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 2021

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Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics, Houda Belaghzal, Tyler M. Borrman, Andrew D. Stephens, Denis L. Lafontaine, Sergey V. Venev, Zhiping Weng, John F. Marko, and Job Dekker

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Simultaneous profiling of multiple chromatin proteins in the same cells [preprint], Sneha Gopalan, Yuqing Wang, Nicholas W. Harper, Manuel Garber, and Thomas G. Fazzio

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An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants, Johnathan D. Guest, Thom Vreven, Jing Zhou, Iain Moal, Jeliazko R. Jeliazkov, Jeffrey J. Gray, Zhiping Weng, and Brian G. Pierce

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YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation [preprint], Lizhi He, Henry E. Pratt, Fengxiang Wei, Mingshi Gao, Zhiping Weng, and Kevin Struhl

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March Mammal Madness and the power of narrative in science outreach, Katie Hinde and Elinor K. Karlsson

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Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions, Jong Hyuk Kim, Kate Megquier, Rachael Thomas, Aaron L. Sarver, Jung Min. Song, Yoon Tae Kim, Nuojin Cheng, Ashley J. Schulte, Michael A. Linden, Paari Murugan, LeAnn Oseth, Colleen L. Forster, Ingegerd Elvers, Ross Swofford, Jason Turner-Maier, Elinor K. Karlsson, Matthew Breen, Kerstin Lindblad-Toh, and Jaime F. Modiano

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Gaining Insight into Vitiligo Genetics through the Lens of a Large Epidemiologic Study, Ken Okamura, Manuel Garber, and John E. Harris

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The testis-specific transcription factor TCFL5 responds to A-MYB to elaborate the male meiotic program in placental mammals [preprint], Deniz M. Ozata, Tianxiong Yu, Katharine Cecchini, Haiwei Mou, Amena Arif, Cansu Colpan, Adriano Biasini, Ildar Gaitendinov, Dirk G. de Rooij, Zhiping Weng, and Phillip D. Zamore

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Multi-tissue integrative analysis of personal epigenomes [preprint], Joel Rozowsky, Jill E. Moore, Henry E. Pratt, Zhiping Weng, and Mark Gerstein

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The Case for Altruism in Institutional Diagnostic Testing [preprint], Ivan Specht, Kian Sani, Yolanda Botti-Lodovico, Michael Hughes, Kristin Heumann, Amy Bronson, John Marshall, Emily Baron, Eric Parrie, Olivia Glennon, Ben Fry, Andres Colubri, and Pardis C. Sabeti

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Annotation of chromatin states in 66 complete mouse epigenomes during development, Arjan van der Velde, Kaili Fan, Junko Tsuji, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, and Zhiping Weng

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Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes, Tianxiong Yu, Kaili Fan, Deniz M. Ozata, Gen Zhang, Yu Fu, William E. Theurkauf, Phillip D. Zamore, and Zhiping Weng

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A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies, Tianxiong Yu, Xiao Huang, Shengqian Dou, Xiaolu Tang, Shiqi Luo, William E. Theurkauf, Jian Lu, and Zhiping Weng

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Investigating the Potential Roles of SINEs in the Human Genome, Xiao-Ou Zhang, Henry E. Pratt, and Zhiping Weng

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Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs, Yang Zhang, Tuan M. Nguyen, Xiao-Ou Zhang, Limei Wang, Tin Phan, John G. Clohessy, and Pier Paolo Pandolfi

Publications from 2020

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Progressive Cactus is a multiple-genome aligner for the thousand-genome era, Joel Armstrong, Elinor K. Karlsson, Guojie Zhang, and Benedict Paten

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Measuring Stability of 3D Chromatin Conformations and Identifying Neuron Specific Chromatin Loops Associated with Schizophrenia Risk, Tyler M. Borrman

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High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides, Tyler M. Borrman, Brian G. Pierce, Thom Vreven, Brian M. Baker, and Zhiping Weng

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Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults [preprint], Yuming Cao, Zhiru Guo, Pranitha Vangala, Elisa Donnard, Ping Liu, Patrick McDonel, Jose Ordovas Montanes, Alex K. Shalek, Robert W. Finberg, Jennifer P. Wang, and Manuel Garber

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Integrated miRNA-/mRNA-Seq of the Habenulo-Interpeduncular Circuit During Acute Nicotine Withdrawal, Alison P. Casserly, Junko Tsuji, Rubing Zhao-Shea, Ciearra B. Smith, Susanna Molas-Casacuberta, Andrew R. Tapper, Zhiping Weng, and Paul D. Gardner

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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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ORAN: A meta-modeling platform to drive real-life and online outbreak simulations, Andres Colubri

