| Year |
Citation |
Score |
| 2020 |
Yan P, Lu JY, Niu J, Gao J, Zhang MQ, Yin Y, Shen X. LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency. Journal of Molecular Cell Biology. PMID 33049031 DOI: 10.1093/jmcb/mjaa056 |
0.316 |
|
| 2020 |
Chen Y, Wang Y, Liu X, Xu J, Zhang MQ. Model-based analysis of chromatin interactions from dCas9-Based CAPTURE-3C-seq. Plos One. 15: e0236666. PMID 32735574 DOI: 10.1371/Journal.Pone.0236666 |
0.409 |
|
| 2020 |
Kong R, Xu X, Liu X, He P, Zhang MQ, Dai Q. 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome. Bmc Bioinformatics. 21: 159. PMID 32349677 DOI: 10.1186/S12859-020-3501-2 |
0.328 |
|
| 2020 |
Ramanand SG, Chen Y, Yuan J, Daescu K, Lambros M, Houlahan KE, Carreira S, Yuan W, Baek G, Sharp A, Paschalis A, Kanchwala M, Gao Y, Aslam A, Safdar N, ... ... Zhang MQ, et al. The landscape of RNA polymerase II associated chromatin interactions in prostate cancer. The Journal of Clinical Investigation. PMID 32343676 DOI: 10.1172/Jci134260 |
0.394 |
|
| 2020 |
Xiong Q, Huang S, Li YH, Lv N, Lv C, Ding Y, Liu WW, Wang LL, Chen Y, Sun L, Zhao Y, Liao SY, Zhang MQ, Zhu BL, Yu L. Single‑cell RNA sequencing of t(8;21) acute myeloid leukemia for risk prediction. Oncology Reports. PMID 32323795 DOI: 10.3892/Or.2020.7507 |
0.34 |
|
| 2020 |
Liu X, Chen Y, Zhang Y, Liu Y, Liu N, Botten GA, Cao H, Orkin SH, Zhang MQ, Xu J. Multiplexed capture of spatial configuration and temporal dynamics of locus-specific 3D chromatin by biotinylated dCas9. Genome Biology. 21: 59. PMID 32138752 DOI: 10.1186/S13059-020-01973-W |
0.411 |
|
| 2019 |
Jia C, Wang LY, Yin GG, Zhang MQ. Single-cell stochastic gene expression kinetics with coupled positive-plus-negative feedback. Physical Review. E. 100: 052406. PMID 31869986 DOI: 10.1103/Physreve.100.052406 |
0.321 |
|
| 2019 |
An Z, Liu P, Zheng J, Si C, Li T, Chen Y, Ma T, Zhang MQ, Zhou Q, Ding S. Sox2 and Klf4 as the Functional Core in Pluripotency Induction without Exogenous Oct4. Cell Reports. 29: 1986-2000.e8. PMID 31722212 DOI: 10.1016/J.Celrep.2019.10.026 |
0.337 |
|
| 2019 |
Xiong L, Xu K, Tian K, Shao Y, Tang L, Gao G, Zhang M, Jiang T, Zhang QC. SCALE method for single-cell ATAC-seq analysis via latent feature extraction. Nature Communications. 10: 4576. PMID 31594952 DOI: 10.1038/S41467-019-12630-7 |
0.311 |
|
| 2019 |
Xiao R, Chen JY, Liang Z, Luo D, Chen G, Lu ZJ, Chen Y, Zhou B, Li H, Du X, Yang Y, San M, Wei X, Liu W, Lécuyer E, ... ... Zhang MQ, et al. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription. Cell. 178: 107-121.e18. PMID 31251911 DOI: 10.1016/J.Cell.2019.06.001 |
0.402 |
|
| 2018 |
Kim YJ, Xie P, Cao L, Zhang MQ, Kim TH. Global transcriptional activity dynamics reveal functional enhancer RNAs. Genome Research. PMID 30352805 DOI: 10.1101/Gr.233486.117 |
0.394 |
|
| 2018 |
Chen F, Li G, Zhang MQ, Chen Y. HiCDB: a sensitive and robust method for detecting contact domain boundaries. Nucleic Acids Research. PMID 30184171 DOI: 10.1093/Nar/Gky789 |
0.342 |
|
| 2018 |
Liu X, Zhang Y, Chen Y, Li M, Shao Z, Zhang MQ, Xu J. CAPTURE: In Situ Analysis of Chromatin Composition of Endogenous Genomic Loci by Biotinylated dCas9. Current Protocols in Molecular Biology. e64. PMID 29927077 DOI: 10.1002/cpmb.64 |
0.322 |
|
| 2018 |
Tan Z, Niu B, Tsang KY, Melhado IG, Ohba S, He X, Huang Y, Wang C, McMahon AP, Jauch R, Chan D, Zhang MQ, Cheah KSE. Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions. Plos Genetics. 14: e1007346. PMID 29659575 DOI: 10.1371/Journal.Pgen.1007346 |
0.394 |
|
| 2018 |
Ma T, Chen L, Shi M, Niu J, Zhang X, Yang X, Zhanghao K, Wang M, Xi P, Jin D, Zhang M, Gao J. Developing novel methods to image and visualize 3D genomes. Cell Biology and Toxicology. PMID 29577183 DOI: 10.1007/S10565-018-9427-Z |
0.335 |
|
| 2018 |
Ray P, Torck A, Quigley L, Wangzhou A, Neiman M, Rao C, Lam T, Kim JY, Kim TH, Zhang MQ, Dussor G, Price TJ. Title: Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq-based resource for pain and sensory neuroscience research. Pain. PMID 29561359 DOI: 10.1097/J.Pain.0000000000001217 |
0.374 |
|
| 2018 |
Djekidel MN, Chen Y, Zhang MQ. FIND: difFerential chromatin INteractions Detection using a spatial Poisson process. Genome Research. PMID 29440282 DOI: 10.1101/Gr.212241.116 |
0.726 |
|
| 2018 |
Li Y, He Y, Liang Z, Wang Y, Chen F, Djekidel MN, Li G, Zhang X, Xiang S, Wang Z, Gao J, Zhang MQ, Chen Y. Alterations of specific chromatin conformation affect ATRA-induced leukemia cell differentiation. Cell Death & Disease. 9: 200. PMID 29422670 DOI: 10.1038/S41419-017-0173-6 |
0.765 |
|
| 2018 |
Jia C, Qian H, Chen M, Zhang MQ. Relaxation rates of gene expression kinetics reveal the feedback signs of autoregulatory gene networks The Journal of Chemical Physics. 148: 095102. DOI: 10.1063/1.5009749 |
0.316 |
|
| 2017 |
Jia C, Zhang MQ, Qian H. Emergent Lévy behavior in single-cell stochastic gene expression. Physical Review. E. 96: 040402. PMID 29347590 DOI: 10.1103/Physreve.96.040402 |
0.305 |
|
| 2017 |
Jia C, Xie P, Chen M, Zhang MQ. Stochastic fluctuations can reveal the feedback signs of gene regulatory networks at the single-molecule level. Scientific Reports. 7: 16037. PMID 29167445 DOI: 10.1038/S41598-017-15464-9 |
0.352 |
|
| 2017 |
Liang Z, Li G, Wang Z, Djekidel MN, Li Y, Qian MP, Zhang MQ, Chen Y. BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions. Nature Communications. 8: 1622. PMID 29158486 DOI: 10.1038/S41467-017-01754-3 |
0.764 |
|
| 2017 |
Fang S, Zhang L, Guo J, Niu Y, Wu Y, Li H, Zhao L, Li X, Teng X, Sun X, Sun L, Zhang MQ, Chen R, Zhao Y. NONCODEV5: a comprehensive annotation database for long non-coding RNAs. Nucleic Acids Research. PMID 29140524 DOI: 10.1093/Nar/Gkx1107 |
0.324 |
|
| 2017 |
Li X, Chen W, Chen Y, Zhang X, Gu J, Zhang MQ. Network embedding-based representation learning for single cell RNA-seq data. Nucleic Acids Research. PMID 28977434 DOI: 10.1093/Nar/Gkx750 |
0.323 |
|
| 2017 |
Guo W, Zhu P, Pellegrini M, Zhang M, Wang X, Ni Z. CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. Bioinformatics (Oxford, England). PMID 28968643 DOI: 10.1093/Bioinformatics/Btx595 |
0.356 |
|
| 2017 |
