Joel
S. Bader, Ph.D.
Curriculum
Vitae
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Assistant Professor, Biomedical Engineering Johns Hopkins University 201C Clark Hall, 3400 N. Charles St. Baltimore, MD 21218 Tel: (410)516-7417 |
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Research Interests
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Genetics: statistical / population genetics, complex
traits, reverse genetics (phenotypic screens, RNAi)
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Functional genomics: regulatory networks, DNA/protein
interactions, microarray analysis
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Proteomics and structural biology: protein-protein
interaction networks, molecular evolution, molecular recognition
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Systems biology: systems-level biological organization,
cellular networks, quantitative models and simulations
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Statistics: data mining, visualization
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Aug 2003 – present |
Assistant Professor, Deparment of Biomedical Engineering, Johns Hopkins University and High-Throughput Biology Center, Johns Hopkins School of Medicine |
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Jun 1999 – Jul 2003 |
Director of Bioinformatics, CuraGen (research director for 6-10 PhDs) |
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Dec 1998 – Jun 1999 |
Principal Investigator, CuraGen |
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Mar 1996 – Dec 1998 |
Group Leader, CuraGen |
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Mar 1995 – Feb 1996 |
Senior Research Scientist, CuraGen |
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Jan 1992 – Jan 1995 |
Post-Doctoral Fellow, Columbia University, Dept. of Chemistry (Laboratory of Bruce J. Berne) |
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Aug 1986 – Dec 1991 |
PhD, UC Berkeley, Theoretical Chemistry (Laboratory of David Chandler) Thesis: “Solvation and electron transfer reaction dynamics” |
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Jul 1989 |
Participant, NATO Advanced Study Institute, Session LI, Les Houches, France |
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Jun 1986 – Aug 1986 |
Research Assistant, UC Berkeley (Laboratory of Peter G. Schultz) |
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Aug 1983 – May 1986 |
BS, Biochemistry, Phi Beta Kappa, Tau Beta Pi, Highest Honors (GPA 4.0/4.0, Class rank 1), Lehigh University |
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Mar 1998 |
Member of IPO working group and prospectus-writing team, CuraGen Corporation |
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Apr 1997 – Apr 1999 |
PI, $2 million direct costs, $3.4 million total budget, “Programmable Nanoscale Engines for Molecular Separation,” Advanced Technology Program, National Institute of Standards and Technology |
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Jul 1996 – Dec 1996 |
PI, $100,000 direct costs, “Novel Liquid-Phase DNA Sequencing,” SBIR Phase I, National Human Genome Research Institute |
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Aug 1986 – Aug 1989 |
NSF Graduate Research Fellow |
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Jul 2002 |
Participant, NIH workshop, Sequencing and resequencing the biome |
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2002 – present |
Editorial board, Pharmacogenomics |
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2001 – present |
Editorial board, American Journal of Pharmacogenomics |
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2000 – present |
Grant reviewer, NIH SSS-Y special emphasis panel (biotech/genomics) |
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Aug 1998 |
Symposium Chair, 216th American Chemical Society Annual Meeting, Computational Chemistry section |
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Nov 2000 |
Lecturer, Expression Arrays, Genetic Networks, and Disease, Functional Genomics Workshop, Institute for Pure and Applied Mathematics, UCLA [ Notes ] |
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Oct 2000 |
Lecturer, Gene Expression Informatics, Cold Spring Harbor Genome Informatics Workshop, Cold Spring Harbor, NY [ Notes ] |
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Oct 1999 |
Lecturer, Gene Expression Informatics, Cold Spring Harbor Genome Informatics Workshop, Cold Spring Harbor, NY [ Notes ] |
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Spring 1999 |
Adjunct Professor, Bioinformatics, University of New Haven MB620, Bioinformatics (40 hours of instruction, masters-level) [ Notes ] |
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Spring 1998 |
Adjunct Professor, Bioinformatics, University of New Haven MB620, Bioinformatics (40 hours of instruction, masters-level) |
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Fall 1988 |
Teaching Assistant, Graduate Statistical Mechanics I, UC Berkeley |
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Spring 1988 |
Teaching Assistant, Graduate Statistical Mechanics II, UC Berkeley |
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Spring 1987 |
Teaching Assistant, Freshman Chemistry, UC Berkeley |
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Summer 1984 |
Teaching Assistant, Organic Chemistry, Lehigh University |
American Association for the Advancement of Science
American Chemical Society
American Physical Society
Phi Beta Kappa
Tau Beta Pi
French, German
Born 1966. US citizen. Married, 2 children.
