2007 | 2006 | 2005 | 2004 | 2003

2006.1: Gay, L. M., H. L. Ng and T. Alber (2006). "A conserved dimer and global conformational changes in the structure of apo-PknE Ser/Thr protein kinase from Mycobacterium tuberculosis." J Mol Biol 360(2): 409-20.

2006.2: Alm, E., K. Huang and A. Arkin (2006). "The evolution of two-component systems in bacteria reveals different strategies for niche adaptation." PLoS Comput Biol 2(11): e143.

2006.3: Anderson, J. C., E. J. Clarke, A. P. Arkin and C. A. Voigt (2006). "Environmentally controlled invasion of cancer cells by engineered bacteria." J Mol Biol 355(4): 619-27.

2006.4: Andrews, S. S. and A. P. Arkin (2006). "Simulating cell biology." Curr Biol 16(14): R523-7.

2006.5: Arkin, A. P. and D. A. Fletcher (2006). "Fast, cheap and somewhat in control." Genome Biol 7(8): 114.

2006.6: Brandis, K. A., I. F. Holmes, S. J. England, N. Sharma, L. Kukreja and S. K. DebBurman (2006). "alpha-Synuclein fission yeast model: concentration-dependent aggregation without plasma membrane localization or toxicity." J Mol Neurosci 28(2): 179-91.

2006.7: Brown, S. D., M. Martin, S. Deshpande, S. Seal, K. Huang, E. Alm, Y. Yang, L. Wu, T. Yan, X. Liu, A. Arkin, K. Chourey, J. Zhou and D. K. Thompson (2006). "Cellular response of Shewanella oneidensis to strontium stress." Appl Environ Microbiol 72(1): 890-900.

2006.8: Chhabra, S. R., Q. He, K. H. Huang, S. P. Gaucher, E. J. Alm, Z. He, M. Z. Hadi, T. C. Hazen, J. D. Wall, J. Zhou, A. P. Arkin and A. K. Singh (2006). "Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough." J Bacteriol 188(5): 1817-28.

2006.9: Clark, M. E., Q. He, Z. He, K. H. Huang, E. J. Alm, X. F. Wan, T. C. Hazen, A. P. Arkin, J. D. Wall, J. Z. Zhou and M. W. Fields (2006). "Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion." Appl Environ Microbiol 72(8): 5578-88.

2006.10: Deutschbauer, A. M., D. Chivian and A. P. Arkin (2006). "Genomics for environmental microbiology." Curr Opin Biotechnol 17(3): 229-35.

2006.11: Feeley, R., M. Frenklach, M. Onsum, T. Russi, A. Arkin and A. Packard (2006). "Model discrimination using data collaboration." J Phys Chem A Mol Spectrosc Kinet Environ Gen Theory 110(21): 6803-13.

2006.12: Ham, T. S., S. K. Lee, J. D. Keasling and A. P. Arkin (2006). "A tightly regulated inducible expression system utilizing the fim inversion recombination switch." Biotechnol Bioeng 94(1): 1-4.

2006.13: He, Q., K. H. Huang, Z. He, E. J. Alm, M. W. Fields, T. C. Hazen, A. P. Arkin, J. D. Wall and J. Zhou (2006). "Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis." Appl Environ Microbiol 72(6): 4370-81.

2006.14: Leaphart, A. B., D. K. Thompson, K. Huang, E. Alm, X. F. Wan, A. Arkin, S. D. Brown, L. Wu, T. Yan, X. Liu, G. S. Wickham and J. Zhou (2006). "Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH." J Bacteriol 188(4): 1633-42.

2006.15: Mukhopadhyay, A., Z. He, E. J. Alm, A. P. Arkin, E. E. Baidoo, S. C. Borglin, W. Chen, T. C. Hazen, Q. He, H. Y. Holman, K. Huang, R. Huang, D. C. Joyner, N. Katz, M. Keller, P. Oeller, A. Redding, J. Sun, J. Wall, J. Wei, Z. Yang, H. C. Yen, J. Zhou and J. D. Keasling (2006). "Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach." J Bacteriol 188(11): 4068-78.

2006.16: Onsum, M. D., K. Wong, P. Herzmark, H. R. Bourne and A. P. Arkin (2006). "Morphology matters in immune cell chemotaxis: membrane asymmetry affects amplification." Phys Biol 3(3): 190-9.

2006.17: Price, M. N., E. J. Alm and A. P. Arkin (2006). "The histidine operon is ancient." J Mol Evol 62(6): 807-8.

