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Karaayvaz M., Cristea S., Gillespie SM., Patel AP., Mylvaganam R., Luo CC., Specht MC., Bernstein BE., Michor F., Ellisen LW. Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nat Commun. 2018 Sep 4;9(1):3588. (PubMed Link)

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. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nat Med. 2018 Aug 20. (PubMed Link)

Beyaz S., Mana MD., Roper J., Kedrin D., Saadatpour A., Hong SJ., Bauer-Rowe KE., Xifaras ME., Akkad A., Arias E., Pinello L., Katz Y., Shinagare S., Abu-Remaileh M., Mihaylova MM., Lamming DW., Dogum R., Guo G., Bell GW., Selig M., Nielsen GP., Gupta N., Ferrone CR., Deshpande V., Yuan GC., Orkin SH., Sabatini DM., Yilmaz ÖH. Author Correction: High-fat diet enhances stemness and tumorigenicity of intestinal progenitors. Nature. 2018 Aug;560(7717):E26. (PubMed Link)

Kimes PK., Reyes A. Reproducible and replicable comparisons using SummarizedBenchmark. Bioinformatics. 2018 Jul 17. (PubMed Link)

Takeda DY., Spisák S., Seo JH., Bell C., O'Connor E., Korthauer K., Ribli D., Csabai I., Solymosi N., Szállási Z., Stillman DR., Cejas P., Qiu X., Long HW., Tisza V., Nuzzo PV., Rohanizadegan M., Pomerantz MM., Hahn WC., Freedman ML. A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer. Cell. 2018 Jun 9. (PubMed Link)

Madsen T., Braun D., Peng G., Parmigiani G., Trippa L. Efficient computation of the joint probability of multiple inherited risk alleles from pedigree data. Genet Epidemiol. 2018 Jun 25. (PubMed Link)

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. 2018 Jun 1. (PubMed Link)

Tsoucas D., Yuan GC. GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection. Genome Biol. 2018 May 10;19(1):58. (PubMed Link)

Kuijjer ML., Paulson JN., Salzman P., Ding W., Quackenbush J. Cancer subtype identification using somatic mutation data. Br J Cancer. 2018 May 16. (PubMed Link)

Han X, Wang R, Zhou Y, Fei L, Sun H, Lai S, Saadatpour A, Zhou Z, Chen H, Ye F, Huang D, Xu Y, Huang W, Jiang M, Jiang X, Mao J, Chen Y, Lu C, Xie J, Fang Q, Wang Y, Yue R, Li T, Huang H, Orkin SH, Yuan GC, Chen M, Guo G. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell. 2018 May 17;173(5):1307. (PubMed Link)

Padi M., Quackenbush J. Detecting phenotype-driven transitions in regulatory network structure. NPJ Syst Biol Appl. 2018 Apr 19;4:16 (PubMed Link)

Huang J., Li K., Cai W., Liu X., Zhang Y., Orkin SH., Xu J., Yuan GC. Dissecting super-enhancer hierarchy based on chromatin interactions. Nat Commun. 2018 Mar 5;9(1):943. (PubMed Link)

Korthauer K., Chakraborty S., Benjamini Y., Irizarry RA. Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing. Biostatistics. 2018 Feb 22. (PubMed Link)

Han X., Wang R., Zhou Y., Fei L., Sun H., Lai S., Saadatpour A., Zhou Z., Chen H., Ye F., Huang D., Xu Y., Huang W., Jiang M., Jiang X., Mao J., Chen Y., Lu C., Xie J., Fang Q., Wang Y., Yue R., Li T., Huang H., Orkin SH., Yuan GC., Chen M., Guo G. Mapping the Mouse Cell Atlas by Microwell-Seq. Cell. 2018 Feb 22;172(5):1091-1107.e17. (PubMed Link)

Ahmad S., Mu X., Yang F., Greenwald E., Park JW., Jacob E., Zhang CZ., Hur S. Breaching Self-Tolerance to Alu Duplex RNA Underlies MDA5-Mediated Inflammation. Cell. 2018 Feb 8;172(4):797-810.e13. (PubMed Link)