Chen FX, Xie P, Collings CK, Cao K, Aoi Y, Marshall SA, Rendleman EJ, Ugarenko M, Ozark PA, Zhang A, Shiekhattar R, Smith ER, Zhang MQ, Shilatifard A. PAF1 regulation of promoter-proximal pause release via enhancer activation. Science (New York, N.Y.). PMID 28860207 DOI: 10.1126/Science.Aan3269 |
0.313 |
|
| 2017 |
Liu X, Zhang Y, Chen Y, Li M, Zhou F, Li K, Cao H, Ni M, Liu Y, Gu Z, Dickerson KE, Xie S, Hon GC, Xuan Z, Zhang MQ, et al. In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell. 170: 1028-1043.e19. PMID 28841410 DOI: 10.1016/J.Cell.2017.08.003 |
0.689 |
|
| 2017 |
Du Z, Zheng H, Huang B, Ma R, Wu J, Zhang X, He J, Xiang Y, Wang Q, Li Y, Ma J, Zhang X, Zhang K, Wang Y, Zhang MQ, et al. Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature. 547: 232-235. PMID 28703188 DOI: 10.1038/Nature23263 |
0.339 |
|
| 2017 |
Liu Z, Lou H, Xie K, Wang H, Chen N, Aparicio OM, Zhang MQ, Jiang R, Chen T. Reconstructing cell cycle pseudo time-series via single-cell transcriptome data. Nature Communications. 8: 22. PMID 28630425 DOI: 10.1038/S41467-017-00039-Z |
0.31 |
|
| 2017 |
Li Y, Ning Q, Shi J, Chen Y, Jiang M, Gao L, Huang W, Jing Y, Huang S, Liu A, Hu Z, Liu D, Wang L, Nervi C, Dai Y, ... Zhang MQ, et al. A novel epigenetic AML1-ETO/THAP10/miR-383 mini-circuitry contributes to t(8;21) leukaemogenesis. Embo Molecular Medicine. PMID 28539478 DOI: 10.15252/Emmm.201607180 |
0.323 |
|
| 2017 |
Dong Q, Han H, Liu X, Wei L, Zhang W, Zhao Z, Zhang MQ, Wang X. HCSGD: An integrated database of human cellular senescence genes. Journal of Genetics and Genomics = Yi Chuan Xue Bao. PMID 28529078 DOI: 10.1016/J.Jgg.2017.04.001 |
0.359 |
|
| 2017 |
Pavlovic M, Ray P, Pavlovic K, Kotamarti A, Chen M, Zhang MQ. DIRECTION: A machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. Bioinformatics (Oxford, England). PMID 28505334 DOI: 10.1093/Bioinformatics/Btx316 |
0.377 |
|
| 2017 |
Ni Y, Cao B, Ma T, Niu G, Huo Y, Huang J, Chen D, Liu Y, Yu B, Zhang MQ, Niu H. Super-resolution imaging of a 2.5 kb non-repetitive DNA in situ in the nuclear genome using molecular beacon probes. Elife. 6. PMID 28485713 DOI: 10.7554/Elife.21660 |
0.338 |
|
| 2016 |
Srivastava S, Potla S, Torck A, Zhang M, Dussor G, Ray P, Price T. (278) A potential role for eIF4A in regulation of nociceptor plasticity: a motif-based genome-wide search for eIF4A targets. The Journal of Pain : Official Journal of the American Pain Society. 17: S45. PMID 28162511 DOI: 10.1016/J.Jpain.2016.01.184 |
0.345 |
|
| 2016 |
Dai Q, Bao C, Hai Y, Ma S, Zhou T, Wang C, Wang Y, Huo W, Liu X, Yao Y, Xuan Z, Chen M, Zhang MQ. MTGIpick allows robust identification of genomic islands from a single genome. Briefings in Bioinformatics. PMID 28025178 DOI: 10.1093/Bib/Bbw118 |
0.646 |
|
| 2016 |
Guo W, Zhang MQ, Wu H. Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements. Scientific Reports. 6: 32207. PMID 27573482 DOI: 10.1038/Srep32207 |
0.363 |
|
| 2016 |
Ma X, Zhan G, Sleumer MC, Chen S, Liu W, Zhang MQ, Liu X. Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT). Nucleic Acids Research. PMID 27557708 DOI: 10.1093/Nar/Gkw734 |
0.344 |
|
| 2016 |
Chen Y, Wang Y, Xuan Z, Chen M, Zhang MQ. De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles. Nucleic Acids Research. PMID 27060148 DOI: 10.1093/Nar/Gkw225 |
0.653 |
|
| 2016 |
Sathe A, Chen Y, Yoo H, Zhang MQ. Abstract 773: Analysis of oncogene affected networks in tumorigenesis of lung cancer Cancer Research. 76: 773-773. DOI: 10.1158/1538-7445.Am2016-773 |
0.317 |
|
| 2016 |
Djekidel MN, Wang M, Zhang MQ, Gao J. HiC-3DViewer: a new tool to visualize Hi-C data in 3D space Quantitative Biology. 5: 183-190. DOI: 10.1007/s40484-017-0091-8 |
0.683 |
|
| 2016 |
Gao J, Yang X, Djekidel MN, Wang Y, Xi P, Zhang MQ. Developing bioimaging and quantitative methods to study 3D genome Quantitative Biology. 4: 129-147. DOI: 10.1007/s40484-016-0065-2 |
0.713 |
|
| 2015 |
Sathe A, Zhang YA, Ma X, Ray P, Cadinu D, Wang YW, Yao X, Liu X, Tang H, Wang Y, Huang Y, Liu C, Gu J, Akerman M, Mo Y, ... ... Zhang MQ, et al. SCT Promoter Methylation is a Highly Discriminative Biomarker for Lung and Many Other Cancers. Ieee Life Sciences Letters. 1: 30-33. PMID 33758771 DOI: 10.1109/lls.2015.2488438 |
0.582 |
|
| 2015 |
Zhang YA, Ma X, Sathe A, Fujimoto J, Wistuba II, Lam S, Yatabe Y, Wang YW, Stastny V, Gao B, Larsen JE, Girard L, Liu X, Song K, Behrens C, ... ... Zhang MQ, et al. Validation of SCT Methylation As a Hallmark Biomarker for Lung Cancers. Journal of Thoracic Oncology : Official Publication of the International Association For the Study of Lung Cancer. PMID 26725182 DOI: 10.1016/J.Jtho.2015.11.004 |
0.309 |
|
| 2015 |
Djekidel MN, Liang Z, Wang Q, Hu Z, Li G, Chen Y, Zhang MQ. 3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. Genome Biology. 16: 288. PMID 26694485 DOI: 10.1186/S13059-015-0851-6 |
0.746 |
|
| 2015 |
Zhao Y, Li H, Fang S, Kang Y, Wu W, Hao Y, Li Z, Bu D, Sun N, Zhang MQ, Chen R. NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Research. PMID 26586799 DOI: 10.1093/Nar/Gkv1252 |
0.311 |
|
| 2015 |
Greer CB, Tanaka Y, Kim YJ, Xie P, Zhang MQ, Park IH, Kim TH. Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery. Cell Reports. PMID 26549458 DOI: 10.1016/J.Celrep.2015.10.013 |
0.417 |
|
| 2015 |
Guo Y, Xu Q, Canzio D, Shou J, Li J, Gorkin DU, Jung I, Wu H, Zhai Y, Tang Y, Lu Y, Wu Y, Jia Z, Li W, Zhang MQ, et al. CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function. Cell. 162: 900-10. PMID 26276636 DOI: 10.1016/J.Cell.2015.07.038 |
0.427 |
|
| 2015 |
Akerman M, Fregoso OI, Das S, Ruse C, Jensen MA, Pappin DJ, Zhang MQ, Krainer AR. Differential connectivity of splicing activators and repressors to the human spliceosome. Genome Biology. 16: 119. PMID 26047612 DOI: 10.1186/S13059-015-0682-5 |
0.343 |
|
| 2015 |
Orozco LD, Morselli M, Rubbi L, Guo W, Go J, Shi H, Lopez D, Furlotte NA, Bennett BJ, Farber CR, Ghazalpour A, Zhang MQ, Bahous R, Rozen R, Lusis AJ, et al. Epigenome-wide association of liver methylation patterns and complex metabolic traits in mice. Cell Metabolism. 21: 905-17. PMID 26039453 DOI: 10.1016/J.Cmet.2015.04.025 |
0.336 |
|
| 2015 |
Wang T, Xiao G, Chu Y, Zhang MQ, Corey DR, Xie Y. Design and bioinformatics analysis of genome-wide CLIP experiments. Nucleic Acids Research. 43: 5263-74. PMID 25958398 DOI: 10.1093/Nar/Gkv439 |
0.376 |
|
| 2015 |
