Zhiping Weng - Publications

Biomedical Engineering Boston University, Boston, MA, United States 

274 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
2021 Belaghzal H, Borrman T, Stephens AD, Lafontaine DL, Venev SV, Weng Z, Marko JF, Dekker J. Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics. Nature Genetics. PMID 33574602 DOI: 10.1038/s41588-021-00784-4  0.56
2021 Yu T, Huang X, Dou S, Tang X, Luo S, Theurkauf WE, Lu J, Weng Z. A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies. Nucleic Acids Research. PMID 33511407 DOI: 10.1093/nar/gkab010  0.8
2021 Yu T, Fan K, Özata DM, Zhang G, Fu Y, Theurkauf WE, Zamore PD, Weng Z. Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes. Nature Communications. 12: 73. PMID 33397987 DOI: 10.1038/s41467-020-20345-3  1
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  0.88
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  1
2020 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. Author Correction: PGBD5 promotes site-specific oncogenic mutations in human tumors. Nature Genetics. PMID 32918070 DOI: 10.1038/s41588-020-00711-z  0.56
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  0.8
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  0.8
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  0.72
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  1
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  0.8
2020 Lu A, Watkins M, Li Q, Robinson SD, Concepcion GP, Yandell M, Weng Z, Olivera BM, Safavi-Hemami H, Fedosov AE. Transcriptomic profiling reveals extraordinary diversity of venom peptides in unexplored predatory gastropods of the genus Clavus. Genome Biology and Evolution. PMID 32333764 DOI: 10.1093/gbe/evaa083  0.56
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  0.8
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  0.8
2020 Espeso-Gil S, Halene T, Bendl J, Kassim B, Ben Hutta G, Iskhakova M, Shokrian N, Auluck P, Javidfar B, Rajarajan P, Chandrasekaran S, Peter CJ, Cote A, Birnbaum R, Liao W, ... ... Weng Z, et al. A chromosomal connectome for psychiatric and metabolic risk variants in adult dopaminergic neurons. Genome Medicine. 12: 19. PMID 32075678 DOI: 10.1186/s13073-020-0715-x  0.6
2020 Sun YH, Zhu J, Xie LH, Li Z, Meduri R, Zhu X, Song C, Chen C, Ricci EP, Weng Z, Li XZ. Author Correction: Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors. Nature Cell Biology. PMID 32066908 DOI: 10.1038/s41556-020-0482-3  0.84
2020 Sun YH, Zhu J, Xie LH, Li Z, Meduri R, Zhu X, Song C, Chen C, Ricci EP, Weng Z, Li XZ. Ribosomes guide pachytene piRNA formation on long intergenic piRNA precursors. Nature Cell Biology. PMID 32015435 DOI: 10.1038/s41556-019-0457-4  0.84
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  0.8
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  0.8
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  0.6
2020 Casserly AP, Tsuji J, Zhao-Shea R, Smith CB, Molas S, Tapper AR, Weng Z, Gardner PD. Integrated miRNA-/mRNA-Seq of the Habenulo-Interpeduncular Circuit During Acute Nicotine Withdrawal. Scientific Reports. 10: 813. PMID 31965003 DOI: 10.1038/s41598-020-57907-w  0.68
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  0.84
2019 Gusev FE, Reshetov DA, Mitchell AC, Andreeva TV, Dincer A, Grigorenko AP, Fedonin G, Halene T, Aliseychik M, Filippova E, Weng Z, Akbarian S, Rogaev EI. Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia. Translational Psychiatry. 9: 256. PMID 31624234 DOI: 10.1038/s41398-019-0596-1  0.6
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  0.88
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  0.8
2019 Li C, Mishra B, Kashyap M, Weng Z, Andrabi SA, Mukhtar SM, Kim AL, Bickers DR, Kopelovich L, Athar M. Patched1 haploinsufficiency severely impacts intermediary metabolism in the skin of Ptch1/ODC transgenic mice. Scientific Reports. 9: 13072. PMID 31506465 DOI: 10.1038/s41598-019-49470-w  0.68
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  0.4
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  0.8
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  0.8
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  0.6
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  0.8
2019 Ge DT, Wang W, Tipping C, Gainetdinov I, Weng Z, Zamore PD. The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria. Molecular Cell. PMID 31076285 DOI: 10.1016/j.molcel.2019.04.006  0.84
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  0.6
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  0.8
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  0.6
2018 Rajarajan P, Borrman T, Liao W, Schrode N, Flaherty E, Casiño C, Powell S, Yashaswini C, LaMarca EA, Kassim B, Javidfar B, Espeso-Gil S, Li A, Won H, Geschwind DH, ... ... Weng Z, et al. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk. Science (New York, N.Y.). 362. PMID 30545851 DOI: 10.1126/science.aat4311  0.6
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  0.84
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  0.8
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  1
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  0.76
