Harvard Catalyst Profiles

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Xiaole Shirley Liu

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Department
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Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01CA234018 (LIU, XIAOLE SHIRLEY) May 15, 2019 - Apr 30, 2023
    NIH/NCI
    Regulators of Cancer Immunotherapy Response
    Role: Principal Investigator
  2. U24CA237617 (LIU, XIAOLE SHIRLEY) Mar 15, 2019 - Feb 29, 2024
    NIH/NCI
    Developing Informatics Technologies to Model Cancer Gene Regulation
    Role: Principal Investigator
  3. U01CA226196 (LIU, XIAOLE SHIRLEY) Apr 6, 2018 - Mar 31, 2021
    NIH/NCI
    Bioinformatics Technology to Characterize Tumor Infiltrating Immune Repertoires
    Role: Principal Investigator
  4. U24CA224316 (LIU, XIAOLE SHIRLEY) Sep 30, 2017 - Jun 30, 2022
    NIH/NCI
    Cancer Immunologic Data Commons
    Role: Principal Investigator
  5. R01HG008927 (LIU, XIAOLE SHIRLEY) Sep 9, 2016 - Jun 30, 2019
    NIH/NHGRI
    Computational Methods for Genome-Wide CRISPR Screens
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Hu X, Zhang J, Liu JS, Li B, Liu XS. Evaluation of immune repertoire inference methods from RNA-seq data. Nat Biotechnol. 2018 11 09; 36(11):1034. PMID: 30412202.
    Citations:    Fields:    
  2. Carey CD, Gusenleitner D, Lipschitz M, Roemer MGM, Stack EC, Gjini E, Hu X, Redd R, Freeman GJ, Neuberg D, Hodi FS, Liu XS, Shipp MA, Rodig SJ. Topological analysis reveals a PD-L1-associated microenvironmental niche for Reed-Sternberg cells in Hodgkin lymphoma. Blood. 2017 11 30; 130(22):2420-2430. PMID: 28893733.
    Citations: 13     Fields:    Translation:HumansCells
  3. 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, Brown M. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Proc Natl Acad Sci U S A. 2017 06 27; 114(26):E5207-E5215. PMID: 28611215.
    Citations: 10     Fields:    Translation:HumansCells
  4. 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. Proc Natl Acad Sci U S A. 2017 03 28; 114(13):3473-3478. PMID: 28289232.
    Citations: 4     Fields:    Translation:HumansCells
  5. Liu XS, Mardis ER. Applications of Immunogenomics to Cancer. Cell. 2017 02 09; 168(4):600-612. PMID: 28187283.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  6. 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. Proc Natl Acad Sci U S A. 2017 01 31; 114(5):1027-1032. PMID: 28082722.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  7. 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. Nat Biotechnol. 2016 Dec; 34(12):1279-1286. PMID: 27798563.
    Citations: 38     Fields:    Translation:HumansCells
  8. 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 Res. 2017 01 04; 45(D1):D658-D662. PMID: 27789702.
    Citations: 22     Fields:    Translation:HumansAnimals
  9. Qin Q, Mei S, Wu Q, Sun H, Li L, Taing L, Chen S, Li F, Liu T, Zang C, Xu H, Chen Y, Meyer CA, Zhang Y, Brown M, Long HW, Liu XS. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. BMC Bioinformatics. 2016 Oct 03; 17(1):404. PMID: 27716038.
    Citations: 7     Fields:    Translation:Humans
  10. 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 Biol. 2016 08 22; 17(1):174. PMID: 27549193.
    Citations: 45     Fields:    Translation:HumansCells
  11. Wang S, Zang C, Xiao T, Fan J, Mei S, Qin Q, Wu Q, Li X, Xu K, He HH, Brown M, Meyer CA, Liu XS. Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles. Genome Res. 2016 10; 26(10):1417-1429. PMID: 27466232.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  12. Zang C, Luyten A, Chen J, Liu XS, Shivdasani RA. NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes. Sci Rep. 2016 07 26; 6:30255. PMID: 27457419.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  13. 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. 2016 11 01; 32(21):3336-3338. PMID: 27402906.
