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Xiaole Shirley Liu - Publications

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41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.578
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  0.559
2020 Hu XS, Zhang J, Liu J, Li B, Liu XS. Abstract B92: Landscape of B-cell immunity and related immune evasion in human cancers Cancer Immunology Research. 8. DOI: 10.1158/2326-6074.Tumimm18-B92  0.369
2019 Köster J, Brown M, Liu XS. A Bayesian model for single cell transcript expression analysis on MERFISH data. Bioinformatics (Oxford, England). 35: 995-1001. PMID 30875429 DOI: 10.1093/Bioinformatics/Bty718  0.596
2019 Jiang P, Gu S, Pan D, Fu J, Sahu A, Hu X, Li Z, Traugh N, Bu X, Li B, Liu J, Freeman GJ, Brown MA, Wucherpfennig KW, Liu XS. Abstract B077: Signatures of T-cell dysfunction and exclusion predict cancer immunotherapy response Cancer Immunology Research. 7. DOI: 10.1158/2326-6074.Cricimteatiaacr18-B077  0.379
2019 Gu SS, Hu XS, Wang XS, Li Z, Traugh N, Bu X, Xing X, Freeman G, Brown M, Liu XS. Abstract A077: Microenvironmental factors shape resistance patterns to immune checkpoint blockade Cancer Immunology Research. 7. DOI: 10.1158/2326-6074.Cricimteatiaacr18-A077  0.646
2019 Gu S, Hu X, Wang X, Jiang P, Li Z, Traugh N, Bu X, Xing X, Freeman GJ, Brown M, Liu XS. Abstract 3779: Clonal tracing reveals different mechanisms of resistance to immune checkpoint blockade Cancer Research. 79: 3779-3779. DOI: 10.1158/1538-7445.Am2019-3779  0.601
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  0.616
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  0.347
2018 Chen CH, Xiao T, Xu H, Jiang P, Meyer CA, Li W, Brown M, Liu XS. Improved design and analysis of CRISPR knockout screens. Bioinformatics (Oxford, England). PMID 29868757 DOI: 10.1093/Bioinformatics/Bty450  0.554
2018 Cornwell M, Vangala M, Taing L, Herbert Z, Köster J, Li B, Sun H, Li T, Zhang J, Qiu X, Pun M, Jeselsohn R, Brown M, Liu XS, Long HW. VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. Bmc Bioinformatics. 19: 135. PMID 29649993 DOI: 10.1186/S12859-018-2139-9  0.559
2018 Gu SSG, Li Z, Bu X, Xing X, Freeman G, Brown M, Liu XS. Abstract A12: Identification of resistance to immune checkpoint blockade Cancer Immunology Research. 6. DOI: 10.1158/2326-6074.Tumimm17-A12  0.642
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  0.34
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  0.623
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  0.615
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  0.337
2016 Fei T, Chen Y, Liu XS, Brown M. Abstract A22: Functional long noncoding RNAs in castration-resistant prostate cancer Cancer Research. 76. DOI: 10.1158/1538-7445.Nonrna15-A22  0.658
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. Abstract B24: High-dimensional genomic data integration and bias correction using MANCIE Cancer Research. 76. DOI: 10.1158/1538-7445.Chromepi15-B24  0.646
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  0.336
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  0.382
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  0.381
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  0.668
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  0.696
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  0.346
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  0.627
2014 Fei T, Chen Y, Du Z, Liu XS, Brown M. Abstract 5238: Integrative analysis of functional long noncoding RNAs during prostate cancer progression Cancer Research. 74: 5238-5238. DOI: 10.1158/1538-7445.Am2014-5238  0.66
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  0.614
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  0.613
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  0.66
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  0.612
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  0.376
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  0.384
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  0.669
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  0.609
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  0.371
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  0.644
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. Abstract 3300: MYC regulation of a “poor prognosis” metastatic cancer cell state Cancer Research. 70: 3300-3300. DOI: 10.1158/1538-7445.Am10-3300  0.626
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  0.63
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  0.549
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  0.342
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  0.316
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