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 2013

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Genome-wide assessment of post-transcriptional control in the fly brain, Shaul Mezan, Reut Ashwal-Fluss, Rom Shenhav, Manuel Garber, and Sebastian Kadener

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Ahead of the curve: next generation estimators of drug resistance in malaria infections, Nicole Mideo, David A. Kennedy, Jane M. Carlton, Jeffrey A. Bailey, Jonathan J. Juliano, and Andrew F. Read

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Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions, Rocco Moretti, Sarel J. Fleishman, Rudi Agius, Mieczyslaw Torchala, Paul A. Bates, Panagiotis L. Kastritis, Joao P.G.L.M Rodrigues, Mikael Trellet, Alexandre M.J.J. Bonvin, Meng Cui, Brian G. Pierce, Howook Hwang, Thom Vreven, Zhiping Weng, and David Baker

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Transposition-driven genomic heterogeneity in the Drosophila brain, Paola N. Perrat, Shamik DasGupta, Jie Wang, William E. Theurkauf, Zhiping Weng, Michael Rosbash, and Scott Waddell

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The Missing Heritability in T1D and Potential New Targets for Prevention, Brian G. Pierce, Ryan Eberwine, Janelle A. Noble, Michael Habib, Hennady P. Shulha, Zhiping Weng, Elizabeth P. Blankenhorn, and John P. Mordes

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A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes, Brian G. Pierce and Zhiping Weng

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Analyses of the effects of all ubiquitin point mutants on yeast growth rate, Benjamin P. Roscoe, Kelly M. Thayer, Konstantin B. Zeldovich, David Fushman, and Daniel N. A. Bolon

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Coordinated cell type-specific epigenetic remodeling in prefrontal cortex begins before birth and continues into early adulthood, Hennady P. Shulha, Iris Cheung, Yin Guo, Schahram Akbarian, and Zhiping Weng

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Recurrent and recent selective sweeps in the piRNA pathway, Alfred Simkin, Alex Wong, Yu-Ping Poh, William E. Theurkauf, and Jeffrey D. Jensen

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Networking development by Boolean logic, Shikui Tu, Thoru Pederson, and Zhiping Weng

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Segment self-repulsion is the major driving force of influenza genome packaging, Sergey V. Venev and Konstantin B. Zeldovich

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Exploring angular distance in protein-protein docking algorithms, Thom Vreven, Howook Hwang, and Zhiping Weng

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Performance of ZDOCK in CAPRI rounds 20-26, Thom Vreven, Brian G. Pierce, Howook Hwang, and Zhiping Weng

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Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium, Jie Wang, Jiali Zhuang, Sowmya Iyer, Xinying Lin, Melissa C. Greven, Bong-Hyun Kim, Jill Moore, Brian G. Pierce, Xianjun Dong, Daniel Virgil, Ewan Birney, Jui-Hung Hung, and Zhiping Weng

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Dynamic Nucleosome Organization at hox Promoters during Zebrafish Embryogenesis, Steven Weicksel, Jia Xu, and Charles G. Sagerstrom

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Rapid reassortment of internal genes in avian influenza A(H7N9) virus, Liangsheng Zhang, Zhenguo Zhang, and Zhiping Weng

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Substitution rates of the internal genes in the novel avian H7N9 influenza virus, Liangsheng Zhang, Zhenguo Zhang, Zhiping Weng, and Weifeng Shi

Publications from 2012

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Understanding transcriptional regulation by integrative analysis of transcription factor binding data, Chao Cheng, Roger Alexander, Rengqiang Min, Jing Leng, Kevin Y. Yip, Joel Rozowsky, Koon-Kiu Yan, Xianjun Dong, Sarah Djebali, Yijun Ruan, Carrie A. Davis, Piero Carninci, Timo Lassman, Thomas R. Gingeras, Roderic Guigo, Ewan Birney, Zhiping Weng, Michael Snyder, and Mark B. Gerstein

