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False gene and chromosome losses in genome assemblies caused by GC content variation and repeats 期刊论文
GENOME BIOLOGY, 2022, 卷号: 23, 期号: 1
作者:  Kim, J;  Lee, C;  Ko, BJ;  Yoo, DA;  Won, S;  Phillippy, AM;  Fedrigo, O;  Zhang, GJ;  Howe, K;  Wood, J;  Durbin, R;  Formenti, G;  Brown, S;  Cantin, L;  Mello, CV;  Cho, S;  Rhie, A;  Kim, H;  Jarvis, ED
Adobe PDF(8635Kb)  |  收藏  |  浏览/下载：1148/0  |  提交时间：2023/04/12
The Earth BioGenome Project 2020: Starting the clock 期刊论文
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2022, 卷号: 119, 期号: 4
作者:  Lewin, HA;  Richards, S;  Aiden, EL;  Allende, ML;  Archibald, JM;  Balint, 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, XY;  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, BP;  Tedersoo, L;  Uliano-Silva, M;  Wang, K;  Wei, XF;  Wetzer, R;  Wilson, JL;  Xu, X;  Yang, HM;  Yoder, AD;  Zhang, GJ
Adobe PDF(1428Kb)  |  收藏  |  浏览/下载：1122/0  |  提交时间：2023/04/12
Towards complete and error-free genome assemblies of all vertebrate species 期刊论文
NATURE, 2021, 卷号: 592, 期号: 7856, 页码: 737-+
作者:  Rhie, A;  McCarthy, SA;  Fedrigo, O;  Damas, J;  Formenti, G;  Koren, S;  Uliano-Silva, M;  Chow, W;  Fungtammasan, A;  Kim, J;  Lee, C;  Ko, BJ;  Chaisson, M;  Gedman, GL;  Cantin, LJ;  Thibaud-Nissen, F;  Haggerty, L;  Bista, I;  Smith, M;  Haase, B;  Mountcastle, J;  Winkler, S;  Paez, S;  Howard, J;  Vernes, SC;  Lama, TM;  Grutzner, F;  Warren, WC;  Balakrishnan, CN;  Burt, D;  George, JM;  Biegler, MT;  Iorns, D;  Digby, A;  Eason, D;  Robertson, B;  Edwards, T;  Wilkinson, M;  Turner, G;  Meyer, A;  Kautt, AF;  Franchini, P;  Detrich, HW;  Svardal, H;  Wagner, M;  Naylor, GJP;  Pippel, M;  Malinsky, M;  Mooney, M;  Simbirsky, M;  Hannigan, BT;  Pesout, T;  Houck, M;  Misuraca, A;  Kingan, SB;  Hall, R;  Kronenberg, Z;  Sovi, I;  Dunn, C;  Ning, Z;  Hastie, A;  Lee, J;  Selvaraj, S;  Green, RE;  Putnam, NH;  Gut, I;  Ghurye, J;  Garrison, E;  Sims, Y;  Collins, J;  Pelan, S;  Torrance, J;  Tracey, A;  Wood, J;  Dagnew, RE;  Guan, D;  London, SE;  Clayton, DF;  Mello, CV;  Friedrich, SR;  Lovell, PV;  Osipova, E;  Al-Ajli, FO;  Secomandi, S;  Kim, H;  Theofanopoulou, C;  Hiller, M;  Zhou, Y;  Harris, RS;  Makova, KD;  Medvedev, P;  Hoffman, J;  Masterson, P;  Clark, K;  Martin, F;  Howe, K;  Flicek, P;  Walenz, BP;  Kwak, W;  Clawson, H;  Diekhans, M;  Nassar, L;  Paten, B;  Kraus, RHS;  Crawford, AJ;  Gilbert, MTP;  Zhang, G;  Venkatesh, B;  Murphy, RW;  Koepfli, KP;  Shapiro, B;  Johnson, WE;  Di Palma, F;  Marques-Bonet, T;  Teeling, EC;  Warnow, T;  Graves, JM;  Ryder, OA;  Haussler, D;  O'Brien, SJ;  Korlach, J;  Lewin, HA;  Howe, K;  Myers, EW;  Durbin, R;  Phillippy, AM;  Jarvis, ED
Adobe PDF(23042Kb)  |  收藏  |  浏览/下载：34/0  |  提交时间：2023/04/12
High-coverage genomes to elucidate the evolution of penguins (vol 8, pg 1, 2019) 期刊论文
GIGASCIENCE, 2020, 卷号: 9, 期号: 3
