Publications by authors named "Zhiping Weng"

100Publications

HIGH RESOLUTION ANALYSIS OF DIFFERENTIAL GENE EXPRESSION DURING SKELETAL MUSCLE ATROPHY AND PROGRAMMED CELL DEATH.

Physiol Genomics 2020 Sep 14. Epub 2020 Sep 14.

Department of Biology, Morrill Science Center, University of Massachusetts, Amherst, Massachusetts, United States.

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http://dx.doi.org/10.1152/physiolgenomics.00047.2020DOI Listing
September 2020

The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility.

Nat Genet 2020 07 29;52(7):728-739. Epub 2020 Jun 29.

Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.

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http://dx.doi.org/10.1038/s41588-020-0657-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383350PMC
July 2020

LogoJS: a Javascript package for creating sequence logos and embedding them in web applications.

Bioinformatics 2020 Jun;36(11):3573-3575

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1093/bioinformatics/btaa192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267833PMC
June 2020

Adaptive Evolution Targets a piRNA Precursor Transcription Network.

Cell Rep 2020 02;30(8):2672-2685.e5

Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.01.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061269PMC
February 2020

Author Correction: Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors.

Nat Cell Biol 2020 03;22(3):353

Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA.

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http://dx.doi.org/10.1038/s41556-020-0482-3DOI Listing
March 2020

Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors.

Nat Cell Biol 2020 02 3;22(2):200-212. Epub 2020 Feb 3.

Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA.

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http://dx.doi.org/10.1038/s41556-019-0457-4DOI Listing
February 2020

Performance of ZDOCK and IRAD in CAPRI rounds 39-45.

Proteins 2020 08 8;88(8):1050-1054. Epub 2020 Feb 8.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.

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http://dx.doi.org/10.1002/prot.25873DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7374054PMC
August 2020

Comprehensive identification of alternative back-splicing in human tissue transcriptomes.

Nucleic Acids Res 2020 02;48(4):1779-1789

Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.

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http://dx.doi.org/10.1093/nar/gkaa005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7038940PMC
February 2020

A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods.

Genome Biol 2020 01 22;21(1):17. Epub 2020 Jan 22.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.

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http://dx.doi.org/10.1186/s13059-019-1924-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977301PMC
January 2020

Integrated miRNA-/mRNA-Seq of the Habenulo-Interpeduncular Circuit During Acute Nicotine Withdrawal.

Sci Rep 2020 01 21;10(1):813. Epub 2020 Jan 21.

Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, University of Massachusetts Medical School, Massachusetts, USA.

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http://dx.doi.org/10.1038/s41598-020-57907-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6972841PMC
January 2020

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.

Authors:
Marc F Lensink Guillaume Brysbaert Nurul Nadzirin Sameer Velankar Raphaël A G Chaleil Tereza Gerguri Paul A Bates Elodie Laine Alessandra Carbone Sergei Grudinin Ren Kong Ran-Ran Liu Xi-Ming Xu Hang Shi Shan Chang Miriam Eisenstein Agnieszka Karczynska Cezary Czaplewski Emilia Lubecka Agnieszka Lipska Paweł Krupa Magdalena Mozolewska Łukasz Golon Sergey Samsonov Adam Liwo Silvia Crivelli Guillaume Pagès Mikhail Karasikov Maria Kadukova Yumeng Yan Sheng-You Huang Mireia Rosell Luis A Rodríguez-Lumbreras Miguel Romero-Durana Lucía Díaz-Bueno Juan Fernandez-Recio Charles Christoffer Genki Terashi Woong-Hee Shin Tunde Aderinwale Sai Raghavendra Maddhuri Venkata Subraman Daisuke Kihara Dima Kozakov Sandor Vajda Kathryn Porter Dzmitry Padhorny Israel Desta Dmitri Beglov Mikhail Ignatov Sergey Kotelnikov Iain H Moal David W Ritchie Isaure Chauvot de Beauchêne Bernard Maigret Marie-Dominique Devignes Maria E Ruiz Echartea Didier Barradas-Bautista Zhen Cao Luigi Cavallo Romina Oliva Yue Cao Yang Shen Minkyung Baek Taeyong Park Hyeonuk Woo Chaok Seok Merav Braitbard Lirane Bitton Dina Scheidman-Duhovny Justas Dapkūnas Kliment Olechnovič Česlovas Venclovas Petras J Kundrotas Saveliy Belkin Devlina Chakravarty Varsha D Badal Ilya A Vakser Thom Vreven Sweta Vangaveti Tyler Borrman Zhiping Weng Johnathan D Guest Ragul Gowthaman Brian G Pierce Xianjin Xu Rui Duan Liming Qiu Jie Hou Benjamin Ryan Merideth Zhiwei Ma Jianlin Cheng Xiaoqin Zou Panagiotis I Koukos Jorge Roel-Touris Francesco Ambrosetti Cunliang Geng Jörg Schaarschmidt Mikael E Trellet Adrien S J Melquiond Li Xue Brian Jiménez-García Charlotte W van Noort Rodrigo V Honorato Alexandre M J J Bonvin Shoshana J Wodak