2006.18: Price, M. N., A. P. Arkin and E. J. Alm (2006). "OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments." BMC Bioinformatics 7: 19.

2006.19: Price, M. N., A. P. Arkin and E. J. Alm (2006). "The life-cycle of operons." PLoS Genet 2(6): e96.

2006.20: Samoilov, M. S. and A. P. Arkin (2006). "Deviant effects in molecular reaction pathways." Nat Biotechnol 24(10): 1235-40.

2006.21: Samoilov, M. S., G. Price and A. P. Arkin (2006). "From fluctuations to phenotypes: the physiology of noise." Sci STKE 2006(366): re17.

2006.22: Akey, D., A. Martins, J. Aniukwu, M. S. Glickman, S. Shuman and J. M. Berger (2006). "Crystal structure and nonhomologous end-joining function of the ligase component of Mycobacterium DNA ligase D." J Biol Chem 281(19): 13412-23.

2006.23: Antczak, A. J., T. Tsubota, P. D. Kaufman and J. M. Berger (2006). "Structure of the yeast histone H3-ASF1 interaction: implications for chaperone mechanism, species-specific interactions, and epigenetics." BMC Struct Biol 6: 26.

2006.24: Clarey, M. G., J. P. Erzberger, P. Grob, A. E. Leschziner, J. M. Berger, E. Nogales and M. Botchan (2006). "Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex." Nat Struct Mol Biol 13(8): 684-90.

2006.25: Corbett, K. D. and J. M. Berger (2006). "Structural basis for topoisomerase VI inhibition by the anti-Hsp90 drug radicicol." Nucleic Acids Res 34(15): 4269-77.

2006.26: Corn, J. E. and J. M. Berger (2006). "Regulation of bacterial priming and daughter strand synthesis through helicase-primase interactions." Nucleic Acids Res 34(15): 4082-8.

2006.27: Erzberger, J. P. and J. M. Berger (2006). "Evolutionary relationships and structural mechanisms of AAA+ proteins." Annu Rev Biophys Biomol Struct 35: 93-114.

2006.28: Erzberger, J. P., M. L. Mott and J. M. Berger (2006). "Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling." Nat Struct Mol Biol 13(8): 676-83.

2006.29: Hagenbach, U., S. Luz, N. Ghafoor, J. M. Berger, F. Grotenhermen, R. Brenneisen and M. Mader (2006). "The treatment of spasticity with Delta(9)-tetrahydrocannabinol in persons with spinal cord injury." Spinal Cord.

2006.30: Hansen, C. L., S. Classen, J. M. Berger and S. R. Quake (2006). "A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination." J Am Chem Soc 128(10): 3142-3.

2006.31: Mougous, J. D., D. H. Lee, S. C. Hubbard, M. W. Schelle, D. J. Vocadlo, J. M. Berger and C. R. Bertozzi (2006). "Molecular basis for G protein control of the prokaryotic ATP sulfurylase." Mol Cell 21(1): 109-22.

2006.32: Recht, J., T. Tsubota, J. C. Tanny, R. L. Diaz, J. M. Berger, X. Zhang, B. A. Garcia, J. Shabanowitz, A. L. Burlingame, D. F. Hunt, P. D. Kaufman and C. D. Allis (2006). "Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis." Proc Natl Acad Sci U S A 103(18): 6988-93.

2006.33: Reynolds, K. A., J. M. Thomson, K. D. Corbett, C. R. Bethel, J. M. Berger, J. F. Kirsch, R. A. Bonomo and T. M. Handel (2006). "Structural and computational characterization of the SHV-1 beta-lactamase-beta-lactamase inhibitor protein interface." J Biol Chem 281(36): 26745-53.

2006.34: Skordalakes, E. and J. M. Berger (2006). "Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor." Cell 127(3): 553-64.

2006.35: Weirich, C. S., J. P. Erzberger, J. S. Flick, J. M. Berger, J. Thorner and K. Weis (2006). "Activation of the DExD/H-box protein Dbp5 by the nuclear-pore protein Gle1 and its coactivator InsP6 is required for mRNA export." Nat Cell Biol 8(7): 668-76.

2006.36: Kechris, K. J., J. C. Lin, P. J. Bickel and A. N. Glazer (2006). "Quantitative exploration of the occurrence of lateral gene transfer by using nitrogen fixation genes as a case study." Proc Natl Acad Sci U S A 103(25): 9584-9.

