Zhiping Weng - Publications

Affiliations: 
Biomedical Engineering Boston University, Boston, MA, United States 

256 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, ... ... Weng Z, et al. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. PMID 35474001 DOI: 10.1038/s41586-021-04226-3  0.673
2021 Moore JE, Zhang XO, Elhajjajy SI, Fan K, Pratt HE, Reese F, Mortazavi A, Weng Z. Integration of high-resolution promoter profiling assays reveals novel, cell type-specific transcription start sites across 115 human cell and tissue types. Genome Research. PMID 34949670 DOI: 10.1101/gr.275723.121  0.727
2021 Jiang T, Zhang XO, Weng Z, Xue W. Deletion and replacement of long genomic sequences using prime editing. Nature Biotechnology. PMID 34650270 DOI: 10.1038/s41587-021-01026-y  0.706
2021 Fan K, Moore JE, Zhang XO, Weng Z. Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes. Nucleic Acids Research. PMID 33978759 DOI: 10.1093/nar/gkab345  0.719
2021 Zhang XO, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annual Review of Genomics and Human Genetics. PMID 33792357 DOI: 10.1146/annurev-genom-111620-100736  0.712
2021 Guest JD, Vreven T, Zhou J, Moal I, Jeliazkov JR, Gray JJ, Weng Z, Pierce BG. An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants. Structure (London, England : 1993). PMID 33539768 DOI: 10.1016/j.str.2021.01.005  0.575
2020 Borrman T, Pierce BG, Vreven T, Baker BM, Weng Z. High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. Bioinformatics (Oxford, England). PMID 33355667 DOI: 10.1093/bioinformatics/btaa1050  0.555
2020 Tsuji J, Thomson T, Chan E, Brown CK, Oppenheimer J, Bigelow C, Dong X, Theurkauf WE, Weng Z, Schwartz LM. HIGH RESOLUTION ANALYSIS OF DIFFERENTIAL GENE EXPRESSION DURING SKELETAL MUSCLE ATROPHY AND PROGRAMMED CELL DEATH. Physiological Genomics. PMID 32926651 DOI: 10.1152/Physiolgenomics.00047.2020  0.71
2020 Li X, Li Z, Zhou H, Gaynor SM, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Aslibekyan S, Ballantyne CM, Bielak LF, Blangero J, Boerwinkle E, Bowden DW, ... ... Weng Z, et al. Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nature Genetics. PMID 32839606 DOI: 10.1038/S41588-020-0676-4  0.322
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Weng Z, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4  0.745
2020 Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, et al. Perspectives on ENCODE. Nature. 583: 693-698. PMID 32728248 DOI: 10.1038/S41586-020-2449-8  0.391
2020 Wu PH, Fu Y, Cecchini K, Özata DM, Arif A, Yu T, Colpan C, Gainetdinov I, Weng Z, Zamore PD. The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility. Nature Genetics. PMID 32601478 DOI: 10.1038/S41588-020-0657-7  0.317
2020 Smith JL, Rodríguez TC, Mou H, Kwan SY, Pratt H, Zhang XO, Cao Y, Liang S, Ozata DM, Yu T, Yin Q, Hazeltine M, Weng Z, Sontheimer EJ, Xue W. YAP1 withdrawal in hepatoblastoma drives therapeutic differentiation of tumor cells to functional hepatocyte-like cells. Hepatology (Baltimore, Md.). PMID 32452550 DOI: 10.1002/Hep.31389  0.67
2020 Jiang T, Henderson JM, Coote K, Cheng Y, Valley HC, Zhang XO, Wang Q, Rhym LH, Cao Y, Newby GA, Bihler H, Mense M, Weng Z, Anderson DG, McCaffrey AP, et al. Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope. Nature Communications. 11: 1979. PMID 32332735 DOI: 10.1038/S41467-020-15892-8  0.706
2020 Pratt H, Weng Z. LogoJS: a Javascript package for creating sequence logos and embedding them in web applications. Bioinformatics (Oxford, England). PMID 32181813 DOI: 10.1093/Bioinformatics/Btaa192  0.334
2020 Parhad SS, Yu T, Zhang G, Rice NP, Weng Z, Theurkauf WE. Adaptive Evolution Targets a piRNA Precursor Transcription Network. Cell Reports. 30: 2672-2685.e5. PMID 32101744 DOI: 10.1016/J.Celrep.2020.01.109  0.377
2020 Vreven T, Vangaveti S, Borrman TM, Gaines JC, Weng Z. Performance of ZDOCK and IRAD in CAPRI rounds 39-45. Proteins. PMID 31994784 DOI: 10.1002/Prot.25873  0.355
2020 Zhang P, Zhang XO, Jiang T, Cai L, Huang X, Liu Q, Li D, Lu A, Liu Y, Xue W, Zhang P, Weng Z. Comprehensive identification of alternative back-splicing in human tissue transcriptomes. Nucleic Acids Research. PMID 31974555 DOI: 10.1093/Nar/Gkaa005  0.701
2020 Moore JE, Pratt HE, Purcaro MJ, Weng Z. A curated benchmark of enhancer-gene interactions for evaluating enhancer-target gene prediction methods. Genome Biology. 21: 17. PMID 31969180 DOI: 10.1186/S13059-019-1924-8  0.367
2020 Özata DM, Yu T, Mou H, Gainetdinov I, Colpan C, Cecchini K, Kaymaz Y, Wu PH, Fan K, Kucukural A, Weng Z, Zamore PD. Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans. Nature Ecology & Evolution. 4: 156-168. PMID 31900453 DOI: 10.1038/S41559-019-1065-1  0.378
2020 Pratt H, Weng Z, Pratt D. 688 Integration Of Gwas And Epigenetic Data To Identify Novel Candidate Genes And Variant Associations In Primary Biliary Cholangitis Gastroenterology. 158. DOI: 10.1016/S0016-5085(20)33876-2  0.304
2019 Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, ... ... Weng Z, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838  0.638
2019 Yu T, Koppetsch BS, Pagliarani S, Johnston S, Silverstein NJ, Luban J, Chappell K, Weng Z, Theurkauf WE. The piRNA Response to Retroviral Invasion of the Koala Genome. Cell. PMID 31607510 DOI: 10.1016/J.Cell.2019.09.002  0.354
2019 Libbrecht MW, Rodriguez OL, Weng Z, Bilmes JA, Hoffman MM, Noble WS. A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types. Genome Biology. 20: 180. PMID 31462275 DOI: 10.1186/S13059-019-1784-2  0.354
2019 Zhang XO, Gingeras TR, Weng Z. Genome-wide analysis of polymerase III-transcribed elements suggests cell-type-specific enhancer function. Genome Research. PMID 31413151 DOI: 10.1101/Gr.249789.119  0.728
2019 Vangaveti S, Vreven T, Zhang Y, Weng Z. Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. Bioinformatics (Oxford, England). PMID 31393558 DOI: 10.1093/Bioinformatics/Btz623  0.369
2019 Rajarajan P, Borrman T, Liao W, Espeso-Gil S, Chandrasekaran S, Jiang Y, Weng Z, Brennand KJ, Akbarian S. Spatial genome exploration in the context of cognitive and neurological disease. Current Opinion in Neurobiology. 59: 112-119. PMID 31255842 DOI: 10.1016/J.Conb.2019.05.007  0.337
2019 Kwan SY, Sheel A, Song CQ, Zhang XO, Jiang T, Dang H, Cao Y, Ozata DM, Mou H, Yin H, Weng Z, Wang XW, Xue W. Depletion of TRRAP induces p53-independent senescence in liver cancer by downregulating mitotic genes. Hepatology (Baltimore, Md.). PMID 31188495 DOI: 10.1002/Hep.30807  0.691
2019 Gusev FE, Reshetov DA, Mitchell AC, Andreeva TV, Dincer A, Grigorenko AP, Fedonin G, Halene T, Aliseychik M, Goltsov AY, Solovyev V, Brizgalov L, Filippova E, Weng Z, Akbarian S, et al. Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. fj201802646R. PMID 30970224 DOI: 10.1096/Fj.201802646R  0.31
