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 2020

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Combining Citizen Science and Genomics to Investigate Tick, Pathogen, and Commensal Microbiome at Single-Tick Resolution, Gaurav Chauhan, Jesse McClure, Jessica Hekman, Patrick W. Marsh, Jeffrey A. Bailey, Rachel F. Daniels, Diane P. Genereux, and Elinor K. Karlsson

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A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods, Jill E. Moore, Henry E. Pratt, Michael J. Purcaro, and Zhiping Weng

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Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans, Deniz M. Ozata, Tianxiong Yu, Haiwei Mou, Ildar Gainetdinov, Cansu Colpan, Katharine Cecchini, Yasin Kaymaz, Pei-Hsuan Wu, Kaili Fan, Alper Kucukural, Zhiping Weng, and Phillip D. Zamore

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Recovery of viable endocrine-specific cells and transcriptomes from human pancreatic islet-engrafted mice, Sambra D. Redick, Linda Leehy, Ann R. Rittenhouse, David M. Blodgett, Alan G. Derr, Alper Kucukural, Manuel Garber, Leonard D. Shultz, Dale L. Greiner, Jennifer P. Wang, David M. Harlan, Rita Bortell, and Agata Jurczyk

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An atlas of cell types in the mammalian epididymis and vas deferens, Vera D. Rinaldi, Elisa Donnard, Kyle Gellatly, Morten Rasmussen, Alper Kucukural, Onur Yukselen, Manuel Garber, Upasna Sharma, and Oliver J. Rando

Publications from 2019

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Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter and giant otter, Annabel C. Beichman, Klaus-Peter Koepfli, Gang Li, William Murphy, Pasha Dobrynin, Sergei Kilver, M. Tim Tinker, Michael J. Murray, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K. Karlsson, Kirk E. Lohmueller, and Robert K. Wayne

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Constrained mutational sampling of amino acids in HIV-1 protease evolution, Jeffrey I. Boucher, Troy W. Whitfield, Ann Dauphin, Gily S. Nachum, Carl Hollins III, Konstantin B. Zeldovich, Ronald Swanstrom, Celia A. Schiffer, Jeremy Luban, and Daniel N. Bolon

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Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals, Nicholas R. Casewell and Elinor K. Karlsson

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Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals, Nicholas R. Casewell, Elinor K. Karlsson, Daniel Petras, Daren C. Card, Vivek Suranse, Alexis M. Mychajliw, David Richards, Ivan Koludarov, Laura-Oana Albulescu, Julien Slagboom, Benjamin-Florian Hempel, Neville M. Ngum, Rosalind J. Kennerley, Jorge L. Brocca, and Gareth Whiteley

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The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria, Daniel Tianfang Ge, Wei Wang, Cindy Tipping, Ildar Gainetdinov, Zhiping Weng, and Phillip D. Zamore

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Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons, Fedor E. Gusev, Anastasia P. Grigorenko, Elena Filippova, Zhiping Weng, Schahram Akbarian, and Evgeny I. Rogaev

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Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia, Fedor E. Gusev, Denis A. Reshetov, Amanda C. Mitchell, Tatiana V. Andreeva, Aslihan Dincer, Anastasia P. Grigorenko, Gennady Fedonin, Tobias Halene, Maria Aliseychik, Elena Filippova, Zhiping Weng, Schahram Akbarian, and Evgeny I. Rogaev

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Molecular Determinants of Epistasis in HIV-1 Protease: Elucidating the Interdependence of L89V and L90M Mutations in Resistance, Mina Henes, Klajdi Kosovrasti, Gordon J. Lockbaum, Florian Leidner, Gily S. Nachum, Ellen A. Nalivaika, Daniel N. Bolon, Nese Kurt Yilmaz, Celia A. Schiffer, and Troy W. Whitfield

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Frequent Loss of IRF2 in Cancers Leads to Immune Evasion through Decreased MHC Class I Antigen Presentation and Increased PD-L1 Expression, Barry Kriegsman, Pranitha Vangala, Benjamin J. Chen, Paul Meraner, Abraham L. Brass, Manuel Garber, and Kenneth L. Rock