2006.37: Ronald, J., H. Tang and R. B. Brem (2006). "Genomewide evolutionary rates in laboratory and wild yeast." Genetics 174(1): 541-4.

2006.38: Chandonia, J. M. and S. E. Brenner (2006). "The impact of structural genomics: expectations and outcomes." Science 311(5759): 347-51.

2006.39: Chandonia, J. M., S. H. Kim and S. E. Brenner (2006). "Target selection and deselection at the Berkeley Structural Genomics Center." Proteins 62(2): 356-70.

2006.40: Leebens-Mack, J., T. Vision, E. Brenner, J. E. Bowers, S. Cannon, M. J. Clement, C. W. Cunningham, C. dePamphilis, R. deSalle, J. J. Doyle, J. A. Eisen, X. Gu, J. Harshman, R. K. Jansen, E. A. Kellogg, E. V. Koonin, B. D. Mishler, H. Philippe, J. C. Pires, Y. L. Qiu, S. Y. Rhee, K. Sjolander, D. E. Soltis, P. S. Soltis, D. W. Stevenson, K. Wall, T. Warnow and C. Zmasek (2006). "Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)." Omics 10(2): 231-7.

2006.41: Leontis, N. B., R. B. Altman, H. M. Berman, S. E. Brenner, J. W. Brown, D. R. Engelke, S. C. Harvey, S. R. Holbrook, F. Jossinet, S. E. Lewis, F. Major, D. H. Mathews, J. S. Richardson, J. R. Williamson and E. Westhof (2006). "The RNA Ontology Consortium: an open invitation to the RNA community." Rna 12(4): 533-41.

2006.42: Mitchell, C. E., S. E. Brenner, J. Garcia-Fortanet and S. V. Ley (2006). "An efficient, asymmetric organocatalyst-mediated conjugate addition of nitroalkanes to unsaturated cyclic and acyclic ketones." Org Biomol Chem 4(10): 2039-49.

2006.43: Smith, A., J. M. Chandonia and S. E. Brenner (2006). "ANDY: a general, fault-tolerant tool for database searching on computer clusters." Bioinformatics 22(5): 618-20.

2006.44: Stefan, L. R., R. Zhang, A. G. Levitan, D. K. Hendrix, S. E. Brenner and S. R. Holbrook (2006). "MeRNA: a database of metal ion binding sites in RNA structures." Nucleic Acids Res 34(Database issue): D131-4.

2006.45: Barrier, A., P. Y. Boelle, F. Roser, J. Gregg, C. Tse, D. Brault, F. Lacaine, S. Houry, M. Huguier, B. Franc, A. Flahault, A. Lemoine and S. Dudoit (2006). "Stage II colon cancer prognosis prediction by tumor gene expression profiling." J Clin Oncol 24(29): 4685-91.

2006.46: Chiappini, F., A. Barrier, R. Saffroy, M. C. Domart, N. Dagues, D. Azoulay, M. Sebagh, B. Franc, S. Chevalier, B. Debuire, S. Dudoit and A. Lemoine (2006). "Exploration of global gene expression in human liver steatosis by high-density oligonucleotide microarray." Lab Invest 86(2): 154-65.

2006.47: Hothorn, T., P. Buhlmann, S. Dudoit, A. Molinaro and M. J. van der Laan (2006). "Survival ensembles." Biostatistics 7(3): 355-73.

2006.48: Keles, S., M. J. van der Laan, S. Dudoit and S. E. Cawley (2006). "Multiple testing methods for ChIP-Chip high density oligonucleotide array data." J Comput Biol 13(3): 579-613.

2006.49: Rubin, D., S. Dudoit and M. van der Laan (2006). "A method to increase the power of multiple testing procedures through sample splitting." Stat Appl Genet Mol Biol 5: Article19.

2006.50: Wang, Y., L. P. Zhao and S. Dudoit (2006). "A fine-scale linkage-disequilibrium measure based on length of haplotype sharing." Am J Hum Genet 78(4): 615-28.

2006.51: Chiang, D. Y., D. A. Nix, R. K. Shultzaberger, A. P. Gasch and M. B. Eisen (2006). "Flexible promoter architecture requirements for coactivator recruitment." BMC Mol Biol 7: 16.

