Hallgren, A., Renneker, S., Lattwein, E., Leonard, D., Eloranta, M.-L., Rönnblom, L., Nordmark, G., Nilsson, P., Andersson, G., Lilliehook, I., Lindblad-Toh, K., Kämpe, O., Hansson-Hamlin, H., 2018. ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease. Sci Rep 8, 4852. doi:10.1038/s41598-018-23034-w

2017

Noh, H.J., Tang, R., Flannick, J., O’Dushlaine, C., Swofford, R., Howrigan, D., Genereux, D.P., Johnson, J., van Grootheest, G., Grunblatt, E., Andersson, E., Djurfeldt, D.R., Patel, P.D., Koltookian, M., M Hultman, C., Pato, M.T., Pato, C.N., Rasmussen, S.A., Jenike, M.A., Hanna, G.L., Stewart, S.E., Knowles, J.A., Ruhrmann, S., Grabe, H.-J., Wagner, M., Ruck, C., Mathews, C.A., Walitza, S., Cath, D.C., Feng, G., Karlsson, E.K., Lindblad-Toh, K., 2017. Integrating evolutionary and regulatory information with a multispecies approach implicates genes and pathways in obsessive-compulsive disorder. Nature Communications 8, 774. doi:10.1038/s41467-017-00831-x

Meadows, J.R.S., Lindblad-Toh, K., 2017. Dissecting evolution and disease using comparative vertebrate genomics. Nat Rev Genet 18, 624–636. doi:10.1038/nrg.2017.51

2016

Ivansson, E.L., Megquier, K., Kozyrev, S.V., Murén, E., Körberg, I.B., Swofford, R., Koltookian, M., Tonomura, N., Zeng, R., Kolicheski, A.L., Hansen, L., Katz, M.L., Johnson, G.C., Johnson, G.S., Coates, J.R., Lindblad-Toh, K., 2016. Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy. Proc Natl Acad Sci U S A 113, E3091–100. doi:10.1073/pnas.1600084113

Melin, M., Rivera, P., Arendt, M., Elvers, I., Murén, E., Gustafson, U., Starkey, M., Borge, K.S., Lingaas, F., Häggström, J., Saellström, S., Rönnberg, H., Lindblad-Toh, K., 2016. Genome-Wide Analysis Identifies Germ-Line Risk Factors Associated with Canine Mammary Tumours. PLoS Genet 12, e1006029.

Truve, K., Dickinson, P., Xiong, A., York, D., Jayashankar, K., Pielberg, G., Koltookian, M., Murén, E., Fuxelius, H.-H., Weishaupt, H., Swartling, F.J., Andersson, G., Hedhammar, Å., Bongcam-Rudloff, E., Forsberg-Nilsson, K., Bannasch, D., Lindblad-Toh, K., 2016. Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus. PLoS Genet 12, e1006000.

Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J., Berlin, A.M., Campbell, M.S., Barrell, D., Martin, K.J., Mulley, J.F., Ravi, V., Lee, A.P., Nakamura, T., Chalopin, D., Fan, S., Wcisel, D., Canestro, C., Sydes, J., Beaudry, F.E.G., Sun, Y., Hertel, J., Beam, M.J., Fasold, M., Ishiyama, M., Johnson, J., Kehr, S., Lara, M., Letaw, J.H., Litman, G.W., Litman, R.T., Mikami, M., Ota, T., Saha, N.R., Williams, L., Stadler, P.F., Wang, H., Taylor, J.S., Fontenot, Q., Ferrara, A., Searle, S.M.J., Aken, B., Yandell, M., Schneider, I., Yoder, J.A., Volff, J.-N., Meyer, A., Amemiya, C.T., Venkatesh, B., Holland, P.W.H., Guiguen, Y., Bobe, J., Shubin, N.H., Di Palma, F., Alföldi, J., Lindblad-Toh, K., Postlethwait, J.H., 2016. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet 48, 427–437. doi:10.1038/ng.3526

2015

Elvers, I., Turner-Maier, J., Swofford, R., Koltookian, M., Johnson, J., Stewart, C., Zhang, C.-Z., Schumacher, S.E., Beroukhim, R., Rosenberg, M., Thomas, R., Mauceli, E., Getz, G., Palma, F.D., Modiano, J.F., Breen, M., Lindblad-Toh, K., Alföldi, J., 2015. Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background. Genome Research 25, 1634–1645. doi:10.1101/gr.194449.115

