July 5th, 2007 by emin

Current and former group members are indicated in bold.

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Technical reports:


  • C. Zuo, K. Chen, K. Hewitt, E. H. Bresnick, S. Keles (2016). A Hierarchical framework for state space matrix inference and clustering. To appear in the Annals of Applied Statistics.
  • Q. Zhang, X. Zeng, S. Younkin, T. Kawli, M. P. Snyder, S. Keles (2016) Systematic evaluation of impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection. To appear in BMC Bioinformatics.
  • C. Zuo, K. Chen, and S. Keles (2016). A MAD-Bayes algorithm for state-space inference and clustering with application to querying large collections of ChIP-seq datasets.  RECOMB 2016.
  • S. Li, L. A. Papale, Q. Zhang, A. Madrid, L. Chen, P. Chopra, S. Keles, P.Jin, R. Alisch (2015). Genome-wide alterations of hippocampal 5-hydroxmethylcytosine  links plasticity genes to acute stress. To appear in  Neurobiology of Disease.


  • A. Wang, R. Welch, B. Zhai, T. Ta, S. Keles, E. Johannsen (2015). EBNA3 proteins regulate EBNA2 binding distinct to RBPJ genomic sites. To appear, Journal of Virology.
  • N. A. Beauchene, K. S. Myers, D. Chung, D. M. Park, A. M. Weisnicht, S. Keles, P. J. Kiley (2015).  The impact of anaerobiosis on expression of the iron-responsive Fur and RhyB regulons. To appear in mBio.
  • L. A. Papale*,  Q. Zhang*,  S. Li, K. ChenS. Keles,  and R. S. Alisch (2015). Genome-wide disruption of  5-hydroxmethylcytosine in a mouse model of autism. To appear in Human Molecular Genetics. *: Joint first authors.
  • X. Zeng, B. Li, R. Welch, C. Rojo-Alfaro, Y. Zheng, C. Dewey, S. Keles (2015).  Perm-seq: Mapping protein-DNA interactions in segmental duplication and highly repetitive regions of genomes with prior-enhanced read mapping. To appear in PLoS Computational Biology. [Software: permseq]
  •  A. J. Marty, A. T. Broman, R. Zarnowski, T. Dwyer, L. M. Bond, A. Lounes-Hadj Sahraoui, J. Fontaine, J. M. Ntambi, S. Keles, C. Kendziorski, G. M. Gauthier (2015). Fungal morphology, iron homeostasis, and lipid metabolism regulated by a GATA transcription factor in Blastomyces dermatitidis. To appear in PLoS Pathogens.
  • C. Zuo, S. Shin, and S. Keles (2015). atSNP: transcription factor binding affinity testing for regulatory SNP detection. To appear in Bioinformatics. [Software: atSNP]
  • K. J. Hewitt, D. H. Kim, P. Devadas, P. Sanalkumar, C. Zuo, R. Sanalkumar, K. D. Johnson, Y-A. Kang, J. Kim, C. N. Dewey, S. Keles.,  and E. H. Bresnick (2015). Hematopoietic Signaling Mechanism Revealed From a Stem/Progenitor Cell Cistrome. To appear in Molecular Cell.  
  • C. Lopez-Anido,  G. Sun, M. Koenning, R. Srinivasan, H. A. Hung, B. Emory, S. Keles, J. Svaren  (2015). Differential Sox10 Genomic Occupancy in Myelinating Glia. To appear in GLIA.
  • L. Xiong, P. Kuan, J. Tian,  S. Keles, S. Wang  (2015). Multivariate boosting  for integrative analysis of high dimensional cancer genomic data.  To appear in Cancer Informatics.
  • H. A. Hung, G. Sun, S. Keles, J. Svaren (2015). Dynamic regulations of Schwann cell enhancers after peripheral nerve injury. To appear in the Journal of Biological Chemistry.  