Pan D., Kobayashi A., Jiang P., Ferrari de Andrade L., Tay RE., Luoma A., Tsoucas D., Qiu X., Lim K., Rao P., Long HW., Yuan GC., Doench J., Brown M., Liu S., Wucherpfennig KW. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science. 2018 Jan 4. (PubMed Link)

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. 2018 Jan (Link)

Reyes A., Huber W. Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues. Nucleic Acids Res. 2017 Nov 30. (epub) (PubMed Link)

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 Res. 2017 Nov 1;77(21):e19-e22. (PubMed Link)

Le X., Chakrabarti S., Michor F., Costa D., Meyerson M. Using population dynamics mathematical modeling to optimize an intermittent dosing regimen for Osimertinib in EGFR-mutant NSCLC. 2017 Nov. J Thoracic Onco (PDF)

Hicks SC., Townes FW., Teng M., Irizarry RA. Missing data and technical variability in single-cell RNA-sequencing experiments. Biostatistics. 2017 Nov 6. (epub) (PubMed Link)

Bhosale PG., Pandey M., Cristea S., Shah M., Patil A., Beerenwinkel N., Schäffer AA., Mahimkar MB. Recurring Amplification at 11q22.1-q22.2 Locus Plays an Important Role in Lymph Node Metastasis and Radioresistance in OSCC. Sci Rep. 2017 Nov 22;7(1):16051. (PubMed Link)

Teng M., Irizarry RA. Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. Genome Res. 2017 Oct 12. (epub) (PubMed Link)

Sonawane AR, Platig J., Fagny M., Chen CY., Paulson JN., Lopes-Ramos CM., DeMeo DL., Quackenbush J., Glass K., Kuijjer ML. Understanding Tissue-Specific Gene Regulation. Cell Rep. 2017 Oct 24;21(4):1077-1088. (PubMed Link)

Paulson JN., Chen CY., Lopes-Ramos CM., Kuijjer ML., Platig J., Sonawane AR., Fagny M., Glass K., Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics. 2017 Oct 3;18(1):437. (PubMed Link)

Parker MM., Chase RP., Lamb A., Reyes A., Saferali A., Yun JH., Himes BE., Silverman EK., Hersh CP., Castaldi PJ. RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking. BMC Med Genomics. 2017 Oct 6;10(1):58. (PubMed Link)

Cheng J., Park DE., Berrios C., White EA., Arora R., Yoon R., Branigan T., Xiao T., Westerling T., Federation A., Zeid R., Strober B., Swanson SK., Florens L., Bradner JE., Brown M., Howley PM., Padi M., Washburn MP., DeCaprio JA. Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis. PLoS Pathog. 2017 Oct 13;13(10):e1006668. (epub) (PubMed Link)

Nakayama RT., Pulice JL., Valencia AM., McBride MJ., McKenzie ZM., Gillespie MA., Ku WL., Teng M., Cui K., Williams RT., Cassel SH., Qing H., Widmer CJ., Demetri GD., Irizarry RA., Zhao K., Ranish JA., Kadoch C. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nat Genet. 2017 Sep 25. (epub) (PubMed Link)

Lopes-Ramos CM., Paulson JN., Chen CY., Kuijjer ML., Fagny M., Platig J., Sonawane AR., DeMeo DL., Quackenbush J., Glass K. Regulatory network changes between cell lines and their tissues of origin. BMC Genomics. 2017 Sep 12;18(1):723. (PubMed Link)

Jadhav U., Saxena M., O'Neill NK., Saadatpour A., Yuan GC., Herbert Z., Murata K., Shivdasani RA. Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells. Cell Stem Cell. 2017 Jun 15. pii: S1934-5909(17)30166-2. (epub) (PubMed Link)

Hsu JH., Hubbell-Engler B., Adelmant G., Huang J., Joyce CE., Vazquez F., Weir BA., Montgomery P., Tsherniak A., Giacomelli AO., Perry JA., Trowbridge J., Fujiwara Y., Cowley GS., Xie H., Kim W., Novina CD., Hahn WC., Marto JA., Orkin SH. Prmt1-mediated translation regulation is a crucial vulnerability of cancer. Cancer Res. 2017 Jun 27. (epub) (PubMed Link)

