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A missense mutation in the proprotein convertase gene furinb causes hepatic cystogenesis during liver development in zebrafish Ellis, Jillian L.; Evason, Kimberley J.; Zhang, Changwen; Fourman, Makenzie N.; Liu, Jiandong; Ninov, Nikolay; Delous, Marion; Vanhollebeke, Benoit; Fiddes, Ian; Otis, Jessica P.; Houvras, Yariv; Farber, Steven A.; Xu, Xiaolei; Lin, Xueying; Stainier, Didier Y. R.; Yin, Chunyue Share Save
A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing (vol 10, 3660, 2019) Petti, Allegra A.; Williams, Stephen R.; Miller, Christopher A.; Fiddes, Ian T.; Srivatsan, Sridhar N.; Chen, David Y.; Fronick, Catrina C.; Fulton, Robert S.; Church, Deanna M.; Ley, Timothy J. Share Save
Benchmarking challenging small variants with linked and long reads 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. Share Save
GENCODE 2021 Frankish, Adam; Diekhans, Mark; Jungreis, Irwin; Lagarde, Julien; Loveland, Jane E.; Mudge, Jonathan M.; Sisu, Cristina; Wright, James C.; Armstrong, Joel; Barnes, If; Berry, Andrew; Bignell, Alexandra; Boix, Carles; Carbonell Sala, Silvia; Cunningham, Fiona; Di Domenico, Tomas; Donaldson, Sarah; Fiddes, Ian T.; Giron, Carlos Garcia; Gonzalez, Jose Manuel; Grego, Tiago; Hardy, Matthew; Hourlier, Thibaut; Howe, Kevin L.; Hunt, Toby; Izuogu, Osagie G.; Johnson, Rory; Martin, Fergal J.; Martinez, Laura; Mohanan, Shamika; Muir, Paul; Navarro, Fabio C. P.; Parker, Anne; Pei, Baikang; Pozo, Fernando; Riera, Ferriol Calvet; Ruffier, Magali; Schmitt, Bianca M.; Stapleton, Eloise; Suner, Marie-Marthe; Sycheva, Irina; Uszczynska-Ratajczak, Barbara; Wolf, Maxim Y.; Xu, Jinuri; Yang, Yucheng T.; Yates, Andrew; Zerbino, Daniel; Zhang, Yan; Choudhary, Jyoti S.; Gerstein, Mark; Guigo, Roderic; Hubbard, Tim J. P.; Kellis, Manolis; Paten, Benedict; Tress, Michael L.; Flicek, Paul Share Save
Transcriptional activity and strain-specific history of mouse pseudogenes Sisu, Cristina; Muir, Paul; Frankish, Adam; Fiddes, Ian; Diekhans, Mark; Thybert, David; Odom, Duncan T.; Flicek, Paul; Keane, Thomas M.; Hubbard, Tim; Harrow, Jennifer; Gerstein, Mark Share Save
A robust benchmark for detection of germline large deletions and insertions (Jun, 10.1038/s41587-020-0538-8, 2020) Zook, Justin M.; Hansen, Nancy F.; Olson, Nathan D.; Chapman, Lesley; Mullikin, James C.; Xiao, Chunlin; Sherry, Stephen; Koren, Sergey; Phillippy, Adam M.; Boutros, Paul C.; Sahraeian, Sayed Mohammad E.; Huang, Vincent; Rouette, Alexandre; Alexander, Noah; Mason, Christopher E.; Hajirasouliha, Iman; Ricketts, Camir; Lee, Joyce; Tearle, Rick; Fiddes, Ian T.; Barrio, Alvaro Martinez; Wala, Jeremiah; Carroll, Andrew; Ghaffari, Noushin; Rodriguez, Oscar L.; Bashir, Ali; Jackman, Shaun; Farrell, John J.; Wenger, Aaron M.; Alkan, Can; Soylev, Arda; Schatz, Michael C.; Garg, Shilpa; Church, George; Marschall, Tobias; Chen, Ken; Fan, Xian; English, Adam C.; Rosenfeld, Jeffrey A.; Zhou, Weichen; Mills, Ryan E.; Sage, Jay M.; Davis, Jennifer R.; Kaiser, Michael D.; Oliver, John S.; Catalano, Anthony P.; Chaisson, Mark J. P.; Spies, Noah; Sedlazeck, Fritz J.; Salit, Marc Share Save
