| Year |
Citation |
Score |
| 2020 |
Qin Q, Fan J, Zheng R, Wan C, Mei S, Wu Q, Sun H, Brown M, Zhang J, Meyer CA, Liu XS. Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. Genome Biology. 21: 32. PMID 32033573 DOI: 10.1186/S13059-020-1934-6 |
0.346 |
|
| 2019 |
Cato L, de Tribolet-Hardy J, Lee I, Rottenberg JT, Coleman I, Melchers D, Houtman R, Xiao T, Li W, Uo T, Sun S, Kuznik NC, Göppert B, Ozgun F, van Royen ME, ... ... Liu XS, et al. ARv7 Represses Tumor-Suppressor Genes in Castration-Resistant Prostate Cancer. Cancer Cell. PMID 30773341 DOI: 10.1016/J.Ccell.2019.01.008 |
0.388 |
|
| 2019 |
Hu X, Zhang J, Wang J, Fu J, Li T, Zheng X, Wang B, Gu S, Jiang P, Fan J, Ying X, Zhang J, Carroll MC, Wucherpfennig KW, Hacohen N, ... ... Liu XS, et al. Landscape of B cell immunity and related immune evasion in human cancers. Nature Genetics. PMID 30742113 DOI: 10.1038/S41588-018-0339-X |
0.302 |
|
| 2019 |
Wang B, Wang M, Zhang W, Xiao T, Chen CH, Wu A, Wu F, Traugh N, Wang X, Li Z, Mei S, Cui Y, Shi S, Lipp JJ, Hinterndorfer M, ... ... Liu XS, et al. Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute. Nature Protocols. PMID 30710114 DOI: 10.1038/S41596-018-0113-7 |
0.339 |
|
| 2018 |
Zheng R, Wan C, Mei S, Qin Q, Wu Q, Sun H, Chen CH, Brown M, Zhang X, Meyer CA, Liu XS. Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. Nucleic Acids Research. PMID 30462313 DOI: 10.1093/Nar/Gky1094 |
0.323 |
|
| 2018 |
Xiao T, Li W, Wang X, Xu H, Yang J, Wu Q, Huang Y, Geradts J, Jiang P, Fei T, Chi D, Zang C, Liao Q, Rennhack J, Andrechek E, ... ... Liu XS, et al. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. Proceedings of the National Academy of Sciences of the United States of America. PMID 29987050 DOI: 10.1073/Pnas.1722617115 |
0.6 |
|
| 2017 |
Mei S, Meyer CA, Zheng R, Qin Q, Wu Q, Jiang P, Li B, Shi X, Wang B, Fan J, Shih C, Brown M, Zang C, Liu XS. Cistrome Cancer: A Web Resource for Integrative Gene Regulation Modeling in Cancer. Cancer Research. 77: e19-e22. PMID 29092931 DOI: 10.1158/0008-5472.Can-17-0327 |
0.611 |
|
| 2017 |
Cao Q, Ma J, Chen CH, Xu H, Chen Z, Li W, Liu XS. CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments. Plos One. 12: e0184281. PMID 28873439 DOI: 10.1371/Journal.Pone.0184281 |
0.521 |
|
| 2017 |
Fei T, Chen Y, Xiao T, Li W, Cato L, Zhang P, Cotter MB, Bowden M, Lis RT, Zhao SG, Wu Q, Feng FY, Loda M, He HH, Liu XS, et al. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Proceedings of the National Academy of Sciences of the United States of America. PMID 28611215 DOI: 10.1073/Pnas.1617467114 |
0.518 |
|
| 2017 |
Li MJ, Zhang J, Liang Q, Xuan C, Wu J, Jiang P, Li W, Zhu Y, Wang P, Fernandez D, Shen Y, Chen Y, Kocher JA, Yu Y, Sham PC, ... ... Liu XS, et al. Exploring genetic associations with ceRNA regulation in the human genome. Nucleic Acids Research. PMID 28472449 DOI: 10.1093/Nar/Gkx331 |
0.519 |
|
| 2017 |
Liu Y, Chen S, Wang S, Soares F, Fischer M, Meng F, Du Z, Lin C, Meyer C, DeCaprio JA, Brown M, Liu XS, He HH. Transcriptional landscape of the human cell cycle. Proceedings of the National Academy of Sciences of the United States of America. PMID 28289232 DOI: 10.1073/Pnas.1617636114 |
0.326 |
|