Han X., Yu H., Huang D., Xu Y., Saadatpour A., Li X., Wang L., Yu J., Pinello L., Lai S. Jiang M., Tian X., Zhang F., Cen Y., Fujiwara Y., Zhu W., Zhou B., Zhou T., Ouyang H., Wang J., Yuan GC., Duan S., Orkin SH., Guo G. A molecular roadmap for induced multi-lineage trans-differentiation of fibroblasts by chemical combinations. Cell Res. 2017 Jun;27(6):843. (PubMed Link)

Garrine M., Mandomando I., Vubil D., Nhampossa T., Acacio S., Li S., Paulson JN., Almeida M., Domman D., Thomson NR., Alonso P., Stine OC. Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing. PLoS Negl Trop Dis. 2017 Jun 16;11(6):e0005671. (PubMed Link)

Yuan GC., Cai L., Elowitz M., Enver T., Fan G., Guo G., Irizarry R., Kharchenko P., Kim J., Orkin S., Quackenbush J., Saadatpour A., Schroeder T., Shivdasani R., Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biol. 2017 May 8;18(1):84. (PubMed Link)

Hill KE., Kelly AD., Kuijjer ML., Barry W., Rattani A., Garbutt CC., Kissick H., Janeway K., Perez-Atayde A., Goldsmith J., Gebhardt MC., Arredouani MS., Cote G., Hornicek F., Choy E., Duan Z., Quackenbush J., Haibe-Kains B., Spentzos D. An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets. J Hematol Oncol. 2017 May 15;10(1):107 (PubMed Link)

Gopalan S., Carja O., Fagny M., Patin E., Myrick JW., McEwen LM., Mah SM., Kobor MS., Froment A., Feldman MW., Quintana-Murci L., Henn BM. Trends in DNA Methylation with Age Replicate Across Diverse Human Populations. Genetics. 2017 May 22. pii: genetics.116.195594. (epub) (PubMed Link)

Chiu HS., Martínez MR., Bansal M., Subramanian A., Golub TR., Yang X., Sumazin P., Califano A. High-throughput validation of ceRNA regulatory networks. BMC Genomics. 2017 May 30;18(1):418. (PubMed Link)

Min L., Zhang C., Qu L., Huang J., Jiang L., Liu J., Pinello L., Yuan GC., Shou C. Gene regulatory pattern analysis reveals essential role of core transcriptional factors' activation in triple-negative breast cancer. Oncotarget. 2017 Mar 28;8(13):21938-21953. (PubMed Link)

Adeegbe D., Liu Y., Lizotte PH., Kamihara Y., Aref AR., Almonte C., Dries R., Li Y., Liu S., Wang X., Warner-Hatten T., Castrillon J., Yuan GC., Poudel-Neupane N., Zhang H., Guerriero JL., Han S., Awad MM., Barbie DA., Ritz J., Jones SS., Hammerman PS., Bradner JE., Quayle SN., Wong KK. Synergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non-small Cell Lung Cancer. Cancer Discov. 2017 Apr 13. pii: CD-16-1020. (PubMed Link)

McDonald TO, Michor F. SIApopr: A computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution. Bioinformatics. 2017 Mar 16. (PubMed Link)

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. Nat Genet. 2017 Mar 30;49(4):482-483. (PubMed Link)

Cellamare M, Ventz S, Baudin E, Mitnick CD, Trippa L. A Bayesian response-adaptive trial in tuberculosis: The endTB trial. Clin Trials. 2017 Feb;14(1):17-28. (PubMed Link)

Chakrabarti S, Hinczewski M, Thirumalai D. Phenomenological and microscopic theories for catch bonds. J Struct Biol. 2017 Jan;197(1):50-56. (PubMed Link)

Love MI, Hogenesch JB, Irizarry RA. Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nat Biotechnol. 2016 Dec;34(12):1287-1291. (PubMed Link)

van IJzendoorn DG, Glass K, Quackenbush J, Kuijjer ML. PyPanda: a Python package for gene regulatory network reconstruction. Bioinformatics. 2016 Nov 1;32(21):3363-3365. Epub 2016 Jul 10. (PubMed Link)

