The Program in Bioinformatics and Integrative Biology (BIB) was established in 2008 at the University of Massachusetts Medical School to address one of the most dynamic and central areas in biomedical research—the ever-increasing quantity of molecular information available to scientists. Research in the BIB Program will include systems biology, computational modeling of regulatory and metabolic networks, docking, comparative genomics, protein design, genomic and proteomic biotechnology, microarray engineering and analysis, pharmacogenomics, structural biology, large scale modeling of biological systems, RNA, computational studies of cancer and neurological disorders and functional genomics, synthetic gene networks and molecular computing and genetics. This collection showcases the journal articles and other publications and presentations written by faculty and researchers of the Program in Bioinformatics and Integrative Biology.

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Publications from 2017

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Discovering cis-Regulatory Motifs, Jui-Hung Hung and Zhiping Weng

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Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding), Jui-Hung Hung and Zhiping Weng

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Mapping Short Sequence Reads to a Reference Genome, Jui-Hung Hung and Zhiping Weng

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Motif Finding, Jui-Hung Hung and Zhiping Weng

Publications from 2016

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How structural adaptability exists alongside HLA-A2 bias in the human alphabeta TCR repertoire, Sydney J. Blevins, Brian G. Pierce, Nishant K. Singh, Timothy P. Riley, Yuan Wang, Timothy T. Spear, Michael I. Nishimura, Zhiping Weng, and Brian M. Baker

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A benchmark testing ground for integrating homology modeling and protein docking, Tanggis Bohnuud, Lingqi Luo, Shoshana J. Wodak, Alexandre M. J. J. Bonvin, Zhiping Weng, Sandor Vajda, Ora Schueler-Furman, and Dima Kozakov

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Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs, Jenny Chen, Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Mitchell Guttman, Jacob H. Hanna, Aviv Regev, and Manuel Garber

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End Sequence Analysis ToolKit (ESAT) expands the extractable from single cell RNA-seq experiments, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim Artyomov, and Manuel Garber

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Unexpected role of interferon-gamma in regulating neuronal connectivity and social behaviour, Anthony J. Filiano, Yang Xu, Nicholas J. Tustison, Rachel L. Marsh, Wendy Baker, Igor Smirnov, Christopher C. Overall, Sachin P. Gadani, Stephen D. Turner, Zhiping Weng, Sayeda Najamussaha Peerzade, Hao Chen, Kevin S. Lee, Michael M. Scott, Mark P. Beenhakker, Vladimir Litvak, and Jonathan Kipnis

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Genomic insights into the Ixodes scapularis tick vector of Lyme disease, Monika Gulia-Nuss,; Daniel R. Caffrey; Neal S. Silverman; Adam R. Wespiser; and Catherine A. Hill

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Forward genetic screen of human transposase genomic rearrangements, Anton G. Henssen, Eileen Jiang, Jiali Zhuang, Luca Pinello, Nicholas D. Socci, Richard Koche, Mithat Gonen, Camila M. Villasante, Scott A. Armstrong, Daniel E. Bauer, Zhiping Weng, and Alex Kentsis

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Analysis of Microarray and RNA-seq Expression Profiling Data, Jui-Hung Hung and Zhiping Weng

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Analyzing Microarray Data, Jui-Hung Hung and Zhiping Weng

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Data Formats in Bioinformatics, Jui-Hung Hung and Zhiping Weng

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Designing Polymerase Chain Reaction Primers Using Primer3Plus, Jui-Hung Hung and Zhiping Weng

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Mapping Billions of Short Reads to a Reference Genome, Jui-Hung Hung and Zhiping Weng

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Peak-Finding Algorithms, Jui-Hung Hung and Zhiping Weng

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Sequence Alignment and Homology Search, Jui-Hung Hung and Zhiping Weng

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Sequence Alignment and Homology Search with BLAST and ClustalW, Jui-Hung Hung and Zhiping Weng

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Visualizing Genomic Annotations with the UCSC Genome Browser, Jui-Hung Hung and Zhiping Weng

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A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance, Li Jiang, Ping Liu, Claudia Bank, Nicholas Renzette, Kristina L. Prachanronarong, L. Safak Yilmaz, Daniel R. Caffrey, Konstantin B. Zeldovich, Celia A. Schiffer, Timothy F. Kowalik, Jeffrey D. Jensen, Robert W. Finberg, Jennifer P. Wang, and Daniel N. Bolon