| 2017 |
Gao W, Li W, Xiao T, Liu XS, Kaelin WG. Inactivation of the PBRM1 tumor suppressor gene amplifies the HIF-response in VHL-/- clear cell renal carcinoma. Proceedings of the National Academy of Sciences of the United States of America. PMID 28082722 DOI: 10.1073/Pnas.1619726114 |
0.367 |
|
| 2016 |
T L, Aron L, Zullo J, Pan Y, Kim H, Chen Y, Yang TH, Kim HM, Drake D, Liu XS, Bennett DA, Colaiácovo MP, Yankner BA. Addendum: REST and stress resistance in ageing and Alzheimer's disease. Nature. PMID 27851730 DOI: 10.1038/Nature20579 |
0.314 |
|
| 2016 |
Zhu S, Li W, Liu J, Chen CH, Liao Q, Xu P, Xu H, Xiao T, Cao Z, Peng J, Yuan P, Brown M, Liu XS, Wei W. Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library. Nature Biotechnology. PMID 27798563 DOI: 10.1038/Nbt.3715 |
0.504 |
|
| 2016 |
Mei S, Qin Q, Wu Q, Sun H, Zheng R, Zang C, Zhu M, Wu J, Shi X, Taing L, Liu T, Brown M, Meyer CA, Liu XS. Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Research. PMID 27789702 DOI: 10.1093/Nar/Gkw983 |
0.6 |
|
| 2016 |
Wang S, Zang C, Xiao T, Fan J, Mei S, Qin Q, Wu Q, Li XL, Xu K, He HH, Brown M, Meyer CA, Liu XS. Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles. Genome Research. PMID 27466232 DOI: 10.1101/Gr.201574.115 |
0.626 |
|
| 2016 |
Ma J, Köster J, Qin Q, Hu S, Li W, Chen C, Cao Q, Wang J, Mei S, Liu Q, Xu H, Liu XS. CRISPR-DO for genome-wide CRISPR design and optimization. Bioinformatics (Oxford, England). PMID 27402906 DOI: 10.1093/Bioinformatics/Btw476 |
0.504 |
|
| 2016 |
Li B, Li T, Pignon JC, Wang B, Wang J, Shukla SA, Dou R, Chen Q, Hodi FS, Choueiri TK, Wu C, Hacohen N, Signoretti S, Liu JS, Liu XS. Landscape of tumor-infiltrating T cell repertoire of human cancers. Nature Genetics. PMID 27240091 DOI: 10.1038/Ng.3581 |
0.31 |
|
| 2016 |
Zang C, Wang T, Deng K, Li B, Hu S, Qin Q, Xiao T, Zhang S, Meyer CA, He HH, Brown M, Liu JS, Xie Y, Liu XS. High-dimensional genomic data bias correction and data integration using MANCIE. Nature Communications. 7: 11305. PMID 27072482 DOI: 10.1038/Ncomms11305 |
0.572 |
|
| 2016 |
Du Z, Sun T, Hacisuleyman E, Fei T, Wang X, Brown M, Rinn JL, Lee MG, Chen Y, Kantoff PW, Liu XS. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nature Communications. 7: 10982. PMID 26975529 DOI: 10.1038/Ncomms10982 |
0.513 |
|
| 2015 |
Xu H, Xu K, He HH, Zang C, Chen CH, Chen Y, Qin Q, Wang S, Wang C, Hu S, Li F, Long H, Brown M, Liu XS. Integrative analysis reveals the transcriptional collaboration between EZH2 and E2F1 in the regulation of cancer-related gene expression. Molecular Cancer Research : McR. PMID 26659825 DOI: 10.1158/1541-7786.Mcr-15-0313 |
0.714 |
|
| 2015 |
Jiang P, Wang H, Li W, Zang C, Li B, Wong YJ, Meyer C, Liu JS, Aster JC, Liu XS. Network analysis of gene essentiality in functional genomics experiments. Genome Biology. 16: 239. PMID 26518695 DOI: 10.1186/S13059-015-0808-9 |
0.608 |
|
| 2015 |
Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M, Liu XS. Sequence determinants of improved CRISPR sgRNA design. Genome Research. PMID 26063738 DOI: 10.1101/Gr.191452.115 |
0.505 |
|
| 2015 |
