Publications & Patents:

• Jaitly, N., Brubaker, M.A., Rubinstein, J.L., Lilien, R.H. Machine Learning in Computational Biology (MLCB), NIPS 2009 workshop. A Bayesian method for 3D reconstruction of macromolecular structure using class averages from single particle electron microscopy.
• Umar, A., Kang, H., Timmermans, A.M, Look, M.P., Meijer-van Gelder, M.E., den Bakker, M.A., Jaitly, N., Martens, J.W., Luider, T.M., Foekens, J.A., Pasa-Tolic, L. Molecular & Cellular Proteomics 2009 Jun;8(6):1278-94. Identification of a putative protein profile associated with tamoxifen therapy resistance in breast cancer.
• Jaitly, N., Mayampurath, A., Littlefield, K., Adkins, J.N., Anderson, G.A., Smith, R.D. BMC Bioinformatics 2009. Mar 17. Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.
• Ansong, C., Yoon, H., Porwollik, S., Mottaz-Brewer, H., Petritis, B.O., Jaitly, N., Adkins, J.N., McClelland, M., Heffron, F., Smith, R.D. PLoS One 2009. 4(3):e4809. Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications of virulence and global protein translation.
• Qian, W.J, Liu, T., et. al. Journal of Proteome Research 2009 Jan; 8(1):290-9. Large-scale multiplexed quantitative discovery proteomics enabled by the use of an (18)O-labeled "universal" reference sample
• Tolmachev, A.V., Monroe, M.E., Purvine, S.O., Moore, R.J., Jaitly, N., Adkins J.N., Anderson, G.A., Smith, R.D. Analytical Chemistry 2008 Nov 15; 80(22):8514-25. Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments
• 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 Proteomics 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.

Selected Projects & Talks:

• Principal Investigator, Lab Directed Research and Development (LDRD) at PNNL. High Performance Data Analysis Pipeline for Intelligent Mass Spectrometry. $500,000 over 3 years. 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 for "...contributions in support of Environmental and Molecular Sciences Laboratorys strategy for achieving high-impact science and marquee capabilities...", Pacific Northwest National Laboratory, November 2006.
• Outstanding Performance Award for "Development and Implementation of Advanced Algorithms for Mass and Time Alignment of Proteomics Data", Pacific Northwest National Laboratory, 2006
• 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