| Year |
Citation |
Score |
| 2021 |
Liu Y, Chen Y, Kong D, Liu X, Fu J, Zhang Y, Zhao Y, Chang Z, Zhao X, Xu K, Jiang C, Fan Z. Short-term effects of cold spells on hospitalisations for acute exacerbation of chronic obstructive pulmonary disease: a time-series study in Beijing, China. Bmj Open. 11: e039745. PMID 33408200 DOI: 10.1136/bmjopen-2020-039745 |
0.52 |
|
| 2020 |
Zeng Z, Fu J, Cibulskis C, Jhaveri A, Gumbs C, Das B, Sanchez-Espiridion B, Janssens S, Taing L, Wang J, Lindsay J, Vilimas T, Zhang J, Tokheim C, Das Sahu A, ... ... Liu XS, et al. Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC network. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 33323402 DOI: 10.1158/1078-0432.CCR-20-3251 |
0.64 |
|
| 2020 |
Wan C, Keany MP, Dong H, Al-Alem LF, Pandya UM, Lazo S, Boehnke K, Lynch KN, Xu R, Zarrella DT, Gu S, Cejas P, Lim K, Long HW, Elias KM, ... ... Liu XS, et al. Enhanced efficacy of simultaneous PD-1 and PD-L1 immune checkpoint blockade in high grade serous ovarian cancer. Cancer Research. PMID 33158814 DOI: 10.1158/0008-5472.CAN-20-1674 |
0.36 |
|
| 2020 |
Shi S, Gu S, Han T, Zhang W, Huang L, Li Z, Pan D, Fu J, Ge J, Brown M, Zhang P, Jiang P, Wucherpfennig KW, Liu XS. Inhibition of MAN2A1 enhances tumor response to anti-PD-L1. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 32723834 DOI: 10.1158/1078-0432.CCR-20-0778 |
0.6 |
|
| 2020 |
Sun Y, Liu X, Li B, Sava-Segal C, Wang A, Zhang M. Effects of Repetition Suppression on Sound Induced Flash Illusion With Aging. Frontiers in Psychology. 11: 216. PMID 32153456 DOI: 10.3389/fpsyg.2020.00216 |
0.68 |
|
| 2020 |
Fu J, Li K, Zhang W, Wan C, Zhang J, Jiang P, Liu XS. Large-scale public data reuse to model immunotherapy response and resistance. Genome Medicine. 12: 21. PMID 32102694 DOI: 10.1186/s13073-020-0721-z |
0.64 |
|
| 2020 |
Zhang Y, Liu X, Kong D, Fu J, Liu Y, Zhao Y, Lian H, Zhao X, Yang J, Fan Z. Effects of Ambient Temperature on Acute Exacerbations of Chronic Obstructive Pulmonary Disease: Results from a Time-Series Analysis of 143318 Hospitalizations. International Journal of Chronic Obstructive Pulmonary Disease. 15: 213-223. PMID 32099346 DOI: 10.2147/COPD.S224198 |
0.52 |
|
| 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 |
0.64 |
|
| 2019 |
Zhang J, Hu X, Wang J, Sahu AD, Cohen D, Song L, Ouyang Z, Fan J, Wang B, Fu J, Gu S, Sade-Feldman M, Hacohen N, Li W, Ying X, ... ... Liu XS, et al. Immune receptor repertoires in pediatric and adult acute myeloid leukemia. Genome Medicine. 11: 73. PMID 31771646 DOI: 10.1186/s13073-019-0681-3 |
0.68 |
|
| 2019 |
Liu X, Zhang Y, Zhao G, Zhang J, Ren S, Fang G. HPWO/ZrO and 1-Butyl-3-methylimidazolium Chloride: A Double-Effect Catalyst for the Degradation of Alkali Lignin. Acs Omega. 4: 18487-18494. PMID 31737806 DOI: 10.1021/acsomega.9b01811 |
0.64 |
|
| 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. Publisher Correction: Landscape of B cell immunity and related immune evasion in human cancers. Nature Genetics. PMID 31101897 DOI: 10.1038/s41588-019-0437-4 |
0.68 |
|
| 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 |
0.56 |
|
| 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 |
0.68 |
|
| 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 |
0.64 |
|
| 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 |
0.56 |
|
| 2018 |
