Integrating Genomes von Zerbino, D. R., Paten, B., Haussler, D.

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A comparative genomics multitool for scientific discovery and conservation von Genereux, Diane P., Serres, Aitor, Armstrong, Joel, Johnson, Jeremy, Marinescu, Voichita D., Muren, Eva, Juan, David, Bejerano, Gill, Casewell, Nicholas R., Chemnick, Leona G., Damas, Joana, Di Palma, Federica, Diekhans, Mark, Fiddes, Ian T., Garber, Manuel, Gladyshev, Vadim N., Goodman, Linda, Haerty, Wilfried, Houck, Marlys L., Hubley, Robert, Kivioja, Teemu, Koepfli, Klaus-Peter, Kuderna, Lukas F. K., Lander, Eric S., Meadows, Jennifer R. S., Murphy, William J., Nash, Will, Noh, Hyun Ji, Nweeia, Martin, Pfenning, Andreas R., Pollard, Katherine S., Ray, David A., Shapiro, Beth, Smit, Arian F. A., Springer, Mark S., Steiner, Cynthia C., Swofford, Ross, Taipale, Jussi, Teeling, Emma C., Turner-Maier, Jason, Alfoldi, Jessica, Birren, Bruce, Ryder, Oliver A., Lewin, Harris A., Paten, Benedict, Marques-Bonet, Tomas, Lindblad-Toh, Kerstin, Karlsson, Elinor K.

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Leveraging base-pair mammalian constraint to understand genetic variation and human disease von Sullivan, Patrick F, Meadows, Jennifer R S, Gazal, Steven, Phan, BaDoi N, Li, Xue, Genereux, Diane P, Dong, Michael X, Bianchi, Matteo, Andrews, Gregory, Sakthikumar, Sharadha, Nordin, Jessika, Roy, Ananya, Christmas, Matthew J, Marinescu, Voichita D, Wang, Chao, Wallerman, Ola, Xue, James, Yao, Shuyang, Sun, Quan, Szatkiewicz, Jin, Wen, Jia, Huckins, Laura M, Lawler, Alyssa, Keough, Kathleen C, Zheng, Zhili, Zeng, Jian, Wray, Naomi R, Li, Yun, Johnson, Jessica, Chen, Jiawen, Paten, Benedict, Reilly, Steven K, Hughes, Graham M, Weng, Zhiping, Pollard, Katherine S, Pfenning, Andreas R, Forsberg-Nilsson, Karin, Karlsson, Elinor K, Lindblad-Toh, Kerstin

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Evolutionary constraint and innovation across hundreds of placental mammals von Christmas, Matthew J, Kaplow, Irene M, Genereux, Diane P, Dong, Michael X, Hughes, Graham M, Li, Xue, Sullivan, Patrick F, Hindle, Allyson G, Andrews, Gregory, Armstrong, Joel C, Bianchi, Matteo, Breit, Ana M, Diekhans, Mark, Fanter, Cornelia, Foley, Nicole M, Goodman, Daniel B, Goodman, Linda, Keough, Kathleen C, Kirilenko, Bogdan, Kowalczyk, Amanda, Lawless, Colleen, Lind, Abigail L, Meadows, Jennifer R S, Moreira, Lucas R, Redlich, Ruby W, Ryan, Louise, Swofford, Ross, Valenzuela, Alejandro, Wagner, Franziska, Wallerman, Ola, Brown, Ashley R, Damas, Joana, Fan, Kaili, Gatesy, John, Grimshaw, Jenna, Johnson, Jeremy, Kozyrev, Sergey V, Lawler, Alyssa J, Marinescu, Voichita D, Morrill, Kathleen M, Osmanski, Austin, Paulat, Nicole S, Phan, BaDoi N, Reilly, Steven K, Schäffer, Daniel E, Steiner, Cynthia, Supple, Megan A, Wilder, Aryn P, Wirthlin, Morgan E, Xue, James R, Birren, Bruce W, Gazal, Steven, Hubley, Robert M, Koepfli, Klaus-Peter, Marques-Bonet, Tomas, Meyer, Wynn K, Nweeia, Martin, Sabeti, Pardis C, Shapiro, Beth, Smit, Arian F A, Springer, Mark S, Teeling, Emma C, Weng, Zhiping, Hiller, Michael, Levesque, Danielle L, Lewin, Harris A, Murphy, William J, Navarro, Arcadi, Paten, Benedict, Pollard, Katherine S, Ray, David A, Ruf, Irina, Ryder, Oliver A, Pfenning, Andreas R, Lindblad-Toh, Kerstin, Karlsson, Elinor K

