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Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing Keskus, Ayse G.; Bryant, Asher; Ahmad, Tanveer; Yoo, Byunggil; Aganezov, Sergey; Goretsky, Anton; Donmez, Ataberk; Lansdon, Lisa A.; Rodriguez, Isabel; Park, Jimin; Liu, Yuelin; Cui, Xiwen; Gardner, Joshua; McNulty, Brandy; Sacco, Samuel; Shetty, Jyoti; Zhao, Yongmei; Tran, Bao; Narzisi, Giuseppe; Helland, Adrienne; Cook, Daniel E.; Chang, Pi-Chuan; Kolesnikov, Alexey; Carroll, Andrew; Molloy, Erin K.; Bi, Chengpeng; Walter, Adam; Gibson, Margaret; Pushel, Irina; Guest, Erin; Pastinen, Tomi; Shafin, Kishwar; Miga, Karen H.; Malikic, Salem; Day, Chi-Ping; Robine, Nicolas; Sahinalp, Cenk; Dean, Michael; Farooqi, Midhat S.; Paten, Benedict; Kolmogorov, Mikhail Share Save
Stochastic modeling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones Hirsch, M. G.; Pal, Soumitra; Mehrabadi, Farid Rashidi; Malikic, Salem; Gruen, Charli; Sassano, Antonella; Perez-Guijarro, Eva; Merlino, Glenn; Sahinalp, S. Cenk; Molloy, Erin K.; Day, Chi-Ping; Przytycka, Teresa M. Share Save
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Melanoma clonal subline analysis reveals genetic factors driving intra-tumor heterogeneity Keskus, Ayse; Goretsky, Anton; Liu, Yuelin; Cui, Xiwen; Ahmad, Tanveer; Guijarro, Eva Perez; Bryant, Asher; Malloy, Erin; Malikic, Salem; Merlino, Glenn; Day, Chi-Ping; Sahinalp, Cenk; Kolmogorov, Mikhail Share Save
Single-cell methylation sequencing data reveals succinct metastatic migration histories and tumor progression models Li, Xuan C.; Liu, Yuelin; Mehrabadi, Farid Rashidi; Schaffer, Alejandro A.; Pratt, Drew; Crawford, David R.; Malikic, Salem; Molloy, Erin K.; Gopalan, Vishaka; Mount, Stephen M.; Ruppin, Eytan; Aldape, Kenneth; Sahinalp, S. Cenk Share Save
Fast intratumor heterogeneity inference from single-cell sequencing data Kizilkale, Can; Mehrabadi, Farid Rashidi; Azer, Erfan Sadeqi; Perez-Guijarro, Eva; Marie, Kerrie L.; Lee, Maxwell P.; Day, Chi-Ping; Merlino, Glenn; Ergun, Funda; Sahinalp, S. Cenk; Malikic, Salem; Buluc, Aydin Share Save
PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data Malikic, Salem; Mehrabadi, Farid Rashidi; Ciccolella, Simone; Rahman, Md. Khaledur; Ricketts, Camir; Haghshenas, Ehsan; Seidman, Daniel; Hach, Faraz; Hajirasouliha, Iman; Sahinalp, S. Cenk Share Save
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Pervasive intra-tumour heterogeneity and subclonal selection across cancer types Dentro, Stefan; Leshchiner, Ignaty; Haase, Kerstin; Wintersinger, Jeff; Deshwar, Amit; Tarabichi, Maxime; Rubanova, Yulia; Yu, Kaixian; Garcia, Ignacio Vazquez; Macintyre, Geoff; Kleinheinz, Kortine; Livitz, Dimitri; Malikic, Salem; Donmez, Nilgun; Sengupta, Subhajit; Ji, Yuan; Demeulemeester, Jonas; Anur, Pavana; Jolly, Clemency; Cmero, Marek; Rosebrock, Daniel; Schumacher, Steve; Fan, Yu; Fittall, Matthew; Yao, Xiaotong; Lee, Juhee; Schlesner, Matthias; Zhu, Hongtu; Adams, David; Getz, Gad; Boutros, Paul; Imielinski, Marcin; Beroukhim, Rameen; Sahinalp, Cenk; Peifer, Martin; Martincorena, Inigo; Markowetz, Florian; Mustonen, Ville; Yuan, Ke; Gerstung, Moritz; Wang, Wenyi; Spellman, Paul; Morris, Quaid; Wedge, David; Van Loo, Peter Share Save
The evolutionary history of 2,658 cancers Jolly, Clemency; Gerstung, Moritz; Leshchiner, Ignaty; Dentro, Stefan C.; Gonzalez, Santiago; Mitchell, Thomas J.; Rubanova, Yulia; Anur, Pavana; Rosebrock, Daniel; Yu, Kaixian; Tarabichi, Maxime; Deshwar, Amit; Wintersinger, Jeff; Kleinheinz, Kortine; Vasquez-Garcia, Ignacio; Haase, Kerstin; Sengupta, Subhajit; Macintyre, Geoff; Malikic, Salem; Donmez, Nilgun; Livitz, Dimitri G.; Cmero, Mark; Demeulemeester, Jonas; Schumacher, Steve; Fan, Yu; Yao, Xiaotong; Lee, Juhee; Schlesner, Matthias; Boutros, Paul C.; Bowtell, David D.; Zhu, Hongtu; Getz, Gad; Imielinski, Marcin; Beroukhim, Rameen; Sahinalp, S. Cenk; Ji, Yuan; Peifer, Martin; Markowetz, Florian; Mustonen, Ville; Juan, Ke; Wang, Wenyi; Morris, Quaid D.; Spellman, Paul T.; Wedge, David C.; Van Loo, Peter Share Save
Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes Numanagic, Ibrahim; Malikic, Salem; Ford, Michael; Qin, Xiang; Toji, Lorraine; Radovich, Milan; Skaar, Todd C.; Pratt, Victoria M.; Berger, Bonnie; Scherer, Steve; Sahinalp, S. Cenk Share Save
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