Hu X, Zhang J, Liu JS, Li B, Liu XS. Evaluation of immune repertoire inference methods from RNA-seq data. Nature Biotechnology. 36: 1034. PMID 30412202 DOI: 10.1038/nbt.4294 |
0.68 |
|
| 2018 |
Liu X, Kong D, Fu J, Zhang Y, Liu Y, Zhao Y, Lian H, Zhao X, Yang J, Fan Z. Association between extreme temperature and acute myocardial infarction hospital admissions in Beijing, China: 2013-2016. Plos One. 13: e0204706. PMID 30332423 DOI: 10.1371/journal.pone.0204706 |
0.52 |
|
| 2018 |
Liu X, Kong D, Liu Y, Fu J, Gao P, Chen T, Fang Q, Cheng K, Fan Z. Effects of the short-term exposure to ambient air pollution on atrial fibrillation. Pacing and Clinical Electrophysiology : Pace. PMID 30225893 DOI: 10.1111/pace.13500 |
0.32 |
|
| 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 |
|
| 2018 |
Liu X, Kong D, Lian H, Zhao X, Zhao Y, Xu Q, Peng B, Wang H, Fang Q, Zhang S, Jin X, Cheng K, Fan Z. Distribution and predictors of hospital charges for haemorrhagic stroke patients in Beijing, China, March 2012 to February 2015: a retrospective study. Bmj Open. 8: e017693. PMID 29602836 DOI: 10.1136/bmjopen-2017-017693 |
0.4 |
|
| 2018 |
Jiang P, Lee W, Li X, Johnson C, Liu JS, Brown M, Aster JC, Liu XS. Genome-Scale Signatures of Gene Interaction from Compound Screens Predict Clinical Efficacy of Targeted Cancer Therapies. Cell Systems. PMID 29428415 DOI: 10.1016/j.cels.2018.01.009 |
0.64 |
|
| 2018 |
Kong D, Liu X, Lian H, Zhao X, Zhao Y, Xu Q, Peng B, Wang H, Fang Q, Zhang S, Cheng K, Jin X, Fan Z. Analysis of Hospital Charges of Inpatients with Acute Ischemic Stroke in Beijing, China, 2012-2015. Neuroepidemiology. 50: 63-73. PMID 29421788 DOI: 10.1159/000484212 |
0.4 |
|
| 2018 |
Chen D, Fang L, Mei S, Li H, Xu X, Des Marais TL, Lu K, Liu XS, Jin C. Erratum: "Regulation of Chromatin Assembly and Cell Transformation by Formaldehyde Exposure in Human Cells". Environmental Health Perspectives. 126: 019001. PMID 29326091 DOI: 10.1289/EHP3193 |
0.32 |
|
| 2017 |
Li T, Fan J, Wang B, Traugh N, Chen Q, Liu JS, Li B, Liu XS. TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells. Cancer Research. 77: e108-e110. PMID 29092952 DOI: 10.1158/0008-5472.CAN-17-0307 |
0.68 |
|
| 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 |
0.68 |
|
| 2017 |
Choi SH, Severson E, Pear WS, Liu XS, Aster JC, Blacklow SC. The common oncogenomic program of NOTCH1 and NOTCH3 signaling in T-cell acute lymphoblastic leukemia. Plos One. 12: e0185762. PMID 29023469 DOI: 10.1371/journal.pone.0185762 |
0.4 |
|
| 2017 |
Chen D, Fang L, Mei S, Li H, Xu X, Des Marais TL, Lu K, Liu XS, Jin C. Regulation of Chromatin Assembly and Cell Transformation by Formaldehyde Exposure in Human Cells. Environmental Health Perspectives. 125: 097019. PMID 28937961 DOI: 10.1289/EHP1275 |
0.32 |
|
| 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 |
0.6 |
|
| 2017 |
Zhang W, Wu S, Cai L, Liu X, Wu H, Xin F, Zhang M, Jiang M. Improved Treatment and Utilization of Rice Straw by Coprinopsis cinerea. Applied Biochemistry and Biotechnology. PMID 28831773 DOI: 10.1007/s12010-017-2579-0 |
0.68 |
|
| 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 |
0.6 |
|
| 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 |
0.64 |
|
| 2017 |
Li B, Li T, Wang B, Dou R, Zhang J, Liu JS, Liu XS. Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA-seq data. Nature Genetics. 49: 482-483. PMID 28358132 DOI: 10.1038/ng.3820 |