Arendt, M.L., Melin, M., Tonomura, N., Koltookian, M., Courtay-Cahen, C., Flindall, N., Bass, J., Boerkamp, K., Megquir, K., Youell, L., Murphy, S., McCarthy, C., London, C., Rutteman, G.R., Starkey, M., Lindblad-Toh, K., 2015. Genome-Wide Association Study of Golden Retrievers Identifies Germ-Line Risk Factors Predisposing to Mast Cell Tumours. PLoS Genet 11, e1005647.

Vieira, N.M., Elvers, I., Alexander, M.S., Moreira, Y.B., Eran, A., Gomes, J.P., Marshall, J.L., Karlsson, E.K., Verjovski-Almeida, S., Lindblad-Toh, K., Kunkel, L.M., Zatz, M., 2015. Jagged 1 Rescues the Duchenne Muscular Dystrophy Phenotype. Cell 163, 1204–1213. doi:10.1016/j.cell.2015.10.049

Wilbe, M., Kozyrev, S.V., Farias, F.H.G., Bremer, H.D., Hedlund, A., Pielberg, G.R., Seppala, E.H., Gustafson, U., Lohi, H., Carlborg, O., Andersson, G., Hansson-Hamlin, H., Lindblad-Toh, K., 2015. Multiple Changes of Gene Expression and Function Reveal Genomic and Phenotypic Complexity in SLE-like Disease. PLoS Genet 11, e1005248.

Webster, M.T., Kamgari, N., Perloski, M., Hoeppner, M.P., Axelsson, E., Hedhammar, Å., Pielberg, G., Lindblad-Toh, K., 2015. Linked genetic variants on chromosome 10 control ear morphology and body mass among dog breeds. BMC Genomics 16, 474. doi:10.1186/s12864-015-1702-2

Tonomura, N., Elvers, I., Thomas, R., Megquier, K., Turner-Maier, J., Howald, C., Sarver, A.L., Swofford, R., Frantz, A.M., Ito, D., Mauceli, E., Arendt, M., Noh, H.J., Koltookian, M., Biagi, T., Fryc, S., Williams, C., Avery, A.C., Kim, J.-H., Barber, L., Burgess, K., Lander, E.S., Karlsson, E.K., Azuma, C., Modiano, J.F., Breen, M., Lindblad-Toh, K., 2015. Genome-wide association study identifies shared risk loci common to two malignancies in golden retrievers. PLoS Genet 11, e1004922.

2014

Tang, R., Noh, H.J., Wang, D., Sigurdsson, S., Swofford, R., Perloski, M., Duxbury, M., Patterson, E.E., Albright, J., Castelhano, M., Auton, A., Boyko, A.R., Feng, G., Lindblad-Toh, K., Karlsson, E.K., 2014. Candidate genes and functional noncoding variants identified in a canine model of obsessive-compulsive disorder. Genome Biology 15, R25. doi:10.1186/gb-2014-15-3-r25

Arendt, M., Fall, T., Lindblad-Toh, K., Axelsson, E., 2014. Amylase activity is associated with AMY2B copy numbers in dog: implications for dog domestication, diet and diabetes. Anim Genet 45, 716–722. doi:10.1111/age.12179

Carneiro, M., Rubin, C.-J., Di Palma, F., Albert, F.W., Alföldi, J., Martinez Barrio, A., Pielberg, G., Rafati, N., Sayyab, S., Turner-Maier, J., Younis, S., Afonso, S., Aken, B., Alves, J.M., Barrell, D., Bolet, G., Boucher, S., Burbano, H.A., Campos, R., Chang, J.L., Duranthon, V., Fontanesi, L., Garreau, H., Heiman, D., Johnson, J., Mage, R.G., Peng, Z., Queney, G., Rogel-Gaillard, C., Ruffier, M., Searle, S., Villafuerte, R., Xiong, A., Young, S., Forsberg-Nilsson, K., Good, J.M., Lander, E.S., Ferrand, N., Lindblad-Toh, K., Andersson, L., 2014. Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science 345, 1074–1079. doi:10.1126/science.1253714