Wang P, Qin J, Qin Y, Zhu Y, Wang LY, Li MJ, Zhang MQ, Wang J. ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks. Nucleic Acids Research. 43: W264-9. PMID 25916854 DOI: 10.7490/F1000Research.1110240.1 |
0.408 |
|
| 2015 |
Huo W, Adams HM, Zhang MQ, Palmer KL. Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing. Journal of Bacteriology. 197: 1939-51. PMID 25825433 DOI: 10.1128/Jb.00130-15 |
0.335 |
|
| 2015 |
Leung D, Jung I, Rajagopal N, Schmitt A, Selvaraj S, Lee AY, Yen CA, Lin S, Lin Y, Qiu Y, Xie W, Yue F, Hariharan M, Ray P, Kuan S, ... ... Zhang MQ, et al. Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature. 518: 350-4. PMID 25693566 DOI: 10.1038/Nature14217 |
0.379 |
|
| 2015 |
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, ... ... Zhang MQ, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248 |
0.378 |
|
| 2015 |
Hu L, Di C, Kai M, Yang YC, Li Y, Qiu Y, Hu X, Yip KY, Zhang MQ, Lu ZJ. A common set of distinct features that characterize noncoding RNAs across multiple species. Nucleic Acids Research. 43: 104-14. PMID 25505163 DOI: 10.1093/Nar/Gku1316 |
0.337 |
|
| 2015 |
Sathe A, Zhang Y, Ma X, Ray P, Cadinu D, Wang Y, Yao X, Liu X, Tang H, Wang Y, Huang Y, Liu C, Gu J, Akerman M, Mo Y, ... ... Zhang MQ, et al. SCT Promoter Methylation Is a Highly Discriminative Biomarker for Lung and Many Other Cancers Ieee Life Sciences Letters. 1: 30-33. DOI: 10.1109/LLS.2015.2488438 |
0.561 |
|
| 2014 |
Liao W, Ouyang W, Zhang MQ, Li MO. Genome Wide Mapping of Foxo1 Binding-sites in Murine T Lymphocytes. Genomics Data. 2: 280-281. PMID 25302145 DOI: 10.1016/J.Gdata.2014.08.006 |
0.357 |
|
| 2014 |
Gu J, Chen Y, Huang H, Yin L, Xie Z, Zhang MQ. Gene module based regulator inference identifying miR-139 as a tumor suppressor in colorectal cancer. Molecular Biosystems. 10: 3249-54. PMID 25286864 DOI: 10.1039/C4Mb00329B |
0.305 |
|
| 2014 |
Lu Y, Zhou X, Jin Z, Cheng J, Shen W, Ji F, Liu L, Zhang X, Zhang M, Cao Y, Han D, Choy K, Yuan H. Resolving the genetic heterogeneity of prelingual hearing loss within one family: Performance comparison and application of two targeted next generation sequencing approaches. Journal of Human Genetics. 59: 599-607. PMID 25231367 DOI: 10.1038/Jhg.2014.78 |
0.322 |
|
| 2014 |
Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP. Genome-wide map of regulatory interactions in the human genome. Genome Research. 24: 1905-17. PMID 25228660 DOI: 10.1101/Gr.176586.114 |
0.451 |
|
| 2014 |
Cheng J, Zhou X, Lu Y, Chen J, Han B, Zhu Y, Liu L, Choy KW, Han D, Sham PC, Zhang MQ, Zhang X, Yuan H. Exome Sequencing Identifies a Novel Frameshift Mutation of MYO6 as the Cause of Autosomal Dominant Nonsyndromic Hearing Loss in a Chinese Family. Annals of Human Genetics. PMID 25227905 DOI: 10.1111/Ahg.12084 |
0.309 |
|
| 2014 |
Rajagopal N, Ernst J, Ray P, Wu J, Zhang M, Kellis M, Ren B. Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. G3 (Bethesda, Md.). 4: 2051-63. PMID 25122670 DOI: 10.1534/G3.114.013565 |
0.377 |
|
| 2014 |
Li W, Wu J, Kim SY, Zhao M, Hearn SA, Zhang MQ, Meistrich ML, Mills AA. Chd5 orchestrates chromatin remodelling during sperm development. Nature Communications. 5: 3812. PMID 24818823 DOI: 10.1038/Ncomms4812 |
0.327 |
|
| 2014 |
Li Y, Ehrhardt K, Zhang MQ, Bleris L. Assembly and validation of versatile transcription activator-like effector libraries. Scientific Reports. 4: 4857. PMID 24798576 DOI: 10.1038/Srep04857 |
0.387 |
|
| 2014 |
He C, Wang X, Zhang MQ. Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alpha-associated long-range interactions. Nucleic Acids Research. 42: 6935-44. PMID 24782518 DOI: 10.1093/Nar/Gku327 |
0.388 |
|
| 2014 |
Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ, Krainer AR, Darnell RB, Zhang C. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Reports. 6: 1139-52. PMID 24613350 DOI: 10.1016/J.Celrep.2014.02.005 |
0.335 |
|
| 2014 |
Guo W, Chung WY, Qian M, Pellegrini M, Zhang MQ. Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic Acids Research. 42: 3009-16. PMID 24343027 DOI: 10.1093/Nar/Gkt1306 |
0.357 |
|
| 2013 |
Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Chen PY, Pellegrini M. BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. Bmc Genomics. 14: 774. PMID 24206606 DOI: 10.1186/1471-2164-14-774 |
0.352 |
|
| 2013 |
Wu D, Gu J, Zhang MQ. FastDMA: an infinium humanmethylation450 beadchip analyzer. Plos One. 8: e74275. PMID 24040221 DOI: 10.1371/Journal.Pone.0074275 |
0.373 |
|
| 2013 |
Rajaram M, Zhang J, Wang T, Li J, Kuscu C, Qi H, Kato M, Grubor V, Weil RJ, Helland A, Borrenson-Dale AL, Cho KR, Levine DA, Houghton AN, Wolchok JD, ... ... Zhang M, et al. Two Distinct Categories of Focal Deletions in Cancer Genomes. Plos One. 8: e66264. PMID 23805207 DOI: 10.1371/Journal.Pone.0066264 |
0.347 |
|
| 2013 |
Ma X, Wang YW, Zhang MQ, Gazdar AF. DNA methylation data analysis and its application to cancer research. Epigenomics. 5: 301-16. PMID 23750645 DOI: 10.2217/Epi.13.26 |
0.349 |
|
| 2013 |
Wang C, Zhang MQ, Zhang Z. Computational identification of active enhancers in model organisms. Genomics, Proteomics & Bioinformatics. 11: 142-50. PMID 23685394 DOI: 10.1016/J.Gpb.2013.04.002 |
0.412 |
|
| 2013 |
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, ... ... Zhang MQ, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 153: 1134-48. PMID 23664764 DOI: 10.1016/J.Cell.2013.04.022 |
0.656 |
|
| 2013 |
Wu J, Anczuków O, Krainer AR, Zhang MQ, Zhang C. OLego: fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Research. 41: 5149-63. PMID 23571760 DOI: 10.1093/Nar/Gkt216 |
0.334 |
|
| 2013 |
Chung W, Schmitz RJ, Biorac T, Ye D, Dudas M, Meredith GD, Adams CC, Ecker JR, Zhang MQ. Constructing Hepitypes: Phasing Local Genotype and DNA Methylation Journal of Neuroscience and Neuroengineering. 2: 335-346. DOI: 10.1166/Jnsne.2013.1067 |
0.379 |
|
| 2012 |
Tang MH, Varadan V, Kamalakaran S, Zhang MQ, Dimitrova N, Hicks J. Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. Frontiers in Oncology. 2: 197. PMID 23293768 DOI: 10.3389/Fonc.2012.00197 |
0.384 |
|
| 2012 |
Xing H, Liao W, Mo Y, Zhang MQ. A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types. Journal of Visualized Experiments : Jove. e4273. PMID 23271069 DOI: 10.3791/4273 |
0.372 |
|
