Featured publications

2022

Dahlqvist J, Ekman D, Sennblad B, Kozyrev SV, Nordin J, Karlsson Å, Meadows JRS, Hellbacher E, Rantapää-Dahlqvist S, Berglin E, Stegmayr B, Baslund B, Palm Ø, Haukeland H, Gunnarsson I, Bruchfeld A, Segelmark M, Ohlsson S, Mohammad AJ, Svärd A, Pullerits R, Herlitz H, Söderbergh A, Rosengren Pielberg G, Hultin Rosenberg L, Bianchi M, Murén E, Omdal R, Jonsson R, Eloranta ML, Rönnblom L, Söderkvist P, Knight A, Eriksson P, Lindblad-Toh K. 2021. Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA. Rheumatology. 2022 Aug 3;61(8):3461-3470. doi: 10.1093/rheumatology/keab912.

Lundtoft C, Sjöwall C, Rantapää-Dahlqvist S, Bengtsson AA, Jönsen A, Pucholt P, Wu YL, Lundström E, Eloranta ML, Gunnarsson I, Baecklund E, Jonsson R, Hammenfors D, Forsblad-d’Elia H, Eriksson P, Mandl T, Bucher S, Norheim KB, Johnsen SJA, Omdal R, Kvarnström M, Wahren-Herlenius M, Truedsson L, Nilsson B, Kozyrev SV, Bianchi M, Lindblad-Toh K; DISSECT consortium; ImmunoArray consortium, Yu CY, Nordmark G, Sandling JK, Svenungsson E, Leonard D, Rönnblom L. 2022. Combined genetic deficiencies of the classical complement pathway are strongly associated with both systemic lupus erythematosus and primary Sjögren’s syndrome. Arthritis Rheumatol. 2022 Jun 21. doi: 10.1002/art.42270. Online ahead of print.

Lundtoft C, Pucholt P, Martin M, Bianchi M, Lundström E, Eloranta ML, Sandling JK, Sjöwall C, Jönsen A, Gunnarsson I, Rantapää-Dahlqvist S, Bengtsson AA, Leonard D, Baecklund E, Jonsson R, Hammenfors D, Forsblad-d’Elia H, Eriksson P, Mandl T, Magnusson Bucher S, Norheim KB, Auglaend Johnsen SJ, Omdal R, Kvarnström M, Wahren-Herlenius M, Notarnicola A, Andersson H, Molberg Ø, Diederichsen LP, Almlöf J, Syvänen AC, Kozyrev SV, Lindblad-Toh K; DISSECT Consortium; ImmunoArray Development Consortium, Nilsson B, Blom AM, Lundberg IE, Nordmark G, Diaz-Gallo LM, Svenungsson E, Rönnblom L. 2022. Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases. Arthritis Rheumatol. 2022 Aug;74(8):1440-1450. doi: 10.1002/art.42122. Epub 2022 Jun 27.

Noh HJ, Turner-Maier J, Schulberg SA, Fitzgerald ML, Johnson J, Allen KN, Hückstädt LA, Batten AJ, Alfoldi J, Costa DP, Karlsson EK, Zapol WM, Buys ES, Lindblad-Toh K, Hindle AG. 2022. The Antarctic Weddell seal genome reveals evidence of selection on cardiovascular phenotype and lipid handling. Commun Biol. 2022 Feb 17;5(1):140. doi: 10.1038/s42003-022-03089-2.

Axelsson E, Ljungvall I, Bhoumik P, Conn LB, Muren E, Ohlsson Å, Olsen LH, Engdahl K, Hagman R, Hanson J, Kryvokhyzha D, Pettersson M, Grenet O, Moggs J, Rio-Espinola AD, Epe C, Taillon B, Tawari N, Mane S, Hawkins T, Hedhammar Å, Gruet P, Häggström J, Lindblad-Toh K. 2022. Correction: The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels. PLoS Genet. 2022 Jan 27;18(1):e1010039. doi: 10.1371/journal.pgen.1010039. eCollection 2022 Jan.

Prouteau A, Mottier S, Primot A, Cadieu E, Bachelot L, Botherel N, Cabillic F, Houel A, Cornevin L, Kergal C, Corre S, Abadie J, Hitte C, Gilot D, Lindblad-Toh K, André C, Derrien T, Hedan B. 2022. Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets. Cancers. 2022 Jan 6;14(2):276. doi: 10.3390/cancers14020276.

Lawniczak MKN, Durbin R, Flicek P, Lindblad-Toh K, Wei X, Archibald JM, Baker WJ, Belov K, Blaxter ML, Marques Bonet T, Childers AK, Coddington JA, Crandall KA, Crawford AJ, Davey RP, Di Palma F, Fang Q, Haerty W, Hall N, Hoff KJ, Howe K, Jarvis ED, Johnson WE, Johnson RN, Kersey PJ, Liu X, Lopez JV, Myers EW, Pettersson OV, Phillippy AM, Poelchau MF, Pruitt KD, Rhie A, Castilla-Rubio JC, Sahu SK, Salmon NA, Soltis PS, Swarbreck D, Thibaud-Nissen F, Wang S, Wegrzyn JL, Zhang G, Zhang H, Lewin HA, Richards S. 2022. Standards recommendations for the Earth BioGenome Project. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115639118. doi: 10.1073/pnas.2115639118.

