Výsledky vyhledávání - Sayed Mohammad Ebrahim Sahraeian

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  1. 1
    SMETANA: Accurate and Scalable Algorithm for Probabilistic Alignment of Large-Scale Biological Networks

    SMETANA: Accurate and Scalable Algorithm for Probabilistic Alignment of Large-Scale Biological Networks Autor Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon

    Vydáno 2013
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  2. 2
    SIFTER search: a web server for accurate phylogeny-based protein function prediction

    SIFTER search: a web server for accurate phylogeny-based protein function prediction Autor Sayed Mohammad Ebrahim Sahraeian, Kevin R. Luo, Steven E. Brenner

    Vydáno 2015
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  3. 3
    Digital genotyping of sorghum – a diverse plant species with a large repeat-rich genome

    Digital genotyping of sorghum – a diverse plant species with a large repeat-rich genome Autor Daryl T. Morishige, Patricia E. Klein, Josie Hilley, Sayed Mohammad Ebrahim Sahraeian, Arun Sharma, John E. Mullet

    Vydáno 2013
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  4. 4
    Deep convolutional neural networks for accurate somatic mutation detection

    Deep convolutional neural networks for accurate somatic mutation detection Autor Sayed Mohammad Ebrahim Sahraeian, Ruolin Liu, Bayo Lau, Karl Podesta, Marghoob Mohiyuddin, Hugo Y. K. Lam

    Vydáno 2019
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  5. 5
    Genetic Structure and Linkage Disequilibrium in a Diverse, Representative Collection of the C4 Model Plant, <i>Sorghum bicolor</i>

    Genetic Structure and Linkage Disequilibrium in a Diverse, Representative Collection of the C4 Model Plant, <i>Sorghum bicolor</i> Autor Yihong Wang, Hari D. Upadhyaya, A. Millie Burrell, Sayed Mohammad Ebrahim Sahraeian, Robert R. Klein, Patricia E. Klein

    Vydáno 2013
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  6. 6
    Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

    Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis Autor Sayed Mohammad Ebrahim Sahraeian, Marghoob Mohiyuddin, Robert Sebra, Hagen Tilgner, Pegah Tootoonchi Afshar, Kin Fai Au, Narges Bani Asadi, Mark Gerstein, Wing Hung Wong, M Snyder, Eric E. Schadt, Hugo Y. K. Lam

    Vydáno 2017
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  7. 7
    Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA

    Towards accurate indel calling for oncopanel sequencing through an international pipeline competition at precisionFDA Autor Binsheng Gong, Samir Lababidi, Rebecca Kusko, Khaled Bouri, Sarah Prezek, Vishal Thovarai, Anish Prasanna, Ezekiel J. Maier, Mahdi Golkaram, Xingqiang Sun, Konstantinos Kyriakidis, João Paulo Kitajima, Sayed Mohammad Ebrahim Sahraeian, Yunfei Guo, Elaine Johanson, Wendell Jones, Weida Tong, Joshua Xu

    Vydáno 2024
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  8. 8
    Small variant benchmark from a complete assembly of X and Y chromosomes

    Small variant benchmark from a complete assembly of X and Y chromosomes Autor Justin Wagner, Nathan D. Olson, Jennifer McDaniel, Lindsay Harris, Brendan J. Pinto, David Jáspez, Adrián Muñoz‐Barrera, Luis A. Rubio‐Rodríguez, José M. Lorenzo-Salazar, Carlos Flores, Sayed Mohammad Ebrahim Sahraeian, Giuseppe Narzisi, Marta Byrska-Bishop, Uday S. Evani, Chunlin Xiao, Juniper A. Lake, Peter Fontana, Craig S. Greenberg, Donald Freed, Mohammed Faizal Eeman Mootor, Paul C. Boutros, Lisa Murray, Kishwar Shafin, Andrew Carroll, Fritz J. Sedlazeck, Melissa A. Wilson, Justin M. Zook