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Exploring the DNA-recognition potential of homeodomains, Stephanie W. Chu, Marcus Blaine Noyes, Ryan G. Christensen, Brian G. Pierce, Lihua Julie Zhu, Zhiping Weng, Gary D. Stormo, and Scot A. Wolfe

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Evolution of the Human Genome: Adaptive Changes, Jessica L. Crisci and Jeffrey D. Jensen

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Recent Progress in Polymorphism-Based Population Genetic Inference, Jessica L. Crisci, Yu-Ping Poh, Angela M. Bean, Alfred Simkin, and Jeffrey D. Jensen

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Modeling gene expression using chromatin features in various cellular contexts, Xianjun Dong, Melissa C. Greven, Anshul Kundaje, Sarah Djebali, James B. Brown, Chao Cheng, Thomas R. Gingeras, Mark B. Gerstein, Roderic Guigo, Ewan Birney, and Zhiping Weng

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An integrated encyclopedia of DNA elements in the human genome, Ian Dunham, Ewan Birney, Bryan R. Lajoie, Amartya Sanyal, Xianjun Dong, Melissa Greven, Xinying Lin, Jie Wang, Troy W. Whitfield, Jiali Zhuang, Job Dekker, Zhiping Weng, Gaurav Jain, and ENCODE Project Consortium (Nature, 2012-09-06)

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Dicer partner proteins tune the length of mature miRNAs in flies and mammals, Ryuya Fukunaga, Bo W. Han, Jui-Hung Hung, Jia Xu, Zhiping Weng, and Phillip D. Zamore

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A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals, Manuel Garber and Ido Amit

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Cutting edge: Evidence for a dynamically driven T cell signaling mechanism, William F. Hawse, Matthew M. Champion, Michelle V. Joyce, Lance M. Hellman, Moushumi Hossain, Veronica Ryan, Brian G. Pierce, Zhiping Weng, and Brian M. Baker

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Unsupervised pattern discovery in human chromatin structure through genomic segmentation, Michael M. Hoffman, Orion J. Buske, Jie Wang, Zhiping Weng, Jeff A. Bilmes, and William Stafford Noble

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Gene set enrichment analysis: performance evaluation and usage guidelines, Jui-Hung Hung, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, and Charles Delisi

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Epigenetic signatures of autism: trimethylated H3K4 landscapes in prefrontal neurons, Hennady P. Shulha, Iris Cheung, Catheryne Whittle, Jie Wang, Daniel Virgil, Cong L. Lin, Yin Guo, Andree Lessard, Schahram Akbarian, and Zhiping Weng

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Human-specific histone methylation signatures at transcription start sites in prefrontal neurons, Hennady P. Shulha, Jessica L. Crisci, Denis Reshetov, Jogender S. Tushir, Iris Cheung, Rahul Bharadwaj, Hsin-Jung Chou, Isaac B. Houston, Cyril J. Peter, Amanda C. Mitchell, Wei-Dong Yao, Richard H. Myers, Jiang-Fan Chen, Todd M. Preuss, Evgeny I. Rogaev, Jeffrey D. Jensen, Zhiping Weng, and Schahram Akbarian

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The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus, Guramrit Singh, Alper Kucukural, Can Cenik, John D. Leszyk, Scott A. Shaffer, Zhiping Weng, and Melissa J. Moore

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Prediction of protein-protein binding free energies, Thom Vreven, Howook Hwang, Brian G. Pierce, and Zhiping Weng

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Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors, Jie Wang, Jiali Zhuang, Sowmya Iyer, Xinying Lin, Troy W. Whitfield, Melissa C. Greven, Brian G. Pierce, Xianjun Dong, Anshul Kundaje, Yong Cheng, Oliver J. Rando, Ewan Birney, Richard M. Myers, William S. Noble, Michael Snyder, and Zhiping Weng

