Publications

From BaderLab

Contents 1 Publications 1.1 2009 1.2 2008 1.3 2007 1.4 2006 1.5 2005 1.6 2004 1.7 2003 1.8 2002 1.9 2001 1.10 2000 and before 2 Non Peer-Reviewed Publications 3 Issued Patents 4 Pending Patent Applicatioins

[edit] Publications

[edit] 2009

• Czar MJ, Anderson JC, Bader JS, Peccoud J. 2009. Gene synthesis demystified. Trends in Biotechnology 27: 63-72.
• Veeramani B, Bader JS. 2009. Metabolic flux correlations, genetic interactions and disease. Journal of Computational Biology. In press.
• Dymond JS, Scheifele LZ, Richardson S, Chandrasegaran C, Bader JS, Boeke JD. 2009. Teaching synthetic biology, bioinformatics, and engineering to undergraduates: the interdisciplinary Build-a-Genome laboratory. Genetics. 181: 13-21.
• Huang H, Maertens AM, Hyland EM, Dai J, Norris A, Boeke JD, Bader JS. 2009. HISTONEHITS: a database for histone mutations and their phenotypes. Genome Research. In press.
• Kut C, Golkhou V, Bader JS. 2009. Analytical approximations for the amplitude and period of a relaxation oscillator. BMC Systems Biology. 3: 6.
• Huang H, Bader JS. 2009. Precision and recall estimates for two-hybrid screens. Bioinformatics 25(3):372-8.

[edit] 2008

• Dai J, Hyland EM, Yuan DS, Huang H, Bader JS, Boeke JD. 2008. Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants. Cell 134(6):1066-78.
• Qi Y, Suhail Y, Lin YY, Boeke JD, Bader JS. 2008. Finding friends and enemies in an enemies-only network: A graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Research 18(12):1991-2004. SFL data and predictions diffusion kernel code
• Lin YY, Qi Y, Lu JY, Pan X, Yuan DS, Zhao Y, Bader JS, Boeke JD. 2008. A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation. Genes and Development 22(15):2062-74.
• Mathivanan et al. 2008. Human Proteinpedia enables sharing of human protein data. Nature Biotechnology 26: 164-167.
• Pan X, Yuan D, Ye P, Bader JS, Boeke JD. 2008. Response to Dr Stephen Cooper's ‘On the use of metaphor to understand, explain, or rationalize redundant genes in yeast’. FEMS Yeast Research. 27-Feb-2008. Response to Cooper S. 2008. On the use of metaphor to understand, explain, or rationalize redundant genes in yeast. FEMS Yeast Research. 22-Feb-2008.
• Bader JS. 2008. Systems approaches for pharmacogenetics and pharmacogenomics. Pharmacogenomics 9: 257-262.

[edit] 2007

• Huang H, Jedynak BM, Bader JS. 2007. Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps. PLoS Comput Biol 3(11): e214.
• Huang H, Zhang LV, Roth FP, Bader JS. 2007. Probabilistic Paths for Protein Complex Inference. Systems Biology and Computational Proteomics. Network weights MIPS Complexes Software (including all the data)
• Liu LA, Bader JS. 2007. Ab initio prediction of transcription factor binding sites. Pac. Symp. Biocomp. 12: 484-495.
• Stuart LM, Boulais J, Charriere GM, Hennessy EJ, Brunet S, Jutras I, Goyette G, Rondeau C, Letarte S, Huang H, Ye P, Morales F, Kocks C, Bader JS, Desjardins M, Ezekowitz RA. A systems biology analysis of the Drosophila phagosome. Nature. 2007 Jan 4;445(7123):95-101. Epub 2006 Dec 6. PMID: 17151602