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Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment, Marc F. Lensink, Zhiping Weng, Thom Vreven, Brian G. Pierce, and Tyler M. Borrman

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Accurate Prediction of Transposon-Derived piRNAs by Integrating Various Sequential and Physicochemical Features, Longqiang Luo, Dingfang Li, Wen Zhang, Shikui Tu, Xiaopeng Zhu, and Gang Tian

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A deep sequencing tool for partitioning clearance rates following antimalarial treatment in polyclonal infections, Nicole Mideo, Jeffrey A. Bailey, Nicholas J. Hathaway, Billy Ngasala, David L. Saunders, Chanthap Lon, Oksana Kharabora, Andrew Jamnik, Sujata Balasubramanian, Anders Bjorkman, Andreas Martensson, Steven R. Meshnick, Andrew F. Read, and Jonathan J. Juliano

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Malaria - how this parasitic infection aids and abets EBV-associated Burkitt lymphomagenesis, Ann M. Moormann and Jeffrey A. Bailey

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RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data., Mercedeh Movassagh, Nawaf Alomran, Prakriti Mudvari, Merve Dede, Cem Dede, Kamran Kowsari, Paula Restrepo, Edmund Cauley, Sonali Bahl, Muzi Li, Wesley Waterhouse, Krasimira Tsaneva-Atanasova, Nathan Edwards, and Anelia Horvath

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Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase, Kristina L. Prachanronarong, Aysegul Ozen, Kelly Thayer, L. Safak Yilmaz, Konstantin B. Zeldovich, Daniel N. Bolon, Timothy F. Kowalik, Jeffrey D. Jensen, Robert W. Finberg, Jennifer P. Wang, Nese Kurt Yilmaz, and Celia A. Schiffer

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A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces, Timothy P. Riley, Cory M. Ayres, Lance M. Hellman, Nishant K. Singh, Michael Cosiano, Jennifer M. Cimons, Michael J. Anderson, Kurt H. Piepenbrink, Brian G. Pierce, Zhiping Weng, and Brian M. Baker

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Computational Modeling of T Cell Receptor Complexes, Timothy P. Riley, Nishant K. Singh, Brian G. Pierce, Zhiping Weng, and Brian M. Baker

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Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals, Upasna Sharma, Colin C. Conine, Jeremy Shea, Ana Boskovic, Alan G. Derr, Xin Y. Bing, Clemence Belleannee, Alper Kucukural, Ryan W. Serra, Fengyun Sun, Lina Song, Benjamin R. Carone, Emiliano P. Ricci, Xin Z. Li, Lucas Fauquier, Melissa J. Moore, Robert Sullivan, Craig C. Mello, Manuel Garber, and Oliver J. Rando

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Genome-wide CRISPR Screen Identifies Regulators of MAPK as Suppressors of Liver Tumors in Mice, Chun-Qing Song, Yingxiang Li, Haiwei Mou, Jill Moore, Angela I. Park, Soren Hough, Zachary Kennedy, Andrew H. Fischer, Darryl Conte Jr., Zhiping Weng, and Wen Xue

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The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans, Wen Tang, Shikui Tu, Heng-Chi Lee, Zhiping Weng, and Craig C. Mello

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DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data, Junko Tsuji and Zhiping Weng

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Performance of ZDOCK and IRAD in CAPRI rounds 28-34, Thom Vreven, Brian G. Pierce, Tyler M. Borrman, and Zhiping Weng

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Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo, Hao Yin, Chun-Qing Song, Joseph R. Dorkin, Lihua Julie Zhu, Yingxiang Li, Qiongqiong Wu, Angela I. Park, Junghoon Yang, Sneha Suresh, Aizhan Bizhanova, Ankit Gupta, Mehmet Fatih Bolukbasi, Stephen Walsh, Roman L. Bogorad, Guangping Gao, Zhiping Weng, Yizhou Dong, Victor Koteliansky, Scot A. Wolfe, Robert Langer, Wen Xue, and Daniel G. Anderson

Publications from 2015

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The PsychENCODE project, Schahram Akbarian, Zhiping Weng, Eugenio Mattei, Michael Purcaro, Junko Tsuji, Geetha Senthil, Thomas Lehner, Pamela Sklar, Nenad Sestan, and PsychENCODE Consortium

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Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains, Guang Bai, Iris Cheung, Hennady P. Shulha, Joana E. Coelho, Ping Li, Xianjun Dong, Mira Jakovcevski, Yumei Wang, Anastasia Grigorenko, Yan Jiang, Andrew Hoss, Krupal Patel, Ming Zheng, Evgeny Rogaev, Richard H. Myers, Zhiping Weng, Schahram Akbarian, and Jiang-Fan Chen

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Novel Observations From Next-Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets, David M. Blodgett, Anetta Nowosielska, Shaked Afik, Susanne Pechhold, Anthony J. Cura, Norman J. Kennedy, Soyoung Kim, Alper Kucukural, Roger J. Davis, Sally C. Kent, Dale L. Greiner, Manuel Garber, David M. Harlan, and Philip J. diLorio Jr.