作者:  Pan, Hailin;  Cole, Theresa L.;  Bi, Xupeng;  Fang, Miaoquan;  Zhou, Chengran;  Yang, Zhengtao;  Ksepka, Daniel T.;  Hart, Tom;  Bouzat, Juan L.;  Argilla, Lisa S.;  Bertelsen, Mads F.;  Boersma, P. Dee;  Bost, Charles-Andre;  Cherel, Yves;  Dann, Peter;  Fiddaman, Steven R.;  Howard, Pauline;  Labuschagne, Kim;  Mattern, Thomas;  Miller, Gary;  Parker, Patricia;  Phillips, Richard A.;  Quillfeldt, Petra;  Ryan, Peter G.;  Taylor, Helen;  Thompson, David R.;  Young, Melanie J.;  Ellegaard, Martin R.;  Gilbert, M. Thomas P.;  Sinding, Mikkel-Holger S.;  Pacheco, George;  Shepherd, Lara D.;  Tennyson, Alan J. D.;  Grosser, Stefanie;  Kay, Emily;  Nupen, Lisa J.;  Ellenberg, Ursula;  Houston, David M.;  Reeve, Andrew Hart;  Johnson, Kathryn;  Masello, Juan F.;  Stracke, Thomas;  McKinlay, Bruce;  Borboroglu, Pablo Garcia;  Zhang, De-Xing;  Zhang, Guojie
Adobe PDF(173Kb)  |  收藏  |  浏览/下载：47/0  |  提交时间：2021/11/09
Dense sampling of bird diversity increases power of comparative genomics 期刊论文
NATURE, 2020, 卷号: 587, 期号: 7833, 页码: 252
作者:  Feng, Shaohong;  Stiller, Josefin;  Deng, Yuan;  Armstrong, Joel;  Fang, Qi;  Reeve, Andrew Hart;  Xie, Duo;  Chen, Guangji;  Guo, Chunxue;  Faircloth, Brant C.;  Petersen, Bent;  Wang, Zongji;  Zhou, Qi;  Diekhans, Mark;  Chen, Wanjun;  Andreu-Sanchez, Sergio;  Margaryan, Ashot;  Howard, Jason Travis;  Parent, Carole;  Pacheco, George;  Sinding, Mikkel-Holger S.;  Puetz, Lara;  Cavill, Emily;  Ribeiro, Angela M.;  Eckhart, Leopold;  Fjeldsa, Jon;  Hosner, Peter A.;  Brumfield, Robb T.;  Christidis, Les;  Bertelsen, Mads F.;  Sicheritz-Ponten, Thomas;  Tietze, Dieter Thomas;  Robertson, Bruce C.;  Song, Gang;  Borgia, Gerald;  Claramunt, Santiago;  Lovette, Irby J.;  Cowen, Saul J.;  Njoroge, Peter;  Dumbacher, John Philip;  Ryder, Oliver A.;  Fuchs, Jerome;  Bunce, Michael;  Burt, David W.;  Cracraft, Joel;  Meng, Guanliang;  Hackett, Shannon J.;  Ryan, Peter G.;  Jonsson, Knud Andreas;  Jamieson, Ian G.;  da Fonseca, Rute R.;  Braun, Edward L.;  Houde, Peter;  Mirarab, Siavash;  Suh, Alexander;  Hansson, Bengt;  Ponnikas, Suvi;  Sigeman, Hanna;  Stervander, Martin;  Frandsen, Paul B.;  van der Zwan, Henriette;  van der Sluis, Rencia;  Visser, Carina;  Balakrishnan, Christopher N.;  Clark, Andrew G.;  Fitzpatrick, John W.;  Bowman, Reed;  Chen, Nancy;  Cloutier, Alison;  Sackton, Timothy B.;  Edwards, Scott V.;  Foote, Dustin J.;  Shakya, Subir B.;  Sheldon, Frederick H.;  Vignal, Alain;  Soares, Andre E. R.;  Shapiro, Beth;  Gonzalez-Solis, Jacob;  Ferrer-Obiol, Joan;  Rozas, Julio;  Riutort, Marta;  Tigano, Anna;  Friesen, Vicki;  Dalen, Love;  Urrutia, Araxi O.;  Szekely, Tamas;  Liu, Yang;  Campana, Michael G.;  Corvelo, Andre;  Fleischer, Robert C.;  Rutherford, Kim M.;  Gemmell, Neil J.;  Dussex, Nicolas;  Mouritsen, Henrik;  Thiele, Nadine;  Delmore, Kira;  Liedvogel, Miriam;  Franke, Andre;  Hoeppner, Marc P.;  Krone, Oliver;  Fudickar, Adam M.;  Mila, Borja;  Ketterson, Ellen D.;  Fidler, Andrew Eric;  Friis, Guillermo;  Parody-Merino, Angela M.;  Battley, Phil F.;  Cox, Murray P.;  Lima, Nicholas Costa Barroso;  Prosdocimi, Francisco;  Parchman, Thomas Lee;  Schlinger, Barney A.;  Loiselle, Bette A.;  