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DolphinNext: A Graphical User Interface for Distributed Data Processing of High Throughput Genomics, Alper Kucukural

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DEBrowser: interactive differential expression analysis and visualization tool for count data, Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, and Manuel Garber

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Depletion of TRRAP induces p53-independent senescence in liver cancer by downregulating mitotic genes, Suet-Yan Kwan, Ankur Sheel, Chun-Qing Song, Xiao-Ou Zhang, Tingting Jiang, Hien Dang, Yueying Cao, Deniz M. Ozata, Haiwei Mou, Hao Yin, Zhiping Weng, Xin Wei Wang, and Wen Xue

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Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment, Marc F. Lensink, Thom Vreven, Sweta Vangaveti, Tyler M. Borrman, Zhiping Weng, and Shoshana J. Wodak

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A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types, Maxwell W. Libbrecht, Oscar L. Rodriguez, Zhiping Weng, Jeffrey A. Bilmes, Michael M. Hoffman, and William Stafford Noble

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The History of Farm Foxes Undermines the Animal Domestication Syndrome, Kathryn A. Lord, Greger Larson, Raymond P. Coppinger, and Elinor K. Karlsson

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Nordic OCD and Related Disorders Consortium: Rationale, design, and methods, David Mataix-Cols, Bjarne Hansen, Manuel Mattheisen, Elinor K. Karlsson, Anjene M. Addington, Julia Boberg, Diana R. Djurfeldt, Matthew Halvorsen, Paul Lichtenstein, Stian Solem, Kerstin Lindblad-Toh, Jan Haavik, Gerd Kvale, Christian Ruck, and James J. Crowley

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Comparative Genomics Reveals Shared Mutational Landscape in Canine Hemangiosarcoma and Human Angiosarcoma, Kate Megquier, Elinor K. Karlsson, and Kerstin Lindblad-Toh

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BarkBase: Epigenomic Annotation of Canine Genomes, Kate Megquier, Xue Li, Kathleen Morrill, Brittney Logan, and Elinor K. Karlsson

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Diverse repertoire of human adipocyte subtypes develops from transcriptionally distinct mesenchymal progenitor cells, So Yun Min, Anand Desai, Zinger Yang, Agastya Sharma, Tiffany DeSouza, Ryan Genga, Alper Kucukural, Lawrence M. Lifshitz, Soren Nielsen, Camilla Scheele, Rene Maehr, Manuel Garber, and Silvia Corvera

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Comprehensive Computational Assessment And Evaluation of Epstein Barr virus (EBV) Variations, miRNAs, And EBERs in eBL, AML And Across Cancers, Mercedeh J. Movassagh

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Sensitive detection of EBV microRNAs across cancer spectrum reveals association with decreased survival in adult acute myelocytic leukemia, Mercedeh J. Movassagh, Cliff Oduor, Catherine Forconi, Ann M. Moormann, and Jeffrey A. Bailey

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Adaptive evolution targets a piRNA precursor transcription network, Swapnil S. Parhad, Tianxiong Yu, Gen Zhang, Nicholas P. Rice, Zhiping Weng, and William E. Theurkauf

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Spatial genome exploration in the context of cognitive and neurological disease, Prashanth Rajarajan, Tyler M. Borrman, Will Liao, Sergio Espeso-Gil, Sandhya Chandrasekaran, Yan Jiang, Zhiping Weng, Kristen J. Brennand, and Schahram Akbarian

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HLA Class II Antigen Processing and Presentation Pathway Components Demonstrated by Transcriptome and Protein Analyses of Islet beta-Cells From Donors With Type 1 Diabetes, Mark A. Russell, Sambra D. Redick, David Blodgett, Jenny Aurielle B. Babon, Chaoxing Yang, Sally C. Kent, Alan G. Derr, Alper Kucukural, Manuel Garber, and David M. Harlan

