California Institute for Quantitative Biosciences (qb3)
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Research
Publications

2007 I 2006 I 2005 I 2004

  • 2007.1: Barth, P., T. Alber and P. B. Harbury (2007). "Accurate, conformation-dependent predictions of solvent effects on protein ionization constants." Proc Natl Acad Sci U S A 104(12): 4898-903.
  • 2007.2: Cellitti, J., M. Llinas, N. Echols, E. A. Shank, B. Gillespie, E. Kwon, S. M. Crowder, F. W. Dahlquist, T. Alber and S. Marqusee (2007). "Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment." Protein Sci 16(5): 842-51.
  • 2007.3: Greenstein, A. E., N. Echols, T. N. Lombana, D. S. King and T. Alber (2007). "Allosteric activation by dimerization of the PknD receptor Ser/Thr protein kinase from Mycobacterium tuberculosis." J Biol Chem 282(15): 11427-35.
  • 2007.4: Greenstein, A. E., J. A. MacGurn, C. E. Baer, A. M. Falick, J. S. Cox and T. Alber (2007). "M. tuberculosis Ser/Thr protein kinase D phosphorylates an anti-anti-sigma factor homolog." PLoS Pathog 3(4): e49.
  • 2007.5: Grundner, C., D. Perrin, R. Hooft van Huijsduijnen, D. Swinnen, J. Gonzalez, C. L. Gee, T. N. Wells and T. Alber (2007). "Structural basis for selective inhibition of Mycobacterium tuberculosis protein tyrosine phosphatase PtpB." Structure 15(4): 499-509.
  • 2007.6: Andrews, S. S. and A. P. Arkin (2007). "A mechanical explanation for cytoskeletal rings and helices in bacteria." Biophys J.
  • 2007.7: Kazakov, A. E., M. J. Cipriano, P. S. Novichkov, S. Minovitsky, D. V. Vinogradov, A. Arkin, A. A. Mironov, M. S. Gelfand and I. Dubchak (2007). "RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes." Nucleic Acids Res 35(Database issue): D407-12.
  • 2007.8: Mukhopadhyay, A., A. M. Redding, M. P. Joachimiak, A. P. Arkin, S. E. Borglin, P. S. Dehal, R. Chakraborty, J. T. Geller, T. C. Hazen, Q. He, D. C. Joyner, V. J. Martin, J. D. Wall, Z. K. Yang, J. Zhou and J. D. Keasling (2007). "Cell wide responses to low oxygen exposure in Desulfovibrio vulgaris Hildenborough." J Bacteriol.
  • 2007.9: Douglas, A. E., K. D. Corbett, J. M. Berger, G. McFadden and T. M. Handel (2007). "Structure of M11L: A myxoma virus structural homolog of the apoptosis inhibitor, Bcl-2." Protein Sci 16(4): 695-703.
  • 2007.10: Mott, M. L. and J. M. Berger (2007). "DNA replication initiation: mechanisms and regulation in bacteria." Nat Rev Microbiol 5(5): 343-54.
  • 2007.11: Lareau, L. F., M. Inada, R. E. Green, J. C. Wengrod and S. E. Brenner (2007). "Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements." Nature 446(7138): 926-9.
  • 2007.12: Yooseph, S., G. Sutton, D. B. Rusch, A. L. Halpern, S. J. Williamson, K. Remington, J. A. Eisen, K. B. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. S. Miller, H. Li, S. T. Mashiyama, M. P. Joachimiak, C. van Belle, J. M. Chandonia, D. A. Soergel, Y. Zhai, K. Natarajan, S. Lee, B. J. Raphael, V. Bafna, R. Friedman, S. E. Brenner, A. Godzik, D. Eisenberg, J. E. Dixon, S. S. Taylor, R. L. Strausberg, M. Frazier and J. C. Venter (2007). "The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families." PLoS Biol 5(3): e16.
  • 2007.13: Barrier, A., F. Roser, P. Y. Boelle, B. Franc, C. Tse, D. Brault, F. Lacaine, S. Houry, P. Callard, C. Penna, B. Debuire, A. Flahault, S. Dudoit and A. Lemoine (2007). "Prognosis of stage II colon cancer by non-neoplastic mucosa gene expression profiling." Oncogene 26(18): 2642-8.
  • 2007.14: Evans, S. N., Y. Shvets and M. Slatkin (2007). "Non-equilibrium theory of the allele frequency spectrum." Theor Popul Biol 71(1): 109-19.
  • 2007.15: Evans, S. N. and D. Steinsaltz (2007). "Damage segregation at fissioning may increase growth rates: A superprocess model." Theor Popul Biol 71(4): 473-90.
  • 2007.16: Fawzi, N. L., Y. Okabe, E. H. Yap and T. Head-Gordon (2007). "Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide." J Mol Biol 365(2): 535-50.