| 2012 |
Wen H, Li Y, Malek SN, Kim YC, Xu J, Chen P, Xiao F, Huang X, Zhou X, Xuan Z, Mankala S, Hou G, Rowley JD, Zhang MQ, Wang SM. New fusion transcripts identified in normal karyotype acute myeloid leukemia. Plos One. 7: e51203. PMID 23251452 DOI: 10.1371/Journal.Pone.0051203 |
0.619 |
|
| 2012 |
Ouyang W, Liao W, Luo CT, Yin N, Huse M, Kim MV, Peng M, Chan P, Ma Q, Mo Y, Meijer D, Zhao K, Rudensky AY, Atwal G, Zhang MQ, et al. Novel Foxo1-dependent transcriptional programs control T(reg) cell function. Nature. 491: 554-9. PMID 23135404 DOI: 10.1038/Nature11581 |
0.537 |
|
| 2012 |
Sleumer MC, Wei G, Wang Y, Chang H, Xu T, Chen R, Zhang MQ. Regulatory elements of Caenorhabditis elegans ribosomal protein genes. Bmc Genomics. 13: 433. PMID 22928635 DOI: 10.1186/1471-2164-13-433 |
0.432 |
|
| 2012 |
Xing H, Mo Y, Liao W, Zhang MQ. Genome-wide localization of protein-DNA binding and histone modification by a Bayesian change-point method with ChIP-seq data. Plos Computational Biology. 8: e1002613. PMID 22844240 DOI: 10.1371/Journal.Pcbi.1002613 |
0.396 |
|
| 2012 |
Li R, Guo W, Gu J, Zhang MQ, Wang X. Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation. Genomics. 100: 297-302. PMID 22824656 DOI: 10.1016/J.Ygeno.2012.07.009 |
0.389 |
|
| 2012 |
Zhang Z, Ma X, Zhang MQ. Bivalent-like chromatin markers are predictive for transcription start site distribution in human. Plos One. 7: e38112. PMID 22768038 DOI: 10.1371/Journal.Pone.0038112 |
0.405 |
|
| 2012 |
Chicas A, Kapoor A, Wang X, Aksoy O, Evertts AG, Zhang MQ, Garcia BA, Bernstein E, Lowe SW. H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proceedings of the National Academy of Sciences of the United States of America. 109: 8971-6. PMID 22615382 DOI: 10.1073/Pnas.1119836109 |
0.389 |
|
| 2012 |
Ma X, Kulkarni A, Zhang Z, Xuan Z, Serfling R, Zhang MQ. A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information. Nucleic Acids Research. 40: e50. PMID 22228832 DOI: 10.1093/Nar/Gkr1135 |
0.619 |
|
| 2011 |
Hu Z, Qian M, Zhang MQ. Novel Markov model of induced pluripotency predicts gene expression changes in reprogramming. Bmc Systems Biology. 5: S8. PMID 22784579 DOI: 10.1186/1752-0509-5-S2-S8 |
0.301 |
|
| 2011 |
Rajan P, Dalgliesh C, Carling PJ, Buist T, Zhang C, Grellscheid SN, Armstrong K, Stockley J, Simillion C, Gaughan L, Kalna G, Zhang MQ, Robson CN, Leung HY, Elliott DJ. Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. Plos One. 6: e29088. PMID 22194994 DOI: 10.1371/Journal.Pone.0029088 |
0.399 |
|
| 2011 |
Wrzeszczynski KO, Varadan V, Byrnes J, Lum E, Kamalakaran S, Levine DA, Dimitrova N, Zhang MQ, Lucito R. Identification of tumor suppressors and oncogenes from genomic and epigenetic features in ovarian cancer. Plos One. 6: e28503. PMID 22174824 DOI: 10.1371/Journal.Pone.0028503 |
0.362 |
|
| 2011 |
Wang LY, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J. EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics. 6: 1505-12. PMID 22139581 DOI: 10.4161/Epi.6.12.18176 |
0.414 |
|
| 2011 |
Watts JA, Zhang C, Klein-Szanto AJ, Kormish JD, Fu J, Zhang MQ, Zaret KS. Study of FoxA pioneer factor at silent genes reveals Rfx-repressed enhancer at Cdx2 and a potential indicator of esophageal adenocarcinoma development. Plos Genetics. 7: e1002277. PMID 21935353 DOI: 10.1371/Journal.Pgen.1002277 |
0.435 |
|
| 2011 |
Wu J, Akerman M, Sun S, McCombie WR, Krainer AR, Zhang MQ. SpliceTrap: a method to quantify alternative splicing under single cellular conditions. Bioinformatics (Oxford, England). 27: 3010-6. PMID 21896509 DOI: 10.1093/Bioinformatics/Btr508 |
0.377 |
|
| 2011 |
Yang S, Yalamanchili HK, Li X, Yao KM, Sham PC, Zhang MQ, Wang J. Correlated evolution of transcription factors and their binding sites. Bioinformatics (Oxford, England). 27: 2972-8. PMID 21896508 DOI: 10.1093/Bioinformatics/Btr503 |
0.35 |
|
| 2011 |
Shen M, Eyras E, Wu J, Khanna A, Josiah S, Rederstorff M, Zhang MQ, Stamm S. Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. Nucleic Acids Research. 39: 9720-30. PMID 21880592 DOI: 10.1093/Nar/Gkr684 |
0.313 |
|
| 2011 |
Qin J, Li MJ, Wang P, Zhang MQ, Wang J. ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Research. 39: W430-6. PMID 21586587 DOI: 10.1093/Nar/Gkr332 |
0.386 |
|
| 2011 |
Zhang Z, Zhang MQ. Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. Bmc Bioinformatics. 12: 155. PMID 21569556 DOI: 10.1186/1471-2105-12-155 |
0.404 |
|
| 2011 |
Renault VM, Thekkat PU, Hoang KL, White JL, Brady CA, Kenzelmann Broz D, Venturelli OS, Johnson TM, Oskoui PR, Xuan Z, Santo EE, Zhang MQ, Vogel H, Attardi LD, Brunet A. The pro-longevity gene FoxO3 is a direct target of the p53 tumor suppressor. Oncogene. 30: 3207-21. PMID 21423206 DOI: 10.1038/Onc.2011.35 |
0.639 |
|
| 2011 |
Wrzeszczynski KO, Varadan V, Kamalakaran S, Levine DA, Dimitrova N, Zhang MQ, Lucito R. Abstract 30: Identification of genomic and epigenetic features of tumor suppressors and oncogenes in ovarian cancer Cancer Research. 71: 30-30. DOI: 10.1158/1538-7445.Am2011-30 |
0.367 |
|
| 2010 |
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, ... ... Zhang MQ, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/Nbt.1682 |
0.385 |
|
| 2010 |
Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan Z, Zhang MQ, Sedel F, Jourdren L, Coulpier F, Triller A, Spector DL, Bessis A. A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. The Embo Journal. 29: 3082-93. PMID 20729808 DOI: 10.1038/Emboj.2010.199 |
0.647 |
|
| 2010 |
Chicas A, Wang X, Zhang C, McCurrach M, Zhao Z, Mert O, Dickins RA, Narita M, Zhang M, Lowe SW. Dissecting the unique role of the retinoblastoma tumor suppressor during cellular senescence. Cancer Cell. 17: 376-87. PMID 20385362 DOI: 10.1016/J.Ccr.2010.01.023 |
0.322 |
|
| 2010 |
Wang SM, Zhang MQ. Transcriptome study for early hematopoiesis—achievement, challenge and new opportunity Journal of Cellular Physiology. 223: 549-552. PMID 20143329 DOI: 10.1002/Jcp.22065 |
0.36 |
|
| 2010 |
Zhang MQ, Smith AD. Challenges in Understanding Genome-Wide DNA Methylation Journal of Computer Science and Technology. 25: 26-34. DOI: 10.1007/S11390-010-9302-8 |
0.483 |
|
| 2009 |
Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ. Updates to the RMAP short-read mapping software. Bioinformatics (Oxford, England). 25: 2841-2. PMID 19736251 DOI: 10.1093/Bioinformatics/Btp533 |
