Publications and Patents

Publications, External Links

Patents

  1. 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 Roche 454 Genome Sequencer 20.
  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 Feb 27, 2001.
  3. Jarvie TP, Bader JS, Went GT. Method for Distance Measurements with Solid-State NMR. US Patent 6027941 issued Feb. 22, 2000.
  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 Aug 17, 1999.

Publications, Local Repository

  1. Chu LH, Rivera CG, Popel AS, Bader JS. Constructing the Angiome – a Global Angiogenesis Protein Interaction Network. Physiol Genomics. 2012 Aug 21. PubMed PMID: 22911453.
  2. Chanda P, Elhaik E, Bader JS. HapZipper: sharing HapMap populations just got easier. Nucleic Acids Res. 2012 Jul 27. [Epub ahead of print] PubMed PMID: 22844100.
  3. Park Y, Bader JS. How networks change with time. Bioinformatics. 2012 Jun 15;28(12):i40-8. PubMed PMID: 22689777; PubMed Central PMCID: PMC3371843.
  4. Chanda P, Yuhki N, Li M, Bader JS, Hartz A, Boerwinkle E, Kao WL, Arking DE. Comprehensive evaluation of imputation performance in African Americans. J Hum Genet. 2012 Jul;57(7):411-21. doi: 10.1038/jhg.2012.43. Epub 2012 May 31. PubMed PMID: 22648186.
  5. Cooper EM, Müller H, Chandrasegaran S, Bader JS, Boeke JD. The Build-a-Genome course. Methods Mol Biol. 2012;852:273-83. PubMed PMID: 22328440.
  6. Richardson SM, Liu S, Boeke JD, Bader JS. Design-A-Gene with GeneDesign.Methods Mol Biol. 2012;852:235-47. PubMed PMID: 22328438.
  7. Muller H, Annaluru N, Schwerzmann JW, Richardson SM, Dymond JS, Cooper EM, Bader JS, Boeke JD, Chandrasegaran S. Assembling large DNA segments in yeast. Methods Mol Biol. 2012;852:133-50. PubMed PMID: 22328431.
  8. Annaluru N, Muller H, Ramalingam S, Kandavelou K, London V, Richardson SM, Dymond JS, Cooper EM, Bader JS, Boeke JD, Chandrasegaran S. Assembling DNA fragments by USER fusion. Methods Mol Biol. 2012;852:77-95. PubMed PMID: 22328427.
  9. Rivera CG, Mellberg S, Claesson-Welsh L, Bader JS, Popel AS. Analysis of VEGF–a regulated gene expression in endothelial cells to identify genes linked to angiogenesis. PLoS One. 2011;6(9):e24887. Epub 2011 Sep 13. PubMed PMID: 21931866; PubMed Central PMCID: PMC3172305.
  10. Karchin R, Ochs MF, Stuart JM, Bader JS. Identification of aberrant pathway and network activity from high-throughput data. Pac Symp Biocomput. 2012;17:1-6. PubMed PMID: 22174257.
  11. Lin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z, Lu JY, Khor CN, Lin CL, Bader JS, Irizarry R, Boeke JD. Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 2012 Feb 8;482(7384):251-5. doi: 10.1038/nature10804. PubMed PMID: 22318606; PubMed Central PMCID:PMC3277212.
  12. Dymond JS, Richardson SM, Coombes CE, Babatz T, Muller H, Annaluru N, Blake WJ, Schwerzmann JW, Dai J, Lindstrom DL, Boeke AC, Gottschling DE, Chandrasegaran S, Bader JS, Boeke JD. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature. 2011 Sep 14;477(7365):471-6. doi:10.1038/nature10403. PubMed PMID: 21918511.
  13. Rivera CG, Rosca EV, Pandey NB, Koskimaki JE, Bader JS, Popel AS. Novel Peptide-Specific Quantitative Structure-Activity Relationship (QSAR) Analysis Applied to Collagen IV Peptides with Antiangiogenic Activity. J Med Chem. 2011 Sep 13. PubMed PMID: 21866962.
  14. Huang H, Chanda P, Alonso A, Bader JS, Arking DE. 2011. Gene-based tests of association. PLoS Genetics 7:e1002177.
  15. Rivera CG, Bader JS, Popel AS. 2011. Angiogenesis-associated crosstalk between collagens, CXC chemokines, and thrombospondin domain-containing proteins. Ann Biomed Eng. Aug;39(8):2213-22. PubMed PMID: 21590489; PubMed Central PMCID: PMC3150481.
  16. Park Y, Bader JS. 2011. Resolving the structure of interactomes with hierarchical agglomerative clustering. BMC Bioinformatics. 2011. 12: S44.
  17. Zou B, Yu H, Babcock JJ, Chanda P, Bader JS, McManus OB, Li M. 2010. Profiling diverse compounds by flux- and electrophysiology-based primary screens for inhibition of human Ether-à-go-go related gene potassium channels. Assay Drug Dev Technol. Dec;8(6):743-54. PubMed PMID: 21158688; PubMed Central PMCID: PMC3002177.
  18. Zhong J, Krawczyk SA, Chaerkady R, Huang H, Goel R, Bader JS, Wong GW, Corkey BE, Pandey A. 2010. Temporal profiling of the secretome during adipogenesis in humans. J Proteome Res. 9(10):5228-38. PubMed PMID: 20707391; PubMed Central PMCID: PMC2948433.