2019 Girdhar K, Hoffman G, Jiang Y, Kundakovic M, Hauberg ME, Wang Y, Shah H, Weng Z, K. Sieberts S, A. Peters M, T. Harris B, Lipska B, Sklar P, Roussos P, Akbarian S. CELL-SPECIFIC HISTONE MODIFICATION MAPS LINK SCHIZOPHRENIA RISK TO THE NEURONAL EPIGENOME European Neuropsychopharmacology. 29: S1009. DOI: 10.1016/J.Euroneuro.2017.08.406  0.307
2018 Davis GM, Tu S, Anderson JWT, Colson RN, Gunzburg MJ, Francisco MA, Ray D, Shrubsole SP, Sobotka JA, Seroussi U, Lao RX, Maity T, Wu MZ, McJunkin K, Morris QD, ... ... Weng Z, et al. The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in . Elife. 7. PMID 30575518 DOI: 10.7554/Elife.35478  0.368
2018 Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, ... ... Weng Z, et al. Comprehensive functional genomic resource and integrative model for the human brain. Science (New York, N.Y.). 362. PMID 30545857 DOI: 10.1126/Science.Aat8464  0.333
2018 Chang TH, Mattei E, Gainetdinov I, Colpan C, Weng Z, Zamore PD. Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster. Molecular Cell. PMID 30527661 DOI: 10.1016/J.Molcel.2018.10.038  0.368
2018 Zhang G, Tu S, Yu T, Zhang XO, Parhad SS, Weng Z, Theurkauf WE. Co-dependent Assembly of Drosophila piRNA Precursor Complexes and piRNA Cluster Heterochromatin. Cell Reports. 24: 3413-3422.e4. PMID 30257203 DOI: 10.1016/J.Celrep.2018.08.081  0.713
2018 Zhang XO, Fu Y, Mou H, Xue W, Weng Z. The temporal landscape of recursive splicing during Pol II transcription elongation in human cells. Plos Genetics. 14: e1007579. PMID 30148885 DOI: 10.1371/Journal.Pgen.1007579  0.695
2018 Fu S, Wang Q, Moore JE, Purcaro MJ, Pratt HE, Fan K, Gu C, Jiang C, Zhu R, Kundaje A, Lu A, Weng Z. Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers. Nucleic Acids Research. PMID 30137428 DOI: 10.1093/Nar/Gky753  0.332
2018 Hu J, Gu L, Ye Y, Zheng M, Xu Z, Lin J, Du Y, Tian M, Luo L, Wang B, Zhang X, Weng Z, Jiang C. Dynamic placement of the linker histone H1 associated with nucleosome arrangement and gene transcription in early Drosophila embryonic development. Cell Death & Disease. 9: 765. PMID 29988149 DOI: 10.1038/S41419-018-0819-Z  0.303
2018 Wu WS, Huang WC, Brown JS, Zhang D, Song X, Chen H, Tu S, Weng Z, Lee HC. pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans. Nucleic Acids Research. PMID 29897582 DOI: 10.1093/Nar/Gky277  0.328
2018 Chen W, Moore J, Ozadam H, Shulha HP, Rhind N, Weng Z, Moore MJ. Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling. Cell. 173: 1031-1044.e13. PMID 29727662 DOI: 10.1016/J.Cell.2018.03.062  0.71
2018 Vreven T, Schweppe DK, Chavez JD, Weisbrod CR, Shibata S, Zheng C, Bruce JE, Weng Z. Integrating cross-linking experiments with ab initio protein-protein docking. Journal of Molecular Biology. PMID 29665372 DOI: 10.1016/J.Jmb.2018.04.010  0.356
2018 Tang W, Seth M, Tu S, Shen EZ, Li Q, Shirayama M, Weng Z, Mello CC. A Sex Chromosome piRNA Promotes Robust Dosage Compensation and Sex Determination in C. elegans. Developmental Cell. PMID 29456136 DOI: 10.1016/J.Devcel.2018.01.025  0.321
2018 Seth M, Shirayama M, Tang W, Shen EZ, Tu S, Lee HC, Weng Z, Mello CC. The Coding Regions of Germline mRNAs Confer Sensitivity to Argonaute Regulation in C. elegans. Cell Reports. PMID 29456100 DOI: 10.1016/J.Celrep.2018.02.009  0.331
2018 Shen EZ, Chen H, Ozturk AR, Tu S, Shirayama M, Tang W, Ding YH, Dai SY, Weng Z, Mello CC. Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline. Cell. PMID 29456082 DOI: 10.1016/J.Cell.2018.02.002  0.352
2018 Zhang D, Tu S, Stubna M, Wu WS, Huang WC, Weng Z, Lee HC. The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes. Science (New York, N.Y.). 359: 587-592. PMID 29420292 DOI: 10.1126/Science.Aao2840  0.329
2018 Fu Y, Yang Y, Zhang H, Farley G, Wang J, Quarles KA, Weng Z, Zamore PD. The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. Elife. 7. PMID 29376823 DOI: 10.7554/Elife.31628  0.354
2018 Mou H, Smith J, Peng L, Yin H, Moore J, Zhang X, Song C, Sheel A, Wu Q, Ozata D, Li Y, Anderson D, Emerson C, Moore M, Weng Z, et al. Abstract 3374: CRISPR/Cas9 mediated genome editing induces exon skipping by alternative splicing or exon deletion Cancer Research. 78: 3374-3374. DOI: 10.1158/1538-7445.Am2018-3374  0.708
2018 Pratt H, Weng Z. Decoding the non-coding genome: Opportunities and challenges of genomic and epigenomic consortium data Current Opinion in Systems Biology. 11: 82-90. DOI: 10.1016/J.Coisb.2018.09.002  0.399
2017 Zhang W, Zhu X, Fu Y, Tsuji J, Weng Z. Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods. Bmc Bioinformatics. 18: 464. PMID 29219070 DOI: 10.1186/S12859-017-1875-6  0.336
2017 Bozler J, Kacsoh BZ, Chen H, Theurkauf WE, Weng Z, Bosco G. A systems level approach to temporal expression dynamics in Drosophila reveals clusters of long term memory genes. Plos Genetics. 13: e1007054. PMID 29084214 DOI: 10.1371/Journal.Pgen.1007054  0.304
2017 Singh NK, Riley TP, Baker SCB, Borrman T, Weng Z, Baker BM. Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes. Journal of Immunology (Baltimore, Md. : 1950). 199: 2203-2213. PMID 28923982 DOI: 10.4049/Jimmunol.1700744  0.326
2017 Pierce BG, Boucher EN, Piepenbrink KH, Ejemel M, Rapp CA, Thomas WD, Sundberg EJ, Weng Z, Wang Y. Structure-Based Design of Hepatitis C Virus Vaccines that Elicit Neutralizing Antibody Responses to a Conserved Epitope. Journal of Virology. PMID 28794021 DOI: 10.1128/Jvi.01032-17  0.58
2017 Fan Y, Yue J, Xiao M, Han-Zhang H, Wang YV, Ma C, Deng Z, Li Y, Yu Y, Wang X, Niu S, Hua Y, Weng Z, Atadja P, Li E, et al. FXR1 regulates transcription and is required for tumor growth in TP53 homozygous deletion human cancers. Elife. 6. PMID 28767039 DOI: 10.7554/Elife.26129  0.335
2017 Mou H, Smith JL, Peng L, Yin H, Moore J, Zhang XO, Song CQ, Sheel A, Wu Q, Ozata DM, Li Y, Anderson DG, Emerson CP, Sontheimer EJ, Moore MJ, ... Weng Z, et al. CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. Genome Biology. 18: 108. PMID 28615073 DOI: 10.1186/S13059-017-1237-8  0.708
2017 Henssen AG, Koche R, Zhuang J, Jiang E, Reed C, Eisenberg A, Still E, MacArthur IC, Rodríguez-Fos E, Gonzalez S, Puiggròs M, Blackford AN, Mason CE, de Stanchina E, Gönen M, ... ... Weng Z, et al. PGBD5 promotes site-specific oncogenic mutations in human tumors. Nature Genetics. PMID 28504702 DOI: 10.1038/Ng.3866  0.328
2017 Moal IH, Barradas-Bautista D, Jiménez-García B, Torchala M, van der Velde A, Vreven T, Weng Z, Bates PA, Fernández-Recio J. IRaPPA: Information retrieval based integration of biophysical models for protein assembly selection. Bioinformatics (Oxford, England). PMID 28200016 DOI: 10.1093/Bioinformatics/Btx068  0.348
2017 Borrman T, Cimons J, Cosiano M, Purcaro M, Pierce BG, Baker BM, Weng Z. ATLAS: A database linking binding affinities with structures for wild-type and mutant TCR-pMHC complexes. Proteins. PMID 28160322 DOI: 10.1002/Prot.25260  0.642