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Plasmodium vivax chloroquine resistance links to pvcrt transcription in a genetic cross, Juliana M. Sa, Derrick K. DeConti, Jeffrey A. Bailey, and Thomas E. Wellems

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Genetic Rescue of Fragile X Syndrome Links FMRP Deficiency to Codon Optimality-Dependent RNA Destabilization, Huan Shu, Elisa Donnard, Botao Liu, and Joel D. Richter

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Integrating ab initio and template-based algorithms for protein-protein complex structure prediction, Sweta Vangaveti, Thom Vreven, Yang Zhang, and Zhiping Weng

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Computational investigation into the fluorescence of luciferin analogues, Thom Vreven and Stephen C. Miller

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Characterizing protein-ligand binding using atomistic simulation and machine learning: Application to drug resistance in HIV-1 protease, Troy W. Whitfield, Debra A. Ragland, Konstantin B. Zeldovich, and Celia A. Schiffer

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The piRNA Response to Retroviral Invasion of the Koala Genome, Tianxiong Yu, Birgit S. Koppetsch, Sara Pagliarani, Stephen Johnston, Noah J. Silverstein, Jeremy Luban, Keith Chappell, Zhiping Weng, and William E. Theurkauf

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Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function, Xiao-Ou Zhang, Thomas R. Gingeras, and Zhiping Weng

Publications from 2018

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Drug-Resistance and Population Structure of Plasmodium falciparum Across the Democratic Republic of Congo Using High-Throughput Molecular Inversion Probes, Ozkan Aydemir, Nicholas J. Hathaway, Patrick W. Marsh, Alice Tran, Thomas Reimonn, and Jeffrey A. Bailey

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The TRIM-NHL protein NHL-2 is a Novel Co-Factor of the CSR-1 and HRDE-1 22G-RNA Pathways, Peter R. Boag, Gregory M. Davis, Shikui Tu, Rhys N. Colson, Joshua W. T. Anderson, Menachem J. Gunzburg, Michelle A. Francisco, Debashish Ray, Tuhin Maity, Monica Z. Wu, Quaid D. Morris, Timothy R. Hughes, Jacqueline A. Wilce, University of Toronto, and Zhiping Weng

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Analysis of the Human Mucosal Response to Cholera Reveals Sustained Activation of Innate Immune Signaling Pathways, Daniel L. Bourque, Diane P. Genereux, Elinor K. Karlsson, Firdausi Qadri, and Jason B. Harris

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Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness, Aneth S. Canale, Sergey V. Venev, Troy W. Whitfield, Daniel R. Caffrey, Wayne A. Marasco, Celia A. Schiffer, Timothy F. Kowalik, Jeffrey D. Jensen, Robert W. Finberg, Konstantin B. Zeldovich, Jennifer P. Wang, and Daniel N. Bolon

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Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster, Timothy Chang, Eugenio Mattei, Ildar Gainetdinov, Cansu Colpan, Zhiping Weng, and Phillip D. Zamore

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Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling, Weijun Chen, Jill E. Moore, Hakan Ozadam, Hennady P. Shulha, Nicholas Rhind, Zhiping Weng, and Melissa J. Moore

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The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans, Gregory M. Davis, Shikui Tu, Jacqueline A. Wilce, Julie M. Claycomb, Zhiping Weng, and Peter R. Boag

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Comparative Analysis of Immune Cells Reveals a Conserved Regulatory Lexicon, Elisa Donnard, Pranitha Vangala, Shaked Afik, Sean M. McCauley, Anetta Nowosielska, Alper Kucukural, Barbara Tabak, Xiaopeng Zhu, William E. Diehl, Patrick McDonel, Nir Yosef, Jeremy Luban, and Manuel Garber

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Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers, Shaliu Fu, Qin Wang, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Kaili Fan, Cuihua Gu, Cizhong Jiang, Ruixin Zhu, Anshul Kundaje, Aiping Lu, and Zhiping Weng

