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Joel Bader, Ph.D.: Key Publications

Joel Bader, Ph.D. Joel Bader, Ph.D.

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Key Publications

Park Y, Bader JS. (2012). How networks change with time. Bioinformatics. 28, i40-i48.  PubMed Link

Lin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z, Lu JY, Khor CN, Lin CL, Bader JS, Irizarry R, Boeke JD. (2012). Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 482, 251-255.  PubMed Link

Karchin R, Ochs MF, Stuart JM, Bader JS. (2012). Identification of aberrant pathway and network activity from high-throughput data. Pac Symp Biocomput. 17, 1-6.  PubMed Link

Rivera CG, Mellberg S, Claesson-Welsh L, Bader JS, Popel AS. (2011). Analysis of VEGF--a regulated gene expression in endothelial cells to identify genes linked to angiogenesis. PLoS One. 6, e24887.  PubMed Link

Rivera CG, Bader JS, Popel AS. (2011). Angiogenesis-associated crosstalk between collagens, CXC chemokines, and thrombospondin domain-containing proteins. Ann Biomed Eng. 39, 2213-2222.  PubMed Link

Bader JS. (2011). Grand network convergence. Genome Biol. 12, 306.  PubMed Link

Rivera CG, Vakil R, Bader JS. (2010). NeMo: Network Module identification in Cytoscape. BMC Bioinformatics. 11 Suppl 1, S61.  PubMed Link

Park Y, Moore C, Bader JS. (2010). Dynamic networks from hierarchical bayesian graph clustering. PLoS One. 5, e8118.  PubMed Link

Bader JS. (2009). New connections, new components, real dynamics. Sci Signal. 2, pe48.  PubMed Link

Huang H, Bader JS. (2009). Precision and recall estimates for two-hybrid screens. Bioinformatics. 25, 372-378.  PubMed Link

Veeramani B, Bader JS. (2009). Metabolic flux correlations, genetic interactions, and disease. J Comput Biol. 16, 291-302.  PubMed Link

Kut C, Golkhou V, Bader JS. (2009). Analytical approximations for the amplitude and period of a relaxation oscillator. BMC Syst Biol. 3, 6.  PubMed Link

Huang H, Maertens AM, Hyland E, Dai J, Norris A, Boeke JD, Bader JS. (2009). HistoneHits: a database for histone mutations and their phenotypes. Genome Res. 19, 674-681.  PubMed Link

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 Res.18, 1991-2004.  PubMed Link

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, et al. (2008). Human Proteinpedia enables sharing of human protein data. Nature Biotechnology. 26, 164-167.  PubMed Link

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.  PubMed Link

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 Res. 8, 349-350.  PubMed Link

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 Dev. 22, 2062-2074.  PubMed Link

Huang J, Jedynak BM, Bader JS. (2007). Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput Biol. 3, e214.  PubMed Link

Liu LA, Bader JS. (2007). Ab initio prediction of transcription factor binding sites.  Pac. Symp. Biocomput. 12, 484-495.  PubMed Link

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.  PubMed Link

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.

Bader JS, Chant J. (2006). Systems biology. When proteomes collide. Science. 311, 187-188.  PubMed Link

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. Proceedings of the National Academy of Sciences, USA. 103, 9773-9778.  PubMed Link

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.  PubMed Link

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. 38, 285-293.  PubMed Link

Liu LA and Bader JS. (2006). Decoding transcriptional regulatory interactions.  Physica D Nonlinear Phenomena. 224, 174-181.  PubMed Link

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.  PubMed Link

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.  PubMed Link

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. 10, 1038.  PubMed Link

Marguiles M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature. 437, 376-380.  PubMed Link

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.  PubMed Link

Bader JS, Chaudhuri A, Rothberg JM, Chant J. (2004). Gaining confidence in high-throughput protein interaction networks. Nat. Biotechnol. 22, 78-85.  PubMed Link

Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, et al. (2003). A protein interaction map of Drosophila melanogaster. Science 301, 1727-1736.  PubMed Link

Bader JS. (2003). Greedily building protein networks with confidence. Bioinformatics 19, 1869-1874.  PubMed Link

Bader JS, Sham P. (2002). Family-based association tests for quantitative traits using pooled DNA.  Eur. J. Hum. Genet. 10, 870-878.  PubMed Link

Sham P, Bader JS, Craig I, O’Donovan M and Owen M. (2002). DNA Pooling: a tool for large-scale association studies. Nat. Rev. Genet. 3, 862-871.  PubMed Link

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