Not logged inAdvancing long-read nanopore genome assembly and accurate variant calling for rare disease detection
Negi, Shloka; Stenton, Sarah L.; Berger, Seth I.; Canigiula, Paolo; Mcnulty, Brandy; Violich, Ivo; Gardner, Joshua; Hillaker, Todd; O'Rourke, Sara M.; O'Leary, Melanie C.; Carbonell, Elizabeth; Austin-Tse, Christina; Lemire, Gabrielle; Serrano, Jillian; Mangilog, Brian; Vannoy, Grace; Kolmogorov, Mikhail; Vilain, Eric; O'Donnell-Luria, Anne; Delot, Emmanuele; Miga, Karen H.; Monlong, Jean; Paten, Benedict .png)
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SavePersonalized pangenome referencesSiren, Jouni; Eskandar, Parsa; Ungaro, Matteo Tommaso; Hickey, Glenn; Eizenga, Jordan M.; Novak, Adam M.; Chang, Xian; Chang, Pi-Chuan; Kolmogorov, Mikhail; Carroll, Andrew; Monlong, Jean; Paten, Benedict Share Save Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome ReferencesTaylor, Dylan J.; Eizenga, Jordan M.; Li, Qiuhui; Das, Arun; Jenike, Katharine M.; Kenny, Eimear E.; Miga, Karen H.; Monlong, Jean; Mccoy, Rajiv C.; Paten, Benedict; Schatz, Michael C. Share Save Share Save Phased nanopore assembly with Shasta and modular graph phasing with GFAseLorig-Roach, Ryan; Meredith, Melissa; Monlong, Jean; Jain, Miten; Olsen, Hugh E.; Mcnulty, Brandy; Porubsky, David; Montague, Tessa G.; Lucas, Julian K.; Condon, Chris; Eizenga, Jordan M.; Juul, Sissel; Mckenzie, Sean K.; Simmonds, Sara E.; Park, Jimin; Asri, Mobin; Koren, Sergey; Eichler, Evan E.; Axel, Richard; Martin, Bruce; Carnevali, Paolo; Miga, Karen H.; Paten, Benedict Share Save Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiringKuzmin, Elena; Baker, Toby M.; Lesluyes, Tom; Monlong, Jean; Abe, Kento T.; Coelho, Paula P.; Schwartz, Michael; Del Corpo, Joseph; Zou, Dongmei; Morin, Genevieve; Pacis, Alain; Yang, Yang; Martinez, Constanza; Barber, Jarrett; Kuasne, Hellen; Li, Rui; Bourgey, Mathieu; Fortier, Anne-Marie; Davison, Peter G.; Omeroglu, Atilla; Guiot, Marie-Christine; Morris, Quaid; Kleinman, Claudia L.; Huang, Sidong; Gingras, Anne-Claude; Ragoussis, Jiannis; Bourque, Guillaume; Van Loo, Peter; Park, Morag Share Save Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylationKolmogorov, Mikhail; Billingsley, Kimberley J.; Mastoras, Mira; Meredith, Melissa; Monlong, Jean; Lorig-Roach, Ryan; Asri, Mobin; Alvarez Jerez, Pilar; Malik, Laksh; Dewan, Ramita; Reed, Xylena; Genner, Rylee M.; Daida, Kensuke; Behera, Sairam; Shafin, Kishwar; Pesout, Trevor; Prabakaran, Jeshuwin; Carnevali, Paolo; Yang, Jianzhi; Rhie, Arang; Scholz, Sonja W.; Traynor, Bryan J.; Miga, Karen H.; Jain, Miten; Timp, Winston; Phillippy, Adam M.; Chaisson, Mark; Sedlazeck, Fritz J.; Blauwendraat, Cornelis; Paten, Benedict Share Save Pangenome graph construction from genome alignments with Minigraph-CactusHickey, Glenn; Monlong, Jean; Ebler, Jana; Novak, Adam M.; Eizenga, Jordan M.; Gao, Yan; Marschall, Tobias; Li, Heng; Paten, Benedict; Abel, Haley J.; Antonacci-Fulton, Lucinda L.; Asri, Mobin; Baid, Gunjan; Baker, Carl A.; Belyaeva, Anastasiya; Billis, Konstantinos; Bourque, Guillaume; Buonaiuto, Silvia; Carroll, Andrew; Chaisson, Mark J. P.; Chang, Pi-Chuan; Chang, Xian H.; Cheng, Haoyu; Chu, Justin; Cody, Sarah; Colonna, Vincenza; Cook, Daniel E.; Cook-Deegan, Robert M.; Cornejo, Omar