0.637 |
|
| 2009 |
Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks JB. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Research. 19: 1593-605. PMID 19581485 DOI: 10.1101/Gr.095190.109 |
0.696 |
|
| 2009 |
Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC, Xavier RJ. An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Research. 37: 4587-602. PMID 19491311 DOI: 10.1093/Nar/Gkp425 |
0.504 |
|
| 2009 |
Kim YC, Wu Q, Chen J, Xuan Z, Jung YC, Zhang MQ, Rowley JD, Wang SM. The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proceedings of the National Academy of Sciences of the United States of America. 106: 8278-83. PMID 19416867 DOI: 10.1073/Pnas.0903390106 |
0.652 |
|
| 2009 |
Rosenfeld JA, Wang Z, Schones DE, Zhao K, DeSalle R, Zhang MQ. Determination of enriched histone modifications in non-genic portions of the human genome. Bmc Genomics. 10: 143. PMID 19335899 DOI: 10.1186/1471-2164-10-143 |
0.752 |
|
| 2009 |
Niida A, Smith AD, Imoto S, Aburatani H, Zhang MQ, Akiyama T. Gene set-based module discovery in the breast cancer transcriptome. Bmc Bioinformatics. 10: 71. PMID 19243633 DOI: 10.1186/1471-2105-10-71 |
0.476 |
|
| 2009 |
Li T, Huang J, Jiang Y, Zeng Y, He F, Zhang MQ, Han Z, Zhang X. Multi-stage analysis of gene expression and transcription regulation in C57/B6 mouse liver development. Genomics. 93: 235-42. PMID 19015022 DOI: 10.1016/J.Ygeno.2008.10.006 |
0.318 |
|
| 2009 |
Wang X, Xuan Z, Zhao X, Li Y, Zhang MQ. High-resolution human core-promoter prediction with CoreBoost_HM. Genome Research. 19: 266-75. PMID 18997002 DOI: 10.1101/Gr.081638.108 |
0.71 |
|
| 2008 |
Niida A, Smith AD, Imoto S, Tsutsumi S, Aburatani H, Zhang MQ, Akiyama T. Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells. Bmc Bioinformatics. 9: 404. PMID 18823535 DOI: 10.1186/1471-2105-9-404 |
0.427 |
|
| 2008 |
Zhang C, Zhang Z, Castle J, Sun S, Johnson J, Krainer AR, Zhang MQ. Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes & Development. 22: 2550-63. PMID 18794351 DOI: 10.1101/Gad.1703108 |
0.4 |
|
| 2008 |
Lin H, Zhang Z, Zhang MQ, Ma B, Li M. ZOOM! Zillions of oligos mapped. Bioinformatics (Oxford, England). 24: 2431-7. PMID 18684737 DOI: 10.1093/Bioinformatics/Btn416 |
0.323 |
|
| 2008 |
Hsieh MC, Das D, Sambandam N, Zhang MQ, Nahlé Z. Regulation of the PDK4 isozyme by the Rb-E2F1 complex. The Journal of Biological Chemistry. 283: 27410-7. PMID 18667418 DOI: 10.1074/Jbc.M802418200 |
0.302 |
|
| 2008 |
Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM. Poly A- transcripts expressed in HeLa cells. Plos One. 3: e2803. PMID 18665230 DOI: 10.1371/Journal.Pone.0002803 |
0.683 |
|
| 2008 |
Fan S, Zhang MQ, Zhang X. Histone Methylation Marks Play Important Roles in Predicting the Methylation Status of CpG Islands Biochemical and Biophysical Research Communications. 374: 559-564. PMID 18656446 DOI: 10.1016/J.Bbrc.2008.07.077 |
0.343 |
|
| 2008 |
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genetics. 40: 897-903. PMID 18552846 DOI: 10.1038/Ng.154 |
0.755 |
|
| 2008 |
Chen G, Li W, Zhang QS, Regulski M, Sinha N, Barditch J, Tully T, Krainer AR, Zhang MQ, Dubnau J. Identification of synaptic targets of Drosophila pumilio. Plos Computational Biology. 4: e1000026. PMID 18463699 DOI: 10.1371/Journal.Pcbi.1000026 |
0.325 |
|
| 2008 |
Wu X, Jiang R, Zhang MQ, Li S. Network-based global inference of human disease genes. Molecular Systems Biology. 4: 189. PMID 18463613 DOI: 10.1038/Msb.2008.27 |
0.333 |
|
| 2008 |
Zhang C, Li WH, Krainer AR, Zhang MQ. RNA landscape of evolution for optimal exon and intron discrimination. Proceedings of the National Academy of Sciences of the United States of America. 105: 5797-802. PMID 18391195 DOI: 10.1073/Pnas.0801692105 |
0.381 |
|
| 2008 |
Smith AD, Xuan Z, Zhang MQ. Using quality scores and longer reads improves accuracy of Solexa read mapping. Bmc Bioinformatics. 9: 128. PMID 18307793 DOI: 10.1186/1471-2105-9-128 |
0.668 |
|
| 2008 |
Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM. Scanning the human genome at kilobase resolution. Genome Research. 18: 751-62. PMID 18292219 DOI: 10.1101/Gr.068304.107 |
0.65 |
|
| 2008 |
Eguchi J, Yan QW, Schones DE, Kamal M, Hsu CH, Zhang MQ, Crawford GE, Rosen ED. Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell Metabolism. 7: 86-94. PMID 18177728 DOI: 10.1016/J.Cmet.2007.11.002 |
0.698 |
|
| 2008 |
Barrera LO, Li Z, Smith AD, Arden KC, Cavenee WK, Zhang MQ, Green RD, Ren B. Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Research. 18: 46-59. PMID 18042645 DOI: 10.1101/Gr.6654808 |
0.54 |
|
| 2008 |
Wang X, Gu J, Zhang MQ, Li Y. Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species. Bioinformatics (Oxford, England). 24: 165-71. PMID 18037683 DOI: 10.1093/Bioinformatics/Btm572 |
0.302 |
|
| 2007 |
Fan S, Fang F, Zhang X, Zhang MQ. Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome. Plos One. 2: e1184. PMID 18030324 DOI: 10.1371/Journal.Pone.0001184 |
0.359 |
|
| 2007 |
Wang X, Bandyopadhyay S, Xuan Z, Zhao X, Zhang MQ, Zhang X. Prediction of transcription start sites based on feature selection using AMOSA. Computational Systems Bioinformatics. Computational Systems Bioinformatics Conference. 6: 183-93. PMID 17951823 |
0.61 |
|
| 2007 |
Jiang B, Zhang MQ, Zhang X. OSCAR: one-class SVM for accurate recognition of cis-elements. Bioinformatics (Oxford, England). 23: 2823-8. PMID 17921174 DOI: 10.1093/Bioinformatics/Btm473 |
0.374 |
|
| 2007 |
Zhang MQ. Computational analyses of eukaryotic promoters Bmc Bioinformatics. 8. PMID 17903284 DOI: 10.1186/1471-2105-8-S6-S3 |
0.339 |
|
| 2007 |
Mignone JL, Roig-Lopez JL, Fedtsova N, Schones DE, Manganas LN, Maletic-Savatic M, Keyes WM, Mills AA, Gleiberman A, Zhang MQ, Enikolopov G. Neural potential of a stem cell population in the hair follicle. Cell Cycle (Georgetown, Tex.). 6: 2161-70. PMID 17873521 DOI: 10.4161/Cc.6.17.4593 |
0.627 |
|
| 2007 |
Zhang C, Hastings ML, Krainer AR, Zhang MQ. Dual-specificity splice sites function alternatively as 5' and 3' splice sites. Proceedings of the National Academy of Sciences of the United States of America. 104: 15028-33. PMID 17848517 DOI: 10.1073/Pnas.0703773104 |
0.379 |
|
| 2007 |