[edit] 2006

• Liu LA, Bader JS. Decoding transcriptional regulatory interactions. Physica D. 2006 Dec;224(1-2):174-181.
• Liu LA, Bader JS. 2006. Decoding transcriptional regulatory interactions. Physica D Nonlinear Phenomena. 224:174-181.
• Bose R, Molina H, Patterson AS, Bitok JK, Periaswamy B, Bader JS, Pandey A, Cole PA. 2006. Phosphoproteomic analysis of Her2/neu signaling and inhibition. PNAS. 103: 9773-9778.(supplement)
• Dorer MS, Kirton D, Bader JS, Isberg RR. 2006. RNA Interference Analysis of Legionella in Drosophila Cells: Exploitation of Early Secretory Apparatus Dynamics. PLoS Pathog 2: e34.
• Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A. 2006. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet. 2006. 38:285-293.
• Bader JS, Chant J. 2006. When proteomes collide. Science 311: 187-188.

[edit] 2005

• Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD. 2005. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell. 124: 1069-1081.
• Qi Y, Ye P, Bader JS. 2005. Genetic Interaction Motif Finding by Expectation Maximization – a novel statistical model for inferring gene modules from synthetic lethality. BMC Bioinformatics 6: 288.
• Ye P, Peyser BP, Pan X, Boeke JD, Spencer FA, Bader JS. 2005. Gene function prediction from congruent synthetic lethal interactions in yeast. Molecular Systems Biology 2005 Nov 22
• Ye P, Peyser BP, Spencer FA, Bader JS. 2005. Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast. BMC Bioinformatics 6: 270.
• Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD. 2005. Global synthetic-lethality analysis and yeast functional profiling. Trends Genet. 2005 Nov 22
• Margulies M, Egholm M, Altman WE, Attiya S, Bader JS*, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM*. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380. *Co-inventors (US Patent 6274320

[edit] 2004

• Pan X, Yuan DS, Xiang D, Wang X, Sookhai-Mahadeo S, Bader JS, Hieter P, Spencer F, Boeke JD. 2004. A robust toolkit for functional profiling of the yeast genome. Mol Cell. 16: 487-496.
• Iossifov I, Krauthammer M, Friedman C, Hatzivassiloglou V, Bader JS, White KP, Rzhetsky A. 2004. Probabilistic inference of molecular networks from noisy data sources. Bioinformatics. 20: 1205-1213.
• Bader JS, Chaudhuri A, Rothberg JM, Chant J. Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol. 2004 Jan;22(1):78-85. Epub 2003 Dec 14. (supplement)

[edit] 2003

• Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Govindan V, 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, Lazovatsk Y, DaSilva A, Zhong J, Stanyon CA, Finley RL, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets. RA, McKenna MP, Chant J, Rothberg JM. 2003. A genome-scale protein interaction map of Drosophila melanogaster. Science. 302: 1727-1736. (supplement)
• Bader JS. Greedily building protein networks with confidence. Bioinformatics. 2003 Oct 12;19(15):1869-74. (supplement)

[edit] 2002

• 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.
• Bader JS, Sham P. Family-based association tests for quantitative traits using pooled DNA. Eur J Hum Genet. 2002 Dec;10(12):870-8
• Bader JS, Deem MW, Hammond RW, Henck SA, Simpson JW, Rothberg JM. 2002. A Brownian-ratchet DNA pump with applications to single-nucleotide polymorphism genotyping. Applied Physics A. 74:1-4.
• Jawaid A, Bader JS, Purcell S, Cherny SS, Sham P. Optimal selection strategies for QTL mapping using pooled DNA samples. Eur J Hum Genet. 2002 Feb;10(2):125-32.

[edit] 2001

• 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. The relative power of SNPs and haplotypes as genetic markers for association tests. Pharmacogenomics. 2001 Feb;2(1):11-24.