Hoeppner, M.P., Lundquist, A., Pirun, M., Meadows, J.R.S., Zamani, N., Johnson, J., Sundstrom, G., Cook, A., FitzGerald, M.G., Swofford, R., Mauceli, E., Moghadam, B.T., Greka, A., Alföldi, J., Abouelleil, A., Aftuck, L., Bessette, D., Berlin, A., Brown, A., Gearin, G., Lui, A., Macdonald, J.P., Priest, M., Shea, T., Turner-Maier, J., Zimmer, A., Lander, E.S., Di Palma, F., Lindblad-Toh, K., Grabherr, M.G., 2014. An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts. PLoS ONE 9, e91172.

2013

Karlsson, E.K., Sigurdsson, S., Ivansson, E., Thomas, R., Elvers, I., Wright, J., Howald, C., Tonomura, N., Perloski, M., Swofford, R., Biagi, T., Fryc, S., Anderson, N., Courtay-Cahen, C., Youell, L., Ricketts, S.L., Mandlebaum, S., Rivera, P., Euler, von, H., Kisseberth, W.C., London, C.A., Lander, E.S., Couto, G., Comstock, K., Starkey, M.P., Modiano, J.F., Breen, M., Lindblad-Toh, K., 2013. Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B. Genome Biology 14, R132. doi:10.1186/gb-2013-14-12-r132

Alföldi, J., Lindblad-Toh, K., 2013. Comparative genomics as a tool to understand evolution and disease. Genome Research 23, 1063–1068. doi:10.1101/gr.157503.113

Amemiya, C.T., Alföldi, J., Lee, A.P., Fan, S., Philippe, H., MacCallum, I., Braasch, I., Manousaki, T., Schneider, I., Rohner, N., Organ, C., Chalopin, D., Smith, J.J., Robinson, M., Dorrington, R.A., Gerdol, M., Aken, B., Biscotti, M.A., Barucca, M., Baurain, D., Berlin, A.M., Blatch, G.L., Buonocore, F., Burmester, T., Campbell, M.S., Canapa, A., Cannon, J.P., Christoffels, A., De Moro, G., Edkins, A.L., Fan, L., Fausto, A.M., Feiner, N., Forconi, M., Gamieldien, J., Gnerre, S., Gnirke, A., Goldstone, J.V., Haerty, W., Hahn, M.E., Hesse, U., Hoffmann, S., Johnson, J., Karchner, S.I., Kuraku, S., Lara, M., Levin, J.Z., Litman, G.W., Mauceli, E., Miyake, T., Mueller, M.G., Nelson, D.R., Nitsche, A., Olmo, E., Ota, T., Pallavicini, A., Panji, S., Picone, B., Ponting, C.P., Prohaska, S.J., Przybylski, D., Saha, N.R., Ravi, V., Ribeiro, F.J., Sauka-Spengler, T., Scapigliati, G., Searle, S.M.J., Sharpe, T., Simakov, O., Stadler, P.F., Stegeman, J.J., Sumiyama, K., Tabbaa, D., Tafer, H., Turner-Maier, J., van Heusden, P., White, S., Williams, L., Yandell, M., Brinkmann, H., Volff, J.-N., Tabin, C.J., Shubin, N., Schartl, M., Jaffe, D.B., Postlethwait, J.H., Venkatesh, B., Di Palma, F., Lander, E.S., Meyer, A., Lindblad-Toh, K., 2013. The African coelacanth genome provides insights into tetrapod evolution. Nature 496, 311–316. doi:10.1038/nature12027

Axelsson, E., Ratnakumar, A., Arendt, M.-L., Maqbool, K., Webster, M.T., Perloski, M., Liberg, O., Arnemo, J.M., Hedhammar, Å., Lindblad-Toh, K., 2013. The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495, 360–364. doi:10.1038/nature11837