    Citations: 6     Fields:    Translation:HumansAnimalsCells
  14. 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. Nat Genet. 2016 07; 48(7):725-32. PMID: 27240091.
    Citations: 39     Fields:    Translation:HumansCells
  15. 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, Mullane S, Hirsch M, Sweeney CJ, Richardson A, Liu XS, Brown M, Shivdasani RA, Long HW. Chromatin immunoprecipitation from fixed clinical tissues reveals tumor-specific enhancer profiles. Nat Med. 2016 06; 22(6):685-91. PMID: 27111282.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  16. 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. Nat Commun. 2016 Apr 13; 7:11305. PMID: 27072482.
    Citations: 4     Fields:    Translation:HumansCells
  17. 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. Nat Commun. 2016 Mar 15; 7:10982. PMID: 26975529.
    Citations: 39     Fields:    Translation:HumansCells
  18. 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. Sci Rep. 2016 Feb 26; 6:22120. PMID: 26916442.
    Citations: 1     Fields:    Translation:HumansCells
  19. Shu S, Lin CY, He HH, Witwicki RM, Tabassum DP, Roberts JM, Janiszewska M, Huh SJ, Liang Y, Ryan J, Doherty E, Mohammed H, Guo H, Stover DG, Ekram MB, Brown J, D'Santos C, Krop IE, Dillon D, McKeown M, Ott C, Qi J, Ni M, Rao PK, Duarte M, Wu SY, Chiang CM, Anders L, Young RA, Winer E, Letai A, Barry WT, Carroll JS, Long H, Brown M, Liu XS, Meyer CA, Bradner JE, Polyak K. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. Nature. 2016 Jan 21; 529(7586):413-417. PMID: 26735014.
    Citations: 90     Fields:    Translation:HumansAnimalsCells
  20. Li W, Köster J, Xu H, Chen CH, Xiao T, Liu JS, Brown M, Liu XS. Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biol. 2015 Dec 16; 16:281. PMID: 26673418.
    Citations: 14     Fields:    
  21. 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. Mol Cancer Res. 2016 Feb; 14(2):163-172. PMID: 26659825.
    Citations: 4     Fields:    Translation:HumansCells
  22. 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 Biol. 2015 Oct 30; 16:239. PMID: 26518695.
    Citations: 8     Fields:    Translation:HumansCells
  23. 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-PGC1a complex and controls mitochondrial function in breast cancer. EMBO J. 2015 Dec 02; 34(23):2953-70. PMID: 26492917.
    Citations: 9     Fields:    Translation:HumansCells
  24. 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 independently of H3K9 trimethylation in mouse ES cells. Genome Res. 2015 Sep; 25(9):1325-35. PMID: 26160163.
    Citations: 5     Fields:    Translation:AnimalsCells
  25. 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 Res. 2015 Aug; 25(8):1147-57. PMID: 26063738.
    Citations: 83     Fields:    Translation:HumansCells
  26. Jiang P, Freedman ML, Liu JS, Liu XS. Inference of transcriptional regulation in cancers. Proc Natl Acad Sci U S A. 2015 Jun 23; 112(25):7731-6. PMID: 26056275.
    Citations: 17     Fields:    Translation:HumansCells
  27. Wang H, Zang C, Liu XS, Aster JC. The role of Notch receptors in transcriptional regulation. J Cell Physiol. 2015 May; 230(5):982-8. PMID: 25418913.
    Citations: 13     Fields:    Translation:HumansAnimalsCells
  28. 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, Balk SP. Lysine-specific demethylase 1 has dual functions as a major regulator of androgen receptor transcriptional activity. Cell Rep. 2014 Dec 11; 9(5):1618-1627. PMID: 25482560.