Proteins 2019 12 25;87(12):1200-1221. Epub 2019 Oct 25.

VIB Structural Biology Research Center, VUB, Brussels, Belgium.

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http://dx.doi.org/10.1002/prot.25838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274794PMC
December 2019

The piRNA Response to Retroviral Invasion of the Koala Genome.

Cell 2019 10 10;179(3):632-643.e12. Epub 2019 Oct 10.

Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800666PMC
October 2019

Genome-wide analysis of polymerase III-transcribed elements suggests cell-type-specific enhancer function.

Genome Res 2019 09 14;29(9):1402-1414. Epub 2019 Aug 14.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

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http://dx.doi.org/10.1101/gr.249789.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6724667PMC
September 2019

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.

Bioinformatics 2020 02;36(3):751-757

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz623DOI Listing
February 2020

Spatial genome exploration in the context of cognitive and neurological disease.

Curr Opin Neurobiol 2019 12 27;59:112-119. Epub 2019 Jun 27.

Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.conb.2019.05.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6889018PMC
December 2019

The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria.

Mol Cell 2019 06 7;74(5):982-995.e6. Epub 2019 May 7.

RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2019.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636356PMC
June 2019

Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin.

Cell Rep 2018 09;24(13):3413-3422.e4

Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.08.081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6235161PMC
September 2018

The temporal landscape of recursive splicing during Pol II transcription elongation in human cells.

PLoS Genet 2018 08 27;14(8):e1007579. Epub 2018 Aug 27.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6110456PMC
August 2018

Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers.

Nucleic Acids Res 2018 11;46(21):11184-11201

Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.

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http://dx.doi.org/10.1093/nar/gky753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265487PMC
November 2018

Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers.

BMC Genomics 2018 Jul 13;19(1):531. Epub 2018 Jul 13.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.

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http://dx.doi.org/10.1186/s12864-018-4933-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044086PMC
July 2018

Dynamic placement of the linker histone H1 associated with nucleosome arrangement and gene transcription in early Drosophila embryonic development.

Cell Death Dis 2018 07 9;9(7):765. Epub 2018 Jul 9.

Institute of Translational Research, Tongji Hospital, the School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, the Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, 200092, China.

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http://dx.doi.org/10.1038/s41419-018-0819-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6037678PMC
July 2018

pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans.

Nucleic Acids Res 2018 07;46(W1):W43-W48

Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/nar/gky277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030828PMC
July 2018

Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling.

Cell 2018 05;173(4):1031-1044.e13

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.03.062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090549PMC
May 2018

Integrating Cross-Linking Experiments with Ab Initio Protein-Protein Docking.

J Mol Biol 2018 06 14;430(12):1814-1828. Epub 2018 Apr 14.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2018.04.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6084434PMC
June 2018

In Vivo Genome Editing Partially Restores Alpha1-Antitrypsin in a Murine Model of AAT Deficiency.