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Functional analysis of transcription factor binding sites in human promoters, Troy W. Whitfield, Jie Wang, Patrick J. Collins, E. Christopher Partridge, Shelley Force Aldred, Nathan D. Trinklein, Richard M. Myers, and Zhiping Weng

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Long-term, efficient inhibition of microRNA function in mice using rAAV vectors, Jun Xie, Stefan L. Ameres, Randall H. Friedline, Jui-Hung Hung, Yu Zhang, Qing Xie, Li Zhong, Qin Su, Ran He, Mengxin Li, Huapeng Li, Xin Mu, Hongwei Zhang, Jennifer A. Broderick, Jason K. Kim, Zhiping Weng, Terence R. Flotte, Phillip D. Zamore, and Guangping Gao

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Genome-wide identification and characterization of replication origins by deep sequencing, Jia Xu, Yoshimi Yanagisawa, Alexander M. Tsankov, Christopher Hart, Keita Aoki, Naveen Kommajosyula, Kathleen E. Steinmann, James Bochicchio, Carsten Russ, Aviv Regev, Oliver J. Rando, Chad Nusbaum, Hironori Niki, Patrice Milos, Zhiping Weng, and Nicholas R. Rhind

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UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery, Fan Zhang, Jie Wang, Jia Xu, Zhao Zhang, Birgit S. Koppetsch, Nadine Schultz, Thom Vreven, Carine Meignin, Ilan Davis, Phillip D. Zamore, Zhiping Weng, and William E. Theurkauf

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Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection, Zhao Zhang, William E. Theurkauf, Zhiping Weng, and Phillip D. Zamore

Publications from 2011

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Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins, Stefan L. Ameres, Jui-Hung Hung, Jia Xu, Zhiping Weng, and Phillip D. Zamore

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Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence, Eugene Berezikov, Nicolas Robine, Anastasia Samsonova, Jakub Orzechowski Westholm, Ammar Naqvi, Jui-Hung Hung, Katsutomo Okamura, Qi Dai, Diane Bortolamiol-Becet, Raquel Martin, Yongjun Zhao, Phillip D. Zamore, Gregory J. Hannon, Marco A. Marra, Zhiping Weng, Norbert Perrimon, and Eric C. Lai

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Molecular basis of a million-fold affinity maturation process in a protein-protein interaction, Daniel A. Bonsor, Sandra Postel, Brian G. Pierce, Ningyan Wang, Penny Zhu, Rebecca A. Buonpane, Zhiping Weng, David M. Kranz, and Eric J. Sundberg

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On Characterizing Adaptive Events Unique to Modern Humans, Jessica L. Crisci, Alex Wong, Jeffrey M. Good, and Jeffrey D. Jensen

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Community-wide assessment of protein-interface modeling suggests improvements to design methodology, Sarel J. Fleishman, Howook Hwang, Thom Vreven, Brian G. Pierce, and Zhiping Weng

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Making enhancers from spare parts of the genome, David Fredman, Xianjun Dong, and Boris Lenhard

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The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1, Bo W. Han, Jui-Hung Hung, Zhiping Weng, Phillip D. Zamore, and Stefan L. Ameres

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Experimental illumination of a fitness landscape, Ryan T. Hietpas, Jeffrey D. Jensen, and Daniel N. A. Bolon

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A machine learning approach for the prediction of protein surface loop flexibility, Howook Hwang, Thom Vreven, Troy W. Whitfield, Kevin Wiehe, and Zhiping Weng

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ACT: aggregation and correlation toolbox for analyses of genome tracks, Justin Jee, Joel Rozowsky, Kevin Y. Yip, Lucas Lochovsky, Robert Bjornson, Guoneng Zhong, Zhengdong Zhang, Yutao Fu, Jie Wang, Zhiping Weng, and Mark B. Gerstein

