High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios von Byrska-Bishop, Marta, Evani, Uday S, Zhao, Xuefang, Basile, Anna O, Abel, Haley J, Regier, Allison A, Corvelo, André, Clarke, Wayne E, Musunuri, Rajeeva, Nagulapalli, Kshithija, Fairley, Susan, Runnels, Alexi, Winterkorn, Lara, Lowy, Ernesto, Paul Flicek, Germer, Soren, Brand, Harrison, Hall, Ira M, Talkowski, Michael E, Narzisi, Giuseppe, Zody, Michael C

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An integrative variant analysis suite for whole exome next-generation sequencing data von Challis, Danny, Yu, Jin, Evani, Uday S, Jackson, Andrew R, Paithankar, Sameer, Coarfa, Cristian, Milosavljevic, Aleksandar, Gibbs, Richard A, Yu, Fuli

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Atlas2 Cloud: a framework for personal genome analysis in the cloud von Evani, Uday S, Challis, Danny, Yu, Jin, Jackson, Andrew R, Paithankar, Sameer, Bainbridge, Matthew N, Jakkamsetti, Adinarayana, Pham, Peter, Coarfa, Cristian, Milosavljevic, Aleksandar, Yu, Fuli

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Integrative transcriptomic analysis of the amyotrophic lateral sclerosis spinal cord implicates glial activation and suggests new risk genes von Humphrey, Jack, Venkatesh, Sanan, Hasan, Rahat, Herb, Jake T., de Paiva Lopes, Katia, Küçükali, Fahri, Byrska-Bishop, Marta, Evani, Uday S., Narzisi, Giuseppe, Fagegaltier, Delphine, Sleegers, Kristel, Phatnani, Hemali, Knowles, David A., Fratta, Pietro, Raj, Towfique

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Recent ultra-rare inherited variants implicate new autism candidate risk genes von Wilfert, Amy B., Turner, Tychele N., Murali, Shwetha C., Hsieh, PingHsun, Sulovari, Arvis, Wang, Tianyun, Coe, Bradley P., Guo, Hui, Hoekzema, Kendra, Bakken, Trygve E., Winterkorn, Lara H., Evani, Uday S., Byrska-Bishop, Marta, Earl, Rachel K., Bernier, Raphael A., Zody, Michael C., Eichler, Evan E.

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Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics von Khurana, Ekta, Fu, Yao, Colonna, Vincenza, Mu, Xinmeng Jasmine, Kang, Hyun Min, Lappalainen, Tuuli, Sboner, Andrea, Lochovsky, Lucas, Chen, Jieming, Harmanci, Arif, Das, Jishnu, Abyzov, Alexej, Balasubramanian, Suganthi, Beal, Kathryn, Chakravarty, Dimple, Challis, Daniel, Chen, Yuan, Clarke, Declan, Clarke, Laura, Cunningham, Fiona, Evani, Uday S., Flicek, Paul, Fragoza, Robert, Garrison, Erik, Gibbs, Richard, Gümüş, Zeynep H., Herrero, Javier, Kitabayashi, Naoki, Kong, Yong, Lage, Kasper, Liluashvili, Vaja, Lipkin, Steven M., MacArthur, Daniel G., Marth, Gabor, Muzny, Donna, Pers, Tune H., Ritchie, Graham R. S., Rosenfeld, Jeffrey A., Sisu, Cristina, Wei, Xiaomu, Wilson, Michael, Xue, Yali, Yu, Fuli, Dermitzakis, Emmanouil T., Yu, Haiyuan, Rubin, Mark A., Tyler-Smith, Chris, Gerstein, Mark

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Proteomic analysis of age‐dependent changes in protein solubility identifies genes that modulate lifespan von Reis‐Rodrigues, Pedro, Czerwieniec, Gregg, Peters, Theodore W., Evani, Uday S., Alavez, Silvestre, Gaman, Emily A., Vantipalli, Maithili, Mooney, Sean D., Gibson, Bradford W., Lithgow, Gordon J., Hughes, Robert E.

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Benchmarking challenging small variants with linked and long reads von Wagner, Justin, Olson, Nathan D., Harris, Lindsay, Khan, Ziad, Farek, Jesse, Mahmoud, Medhat, Stankovic, Ana, Kovacevic, Vladimir, Yoo, Byunggil, Miller, Neil, Rosenfeld, Jeffrey A., Ni, Bohan, Zarate, Samantha, Kirsche, Melanie, Aganezov, Sergey, Schatz, Michael C., Narzisi, Giuseppe, Byrska-Bishop, Marta, Clarke, Wayne, Evani, Uday S., Markello, Charles, Shafin, Kishwar, Zhou, Xin, Sidow, Arend, Bansal, Vikas, Ebert, Peter, Marschall, Tobias, Lansdorp, Peter, Hanlon, Vincent, Mattsson, Carl-Adam, Barrio, Alvaro Martinez, Fiddes, Ian T., Xiao, Chunlin, Fungtammasan, Arkarachai, Chin, Chen-Shan, Wenger, Aaron M., Rowell, William J., Sedlazeck, Fritz J., Carroll, Andrew, Salit, Marc, Zook, Justin M.