[edit] 2000 and before

• Hammond RW, Bader JS, Henck SA, Deem MW, McDermott GA, Bustillo JM, Rothberg JM. Differential Transport of DNA by a rectified Brownian motion device. Electrophoresis. 2000 Jan;21(1):74-80
• Bader JS, Hammond RW, Henck SA, Deem MW, McDermott GA, Bustillo JM, Simpson JW, Mulhern GT, Rothberg JM. DNA transport by a micromachined Brownian ratchet device. Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13165-9.
• Bader JS, Cortis CM, Berne BJ. 1997. Solvation and reorganization energies in polarizable molecular and continuum solvents. Journal of Chemical Physics. 106:2372-2387.
• Bader JS, Berne BJ. 1996. Solvation energies and electronic spectra in polar, polarizable media - simulation tests of dielectric continuum theory. Journal of Chemical Physics. 104:1293-1308.
• Bader JS, Berne BJ, Pollack E, Hanggi P. 1996. The energy relaxation of a nonlinear oscillator coupled to a linear bath. Journal of Chemical Physics. 104:1111-1119.
• Deem MW, Bader JS. 1996. A configurational bias Monte Carlo method for linear and cyclic peptides. Molecular Physics. 87:1245-1260.
• Bader JS, Berne BJ, Pollak E. 1995. Activated rate processes: The reactive flux method for one-dimensional surface diffusion. Journal of Chemical Physics. 102:4037-4055
• Bader JS, Berne BJ. 1995. Fluctuating charge force fields for aqueous solutions. Journal of Molecular Liquids. 65:31-40.
• Bader JS, Berne BJ. 1995. The energy-dependent transmission coefficient and the energy distribution of classical particles escaping from a metastable well. Journal of Chemical Physics. 102:7953-7965.
• Bader JS, Berne BJ. 1994. Quantum and classical relaxation rates from classical simulations. Journal of Chemical Physics. 100:8359-8366.
• Pollak E, Bader J, Berne BJ, Talkner P. Theory of correlated hops in surface diffusion. PHYSICAL REVIEW LETTERS. 1993 May 24;70(21):3299-3302.
• 4. Bader JS, Chandler D. 1992. Computer simulation study of the mean forces between ferrous and ferric ions in water. Journal of Physical Chemistry. 96:6423-6427.
• Bader JS, Kuharski RA, Chandler D. 1990. Role of nuclear tunneling in aqueous ferrous-ferric electron transfer. Journal of Chemical Physics. 93:230-236.
• Bader JS, Chander D. 1989. Computer simulation of photochemically induced electron transfer. Chemical Physics Letters. 157:501-504.
• Kuharski RA, Bader JS, Chandler D, Sprik M, Impey RW. 1988. Molecular model for aqueous ferrous--ferric electron transfer. Journal of Chemical Physics. 89:3248-3256.

[edit] Non Peer-Reviewed Publications

• Mining population-level DNA repositories and SNP databases 2001
• Evolutionary implications of a power-law distribution of protein family sizes 1999

[edit] Issued Patents

• Rothberg JM, Bader JS. Method of sequencing a nucleic acid. US Patent 6274320, issued Aug 14, 2001. Founding patent of 454 Life Sciences; product commercialized as the Genome Sequencer 20 System and distributed by Roche Diagnostics Corporation www.roche-applied-science.com/sis/sequencing/genome/
• 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 Feb 27, 2001.
• Jarvie TP, Bader JS, Went GT. Method for Distance Measurements with Solid-State NMR. US Patent 6027941 issued Feb. 22, 2000.
• 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 Aug 17, 1999.

[edit] Pending Patent Applicatioins

• 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
• 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
• Bader JS. Method for identifying interacting gene products. US Patent Application 60/159,963 filed 18 Oct 2000
• 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
• Bader JS, Liu Y, Dziuda D. Methods for classifying nucleic acids and polypeptides. US Patent Application 60/216,610 (CIP) filed 7 Jul 2000
• 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
• Rothberg JM, Bader JS. Nucleic acid probe arrays. US Patent Application 9/449,402 filed 26 Nov 1999
• 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
• 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
• Bader JS. Geometrical and hierarchical classification based on gene expression. US Patent Application 60/101,009 filed 17 Sep 1998