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DNA-binding-domain fusions enhance the targeting range and precision of Cas9, Mehmet Fatih Bolukbasi, Ankit Gupta, Sarah Oikemus, Alan G. Derr, Manuel Garber, Michael H. Brodsky, Lihua Julie Zhu, and Scot A. Wolfe

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Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs, Min-Te Chou, Bo W. Han, Chiung-Po Hsiao, Phillip D. Zamore, Zhiping Weng, and Jui-Hung Hung

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The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease, Xianjun Dong, Junko Tsuji, Adam Labadorf, Panos Roussos, Jiang-Fan Chen, Richard H. Myers, Schahram Akbarian, and Zhiping Weng

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Glycolytic enzymes localize to ribonucleoprotein granules in Drosophila germ cells, bind Tudor and protect from transposable elements, Ming Gao, Travis Thomson, T Michael Creed, Shikui Tu, Sudan N. Loganathan, Christina A. Jackson, Patrick McCluskey, Yanyan Lin, Scott E. Collier, Zhiping Weng, Paul Lasko, Melanie D. Ohi, and Alexey L. Arkov

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Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production, Bo W. Han, Wei Wang, Chengjian Li, Zhiping Weng, and Phillip D. Zamore

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piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing, Bo W. Han, Wei Wang, Phillip D. Zamore, and Zhiping Weng

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miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement, Andrew G. Hoss, Adam Labadorf, Jeanne C. Latourelle, Vinay K. Kartha, Tiffany C. Hadzi, James F. Gusella, Marcy E. MacDonald, Jiang-Fan Chen, Schahram Akbarian, Zhiping Weng, Jean Paul Vonsattel, and Richard H. Myers

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Functional annotation of native enhancers with a Cas9-histone demethylase fusion, Nicola A. Kearns, Hannah Pham, Barbara Tabak, Ryan M. J. Genga, Noah J. Silverstein, Manuel Garber, and Rene Maehr

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RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression, Adam Labadorf, Andrew Hoss, Valentina Lagomarsino, Jeanne C. Latourelle, Tiffany C. Hadzi, Joli Bregu, Marcy E. MacDonald, James F. Gusella, Jiang-Fan Chen, Schahram Akbarian, Zhiping Weng, and Richard H. Myers

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Using Amplicon Deep Sequencing to Detect Genetic Signatures of Plasmodium vivax Relapse, Jessica T. Lin, Nicholas J. Hathaway, David L. Saunders, Chanthap Lon, Sujata Balasubramanian, Oksana Kharabora, Panita Gosi, Sabaithip Sriwichai, Laurel Kartchner, Char Meng Chuor, Prom Satharath, Charlotte Lanteri, Jeffrey A. Bailey, and Jonathan J. Juliano

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A versatile reporter system for CRISPR-mediated chromosomal rearrangements, Yingxiang Li, Angela I. Park, Haiwei Mou, Cansu Colpan, Aizhan Bizhanova, Elliot Akama-Garren, Nik Joshi, Eric A. Hendrickson, David Feldser, Hao Yin, Daniel G. Anderson, Tyler Jacks, Zhiping Weng, and Wen Xue

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Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified, Georgi K. Marinov, Jie Wang, Dominik Handler, Barbara J. Wold, Zhiping Weng, Gregory J. Hannon, Alexei A. Aravin, Phillip D. Zamore, Julius Brennecke, and Katalin Fejes Toth

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Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome, Jeremy Shea, Ryan W. Serra, Benjamin R. Carone, Hennady P. Shulha, Alper Kucukural, Michael Ziller, Markus Vallaster, Hongcang Gu, Andrew R. Tapper, Paul D. Gardner, Alexander Meissner, Manuel Garber, and Oliver J. Rando