Zhang C, Krainer AR, Zhang MQ. Evolutionary impact of limited splicing fidelity in mammalian genes. Trends in Genetics : Tig. 23: 484-8. PMID 17719121 DOI: 10.1016/J.Tig.2007.08.001 |
0.318 |
|
| 2007 |
Yang Z, Jiang H, Zhao F, Shankar DB, Sakamoto KM, Zhang MQ, Lin S. A highly conserved regulatory element controls hematopoietic expression of GATA-2 in zebrafish. Bmc Developmental Biology. 7: 97. PMID 17708765 DOI: 10.1186/1471-213X-7-97 |
0.435 |
|
| 2007 |
Das D, Zhang MQ. Predictive models of gene regulation: application of regression methods to microarray data. Methods in Molecular Biology (Clifton, N.J.). 377: 95-110. PMID 17634611 DOI: 10.1007/978-1-59745-390-5_5 |
0.384 |
|
| 2007 |
Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell. 128: 1231-45. PMID 17382889 DOI: 10.1016/J.Cell.2006.12.048 |
0.551 |
|
| 2007 |
Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM, Hannon GJ. Critical roles for Dicer in the female germline. Genes & Development. 21: 682-93. PMID 17369401 DOI: 10.1101/Gad.1521307 |
0.675 |
|
| 2007 |
Zhao X, Xuan Z, Zhang MQ. Boosting with stumps for predicting transcription start sites. Genome Biology. 8: R17. PMID 17274821 DOI: 10.1186/Gb-2007-8-2-R17 |
0.663 |
|
| 2007 |
Schones DE, Smith AD, Zhang MQ. Statistical significance of cis-regulatory modules. Bmc Bioinformatics. 8: 19. PMID 17241466 DOI: 10.1186/1471-2105-8-19 |
0.703 |
|
| 2007 |
Smith AD, Sumazin P, Zhang MQ. Tissue-specific regulatory elements in mammalian promoters. Molecular Systems Biology. 3: 73. PMID 17224917 DOI: 10.1038/Msb4100114 |
0.529 |
|
| 2007 |
Jiang C, Xuan Z, Zhao F, Zhang MQ. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Research. 35: D137-40. PMID 17202159 DOI: 10.1093/Nar/Gkl1041 |
0.675 |
|
| 2007 |
Zhang M. Computational Dissection Of Mammalian Regulation Networks Genome Informatics. 19: 197-197. DOI: 10.11234/Gi1990.19.197 |
0.331 |
|
| 2006 |
Kim YC, Jung YC, Xuan Z, Dong H, Zhang MQ, Wang SM. Pan-genome isolation of low abundance transcripts using SAGE tag. Febs Letters. 580: 6721-9. PMID 17113583 DOI: 10.1016/J.Febslet.2006.11.013 |
0.689 |
|
| 2006 |
Martinez MJ, Smith AD, Li B, Zhang MQ, Harrod KS. Computational prediction of novel components of lung transcriptional networks. Bioinformatics (Oxford, England). 23: 21-9. PMID 17050569 DOI: 10.1093/Bioinformatics/Btl531 |
0.463 |
|
| 2006 |
Li J, Zhang MQ, Zhang X. A new method for detecting human recombination hotspots and its applications to the HapMap ENCODE data. American Journal of Human Genetics. 79: 628-639. PMID 16960799 DOI: 10.1086/508066 |
0.31 |
|
| 2006 |
Fang F, Fan S, Zhang X, Zhang MQ. Predicting methylation status of CpG islands in the human brain. Bioinformatics (Oxford, England). 22: 2204-9. PMID 16837523 DOI: 10.1093/Bioinformatics/Btl377 |
0.392 |
|
| 2006 |
Smith PJ, Zhang C, Wang J, Chew SL, Zhang MQ, Krainer AR. An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Human Molecular Genetics. 15: 2490-508. PMID 16825284 DOI: 10.1093/Hmg/Ddl171 |
0.481 |
|
| 2006 |
Das R, Dimitrova N, Xuan Z, Rollins RA, Haghighi F, Edwards JR, Ju J, Bestor TH, Zhang MQ. Computational prediction of methylation status in human genomic sequences. Proceedings of the National Academy of Sciences of the United States of America. 103: 10713-6. PMID 16818882 DOI: 10.1073/Pnas.0602949103 |
0.651 |
|
| 2006 |
Das D, Nahlé Z, Zhang MQ. Adaptively inferring human transcriptional subnetworks. Molecular Systems Biology. 2: 2006.0029. PMID 16760900 DOI: 10.1038/Msb4100067 |
0.441 |
|
| 2006 |
Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Research. 34: e63. PMID 16682442 DOI: 10.1093/Nar/Gkl151 |
0.417 |
|
| 2006 |
Zhang C, Xuan Z, Otto S, Hover JR, McCorkle SR, Mandel G, Zhang MQ. A clustering property of highly-degenerate transcription factor binding sites in the mammalian genome. Nucleic Acids Research. 34: 2238-46. PMID 16670430 DOI: 10.1093/Nar/Gkl248 |
0.683 |
|
| 2006 |
Zhang C, Li HR, Fan JB, Wang-Rodriguez J, Downs T, Fu XD, Zhang MQ. Profiling alternatively spliced mRNA isoforms for prostate cancer classification. Bmc Bioinformatics. 7: 202. PMID 16608523 DOI: 10.1186/1471-2105-7-202 |
0.31 |
|
| 2006 |
Smith AD, Sumazin P, Xuan Z, Zhang MQ. DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proceedings of the National Academy of Sciences of the United States of America. 103: 6275-80. PMID 16606849 DOI: 10.1073/Pnas.0508169103 |
0.7 |
|
| 2006 |
Rollins RA, Haghighi F, Edwards JR, Das R, Zhang MQ, Ju J, Bestor TH. Large-scale structure of genomic methylation patterns. Genome Research. 16: 157-63. PMID 16365381 DOI: 10.1101/Gr.4362006 |
0.381 |
|
| 2005 |
Zhang MQ. Using CorePromoter to find human core promoters Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. PMID 18428749 DOI: 10.1002/0471250953.Bi0209S10 |
0.403 |
|
| 2005 |
Prasanth KV, Prasanth SG, Xuan Z, Hearn S, Freier SM, Bennett CF, Zhang MQ, Spector DL. Regulating gene expression through RNA nuclear retention. Cell. 123: 249-63. PMID 16239143 DOI: 10.1016/J.Cell.2005.08.033 |
0.629 |
|
| 2005 |
Wang J, Smith PJ, Krainer AR, Zhang MQ. Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Research. 33: 5053-62. PMID 16147989 DOI: 10.1093/Nar/Gki810 |
0.503 |
|
| 2005 |
Xuan Z, Zhao F, Wang J, Chen G, Zhang MQ. Genome-wide promoter extraction and analysis in human, mouse, and rat. Genome Biology. 6: R72. PMID 16086854 DOI: 10.1186/Gb-2005-6-8-R72 |
0.709 |
|
| 2005 |
Smith AD, Sumazin P, Das D, Zhang MQ. Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (Oxford, England). 21: i403-12. PMID 15961485 DOI: 10.1093/Bioinformatics/Bti1043 |
0.507 |
|
| 2005 |
Smith AD, Sumazin P, Zhang MQ. Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proceedings of the National Academy of Sciences of the United States of America. 102: 1560-5. PMID 15668401 DOI: 10.1073/Pnas.0406123102 |
0.505 |
|
| 2005 |
Xuan Z, Zhang MQ. From worm to human: bioinformatics approaches to identify FOXO target genes. Mechanisms of Ageing and Development. 126: 209-15. PMID 15610780 DOI: 10.1016/J.Mad.2004.09.021 |
0.677 |
|
| 2005 |
Zhao F, Xuan Z, Liu L, Zhang MQ. TRED: a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies. Nucleic Acids Research. 33: D103-7. PMID 15608156 DOI: 10.1093/Nar/Gki004 |
0.692 |
|
| 2005 |
