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BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis Firtina, Can; Park, Jisung; Alser, Mohammed; Kim, Jeremie S.; Cali, Damla Senol; Shahroodi, Taha; Ghiasi, Nika Mansouri; Singh, Gagandeep; Kanellopoulos, Konstantinos; Alkan, Can; Mutlu, Onur Share Save
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Technology dictates algorithms: recent developments in read alignment Alser, Mohammed; Rotman, Jeremy; Deshpande, Dhrithi; Taraszka, Kodi; Shi, Huwenbo; Baykal, Pelin Icer; Yang, Harry Taegyun; Xue, Victor; Knyazev, Sergey; Singer, Benjamin D.; Balliu, Brunilda; Koslicki, David; Skums, Pavel; Zelikovsky, Alex; Alkan, Can; Mutlu, Onur; Mangul, Serghei 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
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
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GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies Kim, Jeremie S.; Cali, Damla Senol; Xin, Hongyi; Lee, Donghyuk; Ghose, Saugata; Alser, Mohammed; Hassan, Hasan; Ergin, Oguz; Alkan, Can; Mutlu, Onur Share Save
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Targeting PLK1 overcomes T-DM1 resistance via CDK1-dependent phosphorylation and inactivation of Bcl-2/xL in HER2-positive breast cancer Saatci, Ozge; Borgoni, Simone; Akbulut, Ozge; Durmus, Selvi; Raza, Umar; Eyupoglu, Erol; Alkan, Can; Akyol, Aytekin; Kutuk, Ozgur; Wiemann, Stefan; Sahin, Ozgur Share Save
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