  19. Veeramani B, Bader JS. 2010. Predicting functional associations from metabolism using bi-partite network algorithms. BMC Syst Biol. Jul 14;4:95. PMID: 20630077; PMCID: PMC2919484.
  20. Richardson SM, Olson BS, Dymond JS, Burns R, Chandrasegaran S, Boeke JD, Shehu A, Bader JS. 2010. Automated Design of Assemblable, Modular Synthetic Chromosomes. In Parallel Processing and Applied Mathematics (PPAM), 8th International Conference, Lecture Notes in Computer Science. 6068:280-289.
  21. Richardson SM, Nunley PW, Yarrington RM, Boeke JD, Bader JS. 2010. GeneDesign 3.0 is an updated synthetic biology toolkit. Nucleic Acids Res. 2010 May;38(8):2603-6. PMID: 20211837; PMCID: PMC2860129.
  22. Lee PA, Dymond JS, Scheifele LZ, Richardson SM, Foelber K, Boeke JD, Bader JS. 2010. CloneQC: Lightweight sequence verification for synthetic biology. Nucleic Acids Res. May;38(8):2617-23. PMID: 20211841; PMCID: PMC2860120.
  23. Rivera CG, Vakhil R, Bader JS. 2010. NeMo: Network module identification in Cytoscape. BMC Bioinformatics. Jan 18; 11 Suppl. 1:S61
  24. Park Y, Moore C, Bader JS. 2010. Dynamic networks from hierarchical Bayesian graph clustering. PLoS ONE. 5(1): e8118. doi:10.1371/journal.pone.0008118
  25. Kut C, Golkhou V, Bader JS. 2009. Analytical approximations for the amplitude and period of a relaxation oscillator. BMC Systems Biology. 3:6.
  26. 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. 19: 674-681.
  27. Huang H, Bader JS. 2009. Precision and recall estimates for two-hybrid screens. Bioinformatics. 25: 372-378.
  28. Czar MJ, Anderson JC, Bader JS, Peccoud J. 2009. Gene synthesis demystified. Trends in Biotechnology. 27: 63-72.
  29. Dymond J, 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.
  30. Veeramani B, Bader JS. 2009. Metabolic flux correlations, genetic interactions and disease. Journal of Computational Biology. 16: 291-302.
  31. 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: 1991-2004.
  32. 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: 1066-1078.
  33. Guha U, Chaerkady R, Marimuthu A, Patterson AS, Kashyap MK, Harsha HC, Sato M, Bader JS, Lash AE, Minna JD, Pandey A, Varmus HE. 2008. Comparisons of tyrosine phosphorylated proteins in cells expressing lung cancer-specific alleles of EGFR and KRAS. Proc Natl Acad Sci USA. 105: 14112-14117.
  34. Lin YY, Qi Y, Lu JY, Yuan DS, Zhao Y, Bader JS, Boeke JD. 2008. A comprehensive synthetic interaction network governing yeast histone acetylation and deacetylation. Genes and Develop. 22: 2062-2074.
  35. Pan X, Yuan D, Ye P, Bader J, 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. 8: 349-50.
  36. Mathivanan S, (5 authors), Bader JS, (151 authors), Pandey A. 2008. Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26: 164-167.
  37. Huang H, Jedynak B, Bader JS. 2007. Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Computational Biology 3: e214.
  38. Huang H, Zhang LV, Roth FP, Bader JS. 2007. Probabilistic paths for protein complex inference. Springer Lecture Notes in Computer Science, Lecture Notes in Bioinformatics: RECOMB 2006 Satellite Workshops on Systems Biology and Computational Proteomics. 4532: 14-28.
  39. Liu LA, Bader JS. 2007. Ab initio prediction of transcription factor binding sites. Pacific Symposium on Biocomputing. 12: 484-495.
  40. 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. 2007. A systems biology analysis of the Drosophila phagosome. Nature. 445:95-101.
  41. Liu LA, Bader JS. 2006. Decoding transcriptional regulatory interactions. Physica D Nonlinear Phenomena. 224:174-181.
  42. 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. Proc. Natl. Acad. Sci. USA 103: 9773-9778.
  43. Dorer MS, Kirton D, Bader JS, Isberg RR. 2006. RNA Interference Analysis of Legionella in Drosophila Cells: Exploitation of Early Secretory Apparatus Dynamics. PLoS Pathogens. 2: e34.
  44. 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. Nature Genetics. 2006. 38:285-293.
  45. Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD. 2006. Global synthetic-lethality analysis and yeast functional profiling. Trends Genet. 22:56-63.
  46. 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.
  47. 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.