References are available upon request.
1. (author list to be determined) A genome scale protein interaction map of Drosophila (in preparation)
2. Bader JS, Chaudhuri A, Chant J 2003b Pathway discovery by automated analysis of combined interaction/expression networks. (submitted)
3. Bader JS, Chaudhuri A, Chant J 2003a Computational analysis of genome-scale interaction data to define biologically coherent protein interaction networks (submitted)
4. Sham P, Bader JS, Craig I, O’Donovan M, Owen M 2002 DNA pooling: a tool for large-scale association studies. Nature Reviews Genetics 3: 862-871 [ PDF ]
5. Bader JS, Sham P 2002 Family-based association tests for quantitative traits using pooled DNA. Eur J Hum Gen 10: 868-876 [ PDF ]
6. Bader JS, Deem MW, Hammond RW, Henck SA, Simpson JW, Rotherberg JM 2002 A Brownian-ratchet DNA pump with applications to single-nucleotide polymorphism genotyping. Appl Phys A 74: 1-4 [ PDF ]
7. Jawaid A, Bader JS, Purcell S, Cherny SS, Sham P 2002 Optimal selection strategies for QTL mapping using pooled DNA samples. Eur J Hum Gen 10: 125-132 [ PDF ]
8. Bader JS, Bansal A, Sham P 2001 Efficient SNP-based tests of association for quantitative phenotypes using pooled DNA. Genescreen 1: 143-150 [ PDF ]
9. Bader JS 2001 The relative power of SNPs and haplotypes as genetic markers for association tests. J. S. Bader. Pharmacogenomics 2: 11-24 [ PDF ]
10. Hammond RW, Bader JS, Henck SA, Deem MW, McDermott GA, Bustillo JM, Rothberg JM 2000 Differential Transport of DNA by a rectified Brownian motion device. Electrophoresis 21: 74-80 [ PDF ]
11. Bader JS, Hammond RW, Henck SA, Deem MW, McDermott GA, Bustillo JM, Simpson JW, Mulhern GT, Rothberg JM 1999 DNA transport by a micromachined Brownian ratchet device. Proc Natl Acad Sci USA 96: 13165-13169 [ PDF ]
12. Bader JS, Cortis CM, Berne BJ 1997 Solvation and reorganization energies in polarizable molecular and continuum solvents. J Chem Phys 106: 2372-2387 [ PDF ]
13. Bader JS, Berne BJ 1996 Solvation energies and electronic spectra in polar, polarizable media - simulation tests of dielectric continuum theory. J Chem Phys 104: 1293-1308 [ PDF ]
14. Bader JS, Berne BJ, Pollack E, Hanggi P 1996 The energy relaxation of a nonlinear oscillator coupled to a linear bath. J Chem Phys 104: 1111-1119 [ PDF ]
15. Deem MW, Bader JS 1996 A configurational bias Monte Carlo method for linear and cyclic peptides. Mol Phys 87: 1245-1260
16. Bader JS, Berne BJ 1995 The energy-dependent transmission coefficient and the energy distribution of classical particles escaping from a metastable well. J Chem Phys 102: 7953 [ PDF ]
17. Bader JS, Berne BJ, Pollak E 1995 Activated rate processes: The reactive flux method for one-dimensional surface diffusion. J Chem Phys 102: 4037 [ PDF ]
18. Rick SW, Stuart SJ, Bader JS, Berne BJ 1995 Fluctuating charge force fields for aqueous solutions. J Mol Liq 65: 31-40 [ PDF ]
19. Bader JS, Berne BJ 1994 Quantum and classical relaxation rates from classical simulations. J Chem Phys 100: 8359 [ PDF ]