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Simultaneous generation of many RNA-seq libraries in a single reaction, Alexander A. Shishkin, Georgia Giannoukos, Alper Kucukural, Dawn Ciulla, Michele Busby, Christine Surka, Jenny Chen, Roby P. Bhattacharyya, Robert F. Rudy, Milesh M. Patel, Nathaniel Novod, Deborah T. Hung, Andreas Gnirke, Manuel Garber, Mitchell Guttman, and Jonathan Livny

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Absence of Putative Artemisinin Resistance Mutations Among Plasmodium falciparum in Sub-Saharan Africa: A Molecular Epidemiologic Study, Steve M. Taylor, Derrick K. DeConti, Ann M. Moormann, Jeffrey A. Bailey, and Jonathan J. Juliano

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Differential Toxicity of Nuclear RNA Foci versus Dipeptide Repeat Proteins in a Drosophila Model of C9ORF72 FTD/ALS, Helene Tran, Sandra Almeida, Jill Moore, Tania F. Gendron, UmaDevi Chalasani, Yubing Lu, Xing Du, Jeffrey A. Nickerson, Leonard Petrucelli, Zhiping Weng, and Fen-Biao Gao

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Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells, Daniel J. Trombly, Troy W. Whitfield, Srivatsan Padmanabhan, Jonathan A. R. Gordon, Jane B. Lian, Andre J. Van Wijnen, Kaleem Zaidi, Janet L. Stein, and Gary S. Stein

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Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data, Junko Tsuji and Zhiping Weng

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Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes, Shikui Tu, Monica Z. Wu, Jie Wang, Asher D. Cutter, Zhiping Weng, and Julie M. Claycomb

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Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex, Will Van Treuren, Loganathan Ponnusamy, R Jory Brinkerhoff, Antonio Gonzalez, Christian M. Parobek, Jonathan J. Juliano, Theodore G. Andreadis, Richard C. Falco, Lorenza Beati Ziegler, Nicholas J. Hathaway, Corinna Keeler, Michael Emch, Jeffrey A. Bailey, R. Michael Roe, Charles S. Apperson, Rob Knight, and Steven R. Meshnick

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Massively parallel sampling of lattice proteins reveals foundations of thermal adaptation, Sergey V. Venev and Konstantin B. Zeldovich

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Jagged 1 Rescues the Duchenne Muscular Dystrophy Phenotype, Natassia M. Vieira, Ingegerd Elvers, Matthew S. Alexander, Yuri B. Moreira, Alal Eran, Juliana P. Gomes, Jamie L. Marshall, Elinor K. Karlsson, Sergio Verjovski-Almeida, Kerstin Lindblad-Toh, Louis M. Kunkel, and Mayana Zatz

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Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2, Thom Vreven, Iain H. Moal, Anna Vangone, Brian G. Pierce, Panagiotis L. Kastritis, Mieczyslaw Torchala, Raphael Chaleil, Brian Jimenez-Garcia, Paul A. Bates, Juan Fernandez-Recio, Alexandre M. J. J. Bonvin, and Zhiping Weng

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Adenovirus-Mediated Somatic Genome Editing of Pten by CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses, Dan Wang, Haiwei Mou, Shaoyong Li, Yingxiang Li, Soren Hough, Karen Tran, Jia Li, Hao Yin, Daniel G. Anderson, Erik J. Sontheimer, Zhiping Weng, Guangping Gao, and Wen Xue

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Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms, Wei Wang, Bo W. Han, Cindy Tipping, Daniel Tianfang Ge, Zhao Zhang, Zhiping Weng, and Phillip D. Zamore

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Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment, Konstantin B. Zeldovich, Ping Liu, Nicholas Renzette, Matthieu Foll, Serena T. Pham, Sergey V. Venev, Glen R. Gallagher, Daniel N. Bolon, Evelyn A. Kurt-Jones, Jeffrey D. Jensen, Daniel R. Caffrey, Celia A. Schiffer, Timothy F. Kowalik, Jennifer P. Wang, and Robert W. Finberg

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Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes, Jiali Zhuang and Zhiping Weng

Publications from 2014

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High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody, Gregory J. Babcock, Sowmya Iyer, Heidi L. Smith, Yan Wang, Kirk Rowley, Donna M. Ambrosino, Phillip D. Zamore, Brian G. Pierce, Deborah C. Molrine, and Zhiping Weng

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High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm, Benjamin R. Carone, Jui-Hung Hung, Sarah J. Hainer, Min-Te Chou, Dawn M. Carone, Zhiping Weng, Thomas G. Fazzio, and Oliver J. Rando