    Vydáno 2025
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  9. 9
    Curated variation benchmarks for challenging medically relevant autosomal genes

    Curated variation benchmarks for challenging medically relevant autosomal genes Autor Justin Wagner, Nathan D. Olson, Lindsay Harris, Jennifer McDaniel, Haoyu Cheng, Arkarachai Fungtammasan, Yih-Chii Hwang, Richa Gupta, Aaron M. Wenger, William J. Rowell, Ziad Khan, Jesse Farek, Yiming Zhu, Aishwarya Pisupati, Medhat Mahmoud, Chunlin Xiao, Byunggil Yoo, Sayed Mohammad Ebrahim Sahraeian, Danny E. Miller, David Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz‐Barrera, Luis A. Rubio‐Rodríguez, Carlos Flores, Giuseppe Narzisi, Uday S. Evani, Wayne E. Clarke, Joyce Lee, Christopher E. Mason, Stephen E. Lincoln, Karen H. Miga, Mark Ebbert, Alaina Shumate, Heng Li, Chen-Shan Chin, Justin M. Zook, Fritz J. Sedlazeck

    Vydáno 2022
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  10. 10
    Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

    Assessing reproducibility of inherited variants detected with short-read whole genome sequencing Autor Bohu Pan, Luyao Ren, Vitor Onuchic, Meijian Guan, Rebecca Kusko, Steve Bruinsma, Len Trigg, Andreas Scherer, Baitang Ning, Chaoyang Zhang, Christine Glidewell-Kenney, Chunlin Xiao, Eric Donaldson, Fritz J. Sedlazeck, Gary P. Schroth, Gökhan Yavaş, Haiying Grunenwald, Haodong Chen, Heather Meinholz, Joe Meehan, Jing Wang, Jingcheng Yang, Jonathan Foox, Jun Shang, Kelci Miclaus, Lianhua Dong, Leming Shi, Marghoob Mohiyuddin, Mehdi Pirooznia, Ping Gong, Rooz Golshani, Russ Wolfinger, Samir Lababidi, Sayed Mohammad Ebrahim Sahraeian, Stephen T. Sherry, Tao Han, Tao Chen, Tieliu Shi, Wanwan Hou, Weigong Ge, Wen Zou, Wenjing Guo, Wenjun Bao, Wenzhong Xiao, Xiaohui Fan, Yoichi Gondo, Ying Yu, Yongmei Zhao, Zhenqiang Su, Zhichao Liu, Weida Tong, Wenming Xiao, Justin M. Zook, Yuanting Zheng, Huixiao Hong

    Vydáno 2022
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  11. 11
    A robust benchmark for germline structural variant detection

    A robust benchmark for germline structural variant detection Autor Justin M. Zook, Nancy F. Hansen, Nathan D. Olson, Lesley M. Chapman, James C. Mullikin, Chunlin Xiao, Stephen T. Sherry, Sergey Koren, Adam M. Phillippy, Paul C. Boutros, Sayed Mohammad Ebrahim Sahraeian, Vincent Huang, Alexandre Rouette, Noah Alexander, Christopher E. Mason, Iman Hajirasouliha, Camir Ricketts, Joyce Lee, Rick Tearle, Ian T. Fiddes, Álvaro Martínez Barrio, Jeremiah A. Wala, Andrew Carroll, Noushin Ghaffari, Oscar L. Rodriguez, Ali Bashir, Shaun D. Jackman, John J. Farrell, Aaron M. Wenger, Can Alkan, Arda Söylev, Michael C. Schatz, Shilpa Garg, George M. Church, Tobias Marschall, Ken Chen, Xian Fan, Adam C. English, Jeffrey Rosenfeld, Weichen Zhou, Ryan E. Mills, Jay M. Sage, Jennifer R. Davis, Michael D. Kaiser, John S. Oliver, Anthony P. Catalano, Mark Chaisson, Noah Spies, Fritz J. Sedlazeck, Marc Salit