20. Pollak E, Bader JS, Berne BJ, Talkner P 1993 Theory of correlated hops in surface diffusion. Phys Rev Lett 70: 3299 [ PDF ]
21. Bader JS, Chandler D 1992 Computer simulation study of the mean forces between ferrous and ferric ions in water. J Phys Chem 96: 6423
22. Bader JS, Kuharski RA, Chandler D 1990 Role of nuclear tunneling in aqueous ferrous-ferric electron transfer. J Chem Phys 93: 230
23. Bader JS, Chander D 1989 Computer simulation of photochemically induced electron transfer. Chem Phys Lett 157: 501
24. Kuharski RA, Bader JS, Chandler D, Sprik M, Impey RW 1988 Molecular model for aqueous ferrous--ferric electron transfer. J Chem Phys 89: 3248
Publications (Non-peer-reviewed)
1. Bader JS 2001 Mining population-level DNA repositories and SNP databases. Current Drug Discovery July 2001: 31-34 [ PDF ]
2. Bader JS 1999 Evolutionary implications of a power-law distribution of protein family sizes. xxx.lanl.gov physics/990832 [ PDF ]
1. Rothberg JM, Bader JS. Method of sequencing a nucleic acid. US Patent 6274320, issued 14 Aug 2001 [ PDF.GZ ]
2. Bader JS, Rothberg JM, Deem MW, Mulhern GT, Went GT, Simpson J, Henck S. Separation of Charged Particles by a Spatially and Temporally Varying Electric Field. US Patent 6193866 issued 27 Feb 2001 [ PDF.GZ ]
3. Jarvie TP, Bader JS, Went GT. Method for Distance Measurements with Solid-State NMR. US Patent 6027941 issued Feb. 22, 2000 [ PDF.GZ ]
4. Bader JS, Rothberg JM, Deem MW, Mulhern GT, Went GT. Separation of Charged Particles by a Spatially and Temporally Varying Electric Field. US Patent 5938904 issued 17 Aug 1999 [ PDF.GZ ]
Patent Applications (Pending)
1. Bader JS, Bansal A, Sham P. Efficient tests of association for quantitative traits and affected-unaffected studies using pooled DNA. US Patent Application 60/238,391 filed 6 Oct 2001
2. Bader JS. Method of identifying genetic regions associated with disease and predicting responsiveness to therapeutic agents. US Patent Application 60/236,765 filed 28 Sep 2001
3. Bader JS. Method for identifying interacting gene products. US Patent Application 60/159,963 filed 18 Oct 2000
4. Bader JS, Bansal A, Sham P. DNA pooling methods for quantitative traits using unrelated populations or sib pairs. US Patent Application 60/226,465 filed 18 Aug 2000
5. Bader JS, Liu Y, Dziuda D. Methods for classifying nucleic acids and polypeptides. US Patent Application 60/216,610 (CIP) filed 7 Jul 2000
6. Bader JS, Gold S, Gusev V, Li SX, Shenoy S, Crasta OR, Bouffard P. Method of analyzing a nucleic acid. US Patent Application 60/174,685 filed 6 Jan 2000
7. Rothberg JM, Bader JS. Nucleic acid probe arrays. US Patent Application 9/449,402 filed 26 Nov 1999
8. Rothberg JM, Bader JS, Dewell SB, McDade K, Simpson JW, Berka J, Colangelo CM. Method of sequencing a nucleic acid. US Patent Application 9/398,833 filed 16 Sep 1999
9. Bader JS, Liu Y, Gold S, Dziuda D, Gusev V, Judson RS, Went GT. Normalization, scaling, and difference finding among data sets. US Patent Application 60/114,806 filed 5 Jan 1999
10. Bader
JS. Geometrical and hierarchical
classification based on gene expression.