  • 2007.17: Head-Gordon, T. and S. W. Rick (2007). "Consequences of chain networks on thermodynamic, dielectric and structural properties for liquid water." Phys Chem Chem Phys 9(1): 83-91.
  • 2007.18: Johnson, M. E., T. Head-Gordon and A. A. Louis (2007). "Representability problems for coarse-grained water potentials." J Chem Phys 126(14): 144509.
  • 2007.19: Malardier-Jugroot, C. and T. Head-Gordon (2007). "Separable cooperative and localized translational motions of water confined by a chemically heterogeneous environment." Phys Chem Chem Phys 9(16): 1962-71.
  • 2007.20: Kosiol, C., I. Holmes and N. Goldman (2007). "An Empirical Codon Model for Protein Sequence Evolution." Mol Biol Evol.
  • 2007.21: Kim, K., S. Zhang, K. Jiang, L. Cai, I. B. Lee, L. J. Feldman and H. Huang (2007). "Measuring similarities between gene expression profiles through new data transformations." BMC Bioinformatics 8: 29.
  • 2007.22: Bollback, J. P. and J. P. Huelsenbeck (2007). "Clonal interference is alleviated by high mutation rates in large populations." Mol Biol Evol 24(6): 1397-406.
  • 2007.23: Huelsenbeck, J. P. and P. Andolfatto (2007). "Inference of population structure under a Dirichlet process model." Genetics 175(4): 1787-802.
  • 2007.24: Eskenazi, B., A. R. Marks, A. Bradman, K. Harley, D. B. Barr, C. Johnson, N. Morga and N. P. Jewell (2007). "Organophosphate pesticide exposure and neurodevelopment in young Mexican-American children." Environ Health Perspect 115(5): 792-8.
  • 2007.25: Jewell, N. P., X. Lei, A. C. Ghani, C. A. Donnelly, G. M. Leung, L. M. Ho, B. J. Cowling and A. J. Hedley (2007). "Non-parametric estimation of the case fatality ratio with competing risks data: an application to Severe Acute Respiratory Syndrome (SARS)." Stat Med 26(9): 1982-98.
  • 2007.26: Hannig, G., S. G. Bernier, J. G. Hoyt, B. Doyle, E. Clark, R. M. Karp, J. Lorusso and W. F. Westlin (2007). "Suppression of inflammation and structural damage in experimental arthritis through molecular targeted therapy with PPI-2458." Arthritis Rheum 56(3): 850-60.
  • 2007.27: Choi, I. G. and S. H. Kim (2007). "Global extent of horizontal gene transfer." Proc Natl Acad Sci U S A 104(11): 4489-94.
  • 2007.28: Das, D., H. Hyun, Y. Lou, H. Yokota, R. Kim and S. H. Kim (2007). "Crystal structure of a novel single-stranded DNA binding protein from Mycoplasma pneumoniae." Proteins 67(3): 776-82.
  • 2007.29: Das, D., Q. S. Xu, J. Y. Lee, I. Ankoudinova, C. Huang, Y. Lou, A. Degiovanni, R. Kim and S. H. Kim (2007). "Crystal structure of the multidrug efflux transporter AcrB at 3.1A resolution reveals the N-terminal region with conserved amino acids." J Struct Biol 158(3): 494-502.
  • 2007.30: Bunje, P. M. and D. R. Lindberg (2007). "Lineage divergence of a freshwater snail clade associated with post-Tethys marine basin development." Mol Phylogenet Evol 42(2): 373-87.
  • 2007.31: Cellitti, J., R. Bernstein and S. Marqusee (2007). "Exploring subdomain cooperativity in T4 lysozyme II: uncovering the C-terminal subdomain as a hidden intermediate in the kinetic folding pathway." Protein Sci 16(5): 852-62.
  • 2007.32: Cellitti, J., M. Llinas, N. Echols, E. A. Shank, B. Gillespie, E. Kwon, S. M. Crowder, F. W. Dahlquist, T. Alber and S. Marqusee (2007). "Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment." Protein Sci 16(5): 842-51.
  • 2007.33: Park, C., S. Zhou, J. Gilmore and S. Marqusee (2007). "Energetics-based protein profiling on a proteomic scale: identification of proteins resistant to proteolysis." J Mol Biol 368(5): 1426-37.
  • 2007.34: Young, T. A., E. Skordalakes and S. Marqusee (2007). "Comparison of proteolytic susceptibility in phosphoglycerate kinases from yeast and E. coli: modulation of conformational ensembles without altering structure or stability." J Mol Biol 368(5): 1438-47.
  • 2007.35: Sliusarenko, O., D. R. Zusman and G. Oster (2007). "Aggregation during fruiting body formation in Myxococcus xanthus is driven by reducing cell movement." J Bacteriol 189(2): 611-9.