    Citations: 31     Fields:    Translation:HumansCells
  29. 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, Bernstein BE, Blacklow SC, Liu XS, Aster JC, Pear WS. Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proc Natl Acad Sci U S A. 2014 Nov 18; 111(46):E4946-53. PMID: 25369933.
    Citations: 45     Fields:    Translation:HumansAnimalsCells
  30. Meyer CA, Liu XS. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet. 2014 Nov; 15(11):709-21. PMID: 25223782.
    Citations: 62     Fields:    Translation:Cells
  31. 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, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. PMID: 25164756.
    Citations: 86     Fields:    Translation:HumansAnimalsCells
  32. 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 Dev. 2014 Aug 15; 28(16):1827-39. PMID: 25128499.
    Citations: 14     Fields:    Translation:AnimalsCells
  33. 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, Fawell S, Gilliland G, Zhang T, Kremer BE, Knoechel B, Bernstein BE, Pear WS, Liu XS, Aster JC, Sathyanarayanan S. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. Cancer Discov. 2014 Oct; 4(10):1154-67. PMID: 25104330.
    Citations: 33     Fields:    Translation:HumansAnimalsCells
  34. 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, Zhang P, Zhang Y, Liu XS. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol. 2014 Aug 07; 15(8):419. PMID: 25103624.
    Citations: 21     Fields:    Translation:HumansCells
  35. 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, Almendro V, Bessarabova M, Rueda OM, Nikolsky Y, Caldas C, Liu XS, Polyak K. JARID1B is a luminal lineage-driving oncogene in breast cancer. Cancer Cell. 2014 Jun 16; 25(6):762-77. PMID: 24937458.
    Citations: 48     Fields:    Translation:HumansCells
  36. 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. Proc Natl Acad Sci U S A. 2014 May 20; 111(20):7319-24. PMID: 24778216.
    Citations: 64     Fields:    Translation:HumansAnimalsCells
  37. 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, Song M, Tan C, Landis MD, Ferrari M, Shin SJ, Brown M, Chang JC, Liu XS, Glimcher LH. XBP1 promotes triple-negative breast cancer by controlling the HIF1a pathway. Nature. 2014 Apr 03; 508(7494):103-107. PMID: 24670641.
    Citations: 153     Fields:    Translation:HumansAnimalsCells
  38. Wee S, Dhanak D, Li H, Armstrong SA, Copeland RA, Sims R, Baylin SB, Liu XS, Schweizer L. Targeting epigenetic regulators for cancer therapy. Ann N Y Acad Sci. 2014 Feb; 1309:30-6. PMID: 24571255.
    Citations: 18     Fields:    Translation:HumansAnimalsCells
  39. 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 Biol. 2014; 15(12):554. PMID: 25476604.
    Citations: 71     Fields:    Translation:HumansCells
  40. 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. Proc Natl Acad Sci U S A. 2014 Jan 14; 111(2):705-10. PMID: 24374627.
    Citations: 53     Fields:    Translation:HumansCells
  41. 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. 2014 Dec 04; 33(49):5637-48. PMID: 24317510.
    Citations: 10     Fields:    Translation:HumansCells
  42. 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. Nat Methods. 2014 Jan; 11(1):73-78. PMID: 24317252.
    Citations: 62     Fields:    Translation:HumansCells
  43. Zhang Y, Vastenhouw NL, Feng J, Fu K, Wang C, Ge Y, Pauli A, van Hummelen P, Schier AF, Liu XS. Canonical nucleosome organization at promoters forms during genome activation. Genome Res. 2014 Feb; 24(2):260-6. PMID: 24285721.
    Citations: 27     Fields:    Translation:AnimalsCells
  44. 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. Nat Protoc. 2013 Dec; 8(12):2502-15. PMID: 24263090.
    Citations: 60     Fields:    Translation:Cells
  45. 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. 2013 Oct 04; 14:680. PMID: 24093963.
    Citations: 12     Fields:    Translation:HumansCells
  46. 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 a is a central signaling node and therapeutic target for breast cancer stem cells. Cancer Cell. 2013 Sep 09; 24(3):347-64. PMID: 24029232.