2012

Larson, G., Karlsson, E.K., Perri, A., Webster, M.T., Ho, S.Y.W., Peters, J., Stahl, P.W., Piper, P.J., Lingaas, F., Fredholm, M., Comstock, K.E., Modiano, J.F., Schelling, C., Agoulnik, A.I., Leegwater, P.A., Dobney, K., Vigne, J.-D., Vila, C., Andersson, L., Lindblad-Toh, K., 2012. Rethinking dog domestication by integrating genetics, archeology, and biogeography. Proc Natl Acad Sci U S A 109, 8878–8883. doi:10.1073/pnas.1203005109

Axelsson, E., Webster, M.T., Ratnakumar, A., Ponting, C.P., Lindblad-Toh, K., 2012. Death of PRDM9 coincides with stabilization of the recombination landscape in the dog genome. Genome Research 22, 51–63. doi:10.1101/gr.124123.111

Jones, F.C., Grabherr, M.G., Chan, Y.F., Russell, P., Mauceli, E., Johnson, J., Swofford, R., Pirun, M., Zody, M.C., White, S., Birney, E., Searle, S., Schmutz, J., Grimwood, J., Dickson, M.C., Myers, R.M., Miller, C.T., Summers, B.R., Knecht, A.K., Brady, S.D., Zhang, H., Pollen, A.A., Howes, T., Amemiya, C., Baldwin, J., Bloom, T., Jaffe, D.B., Nicol, R., Wilkinson, J., Lander, E.S., Di Palma, F., Lindblad-Toh, K., Kingsley, D.M., 2012. The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484, 55–61. doi:10.1038/nature10944

2011

Lindblad-Toh, K., Garber, M., Zuk, O., Lin, M.F., Parker, B.J., Washietl, S., Kheradpour, P., Ernst, J., Jordan, G., Mauceli, E., Ward, L.D., Lowe, C.B., Holloway, A.K., Clamp, M., Gnerre, S., Alföldi, J., Beal, K., Chang, J., Clawson, H., Cuff, J., Di Palma, F., Fitzgerald, S., Flicek, P., Guttman, M., Hubisz, M.J., Jaffe, D.B., Jungreis, I., Kent, W.J., Kostka, D., Lara, M., Martins, A.L., Massingham, T., Moltke, I., Raney, B.J., Rasmussen, M.D., Robinson, J., Stark, A., Vilella, A.J., Wen, J., Xie, X., Zody, M.C., Baldwin, J., Bloom, T., Chin, C.W., Heiman, D., Nicol, R., Nusbaum, C., Young, S., Wilkinson, J., Worley, K.C., Kovar, C.L., Muzny, D.M., Gibbs, R.A., Cree, A., Dihn, H.H., Fowler, G., Jhangiani, S., Joshi, V., Lee, S., Lewis, L.R., Nazareth, L.V., Okwuonu, G., Santibanez, J., Warren, W.C., Mardis, E.R., Weinstock, G.M., Wilson, R.K., Delehaunty, K., Dooling, D., Fronik, C., Fulton, L., Fulton, B., Graves, T., Minx, P., Sodergren, E., Birney, E., Margulies, E.H., Herrero, J., Green, E.D., Haussler, D., Siepel, A., Goldman, N., Pollard, K.S., Pedersen, J.S., Lander, E.S., Kellis, M., 2011. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478, 476–482. doi:10.1038/nature10530

Olsson, M., Meadows, J.R.S., Truve, K., Rosengren Pielberg, G., Puppo, F., Mauceli, E., Quilez, J., Tonomura, N., Zanna, G., Docampo, M.J., Bassols, A., Avery, A.C., Karlsson, E.K., Thomas, A., Kastner, D.L., Bongcam-Rudloff, E., Webster, M.T., Sanchez, A., Hedhammar, Å., Remmers, E.F., Andersson, L., Ferrer, L., Tintle, L., Lindblad-Toh, K., 2011. A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs. PLoS Genet 7, e1001332. doi:10.1371/journal.pgen.1001332

Lowe, C.B., Kellis, M., Siepel, A., Raney, B.J., Clamp, M., Salama, S.R., Kingsley, D.M., Lindblad-Toh, K., Haussler, D., 2011. Three periods of regulatory innovation during vertebrate evolution. Science 333, 1019–1024. doi:10.1126/science.1202702

