未登录 Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA Gong, Binsheng; Lababidi, Samir; Kusko, Rebecca; Bouri, Khaled; Prezek, Sarah; Thovarai, Vishal; Prasanna, Anish; Maier, Ezekiel J.; Golkaram, Mahdi; Sun, Xingqiang; Kyriakidis, Konstantinos; Kitajima, Joao Paulo; Sahraeian, Sayed Mohammad Ebrahim; Guo, Yunfei; Johanson, Elaine; Jones, Wendell; Tong, Weida; Xu, Joshua 分享 收藏
Curated variation benchmarks for challenging medically relevant autosomal genes 具有挑战性的医学相关常染色体基因的策划变异基准 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. 分享 收藏
Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample Sahraeian, Sayed Mohammad Ebrahim; Fang, Li Tai; Karagiannis, Konstantinos; Moos, Malcolm; Smith, Sean; Santana-Quintero, Luis; Xiao, Chunlin; Colgan, Michael; Hong, Huixiao; Mohiyuddin, Marghoob; Xiao, Wenming 分享 收藏
Assessing reproducibility of inherited variants detected with short-read whole genome sequencing 评估短读全基因组测序检测到的遗传变异的可重复性 Pan, Bohu; Ren, Luyao; Onuchic, Vitor; Guan, Meijian; Kusko, Rebecca; Bruinsma, Steve; Trigg, Len; Scherer, Andreas; Ning, Baitang; Zhang, Chaoyang; Glidewell-Kenney, Christine; Xiao, Chunlin; Donaldson, Eric; Sedlazeck, Fritz J.; Schroth, Gary; Yavas, Gokhan; Grunenwald, Haiying; Chen, Haodong; Meinholz, Heather; Meehan, Joe; Wang, Jing; Yang, Jingcheng; Foox, Jonathan; Shang, Jun; Miclaus, Kelci; Dong, Lianhua; Shi, Leming; Mohiyuddin, Marghoob; Pirooznia, Mehdi; Gong, Ping; Golshani, Rooz; Wolfinger, Russ; Lababidi, Samir; Sahraeian, Sayed Mohammad Ebrahim; Sherry, Steve; Han, Tao; Chen, Tao; Shi, Tieliu; Hou, Wanwan; Ge, Weigong; Zou, Wen; Guo, Wenjing; Bao, Wenjun; Xiao, Wenzhong; Fan, Xiaohui; Gondo, Yoichi; Yu, Ying; Zhao, Yongmei; Su, Zhenqiang; Liu, Zhichao; Tong, Weida; Xiao, Wenming; Zook, Justin M.; Zheng, Yuanting; Hong, Huixiao 分享 收藏
Hidden biases in germline structural variant detection Khayat, Michael M.; Sahraeian, Sayed Mohammad Ebrahim; Zarate, Samantha; Carroll, Andrew; Hong, Huixiao; Pan, Bohu; Shi, Leming; Gibbs, Richard A.; Mohiyuddin, Marghoob; Zheng, Yuanting; Sedlazeck, Fritz J. 分享 收藏
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing Fang, Li Tai; Zhu, Bin; Zhao, Yongmei; Chen, Wanqiu; Yang, Zhaowei; Kerrigan, Liz; Langenbach, Kurt; de Mars, Maryellen; Lu, Charles; Idler, Kenneth; Jacob, Howard; Zheng, Yuanting; Ren, Luyao; Yu, Ying; Jaeger, Erich; Schroth, Gary P.; Abaan, Ogan D.; Talsania, Keyur; Lack, Justin; Shen, Tsai-Wei; Chen, Zhong; Stanbouly, Seta; Tran, Bao; Shetty, Jyoti; Kriga, Yuliya; Meerzaman, Daoud; Nguyen, Cu; Petitjean, Virginie; Sultan, Marc; Cam, Margaret; Mehta, Monika; Hung, Tiffany; Peters, Eric; Kalamegham, Rasika; Sahraeian, Sayed Mohammad Ebrahim; Mohiyuddin, Marghoob; Guo, Yunfei; Yao, Lijing; Song, Lei; Lam, Hugo