0.68 |
|
| 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 |
0.48 |
|
| 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 |
0.56 |
|
| 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 |
0.36 |
|
| 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 |
0.6 |
|
| 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 |
Li B, Severson E, Pignon JC, Zhao H, Li T, Novak J, Jiang P, Shen H, Aster JC, Rodig S, Signoretti S, Liu JS, Liu XS. Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. Genome Biology. 17: 174. PMID 27549193 DOI: 10.1186/s13059-016-1028-7 |
0.56 |
|
| 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 |
0.56 |
|
| 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 |
0.6 |
|
| 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 |
0.68 |
|
| 2016 |
Cejas P, Li L, O'Neill NK, Duarte M, Rao P, Bowden M, Zhou CW, Mendiola M, Burgos E, Feliu J, Moreno-Rubio J, Guadalajara H, Moreno V, García-Olmo D, Bellmunt J, ... ... Liu XS, et al. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles. Nature Medicine. PMID 27111282 DOI: 10.1038/nm.4085 |
0.56 |
|
| 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 |
0.56 |
|
| 2016 |
Yang S, Xu D, Liu X. Evaluation of Round Window Stimulation Performance in Otosclerosis Using Finite Element Modeling. Computational and Mathematical Methods in Medicine. 2016: 3603207. PMID 27034709 DOI: 10.1155/2016/3603207 |
0.64 |
|
| 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 |
0.56 |
|
| 2016 |
Liu Y, Fei T, Zheng X, Brown M, Zhang P, Liu XS, Wang H. An Integrative Pharmacogenomic Approach Identifies Two-drug Combination Therapies for Personalized Cancer Medicine. Scientific Reports. 6: 22120. PMID 26916442 DOI: 10.1038/srep22120 |
0.56 |
|
| 2016 |
Wang A, Liu X, Chen Q, Zhang M. Effect of different directions of attentional shift on inhibition of return in three-dimensional space. Attention, Perception & Psychophysics. PMID 26758976 DOI: 10.3758/s13414-015-1055-6 |
0.68 |
|
| 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 |
0.56 |
|
| 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 |
0.56 |
|
| 2015 |
Liu X, Lian H, Ruan Y, Liang R, Zhao X, Routledge M, Fan Z. Association of Exposure to Particular Matter and Carotid Intima-Media Thickness: A Systematic Review and Meta-Analysis. International Journal of Environmental Research and Public Health. 12: 12924-40. PMID 26501300 DOI: 10.3390/ijerph121012924 |
0.32 |
|
| 2015 |
Zhang J, Wang C, Chen X, Takada M, Fan C, Zheng X, Wen H, Liu Y, Wang C, Pestell RG, Aird KM, Kaelin WG, Liu XS, Zhang Q. EglN2 associates with the NRF1-PGC1α complex and controls mitochondrial function in breast cancer. The Embo Journal. PMID 26492917 DOI: 10.15252/embj.201591437 |
0.56 |
|
| 2015 |
Zhang N, Wang H, Fang Y, Wang J, Zheng X, Liu XS. Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model. Plos Computational Biology. 11: e1004498. PMID 26418249 DOI: 10.1371/journal.pcbi.1004498 |
0.6 |
|
| 2015 |
Fei Q, Yang X, Jiang H, Wang Q, Yu Y, Yu Y, Yi W, Zhou S, Chen T, Lu C, Atadja P, Liu XS, Li E, Zhang Y, Shou J. SetDB1 modulates PRC2 activity at developmental genes independent of H3K9 trimethylation in mouse ES cells. Genome Research. PMID 26160163 DOI: 10.1101/gr.177576.114 |
0.56 |
|
| 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 |