2006.52: Luengo Hendriks, C. L., S. V. Keranen, C. C. Fowlkes, L. Simirenko, G. H. Weber, A. H. DePace, C. Henriquez, D. W. Kaszuba, B. Hamann, M. B. Eisen, J. Malik, D. Sudar, M. D. Biggin and D. W. Knowles (2006). "Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline." Genome Biol 7(12): R123.

2006.53: Mintseris, J. and M. B. Eisen (2006). "Design of a combinatorial DNA microarray for protein-DNA interaction studies." BMC Bioinformatics 7: 429.

2006.54: Moses, A. M., D. A. Pollard, D. A. Nix, V. N. Iyer, X. Y. Li, M. D. Biggin and M. B. Eisen (2006). "Large-scale turnover of functional transcription factor binding sites in Drosophila." PLoS Comput Biol 2(10): e130.

2006.55: Palmer, C., E. M. Bik, M. B. Eisen, P. B. Eckburg, T. R. Sana, P. K. Wolber, D. A. Relman and P. O. Brown (2006). "Rapid quantitative profiling of complex microbial populations." Nucleic Acids Res 34(1): e5.

2006.56: Pennacchio, L. A., N. Ahituv, A. M. Moses, S. Prabhakar, M. A. Nobrega, M. Shoukry, S. Minovitsky, I. Dubchak, A. Holt, K. D. Lewis, I. Plajzer-Frick, J. Akiyama, S. De Val, V. Afzal, B. L. Black, O. Couronne, M. B. Eisen, A. Visel and E. M. Rubin (2006). "In vivo enhancer analysis of human conserved non-coding sequences." Nature 444(7118): 499-502.

2006.57: Pollard, D. A., V. N. Iyer, A. M. Moses and M. B. Eisen (2006). "Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting." PLoS Genet 2(10): e173.

2006.58: Pollard, D. A., A. M. Moses, V. N. Iyer and M. B. Eisen (2006). "Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments." BMC Bioinformatics 7: 376.

2006.59: Wang, Q. F., S. Prabhakar, Q. Wang, A. M. Moses, S. Chanan, M. Brown, M. B. Eisen, J. F. Cheng, E. M. Rubin and D. Boffelli (2006). "Primate-specific evolution of an LDLR enhancer." Genome Biol 7(8): R68.

2006.60: Head-Gordon, T. and M. E. Johnson (2006). "Tetrahedral structure or chains for liquid water." Proc Natl Acad Sci U S A 103(21): 7973-7.

2006.61: Brandis, K. A., I. F. Holmes, S. J. England, N. Sharma, L. Kukreja and S. K. DebBurman (2006). "alpha-Synuclein fission yeast model: concentration-dependent aggregation without plasma membrane localization or toxicity." J Mol Neurosci 28(2): 179-91.

2006.62: Klosterman, P. S., A. V. Uzilov, Y. R. Bendana, R. K. Bradley, S. Chao, C. Kosiol, N. Goldman and I. Holmes (2006). "XRate: a fast prototyping, training and annotation tool for phylo-grammars." BMC Bioinformatics 7: 428.

2006.63: Perry, G. H., H. Vivanco, I. Holmes, J. M. Gwozdz and J. Bourne (2006). "No evidence of Mycobacterium avium subsp. paratuberculosis in in vitro produced cryopreserved embryos derived from subclinically infected cows." Theriogenology 66(5): 1267-73.

2006.64: Jiang, K., S. Zhang, S. Lee, G. Tsai, K. Kim, H. Huang, C. Chilcott, T. Zhu and L. J. Feldman (2006). "Transcription profile analyses identify genes and pathways central to root cap functions in maize." Plant Mol Biol 60(3): 343-63.

2006.65: Tyler, B. M., S. Tripathy, X. Zhang, P. Dehal, R. H. Jiang, A. Aerts, F. D. Arredondo, L. Baxter, D. Bensasson, J. L. Beynon, J. Chapman, C. M. Damasceno, A. E. Dorrance, D. Dou, A. W. Dickerman, I. L. Dubchak, M. Garbelotto, M. Gijzen, S. G. Gordon, F. Govers, N. J. Grunwald, W. Huang, K. L. Ivors, R. W. Jones, S. Kamoun, K. Krampis, K. H. Lamour, M. K. Lee, W. H. McDonald, M. Medina, H. J. Meijer, E. K. Nordberg, D. J. Maclean, M. D. Ospina-Giraldo, P. F. Morris, V. Phuntumart, N. H. Putnam, S. Rash, J. K. Rose, Y. Sakihama, A. A. Salamov, A. Savidor, C. F. Scheuring, B. M. Smith, B. W. Sobral, A. Terry, T. A. Torto-Alalibo, J. Win, Z. Xu, H. Zhang, I. V. Grigoriev, D. S. Rokhsar and J. L. Boore (2006). "Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis." Science 313(5791): 1261-6.