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, Lewin HA. 2022. Why sequence all eukaryotes? Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115636118. doi: 10.1073/pnas.2115636118.

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 SM, 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 JH, 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, Zhang G. 2022. The Earth BioGenome Project 2020: Starting the clock. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115635118. doi: 10.1073/pnas.2115635118.

2021

Letko A, Minor KM, Norton EM, Marinescu VD, Drögemüller M, Ivansson E, Megquier K, Noh HJ, Starkey M, Friedenberg SG, Lindblad-Toh K, Mickelson JR, Drögemüller C. 2021. Genome-Wide Analyses for Osteosarcoma in Leonberger Dogs Reveal the CDKN2A/B Gene Locus as a Major Risk Locus. Genes. 2021 Dec 9;12(12):1964. doi: 10.3390/genes12121964.

Axelsson E, Ljungvall I, Bhoumik P, Conn LB, Muren E, Ohlsson Å, Olsen LH, Engdahl K, Hagman R, Hanson J, Kryvokhyzha D, Pettersson M, Grenet O, Moggs J, Del Rio-Espinola A, Epe C, Taillon B, Tawari N, Mane S, Hawkins T, Hedhammar Å, Gruet P, Häggström J, Lindblad-Toh K. 2021. The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels. PLoS Genet. 2021 Sep 2;17(9):e1009726. doi: 10.1371/journal.pgen.1009726. eCollection Sep.

Arendt M, Ambrosen A, Fall T, Kierczak M, Tengvall K, Meadows JRS, Karlsson Å, Lagerstedt AS, Bergström T, Andersson G, Lindblad-Toh K, Hagman R. 2021. The ABCC4 gene is associated with pyometra in golden retriever dogs. Sci Rep. Aug 17;11(1):16647. doi: 10.1038/s41598-021-95936-1.

Nordin J, Pettersson M, Rosenberg LH, Mathioudaki A, Karlsson Å, Murén E, Tandre K, Rönnblom L, Kastbom A, Cedergren J, Eriksson P, Söderkvist P, Lindblad-Toh K, Meadows JRS. 2021. Association of Protective HLA-A With HLA-B∗27 Positive Ankylosing Spondylitis. Front Genet. 2021 Jul 15;12:659042. doi: 10.3389/fgene.2021.659042.

Bianchi M, Kozyrev SV, Notarnicola A, Hultin Rosenberg L, Karlsson Å, Pucholt P, Rothwell S, Alexsson A, Sandling JK, Andersson H, Cooper RG, Padyukov L, Tjärnlund A, Dastmalchi M; ImmunoArray Development Consortium, The DISSECT consortium, Meadows JRS, Pyndt Diederichsen L, Molberg Ø, Chinoy H, Lamb J, Rönnblom L, Lindblad-Toh K, Lundberg IE. 2021. Contribution of rare genetic variation to disease susceptibility in a large Scandinavian myositis cohort. Arthritis Rheumatol. Jul 19. doi: 10.1002/art.41929.

Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD. 2021. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science. May 28;372(6545):984-989. doi: 10.1126/science.abe2218.

Kim JH, Megquier K, Thomas R, Sarver AL, Song JM, Kim YT, Cheng N, Schulte AJ, Linden MA, Murugan P, Oseth L, Forster CL, Elvers I, Swofford R, Turner-Maier J, Karlsson EK, Breen M, Lindblad-Toh K, Modiano JF. Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions. 2021. Mol Cancer Res. May;19(5):847-861. doi: 10.1158/1541-7786.MCR-20-0937. Epub 2021 Mar 1.

Wang C, Wallerman O, Arendt ML, Sundström E, Karlsson Å, Nordin J, Mäkeläinen S, Pielberg GR, Hanson J, Ohlsson Å, Saellström S, Rönnberg H, Ljungvall I, Häggström J, Bergström TF, Hedhammar Å, Meadows JRS, Lindblad-Toh K. A novel canine reference genome resolves genomic architecture and uncovers transcript complexity. Commun Biol. 2021 Feb 10;4(1):185. doi: 10.1038/s42003-021-01698-x.

2020

Herrera-Álvarez S, Karlsson E, Ryder OA, Lindblad-Toh K, Crawford AJ. 2020. How to make a rodent giant: Genomic basis and tradeoffs of gigantism in the capybara, the world’s largest rodent. Mol Biol Evol. 2020 Nov 10:msaa285. doi: 10.1093/molbev/msaa285. 