2018 Girdhar K, Hoffman GE, Jiang Y, Brown L, Kundakovic M, Hauberg ME, Francoeur NJ, Wang YC, Shah H, Kavanagh DH, Zharovsky E, Jacobov R, Wiseman JR, Park R, Johnson JS, ... ... Weng Z, et al. Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome. Nature Neuroscience. PMID 30038276 DOI: 10.1038/s41593-018-0187-0  0.6
2018 Fu Y, Wu PH, Beane T, Zamore PD, Weng Z. Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers. Bmc Genomics. 19: 531. PMID 30001700 DOI: 10.1186/s12864-018-4933-1  1
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  0.64
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  0.8
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  0.6
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  0.8
2018 Song CQ, Wang D, Jiang T, O'Connor K, Tang Q, Cai L, Li X, Weng Z, Yin H, Gao G, Mueller C, Flotte TR, Xue W. In vivo genome editing partially restores alpha1-antitrypsin in a murine model of AAT deficiency. Human Gene Therapy. PMID 29597895 DOI: 10.1089/hum.2017.225  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  1
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  1
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  0.8
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. Erratum: PGBD5 promotes site-specific oncogenic mutations in human tumors. Nature Genetics. 49: 1558. PMID 28951624 DOI: 10.1038/ng1017-1558b  0.56
2017 Krasemann S, Madore C, Cialic R, Baufeld C, Calcagno N, El Fatimy R, Beckers L, O'Loughlin E, Xu Y, Fanek Z, Greco DJ, Smith ST, Tweet G, Humulock Z, Zrzavy T, ... ... Weng Z, et al. The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases. Immunity. 47: 566-581.e9. PMID 28930663 DOI: 10.1016/j.immuni.2017.08.008  0.8
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  0.56
2017 Parhad SS, Tu S, Weng Z, Theurkauf WE. Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery. Developmental Cell. PMID 28919205 DOI: 10.1016/j.devcel.2017.08.012  0.8
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  0.88
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  0.84
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  0.8
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  0.56
2017 Mou H, Moore J, Malonia SK, Li Y, Ozata DM, Hough S, Song CQ, Smith JL, Fischer A, Weng Z, Green MR, Xue W. Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis. Proceedings of the National Academy of Sciences of the United States of America. PMID 28320962 DOI: 10.1073/pnas.1620861114  0.8
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  0.8
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  0.88
2016 Song CQ, Li Y, Mou H, Moore J, Park A, Pomyen Y, Hough S, Kennedy Z, Fischer A, Yin H, Anderson DG, Conte D, Zender L, Wang XW, Thorgeirsson S, ... Weng Z, et al. Genome-wide CRISPR Screen Identifies Regulators of MAPK as Suppressors of Liver Tumors in Mice. Gastroenterology. PMID 27956228 DOI: 10.1053/j.gastro.2016.12.002  0.8
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  0.68
2016 Srivastava RK, Li C, Weng Z, Agarwal A, Elmets CA, Afaq F, Athar M. Defining cutaneous molecular pathobiology of arsenicals using phenylarsine oxide as a prototype. Scientific Reports. 6: 34865. PMID 27725709 DOI: 10.1038/srep34865  0.68
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  0.88
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  0.88
2016 Hung JH, Weng Z. Mapping Short Sequence Reads to a Reference Genome. Cold Spring Harbor Protocols. PMID 27574204 DOI: 10.1101/pdb.prot093161  1
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  1
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  0.96
2016 Hung JH, Weng Z. Analyzing Microarray Data. Cold Spring Harbor Protocols. PMID 27574201 DOI: 10.1101/pdb.prot093112  1
2016 Hung JH, Weng Z. Sequence Alignment and Homology Search. Cold Spring Harbor Protocols. PMID 27574200 DOI: 10.1101/pdb.top093070  1
2016 Hung JH, Weng Z. Discovering cis-Regulatory Motifs. Cold Spring Harbor Protocols. PMID 27574199 DOI: 10.1101/pdb.prot093203  1
2016 Hung JH, Weng Z. Visualizing Genomic Annotations with the UCSC Genome Browser. Cold Spring Harbor Protocols. PMID 27574198 DOI: 10.1101/pdb.prot093062  1
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  1
2016 Hung JH, Weng Z. Peak-Finding Algorithms. Cold Spring Harbor Protocols. PMID 27574196 DOI: 10.1101/pdb.top093179  1
2016 Hung JH, Weng Z. Motif Finding. Cold Spring Harbor Protocols. PMID 27574195 DOI: 10.1101/pdb.top093195  1
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  1
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  1
2016 Li C, Srivastava RK, Weng Z, Croutch CR, Agarwal A, Elmets CA, Afaq F, Athar M. Molecular Mechanism Underlying Pathogenesis of Lewisite-Induced Cutaneous Blistering and Inflammation: Chemical Chaperones as Potential Novel Antidotes. The American Journal of Pathology. PMID 27528504 DOI: 10.1016/j.ajpath.2016.06.012  0.68
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  0.56
2016 Hung JH, Weng Z. Data Formats in Bioinformatics. Cold Spring Harbor Protocols. 2016: pdb.top093211. PMID 27480726 DOI: 10.1101/pdb.top093211  0.96