2017 Strattan JS, Dreszer TR, Hitz BC, Chan ET, Davidson JM, Gabdank I, Hilton JA, Sloan CA, Weng Z, Kundaje A, Cherry JM. The ENCODE Annotation Pipeline: Standard analyses for ChIP-seq, RNA-seq, DNase-seq, and whole-genome bisulfite experiments F1000research. 6. DOI: 10.7490/F1000Research.1113977.1  0.311
2016 Tsuji J, Weng Z. DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data. Plos One. 11: e0164228. PMID 27736901 DOI: 10.1371/Journal.Pone.0164228  0.323
2016 Vreven T, Pierce BG, Borrman TM, Weng Z. Performance of ZDOCK and IRAD in CAPRI rounds 28-34. Proteins. PMID 27718275 DOI: 10.1002/Prot.25186  0.644
2016 Riley TP, Ayres CM, Hellman LM, Singh NK, Cosiano M, Cimons JM, Anderson MJ, Piepenbrink KH, Pierce BG, Weng Z, Baker BM. A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Engineering, Design & Selection : Peds. PMID 27624308 DOI: 10.1093/Protein/Gzw050  0.623
2016 Hung JH, Weng Z. Mapping Short Sequence Reads to a Reference Genome. Cold Spring Harbor Protocols. PMID 27574204 DOI: 10.1101/Pdb.Prot093161  0.678
2016 Hung JH, Weng Z. Mapping Billions of Short Reads to a Reference Genome. Cold Spring Harbor Protocols. PMID 27574203 DOI: 10.1101/Pdb.Top093153  0.668
2016 Hung JH, Weng Z. Designing Polymerase Chain Reaction Primers Using Primer3Plus. Cold Spring Harbor Protocols. 2016: pdb.prot093096. PMID 27574202 DOI: 10.1101/Pdb.Prot093096  0.638
2016 Hung JH, Weng Z. Analyzing Microarray Data. Cold Spring Harbor Protocols. PMID 27574201 DOI: 10.1101/Pdb.Prot093112  0.668
2016 Hung JH, Weng Z. Sequence Alignment and Homology Search. Cold Spring Harbor Protocols. PMID 27574200 DOI: 10.1101/Pdb.Top093070  0.7
2016 Hung JH, Weng Z. Discovering cis-Regulatory Motifs. Cold Spring Harbor Protocols. PMID 27574199 DOI: 10.1101/Pdb.Prot093203  0.694
2016 Hung JH, Weng Z. Visualizing Genomic Annotations with the UCSC Genome Browser. Cold Spring Harbor Protocols. PMID 27574198 DOI: 10.1101/Pdb.Prot093062  0.69
2016 Hung JH, Weng Z. Sequence Alignment and Homology Search with BLAST and ClustalW. Cold Spring Harbor Protocols. PMID 27574197 DOI: 10.1101/Pdb.Prot093088  0.669
2016 Hung JH, Weng Z. Peak-Finding Algorithms. Cold Spring Harbor Protocols. PMID 27574196 DOI: 10.1101/Pdb.Top093179  0.692
2016 Hung JH, Weng Z. Motif Finding. Cold Spring Harbor Protocols. PMID 27574195 DOI: 10.1101/pdb.top093195  0.676
2016 Hung JH, Weng Z. Analysis of Microarray and RNA-seq Expression Profiling Data. Cold Spring Harbor Protocols. PMID 27574194 DOI: 10.1101/Pdb.Top093104  0.677
2016 Hung JH, Weng Z. Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding). Cold Spring Harbor Protocols. PMID 27574193 DOI: 10.1101/Pdb.Prot093187  0.655
2016 Henssen AG, Jiang E, Zhuang J, Pinello L, Socci ND, Koche R, Gonen M, Villasante CM, Armstrong SA, Bauer DE, Weng Z, Kentsis A. Forward genetic screen of human transposase genomic rearrangements. Bmc Genomics. 17: 548. PMID 27491780 DOI: 10.1186/S12864-016-2877-X  0.326
2016 Hung JH, Weng Z. Data Formats in Bioinformatics. Cold Spring Harbor Protocols. 2016: pdb.top093211. PMID 27480726 DOI: 10.1101/Pdb.Top093211  0.632
2016 Bohnuud T, Luo L, Wodak SJ, Bonvin AM, Weng Z, Vajda S, Schueler-Furman O, Kozakov D. A benchmark testing ground for integrating homology modeling and protein docking. Proteins. PMID 27172383 DOI: 10.1002/Prot.25063  0.383
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Weng Z, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.647
2016 Riley TP, Singh NK, Pierce BG, Weng Z, Baker BM. Computational Modeling of T Cell Receptor Complexes. Methods in Molecular Biology (Clifton, N.J.). 1414: 319-40. PMID 27094300 DOI: 10.1007/978-1-4939-3569-7_19  0.633
2016 Riley TP, Singh NK, Pierce BG, Baker BM, Weng Z. Computational Reprogramming of T Cell Antigen Receptor Binding Properties. Methods in Molecular Biology (Clifton, N.J.). 1414: 305-18. PMID 27094299 DOI: 10.1007/978-1-4939-3569-7_18  0.629
2016 Tang W, Tu S, Lee HC, Weng Z, Mello CC. The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans. Cell. 164: 974-984. PMID 26919432 DOI: 10.1016/J.Cell.2016.02.008  0.317
2016 Blevins SJ, Pierce BG, Singh NK, Riley TP, Wang Y, Spear TT, Nishimura MI, Weng Z, Baker BM. How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire. Proceedings of the National Academy of Sciences of the United States of America. PMID 26884163 DOI: 10.1073/Pnas.1522069113  0.631
2016 Yin H, Song CQ, Dorkin JR, Zhu LJ, Li Y, Wu Q, Park A, Yang J, Suresh S, Bizhanova A, Gupta A, Bolukbasi MF, Walsh S, Bogorad RL, Gao G, ... Weng Z, et al. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nature Biotechnology. PMID 26829318 DOI: 10.1038/Nbt.3471  0.304
2015 Labadorf A, Hoss AG, Lagomarsino V, Latourelle JC, Hadzi TC, Bregu J, MacDonald ME, Gusella JF, Chen JF, Akbarian S, Weng Z, Myers RH. RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression. Plos One. 10: e0143563. PMID 26636579 DOI: 10.1371/Journal.Pone.0143563  0.339
2015 Dong X, Tsuji J, Labadorf A, Roussos P, Chen JF, Myers RH, Akbarian S, Weng Z. The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease. Plos One. 10: e0144398. PMID 26636336 DOI: 10.1371/Journal.Pone.0144398  0.731
2015 Tsuji J, Weng Z. Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data. Briefings in Bioinformatics. PMID 26628557 DOI: 10.1093/Bib/Bbv103  0.322
2015 Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, ... ... Weng Z, et al. The PsychENCODE project. Nature Neuroscience. 18: 1707-1712. PMID 26605881 DOI: 10.1038/Nn.4156  0.65
2015 Wang W, Han BW, Tipping C, Ge DT, Zhang Z, Weng Z, Zamore PD. Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms. Molecular Cell. 59: 819-30. PMID 26340424 DOI: 10.1016/J.Molcel.2015.08.007  0.364
2015 Zhuang J, Weng Z. Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes. Nucleic Acids Research. PMID 26283183 DOI: 10.1093/Nar/Gkv831  0.338
2015 Vreven T, Moal IH, Vangone A, Pierce BG, Kastritis PL, Torchala M, Chaleil R, Jiménez-García B, Bates PA, Fernandez-Recio J, Bonvin AM, Weng Z. Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2. Journal of Molecular Biology. 427: 3031-41. PMID 26231283 DOI: 10.1016/J.Jmb.2015.07.016  0.657
2015 Chou MT, Han BW, Hsiao CP, Zamore PD, Weng Z, Hung JH. Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic Acids Research. PMID 26007652 DOI: 10.1093/Nar/Gkv537  0.67
2015 Han BW, Wang W, Li C, Weng Z, Zamore PD. Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science (New York, N.Y.). 348: 817-21. PMID 25977554 DOI: 10.1126/Science.Aaa1264  0.303
2015 Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF. Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified. Developmental Cell. 32: 765-71. PMID 25805138 DOI: 10.1016/J.Devcel.2015.01.013  0.363
2015 Tu S, Wu MZ, Wang J, Cutter AD, Weng Z, Claycomb JM. Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes. Nucleic Acids Research. 43: 208-24. PMID 25510497 DOI: 10.1093/Nar/Gku1308  0.325