E.; Diekhans, Mark; Doerr, Daniel; Ebert, Peter; Ebler, Jana; Eichler, Evan E.; Eizenga, Jordan M.; Fairley, Susan; Fedrigo, Olivier; Felsenfeld, Adam L.; Feng, Xiaowen; Fischer, Christian; Flicek, Paul; Formenti, Giulio; Frankish, Adam; Fulton, Robert S.; Gao, Yan; Garg, Shilpa; Garrison, Erik; Garrison, Nanibaa' A.; Giron, Carlos Garcia; Green, Richard E.; Groza, Cristian; Guarracino, Andrea; Haggerty, Leanne; Hall, Ira M.; Harvey, William T.; Haukness, Marina; Haussler, David; Heumos, Simon; Hickey, Glenn; Hoekzema, Kendra; Hourlier, Thibaut; Howe, Kerstin; Jain, Miten; Jarvis, Erich D.; Ji, Hanlee P.; Kenny, Eimear E.; Koenig, Barbara A.; Kolesnikov, Alexey; Korbel, Jan O.; Kordosky, Jennifer; Koren, Sergey; Lee, HoJoon; Lewis, Alexandra P.; Liao, Wen-Wei; Lu, Shuangjia; Lu, Tsung-Yu; Lucas, Julian K.; Hugo, Magalhaes; Santiago, Marco-Sola; Marijon, Pierre; Markello, Charles; Marschall, Tobias; Martin, Fergal J.; McCartney, Ann; McDaniel, Jennifer; Miga, Karen H.; Mitchell, Matthew W.; Monlong, Jean; Mountcastle, Jacquelyn; Munson, Katherine M.; Mwaniki, Moses Njagi; Nattestad, Maria; Novak, Adam M.; Nurk, Sergey; Olsen, Hugh E.; Olson, Nathan D.; Pesout, Trevor; Phillippy, Adam M.; Popejoy, Alice B.; Porubsky, David; Prins, Pjotr; Puiu, Daniela; Rautiainen, Mikko; Regier, Allison A.; Rhie, Arang; Sacco, Samuel; Sanders, Ashley D.; Schneider, Valerie A.; Schultz, Baergen, I; Shafin, Kishwar; Sibbesen, Jonas A.; Siren, Jouni; Smith, Michael W.; Sofia, Heidi J.; Abou Tayoun, Ahmad N.; Thibaud-Nissen, Francoise; Tomlinson, Chad; Tricomi, Francesca Floriana; Villani, Flavia; Vollger, Mitchell R.; Wagner, Justin; Walenz, Brian; Wang, Ting; Wood, Jonathan M. D.; Zimin, Aleksey, V; Zook, Justin M. Share Save Evolution of large copy number variants in breast cancer through genetic network rewiringKuzmin, Elena; Monlong, Jean; Bourgey, Mathieu; Lesluyes, Tom; Barker, Toby; Morin, Genevieve; Zou, Dongmei; Schwartz, Michael; Yang, Yang; Pacis, Alain; Martinez, Constanza; Kuasne, Hellen; Fortier, Anne-Marie; Li, Rui; Kleinman, Claudia; Huang, Sidong; van Loo, Peter; Ragoussis, Jiannis; Bourque, Guillaume; Park, Morag Share Save Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition (vol 52, pg 306, 2020)Rodriguez-Martin, Bernardo; Alvarez, Eva G.; Baez-Ortega, Adrian; Zamora, Jorge; Supek, Fran; Demeulemeester, Jonas; Santamarina, Martin; Ju, Young Seok; Temes, Javier; Garcia-Souto, Daniel; Detering, Harald; Li, Yilong; Rodriguez-Castro, Jorge; Dueso-Barroso, Ana; Bruzos, Alicia L.; Dentro, Stefan C.; Blanco, Miguel G.; Contino, Gianmarco; Ardeljan, Daniel; Tojo, Marta; Roberts, Nicola D.; Zumalave, Sonia; Edwards, Paul A.; Weischenfeldt, Joachim; Puiggros, Montserrat; Chong, Zechen; Chen, Ken; Lee, Eunjung Alice; Wala, Jeremiah A.; Raine, Keiran M.; Butler, Adam; Waszak, Sebastian M.; Navarro, Fabio C. P.; Schumacher, Steven E.; Monlong, Jean; Maura, Francesco; Bolli, Niccolo; Bourque, Guillaume; Gerstein, Mark; Park, Peter J.; Wedge, David C.; Beroukhim, Rameen; Torrents, David; Korbel, Jan O.; Martincorena, Inigo; Fitzgerald, Rebecca C.; Van Loo, Peter; Kazazian, Haig H.; Burns, Kathleen H.; Campbell, Peter J.; Tubio, Jose M. C. Share Save Glioblastoma scRNA-seq shows treatment-induced, immune-dependent increase in mesenchymal cancer