Jiang P, Freedman ML, Liu JS, Liu XS. Inference of transcriptional regulation in cancers. Proceedings of the National Academy of Sciences of the United States of America. 112: 7731-6. PMID 26056275 DOI: 10.1073/pnas.1424272112 |
0.364 |
|
| 2015 |
Wang H, Zang C, Liu XS, Aster JC. The role of Notch receptors in transcriptional regulation. Journal of Cellular Physiology. 230: 982-8. PMID 25418913 DOI: 10.1002/Jcp.24872 |
0.548 |
|
| 2015 |
Sun T, Du Z, Fei T, Brown M, Lee GM, Chen Y, Liu XS, Kantoff PW. Long non-coding RNA-mediated PTEN regulation in prostate cancer. Journal of Clinical Oncology. 33: e16081-e16081. DOI: 10.1200/Jco.2015.33.15_Suppl.E16081 |
0.514 |
|
| 2014 |
Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biology. 15: 554. PMID 25476604 DOI: 10.1186/S13059-014-0554-4 |
0.531 |
|
| 2014 |
Yashiro-Ohtani Y, Wang H, Zang C, Arnett KL, Bailis W, Ho Y, Knoechel B, Lanauze C, Louis L, Forsyth KS, Chen S, Chung Y, Schug J, Blobel GA, Liebhaber SA, ... Liu XS, et al. Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proceedings of the National Academy of Sciences of the United States of America. 111: E4946-53. PMID 25369933 DOI: 10.1073/Pnas.1407079111 |
0.543 |
|
| 2014 |
Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, ... Liu XS, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415 |
0.343 |
|
| 2014 |
Luyten A, Zang C, Liu XS, Shivdasani RA. Active enhancers are delineated de novo during hematopoiesis, with limited lineage fidelity among specified primary blood cells. Genes & Development. 28: 1827-39. PMID 25128499 DOI: 10.1101/Gad.240101.114 |
0.531 |
|
| 2014 |
Stoeck A, Lejnine S, Truong A, Pan L, Wang H, Zang C, Yuan J, Ware C, MacLean J, Garrett-Engele PW, Kluk M, Laskey J, Haines BB, Moskaluk C, Zawel L, ... ... Liu XS, et al. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. Cancer Discovery. 4: 1154-67. PMID 25104330 DOI: 10.1158/2159-8290.CD-13-0830 |
0.505 |
|
| 2014 |
Zheng X, Zhao Q, Wu HJ, Li W, Wang H, Meyer CA, Qin QA, Xu H, Zang C, Jiang P, Li F, Hou Y, He J, Wang J, Wang J, ... ... Liu XS, et al. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biology. 15: 419. PMID 25103624 DOI: 10.1186/S13059-014-0419-X |
0.598 |
|
| 2014 |
Wang J, Lin X, Wang S, Wang C, Wang Q, Duan X, Lu P, Wang Q, Wang C, Liu XS, Huang J. PHF8 and REST/NRSF co-occupy gene promoters to regulate proximal gene expression. Scientific Reports. 4: 5008. PMID 24852203 DOI: 10.1038/srep05008 |
0.319 |
|
| 2014 |
Hsieh CL, Fei T, Chen Y, Li T, Gao Y, Wang X, Sun T, Sweeney CJ, Lee GS, Chen S, Balk SP, Liu XS, Brown M, Kantoff PW. Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. Proceedings of the National Academy of Sciences of the United States of America. 111: 7319-24. PMID 24778216 DOI: 10.1073/Pnas.1324151111 |
0.489 |
|
| 2014 |
Lu T, Aron L, Zullo J, Pan Y, Kim H, Chen Y, Yang TH, Kim HM, Drake D, Liu XS, Bennett DA, Colaiácovo MP, Yankner BA. REST and stress resistance in ageing and Alzheimer's disease. Nature. 507: 448-54. PMID 24670762 DOI: 10.1038/Nature13163 |
0.387 |
|
| 2014 |
Chen X, Iliopoulos D, Zhang Q, Tang Q, Greenblatt MB, Hatziapostolou M, Lim E, Tam WL, Ni M, Chen Y, Mai J, Shen H, Hu DZ, Adoro S, Hu B, ... ... Liu XS, et al. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway. Nature. 508: 103-7. PMID 24670641 DOI: 10.1038/Nature13119 |