Alföldi, J., Di Palma, F., Grabherr, M., Williams, C., Kong, L., Mauceli, E., Russell, P., Lowe, C.B., Glor, R.E., Jaffe, J.D., Ray, D.A., Boissinot, S., Shedlock, A.M., Botka, C., Castoe, T.A., Colbourne, J.K., Fujita, M.K., Moreno, R.G., Hallers, ten, B.F., Haussler, D., Heger, A., Heiman, D., Janes, D.E., Johnson, J., de Jong, P.J., Koriabine, M.Y., Lara, M., Novick, P.A., Organ, C.L., Peach, S.E., Poe, S., Pollock, D.D., de Queiroz, K., Sanger, T., Searle, S., Smith, J.D., Smith, Z., Swofford, R., Turner-Maier, J., Wade, J., Young, S., Zadissa, A., Edwards, S.V., Glenn, T.C., Schneider, C.J., Losos, J.B., Lander, E.S., Breen, M., Ponting, C.P., Lindblad-Toh, K., 2011. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477, 587–591. doi:10.1038/nature10390

2010

Meurs, K.M., Mauceli, E., Lahmers, S., Acland, G.M., White, S.N., Lindblad-Toh, K., 2010. Genome-wide association identifies a deletion in the 3′ untranslated region of striatin in a canine model of arrhythmogenic right ventricular cardiomyopathy. Hum Genet 128, 315–324. doi:10.1007/s00439-010-0855-y

Wilbe, M., Jokinen, P., Truve, K., Seppala, E.H., Karlsson, E.K., Biagi, T., Hughes, A., Bannasch, D., Andersson, G., Hansson-Hamlin, H., Lohi, H., Lindblad-Toh, K., 2010. Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex. Nat Genet 42, 250–254. doi:10.1038/ng.525

2009

Rivera, P., Melin, M., Biagi, T., Fall, T., Häggström, J., Lindblad-Toh, K., Euler, von, H., 2009. Mammary tumor development in dogs is associated with BRCA1 and BRCA2. Cancer Res 69, 8770–8774. doi:10.1158/0008-5472.CAN-09-1725

Awano, T., Johnson, G.S., Wade, C.M., Katz, M.L., Johnson, G.C., Taylor, J.F., Perloski, M., Biagi, T., Baranowska, I., Long, S., March, P.A., Olby, N.J., Shelton, G.D., Khan, S., O’Brien, D.P., Lindblad-Toh, K., Coates, J.R., 2009. Genome-wide association analysis reveals a SOD1 mutation in canine degenerative myelopathy that resembles amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A 106, 2794–2799. doi:10.1073/pnas.0812297106

2008

Karlsson, E.K., Lindblad-Toh, K., 2008. Leader of the pack: gene mapping in dogs and other model organisms. Nat Rev Genet 9, 713–725. doi:10.1038/nrg2382

2007

Miller, W., Rosenbloom, K., Hardison, R.C., Hou, M., Taylor, J., Raney, B., Burhans, R., King, D.C., Baertsch, R., Blankenberg, D., Kosakovsky Pond, S.L., Nekrutenko, A., Giardine, B., Harris, R.S., Tyekucheva, S., Diekhans, M., Pringle, T.H., Murphy, W.J., Lesk, A., Weinstock, G.M., Lindblad-Toh, K., Gibbs, R.A., Lander, E.S., Siepel, A., Haussler, D., Kent, W.J., 2007. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research 17, 1797–1808. doi:10.1101/gr.6761107

Karlsson, E.K., Baranowska, I., Wade, C.M., Salmon Hillbertz, N.H.C., Zody, M.C., Anderson, N., Biagi, T.M., Patterson, N., Pielberg, G.R., Kulbokas, E.J.3., Comstock, K.E., Keller, E.T., Mesirov, J.P., Euler, von, H., Kämpe, O., Hedhammar, Å., Lander, E.S., Andersson, G., Andersson, L., Lindblad-Toh, K., 2007. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat Genet 39, 1321–1328. doi:10.1038/ng.2007.10