Mathioudaki A, Ljungström V, Melin M, Arendt ML, Nordin J, Karlsson Å, Murén E, Saksena P, Meadows JRS, Marinescu VD, Sjöblom T, Lindblad-Toh K. 2020. Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort. Sci Rep. Nov 9;10(1):19304. doi: 10.1038/s41598-020-74580-1.

Sandling JK, Pucholt P, Hultin Rosenberg L, Farias FHG, Kozyrev SV, Eloranta ML, Alexsson A, Bianchi M, Padyukov L, Bengtsson C, Jonsson R, Omdal R, Lie BA, Massarenti L, Steffensen R, Jakobsen MA, Lillevang ST; ImmunoArray Development Consortium and DISSECT consortium, Lerang K, Molberg Ø, Voss A, Troldborg A, Jacobsen S, Syvänen AC, Jönsen A, Gunnarsson I, Svenungsson E, Rantapää-Dahlqvist S, Bengtsson AA, Sjöwall C, Leonard D, Lindblad-Toh K, Rönnblom L. 2020. Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing.Ann Rheum Dis. Oct 9:annrheumdis-2020-218636. doi: 10.1136/annrheumdis-2020-218636.

Yavuz S, Bianchi M, Kozyrev S, Bolin K, Leonard D, Pucholt P, Sandling JK, Bengtsson A, Jönsen A, Rantapää-Dahlqvist S, Sjöwall C, Svenungsson E, Gunnarsson I, Lindblad-Toh K, Rönnblom L. 2020. Toll-like receptors revisited; a possible role for TLR1 in lupus nephritis. Ann Rheum Dis. Sep 29:annrheumdis-2020-218373. doi: 10.1136/annrheumdis-2020-218373

Thorlacius GE, Hultin-Rosenberg L, Sandling JK, Bianchi M, Imgenberg-Kreuz J, Pucholt P, Theander E, Kvarnström M, Forsblad-d’Elia H, Bucher SM, Norheim KB, Johnsen SJA, Hammenfors D, Skarstein K, Jonsson MV, Baecklund E, Aqrawi LA, Jensen JL, Palm Ø, Morris AP; DISSECT consortium; the ImmunoArray consortium, Meadows JRS, Rantapää-Dahlqvist S, Mandl T, Eriksson P, Lind L, Omdal R, Jonsson R, Lindblad-Toh K, Rönnblom L, Wahren-Herlenius M, Nordmark G. 2020. Genetic and clinical basis for two distinct subtypes of primary Sjögren’s syndrome. Rheumatology (Oxford). Aug 21:keaa367. doi: 10.1093/rheumatology/keaa367.

Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, Hiller M, Koepfli KP, Pfenning AR, Zhao H, Genereux DP, Swofford R, Pollard KS, Ryder OA, Nweeia MT, Lindblad-Toh K, Teeling EC, Karlsson EK, Lewin HA. 2020. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proc Natl Acad Sci U S A. Sep 8;117(36):22311-22322. doi: 10.1073/pnas.2010146117. Epub 2020 Aug 21.

Tengvall K, Bergvall K, Olsson M, Ardesjö-Lundgren B, Farias FHG, Kierczak M, Hedhammar Å, Lindblad-Toh K, Andersson G. 2020. Transcriptomes from German shepherd dogs reveal differences in immune activity between atopic dermatitis affected and control skin. Immunogenetics. Jul;72(5):315-323. doi: 10.1007/s00251-020-01169-3.

Sakthikumar S, Roy A, Haseeb L, Pettersson ME, Sundström E, Marinescu VD, Lindblad-Toh K, Forsberg-Nilsson K. 2020. Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes. Genome Biol. Jun 9;21(1):127. doi: 10.1186/s13059-020-02035-x.

Bianchi, M., Rafati, N., Karlsson, Å., Murén, E., Rubin, C.-J., Sundberg, K., Andersson, G., Kämpe, O., Hedhammar, Å., Lindblad-Toh, K., Rosengren Pielberg, G., 2020. Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs. BMC Genomics 21, 307–16. doi:10.1186/s12864-020-6700-3

Nordin, J., Ameur, A., Lindblad-Toh, K., Gyllensten, U., Meadows, J.R.S.., 2020. SweHLA: the high confidence HLA typing bio-resource drawn from 1000 Swedish genomes. Eur J Hum Genet. 2020 May;28(5):627-635. doi: 10.1038/s41431-019-0559-2. Epub 2019 Dec 16.

Rohdin, C., Ljungvall, I,, Häggström, J., Leijon, A., Lindblad-Toh, K., Matiasek, K., Rosati, M,, Wohlsein, P., Jäderlund, K.H., 2020. Thoracolumbar meningeal fibrosis in pugs. J Vet Intern Med. 2020 Mar;34(2):797-807. doi: 10.1111/jvim.15716. Epub 2020 Jan 31.

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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 – Selected publications

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.