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Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, and Zhiping Weng

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Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, and Zhiping Weng

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The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology, Yu Fu, Yujing Yang, Han Zhang, Gwen Farley, Junling Wang, Kaycee A. Quarles, Zhiping Weng, and Phillip D. Zamore

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Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome, Kiran Girdhar, Gabriel E. Hoffman, Yan Jiang, Leanne Brown, Marija Kundakovic, Mads E. Hauberg, Nancy J. Francoeur, Ying-Chih Wang, Hardik Shah, David H. Kavanagh, Elizabeth Zharovsky, Rivka Jacobov, Jennifer R. Wiseman, Royce Park, Jessica S. Johnson, Bibi S. Kassim, Laura Sloofman, Eugenio Mattei, Zhiping Weng, Solveig K. Sieberts, Mette A. Peters, Brent T. Harris, Barbara K. Lipska, Pamela Sklar, Panos Roussos, and Schahram Akbarian

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America's lost dogs, Linda Goodman and Elinor K. Karlsson

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A suite of computational tools to interrogate sequence data with local haplotype analysis within complex ​Plasmodium​ infections and other microbial mixtures, Nicholas J. Hathaway

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SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing, Nicholas J. Hathaway, Christian M. Parobek, Jonathan J. Juliano, and Jeffrey A. Bailey

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Inhibition of protein arginine methyltransferase 5 enhances hepatic mitochondrial biogenesis, Lei Huang, Jehnan Liu, Xiao-Ou Zhang, Katelyn Sibley, Sonia M. Najjar, Mary M. Lee, and Joae Qiong Wu

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Dynamic placement of the linker histone H1 associated with nucleosome arrangement and gene transcription in early Drosophila embryonic development, Jian Hu, Liang Gu, Youqiong Ye, Meizhu Zheng, Zhu Xu, Jing Lin, Yanhua Du, Mengxue Tian, Lifang Luo, Beibei Wang, Xiaobai Zhang, Zhiping Weng, and Cizhong Jiang

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ZNFX-1 Functions within Perinuclear Nuage to Balance Epigenetic Signals, Takao Ishidate, Ahmet R. Ozturk, Daniel J. Durning, Rita Sharma, En-Zhi Shen, Hao Chen, Meetu Seth, Masaki Shirayama, and Craig C. Mello

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A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types, Maxwell Wing Libbrecht, Oscar Rodriguez, Zhiping Weng, Michael Hoffman, Jeffrey A. Bilmes, and William Stafford Noble

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Pet genomics medicine runs wild, Lisa Moses, Steve Niemi, and Elinor K. Karlsson

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A comprehensive genomic history of extinct and living elephants, Eleftheria Palkopoulou, Elinor K. Karlsson, and David Reich

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Mutations in influenza A virus neuraminidase and hemagglutinin confer resistance against a broadly neutralizing hemagglutinin stem antibody, Kristina L. Prachanronarong, Aneth S. Canale, Ping Liu, Mohan Somasundaran, Shurong Hou, Yu-Ping Poh, Thomas Han, Quan Zhu, Nicholas Renzette, Konstantin B. Zeldovich, Timothy F. Kowalik, Nese Kurt Yilmaz, Jeffrey D. Jensen, Daniel N. Bolon, Wayne A. Marasco, Robert W. Finberg, Celia A. Schiffer, and Jennifer P. Wang

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Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus, Sofia A. Quinodoz, Barbara Tabak, Patrick McDonel, Manuel Garber, and Mitchell Guttman

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Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk, Prashanth Rajarajan, Tyler M. Borrman, Zhiping Weng, and Schahram Akbarian

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The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans, Meetu Seth, Masaki Shirayama, Wen Tang, En-Zhi Shen, Shikui Tu, Heng-Chi Lee, Zhiping Weng, and Craig C. Mello

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Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline, En-Zhi Shen, Hao Chen, Ahmet R. Ozturk, Shikui Tu, Masaki Shirayama, Wen Tang, Yue-He Ding, Si-Yuan Dai, Zhiping Weng, and Craig C. Mello