  • 2007.36: Beerenwinkel, N., L. Pachter, B. Sturmfels, S. F. Elena and R. E. Lenski (2007). "Analysis of epistatic interactions and fitness landscapes using a new geometric approach." BMC Evol Biol 7: 60.
  • 2007.37: Chatterji, S. and L. Pachter (2007). "Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor." Genomics.
  • 2007.38: Pachter, L. (2007). "Interpreting the unculturable majority." Nat Methods 4(6): 479-80.
  • 2007.39: Schwartz, A. S. and L. Pachter (2007). "Multiple alignment by sequence annealing." Bioinformatics 23(2): e24-9.
  • 2007.40: Ashby, M. N., J. Rine, E. F. Mongodin, K. E. Nelson and D. Dimster-Denk (2007). "Serial Analysis of Ribosomal DNA and the Unexpected Dominance of Rare Members of Microbial Communities." Appl Environ Microbiol.
  • 2007.41: Jeong, H., I. Herskowitz, D. L. Kroetz and J. Rine (2007). "Function-altering SNPs in the human multidrug transporter gene ABCB1 identified using a Saccharomyces-based assay." PLoS Genet 3(3): e39.
  • 2007.42: Larroux, C., B. Fahey, S. M. Degnan, M. Adamski, D. S. Rokhsar and B. M. Degnan (2007). "The NK homeobox gene cluster predates the origin of Hox genes." Curr Biol 17(8): 706-10.
  • 2007.43: Prochnik, S. E., D. S. Rokhsar and A. A. Aboobaker (2007). "Evidence for a microRNA expansion in the bilaterian ancestor." Dev Genes Evol 217(1): 73-7.
  • 2007.44: Glanville, J. G., D. Kirshner, N. Krishnamurthy and K. Sjolander (2007). "Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis." Nucleic Acids Res.
  • 2007.45: Krishnamurthy, N., D. Brown and K. Sjolander (2007). "FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function." BMC Evol Biol 7 Suppl 1: S12.
  • 2007.46: Tor, M., D. Brown, A. Cooper, A. Woods-Tor, K. Sjolander, J. D. G. Jones and E. B. Holub (2007). "Arabidopsis downy mildew resistance gene RPP27 encodes a receptor-like protein similar to CLAVATA2 and tomato Cf-9." Plant Physiol 143(2): 1079.
  • 2007.47: Anderson, E. C. and M. Slatkin (2007). "Estimation of the number of individuals founding colonized populations." Evolution Int J Org Evolution 61(4): 972-83.
  • 2007.48: Evans, S. N., Y. Shvets and M. Slatkin (2007). "Non-equilibrium theory of the allele frequency spectrum." Theor Popul Biol 71(1): 109-19.
  • 2007.49: Hofreiter, M., S. Munzel, N. J. Conard, J. Pollack, M. Slatkin, G. Weiss and S. Paabo (2007). "Sudden replacement of cave bear mitochondrial DNA in the late Pleistocene." Curr Biol 17(4): R122-3.
  • 2007.50: Levy, N., X. Zhao, H. Tang, R. B. Jaffe, T. P. Speed and D. C. Leitman (2007). "Multiple Transcription Factor Elements Collaborate with ER{alpha} to Activate an Inducible Estrogen Response Element in the NKG2E gene." Endocrinology.
  • 2007.51: Qin, X., S. Ahn, T. P. Speed and G. M. Rubin (2007). "Global analyses of mRNA translational control during early Drosophila embryogenesis." Genome Biol 8(4): R63.
  • 2007.52: Beerenwinkel, N., L. Pachter, B. Sturmfels, S. F. Elena and R. E. Lenski (2007). "Analysis of epistatic interactions and fitness landscapes using a new geometric approach." BMC Evol Biol 7: 60.
  • 2007.53: Bembom, O., S. Keles and M. J. van der Laan (2007). "Supervised detection of conserved motifs in DNA sequences with cosmo." Stat Appl Genet Mol Biol 6: Article8.
  • 2007.54: Petersen, M. L., S. G. Deeks and M. J. van der Laan (2007). "Individualized treatment rules: Generating candidate clinical trials." Stat Med.
  • 2007.55: Sinisi, S. E., E. C. Polley, M. L. Petersen, S. Y. Rhee and M. J. van der Laan (2007). "Super learning: an application to the prediction of HIV-1 drug resistance." Stat Appl Genet Mol Biol 6: Article7.
  • 2007.56: Van Der Laan, M. J., E. M. Van Keulen, M. Phaff and J. P. Eerenberg (2007). "Pericardial cyst located in the anterior mediastinum mimicking a thymoma. A presentation of two cases." Minerva Chir 62(2): 133-6.