Platig J, Castaldi PJ, DeMeo D, Quackenbush J. Bipartite Community Structure of eQTLs. PLoS Comput Biol. 2016 Sep 12;12(9):e1005033. (PubMed Link)

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 Aug 22;17(1):174. (PubMed Link)

Yip WK, Bonetti M, Cole BF, Barcella W, Wang XV, Lazar A, Gelber RD. Subpopulation Treatment Effect Pattern Plot (STEPP) analysis for continuous, binary, and count outcomes. Clin Trials. 2016 Aug;13(4):382-90. (PubMed Link)

Altrock PM, Brendel C, Renella R, Orkin SH, Williams DA, Michor F. Mathematical modeling of erythrocyte chimerism informs genetic intervention strategies for sickle cell disease. Am J Hematol. 2016 Sep;91(9):931-7. (PubMed Link)

Giecold G, Marco E, Garcia SP, Trippa L, Yuan GC. Robust lineage reconstruction from high-dimensional single-cell data. Nucleic Acids Res. 2016 Aug 19;44(14):e122. (PubMed Link)

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 Jul;48(7):725-32. (PubMed Link)

Pinello L, Canver MC, Hoban MD, Orkin SH, Kohn DB, Bauer DE, Yuan GC. Analyzing CRISPR genome-editing experiments with CRISPResso. Nat Biotechnol. 2016 Jul 12;34(7):695-7. (Free PMC Article)

Subramanian A, Schwartz R. Erratum to: 'Reference-free inference of tumor phylogenies from single-cell sequencing data'. BMC Genomics. 2016 May 10;17(1):348. (PubMed Link)

Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 Apr 23;17:74. (PubMed Link)

Köster J. Rust-Bio: a fast and safe bioinformatics library. Bioinformatics. 2016 Feb 1;32(3):444-6. (PubMed Link)

Huang J, Liu X, Li D, Shao Z, Cao H, Zhang Y, Trompouki E, Bowman TV, Zon LI, Yuan GC, Orkin SH, Xu J. Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. Dev Cell. 2016 Jan 11;36(1):9-23. (PubMed Link)

Li W, Koster 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. (PubMed Link)

Altrock PM, Liu LL, Michor F. The mathematics of cancer: integrating quantitative models. Nat Rev Cancer. 2015 Dec;15(12):730-45. (PubMed Link)

Love MI, Anders S, Kim V, Huber W. RNA-Seq workflow: gene-level exploratory analysis and differential expression. F1000Res. 2015 Oct 14;4:1070. (Free PMC Article)

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. (PubMed Link)

Saadatpour A, Lai S, Guo G, Yuan GC. Single-Cell Analysis in Cancer Genomics. Trends Genet. 2015 Oct;31(10):576-86. (PubMed Link)

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. (PubMed Link)

Binder AM, LaRocca J, Lesseur C, Marsit CJ, Michels KB. Epigenome-wide and transcriptome-wide analyses reveal gestational diabetes is associated with alterations in the human leukocyte antigen complex. Clin Epigenetics. 2015 Aug 5;7:79. (PubMed Link)

Huang J, Marco E, Pinello L, Yuan GC. Predicting chromatin organization using histone marks. Genome Biol. 2015 Aug 14;16:162. (PubMed Link)

Hicks SC, Irizarry RA. quantro: a data-driven approach to guide the choice of an appropriate normalization method. Genome Biol. 2015 Jun 4;16:117. (Free Article)

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. (PubMed Link)

Jiang P, Liu XS. Big data mining yields novel insights on cancer. Nat Genet. 2015 Feb;47(2):103-4. (PubMed Link)

Saadatpour A, Guo G, Orkin SH, Yuan GC. Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biol. 2014 Dec 3;15(12):525. (Free Article)

Marco E, Karp RL, Guo G, Robson P, Hart AH, Trippa L, Yuan GC. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):E5643-50. (PubMed Link)

Rashid NU, Sperling AS, Bolli N, Wedge DC, Van Loo P, Tai YT, Shammas MA, Fulciniti M, Samur MK, Richardson PG, Magrangeas F, Minvielle S, Futreal PA, Anderson KC, Avet-Loiseau H, Campbell PJ, Parmigiani G, Munshi NC. Differential and limited expression of mutant alleles in multiple myeloma. Blood. 2014 Nov 13;124(20):3110-7. (PubMed Link)