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In vivo genome editing partially restores alpha1-antitrypsin in a murine model of AAT deficiency, Chun-Qing Song, Dan Wang, Tingting Jiang, Kevin O'Connor, Qiushi Tang, Lingling Cai, Xiangrui Li, Zhiping Weng, Hao Yin, Guangping Gao, Christian Mueller, Terence R. Flotte, and Wen Xue

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Systematic pan-cancer analysis of somatic allele frequency, Liam Spurr, Muzi Li, Nawaf Alomran, Qianqian Zhang, Paula Restrepo, Mercedeh Movassagh, Chris Trenkov, Nerissa Tunnessen, Tatiyana Apanasovich, Keith A. Crandall, Nathan Edwards, and Anelia Horvath

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A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans, Wen Tang, Meetu Seth, Shikui Tu, En-Zhi Shen, Qian Li, Masaki Shirayama, Zhiping Weng, and Craig C. Mello

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Thermophilic Adaptation in Prokaryotes Is Constrained by Metabolic Costs of Proteostasis, Sergey V. Venev and Konstantin B. Zeldovich

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Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking, Thom Vreven, Devin K. Schweppe, Juan D. Chavez, Chad R. Weisbrod, Sayaka Shibata, Chunxiang Zheng, James E. Bruce, and Zhiping Weng

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Comprehensive functional genomic resource and integrative model for the human brain, Daifeng Wang, Eugenio Mattei, Jill E. Moore, Zhiping Weng, Daniel H. Geschwind, James A. Knowles, and Mark B. Gerstein

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HIV-1 unmasks the plasticity of innate lymphoid cells, Yetao Wang, Kyle Gellatly, Alan G. Derr, Smita Jaiswal, Alper Kucukural, Patrick McDonel, Thomas C. Greenough, JeanMarie Houghton, Manuel Garber, and Jeremy Luban

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Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection, Eric R. Weiss, Susanna L. Lamers, Jennifer L. Henderson, Alexandre Melnikov, Mohan Somasundaran, Manuel Garber, Liisa K. Selin, Chad Nusbaum, and Katherine Luzuriaga

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pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans, Wei-Sheng Wu, Wei-Che Huang, Jordan S. Brown, Donglei Zhang, Xiaoyan Song, Hao Chen, Shikui Tu, Zhiping Weng, and Heng-Chi Lee

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Identification of Novel Genetic Variations for Amyotrophic Lateral Sclerosis (ALS), Guang Xu

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The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes, Donglei Zhang, Shikui Tu, Michael Stubna, Wei-Sheng Wu, Wei-Che Huang, Zhiping Weng, and Heng-Chi Lee

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Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin, Gen Zhang, Shikui Tu, Tianxiong Yu, Xiao-Ou Zhang, Swapnil S. Parhad, Zhiping Weng, and William E. Theurkauf

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The temporal landscape of recursive splicing during Pol II transcription elongation in human cells, Xiao-Ou Zhang, Yu Fu, Haiwei Mou, Wen Xue, and Zhiping Weng

Publications from 2017

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Defining the 5 and 3 landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq, Shaked Afik, Osnat Bartok, Maxim N. Artyomov, Alexander A. Shishkin, Sabah Kadri, Mor Hanan, Xiaopeng Zhu, Manuel Garber, and Sebastian Kadener

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FLT1 and transcriptome-wide polyadenylation site (PAS) analysis in preeclampsia, Ami Ashar-Patel, Yasin Kaymaz, Augustine Rajakumar, Jeffrey A. Bailey, S. Ananth Karumanchi, and Melissa J. Moore

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ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes, Tyler M. Borrman, Jennifer M. Cimons, Michael Cosiano, Michael Purcaro, Brian G. Pierce, Brian M. Baker, and Zhiping Weng

