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Title	Author(s)	Issue Date
2SNV: Quasispecies reconstruction from PacBio reads Proceeding/Conference:2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)	Artyomenko, Alexander Wu, Nicholas C.Mangul, Serghei Eskin, Eleazar Sun, Ren Zelikovsky, Alex	2015
A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing Journal:BMC Genomics	Zhang, Tian Hao Wu, Nicholas C.Sun, Ren	2016
A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain Journal:Current Biology	Olson, C. Anders Wu, Nicholas C.Sun, Ren	2014
A comprehensive functional map of the hepatitis C virus genome provides a resource for probing viral proteins Journal:mBio	Remenyi, Roland Qi, Hangfei Su, Sheng Yao Chen, Zugen Wu, Nicholas C.Arumugaswami, Vaithilingaraja Truong, Shawna Chu, Virginia Stokelman, Tamar Lo, Hung Hao Anders Olson, C.Wu, Ting Ting Chen, Shu Hwa Lin, Chung Yen Sun, Ren	2014
A Quantitative High-Resolution Genetic Profile Rapidly Identifies Sequence Determinants of Hepatitis C Viral Fitness and Drug Sensitivity Journal:PLoS Pathogens	Qi, Hangfei Olson, C. Anders Wu, Nicholas C.Ke, Ruian Loverdo, Claude Chu, Virginia Truong, Shawna Remenyi, Roland Chen, Zugen Du, Yushen Su, Sheng Yao Al-Mawsawi, Laith Q.Wu, Ting Ting Chen, Shu Hua Lin, Chung Yen Zhong, Weidong Lloyd-Smith, James O.Sun, Ren	2014
Accurate viral population assembly from ultra-deep sequencing data Journal:Bioinformatics	Mangul, Serghei Wu, Nicholas C.Mancuso, Nicholas Zelikovsky, Alex Sun, Ren Eskin, Eleazar	2014
Adaptation in protein fitness landscapes is facilitated by indirect paths Journal:eLife	Wu, Nicholas C.Dai, Lei Olson, C. Anders Lloyd-Smith, James O.Sun, Ren	2016
Annotating protein functional residues by coupling high-throughput fitness profile and homologous-structure analysis Journal:mBio	Du, Yushen Wu, Nicholas C.Jiang, Lin Zhang, Tianhao Gong, Danyang Shu, Sara Wu, Ting Ting Sun, Ren	2016
Applications of High-Fidelity Sequencing Protocol to RNA Viruses Book:Computational Methods for Next Generation Sequencing Data Analysis	Mangul, Serghei Wu, Nicholas C.Nenastyeva, Ekaterina Mancuso, Nicholas Zelikovsky, Alexander Sun, Ren Eskin, Eleazar	2016
Benchmarking of computational error-correction methods for next-generation sequencing data Journal:Genome Biology	Mitchell, Keith Brito, Jaqueline J.Mandric, Igor Wu, Qiaozhen Knyazev, Sergey Chang, Sei Martin, Lana S.Karlsberg, Aaron Gerasimov, Ekaterina Littman, Russell Hill, Brian L.Wu, Nicholas C.Yang, Harry Taegyun Hsieh, Kevin Chen, Linus Littman, Eli Shabani, Taylor Enik, German Yao, Douglas Sun, Ren Schroeder, Jan Eskin, Eleazar Zelikovsky, Alex Skums, Pavel Pop, Mihai Mangul, Serghei	2020
Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment Journal:BMC Genomics	Wu, Nicholas C.Du, Yushen Le, Shuai Young, Arthur P.Zhang, Tian Hao Wang, Yuanyuan Zhou, Jian Yoshizawa, Janice M.Dong, Ling Li, Xinmin Wu, Ting Ting Sun, Ren	2016
Differential antigenic imprinting effects between influenza H1N1 hemagglutinin and neuraminidase in a mouse model Journal:Journal of Virology	Lv, Huibin Teo, Qi Wen Lee, Chang Chun D.Liang, Weiwen Choi, Danbi Mao, Kevin J.Ardagh, Madison R.Gopal, Akshita B.Mehta, Arjun Szlembarski, Matt Bruzzone, Roberto Wilson, Ian A.Wu, Nicholas C.Mok, Chris K.P.	5-Dec-2024
Epistasis mediates the evolution of the receptor binding mode in recent human H3N2 hemagglutinin Journal:Nature Communications	Lei, Ruipeng Liang, Weiwen Ouyang, Wenhao O.Hernandez Garcia, Andrea Kikuchi, Chika Wang, Shengyang McBride, Ryan Tan, Timothy J.C.Sun, Yuanxin Chen, Chunke Graham, Claire S.Rodriguez, Lucia A.Shen, Ivana R.Choi, Danbi Bruzzone, Roberto Paulson, James C.Nair, Satish K.Mok, Chris K.P.Wu, Nicholas C.	18-Jun-2024
Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality Journal:PLoS Genetics	Wu, Nicholas C.Olson, C. Anders Du, Yushen Le, Shuai Tran, Kevin Remenyi, Roland Gong, Danyang Al-Mawsawi, Laith Q.Qi, Hangfei Wu, Ting Ting Sun, Ren	2015
Genome-wide identification of interferon-sensitive mutations enables influenza vaccine design Journal:Science	Du, Yushen Xin, Li Shi, Yuan Zhang, Tian Hao Wu, Nicholas C.Dai, Lei Gong, Danyang Brar, Gurpreet Shu, Sara Luo, Jiadi Reiley, William Tseng, Yen Wen Bai, Hongyan Wu, Ting Ting Wang, Jieru Shu, Yuelong Sun, Ren	2018
High-resolution genetic profile of viral genomes: Why it matters Journal:Current Opinion in Virology	Qi, Hangfei Wu, Nicholas C.Du, Yushen Wu, Ting Ting Sun, Ren	2015
High-throughput identification of loss-of-function mutations for anti-interferon activity in the influenza a virus ns segment Journal:Journal of Virology	Wu, Nicholas C.Young, Arthur P.Al-Mawsawi, Laith Q.Anders Olson, C.Feng, Jun Qi, Hangfei Luan, Harding H.Li, Xinmin Wu, Ting Ting Sun, Ren	2014
High-throughput identification of protein mutant stability computed from a double mutant fitness landscape Journal:Protein Science	Wu, Nicholas C.Olson, C. Anders Sun, Ren	2016
High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution Journal:Scientific Reports	Wu, Nicholas C.Young, Arthur P.Al-Mawsawi, Laith Q.Olson, C. Anders Feng, Jun Qi, Hangfei Chen, Shu Hwa Lu, I. Hsuan Lin, Chung Yen Chin, Robert G.Luan, Harding H.Nguyen, Nguyen Nelson, Stanley F.Li, Xinmin Wu, Ting Ting Sun, Ren	2014
High-throughput profiling of point mutations across the HIV-1 genome Journal:Retrovirology	Al-Mawsawi, Laith Q.Wu, Nicholas C.Olson, C. Anders Shi, Cai C.Qi, Hangfei Zheng, Xiaojuan Wu, Ting Ting Sun, Ren	2014

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