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Long-read whole-genome analysis of human single cells Hard, Joanna; Mold, Jeff E.; Eisfeldt, Jesper; Tellgren-Roth, Christian; Haggqvist, Susana; Bunikis, Ignas; Contreras-Lopez, Orlando; Chin, Chen-Shan; Nordlund, Jessica; Rubin, Carl-Johan; Feuk, Lars; Michaelsson, Jakob; Ameur, Adam Share Save
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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
Curated variation benchmarks for challenging medically relevant autosomal genes 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.; Jaspez, David; Lorenzo-Salazar, Jose M.; Munoz-Barrera, Adrian; Rubio-Rodriguez, 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. Share Save
Dynamic prediction of renal survival among deeply phenotyped kidney transplant recipients using artificial intelligence: an observational, international, multicohort study Raynaud, Marc; Aubert, Olivier; Divard, Gillian; Reese, Peter P.; Kamar, Nassim; Yoo, Daniel; Chin, Chen-Shan; Bailly, Elodie; Buchler, Matthias; Ladriere, Marc; Le Quintrec, Moglie; Delahousse, Michel; Juric, Ivana; Basic-Jukic, Nikolina; Crespo, Marta; Silva Jr, Helio Tedesco; Linhares, Kamilla; Ribeiro de Castro, Maria Cristina; Pujol, Gervasio Soler; Empana, Jean-Philippe; Ulloa, Camilo; Akalin, Enver; Boehmig, Georg; Huang, Edmund; Stegall, Mark D.; Bentall, Andrew J.; Montgomery, Robert A.; Jordan, Stanley C.; Oberbauer, Rainer; Segev, Dorry L.; Friedewald, John J.; Jouven, Xavier; Legendre, Christophe; Lefaucheur, Carmen; Loupy, Alexandre Share Save
Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions Butler, Daniel; Mozsary, Christopher; Meydan, Cem; Foox, Jonathan; Rosiene, Joel; Shaiber, Alon; Danko, David; Afshinnekoo, Ebrahim; MacKay, Matthew; Sedlazeck, Fritz J.; Ivanov, Nikolay A.; Sierra, Maria; Pohle, Diana; Zietz, Michael; Gisladottir, Undina; Ramlall, Vijendra; Sholle, Evan T.; Schenck, Edward J.; Westover, Craig D.; Hassan, Ciaran; Ryon, Krista; Young, Benjamin; Bhattacharya, Chandrima; Ng, Dianna L.; Granados, Andrea C.; Santos, Yale A.; Servellita, Venice; Federman, Scot; Ruggiero, Phyllis; Fungtammasan, Arkarachai; Chin, Chen-Shan; Pearson, Nathaniel M.; Langhorst, Bradley W.; Tanner, Nathan A.; Kim, Youngmi; Reeves, Jason W.; Hether, Tyler D.; Warren, Sarah E.; Bailey, Michael; Gawrys, Justyna; Meleshko, Dmitry; Xu, Dong; Couto-Rodriguez, Mara; Nagy-Szakal, Dorottya; Barrows, Joseph; Wells, Heather; O'Hara, Niamh B.; Rosenfeld, Jeffrey A.; Chen, Ying; Steel, Peter A. D.; Shemesh, Amos J.; Xiang, Jenny; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Iftner, Angelika; Bezdan, Daniela; Sanchez, Elizabeth; Campion, Thomas R., Jr.; Sipley, John; Cong, Lin; Craney, Arryn; Velu, Priya; Melnick, Ari M.; Shapira, Sagi; Hajirasouliha, Iman; Borczuk, Alain; Iftner, Thomas; Salvatore, Mirella; Loda, Massimo; Westblade, Lars F.; Cushing, Melissa; Wu, Shixiu; Levy, Shawn; Chiu, Charles; Schwartz, Robert E.; Tatonetti, Nicholas; Rennert, Hanna; Imielinski, Marcin; Mason, Christopher E. Share Save
Trajectories of glomerular filtration rate and progression to end stage kidney disease after kidney transplantation Raynaud, Marc; Aubert, Olivier; Reese, Peter P.; Bouatou, Yassine; Naesens, Maarten; Kamar, Nassim; Bailly, Elodie; Giral, Magali; Ladriere, Marc; Le Quintrec, Moglie; Delahousse, Michel; Juric, Ivana; Basic-Jukic, Nikolina; Gupta, Gaurav; Akalin, Enver; Yoo, Daniel; Chin, Chen-Shan; Proust-Lima, Cecile; Bohmig, Georg; Oberbauer, Rainer; Stegall, Mark D.; Bentall, Andrew J.; Jordan, Stanley C.; Huang, Edmund; Glotz, Denis; Legendre, Christophe; Montgomery, Robert A.; Segev, Dorry L.; Empana, Jean-Philippe; Grams, Morgan E.; Coresh, Josef; Jouven, Xavier; Lefaucheur, Carmen; Loupy, Alexandre Share Save
Chromosome-scale, haplotype-resolved assembly of human genomes Garg, Shilpa; Fungtammasan, Arkarachai; Carroll, Andrew; Chou, Mike; Schmitt, Anthony; Zhou, Xiang; Mac, Stephen; Peluso, Paul; Hatas, Emily; Ghurye, Jay; Maguire, Jared; Mahmoud, Medhat; Cheng, Haoyu; Heller, David; Zook, Justin M.; Moemke, Tobias; Marschall, Tobias; Sedlazeck, Fritz J.; Aach, John; Chin, Chen-Shan; Church, George M.; Li, Heng Share Save
Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity Hoijer, Ida; Johansson, Josefin; Gudmundsson, Sanna; Chin, Chen-Shan; Bunikis, Ignas; Haggqvist, Susana; Emmanouilidou, Anastasia; Wilbe, Maria; den Hoed, Marcel; Bondeson, Marie-Louise; Feuk, Lars; Gyllensten, Ulf; Ameur, Adam Share Save
A diploid assembly-based benchmark for variants in the major histocompatibility complex Chin, Chen-Shan; Wagner, Justin; Zeng, Qiandong; Garrison, Erik; Garg, Shilpa; Fungtammasan, Arkarachai; Rautiainen, Mikko; Aganezov, Sergey; Kirsche, Melanie; Zarate, Samantha; Schatz, Michael C.; Xiao, Chunlin; Rowell, William J.; Markello, Charles; Farek, Jesse; Sedlazeck, Fritz J.; Bansal, Vikas; Yoo, Byunggil; Miller, Neil; Zhou, Xin; Carroll, Andrew; Barrio, Alvaro Martinez; Salit, Marc; Marschall, Tobias; Dilthey, Alexander T.; Zook, Justin M. Share Save
Effect of sequence depth and length in long-read assembly of the maize inbred NC358 Ou, Shujun; Liu, Jianing; Chougule, Kapeel M.; Fungtammasan, Arkarachai; Seetharam, Arun S.; Stein, Joshua C.; Llaca, Victor; Manchanda, Nancy; Gilbert, Amanda M.; Wei, Sharon; Chin, Chen-Shan; Hufnagel, David E.; Pedersen, Sarah; Snodgrass, Samantha J.; Fengler, Kevin; Woodhouse, Margaret; Walenz, Brian P.; Koren, Sergey; Phillippy, Adam M.; Hannigan, Brett T.; Dawe, R. Kelly; Hirsch, Candice N.; Hufford, Matthew B.; Ware, Doreen Share Save
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome Wenger, Aaron M.; Peluso, Paul; Rowell, William J.; Chang, Pi-Chuan; Hall, Richard J.; Concepcion, Gregory T.; Ebler, Jana; Fungtammasan, Arkarachai; Kolesnikov, Alexey; Olson, Nathan D.; Topfer, Armin; Alonge, Michael; Mahmoud, Medhat; Qian, Yufeng; Chin, Chen-Shan; Phillippy, Adam M.; Schate, Michael C.; Myers, Gene; DePristo, Mark A.; Ruan, Jue; Marschall, Tobias; Sedlazeck, Fritz J.; Zook, Justin M.; Li, Heng; Koren, Sergey; Carroll, Andrew; Rank, David R.; Hunkapiller, Michael W. Share Save
