Bioinformatics Selected Publications

  • Waight JD, Netherby C, Hensen ML, Miller A, Hu Q, Liu S, Bogner PN, Farren MR, Lee KP, Liu K, Abrams SI. Myeloid-derived suppressor cell development is regulated by a STAT/IRF-8 axis. J Clin Invest. 2013; 123(10):4464-4478. PMCID: PMC3784535
  • Yao S, Sucheston LE, Zhao H, Barlow WE, Zirpoli G, Liu S, Moore HC, Thomas Budd G, Hershman DL, Davis W, Ciupak GL, Stewart JA, Isaacs C, Hobday TJ, Salim M, Hortobagyi GN, Gralow JR, Livingston RB, Albain KS, Hayes DF, Ambrosone CB. Germline genetic variants in ABCB1, ABCC1 and ALDH1A1, and risk of hematological and gastrointestinal toxicities in a SWOG Phase III trial S0221 for breast cancer. Pharmacogenomics J. 2013; PMID: 23999597
  • Ochs-Balcom HM, Preus L, Wactawski-Wende J…Liu S, Sucheston LE…et al. Association of DXA-derived Bone Mineral Density and Fat Mass with African Ancestry. J Clin Endocrinol Metab. 2013; 98(4):E713-7. PMCID: PMC3615193
  • Shen H, Morrison CD, Zhang J, Underwood W 3rd, Yang N, Frangou C, Eng K, Head K, Bollag RJ, Kavuri SK, Rojiani AM, Li Y, Yan L, Hill A, Woloszynska-Read A, Wang J, Liu S, Trump DL, Candace JS. 6p22.3 amplification as a biomarker and potential therapeutic target of advanced stage bladder cancer. Oncotarget. 2013 Nov;4(11):2124-34. PMID: 24231253
  • Garcia H, Miecznikowski JC, Safina A, Commane M, Ruusulehto A, Kilpinen S, Leach RW, Attwood K, Li Y, Degan S, Omilian AR, Guryanova O, Papantonopoulou O, Wang J, Buck M, Liu S, Morrison C, Gurova KV. Facilitates chromatin transcription complex is an "accelerator" of tumor transformation and potential marker and target of aggressive cancers. Cell Rep. 2013; 4(1):159-73. PMID: 23831030
  • Liu B, Morrison CD, Johnson CS, Trump DL, Qin M, Conroy JC, Wang J, Liu S. Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges. Oncotarget. 2013; 4(11):1868-81. PMID: 24240121
  • Yao S, Graham K, Shen J, Campbell LE, Singh P, Zirpoli G, Roberts M, Ciupak G, Davis W, Hwang H, Khoury T, Bovbjerg DH, Jandorf L, Pawlish KS, Bandera EV, Liu S, Ambrosone CB, Zhao H. Genetic variants in microRNAs and breast cancer risk in African American and European American women. Breast Cancer Res Treat. 2013; 141(3):447-59. PMCID: PMC3856568
  • Mhawech-Fauceglia P, Wang D, Ali L, Lele S, Huba MA, Liu S, Odunsi K. Intraepithelial T cells and tumor-associated macrophages in ovarian cancer patients. Cancer Immun 2013, 13:1. PMCID: PMC3559189
  • Wawrzyniak JA, Bianchi-Smiraglia A, Bshara W, Mannava S, Ackroyd J, Bagati A, Omilian AR, Im M, Fedtsova N, Miecznikowski JC, Moparthy KC, Zucker SN, Zhu Q, Kozlova NI, Berman AE, Hoek KS, Gudkov AV, Shewach DS, Morrison CD, Nikiforov MA. A purine nucleotide biosynthesis enzyme guanosine monophosphate reductase is a suppressor of melanoma invasion. Cell Rep. 2013; 5(2):493-507. PMID: 24139804
  • Luo W, Hu Q, Wang D, Deeb KK, Ma Y, Morrison CD, Liu S, Johnson CS, Trump DL. Isolation and genome-wide expression and methylation characterization of CD31+ cells from normal and malignant human prostate tissue. Oncotarget. 2013; 4(9):1472-83. PMCID: PMC3824530
  • Bruno AE, Miecznikowski JC, Qin M, Wang J, Liu S. FUSIM: a software tool for simulating fusion transcripts. BMC Bioinformatics 2013; 14(1):13. PMCID: PMC3637076
  • Chakrabarti R, Hwang J, Andres Blanco M… Liu S…et al. Elf5 Inhibits the Epithelial-Mesenchymal Transition in Mammary Gland Development and Breast Cancer Metastasis by Transcriptionally Repressing Snail2. Nature Cell Biology 2012; 14(11):1212-1222. PMCID: PMC3500637
  • Gervasi M, Bianchi-Smiraglia A, Cummings M, Zheng Q, Wang D, Liu S, Bakin A. JunB Contributes to Id2 Repression and the Epithelial-Mesenchymal Transition in Response to Transforming Growth Factor-beta. Journal Cell Biology 2012; 196(5):589-603. PMCID: PMC3307698
  • Yan L, Ma C, Wang D, Hu Q, Qin M, Conroy J, Sucheston L, Ambrosone C, Johnson C, Wang J, Liu S. OSAT: a tool for sample-to-batch allocations in genomics experiments. BMC Genomics 2012; 13:689. PMCID: PMC3548766
  • Han J, Mistriotis P, Lei P, Wang D, Liu S, Andreadis ST. Nanog Reverses the Effects of Organismal Aging on Mesenchymal Stem Cell Proliferation and Myogenic Differentiation Potential. Stem Cells 2012; 30(12):2746-2759. PMCID: PMC3508087
  • Zhu Q, et al. Prioritizing genetic variants for causality on the basis of preferential linkage disequilibrium. American Journal of Human Genetics 2012; 91:422-34. PMCID: PMC3511993