Y. K.; Drabek, Jiri; Vojta, Petr; Maestro, Roberta; Gasparotto, Daniela; Koks, Sulev; Reimann, Ene; Scherer, Andreas; Nordlund, Jessica; Liljedahl, Ulrika; Jensen, Roderick, V; Pirooznia, Mehdi; Li, Zhipan; Xiao, Chunlin; Sherry, Stephen T.; Kusko, Rebecca; Moos, Malcolm; Donaldson, Eric; Tezak, Zivana; Ning, Baitang; Tong, Weida; Li, Jing; Duerken-Hughes, Penelope; Catalanotti, Claudia; Maheshwari, Shamoni; Shuga, Joe; Liang, Winnie S.; Keats, Jonathan; Adkins, Jonathan; Tassone, Erica; Zismann, Victoria; McDaniel, Timothy; Trent, Jeffrey; Foox, Jonathan; Butler, Daniel; Mason, Christopher E.; Hong, Huixiao; Shi, Leming; Wang, Charles; Xiao, Wenming 分享 收藏
A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency Jones, Wendell; Gong, Binsheng; Novoradovskaya, Natalia; Li, Dan; Kusko, Rebecca; Richmond, Todd A.; Johann, Donald J., Jr.; Bisgin, Halil; Sahraeian, Sayed Mohammad Ebrahim; Bushel, Pierre R.; Pirooznia, Mehdi; Wilkins, Katherine; Chierici, Marco; Bao, Wenjun; Basehore, Lee Scott; Lucas, Anne Bergstrom; Burgess, Daniel; Butler, Daniel J.; Cawley, Simon; Chang, Chia-Jung; Chen, Guangchun; Chen, Tao; Chen, Yun-Ching; Craig, Daniel J.; Del Pozo, Angela; Foox, Jonathan; Francescatto, Margherita; Fu, Yutao; Furlanello, Cesare; Giorda, Kristina; Grist, Kira P.; Guan, Meijian; Hao, Yingyi; Happe, Scott; Hariani, Gunjan; Haseley, Nathan; Jasper, Jeff; Jurman, Giuseppe; Kreil, David Philip; Labaj, Pawel; Lai, Kevin; Li, Jianying; Li, Quan-Zhen; Li, Yulong; Li, Zhiguang; Liu, Zhichao; Lopez, Mario Solis; Miclaus, Kelci; Miller, Raymond; Mittal, Vinay K.; Mohiyuddin, Marghoob; Pabon-Pena, Carlos; Parsons, Barbara L.; Qiu, Fujun; Scherer, Andreas; Shi, Tieliu; Stiegelmeyer, Suzy; Suo, Chen; Tom, Nikola; Wang, Dong; Wen, Zhining; Wu, Leihong; Xiao, Wenzhong; Xu, Chang; Yu, Ying; Zhang, Jiyang; Zhang, Yifan; Zhang, Zhihong; Zheng, Yuanting; Mason, Christopher E.; Willey, James C.; Tong, Weida; Shi, Leming; Xu, Joshua 分享 收藏
A robust benchmark for detection of germline large deletions and insertions (Jun, 10.1038/s41587-020-0538-8, 2020) 用于检测种系大缺失和插入的稳健基准 (6月，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 分享 收藏
A robust benchmark for detection of germline large deletions and insertions 用于检测种系大缺失和插入的可靠基准 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 分享 收藏
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Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis Sahraeian, Sayed Mohammad Ebrahim; Mohiyuddin, Marghoob; Sebra, Robert; Tilgner, Hagen; Afshar, Pegah T.; Au, Kin Fai; Asadi, Narges Bani; Gerstein, Mark B.; Wong, Wing Hung; Snyder, Michael P.; Schadt, Eric; Lam, Hugo Y. K. 分享 收藏