Blake, John G.;  Lim, Haw Chuan;  Day, Lainy B.;  Fuxjager, Matthew J.;  Baldwin, Maude W.;  Braun, Michael J.;  Wirthlin, Morgan;  Dikow, Rebecca B.;  Ryder, T. Brandt;  Camenisch, Glauco;  Keller, Lukas F.;  DaCosta, Jeffrey M.;  Hauber, Mark E.;  Louder, Matthew I. M.;  Witt, Christopher C.;  McGuire, Jimmy A.;  Mudge, Joann;  Megna, Libby C.;  Carling, Matthew D.;  Wang, Biao;  Taylor, Scott A.;  Del-Rio, Glaucia;  Aleixo, Alexandre;  Vasconcelos, Ana Tereza Ribeiro;  Mello, Claudio V.;  Weir, Jason T.;  Haussler, David;  Li, Qiye;  Yang, Huanming;  Wang, Jian;  Lei, Fumin;  Rahbek, Carsten;  Gilbert, M. Thomas P.;  Graves, Gary R.;  Jarvis, Erich D.;  Paten, Benedict;  Zhang, Guojie
Adobe PDF(11384Kb)  |  收藏  |  浏览/下载：129/0  |  提交时间：2021/11/09
Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks 期刊论文
GENOME RESEARCH, 2019, 卷号: 29, 期号: 4, 页码: 576-589
作者:  Farre, M;  Kim, J;  Proskuryakova, AA;  Zhang, Y;  Kulemzina, AI;  Li, QY;  Zhou, Y;  Xiong, YQ;  Johnson, JL;  Perelman, PL;  Johnson, WE;  Warren, WC;  Kukekova, AV;  Zhang, GJ;  O'Brien, SJ;  Ryder, OA;  Graphodatsky, AS;  Ma, J;  Lewin, HA;  Larkin, DM
Adobe PDF(988Kb)  |  收藏  |  浏览/下载：1180/0  |  提交时间：2019/11/07
Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks 期刊论文
GENOME RESEARCH, 2019, 卷号: 29, 期号: 4, 页码: 576-589
作者:  Farre, M;  Kim, J;  Proskuryakova, AA;  Zhang, Y;  Kulemzina, AI;  Li, QY;  Zhou, Y;  Xiong, YQ;  Johnson, JL;  Perelman, PL;  Johnson, WE;  Warren, WC;  Kukekova, AV;  Zhang, GJ;  O'Brien, SJ;  Ryder, OA;  Graphodatsky, AS;  Ma, J;  Lewin, HA;  Larkin, DM
Adobe PDF(2175Kb)  |  收藏  |  浏览/下载：93/0  |  提交时间：2023/04/12
An integrated chromosome-scale genome assembly of the Masai giraffe (Giraffa camelopardalis tippelskirchi) 期刊论文
GIGASCIENCE, 2019, 卷号: 8, 期号: 8, 页码: -
作者:  Farre, M;  Li, QY;  Darolti, I;  Zhou, Y;  Damas, J;  Proskuryakova, AA;  Kulemzina, AI;  Chemnick, LG;  Kim, J;  Ryder, OA;  Ma, J;  Graphodatsky, AS;  Zhang, GJ;  Larkin, DM;  Lewin, HA
Adobe PDF(2796Kb)  |  收藏  |  浏览/下载：156/0  |  提交时间：2021/11/18
A near-chromosome-scale genome assembly of the gemsbok (Oryx gazella): an iconic antelope of the Kalahari desert 期刊论文
GIGASCIENCE, 2019, 卷号: 8, 期号: 2
作者:  Farre, M;  Li, QY;  Zhou, Y;  Damas, J;  Chemnick, LG;  Kim, J;  Ryder, OA;  Ma, J;  Zhang, GJ;  Larkin, DM;  Lewin, HA
Adobe PDF(2395Kb)  |  收藏  |  浏览/下载：41/0  |  提交时间：2019/11/04
The yak genome and adaptation to life at high altitude 期刊论文
NATURE GENETICS, 2012, 卷号: 44, 期号: 8, 页码: 946-
作者:  Qiu, Q;  Zhang, GJ;  Ma, T;  Qian, WB;  Wang, JY;  Ye, ZQ;  Cao, CC;  Hu, QJ;  Kim, J;  Larkin, DM;  Auvil, L;  Capitanu, B;  Ma, J;  Lewin, HA;  Qian, XJ;  Lang, YS;  Zhou, R;  Wang, LZ;  Wang, K;  Xia, JQ;  Liao, SG;  Pan, SK;  Lu, X;  Hou, HL;  Wang, Y;  Zang, XT;  Yin, Y;  Ma, H;  Zhang, J;  Wang, ZF;  Zhang, YM;  Zhang, DW;  Yonezawa, T;  Hasegawa, M;  Zhong, Y;  Liu, WB;  Zhang, Y;  Huang, ZY;  Zhang, SX;  Long, RJ;  Yang, HM;  Wang, J;  Lenstra, JA;  Cooper, DN;  Wu, Y;  Wang, J;  Shi, P;  Wang, J;  Liu, JQ
Adobe PDF(864Kb)  |  收藏  |  浏览/下载：1586/0  |  提交时间：2023/02/24