| Year |
Citation |
Score |
| 2023 |
Cao J, Yu T, Xu B, Hu Z, Zhang XO, Theurkauf WE, Weng Z. Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster. Nucleic Acids Research. PMID 36762470 DOI: 10.1093/nar/gkad054 |
0.697 |
|
| 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 |
0.665 |
|
| 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 |
0.72 |
|
| 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 |
0.698 |
|
| 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 |
0.712 |
|
| 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 |
0.705 |
|
| 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 |
0.564 |
|
| 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 |
0.544 |
|
| 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 |
0.698 |
|
| 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 |
0.324 |
|
| 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 |
0.739 |
|
| 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 |
0.395 |
|
| 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 |
0.316 |
|
| 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 |
0.66 |
|
| 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 |
0.698 |
|
| 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 |
0.335 |
|
| 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 |
0.379 |
|
| 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 |
0.353 |
|
| 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 |
0.694 |
|
| 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 |
0.37 |
|
| 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 |
0.381 |
|
| 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 |
0.306 |
|
| 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 |
0.629 |
|
| 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 |
0.357 |
|
| 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 |
0.357 |
|
| 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 |
0.722 |
|
| 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 |
0.366 |
|
| 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 |
0.34 |
|
| 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 |
0.683 |
|
| 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 |
0.312 |
|
| 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 |
0.309 |
|
| 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 |
0.369 |
|
| 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 |
0.335 |
|
| 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 |
0.369 |
|
| 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 |
0.705 |
|
| 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 |
0.687 |
|
| 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 |
0.305 |
|
| 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 |
0.329 |
|
| 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 |
0.704 |
|
| 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 |
0.353 |
|
| 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 |
0.322 |
|
| 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 |
0.333 |
|
| 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 |
0.33 |
|
| 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 |
0.356 |
|
| 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 |
0.701 |
|
| 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 |
0.401 |
|
| 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 |
0.337 |
|
| 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 |
0.305 |
|
| 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 |
0.324 |
|
| 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 |
0.571 |
|
| 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 |
0.337 |
|
| 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 |
0.7 |
|
| 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 |
0.331 |
|
| 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 |
0.346 |
|
| 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 |
0.633 |
|
| 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 |
0.313 |
|
| 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 |
0.324 |
|
| 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 |
0.635 |
|
| 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 |
0.614 |
|
| 2016 |
Hung JH, Weng Z. Mapping Short Sequence Reads to a Reference Genome. Cold Spring Harbor Protocols. PMID 27574204 DOI: 10.1101/Pdb.Prot093161 |
0.674 |
|
| 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 |
0.665 |
|
| 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 |
0.633 |
|
| 2016 |
Hung JH, Weng Z. Analyzing Microarray Data. Cold Spring Harbor Protocols. PMID 27574201 DOI: 10.1101/Pdb.Prot093112 |
0.664 |
|
| 2016 |
Hung JH, Weng Z. Sequence Alignment and Homology Search. Cold Spring Harbor Protocols. PMID 27574200 DOI: 10.1101/Pdb.Top093070 |
0.697 |
|
| 2016 |
Hung JH, Weng Z. Discovering cis-Regulatory Motifs. Cold Spring Harbor Protocols. PMID 27574199 DOI: 10.1101/Pdb.Prot093203 |
0.69 |
|
| 2016 |
Hung JH, Weng Z. Visualizing Genomic Annotations with the UCSC Genome Browser. Cold Spring Harbor Protocols. PMID 27574198 DOI: 10.1101/Pdb.Prot093062 |
0.688 |
|
| 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 |
0.665 |
|
| 2016 |
Hung JH, Weng Z. Peak-Finding Algorithms. Cold Spring Harbor Protocols. PMID 27574196 DOI: 10.1101/Pdb.Top093179 |
0.689 |
|
| 2016 |
Hung JH, Weng Z. Motif Finding. Cold Spring Harbor Protocols. PMID 27574195 DOI: 10.1101/pdb.top093195 |
0.672 |
|
| 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 |
0.673 |
|
| 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 |
0.651 |
|
| 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 |
0.328 |
|
| 2016 |
Hung JH, Weng Z. Data Formats in Bioinformatics. Cold Spring Harbor Protocols. 2016: pdb.top093211. PMID 27480726 DOI: 10.1101/Pdb.Top093211 |
0.627 |
|
| 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 |
0.381 |
|
| 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 |
0.638 |
|
| 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 |
0.624 |
|
| 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 |
0.621 |
|
| 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 |
0.318 |
|
| 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 |
0.623 |
|
| 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 |
0.305 |
|
| 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 |
0.342 |
|
| 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 |
0.72 |
|
| 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 |
0.323 |
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| 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 |
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| 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 |
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| 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 |
0.34 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.319 |
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| 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 |
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| 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 |
0.59 |
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| 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 |