    Citations: 94     Fields:    Translation:HumansCells
  47. 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, Kaspi A, Hu R, Robens J, Nikolskaya T, Haakensen VD, Schnitt SJ, Argani P, Ethington G, Panos L, Grant M, Clark J, Herlihy W, Lin SJ, Chew G, Thompson EW, Greene-Colozzi A, Richardson AL, Rosson GD, Pike M, Garber JE, Nikolsky Y, Blum JL, Au A, Hwang ES, Tamimi RM, Michor F, Haviv I, Liu XS, Sukumar S, Polyak K. Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics. Cell Stem Cell. 2013 Jul 03; 13(1):117-30. PMID: 23770079.
    Citations: 30     Fields:    Translation:HumansCells
  48. 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. Nat Struct Mol Biol. 2013 Jul; 20(7):908-13. PMID: 23728290.
    Citations: 164     Fields:    Translation:HumansCells
  49. Ni M, Chen Y, Fei T, Li D, Lim E, Liu XS, Brown M. Amplitude modulation of androgen signaling by c-MYC. Genes Dev. 2013 Apr 01; 27(7):734-48. PMID: 23530127.
    Citations: 30     Fields:    Translation:HumansCells
  50. 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. 2013 May 15; 29(10):1352-4. PMID: 23508969.
    Citations: 7     Fields:    Translation:HumansAnimalsCells
  51. 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. J Clin Invest. 2013 Mar; 123(3):1109-22. PMID: 23426182.
    Citations: 47     Fields:    Translation:HumansAnimalsCells
  52. 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, Vessella RL, Montironi R, Magi-Galluzzi C, Kantoff PW, Balk SP, Liu XS, Brown M. EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science. 2012 Dec 14; 338(6113):1465-9. PMID: 23239736.
    Citations: 224     Fields:    Translation:HumansAnimalsCells
  53. Verzi MP, Shin H, San Roman AK, Liu XS, Shivdasani RA. Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding. Mol Cell Biol. 2013 Jan; 33(2):281-92. PMID: 23129810.
    Citations: 22     Fields:    Translation:AnimalsCells
  54. Bailey ST, Shin H, Westerling T, Liu XS, Brown M. Estrogen receptor prevents p53-dependent apoptosis in breast cancer. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):18060-5. PMID: 23077249.
    Citations: 37     Fields:    Translation:Humans
  55. Feng J, Liu T, Qin B, Zhang Y, Liu XS. Identifying ChIP-seq enrichment using MACS. Nat Protoc. 2012 Sep; 7(9):1728-40. PMID: 22936215.
    Citations: 225     Fields:    
  56. Meyer CA, Tang Q, Liu XS. Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function. Mol Endocrinol. 2012 Oct; 26(10):1651-9. PMID: 22930692.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  57. 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 Dev. 2012 Jun 15; 26(12):1364-75. PMID: 22713873.
    Citations: 53     Fields:    Translation:HumansCells
  58. He HH, Meyer CA, Chen MW, Jordan VC, Brown M, Liu XS. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 2012 Jun; 22(6):1015-25. PMID: 22508765.
    Citations: 80     Fields:    Translation:HumansCells
  59. 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 Res. 2012 Aug; 40(14):6414-23. PMID: 22495509.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  60. 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. 2011 Oct 18; 20(4):457-71. PMID: 22014572.
    Citations: 132     Fields:    Translation:HumansCells
  61. 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 Res. 2011 Nov 15; 71(22):6940-7. PMID: 21940749.
    Citations: 55     Fields:    Translation:HumansAnimalsCells
  62. 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, Turpaz Y, Liu XS. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 2011 Aug 22; 12(8):R83. PMID: 21859476.
    Citations: 228     Fields:    Translation:Humans
  63. 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. 2011 Jul 12; 20(1):119-31. PMID: 21741601.