0.64 |
|
| 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 |
0.56 |
|
| 2015 |
Jiang P, Liu XS. Big data mining yields novel insights on cancer. Nature Genetics. 47: 103-4. PMID 25627899 DOI: 10.1038/ng.3205 |
0.4 |
|
| 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 |
0.4 |
|
| 2014 |
Meng FL, Du Z, Federation A, Hu J, Wang Q, Kieffer-Kwon KR, Meyers RM, Amor C, Wasserman CR, Neuberg D, Casellas R, Nussenzweig MC, Bradner JE, Liu XS, Alt FW. Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability. Cell. 159: 1538-48. PMID 25483776 DOI: 10.1016/j.cell.2014.11.014 |
0.36 |
|
| 2014 |
Cai C, He HH, Gao S, Chen S, Yu Z, Gao Y, Chen S, Chen MW, Zhang J, Ahmed M, Wang Y, Metzger E, Schüle R, Liu XS, Brown M, et al. Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity. Cell Reports. 9: 1618-27. PMID 25482560 DOI: 10.1016/j.celrep.2014.11.008 |
0.64 |
|
| 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 |
0.64 |
|
| 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 |
0.56 |
|
| 2014 |
Meyer CA, Liu XS. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nature Reviews. Genetics. 15: 709-21. PMID 25223782 DOI: 10.1038/nrg3788 |
0.56 |
|
| 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 |
0.48 |
|
| 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 |
0.6 |
|
| 2014 |
Yamamoto S, Wu Z, Russnes HG, Takagi S, Peluffo G, Vaske C, Zhao X, Moen Vollan HK, Maruyama R, Ekram MB, Sun H, Kim JH, Carver K, Zucca M, Feng J, ... ... Liu XS, et al. JARID1B is a luminal lineage-driving oncogene in breast cancer. Cancer Cell. 25: 762-77. PMID 24937458 DOI: 10.1016/j.ccr.2014.04.024 |
0.48 |
|
| 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 |
0.6 |
|
| 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 |
0.56 |
|
| 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 |
0.48 |
|
| 2014 |
Watanabe H, Ma Q, Peng S, Adelmant G, Swain D, Song W, Fox C, Francis JM, Pedamallu CS, DeLuca DS, Brooks AN, Wang S, Que J, Rustgi AK, Wong KK, ... ... Liu XS, et al. SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas. The Journal of Clinical Investigation. 124: 1636-45. PMID 24590290 DOI: 10.1172/JCI71545 |
0.32 |
|
| 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 |
0.56 |
|
| 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 |
0.56 |
|
| 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 |
0.56 |
|
| 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 |
0.6 |
|
| 2014 |
Wang Q, Huang J, Sun H, Liu J, Wang J, Wang Q, Qin Q, Mei S, Zhao C, Yang X, Liu XS, Zhang Y. CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. Nucleic Acids Research. 42: D450-8. PMID 24253304 DOI: 10.1093/nar/gkt1151 |
0.6 |
|
| 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 |
0.52 |
|
| 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 |
0.56 |
|
| 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 |
0.6 |
|
| 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 |
0.6 |
|
| 2013 |
Tam WL, Lu H, Buikhuisen J, Soh BS, Lim E, Reinhardt F, Wu ZJ, Krall JA, Bierie B, Guo W, Chen X, Liu XS, Brown M, Lim B, Weinberg RA. Protein kinase C α is a central signaling node and therapeutic target for breast cancer stem cells. Cancer Cell. 24: 347-64. PMID 24029232 DOI: 10.1016/j.ccr.2013.08.005 |
0.56 |
|
| 2013 |