Single-cell sequencing of genomic DNA resolves sub-clonal heterogeneity in a melanoma cell line Velazquez-Villarreal, Enrique I.; Maheshwari, Shamoni; Sorenson, Jon; Fiddes, Ian T.; Kumar, Vijay; Yin, Yifeng; Webb, Michelle G.; Catalanotti, Claudia; Grigorova, Mira; Edwards, Paul A.; Carpten, John D.; Craig, David W. Share Save
A robust benchmark for detection of germline large deletions and insertions Zook, Justin M.; Hansen, Nancy F.; Olson, Nathan D.; Chapman, Lesley; Mullikin, James C.; Xiao, Chunlin; Sherry, Stephen; Koren, Sergey; Phillippy, Adam M.; Boutros, Paul C.; Sahraeian, Sayed Mohammad E.; Huang, Vincent; Rouette, Alexandre; Alexander, Noah; Mason, Christopher E.; Hajirasouliha, Iman; Ricketts, Camir; Lee, Joyce; Tearle, Rick; Fiddes, Ian T.; Barrio, Alvaro Martinez; Wala, Jeremiah; Carroll, Andrew; Ghaffari, Noushin; Rodriguez, Oscar L.; Bashir, Ali; Jackman, Shaun; Farrell, John J.; Wenger, Aaron M.; Alkan, Can; Soylev, Arda; Schatz, Michael C.; Garg, Shilpa; Church, George; Marschall, Tobias; Chen, Ken; Fan, Xian; English, Adam C.; Rosenfeld, Jeffrey A.; Zhou, Weichen; Mills, Ryan E.; Sage, Jay M.; Davis, Jennifer R.; Kaiser, Michael D.; Oliver, John S.; Catalano, Anthony P.; Chaisson, Mark J. P.; Spies, Noah; Sedlazeck, Fritz J.; Salit, Marc Share Save
Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing Replogle, Joseph M.; Norman, Thomas M.; Xu, Albert; Hussmann, Jeffrey A.; Chen, Jin; Cogan, J. Zachery; Meer, Elliott J.; Terry, Jessica M.; Riordan, Daniel P.; Srinivas, Niranjan; Fiddes, Ian T.; Arthur, Joseph G.; Alvarado, Luigi J.; Pfeiffer, Katherine A.; Mikkelsen, Tarjei S.; Weissman, Jonathan S.; Adamson, Britt Share Save
Improved reference genome for the domestic horse increases assembly contiguity and composition (vol 1, 197, 2018) Kalbfleisch, Theodore S.; Rice, Edward S.; DePriest, Michael S., Jr.; Walenz, Brian P.; Hestand, Matthew S.; Vermeesch, Joris R.; O'Connell, Brendan L.; Fiddes, Ian T.; Vershinina, Alisa O.; Saremi, Nedda F.; Petersen, Jessica L.; Finno, Carrie J.; Bellone, Rebecca R.; Mccue, Molly E.; Brooks, Samantha A.; Bailey, Ernest; Orlando, Ludovic; Green, Richard E.; Miller, Donald C.; Antczak, Douglas F.; MacLeod, James N. Share Save
A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing Petti, Allegra A.; Williams, Stephen R.; Miller, Christopher A.; Fiddes, Ian T.; Srivatsari, Sridhar N.; Chen, David Y.; Fronick, Catrina C.; Fulton, Robert S.; Church, Deanna M.; Ley, Timothy J. Share Save
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Resolving the full spectrum of human genome variation using Linked-Reads Marks, Patrick; Garcia, Sarah; Barrio, Alvaro Martinez; Belhocine, Kamila; Bernate, Jorge; Bharadwaj, Rajiv; Bjornson, Keith; Catalanotti, Claudia; Delaney, Josh; Fehr, Adrian; Fiddes, Ian T.; Galvin, Brendan; Heaton, Haynes; Herschleb, Jill; Hindson, Christopher; Holt, Esty; Jabara, Cassandra B.; Jett, Susanna; Keivanfar, Nikka; Kyriazopoulou-Panagiotopoulou, Sofia; Lek, Monkol; Lin, Bill; Lowe, Adam; Mahamdallie, Shazia; Maheshwari, Shamoni; Makarewicz, Tony; Marshall, Jamie; Meschi, Francesca; O'Keefe, Christopher J.; Ordonez, Heather; Patel, Pranav; Price, Andrew; Royall, Ariel; Ruark, Elise; Seal, Sheila; Schnall-Levin, Michael; Shah, Preyas; Stafford, David; Williams, Stephen; Wu, Indira; Xu, Andrew Wei; Rahman, Nazneen; MacArthur, Daniel; Church, Deanna M. Share Save