Glass K, Quackenbush J, Silverman EK, Celli B, Rennard SI, Yuan GC, DeMeo DL. Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst Biol. 2014 Nov 28;8:118. (PubMed Link)

Maruvka YE, Tang M, Michor F. On the validity of using increases in 5-year survival rates to measure success in the fight against cancer. PLoS One. 2014 Jul 23;9(7):e83100. (PubMed Link)

Podlaha O, De S, Gonen M, Michor F. Histone modifications are associated with transcript isoform diversity in normal and cancer cells. PLoS Comput Biol. 2014 Jun 5;10(6):e1003611. (Free PMC Article)

Glass K, Girvan M. Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. Sci Rep. 2014 Feb 26;4:4191. (PubMed Link)

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. (PubMed Link)

Platig J, Ott E, Girvan M. Robustness of network measures to link errors. Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Dec;88(6):062812. (Free PDF)

Maruvka YE, Shnerb NM. First principles theories for last name dynamics. Phys Life Rev. 2013 Dec; 10(4):422-3; discussion 426-7. (PubMed Link)

Binder AM, Michels KB. The causal effect of red blood cell folate on genome-wide methylation in cord blood: a Mendelian randomization approach. BMC Bioinformatics. 2013 Dec 4;14:353. (PubMed Link)

Maruvka YE, Shnerb NM, Kessler DA, Ricklefs RE. Model for macroevolutionary dynamics. Proc Natl Acad Sci U S A. 2013 Jul 2;110(27):E2460-9. (PubMed Link)

Glass K, Ott E, Losert W, Girvan M. Implications of functional similarity for gene regulatory interactions. J R Soc Interface. 2012 Jul 7;9(72):1625-36. (PubMed Link)

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, Lieb JD, Liu XS. Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods. 2012 Jun;9(6):609-14. (Free PMC Article)

Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS One. 2013 May 31;8(5):e64832. (PubMed Link)

Podlaha O, Riester M, De S, Michor F. Evolution of the cancer genome. Trends Genet. 2012 Apr;28(4):155-63. (Free PMC Article)

Maruvka YE, Kessler DA, Shnerb NM. The birth-death-mutation process: a new paradigm for fat tailed distributions. PLoS One. 2011;6(11):e26480. (PubMed Link)

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. (PubMed Link)

Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu X. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 2014. Dec (epub). (PubMed Link)

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014. Dec (epub). (PubMed Link)

Marco E, Karp RL, Guo G, Robson P, Hart AH, Trippa L, Yuan GC. Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc Natl Acad Sci U S A. 2014. Dec 30;111(52):E5643-50. (Free PMC article)

Saadatpour A, Guo G, Orkin SH, Yuan GC. Characterizing heterogeneity in leukemic cells using single-cell gene expression analysis. Genome Biol. 2014. Dec 3; 15(12):525. (Free PMC article)

Braun D, Gorfine M, Parmigiani G. Misreported Family Histories and Underestimation of Risk. J Clin Oncol. 2014 Sep 8 (epub). (PubMed Link)

Rashid NU, Sperling AS, Bolli N, Wedge DC, Van Loo P, Tai YT, Shammas MA, Fulciniti M, Samur MK, Richardson PG, Magrangeas F, Minvielle S, Futreal PA, Anderson KC, Avet-Loisseau H, Campbell PJ, Parmigiani G, Munshi NC. Differential and limited expression of mutant alleles in multiple myeloma. 2014 Sep (epub). (PubMed Link)

Samur MK. RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data. PLoS One. 2014 Sep 2; 9(9). (PubMed Link)

Ventz S, Trippa L. Bayesian designs and the control of frequentist characteristics: A practical solution.  Biometrics. 2014 Sep 5(epub). (PubMed Link)

Maruvka YE, Tang M, Michor F. On the Validity of Using Increases in 5-Year Survival Rates to Measure Success in the Fight against Cancer. PLoS One. 2014 Jul 23;9(7):e83100. (PubMed Link)

Podlaha O, De S, Gonen M, Michor F. Histone Modifications Are Associated with Transcript Isoform Diversity in Normal and Cancer Cells. PLoS Comput Biol. 2014 Jun 5;10(6):e1003611. (PubMed Link)

Glass K, Girvan M. Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets. Sci Rep. 2014 Feb 26;4:4191. (PubMed Link)

Maruvka YE, Shnerb NM. First principles theories for last name dynamics. Phys Life Rev. 2013 Dec; 10(4):422-3; discussion 426-7.

