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.
Publications from 2018
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
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
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
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
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
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
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
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
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
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
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
A suite of computational tools to interrogate sequence data with local haplotype analysis within complex Plasmodium infections and other microbial mixtures, Nicholas J. Hathaway
SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing, Nicholas J. Hathaway, Christian M. Parobek, Jonathan J. Juliano, and Jeffrey A. Bailey
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
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
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
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
Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus, Sofia A. Quinodoz, Barbara Tabak, Patrick McDonel, Manuel Garber, and Mitchell Guttman
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
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
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
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
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
Thermophilic Adaptation in Prokaryotes Is Constrained by Metabolic Costs of Proteostasis, Sergey V. Venev and Konstantin B. Zeldovich
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
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
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
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
Identification of Novel Genetic Variations for Amyotrophic Lateral Sclerosis (ALS), Guang Xu
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
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
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
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
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
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
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
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
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
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
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
PGBD5 promotes site-specific oncogenic mutations in human tumors, Anton G. Henssen, Jiali Zhuang, Zhiping Weng, and Alex Kentsis
Discovering cis-Regulatory Motifs, Jui-Hung Hung and Zhiping Weng
Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding), Jui-Hung Hung and Zhiping Weng
Mapping Short Sequence Reads to a Reference Genome, Jui-Hung Hung and Zhiping Weng
Motif Finding, Jui-Hung Hung and Zhiping Weng
Genomic and Transcriptomic Investigation of Endemic Burkitt Lymphoma and Epstein Barr Virus, Yasin Kaymaz
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
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
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
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
Defining a Registry of Candidate Regulatory Elements to Interpret Disease Associated Genetic Variation, Jill E. Moore
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
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
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
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
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
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
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
Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery, Swapnil S. Parhad, Shikui Tu, Zhiping Weng, and William E. Theurkauf
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
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
Analysis, Visualization, and Machine Learning of Epigenomic Data, Michael J. Purcaro
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
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
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
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
Performance of ZDOCK and IRAD in CAPRI rounds 28-34, Thom Vreven, Brian G. Pierce, Tyler M. Borrman, and Zhiping Weng
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
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
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
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
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
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
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
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
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
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
Analysis of Microarray and RNA-seq Expression Profiling Data, Jui-Hung Hung and Zhiping Weng
Analyzing Microarray Data, Jui-Hung Hung and Zhiping Weng
Data Formats in Bioinformatics, Jui-Hung Hung and Zhiping Weng
Designing Polymerase Chain Reaction Primers Using Primer3Plus, Jui-Hung Hung and Zhiping Weng
Mapping Billions of Short Reads to a Reference Genome, Jui-Hung Hung and Zhiping Weng
Peak-Finding Algorithms, Jui-Hung Hung and Zhiping Weng
Sequence Alignment and Homology Search, Jui-Hung Hung and Zhiping Weng
Sequence Alignment and Homology Search with BLAST and ClustalW, Jui-Hung Hung and Zhiping Weng
Visualizing Genomic Annotations with the UCSC Genome Browser, Jui-Hung Hung and Zhiping Weng
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
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
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
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
Malaria - how this parasitic infection aids and abets EBV-associated Burkitt lymphomagenesis, Ann M. Moormann and Jeffrey A. Bailey
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
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
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
Computational Modeling of T Cell Receptor Complexes, Timothy P. Riley, Nishant K. Singh, Brian G. Pierce, Zhiping Weng, and Brian M. Baker
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
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
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
DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data, Junko Tsuji and Zhiping Weng