An expanded evaluation of protein function prediction methods shows an improvement in accuracy 蛋白质功能预测方法的扩展评估显示准确性有所提高 Jiang, Yuxiang; Oron, Tal Ronnen; Clark, Wyatt T.; Bankapur, Asma R.; D'Andrea, Daniel; Lepore, Rosalba; Funk, Christopher S.; Kahanda, Indika; Verspoor, Karin M.; Ben-Hur, Asa; Koo, Da Chen Emily; Penfold-Brown, Duncan; Shasha, Dennis; Youngs, Noah; Bonneau, Richard; Lin, Alexandra; Sahraeian, Sayed M. E.; Martelli, Pier Luigi; Profiti, Giuseppe; Casadio, Rita; Cao, Renzhi; Zhong, Zhaolong; Cheng, Jianlin; Altenhoff, Adrian; Skunca, Nives; Dessimoz, Christophe; Dogan, Tunca; Hakala, Kai; Kaewphan, Suwisa; Mehryary, Farrokh; Salakoski, Tapio; Ginter, Filip; Fang, Hai; Smithers, Ben; Oates, Matt; Gough, Julian; Toronen, Petri; Koskinen, Patrik; Holm, Liisa; Chen, Ching-Tai; Hsu, Wen-Lian; Bryson, Kevin; Cozzetto, Domenico; Minneci, Federico; Jones, David T.; Chapman, Samuel; Dukka, B. K. C.; Khan, Ishita K.; Kihara, Daisuke; Ofer, Dan; Rappoport, Nadav; Stern, Amos; Cibrian-Uhalte, Elena; Denny, Paul; Foulger, Rebecca E.; Hieta, Reija; Legge, Duncan; Lovering, Ruth C.; Magrane, Michele; Melidoni, Anna N.; Mutowo-Meullenet, Prudence; Pichler, Klemens; Shypitsyna, Aleksandra; Li, Biao; Zakeri, Pooya; ElShal, Sarah; Tranchevent, Leon-Charles; Das, Sayoni; Dawson, Natalie L.; Lee, David; Lees, Jonathan G.; Sillitoe, Ian; Bhat, Prajwal; Nepusz, Tamas; Romero, Alfonso E.; Sasidharan, Rajkumar; Yang, Haixuan; Paccanaro, Alberto; Gillis, Jesse; Sedeno-Cortes, Adriana E.; Pavlidis, Paul; Feng, Shou; Cejuela, Juan M.; Goldberg, Tatyana; Hamp, Tobias; Richter, Lothar; Salamov, Asaf; Gabaldon, Toni; Marcet-Houben, Marina; Supek, Fran; Gong, Qingtian; Ning, Wei; Zhou, Yuanpeng; Tian, Weidong; Falda, Marco; Fontana, Paolo; Lavezzo, Enrico; Toppo, Stefano; Ferrari, Carlo; Giollo, Manuel; Piovesan, Damiano; Tosatto, Silvio C. E.; del Pozo, Angela; Fernandez, Jose M.; Maietta, Paolo; Valencia, Alfonso; Tress, Michael L.; Benso, Alfredo; Di Carlo, Stefano; Politano, Gianfranco; Savino, Alessandro; Rehman, Hafeez Ur; Re, Matteo; Mesiti, Marco; Valentini, Giorgio; Bargsten, Joachim W.; van Dijk, Aalt D. J.; Gemovic, Branislava; Glisic, Sanja; Perovic, Vladmir; Veljkovic, Veljko; Veljkovic, Nevena; Almeida-e-Silva, Danillo C.; Vencio, Ricardo Z. N.; Sharan, Malvika; Vogel, Joerg; Kansakar, Lakesh; Zhang, Shanshan; Vucetic, Slobodan; Wang, Zheng; Sternberg, Michael J. E.; Wass, Mark N.; Huntley, Rachael P.; Martin, Maria J.; O'Donovan, Claire; Robinson, Peter N.; Moreau, Yves; Tramontano, Anna; Babbitt, Patricia C.; Brenner, Steven E.; Linial, Michal; Orengo, Christine A.; Rost, Burkhard; Greene, Casey S.; Mooney, Sean D.; Friedberg, Iddo; Radivojac, Predrag 分享 收藏
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