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The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes von Challis, Danny, Antunes, Lilian, Garrison, Erik, Banks, Eric, Evani, Uday S, Muzny, Donna, Poplin, Ryan, Gibbs, Richard A, Marth, Gabor, Yu, Fuli

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Tor1 regulates protein solubility in Saccharomyces cerevisiae von Peters, Theodore W, Rardin, Matthew J, Czerwieniec, Gregg, Evani, Uday S, Reis-Rodrigues, Pedro, Lithgow, Gordon J, Mooney, Sean D, Gibson, Bradford W, Hughes, Robert E

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STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation von Wittkop, Tobias, TerAvest, Emily, Evani, Uday S, Fleisch, K Mathew, Berman, Ari E, Powell, Corey, Shah, Nigam H, Mooney, Sean D

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In silico functional profiling of human disease-associated and polymorphic amino acid substitutions von Mort, Matthew, Evani, Uday S, Krishnan, Vidhya G, Kamati, Kishore K, Baenziger, Peter H, Bagchi, Angshuman, Peters, Brandon J, Sathyesh, Rakesh, Li, Biao, Sun, Yanan, Xue, Bin, Shah, Nigam H, Kann, Maricel G, Cooper, David N, Radivojac, Predrag, Mooney, Sean D

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Bioinformatic Tools for Identifying Disease Gene and SNP Candidates von Mooney, Sean D., Krishnan, Vidhya G., Evani, Uday S.

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Recent ultra-rare inherited variants implicate novel autism candidate risk genes von Wilfert, Amy B., Turner, Tychele N., Murali, Shwetha C., Hsieh, PingHsun, Sulovari, Arvis, Wang, Tianyun, Coe, Bradley P., Guo, Hui, Hoekzema, Kendra, Bakken, Trygve E., Winterkorn, Lara H., Evani, Uday S., Byrska-Bishop, Marta, Earl, Rachel K., Bernier, Raphael A., Zody, Michael C., Eichler, Evan E.

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Enabling Atlas2 personal genome analysis on the cloud von Evani, U. S., Challis, D., Yu, J., Jackson, A. R., Paithankar, S., Bainbridge, M. N., Coarfa, C., Milosavljevic, A., Fuli Yu

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Curated variation benchmarks for challenging medically relevant autosomal genes von Wagner, Justin, Olson, Nathan D., Harris, Lindsay, McDaniel, Jennifer, Cheng, Haoyu, Fungtammasan, Arkarachai, Hwang, Yih-Chii, Gupta, Richa, Wenger, Aaron M., Rowell, William J., Khan, Ziad M., Farek, Jesse, Zhu, Yiming, Pisupati, Aishwarya, Mahmoud, Medhat, Xiao, Chunlin, Yoo, Byunggil, Sahraeian, Sayed Mohammad Ebrahim, Miller, Danny E., Jáspez, David, Lorenzo-Salazar, José M., Muñoz-Barrera, Adrián, Rubio-Rodríguez, Luis A., Flores, Carlos, Narzisi, Giuseppe, Evani, Uday Shanker, Clarke, Wayne E., Lee, Joyce, Mason, Christopher E., Lincoln, Stephen E., Miga, Karen H., Ebbert, Mark T. W., Shumate, Alaina, Li, Heng, Chin, Chen-Shan, Zook, Justin M., Sedlazeck, Fritz J.

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Genome-wide Analyses Identify KIF5A as a Novel ALS Gene von Nicolas, Aude, Kenna, Kevin P, Renton, Alan E, Ticozzi, Nicola, Faghri, Faraz, Chia, Ruth, Dominov, Janice A, Kenna, Brendan J, Nalls, Mike A, Keagle, Pamela, Rivera, Alberto M, van Rheenen, Wouter, Murphy, Natalie A, van Vugt, Joke J.F.A, Geiger, Joshua T, Van der Spek, Rick A, Pliner, Hannah A, Shankaracharya, Smith, Bradley N, Marangi, Giuseppe, Topp, Simon D, Abramzon, Yevgeniya, Gkazi, Athina Soragia, Eicher, John D, Kenna, Aoife, Mora, Gabriele, Calvo, Andrea, Mazzini, Letizia, Riva, Nilo, Mandrioli, Jessica, Caponnetto, Claudia, Battistini, Stefania, Volanti, Paolo, La Bella, Vincenzo, Conforti, Francesca L, Borghero, Giuseppe, Messina, Sonia, Simone, Isabella L, Trojsi, Francesca, Salvi, Fabrizio, Logullo, Francesco O, D'Alfonso, Sandra, Corrado, Lucia, Capasso, Margherita, Ferrucci, Luigi, Moreno, Cristiane de Araujo Martins, Kamalakaran, Sitharthan, Goldstein, David B, Gitler, Aaron D, Harris, Tim, Myers, Richard M, Phatnani, Hemali, Musunuri, Rajeeva Lochan, Evani, Uday Shankar, Abhyankar, Avinash, Zody, Michael C, Kaye, Julia, Finkbeiner, Steven, Wyman, Stacia K, LeNail, Alex, Lima, Leandro, Fraenkel, Ernest, Svendsen, Clive N, Thompson, Leslie M, Van Eyk, Jennifer E, Berry, James D, Miller, Timothy M, Kolb, Stephen J, Cudkowicz, Merit, Baxi, Emily, Benatar, Michael, Taylor, J. Paul, Rampersaud, Evadnie, Wu, Gang, Wuu, Joanne, Lauria, Giuseppe, Verde, Federico, Fogh, Isabella, Tiloca, Cinzia, Comi, Giacomo P, Sorarù, Gianni, Cereda, Cristina, Corcia, Philippe, Laaksovirta, Hannu, Myllykangas, Liisa, Jansson, Lilja, Valori, Miko, Ealing, John, Hamdalla, Hisham, Rollinson, Sara, Pickering-Brown, Stuart, Orrell, Richard W, Sidle, Katie C, Malaspina, Andrea, Hardy, John, Singleton, Andrew B, Johnson, Janel O, Arepalli, Sampath, Sapp, Peter C, McKenna-Yasek, Diane

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An ontology-neutral framework for enrichment analysis von Tirrell, Rob, Evani, Uday, Berman, Ari E, Mooney, Sean D, Musen, Mark A, Shah, Nigam H

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