0.487 |
|
| 2014 |
Wee S, Dhanak D, Li H, Armstrong SA, Copeland RA, Sims R, Baylin SB, Liu XS, Schweizer L. Targeting epigenetic regulators for cancer therapy. Annals of the New York Academy of Sciences. 1309: 30-6. PMID 24571255 DOI: 10.1111/Nyas.12356 |
0.329 |
|
| 2014 |
Wang H, Zang C, Taing L, Arnett KL, Wong YJ, Pear WS, Blacklow SC, Liu XS, Aster JC. NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers. Proceedings of the National Academy of Sciences of the United States of America. 111: 705-10. PMID 24374627 DOI: 10.1073/pnas.1315023111 |
0.547 |
|
| 2014 |
Sulahian R, Casey F, Shen J, Qian ZR, Shin H, Ogino S, Weir BA, Vazquez F, Liu XS, Hahn WC, Bass AJ, Chan V, Shivdasani RA. An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer. Oncogene. 33: 5637-48. PMID 24317510 DOI: 10.1038/Onc.2013.517 |
0.335 |
|
| 2014 |
He HH, Meyer CA, Hu SS, Chen MW, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nature Methods. 11: 73-8. PMID 24317252 DOI: 10.1038/Nmeth.2762 |
0.605 |
|
| 2013 |
Shin H, Liu T, Duan X, Zhang Y, Liu XS. Computational methodology for ChIP-seq analysis. Quantitative Biology. 1: 54-70. PMID 25741452 DOI: 10.1007/s40484-013-0006-2 |
0.413 |
|
| 2013 |
Catic A, Suh CY, Hill CT, Daheron L, Henkel T, Orford KW, Dombkowski DM, Liu T, Liu XS, Scadden DT. Genome-wide Map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation Cell. 155: 1380-1395. PMID 24315104 DOI: 10.1016/J.Cell.2013.11.016 |
0.4 |
|
| 2013 |
Wang S, Sun H, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y, Liu XS. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature Protocols. 8: 2502-15. PMID 24263090 DOI: 10.1038/Nprot.2013.150 |
0.536 |
|
| 2013 |
Wang H, Meyer CA, Fei T, Wang G, Zhang F, Liu XS. A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer. Bmc Genomics. 14: 680. PMID 24093963 DOI: 10.1186/1471-2164-14-680 |
0.303 |
|
| 2013 |
Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, Chen Y, Liu XS. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nature Structural & Molecular Biology. 20: 908-13. PMID 23728290 DOI: 10.1038/Nsmb.2591 |
0.492 |
|
| 2013 |
Ni M, Chen Y, Fei T, Li D, Lim E, Liu XS, Brown M. Amplitude modulation of androgen signaling by c-MYC. Genes & Development. 27: 734-48. PMID 23530127 DOI: 10.1101/Gad.209569.112 |
0.501 |
|
| 2013 |
Sun H, Qin B, Liu T, Wang Q, Liu J, Wang J, Lin X, Yang Y, Taing L, Rao PK, Brown M, Zhang Y, Long HW, Liu XS. CistromeFinder for ChIP-seq and DNase-seq data reuse. Bioinformatics (Oxford, England). 29: 1352-4. PMID 23508969 DOI: 10.1093/Bioinformatics/Btt135 |
0.379 |
|
| 2013 |
Du Z, Li H, Wei Q, Zhao X, Wang C, Zhu Q, Yi X, Xu W, Liu XS, Jin W, Su Z. Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. Molecular Plant. 6: 1463-72. PMID 23355544 DOI: 10.1093/Mp/Sst018 |
0.349 |
|
| 2013 |
Trynka G, Sandor C, Han B, Xu H, Stranger BE, Liu XS, Raychaudhuri S. Chromatin marks identify critical cell types for fine mapping complex trait variants Nature Genetics. 45: 124-130. PMID 23263488 DOI: 10.1038/Ng.2504 |
0.401 |
|
| 2013 |
Verzi MP, Shin H, San Roman AK, Liu XS, Shivdasani RA. Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding. Molecular and Cellular Biology. 33: 281-92. PMID 23129810 DOI: 10.1128/Mcb.01185-12 |