Hum Gene Ther 2018 08 14;29(8):853-860. Epub 2018 May 14.

1 RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts.

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http://dx.doi.org/10.1089/hum.2017.225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6110121PMC
August 2018

A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans.

Dev Cell 2018 03 15;44(6):762-770.e3. Epub 2018 Feb 15.

RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2018.01.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991626PMC
March 2018

The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans.

Cell Rep 2018 02 15;22(9):2254-2264. Epub 2018 Feb 15.

RNA Therapeutics Institute, UMass Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Howard Hughes Medical Institute. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.02.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5918280PMC
February 2018

Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline.

Cell 2018 02 15;172(5):937-951.e18. Epub 2018 Feb 15.

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.02.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5905434PMC
February 2018

The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes.

Science 2018 02 1;359(6375):587-592. Epub 2018 Feb 1.

Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1126/science.aao2840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5939965PMC
February 2018

The genome of the Hi5 germ cell line from , an agricultural pest and novel model for small RNA biology.

Elife 2018 01 29;7. Epub 2018 Jan 29.

RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, United States.

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http://dx.doi.org/10.7554/eLife.31628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5844692PMC
January 2018

Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods.

BMC Bioinformatics 2017 Dec 1;18(Suppl 13):464. Epub 2017 Dec 1.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.

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https://bmcbioinformatics.biomedcentral.com/articles/10.1186
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http://dx.doi.org/10.1186/s12859-017-1875-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5773893PMC
December 2017

A systems level approach to temporal expression dynamics in Drosophila reveals clusters of long term memory genes.

PLoS Genet 2017 Oct 30;13(10):e1007054. Epub 2017 Oct 30.

Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1007054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679645PMC
October 2017

Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes.

J Immunol 2017 10;199(7):2203-2213

Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556;

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http://dx.doi.org/10.4049/jimmunol.1700744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679125PMC
October 2017

Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery.

Dev Cell 2017 10 14;43(1):60-70.e5. Epub 2017 Sep 14.

Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2017.08.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653967PMC
October 2017

Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis.

Proc Natl Acad Sci U S A 2017 04 20;114(14):3648-3653. Epub 2017 Mar 20.

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605;

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http://dx.doi.org/10.1073/pnas.1620861114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389295PMC
April 2017

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.

Bioinformatics 2017 Jun;33(12):1806-1813

Life Science Department, Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btx068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5783285PMC
June 2017

ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes.

Proteins 2017 05 16;85(5):908-916. Epub 2017 Feb 16.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.

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http://dx.doi.org/10.1002/prot.25260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860664PMC
May 2017

Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice.

Gastroenterology 2017 04 10;152(5):1161-1173.e1. Epub 2016 Dec 10.

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts; Program in Molecular Medicine and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2016.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6204228PMC
April 2017

Sequence Alignment and Homology Search.

Cold Spring Harb Protoc 2016 11 1;2016(11). Epub 2016 Nov 1.

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http://dx.doi.org/10.1101/pdb.top093070DOI Listing
November 2016

Visualizing Genomic Annotations with the UCSC Genome Browser.

Cold Spring Harb Protoc 2016 11 1;2016(11). Epub 2016 Nov 1.

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http://dx.doi.org/10.1101/pdb.prot093062DOI Listing
November 2016

Sequence Alignment and Homology Search with BLAST and ClustalW.

Cold Spring Harb Protoc 2016 11 1;2016(11). Epub 2016 Nov 1.

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http://dx.doi.org/10.1101/pdb.prot093088DOI Listing
November 2016

Performance of ZDOCK and IRAD in CAPRI rounds 28-34.

Proteins 2017 03 24;85(3):408-416. Epub 2016 Oct 24.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, 01605.

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http://dx.doi.org/10.1002/prot.25186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5313317PMC
March 2017

DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data.