2016 Labadorf A, Hoss AG, Lagomarsino V, Latourelle JC, Hadzi TC, Bregu J, MacDonald ME, Gusella JF, Chen JF, Akbarian S, Weng Z, Myers RH. Correction: RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression. Plos One. 11: e0160295. PMID 27454300 DOI: 10.1371/journal.pone.0160295  0.72
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  0.32
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  0.52
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  0.52
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  0.68
2016 Weng Z, Liu T, Wu C, Cao Z. Mechanism design and kinematic performance research of snake-like robot with orthogonal active wheels Mechanisms and Machine Science. 36: 603-615. DOI: 10.1007/978-3-319-23327-7_52  0.88
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  0.92
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  0.68
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  0.76
2015 Chaudhary SC, Tang X, Arumugam A, Li C, Srivastava RK, Weng Z, Xu J, Zhang X, Kim AL, McKay K, Elmets CA, Kopelovich L, Bickers DR, Athar M. Shh and p50/Bcl3 signaling crosstalk drives pathogenesis of BCCs in Gorlin syndrome. Oncotarget. PMID 26413810 DOI: 10.18632/oncotarget.5103  0.52
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  0.92
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  0.92
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  0.92
2015 Wang D, Mou H, Li S, Li Y, Hough S, Tran K, Li J, Yin H, Anderson DG, Sontheimer EJ, Weng Z, Gao G, Xue W. Adenovirus-Mediated Somatic Genome Editing of Pten by CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses. Human Gene Therapy. 26: 432-42. PMID 26086867 DOI: 10.1089/hum.2015.087  0.92
2015 Li Y, Park AI, Mou H, Colpan C, Bizhanova A, Akama-Garren E, Joshi N, Hendrickson EA, Feldser D, Yin H, Anderson DG, Jacks T, Weng Z, Xue W. A versatile reporter system for CRISPR-mediated chromosomal rearrangements. Genome Biology. 16: 111. PMID 26018130 DOI: 10.1186/s13059-015-0680-7  0.92
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  0.68
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  0.68
2015 Hoss AG, Labadorf A, Latourelle JC, Kartha VK, Hadzi TC, Gusella JF, MacDonald ME, Chen JF, Akbarian S, Weng Z, Vonsattel JP, Myers RH. miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement. Bmc Medical Genomics. 8: 10. PMID 25889241 DOI: 10.1186/s12920-015-0083-3  0.92
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  0.92
2015 Gao M, Thomson TC, Creed TM, Tu S, Loganathan SN, Jackson CA, McCluskey P, Lin Y, Collier SE, Weng Z, Lasko P, Ohi MD, Arkov AL. Glycolytic enzymes localize to ribonucleoprotein granules in Drosophila germ cells, bind Tudor and protect from transposable elements. Embo Reports. 16: 379-86. PMID 25600116 DOI: 10.15252/embr.201439694  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/pnas.1410434111  0.92
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  0.88
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  0.92
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  0.32
2014 Arumugam A, Weng Z, Chaudhary SC, Afaq F, Elmets CA, Athar M. Keratin-6 driven ODC expression to hair follicle keratinocytes enhances stemness and tumorigenesis by negatively regulating Notch. Biochemical and Biophysical Research Communications. 451: 394-401. PMID 25094045 DOI: 10.1016/j.bbrc.2014.07.129  0.56
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2014 Zhang Z, Koppetsch BS, Wang J, Tipping C, Weng Z, Theurkauf WE, Zamore PD. Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the Tudor-domain protein Qin. The Embo Journal. 33: 536-9. PMID 24652836 DOI: 10.1002/embj.201384895  0.92
2014 Xu J, Weng Z, Arumugam A, Tang X, Chaudhary SC, Li C, Christiano AM, Elmets CA, Bickers DR, Athar M. Hair follicle disruption facilitates pathogenesis to UVB-induced cutaneous inflammation and basal cell carcinoma development in Ptch(+/-) mice. The American Journal of Pathology. 184: 1529-40. PMID 24631180 DOI: 10.1016/j.ajpath.2014.01.013  0.8
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  0.92
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  0.92
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  0.88
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  0.6
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  0.92
2014 Chaudhary SC, Singh T, Talwelkar SS, Srivastava RK, Arumugam A, Weng Z, Elmets CA, Afaq F, Kopelovich L, Athar M. Erb-041, an estrogen receptor-β agonist, inhibits skin photocarcinogenesis in SKH-1 hairless mice by downregulating the WNT signaling pathway. Cancer Prevention Research (Philadelphia, Pa.). 7: 186-98. PMID 24217507 DOI: 10.1158/1940-6207.CAPR-13-0276  0.56
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  0.92
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  0.84
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  0.88
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  0.92
2013 Arumugam A, Weng Z, Talwelkar SS, Chaudhary SC, Kopelovich L, Elmets CA, Afaq F, Athar M. Inhibiting cycloxygenase and ornithine decarboxylase by diclofenac and alpha-difluoromethylornithine blocks cutaneous SCCs by targeting Akt-ERK axis. Plos One. 8: e80076. PMID 24260338 DOI: 10.1371/journal.pone.0080076  0.56
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  0.88