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A structure-based benchmark for protein-protein binding affinity, Panagiotis L. Kastritis, Iain H. Moal, Howook Hwang, Zhiping Weng, Paul A. Bates, Alexandre M. J. J. Bonvin, and Joel Janin

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Adaptation to P element transposon invasion in Drosophila melanogaster, Jaspreet S. Khurana, Jie Wang, Jia Xu, Birgit S. Koppetsch, Travis Thomson, Anetta Nowosielska, Chengjian Li, Phillip D. Zamore, Zhiping Weng, and William E. Theurkauf

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A User's Guide to the Encyclopedia of DNA Elements (ENCODE), Richard M. Meyers, ENCODE Project Consortium, Job Dekker, Bryan R. Lajoie, Amartya Sanyal, Zhiping Weng, Troy W. Whitfield, and Jie Wang

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Accelerating protein docking in ZDOCK using an advanced 3D convolution library, Brian G. Pierce, Yichiro Hourai, and Zhiping Weng

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Extensive genome-wide variability of human cytomegalovirus in congenitally infected infants, Nicholas Renzette, Bornali Bhattacharjee, Jeffrey D. Jensen, Laura L. Gibson, and Timothy F. Kowalik

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On detecting selective sweeps using single genomes, Priyanka Sinha, Aslihan Dincer, Daniel Virgil, Guang Xu, Yu-Ping Poh, and Jeffrey D. Jensen

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Integrating atom-based and residue-based scoring functions for protein-protein docking, Thom Vreven, Howook Hwang, and Zhiping Weng

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MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression, Jun Xie, Qing Xie, Hongwei Zhang, Stefan L. Ameres, Jui-Hung Hung, Qin Su, Ran He, Xin Mu, Seemin Seher Ahmed, Soyeon Park, Hiroki Kato, Chengjian Li, Christian Mueller, Craig C. Mello, Zhiping Weng, Terence R. Flotte, Phillip D. Zamore, and Guangping Gao

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Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells, Ozlem Yildirim, Ruowang Li, Jui-Hung Hung, Poshen B. Chen, Xianjun Dong, Ly-Sha Ee, Zhiping Weng, Oliver J. Rando, and Thomas G. Fazzio

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Heterotypic piRNA Ping-Pong requires qin, a protein with both E3 ligase and Tudor domains, Zhao Zhang, Jia Xu, Birgit S. Koppetsch, Jie Wang, Cindy Tipping, Shengmei Ma, Zhiping Weng, William E. Theurkauf, and Phillip D. Zamore

Publications from 2010

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Target RNA-directed trimming and tailing of small silencing RNAs, Stefan L. Ameres, Michael D. Horwich, Jui-Hung Hung, Jia Xu, Megha Ghildiyal, Zhiping Weng, and Phillip D. Zamore

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Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals, Benjamin R. Carone, Lucas Fauquier, Naomi Habib, Jeremy Shea, Caroline E. Hart, Ruowang Li, Christoph Bock, Chengjian Li, Hongcang Gu, Phillip D. Zamore, Alexander Meissner, Zhiping Weng, Hans A. Hofmann, Nir Friedman, and Oliver J. Rando

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Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex, Iris Cheung, Hennady P. Shulha, Yan Jiang, Anouch Matevossian, Jie Wang, Zhiping Weng, and Schahram Akbarian

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A simple method for improving the specificity of anti-methyl histone antibodies, Caroline M. Connor, Iris Cheung, Andrew Simon, Mira Jakovcevski, Zhiping Weng, and Schahram Akbarian

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Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway, Megha Ghildiyal, Jia Xu, Herve Seitz, Zhiping Weng, and Phillip D. Zamore

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Mutational analysis of the latency-associated nuclear antigen DNA-binding domain of Kaposi's sarcoma-associated herpesvirus reveals structural conservation among gammaherpesvirus origin-binding proteins, Soo-Jin Han, Jianhong Hu, Brian G. Pierce, Zhiping Weng, and Rolf Renne