Multi-platform discovery of haplotype-resolved structural variation in human genomes Chaisson, Mark J. P.; Sanders, Ashley D.; Zhao, Xuefang; Malhotra, Ankit; Porubsky, David; Rausch, Tobias; Gardner, Eugene J.; Rodriguez, Oscar L.; Guo, Li; Collins, Ryan L.; Fan, Xian; Wen, Jia; Handsaker, Robert E.; Fairley, Susan; Kronenberg, Zev N.; Kong, Xiangmeng; Hormozdiari, Fereydoun; Lee, Dillon; Wenger, Aaron M.; Hastie, Alex R.; Antaki, Danny; Anantharaman, Thomas; Audano, Peter A.; Brand, Harrison; Cantsilieris, Stuart; Cao, Han; Cerveira, Eliza; Chen, Chong; Chen, Xintong; Chin, Chen-Shan; Chong, Zechen; Chuang, Nelson T.; Lambert, Christine C.; Church, Deanna M.; Clarke, Laura; Farrell, Andrew; Flores, Joey; Galeev, Timur; Gorkin, David U.; Gujral, Madhusudan; Guryev, Victor; Heaton, William Haynes; Korlach, Jonas; Kumar, Sushant; Kwon, Jee Young; Lam, Ernest T.; Lee, Jong Eun; Lee, Joyce; Lee, Wan-Ping; Lee, Sau Peng; Li, Shantao; Marks, Patrick; Viaud-Martinez, Karine; Meiers, Sascha; Munson, Katherine M.; Navarro, Fabio C. P.; Nelson, Bradley J.; Nodzak, Conor; Noor, Amina; Kyriazopoulou-Panagiotopoulou, Sofia; Pang, Andy W. C.; Qiu, Yunjiang; Rosanio, Gabriel; Ryan, Mallory; Stuetz, Adrian; Spierings, Diana C. J.; Ward, Alistair; Welch, AnneMarie E.; Xiao, Ming; Xu, Wei; Zhang, Chengsheng; Zhu, Qihui; Zheng-Bradley, Xiangqun; Lowy, Ernesto; Yakneen, Sergei; McCarroll, Steven; Jun, Goo; Ding, Li; Koh, Chong Lek; Ren, Bing; Flicek, Paul; Chen, Ken; Gerstein, Mark B.; Kwok, Pui-Yan; Lansdorp, Peter M.; Marth, Gabor T.; Sebat, Jonathan; Shi, Xinghua; Bashir, Ali; Ye, Kai; Devine, Scott E.; Talkowski, Michael E.; Mills, Ryan E.; Marschall, Tobias; Korbel, Jan O.; Eichler, Evan E.; Lee, Charles Share Save
Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus (vol 8, 8924, 2018) Nguyen, Thong T.; Suryamohan, Kushal; Kuriakose, Boney; Janakiraman, Vasantharajan; Reichelt, Mike; Chaudhuri, Subhra; Guillory, Joseph; Divakaran, Neethu; Rabins, P. E.; Goel, Ridhi; Deka, Bhabesh; Sarkar, Suman; Ekka, Preety; Tsai, Yu-Chih; Vargas, Derek; Santhosh, Sam; Mohan, Sangeetha; Chin, Chen-Shan; Korlach, Jonas; Thomas, George; Babu, Azariah; Seshagiri, Somasekar Share Save
Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line Nattestad, Maria; Goodwin, Sara; Ng, Karen; Baslan, Timour; Sedlazeck, Fritz J.; Rescheneder, Philipp; Garvin, Tyler; Fang, Han; Gurtowski, James; Hutton, Elizabeth; Tseng, Elizabeth; Chin, Chen-Shan; Beck, Timothy; Sundaravadanam, Yogi; Kramer, Melissa; Antoniou, Eric; McPherson, John D.; Hicks, James; McCombie, W. Richard; Schatz, Michael C. Share Save
Comprehensive analysis of single molecule sequencing-derived complete genome and whole transcriptome of Hyposidra talaca nuclear polyhedrosis virus Nguyen, Thong T.; Suryamohan, Kushal; Kuriakose, Boney; Janakiraman, Vasantharajan; Reichelt, Mike; Chaudhuri, Subhra; Guillory, Joseph; Divakaran, Neethu; Rabins, P. E.; Goei, Ridhi; Deka, Bhabesh; Sarkars, Suman; Ekka, Preety; Tsai, Yu-Chih; Vargas, Derek; Santhosh, Sam; Mohan, Sangeetha; Chin, Chen-Shan; Korlach, Jonas; Thomas, George; Babus, Azariah; Seshagiri, Somasekar Share Save
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