cells and structural variants in distal neural stem cellsCouturier, Charles P.; Nadaf, Javad; Li, Zhaorong; Baig, Salma; Riva, Gabriele; Le, Phuong; Kloosterman, Daan J.; Monlong, Jean; Meyong, Andriniaina Nkili; Allache, Redouane; Degenhard, Theresa; Al-Rashid, Mariam; Guiot, Marie-Christine; Bourque, Guillaume; Ragoussis, Jiannis; Akkari, Leila; Quintana, Francisco J.; Petrecca, Kevin Share Save Ultra-Rapid Nanopore Whole Genome Genetic Diagnosis of Dilated Cardiomyopathy in an Adolescent With Cardiogenic ShockGorzynski, John E.; Goenka, Sneha D.; Shafin, Kishwar; Jensen, Tanner D.; Fisk, Dianna G.; Grove, Megan E.; Spiteri, Elizabeth; Pesout, Trevor; Monlong, Jean; Bernstein, Jonathan A.; Ceresnak, Scott; Chang, Pi-Chuan; Christle, Jeffrey W.; Chubb, Henry; Dunn, Kyla; Garalde, Daniel R.; Guillory, Joseph; Ruzhnikov, Maura R. Z.; Wright, Chris; Wusthoff, Courtney J.; Xiong, Katherine; Hollander, Seth A.; Berry, Gerald J.; Jain, Miten; Sedlazeck, Fritz J.; Carroll, Andrew; Paten, Benedict; Ashley, Euan A. Share Save Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencingGoenka, Sneha D.; Gorzynski, John E.; Shafin, Kishwar; Fisk, Dianna G.; Pesout, Trevor; Jensen, Tanner D.; Jean Monlong; Pi-Chuan Chang; Baid, Gunjan; Bernstein, Jonathan A.; Christle, Jeffrey W.; Dalton, Karen P.; Garalde, Daniel R.; Grove, Megan E.; Guillory, Joseph; Kolesnikov, Alexey; Nattestad, Maria; Ruzhnikov, Maura R. Z.; Samadi, Mehrzad; Sethia, Ankit; Spiteri, Elizabeth; Wright, Christopher J.; Xiong, Katherine; Zhu, Tong; Jain, Miten; Sedlazeck, Fritz J.; Carroll, Andrew; Paten, Benedict; Ashley, Euan A. Share Save Ultrarapid Nanopore Genome Sequencing in a Critical Care SettingGorzynski, John E.; Goenka, Sneha D.; Shafin, Kishwar; Jensen, Tanner D.; Fisk, Dianna G.; Grove, Megan E.; Spiteri, Elizabeth; Pesout, Trevor; Monlong, Jean; Baid, Gunjan; Bernstein, Jonathan A.; Ceresnak, Scott; Chang, Pi-Chuan; Christle, Jeffrey W.; Chubb, Henry; Dalton, Karen P.; Dunn, Kyla; Garalde, Daniel R.; Guillory, Joseph; Knowles, Joshua W.; Kolesnikov, Alexey; Ma, Michael; Moscarello, Tia; Nattestad, Maria; Perez, Marco; Ruzhnikov, Maura R. Z.; Samadi, Mehrzad; Setia, Ankit; Wright, Chris; Wusthoff, Courtney J.; Xiong, Katherine; Zhu, Tong; Jain, Miten; Sedlazeck, Fritz J.; Carroll, Andrew; Paten, Benedict; Ashley, Euan A. Share Save Invasive growth associated with cold-inducible RNA-binding protein expression drives recurrence of surgically resected brain metastasesDankner, Matthew; Caron, Maxime; Al-Saadi, Tariq; Yu, Wenqing; Ouellet, Veronique; Ezzeddine, Rima; Maritan, Sarah M.; Annis, Matthew G.; Le, Phuong Uyen; Nadaf, Javad; Neubarth, Noah S.; Savage, Paul; Zuo, Dongmei; Couturier, Charles P.; Monlong, Jean; Djambazian, Haig; Altoukhi, Huda; Bourque, Guillaume; Ragoussis, Jiannis; Diaz, Roberto J.; Park, Morag; Guiot, Marie-Christine; Lam, Stephanie; Petrecca, Kevin; Siegel, Peter M. Share Save Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy (vol 11, 3406, 2020)Couturier, Charles P.; Ayyadhury, Shamini; Le, Phuong U.; Nadaf, Javad; Monlong, Jean; Riva, Gabriele; Allache, Redouane; Baig, Salma; Yan, Xiaohua; Bourgey, Mathieu; Lee, Changseok; Wang, Yu Chang David; Yong, V. Wee; Guiot, Marie-Christine; Najafabadi, Hamed; Misic, Bratislav; Antel, Jack; Bourque, Guillaume; Ragoussis, Jiannis; Petrecca, Kevin