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Principles of regulatory information conservation between mouse and human, Yong Cheng, Zhihai Ma, Bong-Hyun Kim, Weisheng Wu, Philip Cayting, Alan P. Boyle, Vasavi Sundaram, Xiaoyun Xing, Nergiz Dogan, Jingjing Li, Ghia Euskirchen, Shin Lin, Yiing Lin, Axel Visel, Trupti Kawli, Xinqiong Yang, Dorrelyn Patacsil, Cheryl A. Keller, Belinda Giardine, Anshul Kundaje, Ting Wang, Len A. Pennacchio, Zhiping Weng, Ross C. Hardison, and Michael P. Snyder

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Endogenous U2.U5.U6 snRNA complexes in S. pombe are intron lariat spliceosomes, Weijun Chen, Hennady P. Shulha, Ami Ashar-Patel, Jing Yang, Karin M. Green, Charles C. Query, Nicholas R. Rhind, Zhiping Weng, and Melissa J. Moore

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Influenza virus drug resistance: a time-sampled population genetics perspective, Matthieu Foll, Yu Ping Poh, Nicholas Renzette, Anna Ferrer Admetlla, Claudia Bank, Hyunjin Shim, Anna Sapfo Malaspinas, Gregory Ewing, Ping Liu, Daniel Wegmann, Daniel R. Caffrey, Konstantin B. Zeldovich, Daniel N. A. Bolon, Jennifer Wang, Timothy F. Kowalik, Celia A. Schiffer, Robert W. Finberg, and Jeffrey D. Jensen

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Backbone flexibility of CDR3 and immune recognition of antigens, Jaafar N. Haidar, Wei Zhu, Jacqueline Lypowy, Brian G. Pierce, Amtul Bari, Kris Persaud, Xenia Luna, Marshall Snavely, Dale Ludwig, and Zhiping Weng

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MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis, Andrew G. Hoss, Vinay K. Kartha, Xianjun Dong, Jeanne C. Latourelle, Alexandra Dumitriu, Tiffany C. Hadzi, Marcy E. Macdonald, James F. Gusella, Schahram Akbarian, Jiang-Fan Chen, Zhiping Weng, and Richard H. Myers

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Binding interface prediction by combining protein-protein docking results, Howook Hwang, Thom Vreven, and Zhiping Weng

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Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells, Nicola A. Kearns, Ryan M. J. Genga, Metewo Selase Enuameh, Manuel Garber, Scot A. Wolfe, and Rene Maehr

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Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease, Manolis Kellis, Job Dekker, Zhiping Weng, and Ross C. Hardison (Proceedings of the National Academy of Sciences of the United States of America, 8-19-2014)

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Defining functional DNA elements in the human genome, Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Job Dekker, Zhiping Weng, Ross C. Hardison, and ENCODE Project Consortium (Proceedings of the National Academy of Sciences of the United States of America, 4-29-2014)

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Blind prediction of interfacial water positions in CAPRI, Marc F. Lensink, Iain H. Moal, Paul A. Bates, Panagiotis L. Kastritis, Adrien S.J. Melquiond, Ezgi Karaca, Christophe Schmitz, Marc van Dijk, Alexandre M.J.J. Bonvin, Miriam Eisenstein, Brian G. Pierce, Howook Hwang, Thom Vreven, and Zhiping Weng

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HIV type 1 (HIV-1) proviral reservoirs decay continuously under sustained virologic control in HIV-1-infected children who received early treatment, Katherine Luzuriaga, Barbara Tabak, Manuel Garber, Ya Hui Chen, Carrie Ziemniak, Margaret M. McManus, Danielle Murray, Matthew Strain, Douglas Richman, Tae-Wook Chun, Coleen K. Cunningham, and Deborah Persaud

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Sickle cell trait is not associated with endemic Burkitt lymphoma: an ethnicity and malaria endemicity-matched case-control study suggests factors controlling EBV may serve as a predictive biomarker for this pediatric cancer, David H. Mulama, Jeffrey A. Bailey, Joslyn Foley, Kiprotich Chelimo, Collins Ouma, Walter G.Z.O. Jura, Juliana A. Otieno, John M. Vulule, and Ann M. Moormann

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Interleukin-6 and interleukin-10 gene promoter polymorphisms and risk of endemic burkitt lymphoma, Cliff I. Oduor, Kiprotich Chelimo, Collins Ouma, David H. Mulama, Joslyn Foley, John M. Vulule, Jeffrey A. Bailey, and Ann M. Moormann