Mikkelsen, T.S., Wakefield, M.J., Aken, B., Amemiya, C.T., Chang, J.L., Duke, S., Garber, M., Gentles, A.J., Goodstadt, L., Heger, A., Jurka, J., Kamal, M., Mauceli, E., Searle, S.M.J., Sharpe, T., Baker, M.L., Batzer, M.A., Benos, P.V., Belov, K., Clamp, M., Cook, A., Cuff, J., Das, R., Davidow, L., Deakin, J.E., Fazzari, M.J., Glass, J.L., Grabherr, M., Greally, J.M., Gu, W., Hore, T.A., Huttley, G.A., Kleber, M., Jirtle, R.L., Koina, E., Lee, J.T., Mahony, S., Marra, M.A., Miller, R.D., Nicholls, R.D., Oda, M., Papenfuss, A.T., Parra, Z.E., Pollock, D.D., Ray, D.A., Schein, J.E., Speed, T.P., Thompson, K., VandeBerg, J.L., Wade, C.M., Walker, J.A., Waters, P.D., Webber, C., Weidman, J.R., Xie, X., Zody, M.C., Graves, J.A.M., Ponting, C.P., Breen, M., Samollow, P.B., Lander, E.S., Lindblad-Toh, K., 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 447, 167–177. doi:10.1038/nature05805

Xie, X., Mikkelsen, T.S., Gnirke, A., Lindblad-Toh, K., Kellis, M., Lander, E.S., 2007. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci U S A 104, 7145–7150. doi:10.1073/pnas.0701811104

2006

Pedersen, J.S., Bejerano, G., Siepel, A., Rosenbloom, K., Lindblad-Toh, K., Lander, E.S., Kent, J., Miller, W., Haussler, D., 2006. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput. Biol. 2, e33. doi:10.1371/journal.pcbi.0020033

Khanna, C., Lindblad-Toh, K., Vail, D., London, C., Bergman, P., Barber, L., Breen, M., Kitchell, B., McNeil, E., Modiano, J.F., Niemi, S., Comstock, K.E., Ostrander, E., Westmoreland, S., Withrow, S., 2006. The dog as a cancer model. Nature Biotechnology 24, 1065–1066. doi:10.1038/nbt0906-1065b