0.315 |
|
| 2013 |
He HH, Meyer CA, Long H, Liu XS, Brown M. A closer look into DNase I hypersensitivity Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-P25 |
0.316 |
|
| 2013 |
Xu K, Wu ZJ, Groner AC, He HH, Cai C, Stack EC, Loda M, Liu T, Morrissey C, Vessella RL, Kantoff PW, Balk SP, Liu XS, Brown M. Polycomb-independent activity of EZH2 in castration resistant prostate cancer Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-O14 |
0.394 |
|
| 2012 |
Xu K, Wu ZJ, Groner AC, He HH, Cai C, Lis RT, Wu X, Stack EC, Loda M, Liu T, Xu H, Cato L, Thornton JE, Gregory RI, Morrissey C, ... ... Liu XS, et al. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science (New York, N.Y.). 338: 1465-9. PMID 23239736 DOI: 10.1126/Science.1227604 |
0.539 |
|
| 2012 |
Feng J, Liu T, Qin B, Zhang Y, Liu XS. Identifying ChIP-seq enrichment using MACS. Nature Protocols. 7: 1728-40. PMID 22936215 DOI: 10.1038/Nprot.2012.101 |
0.385 |
|
| 2012 |
Chen S, Ma J, Wu F, Xiong LJ, Ma H, Xu W, Lv R, Li X, Villen J, Gygi SP, Liu XS, Shi Y. The histone H3 Lys 27 demethylase JMJD3 regulates gene expression by impacting transcriptional elongation. Genes & Development. 26: 1364-75. PMID 22713873 DOI: 10.1101/Gad.186056.111 |
0.334 |
|
| 2012 |
Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, ... ... Liu XS, et al. Systematic evaluation of factors influencing ChIP-seq fidelity. Nature Methods. 9: 609-14. PMID 22522655 DOI: 10.1038/Nmeth.1985 |
0.53 |
|
| 2012 |
Qin B, Zhou M, Ge Y, Taing L, Liu T, Wang Q, Wang S, Chen J, Shen L, Duan X, Hu S, Li W, Long H, Zhang Y, Liu XS. CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinformatics (Oxford, England). 28: 1411-2. PMID 22495751 DOI: 10.1093/Bioinformatics/Bts157 |
0.421 |
|
| 2012 |
Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XS. Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Research. 40: 6414-23. PMID 22495509 DOI: 10.1093/Nar/Gks304 |
0.42 |
|
| 2012 |
Maruyama R, Shipitsin M, Choudhury S, Wu Z, Protopopov A, Yao J, Lo PK, Bessarabova M, Ishkin A, Nikolsky Y, Liu XS, Sukumar S, Polyak K. Altered antisense-to-sense transcript ratios in breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 109: 2820-4. PMID 21098291 DOI: 10.1073/Pnas.1010559107 |
0.338 |
|
| 2012 |
Cai C, He H, Chen S, Liu XS, Brown M, Balk SP. Abstract B12: LSD1 mediates global AR transcription suppression in prostate cancer cells Cancer Research. 72: B12-B12. DOI: 10.1158/1538-7445.Prca2012-B12 |
0.334 |
|
| 2011 |
Tang Q, Chen Y, Meyer C, Geistlinger T, Lupien M, Wang Q, Liu T, Zhang Y, Brown M, Liu XS. A comprehensive view of nuclear receptor cancer cistromes. Cancer Research. 71: 6940-7. PMID 21940749 DOI: 10.1158/0008-5472.Can-11-2091 |
0.562 |
|
| 2011 |
Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, ... ... Liu XS, et al. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biology. 12: R83. PMID 21859476 DOI: 10.1186/Gb-2011-12-8-R83 |
0.533 |
|
| 2011 |
Ni M, Chen Y, Lim E, Wimberly H, Bailey ST, Imai Y, Rimm DL, Liu XS, Brown M. Targeting androgen receptor in estrogen receptor-negative breast cancer. Cancer Cell. 20: 119-31. PMID 21741601 DOI: 10.1016/J.Ccr.2011.05.026 |