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| 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 |
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| 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 |
0.701 |
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| 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 |
0.565 |
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| 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 |
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| 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 |
0.39 |
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| 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 |
0.595 |
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| 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 |
0.333 |
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| 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 |
0.67 |
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| 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 |
0.622 |
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| 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 |
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| 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 |
0.684 |
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| 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 |
0.626 |
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| 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 |
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| 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 |
0.769 |
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| 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 |
0.794 |
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| 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 |
0.57 |
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| 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 |
0.576 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.709 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.645 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
0.323 |
|
| 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 |
0.701 |
|
| 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 |
0.382 |
|
| 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 |
0.755 |
|
| 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 |
0.783 |
|
| 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 |
0.701 |
|
| 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 |
0.792 |
|
| 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 |
0.518 |
|
| 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 |
0.756 |
|
| 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 |
0.784 |
|
| 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 |
0.54 |
|
| 2008 |
Weng Z, Guigó R. In silico meets in vivo. Genome Biology. 9: 302. PMID 18304380 DOI: 10.1186/Gb-2008-9-2-302 |
0.312 |
|
| 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 |
0.729 |
|
| 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 |
0.646 |
|
| 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 |
0.725 |
|
| 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 |
0.736 |
|
| 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 |
0.803 |
|
| 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 |
0.818 |
|
| 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 |
0.746 |
|
| 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 |
0.795 |
|
| 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 |
0.343 |
|
| 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 |
0.308 |
|
| 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 |
0.62 |
|
| 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 |
0.756 |
|
| 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 |
0.753 |
|
| 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 |
0.742 |
|
| 2006 |
Zhu J, Weng Z. FAST: a novel protein structure alignment algorithm. Proteins. 58: 618-27. PMID 15609341 DOI: 10.1002/Prot.20331 |
0.328 |
|
| 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 |
0.398 |
|
| 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 |
0.741 |
|
| 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 |
0.687 |
|
| 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 |
0.801 |
|
| 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 |
0.672 |
|
| 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 |
0.712 |
|
| 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 |
0.788 |
|
| 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 |
0.633 |
|
| 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 |
0.784 |
|
| 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 |
0.352 |
|
| 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 |
0.705 |
|
| 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 |
0.67 |
|
| 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 |
0.753 |
|
| 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 |
0.619 |
|
| 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 |
0.81 |
|
| 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 |
0.741 |
|
| 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 |
0.7 |
|
| 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 |
0.422 |
|
| 2003 |
Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins. 53: 629-39. PMID 14579354 DOI: 10.1002/Prot.10432 |
0.716 |
|
| 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 |
0.705 |
|
| 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 |
0.625 |
|
| 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 |
0.799 |
|
| 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 |
0.722 |
|
| 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 |
0.442 |
|
| 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 |
0.48 |
|
| 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 |
0.621 |
|
| 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 |
0.74 |
|
| 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 |
0.451 |
|
| 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 |
0.667 |
|
| 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 |
0.555 |
|
| 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 |
0.626 |
|
| 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 |
0.696 |
|
| 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 |
0.705 |
|
| 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 |
0.681 |
|
| 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 |
0.335 |
|
| 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 |
0.537 |
|
| 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 |
0.597 |
|
| 1997 |
DeLisi C, Cantor C, Weng Z. Hedgehogs, foxes, and a new science. Nature Biotechnology. 15: 819. PMID 9306387 DOI: 10.1038/Nbt0997-819 |
0.467 |
|
| 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 |
0.532 |
|
| 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 |
0.571 |
|
| 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 |
0.537 |
|
| 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 |
0.777 |
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