    Citations: 110     Fields:    Translation:HumansAnimalsCells
  64. 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, Silver SJ, Kim SY, Park SY, Lee HE, Anderson KS, Richardson AL, Nikolskaya T, Nikolsky Y, Liu XS, Root DE, Hahn WC, Frank DA, Polyak K. The JAK2/STAT3 signaling pathway is required for growth of CD44?CD24? stem cell-like breast cancer cells in human tumors. J Clin Invest. 2011 Jul; 121(7):2723-35. PMID: 21633165.
    Citations: 252     Fields:    Translation:HumansAnimalsCells
  65. Meyer CA, He HH, Brown M, Liu XS. BINOCh: binding inference from nucleosome occupancy changes. Bioinformatics. 2011 Jul 01; 27(13):1867-8. PMID: 21551136.
    Citations: 9     Fields:    Translation:HumansCells
  66. Maruyama R, Choudhury S, Kowalczyk A, Bessarabova M, Beresford-Smith B, Conway T, Kaspi A, Wu Z, Nikolskaya T, Merino VF, Lo PK, Liu XS, Nikolsky Y, Sukumar S, Haviv I, Polyak K. Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium. PLoS Genet. 2011 Apr; 7(4):e1001369. PMID: 21533021.
    Citations: 33     Fields:    Translation:HumansCells
  67. Verzi MP, Shin H, Ho LL, Liu XS, Shivdasani RA. Essential and redundant functions of caudal family proteins in activating adult intestinal genes. Mol Cell Biol. 2011 May; 31(10):2026-39. PMID: 21402776.
    Citations: 40     Fields:    Translation:AnimalsCells
  68. 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 Biol. 2011; 12(2):R11. PMID: 21284836.
    Citations: 10     Fields:    Translation:HumansCells
  69. 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. Proc Natl Acad Sci U S A. 2012 Feb 21; 109(8):2820-4. PMID: 21098291.
    Citations: 26     Fields:    Translation:HumansCells
  70. 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. Dev Cell. 2010 Nov 16; 19(5):713-26. PMID: 21074721.
    Citations: 85     Fields:    Translation:HumansAnimalsCells
  71. 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 Res. 2010 Dec; 20(12):1730-9. PMID: 21045080.
    Citations: 22     Fields:    Translation:HumansCells
  72. 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 Res. 2011 Jan; 39(Database issue):D968-74. PMID: 20972221.
    Citations: 12     Fields:    Translation:Humans
  73. 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 Dev. 2010 Oct 01; 24(19):2219-27. PMID: 20889718.
    Citations: 61     Fields:    Translation:HumansCells
  74. 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. Proc Natl Acad Sci U S A. 2010 Aug 24; 107(34):15157-62. PMID: 20696899.
    Citations: 35     Fields:    Translation:HumansCells
  75. 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, Regan MM, Freedman ML. 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci U S A. 2010 May 25; 107(21):9742-6. PMID: 20453196.
    Citations: 140     Fields:    Translation:HumansCells
  76. 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. 2010 Apr 08; 464(7290):922-6. PMID: 20336069.
    Citations: 124     Fields:    Translation:AnimalsCells
  77. 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. Nat Genet. 2010 Apr; 42(4):343-7. PMID: 20208536.
    Citations: 235     Fields:    Translation:HumansCells
  78. 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, Brugge JS, Ramaswamy S. MYC regulation of a "poor-prognosis" metastatic cancer cell state. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3698-703. PMID: 20133671.
    Citations: 72     Fields:    Translation:Humans
  79. 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, Cepko CL, Gygi SP, Sicinski P. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature. 2010 Jan 21; 463(7279):374-8. PMID: 20090754.
    Citations: 101     Fields:    Translation:AnimalsCells
  80. Boros J, Donaldson IJ, O'Donnell A, Odrowaz ZA, Zeef L, Lupien M, Meyer CA, Liu XS, Brown M, Sharrocks AD. Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery. Genome Res. 2009 Nov; 19(11):1963-73. PMID: 19687146.