    Vydáno 2019
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  12. 12
    A robust benchmark for detection of germline large deletions and insertions

    A robust benchmark for detection of germline large deletions and insertions Autor Justin M. Zook, Nancy F. Hansen, Nathan D. Olson, Lesley M. Chapman, James C. Mullikin, Chunlin Xiao, Stephen T. Sherry, Sergey Koren, Adam M. Phillippy, Paul C. Boutros, Sayed Mohammad Ebrahim Sahraeian, Vincent Huang, Alexandre Rouette, Noah Alexander, Christopher E. Mason, Iman Hajirasouliha, Camir Ricketts, Joyce Lee, Rick Tearle, Ian T. Fiddes, Álvaro Martínez Barrio, Jeremiah A. Wala, Andrew Carroll, Noushin Ghaffari, Oscar L. Rodriguez, Ali Bashir, Shaun D. Jackman, John J. Farrell, Aaron M. Wenger, Can Alkan, Arda Söylev, Michael C. Schatz, Shilpa Garg, George M. Church, Tobias Marschall, Ken Chen, Xian Fan, Adam C. English, Jeffrey Rosenfeld, Weichen Zhou, Ryan E. Mills, Jay M. Sage, Jennifer R. Davis, Michael D. Kaiser, John S. Oliver, Anthony P. Catalano, Mark Chaisson, Noah Spies, Fritz J. Sedlazeck, Marc Salit

    Vydáno 2020
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  13. 13
    precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions

    precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions Autor Nathan D. Olson, Justin Wagner, Jennifer McDaniel, Sarah H. Stephens, Samuel T. Westreich, Anish G. Prasanna, Elaine Johanson, Emily S. Boja, Ezekiel J. Maier, Omar Serang, David Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz‐Barrera, Luis A. Rubio‐Rodríguez, Carlos Flores, Konstantinos Kyriakidis, Andigoni Malousi, Kishwar Shafin, Trevor Pesout, Miten Jain, Benedict Paten, Pi-Chuan Chang, Alexey Kolesnikov, Maria Nattestad, Gunjan Baid, Sidharth Goel, Howard H. Yang, Andrew Carroll, Robert Eveleigh, Mathieu Bourgey, Guillaume Bourque, Gen Li, MA ChouXian, LinQi Tang, DU YuanPing, Shaowei Zhang, Jordi Morata, Raúl Tonda, Genı́s Parra, Jean-Rémi Trotta, Christian Brueffer, Sinem Demirkaya-Budak, Duygu Kabakci-Zorlu, Deniz Turgut, Özem Kalay, Güngör Budak, Kübra Narcı, Elif Acar Arslan, Matthew A. Brown, Ivan J. Johnson, Alexey Dolgoborodov, Vladimir Semenyuk, Amit Jain, H. Serhat Tetikol, Varun Jain, Mike Ruehle, Bryan R. Lajoie, Cooper Roddey, Severine Catreux, Rami Mehio, Mian Umair Ahsan, Qian Liu, Kai Wang, Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Marghoob Mohiyuddin, Calvin Hung, Chirag Jain, Hanying Feng, Zhipan Li, Luoqi Chen, Fritz J. Sedlazeck, Justin M. Zook

    Vydáno 2020
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  14. 14
    A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