Choudhury S, Almendro V, Merino VF, Wu Z, Maruyama R, Su Y, Martins FC, Fackler MJ, Bessarabova M, Kowalczyk A, Conway T, Beresford-Smith B, Macintyre G, Cheng YK, Lopez-Bujanda Z, ... ... Liu XS, et al. Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics. Cell Stem Cell. 13: 117-30. PMID 23770079 DOI: 10.1016/j.stem.2013.05.004 |
0.56 |
|
| 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 |
0.56 |
|
| 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 |
0.56 |
|
| 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 |
0.6 |
|
| 2013 |
Zhang X, Peterson KA, Liu XS, McMahon AP, Ohba S. Gene regulatory networks mediating canonical Wnt signal-directed control of pluripotency and differentiation in embryo stem cells. Stem Cells (Dayton, Ohio). 31: 2667-79. PMID 23505158 DOI: 10.1002/stem.1371 |
0.56 |
|
| 2013 |
Cai C, Wang H, He HH, Chen S, He L, Ma F, Mucci L, Wang Q, Fiore C, Sowalsky AG, Loda M, Liu XS, Brown M, Balk SP, Yuan X. ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer. The Journal of Clinical Investigation. 123: 1109-22. PMID 23426182 DOI: 10.1172/JCI66666 |
0.56 |
|
| 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 |
0.48 |
|
| 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 |
0.56 |
|
| 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 |
0.52 |
|
| 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 |
0.56 |
|
| 2012 |
Xu Y, Xu C, Kato A, Tempel W, Abreu JG, Bian C, Hu Y, Hu D, Zhao B, Cerovina T, Diao J, Wu F, He HH, Cui Q, Clark E, ... ... Liu XS, et al. Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development. Cell. 151: 1200-13. PMID 23217707 DOI: 10.1016/j.cell.2012.11.014 |
0.56 |
|
| 2012 |
Bailey ST, Shin H, Westerling T, Liu XS, Brown M. Estrogen receptor prevents p53-dependent apoptosis in breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 109: 18060-5. PMID 23077249 DOI: 10.1073/pnas.1018858109 |
0.52 |
|
| 2012 |
Benson MJ, Aijö T, Chang X, Gagnon J, Pape UJ, Anantharaman V, Aravind L, Pursiheimo JP, Oberdoerffer S, Liu XS, Lahesmaa R, Lähdesmäki H, Rao A. Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells. Proceedings of the National Academy of Sciences of the United States of America. 109: 16252-7. PMID 22991471 DOI: 10.1073/pnas.1214414109 |
0.56 |
|
| 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 |
0.52 |
|
| 2012 |
Meyer CA, Tang Q, Liu XS. Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function. Molecular Endocrinology (Baltimore, Md.). 26: 1651-9. PMID 22930692 DOI: 10.1210/me.2012-1150 |
0.56 |
|
| 2012 |
Feng J, Meyer CA, Wang Q, Liu JS, Shirley Liu X, Zhang Y. GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. Bioinformatics (Oxford, England). 28: 2782-8. PMID 22923299 DOI: 10.1093/bioinformatics/bts515 |
0.32 |
|
| 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 |
0.48 |
|
| 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 |
0.56 |
|
| 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 |
0.6 |
|
| 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 |
0.6 |
|
| 2011 |
Cai C, He HH, Chen S, Coleman I, Wang H, Fang Z, Chen S, Nelson PS, Liu XS, Brown M, Balk SP. Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1. Cancer Cell. 20: 457-71. PMID 22014572 DOI: 10.1016/j.ccr.2011.09.001 |
0.44 |
|
| 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 |
0.56 |
|
| 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 |
