2007 | 2006 | 2005 | 2004 | 2003

2005.1: Greenstein, A. E., C. Grundner, N. Echols, L. M. Gay, T. N. Lombana, C. A. Miecskowski, K. E. Pullen, P. Y. Sung and T. Alber (2005). "Structure/function studies of Ser/Thr and Tyr protein phosphorylation in Mycobacterium tuberculosis." J Mol Microbiol Biotechnol 9(3-4): 167-81.

2005.2: Grundner, C., L. M. Gay and T. Alber (2005). "Mycobacterium tuberculosis serine/threonine kinases PknB, PknD, PknE, and PknF phosphorylate multiple FHA domains." Protein Sci 14(7): 1918-21.

2005.3: Grundner, C., H. L. Ng and T. Alber (2005). "Mycobacterium tuberculosis protein tyrosine phosphatase PtpB structure reveals a diverged fold and a buried active site." Structure 13(11): 1625-34.

2005.4: Alm, E. J., K. H. Huang, M. N. Price, R. P. Koche, K. Keller, I. L. Dubchak and A. P. Arkin (2005). "The MicrobesOnline Web site for comparative genomics." Genome Res 15(7): 1015-22.

2005.5: Flaherty, P., G. Giaever, J. Kumm, M. I. Jordan and A. P. Arkin (2005). "A latent variable model for chemogenomic profiling." Bioinformatics 21(15): 3286-93.

2005.6: Lee, W., R. P. St Onge, M. Proctor, P. Flaherty, M. I. Jordan, A. P. Arkin, R. W. Davis, C. Nislow and G. Giaever (2005). "Genome-wide requirements for resistance to functionally distinct DNA-damaging agents." PLoS Genet 1(2): e24.

2005.7: Liu, Y., W. Gao, Y. Wang, L. Wu, X. Liu, T. Yan, E. Alm, A. Arkin, D. K. Thompson, M. W. Fields and J. Zhou (2005). "Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions." J Bacteriol 187(7): 2501-7.

2005.8: Price, M. N., E. J. Alm and A. P. Arkin (2005). "Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication." Nucleic Acids Res 33(10): 3224-34.

2005.9: Price, M. N., K. H. Huang, E. J. Alm and A. P. Arkin (2005). "A novel method for accurate operon predictions in all sequenced prokaryotes." Nucleic Acids Res 33(3): 880-92.

2005.10: Price, M. N., K. H. Huang, A. P. Arkin and E. J. Alm (2005). "Operon formation is driven by co-regulation and not by horizontal gene transfer." Genome Res 15(6): 809-19.

2005.11: Rao, C. V., J. R. Kirby and A. P. Arkin (2005). "Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles." Phys Biol 2(3): 148-58.

2005.12: Rodionov, D. A., I. L. Dubchak, A. P. Arkin, E. J. Alm and M. S. Gelfand (2005). "Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks." PLoS Comput Biol 1(5): e55.

2005.13: Samoilov, M., S. Plyasunov and A. P. Arkin (2005). "Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations." Proc Natl Acad Sci U S A 102(7): 2310-5.

2005.14: Schwartz, P., D. Adalsteinsson, P. Colella, A. P. Arkin and M. Onsum (2005). "Numerical computation of diffusion on a surface." Proc Natl Acad Sci U S A 102(32): 11151-6.

2005.15: Weinberger, L. S., J. C. Burnett, J. E. Toettcher, A. P. Arkin and D. V. Schaffer (2005). "Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity." Cell 122(2): 169-82.

2005.16: Wolf, D. M., V. V. Vazirani and A. P. Arkin (2005). "A microbial modified prisoner's dilemma game: how frequency-dependent selection can lead to random phase variation." J Theor Biol 234(2): 255-62.

2005.17: Wolf, D. M., V. V. Vazirani and A. P. Arkin (2005). "Diversity in times of adversity: probabilistic strategies in microbial survival games." J Theor Biol 234(2): 227-53.

2005.18: Akey, D. L. and J. M. Berger (2005). "Structure of the nuclease domain of ribonuclease III from M. tuberculosis at 2.1 A." Protein Sci 14(10): 2744-50.