US Patent Application 60/101,009 filed 17 Sep 1998
1. Protein-protein interactions, microarrays, and cellular networks. Purdue University Bioinformatics Seminar Series, West Lafayette, Indiana, November 12, 2002
2. Biologically coherent cellular networks (poster selected for talk). Gordon Research Conference, Genomics and Structural/Evolutionary Bioinformatics, July 2002
3. CuraGen overview. Euro-Biotech Forum, Paris, France, June 10-12, 2001
4. Genomics, a perspective from biotech. Chemistry Department Symposium, Haverford College, Haverford, PA, February 23, 2000
5. GeneCalling technology for gene expression profiling. ATP National Meeting, San Jose, CA, November 15, 1999
6. Maximizing value from SNPs. SNPs and Pharmacogenomics Global Business Research, San Diego, CA, September 27, 1999
7. Gene networks, clustering, and pharmacogenomics. In Silico Biology, Cambridge Healthtech Institute, June 9, 1999
8. Pharmacogenomics. International Business Communications Nuclear Hormone Receptor Drug Discovery Conference, Scottsdale, AZ, January 1999
9. Pharmacogenomics. Bioinformatics seminar, Cold Spring Harbor, October 30, 1998
10. Phylogenomics and pharmacogenomics. Departmental seminar, Department of Chemistry, New York University, New York, NY, September 19, 1998
11. CuraGen’s tools for DNA diagnostics: applications. NIST/ATP Conference on Tools for DNA Diagnostics, Gaithersberg, Maryland, March 1998
12. NanoNiagara, a nano-Scale, liquid-phase DNA separation device. Departmental seminar, University of Maine, Orono, Maine, November 1997
13. New algorithms for protein simulations. Departmental seminar, Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, April 1996
14. New, rigorous algorithms for sampling protein domains. American Chemical Society National Meeting, New Orleans, Louisiana, March 1996
15. Solvation, absorption, and relaxation: CH2O in H2O. Physical Chemistry Colloquium, Columbia University, New York, New York, September 1994
16. Nuclear tunneling in aqueous ferrous-ferric electron transfer. Meeting of the Electrochemical Society, Toronto, Ontario, October 1992
1. Whole-genome maps of quantitative trait loci (talk) Wellcome Trust, Cold Spring Harbor, August 9, 2001
2. Pharmacogenomics (poster) Pharmacogenomics and Pharmacogenetics, Pasteur Institute, Paris, France, October 12-13, 2000
3. Pharmacogenomics (poster) RECOMB 99 (3rd International Conference on Computational Biology), Lyon, France, April 1999
4. A nanoscale, liquid-phase DNA separation device based on Brownian ratchets (talk) Meeting of the American Physical Society, Los Angeles, California, March 1998
5. Regrowth algorithms for biosimulations (poster) Gordon Conference on Computational Chemistry, Tilton School, Tilton, New Hampshire, July 1996
6. Charge transfer in polar, polarizable fluids: simulation tests of dielectric continuum theories (poster) Gordon Conference on Liquids, Holderness School, Holderness, New Hampshire, August 1995
7. Relaxing in a polarizable solvent (poster) Gordon Conference on Water and Aqueous Solutions, Holderness School, New Hampshire, August 1994
8. Correlated hops in surface diffusion (poster) American Conference on Theoretical Chemistry, Rochester, New York, June 1993
9. Surface diffusion in the low friction regime (talk) Mid-Atlantic Region American Chemical Society, Hofstra University, New York, June 1993
10. Nuclear tunneling in aqueous ferrous-ferric electron transfer (poster) American Chemical Society Symposium on Simulations and Their Critical Experimental Tests, Boston, Massachusetts, August 1990
11. A molecular model for aqueous ferrous-ferric electron transfer (poster) American Chemical Society, Dallas, Texas, 1989