  • C. Yao, B. H. Chen, R. Joehanes, B. Otlu, X. Zhang, C. Liu, T. Huan, O. Tastan, A. Cupples, J. B. Meigs, C. S. Fox, J. E. Freedman, P. Courchesne, C. J. O’Donnell, P. J. Munson, S. Keles, D. Levy (2014).  Integromic analysis of genetic variation and gene expression identifies networks for cardiovascular disease phenotypes. To appear in Circulation.
  • R. S. Alisch, P. Chopra, A. S. Fox, K. Chen, A. T. J. White, P.H. Roseboom, S. Keles, N. H. Kalin (2014). Differentially methylated plasticity genes in the amygdala of young primates are linked to anxious temperament, an at risk phenotype for anxiety and depressive disorders. Journal of Neuroscience 34(47): 15548-15556. 
  • G. Sun, R. Srinivasan, C. Lopez-Anido, H. A. Hung, J. Svaren, and S. Keles (2014). In silico pooling designs for ChIP-seq control experiments. To appear in PLoS One.
  • Q. Zhang and S. Keles (2014). CNV-guided multi-read allocation for ChIP-seq. To appear in Bioinformatics.

  • K. Hewitt, R. Sanalkumar, K. D. Johnson, S. Keles, and E. H. Bresnick (2014). Epigenetic and genetic mechanisms in red cell biology. To appear in Current Opinion in Hematology.
  • A. W. Devilbiss, R. Sanalkumar, K. D. Johnson, S. Keles, and E. H. Bresnick (2014). Hematopoietic transcriptional mechanisms: From locus0specific to genome-wide vantage posints. To appear in Experimental Hematology.


  • M. Bellesi, M. Pfister-Genskow, S. Maret, S. Keles, G. Tononi, and Chiara Cirelli (2013). Effects of sleep and wake on oligodendrocytes and their precursors. To appear in the Journal of Neuroscience.
  • K. Myers, H. Yan, I. Ong, D. Chung, K. Liang, F. Tran, S. Keles, R. Landick, T. Kiley (2013).  Genome-scale analysis of E. coli FNR reveals complex features of transcription factor binding. To appear in PLoS Genetics.
  • C. Zuo and S. Keles (2013).  A statistical framework for power calculations in ChIP-seq experiments. [cssp R package] To appear in Bioinformatics.


  • K. Johnson, A. Hsu, M-J. Ryu, J. Wang, X. Gao, M. Boyer, Y. Liu, Y. Lee, K. Calvo, S. Keles, J. Zhang, S. M. Holland, E. Bresnick (2012). Cis-element mutation in GATA-2-dependent immunodeficiency governs hematopoiesis and vascular integrity. To appear in the Journal of Clinical Investigation.
  • R. Srinivasan, G. Sun, S. Keles, E. A. Jones, S-W. Jang, C. Krueger,  J. J. Moran and J. Svaren (2012). Genome-wide analysis of EGR2/SOX10 binding in myelinating peripheral nerve. Nucleic Acids Research.
  • D. J. Huebert and P-F. Kuan and S. Keles and A. Gasch (2012). Dynamic changes in nucleosome occupancy and genomic expression in Saccharomyces cerevisiae responding to oxidative stress. Molecular and Cellular Biology 32(9): 1645-1653.
  • X. Yang, D. Qiao, K. Meyer, T. Pier, S. Keles and A. Friedl (2012). Angiogenesis induced signal transducer and activator of transcription 5A(STAT5A) is dependent on autocrine activity of proliferin. Journal of Biological Chemistry, 287(9): 6490-502.
  • C. Qiu, A. Kershner, Y. Wang, C. P. Holley, D. Wilinski, S. Keles, J. Kimble, M. Wickens, T. M. Hall (2012). Divergence of Pumilio/fem-3 mRNA binding factor (PUF) protein speci city through variations in an RNA-binding pocket. Journal of Biological Chemistry, 287(9): 6949-57.
  • E. Powell,  E. Shanle, A. Brinkman, J. Li and S. Keles, K. B. Wisinski, W. Huang and W. Xu (2012). Identi cation of Estrogen Receptor alpha/beta heterodimer selective ligands reveals growth-inhibitory effects on human mammary and prostate epithelial cells. PLoS One, 7(2):e30993.
  • E. A. Jones, M. H. Brewer, R. Srinivasan, C. Krueger,  G. Sun,  K. N. Charney, S. Keles, A. Antonellis and J. Svaren (2012). Distal enhancers upstream of the Charcot-Marie-Tooth type 1A disease gene PMP22. Human Molecular Genetics, 21(7): 1581-91.
  • Y. A. Kang, R. Sanalkumar, H. O’Geen,  A. Linnemann, C. J. Chang, E. Bouhassira,P. Farnham, S. Keles and E. Bresnick (2012). Autophagy Driven by a Master Regulator of Hematopoiesis. Molecular and Cellular Biology, 32(1):226-39.
  • K. Liang and S. Keles (2012). Detecting differential binding of transcription factors with ChIP-seq. Bioinformatics, 28(1): 121-2. [R package from Bioconductor: DBChIP]


