Zobrazeno 1 - 10
of 49
pro vyhledávání: '"Sayed Mohammad Ebrahim Sahraeian"'
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
Publikováno v:
Scientific Reports, Vol 14, Iss 1, Pp 1-12 (2024)
Abstract Accurately calling indels with next-generation sequencing (NGS) data is critical for clinical application. The precisionFDA team collaborated with the U.S. Food and Drug Administration’s (FDA’s) National Center for Toxicological Research
Externí odkaz:
https://doaj.org/article/fa59c4fa44684290a436974c57f268f0
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 Schroth, Gokhan Yavas, 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, Steve 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
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-26 (2022)
Abstract Background Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically ass
Externí odkaz:
https://doaj.org/article/a888ae17e58a4cf188efc452ccec0462
Autor:
Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Konstantinos Karagiannis, Malcolm Moos, Sean Smith, Luis Santana-Quintero, Chunlin Xiao, Michael Colgan, Huixiao Hong, Marghoob Mohiyuddin, Wenming Xiao
Publikováno v:
Genome Biology, Vol 23, Iss 1, Pp 1-20 (2022)
Abstract Background Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural network-based somatic mutation
Externí odkaz:
https://doaj.org/article/675a7584d91a4b08951f7e18d9bba393
Autor:
Michael M. Khayat, Sayed Mohammad Ebrahim Sahraeian, Samantha Zarate, Andrew Carroll, Huixiao Hong, Bohu Pan, Leming Shi, Richard A. Gibbs, Marghoob Mohiyuddin, Yuanting Zheng, Fritz J. Sedlazeck
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-15 (2021)
Abstract Background Genomic structural variations (SV) are important determinants of genotypic and phenotypic changes in many organisms. However, the detection of SV from next-generation sequencing data remains challenging. Results In this study, DNA
Externí odkaz:
https://doaj.org/article/0f705634bb9d4e6ebe2949ac7601e5f7
Autor:
Wendell Jones, Binsheng Gong, Natalia Novoradovskaya, Dan Li, Rebecca Kusko, Todd A. Richmond, Donald J. Johann, Halil Bisgin, Sayed Mohammad Ebrahim Sahraeian, Pierre R. Bushel, Mehdi Pirooznia, Katherine Wilkins, Marco Chierici, Wenjun Bao, Lee Scott Basehore, Anne Bergstrom Lucas, Daniel Burgess, Daniel J. Butler, Simon Cawley, Chia-Jung Chang, Guangchun Chen, Tao Chen, Yun-Ching Chen, Daniel J. Craig, Angela 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 Jasper, Giuseppe Jurman, David Philip Kreil, Paweł Łabaj, Kevin Lai, Jianying Li, Quan-Zhen Li, Yulong Li, Zhiguang Li, Zhichao Liu, Mario Solís López, Kelci Miclaus, Raymond Miller, Vinay K. 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
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-38 (2021)
Abstract Background Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a sui
Externí odkaz:
https://doaj.org/article/7cb57d840cc4477294d87b6e0d997c1a
Autor:
Sayed Mohammad Ebrahim Sahraeian, Ruolin Liu, Bayo Lau, Karl Podesta, Marghoob Mohiyuddin, Hugo Y. K. Lam
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-10 (2019)
Somatic mutations are crucial to the understanding of cancer genesis, progression, and treatment, but are still challenging to detect. Here the authors present NeuSomatic, a convolutional neural network approach for accurate somatic mutation detectio
Externí odkaz:
https://doaj.org/article/97e2f4d53235488391827e07f5a633f0
Autor:
Sayed Mohammad Ebrahim Sahraeian, Marghoob Mohiyuddin, Robert Sebra, Hagen Tilgner, Pegah T. Afshar, Kin Fai Au, Narges Bani Asadi, Mark B. Gerstein, Wing Hung Wong, Michael P. Snyder, Eric Schadt, Hugo Y. K. Lam
Publikováno v:
Nature Communications, Vol 8, Iss 1, Pp 1-15 (2017)
RNA-seq is widely used for transcriptome analysis. Here, the authors analyse a wide spectrum of RNA-seq workflows and present a comprehensive analysis protocol named RNACocktail as well as a computational pipeline leveraging the widely used tools for
Externí odkaz:
https://doaj.org/article/0de7f1d5eb3f4b9daae33212abd18a28
Publikováno v:
PLoS ONE, Vol 8, Iss 7, p e67995 (2013)
In this paper we introduce an efficient algorithm for alignment of multiple large-scale biological networks. In this scheme, we first compute a probabilistic similarity measure between nodes that belong to different networks using a semi-Markov rando
Externí odkaz:
https://doaj.org/article/91ee0c563080486fa6887271a1c27daf
Publikováno v:
PLoS ONE, Vol 7, Iss 8, p e41474 (2012)
In this work, we introduce a novel network synthesis model that can generate families of evolutionarily related synthetic protein-protein interaction (PPI) networks. Given an ancestral network, the proposed model generates the network family accordin
Externí odkaz:
https://doaj.org/article/d8b8a131dccf466baecdb5813a421c74
Autor:
Kenneth Idler, Andreas Scherer, Charles Lu, Timothy K. McDaniel, Penelope Duerken-Hughes, K J. Langenbach, Seta Stanbouly, Charles Wang, Victoria Zismann, Keyur Talsania, Leming Shi, Margaret C. Cam, Shamoni Maheshwari, Zhipan Li, Luyao Ren, Petr Vojta, Mehdi Pirooznia, Jonathan J Keats, Rasika Kalamegham, Howard Jacob, Bao Tran, Liz Kerrigan, Baitang Ning, Ene Reimann, Jiri Drabek, Eric F. Donaldson, Zhaowei Yang, Sayed Mohammad Ebrahim Sahraeian, Daoud Meerzaman, Marc Sultan, Jessica Nordlund, Tsai-wei Shen, Sulev Kõks, Christopher E. Mason, Yunfei Guo, Winnie S. Liang, Claudia Catalanotti, Jeffrey M. Trent, Ying Yu, Roderick V. Jensen, Huixiao Hong, Malcolm Moos, Wenming Xiao, Stephen T. Sherry, Jonathan Foox, Joe Shuga, Hugo Y. K. Lam, Chunlin Xiao, Lijing Yao, Li Tai Fang, Wanqiu Chen, Marghoob Mohiyuddin, Monika Mehta, Rebecca Kusko, Roberta Maestro, Yongmei Zhao, Jonathan Adkins, Gary P. Schroth, Daniel Butler, Yuliya Kriga, Ogan D Abaan, Erich Jaeger, Yuanting Zheng, Daniela Gasparotto, Ulrika Liljedahl, Tiffany Hung, Eric Peters, Erica Tassone, Maryellen de Mars, Cu Nguyen, Lei Song, Bin Zhu, Weida Tong, Zivana Tezak, Justin B. Lack, Virginie Petitjean, Jyoti Shetty, Jing Li, Zhong Chen
Publikováno v:
Nat Biotechnol
The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets o