Ph.D dissertation

• Deepayan Sarkar. On the Analysis of Optical Mapping Data. University of Wisconsin-Madison, 2006.

Publications

• Emily C. Knouf, Kavita Garg, Jason D. Arroyo, Yesenia Correa, Deepayan Sarkar, Rachael K. Parkin, Kaitlyn Wurz, Kathy C. O’Briant, Andrew K. Godwin, Nicole D. Urban, Walter L. Ruzzo, Robert Gentleman, Charles W. Drescher, Elizabeth M. Swisher and Muneesh Tewari. An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription.
  Nucleic Acids Research, 2011.
• Brian Teague, Michael S. Waterman, Steven Goldstein, Konstantinos Potamousis, Shiguo Zhou, Susan Reslewic, Deepayan Sarkar, Anton Valouev, Christopher Churas, Jeffrey M. Kidd, Scott Kohn, Rodney Runnheim, Casey Lamers, Dan Forrest, Michael A. Newton, Evan E. Eichler, Marijo Kent-First, Urvashi Surti, Miron Livny, and David C. Schwartz. High-resolution human genome structure by single-molecule analysis.
  Proceedings of the National Academy of Sciences, 107(24):10848-10853, 2010
• Yi Cao, Zizhen Yao, Deepayan Sarkar, Michael Lawrence, Gilson J. Sanchez, Maura H. Parker, Kyle L. MacQuarrie, Jerry Davison, Martin T. Morgan, Walter L. Ruzzo, Robert C. Gentleman, Stephen J. Tapscott. Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming.
  Developmental Cell, 18(4):662-674, 2010
• Kyongryun Lee, Florian Hahne, Deepayan Sarkar, Robert Gentleman. iFlow: A Graphical User Interface for Flow Cytometry Tools in Bioconductor.
  Advances in Bioinformatics, Volume 2009, Article ID 103839, 2009.
• F. Hahne, N. Le Meur, R. R. Brinkman, B. Ellis, P. Haaland, D. Sarkar, J. Spidlen, E. Strain, R. Gentleman. flowCore: a Bioconductor package for high throughput flow cytometry.
  BMC Bioinformatics 10(1):106, 2009.
• D. Sarkar, R. Parkin, S. Wyman, A. Bendoraite, C. Sather, J. Delrow, A. Godwin, C. Drescher, W. Huber, R. Gentleman, M. Tewari. Quality assessment and data analysis for microRNA expression arrays.
  Nucleic Acids Research, 37(2):e17, 2008. [Supplementary material]
• Deepayan Sarkar. Lattice: Multivariate Data Visualization with R.
  Springer, New York, 2008. URL: http://lmdvr.r-forge.r-project.org. ISBN 978-0-387-75968-5
• D. Sarkar, N. Le Meur, R. Gentleman. Using flowViz to visualize flow cytometry data.
  Bioinformatics 24(6):878-9, 2008
• Deepayan Sarkar. Extending lattice: using generics and methods to implement new visualization methods within the Trellis framework.
  Computational Statistics, 2008. doi:10.1007/s00180-007-0098-0.
• V. J. Carey, J. Gentry, D. Sarkar, R. Gentleman, and S. Ramaswamy. SGDI: system for genomic data integration.
  In Proceedings of the Pacific Symposium on Biocomputing 2008 141-152, 2008
• T. Chiang, D. Scholtens, D. Sarkar, R. Gentleman, W. Huber. Coverage and error models of protein-protein interaction data by directed graph analysis.
  Genome Biology, 8 (9):R186, 2007
• M. A. Newton, A. Noueiry, D. Sarkar, P. Ahlquist. Detecting differential gene expression with a semiparametric hierarchical mixture method.
  Biostatistics, 5 (2):155-176, 2004
• M. G. Edwards, D. Sarkar, R. Klopp, J. D. Morrow, R. Weindruch, T.A. Prolla. Age-related impairment of the transcriptional responses to oxidative stress in the mouse heart.
  Physiological Genomics 13 (2):119-127, 2003
• Deepayan Sarkar. Some Notes on lattice.
  In Proceedings of the 3rd International Workshop on Distributed Statistical Computing, 2003
• Deepayan Sarkar. Lattice.
  R News 2/2:19-23, 2002