  • A. Linnemann, H. O’Geen, S. Keles, P. J. Farnham, and E. H. Bresnick (2011) Genetic framework for GATA factor function in vascular biology. PNAS, 108(33): 13641-13646.  


  • E. H. Bresnick, H-Y. Lee,  T. Fujiwara, K. D. Johnson and S. Keles (2010). GATA switches as developmental drivers. Journal of Biological Chemistry, 285(41):31087-31093.
  • S. W. Jang*, R. Srinivasan*, E. A. Jones, G. Sun , S. Keles, C. Krueger, L. W. Chang, R. Nagarajan, and J. Svaren (2010) Locus-wide identification of EGR2/Krox20 regulatory targets in myelin genes. Journal of Neurochemistry,  115(6):1409-1420. *: Joint first authors.
  • J. R. Tietjen, D. W. Zhang, and J. B. Rodriguez-Molina, B. E. White, M. Sohail Akhtar, M. Heidemann, X. Li, R. D. Chapman, K. Shokat, S. Keles, D. Eick , A. Z. Ansari (2010). Chemical-genomic dissection of  the CTD code. Nature Structural and Molecular Biology, 17: 1154-1161.
  • K. H. Eng*, D. Kvitek*, S. Keles, A. P. Gasch (2010). Transient genotype-environment interactions following environmental shock provide a source of expression variation for essenial genes. Genetics, 184(2):587-93. Highlighted paper. *: Joint first authors.
  • Y. A. Bochkov, K. M. Hanson, S. Keles, R. A. Brockman-Schnedier, N. N. Jarjour,  J. E. Gern (2010). Rhinovirus-induced modulation of gene expression in bronchial epithelial cells from subjects with asthma.  Mucosal Immunology, Jan;3(1):69-80.


  • T. Fujiwara*, H. O’Green*, S. Keles*, K. Blahnik, A. K. Linneman, Y-A. Kang, K. Choi, P. J. Farnham, and E. Bresnick (2009). Discovering hematopoietic mechanisms through genomewide analysis of GATA factor chromatin occupancy. *: Joint first authors. Molecular Cell, 25;36(4):667-81.





  • H. Cinar, S. Keles, and Y. Jin (2005). Expression profiling of GABAergic motor neurons in Caenorhabditis elegans. Current Biology, 15 (4): 340 -346. (Journal website)




  • S. Keles, M.R. Segal (2002). Residual-based tree-structured survival analysis. Statistics in Medicine, 21: 313-326. (Journal website)

Tech reports and sufficiently different prior versions of published papers:




  • R01 (2R01 HG003747) grant from NIH/NHGRI.
  • R21 (R21 HG006716) grant from NIH/NHGRI.
  • U01 (U01 HG007019) grant from NIH/NHGRI.


  • Research starter award from the PhRMA Foundation.

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