PLoS One 2016 13;11(10):e0164228. Epub 2016 Oct 13.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0164228PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5063419PMC
May 2017

Defining cutaneous molecular pathobiology of arsenicals using phenylarsine oxide as a prototype.

Sci Rep 2016 10 11;6:34865. Epub 2016 Oct 11.

Department of Dermatology and Skin Diseases Research Center, University of Alabama at Birmingham, Alabama, USA.

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http://www.nature.com/articles/srep34865
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http://dx.doi.org/10.1038/srep34865DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5057142PMC
October 2016

A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces.

Protein Eng Des Sel 2016 Dec 13;29(12):595-606. Epub 2016 Sep 13.

Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA

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http://dx.doi.org/10.1093/protein/gzw050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5181382PMC
December 2016

Mapping Short Sequence Reads to a Reference Genome.

Cold Spring Harb Protoc 2017 02 1;2017(2). Epub 2017 Feb 1.

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http://dx.doi.org/10.1101/pdb.prot093161DOI Listing
February 2017

Mapping Billions of Short Reads to a Reference Genome.

Cold Spring Harb Protoc 2017 01 3;2017(1). Epub 2017 Jan 3.

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http://dx.doi.org/10.1101/pdb.top093153DOI Listing
January 2017

Designing Polymerase Chain Reaction Primers Using Primer3Plus.

Cold Spring Harb Protoc 2016 09 1;2016(9). Epub 2016 Sep 1.

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http://dx.doi.org/10.1101/pdb.prot093096DOI Listing
September 2016

Analyzing Microarray Data.

Cold Spring Harb Protoc 2017 03 1;2017(3). Epub 2017 Mar 1.

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http://dx.doi.org/10.1101/pdb.prot093112DOI Listing
March 2017

Discovering cis-Regulatory Motifs.

Cold Spring Harb Protoc 2017 02 1;2017(2). Epub 2017 Feb 1.

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http://dx.doi.org/10.1101/pdb.prot093203DOI Listing
February 2017

Peak-Finding Algorithms.

Cold Spring Harb Protoc 2017 03 1;2017(3). Epub 2017 Mar 1.

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http://dx.doi.org/10.1101/pdb.top093179DOI Listing
March 2017

Motif Finding.

Cold Spring Harb Protoc 2017 02 1;2017(2). Epub 2017 Feb 1.

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http://dx.doi.org/10.1101/pdb.top093195DOI Listing
February 2017

Analysis of Microarray and RNA-seq Expression Profiling Data.

Cold Spring Harb Protoc 2017 03 1;2017(3). Epub 2017 Mar 1.

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http://dx.doi.org/10.1101/pdb.top093104DOI Listing
March 2017

Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding).

Cold Spring Harb Protoc 2017 02 1;2017(2). Epub 2017 Feb 1.

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http://dx.doi.org/10.1101/pdb.prot093187DOI Listing
February 2017

Forward genetic screen of human transposase genomic rearrangements.

BMC Genomics 2016 Aug 4;17:548. Epub 2016 Aug 4.

Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

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http://dx.doi.org/10.1186/s12864-016-2877-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973553PMC
August 2016

Data Formats in Bioinformatics.

Cold Spring Harb Protoc 2016 08 1;2016(8). Epub 2016 Aug 1.

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http://dx.doi.org/10.1101/pdb.top093211DOI Listing
August 2016

Activating transcription factor 4 underlies the pathogenesis of arsenic trioxide-mediated impairment of macrophage innate immune functions.

Toxicol Appl Pharmacol 2016 10 25;308:46-58. Epub 2016 Jul 25.

Department of Dermatology and Skin Diseases Research Center, University of Alabama at Birmingham, Birmingham, AL, USA. Electronic address:

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http://dx.doi.org/10.1016/j.taap.2016.07.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5978774PMC
October 2016

A benchmark testing ground for integrating homology modeling and protein docking.

Proteins 2017 01 13;85(1):10-16. Epub 2016 Nov 13.

Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.

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http://dx.doi.org/10.1002/prot.25063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5817996PMC
January 2017

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Authors:
Marc F Lensink Sameer Velankar Andriy Kryshtafovych Shen-You Huang Dina Schneidman-Duhovny Andrej Sali Joan Segura Narcis Fernandez-Fuentes Shruthi Viswanath Ron Elber Sergei Grudinin Petr Popov Emilie Neveu Hasup Lee Minkyung Baek Sangwoo Park Lim Heo Gyu Rie Lee Chaok Seok Sanbo Qin Huan-Xiang Zhou David W Ritchie Bernard Maigret Marie-Dominique Devignes Anisah Ghoorah Mieczyslaw Torchala Raphaël A G Chaleil Paul A Bates Efrat Ben-Zeev Miriam Eisenstein Surendra S Negi Zhiping Weng Thom Vreven Brian G Pierce Tyler M Borrman Jinchao Yu Françoise Ochsenbein Raphaël Guerois Anna Vangone João P G L M Rodrigues Gydo van Zundert Mehdi Nellen Li Xue Ezgi Karaca Adrien S J Melquiond Koen Visscher Panagiotis L Kastritis Alexandre M J J Bonvin Xianjin Xu Liming Qiu Chengfei Yan Jilong Li Zhiwei Ma Jianlin Cheng Xiaoqin Zou Yang Shen Lenna X Peterson Hyung-Rae Kim Amit Roy Xusi Han Juan Esquivel-Rodriguez Daisuke Kihara Xiaofeng Yu Neil J Bruce Jonathan C Fuller Rebecca C Wade Ivan Anishchenko Petras J Kundrotas Ilya A Vakser Kenichiro Imai Kazunori Yamada Toshiyuki Oda Tsukasa Nakamura Kentaro Tomii Chiara Pallara Miguel Romero-Durana Brian Jiménez-García Iain H Moal Juan Férnandez-Recio Jong Young Joung Jong Yun Kim Keehyoung Joo Jooyoung Lee Dima Kozakov Sandor Vajda Scott Mottarella David R Hall Dmitri Beglov Artem Mamonov Bing Xia Tanggis Bohnuud Carlos A Del Carpio Eichiro Ichiishi Nicholas Marze Daisuke Kuroda Shourya S Roy Burman Jeffrey J Gray Edrisse Chermak Luigi Cavallo Romina Oliva Andrey Tovchigrechko Shoshana J Wodak

Proteins 2016 09 1;84 Suppl 1:323-48. Epub 2016 Jun 1.

Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1002/prot.25007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030136PMC
September 2016

Computational Modeling of T Cell Receptor Complexes.

Methods Mol Biol 2016 ;1414:319-40

Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN, 46556, USA.

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http://dx.doi.org/10.1007/978-1-4939-3569-7_19DOI Listing
December 2016

Computational Reprogramming of T Cell Antigen Receptor Binding Properties.

Methods Mol Biol 2016 ;1414:305-18

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.

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http://dx.doi.org/10.1007/978-1-4939-3569-7_18DOI Listing
December 2016

The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans.

Cell 2016 Feb;164(5):974-84

RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.02.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4785802PMC
February 2016

How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire.

Proc Natl Acad Sci U S A 2016 Mar 16;113(9):E1276-85. Epub 2016 Feb 16.

Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556; Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556;

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http://dx.doi.org/10.1073/pnas.1522069113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4780628PMC
March 2016

The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease.

PLoS One 2015 4;10(12):e0144398. Epub 2015 Dec 4.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0144398PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670094PMC
June 2016

The PsychENCODE project.

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1038/nn.4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675669PMC
December 2015

Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms.

Mol Cell 2015 Sep;59(5):819-30

RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.08.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560842PMC
September 2015

Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes.

Nucleic Acids Res 2015 Sep 17;43(17):8146-56. Epub 2015 Aug 17.

Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkv831DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787836PMC
September 2015