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Differing patterns of selection and geospatial genetic diversity within two leading Plasmodium vivax candidate vaccine antigens, Christian M. Parobek, Jeffrey A. Bailey, Nicholas J. Hathaway, Duong Socheat, William O. Rogers, and Jonathan J. Juliano

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Computational design of the affinity and specificity of a therapeutic T cell receptor, Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, and Brian M. Baker

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Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes, Brian G. Pierce, Thom Vreven, and Zhiping Weng

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ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers, Brian G. Pierce, Kevin Wiehe, Howook Hwang, Bong-Hyun Kim, Thom Vreven, and Zhiping Weng

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On the prospect of identifying adaptive loci in recently bottlenecked populations, Yu-Ping Poh, Vera S. Domingues, Hopi E. Hoekstra, and Jeffrey D. Jensen

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Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro, Nicholas Renzette, Daniel R. Caffrey, Konstantin B. Zeldovich, Ping Liu, Glen R. Gallagher, Daniel Aiello, Alyssa J. Porter, Evelyn A. Kurt-Jones, Daniel N. Bolon, Yu-Ping Poh, Jeffrey D. Jensen, Celia A. Schiffer, Timothy F. Kowalik, Robert W. Finberg, and Jennifer P. Wang

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Epstein-barr virus latent membrane protein 1 genetic variability in peripheral blood B cells and oropharyngeal fluids, Nicholas Renzette, Mohan Somasundaran, Frank E. Brewster, James Coderre, Eric R. Weiss, Margaret M. McManus, Thomas C. Greenough, Barbara Tabak, Manuel Garber, Timothy F. Kowalik, and Katherine Ruiz De Luzuriaga

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Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions, Yutaka Saito, Junko Tsuji, and Toutai Mituyama

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Regulation of histone H3K4 methylation in brain development and disease, Erica Shen, Hennady P. Shulha, Zhiping Weng, and Schahram Akbarian

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Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies, Beatriz Trastoy, Joseph V. Lomino, Brian G. Pierce, Lester G. Carter, Sebastian Gunther, John P. Giddens, Greg A. Snyder, Thomas M. Weiss, Zhiping Weng, Lai-Xi Wang, and Eric J. Sundberg

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Evaluating template-based and template-free protein-protein complex structure prediction, Thom Vreven, Howook Hwang, Brian G. Pierce, and Zhiping Weng

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The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs, Wei Wang, Mayu Yoshikawa, Bo W. Han, Natsuko Izumi, Yukihide Tomari, Zhiping Weng, and Phillip D. Zamore

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Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals, Stefan Washietl, Manolis Kellis, and Manuel Garber

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A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters, Ozlem Yildirim, Jui-Hung Hung, Ryan J. Cedeno, Zhiping Weng, Christopher J. Lengner, and Oliver J. Rando

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Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the Tudor-domain protein Qin, Zhao Zhang, Birgit S. Koppetsch, Jie Wang, Cindy Tipping, Zhiping Weng, William E. Theurkauf, and Phillip D. Zamore

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The HP1 homolog rhino anchors a nuclear complex that suppresses piRNA precursor splicing, Zhao Zhang, Jie Wang, Nadine McGinnis-Schultz, Fan Zhang, Swapnil S. Parhad, Shikui Tu, Thom Vreven, Phillip D. Zamore, Zhiping Weng, and William E. Theurkauf

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TEMP: a computational method for analyzing transposable element polymorphism in populations, Jiali Zhuang, Jie Wang, William E. Theurkauf, and Zhiping Weng

Publications from 2013

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Diversity of T cell epitopes in Plasmodium falciparum circumsporozoite protein likely due to protein-protein interactions, Nagesh R. Aragam, Kelly M. Thayer, Nabi Nge, Irving Hoffman, Francis Martinson, Debbie Kamwendo, Feng-Chang Lin, Colin Sutherland, Jeffrey A. Bailey, and Jonathan J. Juliano

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Hdac6 regulates Tip60-p400 function in stem cells, Poshen B. Chen, Jui-Hung Hung, Taylor L. Hickman, Andrew H. Coles, James F. Carey, Zhiping Weng, Feixia Chu, and Thomas G. Fazzio

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The impact of equilibrium assumptions on tests of selection, Jessica L. Crisci, Yu-Ping Poh, Shivani Mahajan, and Jeffrey D. Jensen