November 8, 2008

About

I am currently a PhD student at the Computer Science department in the University of Toronto under the supervision of Geoffrey Hinton. My interests lie in Machine Learning and Bioinformatics.

Publications

  • Sorensen, C.M., Ding, J., Jaitly, N., et. al. Journal of Chromatography B Analytical Technologies in the Biomedical and Life Sciences. 2008 May 7. Application of the accurate mass and time tag approach in studies of the human blood lipidome.
  • Polpitiya A.D., Qian, W.J., Jaitly N., et. al. Bioinformatics. 2008 Jul 1;24(13):1556-8. DAnTE: A statistical tool for quantitative analysis of omics data.
  • Ham B.M., et. al. Journal of Proteome Research. 2008 Jun; 7(6):2215-21. The influence of sample preparation and replicate analyses on HeLa Cell phosphoproteome coverage.
  • Mayampurath A.M., Jaitly N., Purvine S.O., Monroe M.M., Auberry K.A., Adkins J.N., Smith R.D. Bioinformatics. 2008 Apr 1;24(7):1021-3. DeconMSn: A software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra.
  • Petyuk, V.A., Jaitly, et. Al. Analytical Chemistry 2008 Feb 1;80(3):693-706.Elimination of systematic mass measurement errors in liquid chromatography-mass spectrometry based proteomics using regression models and a priori partial knowledge of the sample content.
  • Yang, F., Jaitly, N., Jayachandran, H., et. Al. Journal of Proteome Reseach 2007 Nov;6(11):4489-97. Epub 2007 Oct 12. Applying a Targeted Label-Free Approach Using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition.
  • Gupta, N., Tanner, S., Jaitly, N., Adkins, J.N., Liptono, M., Edwards, R., Romine, M., Osterman, A., Bafna, V., Smith, R.D., Pevzner, P.A. Genome Research.2007 Sep; 17(9): 1362-77. Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation.
  • Liu, T., Belov, M.E., Jaitly, N., Qian, W.J., Smith, R.D. Chemical Reviews 2007 Aug; 107(8): 3621-53. Accurate Mass Measurements in Proteomics.
  • Ding, J., Sorensen, C.M., Zhang, Q., Jiang, H., Jaitly, N., Livesay, E.A., Shen, Y., Smith, R.D., Metz, T.O. Analytical Chemistry 2007 Aug 15; 79(16): 6081-93. Capillary LC coupled with high-mass measurement accuracy mass spectrometry for metaboloic profiling.
  • Monroe, M.E., Tolic, N., Jaitly, N., Shaw, J.L., Adkins, J.N., Smith, R.D. Bioinformatics Aug 1;23(15):2021-3. VIPER: an advanced software package to support high-throughput LC-MS peptide identification.
  • Jaitly, N., Monroe, M.E., Petyuk, V.A., Clauss, T.R.W, Adkins, J.N., Smith, R.D. Analytical Chemistry 2006 Nov 1;78(21):7397-409. Robust Algorithm for Alignment of Liquid Chromatography-Mass Spectrometry Analyses in an Accurate Mass and Time Tag Data Analysis Pipeline.
  • Kearney, P. et. al. (US Patent Application being filed 2006). TAT-001 and Methods of Assessing and Treating Cancer.
  • Sharma, S., Simpson, D.C., Jaitly, N., Mayampurath, A.M., Smith, R.D., Pasa-Tolic, L. Journal of Proteome Research.2007 Feb; 6(2):602-10. Proteomic Profiling of Intact Proteins Using WAX-RPLC 2-D Separations and FTICR Mass Spectrometry
  • Petyuk, V.A. et.al. Genome Research. 2007 Mar;17(3):328-36. Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry.
  • Tolmachev A.V., Monroe M.E., Jaitly N., Petyuk V.A., Adkins J.N., Smith R.D. Analytical Chemistry. 2006 Dec 15;78(24):8374-85. Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration
  • Norbeck, A.D., Callister, S.J., Monroe, M.E., Jaitly, N., Elias, D.A., Lipton, M.S., Smith, R.D. Journal of Microbiological Methods. 2006 Dec;67(3):473-86. Proteomic approaches to bacterial differentiation.
  • Kiebel GR, Auberry KJ, Jaitly N, Clark DA, Monroe ME, Peterson ES, Tolic N, Anderson GA, Smith RD. Proteomics. 2006 Mar;6(6):1783-90. PRISM: A Data Management System for High-Throughput Proteomics.
  • McIntire, T.M., Lea, A.S., Gaspar, D.J., Jaitly, N., Dubowski, Y., Li, Q., Finlayson-Pitts, B.J. Phys Chem Chem Phys. 2005 Oct 21;7(20):3605-9. Unusual Aggregates from the Oxidation of Alkene Self-Assembled Monolayers: A Previously Unrecognized Mechanism for SAM Ozonolysis?
  • Kearney, P, Jaitly, D., Eng, K. (US Patent Application# 20060122785). Constellation Mapping: Software and Methods to match complex peptide maps using nonlinear alignment methods.
  • Jaitly, D, Page-Belanger, R., Faubert, D, Thibault, P, Kearney, P. MSMS Peak Identification through Maximum Likelihood Methods And its Application to Analysis of Tandem Mass Spectrometry data. ISMB 2004.
  • Swamy, S, Furtos-Matei, A, Jaitly, N, Kearney, P, Thibault, P. GlycoTrack: Tool for Automated N-Linked Glycopeptide Identification and Analysis. Poster, PSB 2003 (Also, US Patent Application# 20040248317).
  • Jaitly, D, Kearney, P,Lin, G and Ma, B. Methods for Reconstructing the History of Tandem Repeats and Their Application to the Human Genome. Journal of Computer and System Sciences 65(3): 494-507. 2002.