0.438 |
|
| 2011 |
Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y, Mahapatra S, Kapranov P, Tahiliani M, Daley GQ, Liu XS, Ecker JR, Milos PM, et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. 473: 394-7. PMID 21552279 DOI: 10.1038/Nature10102 |
0.307 |
|
| 2011 |
Wang X, Laurie JD, Liu T, Wentz J, Liu XS. Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites. Genomics. 97: 235-43. PMID 21295131 DOI: 10.1016/J.Ygeno.2011.01.006 |
0.324 |
|
| 2011 |
Chen Y, Meyer CA, Liu T, Li W, Liu JS, Liu XS. MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biology. 12: R11. PMID 21284836 DOI: 10.1186/Gb-2011-12-2-R11 |
0.51 |
|
| 2010 |
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, ... ... Liu XS, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (New York, N.Y.). 330: 1775-87. PMID 21177976 DOI: 10.1126/Science.1196914 |
0.417 |
|
| 2010 |
Verzi MP, Shin H, He HH, Sulahian R, Meyer CA, Montgomery RK, Fleet JC, Brown M, Liu XS, Shivdasani RA. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Developmental Cell. 19: 713-26. PMID 21074721 DOI: 10.1016/J.Devcel.2010.10.006 |
0.316 |
|
| 2010 |
Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Maruyama R, Bessarabova M, Nikolskaya T, Sukumar S, Schwartzman A, Liu JS, Polyak K, Liu XS. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Research. 20: 1730-9. PMID 21045080 DOI: 10.1101/Gr.108217.110 |
0.324 |
|
| 2010 |
He HH, Meyer CA, Shin H, Bailey ST, Wei G, Wang Q, Zhang Y, Xu K, Ni M, Lupien M, Mieczkowski P, Lieb JD, Zhao K, Brown M, Liu XS. Nucleosome dynamics define transcriptional enhancers. Nature Genetics. 42: 343-7. PMID 20208536 DOI: 10.1038/Ng.545 |
0.575 |
|
| 2009 |
Shin H, Liu T, Manrai AK, Liu XS. CEAS: cis-regulatory element annotation system. Bioinformatics (Oxford, England). 25: 2605-6. PMID 19689956 DOI: 10.1093/Bioinformatics/Btp479 |
0.397 |
|
| 2009 |
Wang Q, Li W, Zhang Y, Yuan X, Xu K, Yu J, Chen Z, Beroukhim R, Wang H, Lupien M, Wu T, Regan MM, Meyer CA, Carroll JS, Manrai AK, ... ... Liu XS, et al. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell. 138: 245-56. PMID 19632176 DOI: 10.1016/J.Cell.2009.04.056 |
0.348 |
|
| 2009 |
Xia X, Lemieux ME, Li W, Carroll JS, Brown M, Liu XS, Kung AL. Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis. Proceedings of the National Academy of Sciences of the United States of America. 106: 4260-5. PMID 19255431 DOI: 10.1073/Pnas.0810067106 |
0.318 |
|
| 2009 |
Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. Differential chromatin marking of introns and expressed exons by H3K36me3. Nature Genetics. 41: 376-81. PMID 19182803 DOI: 10.1038/Ng.322 |
0.374 |
|
| 2008 |
Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song JS, Fisher DE. Chromatin structure analyses identify miRNA promoters. Genes & Development. 22: 3172-83. PMID 19056895 DOI: 10.1101/Gad.1706508 |
0.367 |
|
| 2008 |
Zhang Y, Shin H, Song JS, Lei Y, Liu XS. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. Bmc Genomics. 9: 537. PMID 19014516 DOI: 10.1186/1471-2164-9-537 |
0.412 |
|
| 2008 |
Holmes KA, Song JS, Liu XS, Brown M, Carroll JS. Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity. Cancer Research. 68: 7380-5. PMID 18794125 DOI: 10.1158/0008-5472.Can-08-0133 |