0.56 |
|
| 2011 |
Marotta LL, Almendro V, Marusyk A, Shipitsin M, Schemme J, Walker SR, Bloushtain-Qimron N, Kim JJ, Choudhury SA, Maruyama R, Wu Z, Gönen M, Mulvey LA, Bessarabova MO, Huh SJ, ... ... Liu XS, et al. The JAK2/STAT3 signaling pathway is required for growth of CD44âºCD24â» stem cell-like breast cancer cells in human tumors. The Journal of Clinical Investigation. 121: 2723-35. PMID 21633165 DOI: 10.1172/JCI44745 |
0.56 |
|
| 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 |
0.56 |
|
| 2011 |
Meyer CA, He HH, Brown M, Liu XS. BINOCh: binding inference from nucleosome occupancy changes. Bioinformatics (Oxford, England). 27: 1867-8. PMID 21551136 DOI: 10.1093/bioinformatics/btr279 |
0.56 |
|
| 2011 |
Verzi MP, Shin H, Ho LL, Liu XS, Shivdasani RA. Essential and redundant functions of caudal family proteins in activating adult intestinal genes. Molecular and Cellular Biology. 31: 2026-39. PMID 21402776 DOI: 10.1128/MCB.01250-10 |
0.52 |
|
| 2011 |
Feng D, Liu T, Sun Z, Bugge A, Mullican SE, Alenghat T, Liu XS, Lazar MA. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science (New York, N.Y.). 331: 1315-9. PMID 21393543 DOI: 10.1126/science.1198125 |
0.56 |
|
| 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 |
0.56 |
|
| 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 |
0.56 |
|
| 2011 |
Cao Q, Zhou M, Wang X, Meyer CA, Zhang Y, Chen Z, Li C, Liu XS. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Research. 39: D968-74. PMID 20972221 DOI: 10.1093/nar/gkq997 |
0.6 |
|
| 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 |
0.56 |
|
| 2010 |
Ko M, Huang Y, Jankowska AM, Pape UJ, Tahiliani M, Bandukwala HS, An J, Lamperti ED, Koh KP, Ganetzky R, Liu XS, Aravind L, Agarwal S, Maciejewski JP, Rao A. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature. 468: 839-43. PMID 21057493 DOI: 10.1038/nature09586 |
0.56 |
|
| 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 |
0.56 |
|
| 2010 |
Lupien M, Meyer CA, Bailey ST, Eeckhoute J, Cook J, Westerling T, Zhang X, Carroll JS, Rhodes DR, Liu XS, Brown M. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance. Genes & Development. 24: 2219-27. PMID 20889718 DOI: 10.1101/gad.1944810 |
0.56 |
|
| 2010 |
Verzi MP, Hatzis P, Sulahian R, Philips J, Schuijers J, Shin H, Freed E, Lynch JP, Dang DT, Brown M, Clevers H, Liu XS, Shivdasani RA. TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions. Proceedings of the National Academy of Sciences of the United States of America. 107: 15157-62. PMID 20696899 DOI: 10.1073/pnas.1003822107 |
0.56 |
|
| 2010 |
Ahmadiyeh N, Pomerantz MM, Grisanzio C, Herman P, Jia L, Almendro V, He HH, Brown M, Liu XS, Davis M, Caswell JL, Beckwith CA, Hills A, Macconaill L, Coetzee GA, et al. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proceedings of the National Academy of Sciences of the United States of America. 107: 9742-6. PMID 20453196 DOI: 10.1073/pnas.0910668107 |
0.56 |
|
| 2010 |
Vastenhouw NL, Zhang Y, Woods IG, Imam F, Regev A, Liu XS, Rinn J, Schier AF. Chromatin signature of embryonic pluripotency is established during genome activation. Nature. 464: 922-6. PMID 20336069 DOI: 10.1038/nature08866 |
0.56 |
|
| 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 |
0.6 |
|
| 2010 |