2005.19: Corbett, K. D. and J. M. Berger (2005). "Structural dissection of ATP turnover in the prototypical GHL ATPase TopoVI." Structure 13(6): 873-82.

2005.20: Corbett, K. D., A. J. Schoeffler, N. D. Thomsen and J. M. Berger (2005). "The structural basis for substrate specificity in DNA topoisomerase IV." J Mol Biol 351(3): 545-61.

2005.21: Corn, J. E., P. J. Pease, G. L. Hura and J. M. Berger (2005). "Crosstalk between primase subunits can act to regulate primer synthesis in trans." Mol Cell 20(3): 391-401.

2005.22: Cunningham, E. L. and J. M. Berger (2005). "Unraveling the early steps of prokaryotic replication." Curr Opin Struct Biol 15(1): 68-76.

2005.23: Fennell-Fezzie, R., S. D. Gradia, D. Akey and J. M. Berger (2005). "The MukF subunit of Escherichia coli condensin: architecture and functional relationship to kleisins." Embo J 24(11): 1921-30.

2005.24: Schoeffler, A. J. and J. M. Berger (2005). "Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism." Biochem Soc Trans 33(Pt 6): 1465-70.

2005.25: Skordalakes, E., A. P. Brogan, B. S. Park, H. Kohn and J. M. Berger (2005). "Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin." Structure 13(1): 99-109.

2005.26: van Zwet, E. W., K. J. Kechris, P. J. Bickel and M. B. Eisen (2005). "Estimating motifs under order restrictions." Stat Appl Genet Mol Biol 4: Article1.

2005.27: Brem, R. B. and L. Kruglyak (2005). "The landscape of genetic complexity across 5,700 gene expression traits in yeast." Proc Natl Acad Sci U S A 102(5): 1572-7.

2005.28: Brem, R. B., J. D. Storey, J. Whittle and L. Kruglyak (2005). "Genetic interactions between polymorphisms that affect gene expression in yeast." Nature 436(7051): 701-3.

2005.29: Ronald, J., R. B. Brem, J. Whittle and L. Kruglyak (2005). "Local regulatory variation in Saccharomyces cerevisiae." PLoS Genet 1(2): e25.

2005.30: Blanchette, M., R. E. Green, S. E. Brenner and D. C. Rio (2005). "Global analysis of positive and negative pre-mRNA splicing regulators in Drosophila." Genes Dev 19(11): 1306-14.

2005.31: Bourne, P. E., S. E. Brenner and M. B. Eisen (2005). "PLoS Computational Biology: a new community journal." PLoS Comput Biol 1(1): e4.

2005.32: Carninci, P., T. Kasukawa, S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. E. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, L. Baxter, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. Krishnan, A. Kruger, S. K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, D. L Crooks, G. E., R. E. Green and S. E. Brenner (2005). "Pairwise alignment incorporating dipeptide covariation." Bioinformatics 21(19): 3704-10.

2005.33: Engelhardt, B. E., M. I. Jordan, K. E. Muratore and S. E. Brenner (2005). "Protein molecular function prediction by Bayesian phylogenomics." PLoS Comput Biol 1(5): e45.

2005.34: Hendrix, D. K., S. E. Brenner and S. R. Holbrook (2005). "RNA structural motifs: building blocks of a modular biomolecule." Q Rev Biophys 38(3): 221-43.

2005.35: Kim, S. H., D. H. Shin, J. Liu, V. Oganesyan, S. Chen, Q. S. Xu, J. S. Kim, D. Das, U. Schulze-Gahmen, S. R. Holbrook, E. L. Holbrook, B. A. Martinez, N. Oganesyan, A. DeGiovanni, Y. Lou, M. Henriquez, C. Huang, J. Jancarik, R. Pufan, I. G. Choi, J. M. Chandonia, J. Hou, B. Gold, H. Yokota, S. E. Brenner, P. D. Adams and R. Kim (2005). "Structural genomics of minimal organisms and protein fold space." J Struct Funct Genomics 6(2-3): 63-70.

2005.36: Mitchell, C. E., S. E. Brenner and S. V. Ley (2005). "A versatile organocatalyst for the asymmetric conjugate addition of nitroalkanes to enones." Chem Commun (Camb)(42): 5346-8.