2015 Bai G, Cheung I, Shulha HP, Coelho JE, Li P, Dong X, Jakovcevski M, Wang Y, Grigorenko A, Jiang Y, Hoss A, Patel K, Zheng M, Rogaev E, Myers RH, ... Weng Z, et al. Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains. Human Molecular Genetics. 24: 1441-56. PMID 25480889 DOI: 10.1093/Hmg/Ddu561  0.799
2015 Han BW, Wang W, Zamore PD, Weng Z. piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. Bioinformatics (Oxford, England). 31: 593-5. PMID 25342065 DOI: 10.1093/Bioinformatics/Btu647  0.317
2014 Wang W, Yoshikawa M, Han BW, Izumi N, Tomari Y, Weng Z, Zamore PD. The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs. Molecular Cell. 56: 708-16. PMID 25453759 DOI: 10.1016/J.Molcel.2014.10.016  0.301
2014 Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, ... ... Weng Z, et al. Principles of regulatory information conservation between mouse and human. Nature. 515: 371-5. PMID 25409826 DOI: 10.1038/Nature13985  0.411
2014 Pierce BG, Vreven T, Weng Z. Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. Bmc Bioinformatics. 15: 319. PMID 25260513 DOI: 10.1186/1471-2105-15-319  0.6
2014 Shen E, Shulha H, Weng Z, Akbarian S. Regulation of histone H3K4 methylation in brain development and disease. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 369. PMID 25135975 DOI: 10.1098/Rstb.2013.0514  0.707
2014 Yildirim O, Hung JH, Cedeno RJ, Weng Z, Lengner CJ, Rando OJ. A system for genome-wide histone variant dynamics in ES cells reveals dynamic MacroH2A2 replacement at promoters. Plos Genetics. 10: e1004515. PMID 25102063 DOI: 10.1371/Journal.Pgen.1004515  0.671
2014 Carone BR, Hung JH, Hainer SJ, Chou MT, Carone DM, Weng Z, Fazzio TG, Rando OJ. High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm. Developmental Cell. 30: 11-22. PMID 24998598 DOI: 10.1016/J.Devcel.2014.05.024  0.704
2014 Babcock GJ, Iyer S, Smith HL, Wang Y, Rowley K, Ambrosino DM, Zamore PD, Pierce BG, Molrine DC, Weng Z. High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody. Plos One. 9: e100325. PMID 24956119 DOI: 10.1371/Journal.Pone.0100325  0.574
2014 Zhang Z, Wang J, Schultz N, Zhang F, Parhad SS, Tu S, Vreven T, Zamore PD, Weng Z, Theurkauf WE. The HP1 homolog rhino anchors a nuclear complex that suppresses piRNA precursor splicing. Cell. 157: 1353-63. PMID 24906152 DOI: 10.1016/J.Cell.2014.04.030  0.369
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, ... ... Weng Z, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/Pnas.1318948111  0.387
2014 Trastoy B, Lomino JV, Pierce BG, Carter LG, Günther S, Giddens JP, Snyder GA, Weiss TM, Weng Z, Wang LX, Sundberg EJ. Crystal structure of Streptococcus pyogenes EndoS, an immunomodulatory endoglycosidase specific for human IgG antibodies. Proceedings of the National Academy of Sciences of the United States of America. 111: 6714-9. PMID 24753590 DOI: 10.1073/Pnas.1322908111  0.604
2014 Zhuang J, Wang J, Theurkauf W, Weng Z. TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Research. 42: 6826-38. PMID 24753423 DOI: 10.1093/Nar/Gku323  0.33
2014 Hoss AG, Kartha VK, Dong X, Latourelle JC, Dumitriu A, Hadzi TC, Macdonald ME, Gusella JF, Akbarian S, Chen JF, Weng Z, Myers RH. MicroRNAs located in the Hox gene clusters are implicated in huntington's disease pathogenesis. Plos Genetics. 10: e1004188. PMID 24586208 DOI: 10.1371/Journal.Pgen.1004188  0.683
2014 Pierce BG, Hellman LM, Hossain M, Singh NK, Vander Kooi CW, Weng Z, Baker BM. Computational design of the affinity and specificity of a therapeutic T cell receptor. Plos Computational Biology. 10: e1003478. PMID 24550723 DOI: 10.1371/Journal.Pcbi.1003478  0.631
2014 Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics (Oxford, England). 30: 1771-3. PMID 24532726 DOI: 10.1093/Bioinformatics/Btu097  0.795
2014 Chen W, Shulha HP, Ashar-Patel A, Yan J, Green KM, Query CC, Rhind N, Weng Z, Moore MJ. Endogenous U2·U5·U6 snRNA complexes in S. pombe are intron lariat spliceosomes. Rna (New York, N.Y.). 20: 308-20. PMID 24442611 DOI: 10.1261/Rna.040980.113  0.691
2014 Haidar JN, Zhu W, Lypowy J, Pierce BG, Bari A, Persaud K, Luna X, Snavely M, Ludwig D, Weng Z. Backbone flexibility of CDR3 and immune recognition of antigens. Journal of Molecular Biology. 426: 1583-99. PMID 24380763 DOI: 10.1016/J.Jmb.2013.12.024  0.636
2014 Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, ... ... Weng Z, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439  0.788
2014 Hwang H, Vreven T, Weng Z. Binding interface prediction by combining protein-protein docking results. Proteins. 82: 57-66. PMID 23836482 DOI: 10.1002/Prot.24354  0.773
2014 Vreven T, Hwang H, Pierce BG, Weng Z. Evaluating template-based and template-free protein-protein complex structure prediction. Briefings in Bioinformatics. 15: 169-76. PMID 23818491 DOI: 10.1093/Bib/Bbt047  0.795
2014 Babcock GJ, Iyer S, Smith HL, Wang Y, Rowley K, Ambrosino DM, Zamore PD, Pierce BG, Molrine DC, Weng Z. Changes in viral loads and epitope sequence distributions in placebo subjects. Plos One. DOI: 10.1371/Journal.Pone.0100325.G002  0.578
2014 Pierce BG, Hellman LM, Hossain M, Singh NK, Kooi CWV, Weng Z, Baker BM. Scores from ZAFFI (ZF) and Rosetta (Ros), predicted peptide contacts, and measured energies (in kcal/mol) for DMF5 point mutants binding to ELA/HLA-A2 and AAG/HLA-A2. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1003478.T002  0.586
2013 Chen PB, Hung JH, Hickman TL, Coles AH, Carey JF, Weng Z, Chu F, Fazzio TG. Hdac6 regulates Tip60-p400 function in stem cells. Elife. 2: e01557. PMID 24302573 DOI: 10.7554/Elife.01557  0.674
2013 Vreven T, Pierce BG, Hwang H, Weng Z. Performance of ZDOCK in CAPRI rounds 20-26. Proteins. 81: 2175-82. PMID 24123140 DOI: 10.1002/Prot.24432  0.803
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Weng Z, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.793
2013 Pierce BG, Eberwine R, Noble JA, Habib M, Shulha HP, Weng Z, Blankenhorn EP, Mordes JP. The Missing Heritability in T1D and Potential New Targets for Prevention. Journal of Diabetes Research. 2013: 737485. PMID 23691517 DOI: 10.1155/2013/737485  0.764
2013 Shulha HP, Cheung I, Guo Y, Akbarian S, Weng Z. Coordinated cell type-specific epigenetic remodeling in prefrontal cortex begins before birth and continues into early adulthood. Plos Genetics. 9: e1003433. PMID 23593028 DOI: 10.1371/Journal.Pgen.1003433  0.705
2013 Dong X, Weng Z. The correlation between histone modifications and gene expression. Epigenomics. 5: 113-6. PMID 23566087 DOI: 10.2217/Epi.13.13  0.721
2013 Perrat PN, DasGupta S, Wang J, Theurkauf W, Weng Z, Rosbash M, Waddell S. Transposition-driven genomic heterogeneity in the Drosophila brain. Science (New York, N.Y.). 340: 91-5. PMID 23559253 DOI: 10.1126/Science.1231965  0.304
2013 Li XZ, Roy CK, Dong X, Bolcun-Filas E, Wang J, Han BW, Xu J, Moore MJ, Schimenti JC, Weng Z, Zamore PD. An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Molecular Cell. 50: 67-81. PMID 23523368 DOI: 10.1016/J.Molcel.2013.02.016  0.722