2006.66: Alfaro, M. E. and J. P. Huelsenbeck (2006). "Comparative performance of Bayesian and AIC-based measures of phylogenetic model uncertainty." Syst Biol 55(1): 89-96.

2006.67: Huelsenbeck, J. P., S. Jain, S. W. Frost and S. L. Pond (2006). "A Dirichlet process model for detecting positive selection in protein-coding DNA sequences." Proc Natl Acad Sci U S A 103(16): 6263-8.

2006.68: Ronquist, F., B. Larget, J. P. Huelsenbeck, J. B. Kadane, D. Simon and P. van der Mark (2006). "Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees"." Science 312(5772): 367; author reply 367.

2006.69: Arnon, S. S., R. Schechter, S. E. Maslanka, N. P. Jewell and C. L. Hatheway (2006). "Human botulism immune globulin for the treatment of infant botulism." N Engl J Med 354(5): 462-71.

2006.70: Eskenazi, B., A. R. Marks, A. Bradman, L. Fenster, C. Johnson, D. B. Barr and N. P. Jewell (2006). "In utero exposure to dichlorodiphenyltrichloroethane (DDT) and dichlorodiphenyldichloroethylene (DDE) and neurodevelopment among young Mexican American children." Pediatrics 118(1): 233-41.

2006.71: Blei, D. M., K. Franks, M. I. Jordan and I. S. Mian (2006). "Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span." BMC Bioinformatics 7: 250.

2006.72: Cooper, A. C., R. M. Karp, E. J. Clark, N. R. Taghizadeh, J. G. Hoyt, M. T. Labenski, M. J. Murray, G. Hannig, W. F. Westlin and C. D. Thompson (2006). "A novel methionine aminopeptidase-2 inhibitor, PPI-2458, inhibits non-Hodgkin's lymphoma cell proliferation in vitro and in vivo." Clin Cancer Res 12(8): 2583-90.

2006.73: Hannig, G., D. D. Lazarus, S. G. Bernier, R. M. Karp, J. Lorusso, D. Qiu, M. T. Labenski, J. D. Wakefield, C. D. Thompson and W. F. Westlin (2006). "Inhibition of melanoma tumor growth by a pharmacological inhibitor of MetAP-2, PPI-2458." Int J Oncol 28(4): 955-63.

2006.74: Scott, J., T. Ideker, R. M. Karp and R. Sharan (2006). "Efficient algorithms for detecting signaling pathways in protein interaction networks." J Comput Biol 13(2): 133-44.

2006.75: Chandonia, J. M. and S. H. Kim (2006). "Structural proteomics of minimal organisms: conservation of protein fold usage and evolutionary implications." BMC Struct Biol 6: 7.

2006.76: Chandonia, J. M., S. H. Kim and S. E. Brenner (2006). "Target selection and deselection at the Berkeley Structural Genomics Center." Proteins 62(2): 356-70.

2006.77: Choi, I. G. and S. H. Kim (2006). "Evolution of protein structural classes and protein sequence families." Proc Natl Acad Sci U S A 103(38): 14056-61.

2006.78: Grant, M. R., S. H. Kim and C. A. Hunt (2006). "Simulating in vitro epithelial morphogenesis in multiple environments." Comput Syst Bioinformatics Conf: 381-4.

2006.79: Kim, J. S., D. H. Shin, R. Pufan, C. Huang, H. Yokota, R. Kim and S. H. Kim (2006). "Crystal structure of ScpB from Chlorobium tepidum, a protein involved in chromosome partitioning." Proteins 62(2): 322-8.

2006.80: Sims, G. E. and S. H. Kim (2006). "A method for evaluating the structural quality of protein models by using higher-order phi-psi pairs scoring." Proc Natl Acad Sci U S A 103(12): 4428-32.

2006.81: Simison, W. B., D. R. Lindberg and J. L. Boore (2006). "Rolling circle amplification of metazoan mitochondrial genomes." Mol Phylogenet Evol 39(2): 562-7.

2006.82: de los Rios, M. A., B. K. Muralidhara, D. Wildes, T. R. Sosnick, S. Marqusee, P. Wittung-Stafshede, K. W. Plaxco and I. Ruczinski (2006). "On the precision of experimentally determined protein folding rates and phi-values." Protein Sci 15(3): 553-63.