  48. 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 2005.0026
  49. 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.
  50. 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.
  51. 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. Molecular Cell. 16: 487-496.
  52. 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.
  53. Bader JS, Chaudhuri A, Rothberg JM, Chant J. 2004. Gaining confidence in high-throughput protein interaction networks. Nature Biotechnology. 22: 78-85.
  54. Giot L, Bader JS (contributing equally), 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.
  55. Bader JS. 2003. Greedily building protein networks with confidence. Bioinformatics. 19: 1869-1874.
  56. 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.
  57. Bader JS, Sham P. 2002. Family-based association tests for quantitative traits using pooled DNA. European Journal of Human Genetics. 10: 868-876.
  58. Jawaid A, Bader JS, Purcell S, Cherny SS, Sham P. Feb 2002. Optimal selection strategies for QTL mapping using pooled DNA samples. European Journal of Human Genetics. 10:125-132.
  59. 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.
  60. Bader JS. The relative power of SNPs and haplotype as genetic markers for association tests. Pharmacogenomics. 2001 Feb;2(1):11-24. PubMed PMID: 11258193.
  61. Bader JS, Bansal A, Sham P. 2001. Efficient SNP-based tests of association for quantitative phenotypes using pooled DNA. Genescreen. 1:143-150.
  62. 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.
  63. Bader JS, Hammond RW, Henck SA, Deem MW, McDermott GA, Bustillo JM, Simpson JW, Mulhern GT, Rothberg JM. Nov 1999. DNA transport by a micromachined Brownian ratchet device. Proceedings of the National Academy of Sciences of the United States of America. 96:13165-13169.
  64. Bader JS, Cortis CM, Berne BJ. 1997. Solvation and reorganization energies in polarizable molecular and continuum solvents. Journal of Chemical Physics. 106:2372-2387.
  65. 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.
  66. 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.
  67. Deem MW, Bader JS. 1996. A configurational bias Monte Carlo method for linear and cyclic peptides. Molecular Physics. 87:1245-1260.
  68. Rick SW, Stuart SJ, Bader JS, Berne BJ. 1995. Fluctuating charge force fields for aqueous solutions. Journal of Molecular Liquids. 65:31-40.
  69. 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.
  70. 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.
  71. Bader JS, Berne BJ. 1994. Quantum and classical relaxation rates from classical simulations. Journal of Chemical Physics. 100:8359-8366.
  72. Pollak E, Bader JS, Berne BJ, Talkner P. 1993. Theory of correlated hops in surface diffusion. Physical Review Letters. 70:3299-3302.
  73. 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.
  74. Bader JS, Kuharski RA, Chandler D. 1990. Role of nuclear tunneling in aqueous ferrous-ferric electron transfer. Journal of Chemical Physics. 93:230-236.
  75. Bader JS, Chander D. 1989. Computer simulation of photochemically induced electron transfer. Chemical Physics Letters. 157:501-504.
  76. 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.

Book Chapters and Invited Publications

  1. Bader JS. 2011. Meeting report: Grand network convergence. Genome Biology 12: 306.
  2. Bader JS. 2009. New connections, new components, real dynamics. Science Signaling 2: pe48.
  3. Bader JS. 2008. Systems approaches for pharmacogenetics and pharmacogenomics. Pharmacogenomics 9: 257-262.
  4. Liu LA, Bader JS. 2009. Structure-based ab initio prediction of transcription factor binding sites. In Jason McDermott, Ram Samudrala, and Roger Bumgarner, editors, Computational Systems Biology. Humana Press. Methods Mol. Biol. 541: 1-19.
  5. Bader JS, Chant J. 2006. When proteomes collide. Science 311: 187-188.
  6. Bader JS. 2005. Functional inference from probabilistic protein interaction networks. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. ed. MJ Dunn and RL Winslow. John Wiley & Sons.
  7. Bader JS. 2005. The Drosophila protein interaction network may be neither power-law nor scale-free. In Power Laws, Scale-Free Networks and Genome Biology, ed. EV Koonin, Landes / Eurekah Bioscience

 

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