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A systems level approach to temporal expression dynamics in Drosophila reveals clusters of long term memory genes, Julianna Bozler, Balint Z. Kacsoh, Hao Chen, William E. Theurkauf, Zhiping Weng, and Giovanni Bosco

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Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data, Srinivas Niranj Chandrasekaran and Charles W. Carter Jr

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Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints, Yvonne H. Chan, Sergey V. Venev, Konstantin B. Zeldovich, and C. Robert Matthews

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Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation, Hsin-Jung Chou, Elisa Donnard, H. Tobias Gustafsson, Manuel Garber, and Oliver J. Rando

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High pathogen burden in childhood promotes the development of unconventional innate-like CD8+ T cells, Yves T. Falanga, Michela Frascoli, Yasin Kaymaz, Catherine Forconi, John Michael Ong'echa, Jeffrey A. Bailey, Leslie J. Berg, and Ann M. Moormann

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PGBD5 promotes site-specific oncogenic mutations in human tumors, Anton G. Henssen, Jiali Zhuang, Zhiping Weng, and Alex Kentsis

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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

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Genomic and Transcriptomic Investigation of Endemic Burkitt Lymphoma and Epstein Barr Virus, Yasin Kaymaz

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Comprehensive Transcriptome and Mutational Profiling of Endemic Burkitt Lymphoma Reveals EBV Type-Specific Differences., Yasin Kaymaz, Cliff I. Oduor, Hongbo Yu, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, and Jeffrey A. Bailey

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Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping, Kyle Klein, Weitao Wang, Tyler M. Borrman, Saki Chan, Denghong Zhang, Zhiping Weng, Alex Hastie, Chunlong Chen, David M. Gilbert, and Nicholas R. Rhind

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The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases, Susanne Krasemann, Yang Xu, Zhiping Weng, Hao Chen, Vladimir Litvak, and Oleg Butovsky

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A deep sequencing approach to estimate Plasmodium falciparum complexity of infection (COI) and explore apical membrane antigen 1 diversity, Robin H. Miller, Nicholas J. Hathaway, Oksana Kharabora, Kashamuka Mwandagalirwa, Antoinette Tshefu, Steven R. Meshnick, Steve M. Taylor, Jonathan J. Juliano, V. Ann Stewart, and Jeffrey A. Bailey

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IRaPPA: information retrieval based integration of biophysical models for protein assembly selection, Iain H. Moal, Didier Barradas-Bautista, Brian Jimenez-Garcia, Mieczyslaw Torchala, Arjan van der Velde, Thom Vreven, Zhiping Weng, Paul A. Bates, and Juan Fernandez-Recio

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Defining a Registry of Candidate Regulatory Elements to Interpret Disease Associated Genetic Variation, Jill E. Moore

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Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis, Haiwei Mou, Jill Moore, Sunil K. Malonia, Yingxiang Li, Deniz M. Ozata, Soren Hough, Chun-Qing Song, Jordan L. Smith, Andrew H. Fischer, Zhiping Weng, Michael R. Green, and Wen Xue

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CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion, Haiwei Mou, Jordan L. Smith, Lingtao Peng, Jill Moore, Xiao-Ou Zhang, Chun-Qing Song, Ankur Sheel, Deniz M. Ozata, Yingxiang Li, Charles P. Emerson Jr., Erik J. Sontheimer, Melissa J. Moore, Zhiping Weng, and Wen Xue

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Surveillance for sulfadoxine-pyrimethamine resistant malaria parasites in the Lake and Southern Zones, Tanzania, using pooling and next-generation sequencing, Jeremiah M. Ngondi, Nicholas J. Hathaway, Jeffrey A. Bailey, and Julie Gutman

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Coxsackievirus-Induced Proteomic Alterations in Primary Human Islets Provide Insights for the Etiology of Diabetes, Julius O. Nyalwidhe, Glen R. Gallagher, Lindsey M. Glenn, Margaret A. Morris, Pranitha Vangala, Agata Jurczyk, Rita Bortell, David M. Harlan, Jennifer P. Wang, and Jerry L. Nadler