    Citations: 56     Fields:    Translation:HumansCells
  81. 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, Jänne OA, Balk SP, Mehra R, Han B, Chinnaiyan AM, Rubin MA, True L, Fiorentino M, Fiore C, Loda M, Kantoff PW, Liu XS, Brown M. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell. 2009 Jul 23; 138(2):245-56. PMID: 19632176.
    Citations: 352     Fields:    Translation:HumansCells
  82. Lupien M, Eeckhoute J, Meyer CA, Krum SA, Rhodes DR, Liu XS, Brown M. Coactivator function defines the active estrogen receptor alpha cistrome. Mol Cell Biol. 2009 Jun; 29(12):3413-23. PMID: 19364822.
    Citations: 33     Fields:    Translation:HumansCells
  83. 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. Proc Natl Acad Sci U S A. 2009 Mar 17; 106(11):4260-5. PMID: 19255431.
    Citations: 133     Fields:    Translation:HumansCells
  84. 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 Res. 2009 Mar; 19(3):372-80. PMID: 19129543.
    Citations: 55     Fields:    Translation:HumansCells
  85. Liu XS, Meyer CA. ChIP-Chip: algorithms for calling binding sites. Methods Mol Biol. 2009; 556:165-75. PMID: 19488878.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  86. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137. PMID: 18798982.
    Citations: 2870     Fields:    Translation:HumansCells
  87. Holmes KA, Song JS, Liu XS, Brown M, Carroll JS. Nkx3-1 and LEF-1 function as transcriptional inhibitors of estrogen receptor activity. Cancer Res. 2008 Sep 15; 68(18):7380-5. PMID: 18794125.
    Citations: 14     Fields:    Translation:HumansAnimalsCells
  88. 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. Mol Endocrinol. 2008 Nov; 22(11):2420-32. PMID: 18787043.
    Citations: 15     Fields:    Translation:HumansCells
  89. 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. 2008 Mar 21; 132(6):958-70. PMID: 18358809.
    Citations: 410     Fields:    Translation:HumansCells
  90. Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 2008 Mar; 18(3):393-403. PMID: 18258921.
    Citations: 73     Fields:    Translation:HumansCells
  91. Li W, Carroll JS, Brown M, Liu xS. xMAN: extreme MApping of OligoNucleotides. BMC Genomics. 2008; 9 Suppl 1:S20. PMID: 18366610.
    Citations: 12     Fields:    
  92. Liu XS. Getting started in tiling microarray analysis. PLoS Comput Biol. 2007 Oct; 3(10):1842-4. PMID: 17967045.
    Citations: 18     Fields:    Translation:HumansAnimalsCells
  93. 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. Mol Cell. 2007 Aug 03; 27(3):380-92. PMID: 17679089.
    Citations: 253     Fields:    Translation:HumansCells
  94. 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, Gingeras TR, Liu XS, Brown M. Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006 Nov; 38(11):1289-97. PMID: 17013392.
    Citations: 615     Fields:    Translation:HumansCells
  95. Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 2006 Aug 15; 103(33):12457-62. PMID: 16895995.
    Citations: 246     Fields:    Translation:Humans
  96. Swinburne IA, Meyer CA, Liu XS, Silver PA, Brodsky AS. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Res. 2006 Jul; 16(7):912-21. PMID: 16769980.
    Citations: 22     Fields:    Translation:HumansCells
  97. 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 Biol. 2005; 6(8):R64. PMID: 16086846.
    Citations: 46     Fields:    Translation:HumansCells
  98. 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. 2005 Jul 15; 122(1):33-43. PMID: 16009131.
    Citations: 542     Fields:    Translation:HumansAnimalsCells
  99. 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. 2005 Jun; 21 Suppl 1:i274-82. PMID: 15961467.
    Citations: 41     Fields:    Translation:HumansCells
  100. 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. Mol Cell. 2005 Mar 18; 17(6):773-82. PMID: 15780934.
    Citations: 32     Fields:    Translation:Cells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.