2005.37: Price, G. A., G. E. Crooks, R. E. Green and S. E. Brenner (2005). "Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap." Bioinformatics 21(20): 3824-31.

2005.38: Barrier, A., P. Y. Boelle, A. Lemoine, C. Tse, D. Brault, F. Chiappini, F. Lacaine, S. Houry, M. Huguier, A. Flahault and S. Dudoit (2005). "Gene expression profiling of nonneoplastic mucosa may predict clinical outcome of colon cancer patients." Dis Colon Rectum 48(12): 2238-48.

2005.39: Barrier, A., A. Lemoine, P. Y. Boelle, C. Tse, D. Brault, F. Chiappini, J. Breittschneider, F. Lacaine, S. Houry, M. Huguier, M. J. Van der Laan, T. Speed, B. Debuire, A. Flahault and S. Dudoit (2005). "Colon cancer prognosis prediction by gene expression profiling." Oncogene 24(40): 6155-64.

2005.40: Barrier, A., N. Olaya, F. Chiappini, F. Roser, O. Scatton, C. Artus, B. Franc, S. Dudoit, A. Flahault, B. Debuire, D. Azoulay and A. Lemoine (2005). "Ischemic preconditioning modulates the expression of several genes, leading to the overproduction of IL-1Ra, iNOS, and Bcl-2 in a human model of liver ischemia-reperfusion." Faseb J 19(12): 1617-26.

2005.41: van der Laan, M. J., M. D. Birkner and A. E. Hubbard (2005). "Empirical Bayes and resampling based multiple testing procedure controlling tail probability of the proportion of false positives." Stat Appl Genet Mol Biol 4: Article29.

2005.42: Bourne, P. E., S. E. Brenner and M. B. Eisen (2005). "PLoS Computational Biology: a new community journal." PLoS Comput Biol 1(1): e4.

2005.43: Fraser, H. B., P. Khaitovich, J. B. Plotkin, S. Paabo and M. B. Eisen (2005). "Aging and gene expression in the primate brain." PLoS Biol 3(9): e274.

2005.44: Levy, O., J. L. Ptacin, P. J. Pease, J. Gore, M. B. Eisen, C. Bustamante and N. R. Cozzarelli (2005). "Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase." Proc Natl Acad Sci U S A 102(49): 17618-23.

2005.45: Nix, D. A. and M. B. Eisen (2005). "GATA: a graphic alignment tool for comparative sequence analysis." BMC Bioinformatics 6: 9.

2005.46: Salzberg, S. L., J. C. Dunning Hotopp, A. L. Delcher, M. Pop, D. R. Smith, M. B. Eisen and W. C. Nelson (2005). "Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species." Genome Biol 6(7): 402.

2005.47: Salzberg, S. L., J. C. Hotopp, A. L. Delcher, M. Pop, D. R. Smith, M. B. Eisen and W. C. Nelson (2005). "Serendipitous discovery of Wolbachia genomes in multiple Drosophila species." Genome Biol 6(3): R23.

2005.48: van Zwet, E. W., K. J. Kechris, P. J. Bickel and M. B. Eisen (2005). "Estimating motifs under order restrictions." Stat Appl Genet Mol Biol 4: Article1.

2005.49: Wall, D. P., A. E. Hirsh, H. B. Fraser, J. Kumm, G. Giaever, M. B. Eisen and M. W. Feldman (2005). "Functional genomic analysis of the rates of protein evolution." Proc Natl Acad Sci U S A 102(15): 5483-8.

2005.50: Fawzi, N. L., V. Chubukov, L. A. Clark, S. Brown and T. Head-Gordon (2005). "Influence of denatured and intermediate states of folding on protein aggregation." Protein Sci 14(4): 993-1003.

2005.51: Marianayagam, N. J., N. L. Fawzi and T. Head-Gordon (2005). "Protein folding by distributed computing and the denatured state ensemble." Proc Natl Acad Sci U S A 102(46): 16684-9.

2005.52: Russo, D., R. K. Murarka, J. R. Copley and T. Head-Gordon (2005). "Molecular view of water dynamics near model peptides." J Phys Chem B Condens Matter Mater Surf Interfaces Biophys 109(26): 12966-75.

