8631 W. Third Street                            Parag Mallick      Work Phone: --- --- ----

Suite 1001E , Los Angeles, CA 90048                                                               Home Phone: --- --- ----

Parag.Mallick@cshs.org                                                                             Web Page

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Summary                                                                                                                                           

Interdisciplinary quantitative scientist with diverse academic and industry experience in translational research, information technology, bioinformatics, genomics, proteomics and graphic design.

 

Skills

Molecular Biology, Protein Chemistry and Proteomics: Yeast and Bacterial Cloning, Expression and Protein Purification, Northern & Western Blotting, HPLC, Protein Biophysical Characterization, Fluorimetry, Mammalian Cell Culture, Quantitative, liquid chromatographic tandem mass spectrometry. Bioinformatics and Genomics: Genome scale structure, function, interaction and regulatory network analysis, cDNA and Oligo Microarray Data Analysis, PSI-BLAST, Ensembl, RefSeq, Pattern Theory. Computer Related: Macintosh, Unix, Windows, C/C++, PERL, HTML, SQL, XML, JAVA, Macintosh Assembly, TCL/TK, Pascal, Scheme, PHP, Python, Design Patterns, OOP, CGI, Threads Programming, Socket Programming, Inter-process communication. Design: QuarkXpress, InDesign, Illustrator, Freehand, Photoshop.

 

Experience

Academic

Director of Clinical Proteomics                        Cedars-Sinai                                                           Nov 2004 – Present

Developing systems biology research group in division of Haemotology-Oncology and directing quantitative proteomics efforts of Clinical Outcomes Program.

Assistant Professor of Biochemistry                     UCLA                                                                 July 2005 – Present

 Developing and teaching coursework within the Bioinformatics program. 

Bioinformatics and Genomics

Consultant                                           Protein Pathways, Los Angeles, CA                               Oct 1999 – Dec 2002

Implemented parallel and distributed algorithms and software tools for analysis and discovery of protein functional networks.  Developed tools for microarray data analysis and database integration. 

Bioinformatics Liaison               TB Structural Genomics Consortium                             Oct 2000 – Dec 2002

Coordinated a distributed team to develop a structural proteomics lab information management system for 70 labs in 12 countries.  Developed bayesian target selection framework, reporting algorithms, XML languages for distributing lab protocols.

Selected Web & Software Development

Production & Copy Editor                ACM Crossroads Magazine                                           Jan 1995 – Present

Layout, design, and edit of online and print versions of Crossroads.

Developer and Owner                                        Midnight Media                                                       July 1995 – Present

Software design and backbone development for web utility software tools Framework, Gradient Page Designer and Connect 4 game.  Contracted website development.  Developed products include secure online ordering and inventory control systems, sequencing analysis, secure toolkit licensing and distribution, online betting for horse racing, and product display.

Graphic Design

Production Manager                                  Student Life Newspaper                                         Aug 1994 – Aug 1997

Coordinated team of designers and editors for semi-weekly creation and manipulation of articles, graphics, images, page designs and issue layouts.  

Business Manager & Designer                   Campus Graphics                                                Aug 1994 – Aug 1997

Managed payroll and solicited clients.  Worked with clients to designed advertisements, posters, leaflets, stickers, etc.

 

 

 

Teaching Experience

Introductory Biochemistry, Biochemistry Laboratory, Bioinformatics Brainstorm Seminar, Statistical Methods in Bioinformatics, Assisted Development of UCLA Bioinformatics Program.

 

 

Education

Postdoctoral Fellow                         Institute for Systems Biology, Seattle, WA                       Dec 2002 – Nov 2004

         Mentor: Ruedi Aebersold        

         Research Area: Medical and quantitative mass spectrometry based proteomics

 

Doctor of Philosophy                      University of California, Los Angeles, CA                        Oct 1997 – Dec 2002

         Department of Chemistry and Biochemistry

         Mentor: David Eisenberg

Thesis Topic: Genome Scale Fold Assignment: Exploring Fold, Function and the Twilight Zone

 

Bachelor of Science                              Washington University, St. Louis, MO                        Aug 1994 – May 1997

         Departments of Computer Science and Chemistry

         Undergraduate Honours Thesis Research in Biochemistry and Molecular Biophysics,

         Mentor: Jay Ponder

         Thesis Topic: Novel Methods for Protein Threading and Fold Recognition

 

         Undergraduate Honours Thesis Research in Computer Science,

         Mentor: Keith Bennett

Thesis Topic: Handling the International Space Station Communication Barrier Through the Incorporation of a Virtual Time Machine

 

Publications (current and forthcoming)

Prakash A, Mallick P, Whiteaker J, Zhang H, Paulovich A, Flory M, Lee H, Aebersold R, Schwikowski Algorithms for Constructing Signal Maps between Mass Spectrometry Experiments. Submitted Molecular and Cellular Proteomics

Desiere FÉThe PeptideAtlas Project.  In Press Nucleic Acids Research

Katz JE, Mallick P, Agus DB. A perspective on protein profiling of blood. BJU Int. 2005 Sep;96(4):477-82.