2013 Vreven T, Hwang H, Weng Z. Exploring angular distance in protein-protein docking algorithms. Plos One. 8: e56645. PMID 23437194 DOI: 10.1371/Journal.Pone.0056645  0.744
2013 Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Research. 41: D171-6. PMID 23203885 DOI: 10.1093/Nar/Gks1221  0.811
2013 Pierce BG, Weng Z. A flexible docking approach for prediction of T cell receptor-peptide-MHC complexes. Protein Science : a Publication of the Protein Society. 22: 35-46. PMID 23109003 DOI: 10.1002/Pro.2181  0.651
2013 Chen PB, Hung J, Hickman TL, Coles AH, Carey JF, Weng Z, Chu F, Fazzio TG. Author response: Hdac6 regulates Tip60-p400 function in stem cells Elife. DOI: 10.7554/Elife.01557.035  0.637
2012 Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell. 151: 912. PMID 30360291 DOI: 10.1016/J.Cell.2012.10.029  0.636
2012 Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, Yao WD, Myers RH, Chen JF, Preuss TM, Rogaev EI, ... ... Weng Z, et al. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. Plos Biology. 10: e1001427. PMID 23185133 DOI: 10.1371/Journal.Pbio.1001427  0.725
2012 Zhang F, Wang J, Xu J, Zhang Z, Koppetsch BS, Schultz N, Vreven T, Meignin C, Davis I, Zamore PD, Weng Z, Theurkauf WE. UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery. Cell. 151: 871-84. PMID 23141543 DOI: 10.1016/J.Cell.2012.09.040  0.311
2012 Singh G, Kucukural A, Cenik C, Leszyk JD, Shaffer SA, Weng Z, Moore MJ. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell. 151: 750-64. PMID 23084401 DOI: 10.1016/J.Cell.2012.10.007  0.362
2012 Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell. 151: 533-46. PMID 23063653 DOI: 10.1016/J.Cell.2012.09.027  0.65
2012 Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, ... Weng Z, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Research. 22: 1798-812. PMID 22955990 DOI: 10.1101/Gr.139105.112  0.814
2012 Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, ... ... Weng Z, et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Research. 22: 1658-67. PMID 22955978 DOI: 10.1101/Gr.136838.111  0.738
2012 Whitfield TW, Wang J, Collins PJ, Partridge EC, Aldred SF, Trinklein ND, Myers RM, Weng Z. Functional analysis of transcription factor binding sites in human promoters. Genome Biology. 13: R50. PMID 22951020 DOI: 10.1186/Gb-2012-13-9-R50  0.348
2012 Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biology. 13: R53. PMID 22950368 DOI: 10.1186/Gb-2012-13-9-R53  0.718
2012 Hawse WF, Champion MM, Joyce MV, Hellman LM, Hossain M, Ryan V, Pierce BG, Weng Z, Baker BM. Cutting edge: Evidence for a dynamically driven T cell signaling mechanism. Journal of Immunology (Baltimore, Md. : 1950). 188: 5819-23. PMID 22611242 DOI: 10.4049/Jimmunol.1200952  0.62
2012 Chu SW, Noyes MB, Christensen RG, Pierce BG, Zhu LJ, Weng Z, Stormo GD, Wolfe SA. Exploring the DNA-recognition potential of homeodomains. Genome Research. 22: 1889-98. PMID 22539651 DOI: 10.1101/Gr.139014.112  0.635
2012 Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, et al. Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biology. 13: R27. PMID 22531001 DOI: 10.1186/Gb-2012-13-4-R27  0.381
2012 Xie J, Ameres SL, Friedline R, Hung JH, Zhang Y, Xie Q, Zhong L, Su Q, He R, Li M, Li H, Mu X, Zhang H, Broderick JA, Kim JK, ... Weng Z, et al. Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nature Methods. 9: 403-9. PMID 22388288 DOI: 10.1038/Nmeth.1903  0.627
2012 Vreven T, Hwang H, Pierce BG, Weng Z. Prediction of protein-protein binding free energies. Protein Science : a Publication of the Protein Society. 21: 396-404. PMID 22238219 DOI: 10.1002/Pro.2027  0.797
2012 Shulha HP, Cheung I, Whittle C, Wang J, Virgil D, Lin CL, Guo Y, Lessard A, Akbarian S, Weng Z. Epigenetic signatures of autism: trimethylated H3K4 landscapes in prefrontal neurons. Archives of General Psychiatry. 69: 314-24. PMID 22065254 DOI: 10.1001/Archgenpsychiatry.2011.151  0.657
2012 Hung JH, Yang TH, Hu Z, Weng Z, DeLisi C. Gene set enrichment analysis: performance evaluation and usage guidelines. Briefings in Bioinformatics. 13: 281-91. PMID 21900207 DOI: 10.1093/Bib/Bbr049  0.783
2011 Yildirim O, Li R, Hung JH, Chen PB, Dong X, Ee LS, Weng Z, Rando OJ, Fazzio TG. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell. 147: 1498-510. PMID 22196727 DOI: 10.1016/J.Cell.2011.11.054  0.796
2011 Zhang Z, Xu J, Koppetsch BS, Wang J, Tipping C, Ma S, Weng Z, Theurkauf WE, Zamore PD. Heterotypic piRNA Ping-Pong requires qin, a protein with both E3 ligase and Tudor domains. Molecular Cell. 44: 572-84. PMID 22099305 DOI: 10.1016/J.Molcel.2011.10.011  0.362
2011 Han BW, Hung JH, Weng Z, Zamore PD, Ameres SL. The 3'-to-5' exoribonuclease Nibbler shapes the 3' ends of microRNAs bound to Drosophila Argonaute1. Current Biology : Cb. 21: 1878-87. PMID 22055293 DOI: 10.1016/J.Cub.2011.09.034  0.645
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Weng Z, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031  0.788
2011 Pierce BG, Hourai Y, Weng Z. Accelerating protein docking in ZDOCK using an advanced 3D convolution library. Plos One. 6: e24657. PMID 21949741 DOI: 10.1371/Journal.Pone.0024657  0.641
2011 Li C, Xu J, Li F, Chaudhary SC, Weng Z, Wen J, Elmets CA, Ahsan H, Athar M. Unfolded protein response signaling and MAP kinase pathways underlie pathogenesis of arsenic-induced cutaneous inflammation. Cancer Prevention Research (Philadelphia, Pa.). 4: 2101-9. PMID 21911445 DOI: 10.1158/1940-6207.Capr-11-0343  0.303
2011 Vreven T, Hwang H, Weng Z. Integrating atom-based and residue-based scoring functions for protein-protein docking. Protein Science : a Publication of the Protein Society. 20: 1576-86. PMID 21739500 DOI: 10.1002/Pro.687  0.763
2011 Bonsor DA, Postel S, Pierce BG, Wang N, Zhu P, Buonpane RA, Weng Z, Kranz DM, Sundberg EJ. Molecular basis of a million-fold affinity maturation process in a protein-protein interaction. Journal of Molecular Biology. 411: 321-8. PMID 21689661 DOI: 10.1016/J.Jmb.2011.06.009  0.638
2011 Hwang H, Vreven T, Whitfield TW, Wiehe K, Weng Z. A machine learning approach for the prediction of protein surface loop flexibility. Proteins. 79: 2467-74. PMID 21633973 DOI: 10.1002/Prot.23070  0.795
2011 Jee J, Rozowsky J, Yip KY, Lochovsky L, Bjornson R, Zhong G, Zhang Z, Fu Y, Wang J, Weng Z, Gerstein M. ACT: aggregation and correlation toolbox for analyses of genome tracks. Bioinformatics (Oxford, England). 27: 1152-4. PMID 21349863 DOI: 10.1093/Bioinformatics/Btr092  0.736
2011 Kastritis PL, Moal IH, Hwang H, Weng Z, Bates PA, Bonvin AM, Janin J. A structure-based benchmark for protein-protein binding affinity. Protein Science : a Publication of the Protein Society. 20: 482-91. PMID 21213247 DOI: 10.1002/Pro.580  0.767