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  0.92
2013 Zhang L, Zhang Z, Weng Z, Shi W. Substitution rates of the internal genes in the novel avian H7N9 influenza virus. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 57: 1213-5. PMID 23821733 DOI: 10.1093/cid/cit447  1
2013 Zhang L, Zhang Z, Weng Z. Rapid reassortment of internal genes in avian influenza A(H7N9) virus. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 57: 1059-61. PMID 23788242 DOI: 10.1093/cid/cit414  1
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  0.88
2013 Li C, Weng Z, Doran SF, Srivastava RK, Afaq F, Matalon S, Athar M. Chlorine induces the unfolded protein response in murine lungs and skin. American Journal of Respiratory Cell and Molecular Biology. 49: 197-203. PMID 23668485 DOI: 10.1165/rcmb.2012-0488RC  0.68
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  0.92
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  1
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  0.92
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  1
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  0.84
2013 Tu S, Pederson T, Weng Z. Networking development by Boolean logic. Nucleus (Austin, Tex.). 4: 89-91. PMID 23412653 DOI: 10.4161/nucl.23986  0.8
2013 Chaudhary SC, Singh T, Kapur P, Weng Z, Arumugam A, Elmets CA, Kopelovich L, Athar M. Nitric oxide-releasing sulindac is a novel skin cancer chemopreventive agent for UVB-induced photocarcinogenesis. Toxicology and Applied Pharmacology. 268: 249-55. PMID 23274568 DOI: 10.1016/j.taap.2012.12.009  0.52
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  0.92
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  0.88
2013 Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics, Acm-Bcb 2013. 813-814. DOI: 10.1145/2506583.2506701  0.92
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: 915-916. PMID 30360293 DOI: 10.1016/j.cell.2012.10.032  0.44
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  1
2012 Zhang Z, Theurkauf WE, Weng Z, Zamore PD. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence. 3: 9. PMID 23273270 DOI: 10.1186/1758-907X-3-9  0.92
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  0.92
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  0.92
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  0.44
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2012 Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nature Methods. 9: 473-6. PMID 22426492 DOI: 10.1038/nmeth.1937  0.92
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  0.92
2012 Singh T, Chaudhary SC, Kapur P, Weng Z, Elmets CA, Kopelovich L, Athar M. Nitric oxide donor exisulind is an effective inhibitor of murine photocarcinogenesis Photochemistry and Photobiology. 88: 1141-1148. PMID 22364235 DOI: 10.1111/j.1751-1097.2012.01093.x  0.52
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  0.88
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  0.92
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  0.92
2011 Khurana JS, Wang J, Xu J, Koppetsch BS, Thomson TC, Nowosielska A, Li C, Zamore PD, Weng Z, Theurkauf WE. Adaptation to P element transposon invasion in Drosophila melanogaster. Cell. 147: 1551-63. PMID 22196730 DOI: 10.1016/j.cell.2011.11.042  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.88
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  0.76
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  0.84
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  0.88
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2010 Carone BR, Fauquier L, Habib N, Shea JM, Hart CE, Li R, Bock C, Li C, Gu H, Zamore PD, Meissner A, Weng Z, Hofmann HA, Friedman N, Rando OJ. Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell. 143: 1084-96. PMID 21183072 DOI: 10.1016/j.cell.2010.12.008  0.92
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  0.92
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  0.92
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  0.92
2010 Xu J, Timares L, Heilpern C, Weng Z, Li C, Xu H, Pressey JG, Elmets CA, Kopelovich L, Athar M. Targeting wild-type and mutant p53 with small molecule CP-31398 blocks the growth of rhabdomyosarcoma by inducing reactive oxygen species-dependent apoptosis. Cancer Research. 70: 6566-76. PMID 20682800 DOI: 10.1158/0008-5472.CAN-10-0942  0.76
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  0.88
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  0.92
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  0.92
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  0.84
2010 McNally B, Singer A, Yu Z, Sun Y, Weng Z, Meller A. Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Letters. 10: 2237-44. PMID 20459065 DOI: 10.1021/nl1012147  0.92
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  0.92
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  0.92
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  0.92
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  0.92
2010 Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. Rna (New York, N.Y.). 16: 43-56. PMID 19917635 DOI: 10.1261/rna.1972910  0.92