2006.83: Freedman, T. S., H. Sondermann, G. D. Friedland, T. Kortemme, D. Bar-Sagi, S. Marqusee and J. Kuriyan (2006). "A Ras-induced conformational switch in the Ras activator Son of sevenless." Proc Natl Acad Sci U S A 103(45): 16692-7.

2006.84: Wildes, D., L. M. Anderson, A. Sabogal and S. Marqusee (2006). "Native state energetics of the Src SH2 domain: evidence for a partially structured state in the denatured ensemble." Protein Sci 15(7): 1769-79.

2006.85: Adelman, J. L., Y. J. Jeong, J. C. Liao, G. Patel, D. E. Kim, G. Oster and S. S. Patel (2006). "Mechanochemistry of transcription termination factor Rho." Mol Cell 22(5): 611-21.

2006.86: Eide, J. L., A. K. Chakraborty and G. F. Oster (2006). "Simple models for extracting mechanical work from the ATP hydrolysis cycle." Biophys J 90(12): 4281-94.

2006.87: Liu, J., M. Kaksonen, D. G. Drubin and G. Oster (2006). "Endocytic vesicle scission by lipid phase boundary forces." Proc Natl Acad Sci U S A 103(27): 10277-82.

2006.88: Sliusarenko, O., J. Chen and G. Oster (2006). "From biochemistry to morphogenesis in myxobacteria." Bull Math Biol 68(5): 1039-51.

2006.89: Sliusarenko, O., J. Neu, D. R. Zusman and G. Oster (2006). "Accordion waves in Myxococcus xanthus." Proc Natl Acad Sci U S A 103(5): 1534-9.

2006.90: Xing, J., F. Bai, R. Berry and G. Oster (2006). "Torque-speed relationship of the bacterial flagellar motor." Proc Natl Acad Sci U S A 103(5): 1260-5.

2006.91: Caspi, A. and L. Pachter (2006). "Identification of transposable elements using multiple alignments of related genomes." Genome Res 16(2): 260-70.

2006.92: Chatterji, S. and L. Pachter (2006). "Reference based annotation with GeneMapper." Genome Biol 7(4): R29.

2006.93: Dewey, C. N., P. M. Huggins, K. Woods, B. Sturmfels and L. Pachter (2006). "Parametric alignment of Drosophila genomes." PLoS Comput Biol 2(6): e73.

2006.94: Dewey, C. N. and L. Pachter (2006). "Evolution at the nucleotide level: the problem of multiple whole-genome alignment." Hum Mol Genet 15 Spec No 1: R51-6.

2006.95: Lall, S., D. Grun, A. Krek, K. Chen, Y. L. Wang, C. N. Dewey, P. Sood, T. Colombo, N. Bray, P. Macmenamin, H. L. Kao, K. C. Gunsalus, L. Pachter, F. Piano and N. Rajewsky (2006). "A genome-wide map of conserved microRNA targets in C. elegans." Curr Biol 16(5): 460-71.

2006.96: Levy, D., R. Yoshida and L. Pachter (2006). "Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates." Mol Biol Evol 23(3): 491-8.

2006.97: Babiarz, J. E., J. E. Halley and J. Rine (2006). "Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae." Genes Dev 20(6): 700-10.

2006.98: Davies, B. S. and J. Rine (2006). "A role for sterol levels in oxygen sensing in Saccharomyces cerevisiae." Genetics 174(1): 191-201.

2006.99: Kirchmaier, A. L. and J. Rine (2006). "Cell cycle requirements in assembling silent chromatin in Saccharomyces cerevisiae." Mol Cell Biol 26(3): 852-62.

2006.100: Neff, M. W. and J. Rine (2006). "A fetching model organism." Cell 124(2): 229-31.

2006.101: Roberts, T. M., M. S. Kobor, S. A. Bastin-Shanower, M. Ii, S. A. Horte, J. W. Gin, A. Emili, J. Rine, S. J. Brill and G. W. Brown (2006). "Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4." Mol Biol Cell 17(1): 539-48.

2006.102: Shoguchi, E., T. Kawashima, Y. Satou, M. Hamaguchi, I. T. Sin, Y. Kohara, N. Putnam, D. S. Rokhsar and N. Satoh (2006). "Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis." Genome Res 16(2): 297-303.

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