2005.53: Graham, K. L., F. E. Fleming, P. Halasz, M. J. Hewish, H. S. Nagesha, I. H. Holmes, Y. Takada and B. S. Coulson (2005). "Rotaviruses interact with alpha4beta7 and alpha4beta1 integrins by binding the same integrin domains as natural ligands." J Gen Virol 86(Pt 12): 3397-408.

2005.54: Holmes, I. (2005). "Accelerated probabilistic inference of RNA structure evolution." BMC Bioinformatics 6: 73.

2005.55: Holmes, I. (2005). "Using evolutionary Expectation Maximization to estimate indel rates." Bioinformatics 21(10): 2294-300.

2005.56: Kalawsky, R. S., S. P. Nee, I. Holmes and P. V. Coveney (2005). "A grid-enabled lightweight computational steering client: a .NET PDA implementation." Philos Transact A Math Phys Eng Sci 363(1833): 1885-94.

2005.57: Zhao, X., H. Huang and T. P. Speed (2005). "Finding short DNA motifs using permuted Markov models." J Comput Biol 12(6): 894-906.

2005.58: Bradman, A., J. Chevrier, I. Tager, M. Lipsett, J. Sedgwick, J. Macher, A. B. Vargas, E. B. Cabrera, J. M. Camacho, R. Weldon, K. Kogut, N. P. Jewell and B. Eskenazi (2005). "Association of housing disrepair indicators with cockroach and rodent infestations in a cohort of pregnant Latina women and their children." Environ Health Perspect 113(12): 1795-801.

2005.59: Chen, Y. Q., N. P. Jewell, X. Lei and S. C. Cheng (2005). "Semiparametric estimation of proportional mean residual life model in presence of censoring." Biometrics 61(1): 170-8.

2005.60: Engelhardt, B. E., M. I. Jordan, K. E. Muratore and S. E. Brenner (2005). "Protein molecular function prediction by Bayesian phylogenomics." PLoS Comput Biol 1(5): e45.

2005.61: Flaherty, P., G. Giaever, J. Kumm, M. I. Jordan and A. P. Arkin (2005). "A latent variable model for chemogenomic profiling." Bioinformatics 21(15): 3286-93.

2005.62: Gyaneshwar, P., O. Paliy, J. McAuliffe, A. Jones, M. I. Jordan and S. Kustu (2005). "Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation." Proc Natl Acad Sci U S A 102(9): 3453-8.

2005.63: Gyaneshwar, P., O. Paliy, J. McAuliffe, D. L. Popham, M. I. Jordan and S. Kustu (2005). "Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses." J Bacteriol 187(3): 1074-90.

2005.64: Lee, W., R. P. St Onge, M. Proctor, P. Flaherty, M. I. Jordan, A. P. Arkin, R. W. Davis, C. Nislow and G. Giaever (2005). "Genome-wide requirements for resistance to functionally distinct DNA-damaging agents." PLoS Genet 1(2): e24.

2005.65: McAuliffe, J. D., M. I. Jordan and L. Pachter (2005). "Subtree power analysis and species selection for comparative genomics." Proc Natl Acad Sci U S A 102(22): 7900-5.

2005.66: Sharan, R., T. Ideker, B. Kelley, R. Shamir and R. M. Karp (2005). "Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data." J Comput Biol 12(6): 835-46.

2005.67: Sharan, R., S. Suthram, R. M. Kelley, T. Kuhn, S. McCuine, P. Uetz, T. Sittler, R. M. Karp and T. Ideker (2005). "Conserved patterns of protein interaction in multiple species." Proc Natl Acad Sci U S A 102(6): 1974-9.

2005.68: Card, G. L., L. Blasdel, B. P. England, C. Zhang, Y. Suzuki, S. Gillette, D. Fong, P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. Milburn, S. H. Kim, J. Schlessinger and K. Y. Zhang (2005). "A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design." Nat Biotechnol 23(2): 201-7.

2005.69: Chen, S., A. F. Yakunin, M. Proudfoot, R. Kim and S. H. Kim (2005). "Structural and functional characterization of a 5,10-methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087)." Proteins 61(2): 433-43.

2005.70: Hou, J., S. R. Jun, C. Zhang and S. H. Kim (2005). "Global mapping of the protein structure space and application in structure-based inference of protein function." Proc Natl Acad Sci U S A 102(10): 3651-6.