  • Mannava S, Zhuang D, Nair J… Liu S, Lee K, Nikiforov M…et al. KLF9 is a Novel Transcriptional Regulator of Bortezomib- and LBH589-induced Apoptosis in Multiple Myeloma Cells. Blood 2012; 119(6):1450-1458. PMCID: PMC3286209
  • Mhawech-Fauceglia P, Wang D, Samrao D, Godoy H, Pejovic T, Liu S, Lele S. Pair-Box (PAX8) Protein-Positive Expression is Associated with Poor Disease Outcome in Women with Endometrial Cancer. British Journal of Cancer 2012; 107(2):370-374. PMCID: PMC3394976
  • McCann SE, Liu S, Wang D, Shen J, Hu Q, Hong CC, Newman VA, Zhao H. Reduction of Dietary Glycaemic Load Modifies the Expression of microRNA Potentially Associated with Energy Balance and Cancer Pathways in Pre-Menopausal Women. British Journal of Nutrition. 2012; 30:1-8. PMID: 22647265
  • Zhao H, Shen J, Wang D, Gregory S, Medico L, Hu Q, Yan L, Odunsi K, Lele SB, Liu S. Associations Between Gene Expression Variations and Ovarian Cancer Risk Alleles Identified from Genome Wide Association Studies. PLoS ONE, 2012; 7(11):e47962. PMCID: PMC3487879
  • Wang D, Yan L, Hu Q, Sucheston L, Higgins M, Ambrosone C, Johnson C, Smiraglia D, Liu S. IMA: An R package for high-throughput analysis of Illumina’s 450K Infinium methylation data. Bioinformatics 2012; 28:729-30. PMCID: PMC3289916
  • Koman IE, Commane M, Paszkiewicz G… Liu S, Morrison C, Gudkov A, Gurova K…et al. Targeting FACT Complex Suppresses Mammary Tumorigenesis in Her2/neu Transgenic Mice. Cancer Prev Res 2012; 5(8):1025-1035. PMID: 22689915
  • Shen J, Wang D, Gregory S, Medico L, Hu Q, Yan L, Odunsi A, Lele S, Ambrosone C, Liu S, Zhao H. Evaluation of microRNA Expression Profiles and their Associations with Risk Alleles in Lymphoblastoid Cell Lines of Familial Ovarian Cancer. Carcinogenesis 2012; 33(3):604-612. PMCID: PMC3291866
  • Heemers HV, Schmidt LJ, Sun Z, Regan KM, Anderson SK, Duncan K, Wang D, Liu S, Ballman KV, Tindall DJ. Identification of a Clinically Relevant Androgen-Dependent Gene Signature in Prostate Cancer. Cancer Research 2011; 71(5):1978-1988. PMCID: PMC3077061
  • Liu S, Lin L, Jiang P, Wang D, Xing Y. A Comparison of RNA-Seq and High-Density Exon Array for Detecting Differential Gene Expression between Closely Related Species. Nucleic Acids Research 2011; 39:578-588. PMCID: PMC3025565
  • Mhawech-Fauceglia P, Wang D, Kesterson J, Beck A, Bentley K, Shroff S, Syriac S, Frederick P, Liu S, Odunsi K. Aldolase mRNA Expression in Endometrial Cancer and the Role of Clotrimazole in Endometrial Cancer Cell Viability and Morphology. Histopathology 2011; 59(5):1015-1018. PMID: 21939454.
  • Sucheston L, Zhao H, Yao S… Liu S, Ambrosone CB…et al. Genetic Predictors of Taxane-induced Neurotoxicity in a SWOG Phase III Adjuvant Breast Cancer Treatment Trial. Breast Cancer Research and Treatment 2011; 130(3):993-1002. PMCID: PMC3532924
  • Miecznikowski JC, Wang D, Liu S, Sucheston L, Gold D. Comparative Survival Analysis of Breast Cancer Microarray Studies Identifies Important Prognostic Genetic Pathways. BMC Cancer 2010; 10:573. PMCID: PMC2972286
  • Nagarajan P, Chin SS, Wang D, Liu S, Sinha S, Garrett-Sinha LA. Ets1 blocks terminal differentiation of keratinocytes and induces expression of matrix metalloproteases and innate immune mediators. Journal of Cell Science 2010; 123:3566-3575. PMCID: PMC2959112
  • Mhawech-Fauceglia P, Wang D, Kesterson J, Clark K, Monhollen L, Odunsi K, Lele S, Liu S. Microarray Analysis Reveals Distinct Gene Expression Profiles Among Different Tumor Histology, Stage and Disease Outcomes in Endometrial Adenocarcinoma. PLoS ONE 2010; 5(11):e15415. PMCID: PMC2975707
  • Romano RA, Smalley K, Liu S, Sinha S. Abnormal Hair Follicle Development and Altered cell fate of Follicular Keratinocytes in Transgenic Mice Expressing DNp63a. Development 2010; 137:1431-1439. PMCID: PMC2972286
  • Zhao H, Shen J, Medico L, Wang D, Ambrosone CB, Liu S. A Pilot Study of Circulating miRNAs as Potential Biomarkers of Early Stage Breast Cancer. PLoS ONE 2010; 5(10):e13735. PMCID: PMC2966402
  • Khoury T, Kanehira K, Wang D, Ademuyiwa F, Mojica W, Cheney R, Morrison C, Conroy J, Nowak N, Liu S. Breast Carcinoma with Amplified HER2: A Gene Expression Signature Specific for Trastuzumab Resistance and Poor Prognosis. Modern Pathology 2010; 23:1364-1378. PMID: 20657551