Publications, Peer-Reviewed

Bader JS, Chaudhuri A, Rothberg JM, Chant J 2004 Gaining confidence in high-throughput protein interaction networks. Nat Biotech 22: 78-85

Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, GodwinB, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley Jr. RL, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM 2003 A protein interaction map of Drosophila melanogaster Science 302: 1727-1736

Bader JS 2003 Greedily building protein networks with confidence. Bioinformatics. 19: 1869-1874.

Sham P, Bader JS, Craig I, O'Donovan M, Owen M 2002 Efficient association studies using pooled DNA: promise and pitfalls. Nature Reviews Genetics 3: 862-871

Bader JS, Sham P 2002 Family-based association tests for quantitative traits using pooled DNA. Eur J Hum Gen 10: 868-876

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

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

Bader JS, Bansal A, Sham P 2001 Efficient SNP-based tests of association for quantitative phenotypes using pooled DNA. Genescreen 1: 143-150

Bader JS 2001 The relative power of SNPs and haplotypes as genetic markers for association tests. J. S. Bader. Pharmacogenomics 2: 11-24

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

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

Bader JS, Cortis CM, Berne BJ 1997 Solvation and reorganization energies in polarizable molecular and continuum solvents. J Chem Phys 106: 2372-2387

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

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

Deem MW, Bader JS 1996 A configurational bias Monte Carlo method for linear and cyclic peptides. Mol Phys 87: 1245-1260

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

Bader JS, Berne BJ, Pollak E 1995 Activated rate processes: The reactive flux method for one-dimensional surface diffusion. J Chem Phys 102: 4037

Rick SW, Stuart SJ, Bader JS, Berne BJ 1995 Fluctuating charge force fields for aqueous solutions. J Mol Liq 65: 31-40

Bader JS, Berne BJ 1994 Quantum and classical relaxation rates from classical simulations. J Chem Phys 100: 8359

Pollak E, Bader JS, Berne BJ, Talkner P 1993 Theory of correlated hops in surface diffusion. Phys Rev Lett 70: 3299

Bader JS, Chandler D 1992 Computer simulation study of the mean forces between ferrous and ferric ions in water. J Phys Chem 96: 6423

Bader JS, Kuharski RA, Chandler D 1990 Role of nuclear tunneling in aqueous ferrous-ferric electron transfer. J Chem Phys 93: 230

Bader JS, Chander D 1989 Computer simulation of photochemically induced electron transfer. Chem Phys Lett 157: 501

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

Bader JS 2001 Mining population-level DNA repositories and SNP databases. Current Drug Discovery July 2001: 31-34

Bader JS 1999 Evolutionary implications of a power-law distribution of protein family sizes. xxx.lanl.gov physics/990832