2005

Lindblad-Toh, K., Wade, C.M., Mikkelsen, T.S., Karlsson, E.K., Jaffe, D.B., Kamal, M., Clamp, M., Chang, J.L., Kulbokas, E.J.3., Zody, M.C., Mauceli, E., Xie, X., Breen, M., Wayne, R.K., Ostrander, E.A., Ponting, C.P., Galibert, F., Smith, D.R., DeJong, P.J., Kirkness, E., Alvarez, P., Biagi, T., Brockman, W., Butler, J., Chin, C.-W., Cook, A., Cuff, J., Daly, M.J., DeCaprio, D., Gnerre, S., Grabherr, M., Kellis, M., Kleber, M., Bardeleben, C., Goodstadt, L., Heger, A., Hitte, C., Kim, L., Koepfli, K.-P., Parker, H.G., Pollinger, J.P., Searle, S.M.J., Sutter, N.B., Thomas, R., Webber, C., Baldwin, J., Abebe, A., Abouelleil, A., Aftuck, L., Ait-Zahra, M., Aldredge, T., Allen, N., An, P., Anderson, S., Antoine, C., Arachchi, H., Aslam, A., Ayotte, L., Bachantsang, P., Barry, A., Bayul, T., Benamara, M., Berlin, A., Bessette, D., Blitshteyn, B., Bloom, T., Blye, J., Boguslavskiy, L., Bonnet, C., Boukhgalter, B., Brown, A., Cahill, P., Calixte, N., Camarata, J., Cheshatsang, Y., Chu, J., Citroen, M., Collymore, A., Cooke, P., Dawoe, T., Daza, R., Decktor, K., DeGray, S., Dhargay, N., Dooley, K., Dooley, K., Dorje, P., Dorjee, K., Dorris, L., Duffey, N., Dupes, A., Egbiremolen, O., Elong, R., Falk, J., Farina, A., Faro, S., Ferguson, D., Ferreira, P., Fisher, S., FitzGerald, M., Foley, K., Foley, C., Franke, A., Friedrich, D., Gage, D., Garber, M., Gearin, G., Giannoukos, G., Goode, T., Goyette, A., Graham, J., Grandbois, E., Gyaltsen, K., Hafez, N., Hagopian, D., Hagos, B., Hall, J., Healy, C., Hegarty, R., Honan, T., Horn, A., Houde, N., Hughes, L., Hunnicutt, L., Husby, M., Jester, B., Jones, C., Kamat, A., Kanga, B., Kells, C., Khazanovich, D., Kieu, A.C., Kisner, P., Kumar, M., Lance, K., Landers, T., Lara, M., Lee, W., Leger, J.-P., Lennon, N., Leuper, L., LeVine, S., Liu, J., Liu, X., Lokyitsang, Y., Lokyitsang, T., Lui, A., Macdonald, J., Major, J., Marabella, R., Maru, K., Matthews, C., McDonough, S., Mehta, T., Meldrim, J., Melnikov, A., Meneus, L., Mihalev, A., Mihova, T., Miller, K., Mittelman, R., Mlenga, V., Mulrain, L., Munson, G., Navidi, A., Naylor, J., Nguyen, T., Nguyen, N., Nguyen, C., Nguyen, T., Nicol, R., Norbu, N., Norbu, C., Novod, N., Nyima, T., Olandt, P., O’Neill, B., O’Neill, K., Osman, S., Oyono, L., Patti, C., Perrin, D., Phunkhang, P., Pierre, F., Priest, M., Rachupka, A., Raghuraman, S., Rameau, R., Ray, V., Raymond, C., Rege, F., Rise, C., Rogers, J., Rogov, P., Sahalie, J., Settipalli, S., Sharpe, T., Shea, T., Sheehan, M., Sherpa, N., Shi, J., Shih, D., Sloan, J., Smith, C., Sparrow, T., Stalker, J., Stange-Thomann, N., Stavropoulos, S., Stone, C., Stone, S., Sykes, S., Tchuinga, P., Tenzing, P., Tesfaye, S., Thoulutsang, D., Thoulutsang, Y., Topham, K., Topping, I., Tsamla, T., Vassiliev, H., Venkataraman, V., Vo, A., Wangchuk, T., Wangdi, T., Weiand, M., Wilkinson, J., Wilson, A., Yadav, S., Yang, S., Yang, X., Young, G., Yu, Q., Zainoun, J., Zembek, L., Zimmer, A., Lander, E.S., 2005. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803–819. doi:10.1038/nature04338

Xie, X., Lu, J., Kulbokas, E.J., Golub, T.R., Mootha, V., Lindblad-Toh, K., Lander, E.S., Kellis, M., 2005. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434, 338–345. doi:10.1038/nature03441

2004

Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., Mauceli, E., Bouneau, L., Fischer, C., Ozouf-Costaz, C., Bernot, A., Nicaud, S., Jaffe, D., Fisher, S., Lutfalla, G., Dossat, C., Segurens, B., Dasilva, C., Salanoubat, M., Levy, M., Boudet, N., Castellano, S., Anthouard, V., Jubin, C., Castelli, V., Katinka, M., Vacherie, B., Biemont, C., Skalli, Z., Cattolico, L., Poulain, J., De Berardinis, V., Cruaud, C., Duprat, S., Brottier, P., Coutanceau, J.-P., Gouzy, J., Parra, G., Lardier, G., Chapple, C., McKernan, K.J., McEwan, P., Bosak, S., Kellis, M., Volff, J.-N., Guigó, R., Zody, M.C., Mesirov, J., Lindblad-Toh, K., Birren, B., Nusbaum, C., Kahn, D., Robinson-Rechavi, M., Laudet, V., Schachter, V., Quetier, F., Saurin, W., Scarpelli, C., Wincker, P., Lander, E.S., Weissenbach, J., Roest Crollius, H., 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946–957. doi:10.1038/nature03025

2003

Jaffe, D.B., Butler, J., Gnerre, S., Mauceli, E., Lindblad-Toh, K., Mesirov, J.P., Zody, M.C., Lander, E.S., 2003. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Research 13, 91–96. doi:10.1101/gr.828403