Projects and Talks:

  • Refereed talk in "Advances in Bioinformatics Research" Session, ASMS 2008. A Statistical Approach to Quantifying Uncertainties in the Accurate Mass and Time (AMT) tag pipeline. June 2008, Denver, CO
  • Taught Tutorial at US Human Proteomics Organization (HUPO) with Matthew E. Monroe of PNNL and Jake Jaffe of the Broad Institute, M.I.T. Data Extraction and Analysis for LC-MS Based Proteomcis. March 2008, Bethesda, MD.
  • Principal Investigator, Lab Directed Research and Development (LDRD) at PNNL. High Performance Data Analysis Pipeline for Intelligent Mass Spectrometry. $500,000 over 3 years, starting 2007.
  • Invited talk at the Training Program in Bioinformatics in Texas A&M University. Challenges in Interpretation of Proteomics Data from Mass Spectrometry Experiments. October 2007
  • Taught Tutorial at US Human Proteomics Organization (HUPO) with Matthew E. Monroe of PNNL and Jake Jaffe of the Broad Institute, M.I.T. Data Extraction and Analysis for LC-MS Based Proteomcis. March 2007.
  • Short Presentation at Intelligent Systems for Molecular Biology. MSMS Peak Identification through Maximum Likelihood Methods And its Application to Analysis of Tandem Mass Spectrometry data. 2004

Awards and Honors:

  • Nominated for Environmental and Molecular Sciences Laboratory (EMSL) Director’s Award, Environmental and Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory, November 2006.
  • Outstanding Performance Award, Pacific Northwest National Laboratory, 2006 for Development and Implementation of Advanced Algorithms for Mass and Time Alignment of Proteomics Data
  • Outstanding Performance Award, Pacific Northwest National Laboratory, 2005.
  • Ranked 63rd in William Lowell Putnam Mathematics Competition, Dec 1996.
  • Ranked in the top 31 in the Indian National Mathematics Olympiads, 1993.
  • Dean’s List

Contact:

  • Email:

    ndjaitly AT cs DOT toronto DOT edu

  • Office:

    Dept of Computer Science
    Pratt Bldg, Room 286
    6 King's College Rd
    University of Toronto
    Toronto, ON M5S 3G4, Canada
    Map

  • Mailing:

    Navdeep Jaitly c/o Ryan Lilien
    UofT - Dept of Computer Science
    10 King's College Rd., Room 3302
    Toronto, Ontario M5S 3G4
    Canada