2011 Xie J, Xie Q, Zhang H, Ameres SL, Hung JH, Su Q, He R, Mu X, Seher Ahmed S, Park S, Kato H, Li C, Mueller C, Mello CC, Weng Z, et al. MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression. Molecular Therapy : the Journal of the American Society of Gene Therapy. 19: 526-35. PMID 21179009 DOI: 10.1038/Mt.2010.279  0.656
2011 Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, et al. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research. 21: 203-15. PMID 21177969 DOI: 10.1101/Gr.116657.110  0.644
2011 Ameres SL, Hung JH, Xu J, Weng Z, Zamore PD. Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. Rna (New York, N.Y.). 17: 54-63. PMID 21106652 DOI: 10.1261/Rna.2498411  0.67
2010 Khurana JS, Xu J, Weng Z, Theurkauf WE. Distinct functions for the Drosophila piRNA pathway in genome maintenance and telomere protection. Plos Genetics. 6: e1001246. PMID 21179579 DOI: 10.1371/Journal.Pgen.1001246  0.338
2010 Hwang H, Vreven T, Pierce BG, Hung JH, Weng Z. Performance of ZDOCK and ZRANK in CAPRI rounds 13-19 Proteins: Structure, Function and Bioinformatics. 78: 3104-3110. PMID 20936681 DOI: 10.1002/Prot.22764  0.79
2010 Hwang H, Vreven T, Janin J, Weng Z. Protein-protein docking benchmark version 4.0. Proteins. 78: 3111-4. PMID 20806234 DOI: 10.1002/Prot.22830  0.759
2010 Pierce BG, Haidar JN, Yu Y, Weng Z. Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains. Biochemistry. 49: 7050-9. PMID 20681514 DOI: 10.1021/Bi901969A  0.616
2010 Ameres SL, Horwich MD, Hung JH, Xu J, Ghildiyal M, Weng Z, Zamore PD. Target RNA-directed trimming and tailing of small silencing RNAs. Science (New York, N.Y.). 328: 1534-9. PMID 20558712 DOI: 10.1126/Science.1187058  0.645
2010 Landolin JM, Johnson DS, Trinklein ND, Aldred SF, Medina C, Shulha H, Weng Z, Myers RM. Sequence features that drive human promoter function and tissue specificity. Genome Research. 20: 890-8. PMID 20501695 DOI: 10.1101/Gr.100370.109  0.805
2010 Han SJ, Hu J, Pierce B, Weng Z, Renne R. 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. The Journal of General Virology. 91: 2203-15. PMID 20484563 DOI: 10.1099/Vir.0.020958-0  0.652
2010 Connor C, Cheung I, Simon A, Jakovcevski M, Weng Z, Akbarian S. A simple method for improving the specificity of anti-methyl histone antibodies. Epigenetics. 5: 392-5. PMID 20458167 DOI: 10.4161/Epi.5.5.11874  0.322
2010 Cheung I, Shulha HP, Jiang Y, Matevossian A, Wang J, Weng Z, Akbarian S. Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex. Proceedings of the National Academy of Sciences of the United States of America. 107: 8824-9. PMID 20421462 DOI: 10.1073/Pnas.1001702107  0.707
2010 Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nature Structural & Molecular Biology. 17: 635-40. PMID 20418883 DOI: 10.1038/Nsmb.1794  0.38
2010 Hung JH, Whitfield TW, Yang TH, Hu Z, Weng Z, DeLisi C. Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biology. 11: R23. PMID 20187943 DOI: 10.1186/Gb-2010-11-2-R23  0.782
2009 Klattenhoff C, Xi H, Li C, Lee S, Xu J, Khurana JS, Zhang F, Schultz N, Koppetsch BS, Nowosielska A, Seitz H, Zamore PD, Weng Z, Theurkauf WE. The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell. 138: 1137-49. PMID 19732946 DOI: 10.1016/J.Cell.2009.07.014  0.765
2009 Li C, Vagin VV, Lee S, Xu J, Ma S, Xi H, Seitz H, Horwich MD, Syrzycka M, Honda BM, Kittler EL, Zapp ML, Klattenhoff C, Schulz N, Theurkauf WE, ... Weng Z, et al. Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell. 137: 509-21. PMID 19395009 DOI: 10.1016/J.Cell.2009.04.027  0.792
2009 Yu L, Coelho JE, Zhang X, Fu Y, Tillman A, Karaoz U, Fredholm BB, Weng Z, Chen JF. Uncovering multiple molecular targets for caffeine using a drug target validation strategy combining A 2A receptor knockout mice with microarray profiling. Physiological Genomics. 37: 199-210. PMID 19258493 DOI: 10.1152/Physiolgenomics.90353.2008  0.704
2009 Haidar JN, Pierce B, Yu Y, Tong W, Li M, Weng Z. Structure-based design of a T-cell receptor leads to nearly 100-fold improvement in binding affinity for pepMHC. Proteins. 74: 948-60. PMID 18767161 DOI: 10.1002/Prot.22203  0.796
2008 Lee S, Kasif S, Weng Z, Cantor CR. Quantitative analysis of single nucleotide polymorphisms within copy number variation. Plos One. 3: e3906. PMID 19093001 DOI: 10.1371/Journal.Pone.0003906  0.556
2008 Fu Y, Sinha M, Peterson CL, Weng Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. Plos Genetics. 4: e1000138. PMID 18654629 DOI: 10.1371/Journal.Pgen.1000138  0.757
2008 Hwang H, Pierce B, Mintseris J, Janin J, Weng Z. Protein-protein docking benchmark version 3.0. Proteins. 73: 705-9. PMID 18491384 DOI: 10.1002/Prot.22106  0.785
2008 Ghildiyal M, Seitz H, Horwich MD, Li C, Du T, Lee S, Xu J, Kittler EL, Zapp ML, Weng Z, Zamore PD. Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science (New York, N.Y.). 320: 1077-81. PMID 18403677 DOI: 10.1126/Science.1157396  0.576
2008 Weng Z, Guigó R. In silico meets in vivo. Genome Biology. 9: 302. PMID 18304380 DOI: 10.1186/Gb-2008-9-2-302  0.31
2008 Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, ... ... Weng Z, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Research. 18: 393-403. PMID 18258921 DOI: 10.1101/Gr.7080508  0.792
2008 Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE. High-resolution mapping and characterization of open chromatin across the genome. Cell. 132: 311-22. PMID 18243105 DOI: 10.1016/J.Cell.2007.12.014  0.733
2008 Pierce B, Weng Z. A combination of rescoring and refinement significantly improves protein docking performance. Proteins. 72: 270-9. PMID 18214977 DOI: 10.1002/Prot.21920  0.656
2008 Zhang X, Guo C, Chen Y, Shulha HP, Schnetz MP, LaFramboise T, Bartels CF, Markowitz S, Weng Z, Scacheri PC, Wang Z. Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies. Nature Methods. 5: 163-5. PMID 18176569 DOI: 10.1038/Nmeth1170  0.731
2007 Wiehe K, Peterson MW, Pierce B, Mintseris J, Weng Z. Protein-protein docking: Overview and performance analysis Methods in Molecular Biology. 413: 283-314. PMID 18075170 DOI: 10.1007/978-1-59745-574-9_11  0.799
2007 Wiehe K, Pierce B, Tong WW, Hwang H, Mintseris J, Weng Z. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI. Proteins. 69: 719-25. PMID 17803212 DOI: 10.1002/Prot.21747  0.787
2007 Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RD, Chenoweth JG, Tesar PJ, Furey TS, Ren B, Weng Z, Crawford GE. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. Plos Genetics. 3: e136. PMID 17708682 DOI: 10.1371/Journal.Pgen.0030136  0.797
2007 Mintseris J, Pierce B, Wiehe K, Anderson R, Chen R, Weng Z. Integrating statistical pair potentials into protein complex prediction. Proteins. 69: 511-20. PMID 17623839 DOI: 10.1002/Prot.21502  0.799
2007 Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z. Nucleosome positioning signals in genomic DNA. Genome Research. 17: 1170-7. PMID 17620451 DOI: 10.1101/Gr.6101007  0.738
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.802