2005.71: Kim, J. S., A. DeGiovanni, J. Jancarik, P. D. Adams, H. Yokota, R. Kim and S. H. Kim (2005). "Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications." Proc Natl Acad Sci U S A 102(9): 3248-53.

2005.72: Kim, S. H., D. H. Shin, J. Liu, V. Oganesyan, S. Chen, Q. S. Xu, J. S. Kim, D. Das, U. Schulze-Gahmen, S. R. Holbrook, E. L. Holbrook, B. A. Martinez, N. Oganesyan, A. DeGiovanni, Y. Lou, M. Henriquez, C. Huang, J. Jancarik, R. Pufan, I. G. Choi, J. M. Chandonia, J. Hou, B. Gold, H. Yokota, S. E. Brenner, P. D. Adams and R. Kim (2005). "Structural genomics of minimal organisms and protein fold space." J Struct Funct Genomics 6(2-3): 63-70.

2005.73: Liu, J., C. Huang, D. H. Shin, H. Yokota, J. Jancarik, J. S. Kim, P. D. Adams, R. Kim and S. H. Kim (2005). "Crystal structure of a heat-inducible transcriptional repressor HrcA from Thermotoga maritima: structural insight into DNA binding and dimerization." J Mol Biol 350(5): 987-96.

2005.74: Liu, J., Y. Lou, H. Yokota, P. D. Adams, R. Kim and S. H. Kim (2005). "Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters." J Biol Chem 280(16): 15960-6.

2005.75: Liu, J., Y. Lou, H. Yokota, P. D. Adams, R. Kim and S. H. Kim (2005). "Crystal structures of an NAD kinase from Archaeoglobus fulgidus in complex with ATP, NAD, or NADP." J Mol Biol 354(2): 289-303.

2005.76: Liu, J., N. Oganesyan, D. H. Shin, J. Jancarik, H. Yokota, R. Kim and S. H. Kim (2005). "Structural characterization of an iron-sulfur cluster assembly protein IscU in a zinc-bound form." Proteins 59(4): 875-81.

2005.77: Oganesyan, N., S. H. Kim and R. Kim (2005). "On-column protein refolding for crystallization." J Struct Funct Genomics 6(2-3): 177-82.

2005.78: Oganesyan, V., C. Huang, P. D. Adams, J. Jancarik, H. A. Yokota, R. Kim and S. H. Kim (2005). "Structure of a NAD kinase from Thermotoga maritima at 2.3 A resolution." Acta Crystallograph Sect F Struct Biol Cryst Commun 61(Pt 7): 640-6.

2005.79: Oganesyan, V., N. Oganesyan, P. D. Adams, J. Jancarik, H. A. Yokota, R. Kim and S. H. Kim (2005). "Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus." J Bacteriol 187(12): 4238-44.

2005.80: Rodier, F., S. H. Kim, T. Nijjar, P. Yaswen and J. Campisi (2005). "Cancer and aging: the importance of telomeres in genome maintenance." Int J Biochem Cell Biol 37(5): 977-90.

2005.81: Schulze-Gahmen, U., S. Aono, S. Chen, H. Yokota, R. Kim and S. H. Kim (2005). "Structure of the hypothetical Mycoplasma protein MPN555 suggests a chaperone function." Acta Crystallogr D Biol Crystallogr 61(Pt 10): 1343-7.

2005.82: Shin, D. H., N. Oganesyan, J. Jancarik, H. Yokota, R. Kim and S. H. Kim (2005). "Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum." J Biol Chem 280(18): 18326-35.

2005.83: Sims, G. E., I. G. Choi and S. H. Kim (2005). "Protein conformational space in higher order phi-Psi maps." Proc Natl Acad Sci U S A 102(3): 618-21.

2005.84: Xu, Q. S., J. Jancarik, Y. Lou, K. Kuznetsova, A. F. Yakunin, H. Yokota, P. Adams, R. Kim and S. H. Kim (2005). "Crystal structures of a phosphotransacetylase from Bacillus subtilis and its complex with acetyl phosphate." J Struct Funct Genomics 6(4): 269-79.