    A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency Autor Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd Richmond, Donald J. Johann, Halil Bişğin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee S Basehore, Anne Bergstrom Lucas, Daniel L. Burgess, Daniel Butler, Simon Cawley, Chia-Jung Chang, Guangchun Chen, Tao Chen, Yun-Ching Chen, Daniel J. Craig, Ángela del Pozo, Jonathan Foox, Margherita Francescatto, Yutao Fu, Cesare Furlanello, Kristina Giorda, Kira P. Grist, Meijian Guan, Yingyi Hao, Scott Happe, Gunjan Hariani, Nathan Haseley, Jeff S. Jasper, Giuseppe Jurman, David P. Kreil, Paweł P. Łabaj, Kevin Lai, Jianying Li, Quan‐Zhen Li, Yulong Li, Zhiguang Li, Zhichao Liu, Mario Solís, Kelci Miclaus, Raymond D. Miller, Vinay Kumar Mittal, Marghoob Mohiyuddin, Carlos Pabón-Peña, Barbara L. Parsons, Fujun Qiu, Andreas Scherer, Tieliu Shi, Suzy Stiegelmeyer, Chen Suo, Nikola Tom, Dong Wang, Zhining Wen, Leihong Wu, Wenzhong Xiao, Chang Xu, Ying Yu, Jiyang Zhang, Yifan Zhang, Zhihong Zhang, Yuanting Zheng, Christopher E. Mason, James C. Willey, Weida Tong, Leming Shi, Joshua Xu

    Vydáno 2021
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  15. 15
    PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

    PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions Autor Nathan D. Olson, Justin Wagner, Jennifer McDaniel, Sarah H. Stephens, Samuel T. Westreich, Anish G. Prasanna, Elaine Johanson, Emily S. Boja, Ezekiel J. Maier, Omar Serang, David Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz‐Barrera, Luis A. Rubio‐Rodríguez, Carlos Flores, Konstantinos Kyriakidis, Andigoni Malousi, Kishwar Shafin, Trevor Pesout, Miten Jain, Benedict Paten, Pi-Chuan Chang, Alexey Kolesnikov, Maria Nattestad, Gunjan Baid, Sidharth Goel, Howard H. Yang, Andrew Carroll, Robert Eveleigh, Mathieu Bourgey, Guillaume Bourque, Gen Li, Chouxian Ma, LinQi Tang, Yuanping Du, Shaowei Zhang, Jordi Morata, Raúl Tonda, Genı́s Parra, Jean-Rémi Trotta, Christian Brueffer, Sinem Demirkaya-Budak, Duygu Kabakci-Zorlu, Deniz Turgut, Özem Kalay, Güngör Budak, Kübra Narcı, Elif Acar Arslan, Matthew A. Brown, Ivan J. Johnson, Alexey Dolgoborodov, Vladimir Semenyuk, Amit Jain, H. Serhat Tetikol, Varun Jain, Mike Ruehle, Bryan R. Lajoie, Cooper Roddey, Severine Catreux, Rami Mehio, Mian Umair Ahsan, Qian Liu, Kai Wang, Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Marghoob Mohiyuddin, Calvin Hung, Chirag Jain, Hanying Feng, Zhipan Li, Luoqi Chen, Fritz J. Sedlazeck, Justin M. Zook

    Vydáno 2022
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  16. 16
    An expanded evaluation of protein function prediction methods shows an improvement in accuracy