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Preventing Outbreaks through Interactive, Experiential Real-Life Simulations, Andres Colubri, Molly Kemball, Kian Sani, Chloe Boehm, Karen Mutch-Jones, Ben Fry, Todd Brown, and Pardis C. Sabeti

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The meadow jumping mouse genome and transcriptome suggest mechanisms of hibernation [preprint], Qian Cong, Ethan A. Brem, Jing Zhang, Jessica Alfoldi, Jeremy Johnson, Elinor K. Karlsson, Kerstin Lindblad-Toh, Jason L. Malaney, and William J. Israelsen

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Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates, Joana Damas, Elinor K. Karlsson, and Harris A. Lewin

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Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates [preprint], Joana Damas, Elinor K. Karlsson, and Harris A. Lewin

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Single Cell Transcriptomics Reveals Dysregulated Cellular and Molecular Networks in a Fragile X Syndrome model [preprint], Elisa Donnard, Huan Shu, and Manuel Garber

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Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities, Julie A. Dragon, Chris Gates, Shannan Ho Sui, John N. Hutchinson, R. Krishna Murthy Karuturi, Alper Kucukural, Shawn Polson, Alberto Riva, Matthew Lee Settles, Jyothi Thimmapuram, and Stuart S. Levine

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Expanded encyclopaedias of DNA elements in the human and mouse genomes, ENCODE Project Consortium, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Job Dekker, J. Michael Cherry, Richard M. Myers, Bing Ren, Brenton R. Graveley, Mark B. Gerstein, Len A. Pennacchio, Michael P. Snyder, Bradley E. Bernstein, Barbara Wold, Ross C. Hardison, Thomas R. Gingeras, John A. Stamatoyannopoulos, and Zhiping Weng

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Perspectives on ENCODE, ENCODE Project Consortium, Michael P. Snyder, Jill E. Moore, and Zhiping Weng

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A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons, Sergio Espeso-Gil, Tyler M. Borrman, Zhiping Weng, and Schahram Akbarian

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Genetic and Epigenetic Features of Promoters with Ubiquitous Chromatin Accessibility Support Ubiquitous Transcription of Cell-essential Genes [preprint], Kaili Fan, Jill E. Moore, Xiao-Ou Zhang, and Zhiping Weng

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The Tec kinase ITK differentially optimizes NFAT, NF-κB, and MAPK signaling during early T cell activation to regulate graded gene induction [preprint], Michael P. Gallagher, James M. Conley, Pranitha Vangala, Andrea Reboldi, Manuel Garber, and Leslie J. Berg

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Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope, Tingting Jiang, Xiao-Ou Zhang, Yueying Cao, Zhiping Weng, and Wen Xue

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Epstein-Barr Virus Genomes Reveal Population Structure and Type 1 Association with Endemic Burkitt Lymphoma, Yasin Kaymaz, Cliff I. Oduor, Ozkan Aydemir, Micah A. Luftig, Juliana A. Otieno, John Michael. Ong'echa, Jeffrey A. Bailey, and Ann M. Moormann

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An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes, Nathan D. Lawson, Rui Li, Masahiro Shin, Ann S. Grosse, Onur Yukselen, Oliver A. Stone, Alper Kucukural, and Lihua Julie Zhu

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Reduced Neurog3 Gene Dosage Shifts Enteroendocrine Progenitor Toward Goblet Cell Lineage in the Mouse Intestine, Joyce H. Li, Subir Ray, Alper Kucukural, Gerard Gradwohl, and Andrew B. Leiter

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Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale, Xihao Li, Jill E. Moore, Zhiping Weng, and Xihong Lin

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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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Transcriptomic profiling reveals extraordinary diversity of venom peptides in unexplored predatory gastropods of the genus Clavus, Aiping Lu, Maren Watkins, Qing Li, Samuel D. Robinson, Gisela P. Concepcion, Mark Yandell, Zhiping Weng, Baldomero M. Olivera, Helena Safavi-Hemami, and Alexander E. Fedosov

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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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Proteomic and Transcriptional Profiles of Human Stem Cell-Derived beta Cells Following Enteroviral Challenge, Julius O. Nyalwidhe, Agata Jurczyk, Basanthi Satish, Sambra D. Redick, Natasha Qaisar, Melanie I. Trombly, Pranitha Vangala, Riccardo Racicot, Rita Bortell, David M. Harlan, Dale L. Greiner, Michael A. Brehm, Jerry L. Nadler, and Jennifer P. Wang

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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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Adaptive Evolution Targets a piRNA Precursor Transcription Network, Swapnil Parhad, Tianxiong Yu, Gen Zhang, Nicholas P. Rice, Zhiping Weng, and William E. Theurkauf