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Identification of functional modules that correlate with phenotypic difference: the influence of network topology, Jui-Hung Hung, Troy W. Whitfield, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, and Charles Delisi

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Protein-protein docking benchmark version 4.0, Howook Hwang, Thom Vreven, Joel Janin, and Zhiping Weng

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Performance of ZDOCK and ZRANK in CAPRI rounds 13-19, Howook Hwang, Thom Vreven, Brian G. Pierce, Jui-Hung Hung, and Zhiping Weng

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Distinct functions for the Drosophila piRNA pathway in genome maintenance and telomere protection, Jaspreet S. Khurana, Jia Xu, Zhiping Weng, and William E. Theurkauf

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Sequence features that drive human promoter function and tissue specificity, Jane M. Landolin, David S. Johnson, Nathan D. Trinklein, Shelley Force Aldred, Catherine Medina, Hennady P. Shulha, Zhiping Weng, and Richard M. Myers

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Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays, Ben McNally, Alon Singer, Zhiliang Yu, Yingjie Sun, Zhiping Weng, and Amit Meller

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Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells, Zarmik Moqtaderi, Jie Wang, Debasish Raha, Robert J. White, Michael Snyder, Zhiping Weng, and Kevin Struhl

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Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains, Brian G. Pierce, Jaafar N. Haidar, Yong Yu, and Zhiping Weng

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Genome mapping and characterization of the Anopheles gambiae heterochromatin, Maria V. Sharakhova, Phillip George, Irina V. Brusentsova, Scotland C. Leman, Jeffrey A. Bailey, Christopher D. Smith, and Igor V. Sharakhov

Publications from 2009

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Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC, Jaafar N. Haidar, Brian G. Pierce, Yong Yu, Weiwei Tong, Michael Li, and Zhiping Weng

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The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters, Carla Andrea Klattenhoff, Hualin Xi, Chengjian Li, Soohyun Lee, Jia Xu, Jaspreet S. Khurana, Fan Zhang, Nadine Schultz, Birgit S. Koppetsch, Anetta Nowosielska, Herve Seitz, Phillip D. Zamore, Zhiping Weng, and William E. Theurkauf

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Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies, Chengjian Li, Vasily V. Vagin, Soohyun Lee, Jia Xu, Shengmei Ma, Hualin Xi, Herve Seitz, Michael D. Horwich, Monika Syrzycka, Barry M. Honda, Ellen L. W. Kittler, Maria L. Zapp, Carla Andrea Klattenhoff, Nadine Schultz, William E. Theurkauf, Zhiping Weng, and Phillip D. Zamore

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Uncovering multiple molecular targets for caffeine using a drug target validation strategy combining A 2A receptor knockout mice with microarray profiling, Liqun Yu, Joana E. Coelho, Xiaoling Zhang, Yutao Fu, Abigail Tillman, Ulas Karaoz, Bertil B. Fredholm, Zhiping Weng, and Jiang-Fan Chen

Publications from 2008

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The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome, Yutao Fu, Manisha Sinha, Craig L. Peterson, and Zhiping Weng

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Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells, Megha Ghildiyal, Herve Seitz, Michael D. Horwich, Chengjian Li, Tingting Du, Soohyun Lee, Jia Xu, Ellen L. W. Kittler, Maria L. Zapp, Zhiping Weng, and Phillip D. Zamore

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Protein-protein docking benchmark version 3.0, Howook Hwang, Brian G. Pierce, Julian Mintseris, Joel Janin, and Zhiping Weng

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Quantitative analysis of single nucleotide polymorphisms within copy number variation, Soohyun Lee, Simon Kasif, Zhiping Weng, and Charles R. Cantor

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In Silico Meets in Vivo, Zhiping Weng and Roderic Guigo

Publications from 2007

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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, ENCODE Project Consortium, Zhiping Weng, and Job Dekker