 Joel Bader, Ph.D. Additional Information |
Key Publications
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. [Epub ahead of print] PubMed Link
HOT PAPER!
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
HOT PAPER!
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
HOT PAPER!
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
HOT PAPER!
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