Kuester B, Shirle M, Mallick P Aebersold R.  Innovation: Scoring Proteomes with Proteotypic Peptide Probes. Nature Reviews Molecular Cellular Biology 2005, 6 : 577-583,

Zhang H, Yi E, Li X, Mallick P, Aebersold R: High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Mol Cell Proteomics. 2005 Feb;4(2):144-55

Desiere F*..Mallick P*, É , Aebersold R: Annotation of the Human Genome with Peptide Sequences obtained by High-Throughput Mass Spectrometry., Genome Biology.2004,6:R9

Kleiger G, Panina EM, Mallick P, Eisenberg D: PFIT and PFRIT: bioinformatic algorithms for detecting glycosidase function from structure and sequence. Protein Sci 2004, 13:221-229.

Strong M, Mallick P, Pellegrini M, Thompson MJ, Eisenberg D: Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. Genome Biol 2003, 4:R59.

Mallick P, Marcotte E:  Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions and interactions. Proteins and Proteomics: A Laboratory Manual, Dec. 2002, Cold Spring Harbor Laboratory Press

Mallick P, Boutz DR, Eisenberg D, Yeates TO: Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc Natl Acad Sci U S A 2002, 99:9679-9684.

Mallick P, Weiss R, Eisenberg D: The directional atomic solvation energy: an atom-based potential for the assignment of protein sequences to known folds. Proc Natl Acad Sci U S A 2002, 99:16041-16046.

Kleiger G, Grothe R, Mallick P, Eisenberg D: GXXXG and AXXXA: common alpha-helical interaction motifs in proteins, particularly in extremophiles. Biochemistry 2002, 41:5990-5997.

French SW, Shen RR, Koh PJ, Malone CS, Mallick P, Teitell MA: A modeled hydrophobic domain on the TCL1 oncoprotein mediates association with AKT at the cytoplasmic membrane. Biochemistry 2002, 41:6376-6382.

Mallick P: The accidental bioinformaticist. J Cell Biochem 2000, 80:208-209.

Kleiger G, Beamer LJ, Grothe R, Mallick P, Eisenberg D: The 1.7 A crystal structure of BPI: a study of how two dissimilar amino acid sequences can adopt the same fold. J Mol Biol 2000, 299:1019-1034.

Mallick P, Goodwill KE, Fitz-Gibbon S, Miller JH, Eisenberg D: Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing. Proc Natl Acad Sci U S A 2000, 97:2450-2455.

 

Selected Invited Talks

Gifts and Dreams. Keynote Speaker, Washington University Engineering Honours Banquet, Dec 1997

From Genome To Function, 3rd Critical Assessment of Structure Prediction, Dec 1998

Computational Analysis of Genome Sequences, Department of Energy Computational Structural Biology Research Meeting, Dec 1998

Whole Genome Structure Prediction, Assessing Resources for Genomics, Proteomics..., May 1999

Protein Structure Prediction, Bioinformatics Seminar Series, CSU Northridge, Nov 1999

Interfacing with the TB Structural Genomics Consortium, Keystone Symposium, January 2001

Bioinformatics of the TB SGC, NIH Meeting on Structural Genomics Bottlenecks, November 2001.

Bioinformatics of the TB SGC, Structural Genomics of Pathogenic Protozoa Meeting, Apr 2002.

Using Bioinformatics to Discover Cell Biology, Syddansk University Seminar, May 2002.

Developing Empirical Energy Functions For Structure Prediction, SAC-CASP, Dec 2002.

Approaches to Serum Marker Discovery, NSF-IPAM Proteomics, Apr 2004

 

Professional Organizations

American Association for the Advancement of Science, American Chemical Society, Association for Computing Machinery, American Society for Mass Spectrometry, Golden Key National Honorary Society, Human Proteome Organization, The Institute of Electrical and Electronics Engineers, International Society for Computational Biology, Mars Society, National Space Society, Protein Society.

 

Honours, Awards and Fellowships

Dean's List, College Honours, Class of 1983 Scholarship, 1996 Leadershape Institute Scholarship, 1998 UCLA Chemistry Graduate Teaching Excellence Award, 1999 Upjohn Fellowship, 1999 NIH-NIGMS Biotechnology Fellowship, 2000-2002 NSF IGERT Fellowship

 

Personal Interests

Volunteering (principally Habitat for Humanity and Aids Research Alliance), Juggling (Member of Los Angeles Troupes, Cirque Berzerk, The MUMs), Magic (Member, Magic Castle, Hollywood), Performance Art, Triathlons (Olympic Distance), Rock climbing, Volleyball, Tennis, Fiction Writing, Poetry, Piano, Graphic arts, Paper Collage Art, Cooking, Woodworking.