ANSHUL BHARAT KUNDAJE

e-mail:

REFEREED PUBLICATIONS:

• Steve Lianoglou, Anshul Kundaje, Christina Leslie, Inferring active signaling pathways by boosting the phosphorylation network, Accepted to NIPS Workshop on Computational Biology, Nov 2006.

• Anshul Kundaje, Changgui Lan, Mei Zhou, Christina Leslie, Li Zhang, A Predictive Model of the Oxygen Sensing and Regulatory Network in Yeast, Submitted to Nature Biotechnology, Sep 2006.

• Anshul Kundaje, Manuel Middendorf, Mihir Shah, Chris Wiggins, Yoav Freund, Christina Leslie, A classification-based framework for predicting and analyzing gene regulatory response, BMC Bioinformatics, Vol. 7(5), Mar 2006.

• Manuel Middendorf, Anshul Kundaje, Mihir Shah, Yoav Freund, Chris Wiggins, Christina Leslie, Motif Discovery through predictive modeling of gene regulation, RECOMB (Research in Computational Biology), May 2005.

• Anshul Kundaje, Manuel Middendorf, Feng Gao, Chris Wiggins, Christina Leslie, Combining Sequence and Time Series Expression Data To Learn Transcriptional Modules, IEEE/ACM Transactions on Computational Biology and Bioinformatics, May 2005.

• Gustavo Stolovitzky, Anshul Kundaje, Glenn Held, Keith Duggar, Christian Haudenschild, Daixing Zhou, Tom Vasicek, Kelly Smith, Alan Aderem, Jared Roach, Statistical analysis of MPSS measurements: application to the study of LPS activated macrophage gene expression, PNAS (Proceedings of the National Academy of Sciences), Vol. 102(5), pp. 1402-1407, Feb 2005.

• Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina Leslie, Predicting genetic regulatory response using classification: Yeast stress response, Lecture Notes in Computer Science, Vol. 3318(), pp. 1-13, Jan 2005.

• Manuel Middendorf, Anshul Kundaje, Chris Wiggins, Yoav Freund, Christina Leslie, Predicting genetic regulatory response using classification, Bioinformatics, Vol. 20(), pp. 232-240, Aug 2004.

• David Sussilo, Anshul Kundaje, Dimitris Anastassiou, Spectrogram Analysis of Genomes, EURASIP Journal of Applied Signal Processing, Nov 2003.

POSTER SESSIONS AND INVITED TALKS:

• Poster on hypoxia regulatory networks presented at the 2006 Cold Spring Harbor Labs Meeting on Sytems biology: Global regulation of gene expression

• Selected talk on hypoxia regulatory networks in yeast at the 2006 Annual Yeast Molecular Biology meeting in Princeton

• Selected talk on predictive modeling of gene regulation at the RECOMB 2004 Satellite Workshop on Regulatory Genomics

• Selected talk on a classification based framework of learning gene regulatory networks at the NIPS workshop on Methods in Computational Biology

• Invited talk at IBM TJ Watson Research center (2001) on using sequence and expression data to learn transcriptional modules

HIGHER EDUCATION:

• Currently pursuing a PhD in Computer Science (Computational Biology), Columbia University in the City of New York (09/2003 - Present)
  Advisors:
  Prof. Christina Leslie (Center for Computational Learning systems)

• Masters in Electrical Engineering
  Columbia University in The City of New York, (09/2001-12/2002)
  (CGPA 3.72)

• Bachelor of Engineering (Electrical), (07/1997 ? 06/2001)
  Veermata Jijabai Technological Institute (V. J. T. I.),
  Mumbai University, Mumbai (Bombay), India.
  Overall Result (1st to 8th Semester): ?Distinction?-75%
  Top student in Mumbai University (Electrical Engineering)

WORK EXPERIENCE:

• (01/02-09/02) Worked as an intern at the Functional Genomics and Systems Biology group at IBM T.J. Watson Research Center. Worked on statistical noise analysis of massively parallel signature sequencing (MPSS) data in collaboration with Lynx Therapeutics and Institute for Systems biology (Alan Aderem lab).
  Manager: Gustavo Stolovitzky

COMPUTATIONAL SKILLS:

• Machine learning: Boosting, Support vector machines, Graphical models and Bayesian networks with applications in Computational genomics.

• Algorithms and Computational learning theory

• Programming in C, C++, MATLAB, Simulink, PERL

• Operating systems: Windows, Unix & Linux Kernel and system programming

BIOLOGICAL TOOLS AND RESOURCES:

• General molecular biology, gene regulation, yeast biology and genetics, immunology and molecular basis of cancer.

• Gene expression measurement technologies - cDNA, Affymetrix oligoarrays (Yeast, Human), SAGE, MPSS.

• Statistical noise analysis of microarray data.

• Databases: Genbank, SGD, YPD, CYGD, MIPS, PFAM, SCOP, SWISS-PROT, PDB, WormPD, FlyBase

• NCBI Tools and Protein structural analysis tools

SCHOLARSHIPS AND ASSISTANTSHIPS:

• Teaching Assistant: Computational Genomics (Summer 02, Spring 04)
  Machine Learning Spring 06, Computer Networks Spring 2002

• Research Assistant: Computational Biology Group, Columbia University (02-Present)

• Prof. P.R Dandavate Memorial Award: Highest GPA in the Bachelor?s Program

• D.D. & L.H. Prize: Consistent Academic Career in the Bachelor?s Program

• M.B.P. Memorial Foundation Award: Highest GPA in final Year of Bachelors Program

• National Scholarship of Central Board Of Secondary Education for scoring 100 % marks in Maths in the Class 10 examination, conducted by the Central Board.