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A user's guide to the encyclopedia of DNA elements (ENCODE) von Consortium, The ENCODEProject

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Cactus graphs for genome comparisons von Paten, Benedict, Diekhans, Mark, Earl, Dent, John, John St, Ma, Jian, Suh, Bernard, Haussler, David

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Guilt by multiple association von Ettwiller, L, Paten, B

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Integrating Genomes : Computational Biology von ZERBINO, D. R, PATEN, B, HAUSSLER, D

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Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020) von 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

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Functional genomics: Guilt by multiple association von Ettwiller, L, Paten, B

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The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates von Ettwiller, Laurence, Paten, Benedict, Souren, Marcel, Loosli, Felix, Wittbrodt, Jochen, Birney, Ewan

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Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci von Lilue, J, Doran, AG, Fiddes, IT, Abrudan, M, Armstrong, J, Bennett, R, Chow, W, Collins, J, Collins, S, Czechanski, A, Danecek, P, Diekhans, M, Dolle, D-D, Dunn, M, Durbin, R, Earl, D, Ferguson-Smith, A, Flicek, P, Flint, J, Frankish, A, Fu, B, Gerstein, M, Gilbert, J, Goodstadt, L, Harrow, J, Howe, K, Ibarra-Soria, X, Kolmogorov, M, Lelliott, CJ, Logan, DW, Loveland, J, Mathews, CE, Mott, R, Muir, P, Nachtweide, S, Navarro, FCP, Odom, DT, Park, N, Pelan, S, Pham, SK, 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, DJ, Paten, B, Keane, TM

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BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2 von Cline, M.S., Liao, R.G., Parsons, M.T., Paten, B., Alquaddoomi, F., Antoniou, A., Baxter, S., Brody, L., Cook-Deegan, R., Coffin, A., Couch, F.J., Craft, B., Currie, R., Dlott, C.C., Dolman, L., Dunnen, J.T. den, Dyke, S.O.M., Domchek, S.M., Fischmann, Z., Garber, J., Goldman, M.J., Harrison, S., Haussler, D., Kato, K., Knoppers, B., Markello, C., Nussbaum, R., Offit, K., Plon, S.E., Rashbass, J., Rehm, H.L., Robson, M., Rubinstein, W.S., Stoppa-Lyonnet, D., Tavtigian, S., Zhang, C., Zimmermann, M., Burn, J., Chanock, S., Ratsch, G., Spurdle, A.B., Andreoletti, G., Baker, D., Brenner, S., Brush, M., Caputo, S., Castera, L., Cunningham, F., Hoya, M. de la, Dolinsky, J., Dwight, S., Eccles, D., Feng, B., Flicek, P., Gaudet, P., Garcia, E.G., Haendel, M., Haeussler, M., Hahnen, E., Houdayer, C., Hunt, S., James, P., Lebo, M., Lee, J., Lerner-Ellis, J., Lin, M., Lincoln, S., Malheiro, A., Natzijl-Visser, E., Ngeow, J., North, K., Parkinson, H., Paschall, J., Patrinos, G., Radice, P., Rainville, I., Rasmussen, M., Riley, G., Rouleau, E., Schmutzler, R., Shefchek, K., Sofia, H., Southey, M., Stuart, J., Thomas, J., Toland, A., Turn-Bull, C., Vaur, D., Vreeswijk, M.P.G., Walker, L., Walsh, M., Wappenschmidt, B., Weitzel, J., Wright, M., Zalunin, V., Zaranek, A., Zerbino, D., Zhou, A., Zhou, J., Zook, J.

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A 3-way hybrid approach to generate a new high quality chimpanzee reference genome (Pan_tro_3.0) von Kuderna, LFK, Tomlinson, C, Hillier, LW, Tran, A, Fiddes, I, Armstrong, J, Laayouni, H, Gordon, D, Huddleston, J, Perez, RG, Povolotskaya, I, Armero, AS, Garrido, JG, Ho, D, Ribeca, P, Alioto, T, Green, RE, Paten, B, Navarro, A, Betranpetit, J, Herrero, J, Eichler, EE, Sharp, AJ, Feuk, L, Warren, WC, Marques-Bonet, T