2010 Reynolds SM, Weng Z, Bilmes JA, Noble WS. Predicting nucleosome positioning using multiple evidence tracks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6044: 441-455. DOI: 10.1007/978-3-642-12683-3_29  0.92
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  0.92
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  0.92
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  0.92
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  1
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.92
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  0.84
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  0.6
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  0.92
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  1
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  0.92
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  1
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  0.92
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  0.92
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  0.92
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  1
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  0.92
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  0.92
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  0.92
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  0.92
2007 Kothe DL, Decker JM, Li Y, Weng Z, Bibollet-Ruche F, Zammit KP, Salazar MG, Chen Y, Salazar-Gonzalez JF, Moldoveanu Z, Mestecky J, Gao F, Haynes BF, Shaw GM, Muldoon M, et al. Antigenicity and immunogenicity of HIV-1 consensus subtype B envelope glycoproteins. Virology. 360: 218-34. PMID 17097711 DOI: 10.1016/j.virol.2006.10.017  0.52
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  0.92
2006 Kothe DL, Li Y, Decker JM, Bibollet-Ruche F, Zammit KP, Salazar MG, Chen Y, Weng Z, Weaver EA, Gao F, Haynes BF, Shaw GM, Korber BT, Hahn BH. Ancestral and consensus envelope immunogens for HIV-1 subtype C. Virology. 352: 438-49. PMID 16780913 DOI: 10.1016/j.virol.2006.05.011  0.52
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  1
2006 Zhu J, Weng Z. FAST: a novel protein structure alignment algorithm. Proteins. 58: 618-27. PMID 15609341 DOI: 10.1002/PROT.20331  0.48
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  1
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  0.56
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  0.84
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  1
2005 Anderson RJ, Weng Z, Campbell RK, Jiang X. Main-chain conformational tendencies of amino acids. Proteins. 60: 679-89. PMID 16021632 DOI: 10.1002/prot.20530  0.4
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  0.92
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  1
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  0.92
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  1
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  1
2004 Mintseris J, Weng Z. Optimizing protein representations with information theory. Genome Informatics. International Conference On Genome Informatics. 15: 160-9. PMID 15712119  1
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  0.84
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  1
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  1
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  0.84
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  0.84
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  0.92
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  0.84
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  1
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  0.84
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  0.76
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  0.84
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  1
2003 Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins. 53: 629-39. PMID 14579354 DOI: 10.1002/prot.10432  1
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  1
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  0.76
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  0.84
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  0.92
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  1
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  1
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  1
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  0.32
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  0.92
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  0.44
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  0.76
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  0.56
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  1
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  0.84
2002 Weng Z, DeLisi C. Protein therapeutics: promises and challenges for the 21st century. Trends in Biotechnology. 20: 29-35. PMID 11742675  0.92
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  0.32
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  0.92
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.  0.92
1997 DeLisi C, Cantor C, Weng Z. Hedgehogs, foxes, and a new science. Nature Biotechnology. 15: 819. PMID 9306387 DOI: 10.1038/NBT0997-819  0.36
Show low-probability matches.