Wolfer A, Wittner BS, Irimia D, Flavin RJ, Lupien M, Gunawardane RN, Meyer CA, Lightcap ES, Tamayo P, Mesirov JP, Liu XS, Shioda T, Toner M, Loda M, Brown M, et al. MYC regulation of a "poor-prognosis" metastatic cancer cell state. Proceedings of the National Academy of Sciences of the United States of America. 107: 3698-703. PMID 20133671 DOI: 10.1073/pnas.0914203107 |
0.56 |
|
| 2010 |
Bienvenu F, Jirawatnotai S, Elias JE, Meyer CA, Mizeracka K, Marson A, Frampton GM, Cole MF, Odom DT, Odajima J, Geng Y, Zagozdzon A, Jecrois M, Young RA, Liu XS, et al. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature. 463: 374-8. PMID 20090754 DOI: 10.1038/nature08684 |
0.56 |
|
| 2010 |
Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. Reply to Evidence against a genomic code for nucleosome positioning Nature Structural and Molecular Biology. 17: 920-923. DOI: 10.1038/nsmb0810-920 |
0.56 |
|
| 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 |
0.52 |
|
| 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 |
0.56 |
|
| 2009 |
Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nature Structural & Molecular Biology. 16: 847-52. PMID 19620965 DOI: 10.1038/nsmb.1636 |
0.56 |
|
| 2009 |
Liu XS, Meyer CA. ChIP-Chip: algorithms for calling binding sites. Methods in Molecular Biology (Clifton, N.J.). 556: 165-75. PMID 19488878 DOI: 10.1007/978-1-60327-192-9_12 |
0.56 |
|
| 2009 |
Wang X, Elling AA, Li X, Li N, Peng Z, He G, Sun H, Qi Y, Liu XS, Deng XW. Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. The Plant Cell. 21: 1053-69. PMID 19376930 DOI: 10.1105/tpc.109.065714 |
0.48 |
|
| 2009 |
Lupien M, Eeckhoute J, Meyer CA, Krum SA, Rhodes DR, Liu XS, Brown M. Coactivator function defines the active estrogen receptor alpha cistrome. Molecular and Cellular Biology. 29: 3413-23. PMID 19364822 DOI: 10.1128/MCB.00020-09 |
0.56 |
|
| 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 |
0.56 |
|
| 2009 |
Eeckhoute J, Lupien M, Meyer CA, Verzi MP, Shivdasani RA, Liu XS, Brown M. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Research. 19: 372-80. PMID 19129543 DOI: 10.1101/gr.084582.108 |
0.56 |
|
| 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 |
0.56 |
|
| 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 |
0.52 |
|
| 2008 |
Lefterova MI, Zhang Y, Steger DJ, Schupp M, Schug J, Cristancho A, Feng D, Zhuo D, Stoeckert CJ, Liu XS, Lazar MA. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes & Development. 22: 2941-52. PMID 18981473 DOI: 10.1101/gad.1709008 |
0.56 |
|
| 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 |
0.32 |
|
| 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 |
0.56 |
|
| 2008 |
Li W, Carroll JS, Brown M, Liu xS. xMAN: extreme MApping of OligoNucleotides. Bmc Genomics. 9: S20. PMID 18366610 DOI: 10.1186/1471-2164-9-S1-S20 |
0.4 |
|
| 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 |
0.56 |
|
| 2008 |
Stayrook KR, Rogers PM, Savkur RS, Wang Y, Su C, Varga G, Bu X, Wei T, Nagpal S, Liu XS, Burris TP. Regulation of human 3 alpha-hydroxysteroid dehydrogenase (AKR1C4) expression by the liver X receptor alpha. Molecular Pharmacology. 73: 607-12. PMID 18024509 DOI: 10.1124/mol.107.039099 |
0.32 |
|
| 2008 |
Gottardo R, Li W, Johnson WE, Liu XS. A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments. Biometrics. 64: 468-78. PMID 17888037 DOI: 10.1111/j.1541-0420.2007.00899.x |
0.56 |
|
| 2007 |