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A user's guide to the Encyclopedia of DNA elements (ENCODE) von Wang, L, Issner, R, Ward, LD, Batut, P, Chakrabortty, S, Jha, S, Lin, W, Wang, H, Bell, K, Antonarakis, SE, Guigo, R, Abdelhamid, RF, Hannon, G, Fejes, K, Preall, J, Howald, C, Ruan, X, Poh, WT, Furey, TS, Boyle, AP, Vales, T, Battenhouse, A, Kim, SKC, Bansal, A, Pusey, B, Muratet, MA, Bowling, KM, Parker, SL, Absher, DM, Williams, B, Marinov, G, Pepke, S, McCue, K, DeSalvo, G, Fisher, K, Sidow, A, Batzoglou, S, Kundaje, A, Hubbard, T, Harrow, J, Kokocinski, F, Despacio-Reyes, G, Saunders, G, Boychenko, V, Brent, M, Khurana, E, Lam, H, Cayting, P, Robilotto, R, Lu, Z, Knowles, DG, Harte, R, Diekhans, M, Landt, SG, Lacroute, P, Xu, Y, Reed, B, Hariharan, M, Rozowsky, J, Weissman, SM, Frietze, S, O'Geen, H, Kaul, R, Thurman, RE, Weaver, M, Roach, V, Johnson, A, Rynes, E, Vong, S, Frum, T, Johnson, EM, Haugen, E, Humbert, R, Shafer, T, Learned, K, Fujita, PA, Kuhn, RM, Luscombe, NM, Boley, N, Brown, JB, Sboner, A, Cheng, C, Yan, K-K, Bhardwaj, N, Gibson, T, Du, J, Harris, RS, Suh, B, Paten, B, Hoffman, MM, Penalva, LO, Victorsen, A, Jameel, N, Bild, N, Whitfield, TW, Trinklein, ND, Giddings, MC, Gunawardena, H, Risk, B, Lowdon, RF

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Long-term dynamics of honey bee colonies following exposure to chemical stress von Colin, Théotime, Meikle, William G., Paten, Amy M., Barron, Andrew B.

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The Human Pangenome Project: a global resource to map genomic diversity von Wang, Ting, Antonacci-Fulton, Lucinda, Howe, Kerstin, Lawson, Heather A., Lucas, Julian K., Phillippy, Adam M., Popejoy, Alice B., Asri, Mobin, Carson, Caryn, Chaisson, Mark J. P., Chang, Xian, Cook-Deegan, Robert, Felsenfeld, Adam L., Fulton, Robert S., Garrison, Erik P., Garrison, Nanibaa’ A., Graves-Lindsay, Tina A., Ji, Hanlee, Kenny, Eimear E., Koenig, Barbara A., Li, Daofeng, Marschall, Tobias, McMichael, Joshua F., Novak, Adam M., Purushotham, Deepak, Schneider, Valerie A., Schultz, Baergen I., Smith, Michael W., Sofia, Heidi J., Weissman, Tsachy, Flicek, Paul, Li, Heng, Miga, Karen H., Paten, Benedict, Jarvis, Erich D., Hall, Ira M., Eichler, Evan E., Haussler, David

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Non-additive gene interactions underpin molecular and phenotypic responses in honey bee larvae exposed to imidacloprid and thymol von Paten, Amy M., Colin, Théotime, Coppin, Chris W., Court, Leon N., Barron, Andrew B., Oakeshott, John G., Morgan, Matthew J.

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The human body at cellular resolution: the NIH Human Biomolecular Atlas Program von Snyder, Michael P, Lin, Shin, Posgai, Amanda, Atkinson, Mark, Regev, Aviv, Rood, Jennifer, Rozenblatt-Rosen, Orit

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Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer von Walker, Nicolas J., Rashid, Mamunur, Yu, Shirong, Bignell, Helen, Lumby, Casper K., Livi, Carmen M., Howell, Kate, Morley, David J., Morganella, Sandro, Barrell, Daniel, Caim, Shabhonam, Gosal, Walraj, Füllgrabe, Jens, Charlesworth, Thomas J., Vasquez, Louella, Ahdesmäki, Miika, Eizenga, Jordan, Prabhat, Parul, Proutski, Vitali, Murat-Onana, Marie Laurie, Greenwood, Catherine J., Kirkwood, Lisa, Maisuria-Armer, Meeta, Li, Mengjie, Coats, Emma, Winfield, Victoria, MacBean, Lachlan, Stock, Toby, Tomé-Fernandez, Alice, Chan, Yat, Sheikh, Nasir, Golder, Paula, Steward, Michael, Ost, Tobias W. B., Stewart, Douglas, Vilella, Albert, Noursalehi, Mojtaba, Paten, Benedict, Lucarelli, Debora, Mason, Joanne, Ridge, Gareth, Mellad, Jason, Shirodkar, Suman, Balasubaramanian, Shankar, Holbrook, Joanna D.

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