2007 Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z. Transcription factor binding and modified histones in human bidirectional promoters. Genome Research. 17: 818-27. PMID 17568000 DOI: 10.1101/Gr.5623407  0.817
2007 Xi H, Yu Y, Fu Y, Foley J, Halees A, Weng Z. Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Research. 17: 798-806. PMID 17567998 DOI: 10.1101/Gr.5754707  0.814
2007 Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Research. 17: 787-97. PMID 17567997 DOI: 10.1101/Gr.5573107  0.747
2007 Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Research. 17: 720-31. PMID 17567992 DOI: 10.1101/Gr.5716607  0.794
2007 Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, ... ... Weng Z, et al. The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Research. 17: 691-707. PMID 17567990 DOI: 10.1101/Gr.5704207  0.341
2007 Takehisa J, Kraus MH, Decker JM, Li Y, Keele BF, Bibollet-Ruche F, Zammit KP, Weng Z, Santiago ML, Kamenya S, Wilson ML, Pusey AE, Bailes E, Sharp PM, Shaw GM, et al. Generation of infectious molecular clones of simian immunodeficiency virus from fecal consensus sequences of wild chimpanzees. Journal of Virology. 81: 7463-75. PMID 17494082 DOI: 10.1128/Jvi.00551-07  0.307
2007 Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins. 67: 1078-86. PMID 17373710 DOI: 10.1002/Prot.21373  0.629
2007 Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, Wang W, Weng Z, Green RD, Crawford GE, Ren B. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nature Genetics. 39: 311-318. PMID 17277777 DOI: 10.1038/Ng1966  0.757
2006 Zeller KI, Zhao X, Lee CWH, Kuo PC, Yao F, Yustein JT, Hong SO, Orlov YL, Shahab A, How CY, Fu Y, Weng Z, Kuznetsov VA, Sung WK, Ruan Y, et al. Global mapping of c-Myc binding sites and target gene networks in human B cells Proceedings of the National Academy of Sciences of the United States of America. 103: 17834-17839. PMID 17093053 DOI: 10.1073/Pnas.0604129103  0.754
2006 Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, et al. A global map of p53 transcription-factor binding sites in the human genome. Cell. 124: 207-19. PMID 16413492 DOI: 10.1016/J.Cell.2005.10.043  0.743
2006 Zhu J, Weng Z. FAST: a novel protein structure alignment algorithm. Proteins. 58: 618-27. PMID 15609341 DOI: 10.1002/Prot.20331  0.33
2006 Lin JM, Weng Z. Systematic detection of statistically overrepresented DNA motif association rules. Genome Informatics. 17: 124-133. DOI: 10.11234/Gi1990.17.124  0.396
2005 Fu Y, Weng Z. Improvement of TRANSFAC matrices using multiple local alignment of transcription factor binding site sequences. Genome Informatics. International Conference On Genome Informatics. 16: 68-72. PMID 16362908 DOI: 10.11234/Gi1990.16.68  0.743
2005 Szustakowski JD, Kasif S, Weng Z. Less is more: towards an optimal universal description of protein folds. Bioinformatics (Oxford, England). 21: ii66-71. PMID 16204127 DOI: 10.1093/Bioinformatics/Bti1111  0.69
2005 Leyfer D, Weng Z. Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering. Bioinformatics (Oxford, England). 21: ii197-203. PMID 16204103 DOI: 10.1093/Bioinformatics/Bti1131  0.8
2005 Yu L, Haverty PM, Mariani J, Wang Y, Shen HY, Schwarzschild MA, Weng Z, Chen JF. Genetic and pharmacological inactivation of adenosine A2A receptor reveals an Egr-2-mediated transcriptional regulatory network in the mouse striatum. Physiological Genomics. 23: 89-102. PMID 16046619 DOI: 10.1152/Physiolgenomics.00068.2005  0.671
2005 Mintseris J, Weng Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 102: 10930-5. PMID 16043700 DOI: 10.1073/Pnas.0502667102  0.726
2005 Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z. Protein-Protein Docking Benchmark 2.0: an update. Proteins. 60: 214-6. PMID 15981264 DOI: 10.1002/Prot.20560  0.789
2005 Wiehe K, Pierce B, Mintseris J, Tong WW, Anderson R, Chen R, Weng Z. ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins. 60: 207-13. PMID 15981263 DOI: 10.1002/Prot.20559  0.787
2005 Yanai I, Yu Y, Zhu X, Cantor CR, Weng Z. An avidin-like domain that does not bind biotin is adopted for oligomerization by the extracellular mosaic protein fibropellin. Protein Science : a Publication of the Protein Society. 14: 417-23. PMID 15659374 DOI: 10.1110/Ps.04898705  0.644
2005 Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ, Makeev VJ, Mironov AA, Noble WS, Pavesi G, Pesole G, ... ... Weng Z, et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology. 23: 137-44. PMID 15637633 DOI: 10.1038/Nbt1053  0.787
2005 Pierce B, Tong W, Weng Z. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. Bioinformatics (Oxford, England). 21: 1472-8. PMID 15613396 DOI: 10.1093/Bioinformatics/Bti229  0.788
2005 Burden HE, Weng Z. Identification of conserved structural features at sequentially degenerate locations in transcription factor binding sites. Genome Informatics. 16: 49-58. DOI: 10.11234/Gi1990.16.49  0.351
2005 Haverty PM, Weng Z, Hansen U. Transcriptional Regulatory Networks Activated by PI3K and ERK Transduced Growth Signals in Human Glioblastoma Cells Journal of Computer Science and Technology. 20: 439-445. DOI: 10.1007/S11390-005-0439-9  0.684
2004 Mintseris J, Weng Z. Optimizing protein representations with information theory. Genome Informatics. International Conference On Genome Informatics. 15: 160-9. PMID 15712119 DOI: 10.11234/Gi1990.15.160  0.72
2004 Haverty PM, Hsiao LL, Gullans SR, Hansen U, Weng Z. Limited agreement among three global gene expression methods highlights the requirement for non-global validation. Bioinformatics (Oxford, England). 20: 3431-41. PMID 15256402 DOI: 10.1093/Bioinformatics/Bth421  0.669
2004 Fu Y, Frith MC, Haverty PM, Weng Z. MotifViz: an analysis and visualization tool for motif discovery. Nucleic Acids Research. 32: W420-3. PMID 15215422 DOI: 10.1093/Nar/Gkh426  0.8
2004 Hu Z, Fu Y, Halees AS, Kielbasa SM, Weng Z. SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. Nucleic Acids Research. 32: W235-41. PMID 15215387 DOI: 10.1093/Nar/Gkh483  0.804
2004 Haverty PM, Frith MC, Weng Z. CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. Nucleic Acids Research. 32: W213-6. PMID 15215383 DOI: 10.1093/Nar/Gkh402  0.755
2004 Halees AS, Weng Z. PromoSer: improvements to the algorithm, visualization and accessibility. Nucleic Acids Research. 32: W191-4. PMID 15215378 DOI: 10.1093/Nar/Gkh433  0.767
2004 Leyfer D, Bond A, Tworog E, Perron D, Maska S, Brito A, Kamens J, Weng Z, Voss J. cis-Element clustering correlates with dose-dependent pro- and antisignaling effects of IL18. Genes and Immunity. 5: 354-62. PMID 15190265 DOI: 10.1038/Sj.Gene.6364099  0.769
2004 Yu L, Frith MC, Suzuki Y, Peterfreund RA, Gearan T, Sugano S, Schwarzschild MA, Weng Z, Fink JS, Chen JF. Characterization of genomic organization of the adenosine A2A receptor gene by molecular and bioinformatics analyses. Brain Research. 1000: 156-73. PMID 15053963 DOI: 10.1016/J.Brainres.2003.11.072  0.624
