Research Interests:

• Protein protein interactions
• Motif annotation (TOMTOM).
• Motif analysis pipeline (MPIPE).
• Gene structure: Prediction and analysis (SpliceNest).
• Expression patterns of genes/isoforms (T-STAG).
• Biochemical pathways.

Short Vita:

• June, 2007 - Present: Research Scientist in Bioinformatics at the Biotechnology High Performance Software Applications Institute.
• Feb, 2006 - June, 2007: Postdoc Research in Bioinformatics at the Department of genome sciences, University of Washington.
• May, 2005 - Jan, 2006: Postdoc Research in Bioinformatics at the Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics.
• 2002 - May, 2005: PhD Thesis Research in Bioinformatics at the Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics and Dept. of Mathematics and Computer Science, FU-Berlin. Thesis (pdf).
• 2001 - 2002: Master in Biochemical Engineering and Biotechnology at the Indian Institute of Technology, Delhi
• 1997 - 2001: Bachelors in Biochemical Engineering and Biotechnology at the Indian Institute of Technology, Delhi
• July, 1978: Born in Ghaziabad, Northern India.

Degrees:

• 2005 Mathematics / Bioinformatics: Phd
  Freie University, Berlin, Germany
  Thesis: EST-based detection and analysis of mammalian transcripts.
  Supervisor: Prof. Dr. Martin Vingron & Dr. Stefan Haas, MPI for molecular genetics, Berlin.
• 2002 Biochemical Engineering and Biotechnology: Masters
  Indian Institute of Technology, Delhi, India
  Thesis: Bayesian Gene Structure Prediction Algorithms
  Supervisor: Prof. J. K. Deb, IIT Delhi. & Ms Sudeshna, IBM India Research Lab, Delhi.
• 2001 Biochemical Engineering and Biotechnology: Bachelors
  Indian Institute of Technology, Delhi, India
  Thesis: Metabolic Control Analysic of Biochemical Pathways for Target Identification in Drug Development
  Supervisor: Dr Santanu Datta, Astra Zeneca Labs, Bangalore.

Papers:

• S.Gupta, J. Dennis, R. E. Thurman, R. Kingston, J. Stamatoyannopoulos, and W. S. Noble (2008).
  Predicting human nucleosome occupancy from primary sequence.
  PloS Computational Biology, in press.
• S.Gupta, J. Stamatoyannopoulos, T. Bailey and W. S. Noble (2007).
  Quantifying similarity between motifs.
  Genome Biology, 8:R24.
• S.Gupta, M. Vingron and S.A. Haas (2004).
  T-STAG: Resource and web-interface for Tissue-Specific Transcripts And Genes.
  Nucleic Acids Research, 33, W654-W658.
• S.Gupta, D. Zink, B. Korn, M. Vingron and S.A. Haas (2004).
  Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing.
  BMC Genomics, 5:72.
• S.Gupta, D. Zink, B. Korn, M. Vingron and S.A. Haas (2004).
  Genome wide identification and classification of Alternative Splicing based on EST data.
  Bioinformatics, 20(16): 2579-2585.

Conference contributions:

• S.Gupta, D. Zink, B. Korn, M. Vingron and S.A. Haas (2004).
  Evaluation of the tissue related sensitivity of Expressed Sequence Tag (EST) data using RT-PCR experiments.
  Paper in Proceedings of Bioinformatics Research and Education Workshop (BREW).
• Genome wide prediction of tissue and tumor specific alternative splicing based on EST data.
  European Conference for Computational Biology (Poster Abstracts, ECCB 2003 & GCB 2003).
• Automated Identification and Classification of alternative splice isoforms derived from EST data assembly.
  Research in Computational Molecular Biology (Poster Abstracts, RECOMB 2003).
• Predicting "Good" drug targets based on Metabolic Control Analysis.
  European Conference for Computational Biology (Poster Abstracts, ECCB 2002).

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