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Structurally Conserved Primate LncRNAs Are Transiently Expressed during Human Cortical Differentiation and Influence Cell-Type-Specific Genes Field, Andrew R.; Jacobs, Frank M. J.; Fiddes, Ian T.; Phillips, Alex P. R.; Reyes-Ortiz, Andrea M.; LaMontagne, Erin; Whitehead, Lila; Meng, Vincent; Rosenkrantz, Jimi L.; Olsen, Mari; Hauessler, Max; Katzman, Sol; Salama, Sofie R.; Haussler, David Share Save
Improved reference genome for the domestic horse increases assembly contiguity and composition Kalbfleisch, Theodore S.; Rice, Edward S.; DePriest, Michael S., Jr.; Walenz, Brian P.; Hestand, Matthew S.; Vermeesch, Joris R.; O'Connell, Brendan L.; Fiddes, Ian T.; Vershinina, Alisa O.; Saremi, Nedda F.; Petersen, Jessica L.; Finno, Carrie J.; Bellone, Rebecca R.; McCue, Molly E.; Brooks, Samantha A.; Bailey, Ernest; Orlando, Ludovic; Greene, Richard E.; Miller, Donald C.; Antczak, Douglas F.; MacLeod, James N. Share Save
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GENCODE reference annotation for the human and mouse genomes Frankish, Adam; Diekhans, Mark; Ferreira, Anne-Maud; Johnson, Rory; Jungreis, Irwin; Loveland, Jane; Mudge, Jonathan M.; Sisu, Cristina; Wright, James; Armstrong, Joel; Barnes, If; Berry, Andrew; Bignell, Alexandra; Sala, Silvia Carbonell; Chrast, Jacqueline; Cunningham, Fiona; Di Domenico, Tomas; Donaldson, Sarah; Fiddes, Ian T.; Giron, Carlos Garcia; Gonzalez, Jose Manuel; Grego, Tiago; Hardy, Matthew; Hourlier, Thibaut; Hunt, Toby; Izuogu, Osagie G.; Lagarde, Julien; Martin, Fergal J.; Martinez, Laura; Mohanan, Shamika; Muir, Paul; Navarro, Fabio C. P.; Parker, Anne; Pei, Baikang; Pozo, Fernando; Ruffier, Magali; Schmitt, Bianca M.; Stapleton, Eloise; Suner, Marie-Marthe; Sycheva, Irina; Uszczynska-Ratajczak, Barbara; Xu, Jinuri; Yates, Andrew; Zerbino, Daniel; Zhang, Yan; Aken, Bronwen; Choudhary, Jyoti S.; Gerstein, Mark; Guigo, Roderic; Hubbard, Tim J. P.; Kellis, Manolis; Paten, Benedict; Reymond, Alexandre; Tress, Michael L.; Flicek, Paul Share Save
Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci Lilue, Jingtao; Doran, Anthony G.; Fiddes, Ian T.; Abrudan, Monica; Armstrong, Joel; Bennett, Ruth; Chow, William; Collins, Joanna; Collins, Stephan; Czechanski, Anne; Danecek, Petr; Diekhans, Mark; Dolle, Dirk-Dominik; Dunn, Matt; Durbin, Richard; Earl, Dent; Ferguson-Smith, Anne; Flicek, Paul; Flint, Jonathan; Frankish, Adam; Fu, Beiyuan; Gerstein, Mark; Gilbert, James; Goodstadt, Leo; Harrow, Jennifer; Howe, Kerstin; Ibarra-Soria, Ximena; Kolmogorov, Mikhail; Lelliott, Chris J.; Logan, Darren W.; Loveland, Jane; Mathews, Clayton E.; Mott, Richard; Muir, Paul; Nachtweide, Stefanie; Navarro, Fabio C. P.; Odom, Duncan T.; Park, Naomi; Pelan, Sarah; Pham, Son K.; Quail, Mike; Reinholdt, Laura; Romoth, Lars; Shirley, Lesley; Sisu, Cristina; Sjoberg-Herrera, Marcela; Stanke, Mario; Steward, Charles; Thomas, Mark; Threadgold, Glen; Thybert, David; Torrance, James; Wong, Kim; Wood, Jonathan; Yalcin, Binnaz; Yang, Fengtang; Adams, David J.; Paten, Benedict; Keane, Thomas M. Share Save
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