2005.85: Cecconi, C., E. A. Shank, C. Bustamante and S. Marqusee (2005). "Direct observation of the three-state folding of a single protein molecule." Science 309(5743): 2057-60.

2005.86: Maxwell, K. L., D. Wildes, A. Zarrine-Afsar, M. A. De Los Rios, A. G. Brown, C. T. Friel, L. Hedberg, J. C. Horng, D. Bona, E. J. Miller, A. Vallee-Belisle, E. R. Main, F. Bemporad, L. Qiu, K. Teilum, N. D. Vu, A. M. Edwards, I. Ruczinski, F. M. Poulsen, B. B. Kragelund, S. W. Michnick, F. Chiti, Y. Bai, S. J. Hagen, L. Serrano, M. Oliveberg, D. P. Raleigh, P. Wittung-Stafshede, S. E. Radford, S. E. Jackson, T. R. Sosnick, S. Marqusee, A. R. Davidson and K. W. Plaxco (2005). "Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins." Protein Sci 14(3): 602-16.

2005.87: Park, C. and S. Marqusee (2005). "Pulse proteolysis: a simple method for quantitative determination of protein stability and ligand binding." Nat Methods 2(3): 207-12.

2005.88: Liao, J. C., Y. J. Jeong, D. E. Kim, S. S. Patel and G. Oster (2005). "Mechanochemistry of t7 DNA helicase." J Mol Biol 350(3): 452-75.

2005.89: Oster, G. (2005). "Q & A. [interview]." Curr Biol 15(1): R5-7.

2005.90: Xing, J., J. C. Liao and G. Oster (2005). "Making ATP." Proc Natl Acad Sci U S A 102(46): 16539-46.

2005.91: Xing, J., H. Wang and G. Oster (2005). "From continuum Fokker-Planck models to discrete kinetic models." Biophys J 89(3): 1551-63.

2005.92: Chatterji, S. and L. Pachter (2005). "Large multiple organism gene finding by collapsed Gibbs sampling." J Comput Biol 12(6): 599-608.

2005.93: Chen, K. and L. Pachter (2005). "Bioinformatics for whole-genome shotgun sequencing of microbial communities." PLoS Comput Biol 1(2): 106-12.

2005.94: McAuliffe, J. D., M. I. Jordan and L. Pachter (2005). "Subtree power analysis and species selection for comparative genomics." Proc Natl Acad Sci U S A 102(22): 7900-5.

2005.95: Davies, B. S., H. S. Wang and J. Rine (2005). "Dual activators of the sterol biosynthetic pathway of Saccharomyces cerevisiae: similar activation/regulatory domains but different response mechanisms." Mol Cell Biol 25(16): 7375-85.

2005.96: Lynch, P. J., H. B. Fraser, E. Sevastopoulos, J. Rine and L. N. Rusche (2005). "Sum1p, the origin recognition complex, and the spreading of a promoter-specific repressor in Saccharomyces cerevisiae." Mol Cell Biol 25(14): 5920-32.

2005.97: Olaharski, A. J., J. Rine, B. L. Marshall, J. Babiarz, L. Zhang, E. Verdin and M. T. Smith (2005). "The flavoring agent dihydrocoumarin reverses epigenetic silencing and inhibits sirtuin deacetylases." PLoS Genet 1(6): e77.

2005.98: Rine, J. (2005). "Cell biology. Twists in the tale of the aging yeast." Science 310(5751): 1124-5.

2005.99: Keys, D. N., B. I. Lee, A. Di Gregorio, N. Harafuji, J. C. Detter, M. Wang, O. Kahsai, S. Ahn, C. Zhang, S. A. Doyle, N. Satoh, Y. Satou, H. Saiga, A. T. Christian, D. S. Rokhsar, T. L. Hawkins, M. Levine and P. M. Richardson (2005). "A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis." Proc Natl Acad Sci U S A 102(3): 679-83.

2005.100: Mahony, S., D. Hendrix, A. Golden, T. J. Smith and D. S. Rokhsar (2005). "Transcription factor binding site identification using the self-organizing map." Bioinformatics 21(9): 1807-14.

2005.101: Brown, D., N. Krishnamurthy, J. M. Dale, W. Christopher and K. Sjolander (2005). "Subfamily hmms in functional genomics." Pac Symp Biocomput: 322-33.