0.486 |
|
| 2008 |
Agoulnik IU, Bingman WE, Nakka M, Li W, Wang Q, Liu XS, Brown M, Weigel NL. Target gene-specific regulation of androgen receptor activity by p42/p44 mitogen-activated protein kinase. Molecular Endocrinology (Baltimore, Md.). 22: 2420-32. PMID 18787043 DOI: 10.1210/Me.2007-0481 |
0.329 |
|
| 2008 |
Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell. 132: 958-70. PMID 18358809 DOI: 10.1016/J.Cell.2008.01.018 |
0.352 |
|
| 2007 |
Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS. Model-based analysis of two-color arrays (MA2C). Genome Biology. 8: R178. PMID 17727723 DOI: 10.1186/Gb-2007-8-8-R178 |
0.377 |
|
| 2007 |
Wang Q, Li W, Liu XS, Carroll JS, Jänne OA, Keeton EK, Chinnaiyan AM, Pienta KJ, Brown M. A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Molecular Cell. 27: 380-92. PMID 17679089 DOI: 10.1016/J.Molcel.2007.05.041 |
0.351 |
|
| 2007 |
Ozsolak F, Song JS, Liu XS, Fisher DE. High-throughput mapping of the chromatin structure of human promoters. Nature Biotechnology. 25: 244-8. PMID 17220878 DOI: 10.1038/Nbt1279 |
0.502 |
|
| 2006 |
Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, ... ... Liu XS, et al. Genome-wide analysis of estrogen receptor binding sites. Nature Genetics. 38: 1289-97. PMID 17013392 DOI: 10.1038/Ng1901 |
0.537 |
|
| 2006 |
Ji X, Li W, Song J, Wei L, Liu XS. CEAS: cis-regulatory element annotation system. Nucleic Acids Research. 34: W551-4. PMID 16845068 DOI: 10.1093/Nar/Gkl322 |
0.52 |
|
| 2006 |
Nelson EA, Walker SR, Li W, Liu XS, Frank DA. Identification of human STAT5-dependent gene regulatory elements based on interspecies homology. The Journal of Biological Chemistry. 281: 26216-24. PMID 16840779 DOI: 10.1074/Jbc.M605001200 |
0.352 |
|
| 2006 |
Palomero T, Odom DT, O'Neil J, Ferrando AA, Margolin A, Neuberg DS, Winter SS, Larson RS, Li W, Liu XS, Young RA, Look AT. Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia. Blood. 108: 986-92. PMID 16621969 DOI: 10.1182/Blood-2005-08-3482 |
0.323 |
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| 2005 |
Carroll JS, Liu XS, Brodsky AS, Li W, Meyer CA, Szary AJ, Eeckhoute J, Shao W, Hestermann EV, Geistlinger TR, Fox EA, Silver PA, Brown M. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell. 122: 33-43. PMID 16009131 DOI: 10.1016/J.Cell.2005.05.008 |
0.38 |
|
| 2005 |
Li W, Meyer CA, Liu XS. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics (Oxford, England). 21: i274-82. PMID 15961467 DOI: 10.1093/Bioinformatics/Bti1046 |
0.379 |
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| 2004 |
Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS. A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Research. 32: W204-7. PMID 15215381 DOI: 10.1093/Nar/Gkh461 |
0.512 |
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| 2003 |
Conlon EM, Liu XS, Lieb JD, Liu JS. Integrating regulatory motif discovery and genome-wide expression analysis. Proceedings of the National Academy of Sciences of the United States of America. 100: 3339-44. PMID 12626739 DOI: 10.1073/pnas.0630591100 |
0.306 |
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