Long F, Liu H, Hahn C, Sumazin P, Zhang MQ, Zilberstein A. Genome-wide prediction and analysis of function-specific transcription factor binding sites. In Silico Biology. 4: 395-410. PMID 15506990 |
0.323 |
|
| 2005 |
Sumazin P, Chen G, Hata N, Smith AD, Zhang T, Zhang MQ. DWE: discriminating word enumerator. Bioinformatics (Oxford, England). 21: 31-8. PMID 15333453 DOI: 10.1093/Bioinformatics/Bth471 |
0.471 |
|
| 2005 |
Schones DE, Sumazin P, Zhang MQ. Similarity of position frequency matrices for transcription factor binding sites. Bioinformatics (Oxford, England). 21: 307-13. PMID 15319260 DOI: 10.1093/Bioinformatics/Bth480 |
0.669 |
|
| 2004 |
Dike S, Balija VS, Nascimento LU, Xuan Z, Ou J, Zutavern T, Palmer LE, Hannon G, Zhang MQ, McCombie WR. The mouse genome: experimental examination of gene predictions and transcriptional start sites. Genome Research. 14: 2424-9. PMID 15574821 DOI: 10.1101/Gr.3158304 |
0.69 |
|
| 2004 |
Das D, Banerjee N, Zhang MQ. Interacting models of cooperative gene regulation. Proceedings of the National Academy of Sciences of the United States of America. 101: 16234-9. PMID 15534222 DOI: 10.1073/Pnas.0407365101 |
0.422 |
|
| 2004 |
Zhang J, Li F, Li J, Zhang MQ, Zhang X. Evidence and characteristics of putative human alpha recombination hotspots. Human Molecular Genetics. 13: 2823-8. PMID 15385449 DOI: 10.1093/Hmg/Ddh310 |
0.353 |
|
| 2004 |
Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ. Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biology. 5: R56. PMID 15287978 DOI: 10.1186/Gb-2004-5-8-R56 |
0.446 |
|
| 2004 |
Chen G, Hata N, Zhang MQ. Transcription factor binding element detection using functional clustering of mutant expression data. Nucleic Acids Research. 32: 2362-71. PMID 15115798 DOI: 10.1093/Nar/Gkh557 |
0.414 |
|
| 2003 |
Zhang MQ. Prediction, annotation, and analysis of human promoters Cold Spring Harbor Symposia On Quantitative Biology. 68: 217-225. PMID 15338621 DOI: 10.1101/Sqb.2003.68.217 |
0.314 |
|
| 2003 |
Banerjee N, Zhang MQ. Identifying cooperativity among transcription factors controlling the cell cycle in yeast. Nucleic Acids Research. 31: 7024-7031. PMID 14627835 DOI: 10.1093/Nar/Gkg894 |
0.447 |
|
| 2003 |
Davuluri RV, Zhang MQ. Computer software to find genes in plant genomic DNA. Methods in Molecular Biology (Clifton, N.J.). 236: 87-108. PMID 14501060 DOI: 10.1385/1-59259-413-1:87 |
0.63 |
|
| 2003 |
Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR. ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Research. 31: 3568-71. PMID 12824367 DOI: 10.1093/Nar/Gkg616 |
0.455 |
|
| 2003 |
Li Z, Van Calcar S, Qu C, Cavenee WK, Zhang MQ, Ren B. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proceedings of the National Academy of Sciences of the United States of America. 100: 8164-9. PMID 12808131 DOI: 10.1073/Pnas.1332764100 |
0.376 |
|
| 2003 |
Xuan Z, Wang J, Zhang MQ. Computational comparison of two mouse draft genomes and the human golden path. Genome Biology. 4: R1. PMID 12537546 DOI: 10.1186/Gb-2002-4-1-R1 |
0.684 |
|
| 2003 |
Kato M, Hata N, Banerjee N, Zhang MQ. Integrative Method for Identifying Combinatorial Regulation of Transcription Factors Genome Informatics. 14: 358-359. DOI: 10.11234/Gi1990.14.358 |
0.431 |
|
| 2002 |
Carmell MA, Xuan Z, Zhang MQ, Hannon GJ. The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes & Development. 16: 2733-42. PMID 12414724 DOI: 10.1101/Gad.1026102 |
0.609 |
|
| 2002 |
Nahle Z, Polakoff J, Davuluri RV, McCurrach ME, Jacobson MD, Narita M, Zhang MQ, Lazebnik Y, Bar-Sagi D, Lowe SW. Direct coupling of the cell cycle and cell death machinery by E2F. Nature Cell Biology. 4: 859-64. PMID 12389032 DOI: 10.1038/Ncb868 |
0.565 |
|
| 2002 |
Zhang Y, Mei P, Lou R, Zhang MQ, Wu G, Qiang B, Zhang Z, Shen Y. Gene expression profiling in developing human hippocampus. Journal of Neuroscience Research. 70: 200-8. PMID 12271469 DOI: 10.1002/Jnr.10322 |
0.362 |
|
| 2002 |
Zhang MQ. Extracting functional information from microarrays: A challenge for functional genomics Proceedings of the National Academy of Sciences of the United States of America. 99: 12509-12511. PMID 12271149 DOI: 10.1073/Pnas.212532499 |
0.404 |
|
| 2002 |
Zhang MQ. Computational prediction of eukaryotic protein-coding genes Nature Reviews Genetics. 3: 698-709. PMID 12209144 DOI: 10.1038/Nrg890 |
0.389 |
|
| 2002 |
Xuan Z, McCombie WR, Zhang MQ. GFScan: a gene family search tool at genomic DNA level. Genome Research. 12: 1142-9. PMID 12097353 DOI: 10.1101/Gr.220102 |
0.634 |
|
| 2002 |
Banerjee N, Zhang MQ. Functional genomics as applied to mapping transcription regulatory networks Current Opinion in Microbiology. 5: 313-317. PMID 12057687 DOI: 10.1016/S1369-5274(02)00322-3 |
0.425 |
|
| 2002 |
Zhang T, Zhang M. Promoter Extraction from GenBank (PEG): automatic extraction of eukaryotic promoter sequences in large sets of genes. Bioinformatics (Oxford, England). 17: 1232-3. PMID 11751235 DOI: 10.1093/Bioinformatics/17.12.1232 |
0.336 |
|
| 2002 |
Kato M, Hata N, Banerjee N, Zhang MQ. Inferring Combinatorial Regulation of Binding Sites and Transcription Factors on Gene Expression Genome Informatics. 13: 303-304. DOI: 10.11234/Gi1990.13.303 |
0.379 |
|
| 2001 |
Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nature Genetics. 29: 412-7. PMID 11726928 DOI: 10.1038/Ng780 |
0.635 |
|
| 2001 |
Weinmann AS, Bartley SM, Zhang T, Zhang MQ, Farnham PJ. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Molecular and Cellular Biology. 21: 6820-32. PMID 11564866 DOI: 10.1128/Mcb.21.20.6820-6832.2001 |
0.415 |
|
| 2001 |
Kel AE, Kel-Margoulis OV, Farnham PJ, Bartley SM, Wingender E, Zhang MQ. Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. Journal of Molecular Biology. 309: 99-120. PMID 11491305 DOI: 10.1006/Jmbi.2001.4650 |
0.445 |
|
| 2001 |
Zhang MQ. Discriminant analysis and its application in DNA sequence motif recognition. Briefings in Bioinformatics. 1: 331-42. PMID 11465051 DOI: 10.1093/Bib/1.4.331 |
0.341 |
|
| 2001 |
Tabaska JE, Davuluri RV, Zhang MQ. Identifying the 3'-terminal exon in human DNA. Bioinformatics (Oxford, England). 17: 602-7. PMID 11448878 DOI: 10.1093/Bioinformatics/17.7.602 |
0.585 |
|
| 2001 |