2002

Waterston, R.H., Lindblad-Toh, K., Birney, E., Rogers, J., Abril, J.F., Agarwal, P., Agarwala, R., Ainscough, R., Alexandersson, M., An, P., Antonarakis, S.E., Attwood, J., Baertsch, R., Bailey, J., Barlow, K., Beck, S., Berry, E., Birren, B., Bloom, T., Bork, P., Botcherby, M., Bray, N., Brent, M.R., Brown, D.G., Brown, S.D., Bult, C., Burton, J., Butler, J., Campbell, R.D., Carninci, P., Cawley, S., Chiaromonte, F., Chinwalla, A.T., Church, D.M., Clamp, M., Clee, C., Collins, F.S., Cook, L.L., Copley, R.R., Coulson, A., Couronne, O., Cuff, J., Curwen, V., Cutts, T., Daly, M., David, R., Davies, J., Delehaunty, K.D., Deri, J., Dermitzakis, E.T., Dewey, C., Dickens, N.J., Diekhans, M., Dodge, S., Dubchak, I., Dunn, D.M., Eddy, S.R., Elnitski, L., Emes, R.D., Eswara, P., Eyras, E., Felsenfeld, A., Fewell, G.A., Flicek, P., Foley, K., Frankel, W.N., Fulton, L.A., Fulton, R.S., Furey, T.S., Gage, D., Gibbs, R.A., Glusman, G., Gnerre, S., Goldman, N., Goodstadt, L., Grafham, D., Graves, T.A., Green, E.D., Gregory, S., Guigó, R., Guyer, M., Hardison, R.C., Haussler, D., Hayashizaki, Y., Hillier, L.W., Hinrichs, A., Hlavina, W., Holzer, T., Hsu, F., Hua, A., Hubbard, T., Hunt, A., Jackson, I., Jaffe, D.B., Johnson, L.S., Jones, M., Jones, T.A., Joy, A., Kamal, M., Karlsson, E.K., Karolchik, D., Kasprzyk, A., Kawai, J., Keibler, E., Kells, C., Kent, W.J., Kirby, A., Kolbe, D.L., Korf, I., Kucherlapati, R.S., Kulbokas, E.J., Kulp, D., Landers, T., Leger, J.P., Leonard, S., Letunic, I., Levine, R., Li, J., Li, M., Lloyd, C., Lucas, S., Ma, B., Maglott, D.R., Mardis, E.R., Matthews, L., Mauceli, E., Mayer, J.H., McCarthy, M., McCombie, W.R., McLaren, S., McLay, K., McPherson, J.D., Meldrim, J., Meredith, B., Mesirov, J.P., Miller, W., Miner, T.L., Mongin, E., Montgomery, K.T., Morgan, M., Mott, R., Mullikin, J.C., Muzny, D.M., Nash, W.E., Nelson, J.O., Nhan, M.N., Nicol, R., Ning, Z., Nusbaum, C., O’Connor, M.J., Okazaki, Y., Oliver, K., Overton-Larty, E., Pachter, L., Parra, G., Pepin, K.H., Peterson, J., Pevzner, P., Plumb, R., Pohl, C.S., Poliakov, A., Ponce, T.C., Ponting, C.P., Potter, S., Quail, M., Reymond, A., Roe, B.A., Roskin, K.M., Rubin, E.M., Rust, A.G., Santos, R., Sapojnikov, V., Schultz, B., Schultz, J., Schwartz, M.S., Schwartz, S., Scott, C., Seaman, S., Searle, S., Sharpe, T., Sheridan, A., Shownkeen, R., Sims, S., Singer, J.B., Slater, G., Smit, A., Smith, D.R., Spencer, B., Stabenau, A., Stange-Thomann, N., Sugnet, C., Suyama, M., Tesler, G., Thompson, J., Torrents, D., Trevaskis, E., Tromp, J., Ucla, C., Ureta-Vidal, A., Vinson, J.P., Niederhausern, Von, A.C., Wade, C.M., Wall, M., Weber, R.J., Weiss, R.B., Wendl, M.C., West, A.P., Wetterstrand, K., Wheeler, R., Whelan, S., Wierzbowski, J., Willey, D., Williams, S., Wilson, R.K., Winter, E., Worley, K.C., Wyman, D., Yang, S., Yang, S.-P., Zdobnov, E.M., Zody, M.C., Lander, E.S., 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562.