O'Neil J, Tchinda J, Gutierrez A, Moreau L, Maser RS, Wong KK, Li W, McKenna K, Liu XS, Feng B, Neuberg D, Silverman L, DeAngelo DJ, Kutok JL, Rothstein R, et al. Alu elements mediate MYB gene tandem duplication in human T-ALL. The Journal of Experimental Medicine. 204: 3059-66. PMID 18070937 DOI: 10.1084/jem.20071637 |
0.56 |
|
| 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 |
0.44 |
|
| 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 |
0.56 |
|
| 2007 |
Litovchick L, Sadasivam S, Florens L, Zhu X, Swanson SK, Velmurugan S, Chen R, Washburn MP, Liu XS, DeCaprio JA. Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. Molecular Cell. 26: 539-51. PMID 17531812 DOI: 10.1016/j.molcel.2007.04.015 |
0.56 |
|
| 2007 |
Song JS, Maghsoudi K, Li W, Fox E, Quackenbush J, Shirley Liu X. Microarray blob-defect removal improves array analysis. Bioinformatics (Oxford, England). 23: 966-71. PMID 17332024 DOI: 10.1093/bioinformatics/btm043 |
0.6 |
|
| 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 |
0.52 |
|
| 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 |
0.56 |
|
| 2006 |
Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip. Proceedings of the National Academy of Sciences of the United States of America. 103: 12457-62. PMID 16895995 DOI: 10.1073/pnas.0601180103 |
0.56 |
|
| 2006 |
Zhang Y, Liu XS, Liu QR, Wei L. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Research. 34: 3465-75. PMID 16849434 DOI: 10.1093/nar/gkl473 |
0.52 |
|
| 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 |
0.56 |
|
| 2006 |
Lieb JD, Beck S, Bulyk ML, Farnham P, Hattori N, Henikoff S, Liu XS, Okumura K, Shiota K, Ushijima T, Greally JM. Applying whole-genome studies of epigenetic regulation to study human disease. Cytogenetic and Genome Research. 114: 1-15. PMID 16717444 DOI: 10.1159/000091922 |
0.56 |
|
| 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 |
0.56 |
|
| 2005 |
Brodsky AS, Meyer CA, Swinburne IA, Hall G, Keenan BJ, Liu XS, Fox EA, Silver PA. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biology. 6: R64. PMID 16086846 DOI: 10.1186/gb-2005-6-8-r64 |
0.32 |
|
| 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 |
0.56 |
|
| 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 |
0.56 |
|
| 2005 |
Hong P, Liu XS, Zhou Q, Lu X, Liu JS, Wong WH. A boosting approach for motif modeling using ChIP-chip data. Bioinformatics (Oxford, England). 21: 2636-43. PMID 15817698 DOI: 10.1093/bioinformatics/bti402 |
0.64 |
|
| 2005 |
Ben-Yehuda S, Fujita M, Liu XS, Gorbatyuk B, Skoko D, Yan J, Marko JF, Liu JS, Eichenberger P, Rudner DZ, Losick R. Defining a centromere-like element in Bacillus subtilis by Identifying the binding sites for the chromosome-anchoring protein RacA. Molecular Cell. 17: 773-82. PMID 15780934 DOI: 10.1016/j.molcel.2005.02.023 |
0.32 |
|
| 2004 |
Yildiz FH, Liu XS, Heydorn A, Schoolnik GK. Molecular analysis of rugosity in a Vibrio cholerae O1 El Tor phase variant. Molecular Microbiology. 53: 497-515. PMID 15228530 DOI: 10.1111/j.1365-2958.2004.04154.x |
0.32 |
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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 |
0.32 |
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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 |
0.32 |
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| Show low-probability matches. |