Wu Q, Zhang T, Cheng JF, Kim Y, Grimwood J, Schmutz J, Dickson M, Noonan JP, Zhang MQ, Myers RM, Maniatis T. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Genome Research. 11: 389-404. PMID 11230163 DOI: 10.1101/Gr.167301 |
0.354 |
|
| 2001 |
Farnham P, Graveel C, Kirmizis A, Bartley S, Kel A, Kel-Margoulis O, Wingender E, Zhang M, Jatkoe T, Madore S. Use of chromatin immunoprecipitation to study transcriptional deregulation in cancer cells Nature Genetics. 27: 53-53. DOI: 10.1038/87076 |
0.332 |
|
| 2000 |
Stamm S, Zhu J, Nakai K, Stoilov P, Stoss O, Zhang MQ. An alternative-exon database and its statistical analysis. Dna and Cell Biology. 19: 739-756. PMID 11177572 DOI: 10.1089/104454900750058107 |
0.344 |
|
| 2000 |
Davuluri RV, Suzuki Y, Sugano S, Zhang MQ. CART Classification of Human 5′ UTR Sequences Genome Research. 10: 1807-1816. PMID 11076865 DOI: 10.1101/Gr.Gr-1460R |
0.624 |
|
| 2000 |
Ioshikhes IP, Zhang MQ. Large-scale human promoter mapping using CpG islands. Nature Genetics. 26: 61-63. PMID 10973249 DOI: 10.1038/79189 |
0.724 |
|
| 2000 |
Liu HX, Chew SL, Cartegni L, Zhang MQ, Krainer AR. Exonic splicing enhancer motif recognized by human SC35 under splicing conditions. Molecular and Cellular Biology. 20: 1063-71. PMID 10629063 DOI: 10.1128/Mcb.20.3.1063-1071.2000 |
0.346 |
|
| 2000 |
Machida M, Yamazaki S, Kunihiro S, Tanaka T, Kushida N, Jinnno K, Haikawa Y, Yamazaki J, Yamamoto S, Sekine M, Oguchi A, Nagai Y, Sakai M, Aoki K, Ogura K, ... ... Zhang MQ, et al. A 38 kb segment containing the cdc2 gene from the left arm of fission yeast chromosome II: sequence analysis and characterization of the genomic DNA and cDNAs encoded on the segment. Yeast (Chichester, England). 16: 71-80. PMID 10620777 DOI: 10.1002/(Sici)1097-0061(20000115)16:1<71::Aid-Yea505>3.0.Co;2-5 |
0.37 |
|
| 2000 |
Getz G, Levine E, Domany E, Zhang M. Super-paramagnetic clustering of yeast gene expression profiles Physica a: Statistical Mechanics and Its Applications. 279: 457-464. DOI: 10.1016/S0378-4371(99)00524-5 |
0.331 |
|
| 1999 |
Mayeda A, Badolato J, Kobayashi R, Zhang MQ, Gardiner EM, Krainer AR. Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. The Embo Journal. 18: 4560-70. PMID 10449421 DOI: 10.1093/Emboj/18.16.4560 |
0.306 |
|
| 1999 |
Zhang MQ. Promoter analysis of co-regulated genes in the yeast genome. Computers & Chemistry. 23: 233-50. PMID 10404618 DOI: 10.1016/S0097-8485(99)00020-0 |
0.437 |
|
| 1999 |
Ioshikhes I, Trifonov EN, Zhang MQ. Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure Proceedings of the National Academy of Sciences of the United States of America. 96: 2891-2895. PMID 10077607 DOI: 10.1073/Pnas.96.6.2891 |
0.712 |
|
| 1999 |
Zhang MQ. Large-scale gene expression data analysis: a new challenge to computational biologists. Genome Research. 9: 681-688. DOI: 10.1101/Gr.9.8.681 |
0.392 |
|
| 1998 |
Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell. 9: 3273-97. PMID 9843569 DOI: 10.1091/Mbc.9.12.3273 |
0.374 |
|
| 1998 |
Zhang MQ. Identification of protein-coding regions in Arabidopsis thaliana genome based on quadratic discriminant analysis Plant Molecular Biology. 37: 803-806. PMID 9678575 DOI: 10.1023/A:1006023912378 |
0.358 |
|
| 1998 |
Chen T, Zhang MQ. Pombe: A gene-finding and exon-intron structure prediction system for fission yeast Yeast. 14: 701-710. PMID 9675815 DOI: 10.1002/(Sici)1097-0061(19980615)14:8<701::Aid-Yea247>3.0.Co;2-# |
0.344 |
|
| 1998 |
Liu HX, Zhang M, Krainer AR. Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes & Development. 12: 1998-2012. PMID 9649504 DOI: 10.1101/Gad.12.13.1998 |
0.343 |
|
| 1998 |
Zhang MQ. Statistical Features of Human Exons and Their Flanking Regions Human Molecular Genetics. 7: 919-932. PMID 9536098 DOI: 10.1093/Hmg/7.5.919 |
0.4 |
|
| 1998 |
Zhang MQ. Identification of human gene core promoters in silico Genome Research. 8: 319-326. PMID 9521935 DOI: 10.1101/Gr.8.3.319 |
0.419 |
|
| 1997 |
Zhang MQ. Identification of protein coding regions in the human genome by quadratic discriminant analysis Proceedings of the National Academy of Sciences of the United States of America. 94: 565-568. PMID 9012824 DOI: 10.1073/Pnas.94.2.565 |
0.349 |
|
| 1994 |
Zhang MQ, Marr TG. Fission yeast gene structure and recognition. Nucleic Acids Research. 22: 1750-9. PMID 8202381 DOI: 10.1093/Nar/22.9.1750 |
0.34 |
|
| 1994 |
Stamm S, Zhang MQ, Marr TG, Helfman DM. A sequence compilation and comparison of exons that are alternatively spliced in neurons Nucleic Acids Research. 22: 1515-1526. PMID 8202349 DOI: 10.1093/Nar/22.9.1515 |
0.34 |
|
| 1993 |
Zhang MQ, Marr TG. Genome mapping by nonrandom anchoring: a discrete theoretical analysis. Proceedings of the National Academy of Sciences of the United States of America. 90: 600-4. PMID 8421694 DOI: 10.1073/Pnas.90.2.600 |
0.307 |
|
| 1993 |
Zhang MQ, Marr TG. Genome mapping by random anchoring: A discrete theoretical analysis Journal of Statistical Physics. 73: 611-623. DOI: 10.1007/Bf01054342 |
0.313 |
|
| 1990 |
Percus J, Zhang M. The quasi-one dimensional hard square gas Molecular Physics. 69: 347-355. DOI: 10.1080/00268979000100241 |
0.482 |
|
| 1990 |
Zhang MQ, Percus JK. A recursive density functional formalism for nonuniform fluids The Journal of Chemical Physics. 92: 6779-6785. DOI: 10.1063/1.458264 |
0.486 |
|
| 1989 |
Percus JK, Zhang MQ. Direct correlations of the capillary wave model and construction of the free energy density functional for the liquid–vapor interface system The Journal of Chemical Physics. 90: 3795-3799. DOI: 10.1063/1.455837 |
0.484 |
|
| 1989 |
Zhang MQ, Percus JK. Inhomogeneous Ising model on a multiconnected network Journal of Statistical Physics. 56: 695-708. DOI: 10.1007/Bf01016775 |
0.487 |
|
| 1988 |
Ord G, Percus J, Zhang M. Energetics of a discrete interface Nuclear Physics B. 305: 271-285. DOI: 10.1016/0550-3213(88)90296-9 |
0.492 |
|
| 1988 |
Zhang MQ, Wang J-, Lebowitz JL, Vall�s JL. Power law decay of correlations in stationary nonequilibrium lattice gases with conservative dynamics Journal of Statistical Physics. 52: 1461-1478. DOI: 10.1007/Bf01011660 |
0.559 |
|
| 1986 |
Krug J, Lebowitz JL, Spohn H, Zhang MQ. The fast rate limit of driven diffusive systems Journal of Statistical Physics. 44: 535-565. DOI: 10.1007/Bf01011309 |
0.416 |
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