Share Save Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchyCouturier, Charles P.; Ayyadhury, Shamini; Le, Phuong U.; Nadaf, Javad; Monlong, Jean; Riva, Gabriele; Allache, Redouane; Baig, Salma; Yan, Xiaohua; Bourgey, Mathieu; Lee, Changseok; Wang, Yu Chang David; Yong, V. Wee; Guiot, Marie-Christine; Najafabadi, Hamed; Misic, Bratislav; Antel, Jack; Bourque, Guillaume; Ragoussis, Jiannis; Petrecca, Kevin Share Save Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomesShafin, Kishwar; Pesout, Trevor; Lorig-Roach, Ryan; Haukness, Marina; Olsen, Hugh E.; Bosworth, Colleen; Armstrong, Joel; Tigyi, Kristof; Maurer, Nicholas; Koren, Sergey; Sedlazeck, Fritz J.; Marschall, Tobias; Mayes, Simon; Costa, Vania; Zook, Justin M.; Liu, Kelvin J.; Kilburn, Duncan; Sorensen, Melanie; Munson, Katy M.; Vollger, Mitchell R.; Monlong, Jean; Garrison, Erik; Eichler, Evan E.; Salama, Sofie; Haussler, David; Green, Richard E.; Akeson, Mark; Phillippy, Adam; Miga, Karen H.; Carnevali, Paolo; Jain, Miten; Paten, Benedict Share Save Genotyping structural variants in pangenome graphs using the vg toolkitHickey, Glenn; Heller, David; Monlong, Jean; Sibbesen, Jonas A.; Siren, Jouni; Eizenga, Jordan; Dawson, Eric T.; Garrison, Erik; Novak, Adam M.; Paten, Benedict Share Save Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotranspositionRodriguez-Martin, Bernardo; Alvarez, Eva G.; Baez-Ortega, Adrian; Zamora, Jorge; Supek, Fran; Demeulemeester, Jonas; Santamarina, Martin; Ju, Young Seok; Temes, Javier; Garcia-Souto, Daniel; Detering, Harald; Li, Yilong; Rodriguez-Castro, Jorge; Dueso-Barroso, Ana; Bruzos, Alicia L.; Dentro, Stefan C.; Blanco, Miguel G.; Contino, Gianmarco; Ardeljan, Daniel; Tojo, Marta; Roberts, Nicola D.; Zumalave, Sonia; Edwards, Paul A. W.; Weischenfeldt, Joachim; Puiggros, Montserrat; Chong, Zechen; Chen, Ken; Lee, Eunjung Alice; Wala, Jeremiah A.; Raine, Keiran; Butler, Adam; Waszak, Sebastian M.; Navarro, Fabio C. P.; Schumacher, Steven E.; Monlong, Jean; Maura, Francesco; Bolli, Niccolo; Bourque, Guillaume; Gerstein, Mark; Park, Peter J.; Wedge, David C.; Beroukhim, Rameen; Torrents, David; Korbel, Jan O.; Martincorena, Inigo; Fitzgerald, Rebecca C.; Van Loo, Peter; Kazazian, Haig H.; Burns, Kathleen H.; Campbell, Peter J.; Tubio, Jose M. C.; Akdemir, Kadir C.; Boutros, Paul C.; Bowtell, David D. L.; Brors, Benedikt; Chan, Kin; Cortes-Ciriano, Isidro; Dunford, Andrew J.; Edwards, Paul A.; Estivill, Xavier; Etemadmoghadam, Dariush; Feuerbach, Lars; Fink, J. Lynn; Frenkel-Morgenstern, Milana; Garsed, Dale W.; Gordenin, Dmitry A.; Haan, David; Haber, James E.; Hess, Julian M.; Hutter, Barbara; Imielinski, Marcin; Jones, David T. W.; Kazanov, Marat D.; Klimczak, Leszek J.; Koh, Youngil; Kumar, Kiran; Lee, Jake June-Koo; Lynch, Andy G.; Macintyre, Geoff; Markowetz, Florian; Martinez-Fundichely, Alexander; Meyerson, Matthew; Miyano, Satoru; Nakagawa, Hidewaki; Ossowski, Stephan; Pearson, John, V; Rippe, Karsten; Roberts, Steven A.; Scully, Ralph; Shackleton, Mark; Sidiropoulos, Nikos; Sieverling, Lina; Stewart, Chip; Villasante, Izar; Waddell, Nicola; Yang, Lixing; Yao, Xiaotong; Yoon, Sung-Soo; Zhang, Cheng-Zhong Share Save 
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