    An expanded evaluation of protein function prediction methods shows an improvement in accuracy Autor Yuxiang Jiang, Tal Oron, Wyatt T. Clark, Asma Bankapur, Daniel D’Andrea, Rosalba Lepore, Christopher S. Funk, Indika Kahanda, Karin Verspoor, Asa Ben‐Hur, Da Chen Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah Youngs, Richard Bonneau, Alexandra J. Lin, Sayed Mohammad Ebrahim Sahraeian, Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio, Renzhi Cao, Zhaolong Zhong, Jianlin Cheng, Adrian Altenhoff, Nives Škunca, Christophe Dessimoz, Tunca Doğan, Kai Hakala, Suwisa Kaewphan, Farrokh Mehryary, Tapio Salakoski, Filip Ginter, Hai Fang, Ben Smithers, Matt E. Oates, Julian Gough, Petri Törönen, Patrik Koskinen, Liisa Holm, Ching-Tai Chen, Wen−Lian Hsu, Kevin Bryson, Domenico Cozzetto, Federico Minneci, David T. Jones, Samuel Chapman, Dukka Bkc, Ishita Khan, Daisuke Kihara, Dan Ofer, Nadav Rappoport, Amos Stern, Elena Cibrián–Uhalte, Paul Denny, Rebecca E. Foulger, Reija Hieta, Duncan Legge, Ruth C. Lovering, Michele Magrane, Anna N. Melidoni, Prudence Mutowo, Klemens Pichler, Aleksandra Shypitsyna, Biao Li, Pooya Zakeri, Sarah ElShal, Léon-Charles Tranchevent, Sayoni Das, Natalie L. Dawson, David Lee, Jonathan Lees, Ian Sillitoe, Prajwal Bhat, Tamás Nepusz, Alfonso E. Romero, Rajkumar Sasidharan, Haixuan Yang, Alberto Paccanaro, Jesse Gillis, Adriana E. Sedeño-Cortés, Paul Pavlidis, Shou Feng, Juan Miguel Cejuela, Tatyana Goldberg, Tobias Hamp, Lothar Richter, Asaf Salamov, Toni Gabaldón, Marina Marcet‐Houben, Fran Supek, Qingtian Gong, Wei Ning, Yuanpeng Zhou, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Stefano Toppo, Carlo Ferrari, Manuel Giollo

    Vydáno 2016
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  17. 17
    Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

    Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing Autor Li Tai Fang, Bin Zhu, Yongmei Zhao, Wanqiu Chen, Zhaowei Yang, Liz Kerrigan, Kurt J. Langenbach, Maryellen de Mars, Charles Lu, Kenneth B. Idler, Howard J. Jacob, Yuanting Zheng, Luyao Ren, Ying Yu, Erich Jaeger, Gary P. Schroth, Ogan D. Abaan, Keyur Talsania, Justin Lack, Tsai-Wei Shen, Zhong Chen, Seta Stanbouly, Bao Tran, Jyoti Shetty, Yuliya Kriga, Daoud Meerzaman, Cu Nguyen, Virginie Petitjean, Marc Sultan, Margaret C. Cam, Monika Mehta, Tiffany Hung, Eric Peters, Rasika Kalamegham, Sayed Mohammad Ebrahim Sahraeian, Marghoob Mohiyuddin, Yunfei Guo, Lijing Yao, Lei Song, Hugo Y. K. Lam, Jir̆ı́ Drábek, Petr Vojta, Roberta Maestro, Daniela Gasparotto, Sulev Kõks, Ene Reimann, Andreas Scherer, Jessica Nordlund, Ulrika Liljedahl, Roderick V. Jensen, Mehdi Pirooznia, Zhipan Li, Chunlin Xiao, Stephen T. Sherry, Rebecca Kusko, Malcolm Moos, Eric Donaldson, Živana Težak, Baitang Ning, Weida Tong, Jing Li, Penelope Duerken-Hughes, Claudia Catalanotti, Shamoni Maheshwari, Joe Shuga, Winnie S. Liang, Jonathan J. Keats, Jonathan Adkins, Erica E. Tassone, Victoria Zismann, Timothy K. McDaniel, Jeffrey M. Trent, Jonathan Foox, Daniel Butler, Christopher E. Mason, Huixiao Hong, Leming Shi, Charles Wang, Wenming Xiao, Ogan D. Abaan, Meredith Ashby, Ozan Aygün, Xiaopeng Bian, Thomas M. Blomquist, Pierre R. Bushel, Margaret C. Cam, Fabien Campagne, Qingrong Chen, Tao Chen, Xin Chen, Yunching Chen, Han‐Yu Chuang, Maryellen de Mars, Youping Deng, Eric Donaldson, Jir̆ı́ Drábek, Ben Ernest, Jonathan Foox, Don Freed, Paul G. Giresi

    Vydáno 2021
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