Pinello L, Lo Bosco G, GC Yuan. Applications of alignment-free methods in epigenomics. Briefings in Bioinformatics 2013; Nov 6 (epub)

Marco E, Dorn JF, Hsu PH, Jaqaman K, Sorger PK, Danuser G. S. cerevisiae Chromosomes Biorient via Gradual Resolution of Syntely between S Phase and Anaphase. Cell. 2013 Aug 29;154(5):1127-39 (PubMed Link)

Glass K, Huttenhower C, Quackenbush J, Yuan GC. Passing messages between biological networks to refine predicted interactions. PLoS One 2013; 8(5):e64832. PMCID: PMC3669401 (PubMed Link)

Chakraborty, S, Datta S. svapls: an R package to correct for hidden factors of variability in gene expression studies. BMC Bioinformatics 2013; 14(1):236. PMCID: PMC3733742

Maruvka YE, Shnerb NM, Kessler DA, Ricklefs RE. Model for macroevolutionary dynamics. Proc Natl Acad Sci USA 2013 Jul 2; 110(27):E2460-9. PMCID: PMC3703965 (PubMed Link)

Kuijjer ML, Peterse EF, van den Akker BE, Briaire-de Bruijn IH, Serra M, Meza-Zepeda LA, Myklebost O, Hassan AB, Hogendoorn PC, Cleton-Jansen AM. R/IGF1R signaling as potential target for treatment of high-grade osteosarcoma.  BMC Cancer 2013 May 20; 13:245. PMCID: PMC3672007 (PubMed Link)

Liu L, De S, Michor F (2013) DNA replication timing and higher-order nuclear organization determine single nucleotide substitution patterns in cancer genomes. Nature Communications 4, 1052. (PDF)

De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, Cerchietti L, Gascoyne RD, Melnick A+, Michor F+ (2013) Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genetics 9, e1003137. (PDF)

Tomasetti C, Vogelstein B, Parmigiani G. Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation, Proc Natl Acad Sci USA, published ahead of print January 23, 2013, doi:10.1073/pnas.1221068110.

Waldron L, Simpson PT, Parmigiani G, Huttenhower C. Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. BMC Cancer 2012; 12(1):124.

Waldron L, Ogino S, Hoshida Y, Shima K, McCart Reed AE, Simpson PT, Baba Y, Nosho K, Segata N, Vargas AC, Cummings MC, Lakhani SR, Kirkner GJ, Giovannucci E, Quackenbush J, Golub TR, Fuchs CS, Parmigiani G, Huttenhower C. Expression profiling of archival tumors for long-term health studies. Clin Cancer Res 2012; Nov 7 epub.

Tomasetti C. Stochastic modeling of multiple random genetic mutations under the cancer stem cell hypothesis, Mathematical Population Studies 2012, 19(4):200-213.

Tomasetti C. On the probability of random genetic mutations for various types of tumor growth, Bulletin of Mathematical Biology 2012, 74(6):1379-1395.

De S, Michor F (2012) Analyzing the association of SCNA boundaries with replication timing. Nature Biotechnology 30, 1045-46. (PDF)

Foo J, Chmielecki J, Pao W, Michor F (2012) Effects of pharmacokinetic processes and varied dosing schedules on the dynamics of acquired resistance to erlotinib in EGFR-mutant lung cancer. Journal of Thoracic Oncology 7, 1583-93. (PDF)

Tang M, Foo J, Gonen M, Guilhot J, Mahon F-X, Michor F (2012) Selection pressure exerted by imatinib therapy leads to disparate outcomes of imatinib discontinuation trials. Haematologica 97, 1553-61.(PDF)