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The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility, Pei-Hsuan Wu, Yu Fu, Katharine Cecchini, Deniz M. Ozata, Amena Arif, Tianxiong Yu, Cansu Colpan, Ildar Gainetdinov, Zhiping Weng, and Phillip D. Zamore

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LogoJS: a Javascript package for creating sequence logos and embedding them in web applications, Henry E. Pratt and Zhiping Weng

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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 [preprint], Vera D. Rinaldi, Elisa Donnard, Kyle Gellatly, Morten Rasmussen, Alper Kucukural, Onur Yukselen, Manuel Garber, Upasna Sharma, and Oliver J. Rando

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An atlas of cell types in the mouse 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

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FMRP Links Optimal Codons to mRNA stability in Neurons [preprint], Huan Shu, Elisa Donnard, Botao Liu, Ruijia Wang, and Joel D. Richter

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YAP1 withdrawal in hepatoblastoma drives therapeutic differentiation of tumor cells to functional hepatocyte-like cells, Jordan L. Smith, Tomas Rodriguez, Haiwei Mou, Suet-Yan Kwan, Henry E. Pratt, Xiao-Ou Zhang, Yueying Cao, Shun-Qing Liang, Deniz M. Ozata, Tianxiong Yu, Qiangzong Yin, Max Hazeltine, Zhiping Weng, Erik J. Sontheimer, and Wen Xue

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Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors, Yu H. Sun, Jiang Zhu, Li Huitong Xie, Ziwei Li, Rajyalakshmi Meduri, Xiaopeng Zhu, Chi Song, Chen Chen, Emiliano P. Ricci, Zhiping Weng, and Xin Zhiguo Li

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Humanity's Best Friend: A Dog-Centric Approach to Addressing Global Challenges, Naomi Sykes, Elinor K. Karlsson, and Greger Larson

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High-resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death, Junko Tsuji, Travis Thomson, Elizabeth Chan, Christine K. Brown, Julia Oppenheimer, Carol Bigelow, Xianjun Dong, William E. Theurkauf, Zhiping Weng, and Lawrence M. Schwartz

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Role of Cis-regulatory Elements in Transcriptional Regulation: From Evolution to 4D Interactions, Pranitha Vangala

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High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection, Pranitha Vangala, Rachel Murphy, Sofia A. Quinodoz, Kyle J. Gellatly, Patrick E. McDonel, Mitchell Guttman, and Manuel Garber

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Performance of ZDOCK and IRAD in CAPRI rounds 39-45, Thom Vreven, Sweta Vangaveti, Tyler M. Borrman, Jennifer C. Gaines, and Zhiping Weng

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HIV-1-induced cytokines deplete homeostatic innate lymphoid cells and expand TCF7-dependent memory NK cells, Yetao Wang, Lawrence M. Lifshitz, Kyle Gellatly, Sean M. McCauley, Pranitha Vangala, Kyusik Kim, Alan G. Derr, Smita Jaiswal, Alper Kucukural, Patrick McDonel, Thomas C. Greenough, JeanMarie Houghton, Manuel Garber, and Jeremy Luban

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DolphinNext: a distributed data processing platform for high throughput genomics, Onur Yukselen, Osman Turkyilmaz, Ahmet R. Ozturk, Manuel Garber, and Alper Kucukural

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Comprehensive identification of alternative back-splicing in human tissue transcriptomes, Peng Zhang, Xiao-Ou Zhang, Tingting Jiang, Lingling Cai, Xiao Huang, Qi Liu, Dan Li, Aiping Lu, Yan Liu, Wen Xue, Peng Zhang, and Zhiping Weng

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Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity, Xuming Zhou, Elinor K. Karlsson, and Vadim N. Gladyshev

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SARS-CoV-2 Receptor ACE2 Is an Interferon-Stimulated Gene in Human Airway Epithelial Cells and Is Detected in Specific Cell Subsets across Tissues, Carly G. K. Ziegler, Yuming Cao, Zhiru Guo, Jennifer P. Wang, Robert W. Finberg, Manuel Garber, Alex K. Shalek, Jose Ordovas-Montanes, and HCA Lung Biological Network

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A comparative genomics multitool for scientific discovery and conservation, Zoonomia Consortium, Diane P. Genereux, Manuel Garber, Kerstin Lindblad-Toh, and Elinor K. Karlsson

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, 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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Epstein Barr virus genomes reveal population structure and type 1 association with endemic Burkitt lymphoma [preprint], Yasin Kaymaz, Cliff Oduor, Ozkan Aydemir, Micah Luftig, Juliana Otieno, John Michael Ong'echa, Jeffrey A. Bailey, and Ann M. Moormann

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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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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 [preprint], 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 [preprint], 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 [preprint], 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