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 2018

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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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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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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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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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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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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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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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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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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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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

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

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

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Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma, Cliff I. Oduor, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John Michael Ong'echa, Ann M. Moormann, and Jeffrey A. Bailey

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Human and Epstein-Barr Virus miRNA Profiling as Predictive Biomarkers for Endemic Burkitt Lymphoma, Cliff I. Oduor, Mercedeh Movassagh, Yasin Kaymaz, Kiprotich Chelimo, Juliana A. Otieno, John M. Ong'echa, Ann M. Moormann, and Jeffrey A. Bailey

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The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution, Louise Ormond, Ping Liu, Sebastian Matuszewski, Nicholas Renzette, Claudia Bank, Konstantin B. Zeldovich, Daniel N. Bolon, Timothy F. Kowalik, Robert W. Finberg, Jeffrey D. Jensen, and Jennifer P. Wang

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Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery, Swapnil S. Parhad, Shikui Tu, Zhiping Weng, and William E. Theurkauf

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Partner-Drug Resistance and Population Substructuring of Artemisinin-Resistant Plasmodium falciparum in Cambodia, Christian M. Parobek, Jonathan B. Parr, Nicholas F. Brazeau, Chanthap Lon, Suwanna Chaorattanakawee, Panita Gosi, Eric J. Barnett, Lauren D. Norris, Steven R. Meshnick, Michele D. Spring, Charlotte A. Lanteri, Jeffrey A. Bailey, David L. Saunders, Jessica T. Lin, and Jonathan J. Juliano

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Structure-Based Design of Hepatitis C Virus Vaccines That Elicit Neutralizing Antibody Responses to a Conserved Epitope, Brian G. Pierce, Elisabeth N. Boucher, Kurt H. Piepenbrink, Ejemel Monir, Chelsea A. Rapp, William D. Thomas Jr., Eric J. Sundberg, Zhiping Weng, and Yan Wang

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Analysis, Visualization, and Machine Learning of Epigenomic Data, Michael J. Purcaro

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Elucidating the Interdependence of Drug Resistance from Combinations of Mutations, Debra A. Ragland, Troy W. Whitfield, Sook-Kyung Lee, Ronald Swanstrom, Konstantin B. Zeldovich, Nese Kurt Yilmaz, and Celia A. Schiffer

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Overexpressed somatic alleles are enriched in functional elements in Breast Cancer, Paula Restrepo, Mercedeh Movassagh, Nawaf Alomran, Christian Miller, Muzi Li, Chris Trenkov, Yulian Manchev, Sonali Bahl, Stephanie Warnken, Liam Spurr, Tatiyana Apanasovich, Keith Crandall, Nathan Edwards, and Anelia Horvath

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Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes, Nishant K. Singh, Timothy P. Riley, Sarah Catherine B. Baker, Tyler M. Borrman, Zhiping Weng, and Brian M. Baker

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Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase 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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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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Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods, Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, and Zhiping Weng

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GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases, Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Herve Pages, Alper Kucukural, Manuel Garber, and Scot A. Wolfe

Publications from 2016

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An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy, Claudia Bank, Nicholas Renzette, Ping Liu, Sebastian Matuszewski, Hyunjin Shim, Matthieu Foll, Daniel N. Bolon, Konstantin B. Zeldovich, Timothy F. Kowalik, Robert W. Finberg, Jennifer P. Wang, and Jeffrey D. Jensen

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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 information from single-cell RNA-seq data, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David M. Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim N. 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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RSQ: a statistical method for quantification of isoform-specific structurome using transcriptome-wide structural profiling data, Yunfei Wang, University of Texas at Dallas, Xiaopeng Zhu, Ming Sun, Yong Chen, Michael Q. Zhang, University of Texas at Dallas, Yiwen Chen, Shikui Tu, Qi Dai, Haozhe Wang, and Boyang Bai

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High Epstein-Barr Virus Load and Genomic Diversity Are Associated with Generation of gp350-Specific Neutralizing Antibodies following Acute Infectious Mononucleosis, Eric R. Weiss, Galit Alter, Javier Gordon Ogembo, Jennifer L. Henderson, Barbara Tabak, Yasin Bakis, Mohan Somasundaran, Manuel Garber, Liisa K. Selin, and Katherine Luzuriaga

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

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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