2004 Haverty PM, Weng Z. CisML: an XML-based format for sequence motif detection software. Bioinformatics (Oxford, England). 20: 1815-7. PMID 15001475 DOI: 10.1093/Bioinformatics/Bth162  0.66
2004 Frith MC, Fu Y, Yu L, Chen JF, Hansen U, Weng Z. Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Research. 32: 1372-81. PMID 14988425 DOI: 10.1093/Nar/Gkh299  0.809
2004 Frith MC, Halees AS, Hansen U, Weng Z. Site2genome: locating short DNA sequences in whole genomes. Bioinformatics (Oxford, England). 20: 1468-9. PMID 14962939 DOI: 10.1093/Bioinformatics/Bth094  0.793
2004 Frith MC, Hansen U, Spouge JL, Weng Z. Finding functional sequence elements by multiple local alignment. Nucleic Acids Research. 32: 189-200. PMID 14704356 DOI: 10.1093/Nar/Gkh169  0.746
2004 Haverty PM, Hansen U, Weng Z. Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Research. 32: 179-88. PMID 14704355 DOI: 10.1093/Nar/Gkh183  0.699
2003 Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins. 53: 693-707. PMID 14579360 DOI: 10.1002/Prot.10460  0.432
2003 Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins. 53: 629-39. PMID 14579354 DOI: 10.1002/Prot.10432  0.73
2003 Peters B, Tong W, Sidney J, Sette A, Weng Z. Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinformatics (Oxford, England). 19: 1765-72. PMID 14512347 DOI: 10.1093/Bioinformatics/Btg247  0.733
2003 Weng Z. Managing biological sequence and protein structure data. Omics : a Journal of Integrative Biology. 7: 25-6. PMID 12831551 DOI: 10.1089/153623103322006544  0.347
2003 Frith MC, Li MC, Weng Z. Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Research. 31: 3666-8. PMID 12824389 DOI: 10.1093/Nar/Gkg540  0.63
2003 Halees AS, Leyfer D, Weng Z. PromoSer: A large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Research. 31: 3554-9. PMID 12824364 DOI: 10.1093/Nar/Gkg549  0.798
2003 Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins. 52: 88-91. PMID 12784372 DOI: 10.1002/Prot.10390  0.737
2003 Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins. 52: 80-7. PMID 12784371 DOI: 10.1002/Prot.10389  0.451
2003 Chen R, Tong W, Mintseris J, Li L, Weng Z. ZDOCK predictions for the CAPRI challenge. Proteins. 52: 68-73. PMID 12784369 DOI: 10.1002/Prot.10388  0.794
2003 Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins. 51: 397-408. PMID 12696051 DOI: 10.1002/Prot.10334  0.489
2003 Hu Z, Frith M, Niu T, Weng Z. SeqVISTA: a graphical tool for sequence feature visualization and comparison. Bmc Bioinformatics. 4: 1. PMID 12513700 DOI: 10.1186/1471-2105-4-1  0.627
2002 Kasif S, Weng Z, Derti A, Beigel R, DeLisi C. A computational framework for optimal masking in the synthesis of oligonucleotide microarrays. Nucleic Acids Research. 30: e106. PMID 12384608 DOI: 10.1093/Nar/Gnf105  0.786
2002 Wong JY, Weng Z, Moll S, Kim S, Brown CT. Identification and validation of a novel cell-recognition site (KNEED) on the 8th type III domain of fibronectin. Biomaterials. 23: 3865-70. PMID 12164191 DOI: 10.1016/S0142-9612(02)00127-8  0.325
2002 Frith MC, Spouge JL, Hansen U, Weng Z. Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Research. 30: 3214-24. PMID 12136103 DOI: 10.1093/Nar/Gkf438  0.744
2002 Resendes BL, Robertson NG, Szustakowski JD, Resendes RJ, Weng Z, Morton CC. Gene discovery in the auditory system: characterization of additional cochlear-expressed sequences. Journal of the Association For Research in Otolaryngology : Jaro. 3: 45-53. PMID 12083723 DOI: 10.1007/S101620020005  0.706
2002 Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins. 47: 281-94. PMID 11948782 DOI: 10.1002/Prot.10092  0.461
2002 Haverty PM, Weng Z, Best NL, Auerbach KR, Hsiao LL, Jensen RV, Gullans SR. HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues. Nucleic Acids Research. 30: 214-7. PMID 11752297 DOI: 10.1093/Nar/30.1.214  0.666
2002 Weng Z, DeLisi C. Protein therapeutics: promises and challenges for the 21st century. Trends in Biotechnology. 20: 29-35. PMID 11742675 DOI: 10.1016/S0167-7799(01)01846-7  0.556
2002 Frith MC, Hansen U, Weng Z. Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics (Oxford, England). 17: 878-89. PMID 11673232 DOI: 10.1093/Bioinformatics/17.10.878  0.632
2002 Frith MC, Graber JH, Weng Z, Spouge JL. Gapless Local Alignment of Multiple Sequences Genome Informatics. 13: 436-437. DOI: 10.11234/Gi1990.13.436  0.701
2001 Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV, Misra J, Dillon W, Lee KF, Clark KE, Haverty P, Weng Z, Mutter GL, Frosch MP, MacDonald ME, Milford EL, et al. A compendium of gene expression in normal human tissues. Physiological Genomics. 7: 97-104. PMID 11773596 DOI: 10.1152/Physiolgenomics.00040.2001  0.657
2000 Szustakowski JD, Weng Z. Protein structure alignment using a genetic algorithm. Proteins. 38: 428-40. PMID 10707029 DOI: 10.1002/(Sici)1097-0134(20000301)38:4<428::Aid-Prot8>3.0.Co;2-N  0.707
1999 Camacho CJ, Weng Z, Vajda S, DeLisi C. Free energy landscapes of encounter complexes in protein-protein association. Biophysical Journal. 76: 1166-78. PMID 10049302 DOI: 10.1016/S0006-3495(99)77281-4  0.685
1999 Skvorak AB, Weng Z, Yee AJ, Robertson NG, Morton CC. Human cochlear expressed sequence tags provide insight into cochlear gene expression and identify candidate genes for deafness. Human Molecular Genetics. 8: 439-52. PMID 9949203 DOI: 10.1093/Hmg/8.3.439  0.332
1998 Weng Z, Gulukota K, Vaughn DE, Bjorkman PJ, DeLisi C. Computational determination of the structure of rat Fc bound to the neonatal Fc receptor. Journal of Molecular Biology. 282: 217-25. PMID 9735282 DOI: 10.1006/Jmbi.1998.2020  0.775
1998 Weng Z, DeLisi C. Toward a predictive understanding of molecular recognition. Immunological Reviews. 163: 251-66. PMID 9700515 DOI: 10.1111/J.1600-065X.1998.Tb01201.X  0.539
1998 Zhang C, Kimura SR, Weng Z, Vajda S, Brower RC, Delisi C. The waters of life Journal of the Franklin Institute. 335: 213-240. DOI: 10.1016/S0016-0032(97)00020-3  0.78
1997 DeLisi C, Cantor C, Weng Z. Hedgehogs, foxes, and a new science. Nature Biotechnology. 15: 819. PMID 9306387 DOI: 10.1038/Nbt0997-819  0.468
1997 Weng Z, Delisi C, Vajda S. Empirical free energy calculation: Comparison to calorimetric data Protein Science. 6: 1976-1984. PMID 9300497 DOI: 10.1002/Pro.5560060918  0.534
1996 Weng Z, Vajda S, Delisi C. Prediction of protein complexes using empirical free energy functions Protein Science. 5: 614-626. PMID 8845751 DOI: 10.1002/Pro.5560050406  0.573
1995 Vajda S, Weng Z, Delisi C. Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments Protein Engineering, Design and Selection. 8: 1081-1092. PMID 8819974 DOI: 10.1093/Protein/8.11.1081  0.54
1994 Vajda S, Weng Z, Rosenfeld R, DeLisi C. Effect of conformational flexibility and solvation on receptor - Ligand binding free energies Biochemistry. 33: 13977-13988. PMID 7947806 DOI: 10.1021/Bi00251A004  0.778
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