Podlaha O, Riester M, De S, Michor F (2012) Evolution of the cancer genome. Trends in Genetics 28, 155-163. (PDF)

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, Lieb JD, Liu XS. Systematic evaluation of factors influenicng ChIP-seq fidelity. Nat Methods 2012; 9(6):609-614. epub April 22. [Abstract] [Full Paper]

He HH, Meyer CA, Chen MW, Jordan VC, Brown M, Liu XS. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Research 2012; 22(6):1015-25. epub April 16. [Abstract] [Full Paper]

Larson JL, Yuan GC. Chromatin states accurately classify cell differentiation status. PLoS ONE. 2012. 7(2): e31414. doi:10.1371/journal.pone.0031414 [paper]

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. PMCID:PMC3188793.
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Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I, Cheung MS, Ercan S, Ikegami K, Jensen M, Kolasinska-Zwierz P, Rosenbaum H, Shin H, Taing S, Takasaki T, Iniguez AL, Desai A, Dernburg AF, Kimura H, Lieb JD, Ahringer J, Strome S, Liu XS. Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res 2011; 21(2):227-36.
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Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin HG, 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; 12(8):R83. [Abstract] [Full Paper]

Pinello L, Lo Bosco G, Hanlon B, Yuan GC. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics. 2011 Oct 21;12:408. [paper] [Software].

Tang M, Gonen M, Quintas-Cardama A, Cortes J, Kantarjian H, Field C, Hughes TP, Branford S, Michor F (2011) Dynamics of chronic myeloid leukemia response to long-term targeted therapy reveal treatment effects on leukemic stem cells. Blood 118, 1622-1631. (PDF)

De S, Michor F (2011) DNA secondary structures and epigenetic determinants of cancer genome evolution. Nature Structural and Molecular Biology 18, 950-955. (PDF)

Cheng Y-K, Beroukhim R, Levine RL, Mellinghoff IK, Michor F (2011) Reply to Parsons: Many tumor types follow the monoclonal model of tumor initiation. Proc Natl Acad Sci U S A 108, E16. (PDF)

Tomasetti C. A new hypothesis: imatinib affects leukemic stem cells in the same way it affects all other leukemic cells, Blood Cancer J 2011, 1:e19; doi:10.1038/bcj.2011.17.

Tomasetti C, Levy D. Role of symmetric and asymmetric division of stem cells in developing drug resistance, Proc Natl Acad Sci USA 2010, 107(39):16766-16771.

Tomasetti C, Levy D. An elementary approach to modeling drug resistance in cancer, Math Biosci Eng 2010, 7(4):905-918.

Foo J, Leder K, Michor F (2010) Stochastic dynamics of cancer initiation. Physical Biology 8, 015002. (PDF)

Leder K, Holland EC, Michor F (2010) The therapeutic implications of plasticity of the cancer stem cell phenotype. PLoS ONE 5, e14366. (PDF)

He HH, Meyer C, 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 defines transcriptional enhancers. Nat Genet 2010; 42:343-7.PMCID:PMC2932437 [Abstract] [Full Paper]

Wu ZJ, Meyer CA, Choudhury S, Shipitsin M, Bessarabova M, Nikolsky Y, Sukumar S, Schwartzman A, Liu JS, Polyak K, Liu XS. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res 2010; 20(12):1730-9. PMCID:PMC2989999
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Liu Y, Shao Z, Yuan GC. Prediction of Polycomb target plasticity in mouse embryonic stem cells. Genomics. 2010 Jul;96(1):17-26. (cover article) [paper]

Shin H, Liu T, Manrai AK, Liu XS. CEAS: Cis-regulatory element annotation system. Bioinformatics 2009;25(19):2605-6.
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Wang X, Elling A, 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. Plant Cell. 2009;21(4):1053-69. PMCID:PMC2685623.
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Zhang Y, Moqtaderi Z, Rattner B, Zhenhai Zhang Z, Euskirchen G, Snyder M, Kadonaga JT, Pugh BF, Liu XS, Struhl K. Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo: evidence against a nucleosome code. Nat Struct Mol Biol. 2009;16(8):847-52. PMCID:PMC2823114.
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