2005.102: Chisholm, S. T., D. Dahlbeck, N. Krishnamurthy, B. Day, K. Sjolander and B. J. Staskawicz (2005). "Molecular characterization of proteolytic cleavage sites of the Pseudomonas syringae effector AvrRpt2." Proc Natl Acad Sci U S A 102(6): 2087-92.

2005.103: Fritz-Laylin, L. K., N. Krishnamurthy, M. Tor, K. V. Sjolander and J. D. Jones (2005). "Phylogenomic analysis of the receptor-like proteins of rice and Arabidopsis." Plant Physiol 138(2): 611-23.

2005.104: Middleton, R., K. Sjolander, N. Krishnamurthy, J. Foley and P. Zambryski (2005). "Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion." Proc Natl Acad Sci U S A 102(5): 1685-90.

2005.105: von Zychlinski, A., T. Kleffmann, N. Krishnamurthy, K. Sjolander, S. Baginsky and W. Gruissem (2005). "Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions." Mol Cell Proteomics 4(8): 1072-84.

2005.106: Novembre, J., A. P. Galvani and M. Slatkin (2005). "The geographic spread of the CCR5 Delta32 HIV-resistance allele." PLoS Biol 3(11): e339.

2005.107: Saunders, M. A., M. Slatkin, C. Garner, M. F. Hammer and M. W. Nachman (2005). "The extent of linkage disequilibrium caused by selection on G6PD in humans." Genetics 171(3): 1219-29.

2005.108: Slatkin, M. (2005). "Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations." Mol Ecol 14(1): 67-73.

2005.109: Wood, E. T., D. A. Stover, M. Slatkin, M. W. Nachman and M. F. Hammer (2005). "The beta -globin recombinational hotspot reduces the effects of strong selection around HbC, a recently arisen mutation providing resistance to malaria." Am J Hum Genet 77(4): 637-42.

2005.110: Barrier, A., A. Lemoine, P. Y. Boelle, C. Tse, D. Brault, F. Chiappini, J. Breittschneider, F. Lacaine, S. Houry, M. Huguier, M. J. Van der Laan, T. Speed, B. Debuire, A. Flahault and S. Dudoit (2005). "Colon cancer prognosis prediction by gene expression profiling." Oncogene 24(40): 6155-64.

2005.111: Zhao, X., H. Huang and T. P. Speed (2005). "Finding short DNA motifs using permuted Markov models." J Comput Biol 12(6): 894-906.

2005.112: Sturmfels, B. and S. Sullivant (2005). "Toric ideals of phylogenetic invariants." J Comput Biol 12(4): 457-81.

2005.113: Sturmfels, B. and S. Sullivant (2005). "Toric ideals of phylogenetic invariants." J Comput Biol 12(2): 204-28.

2005.114: Barrier, A., A. Lemoine, P. Y. Boelle, C. Tse, D. Brault, F. Chiappini, J. Breittschneider, F. Lacaine, S. Houry, M. Huguier, M. J. Van der Laan, T. Speed, B. Debuire, A. Flahault and S. Dudoit (2005). "Colon cancer prognosis prediction by gene expression profiling." Oncogene 24(40): 6155-64.

2005.115: Birkner, M. D., S. E. Sinisi and M. J. van der Laan (2005). "Multiple testing and data adaptive regression: an application to HIV-1 sequence data." Stat Appl Genet Mol Biol 4: Article8.

2005.116: Mukherjee, S., S. J. Roberts and M. J. van der Laan (2005). "Data-adaptive test statistics for microarray data." Bioinformatics 21 Suppl 2: ii108-ii114.

2005.117: van der Laan, M. J., M. D. Birkner and A. E. Hubbard (2005). "Empirical Bayes and resampling based multiple testing procedure controlling tail probability of the proportion of false positives." Stat Appl Genet Mol Biol 4: Article29.

2005.118: Xing, B. and M. J. van der Laan (2005). "A causal inference approach for constructing transcriptional regulatory networks." Bioinformatics 21(21): 4007-13.

2005.119: Xing, B. and M. J. van der Laan (2005). "A statistical method for constructing transcriptional regulatory networks using gene expression and sequence data." J Comput Biol 12(2): 229-46.