52: Journal of Molecular Biology , (2007) in press
Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus Eisenmesser E, Thai V, Renesto P, Fowler A, Brown D, Davis T, Gu W, Pollock DD, Kern D, and Raoult D
51: Journal of Molecular Evolution , (2007) in press
Coevolutionary patterns in cytochrome c oxidase
subunit I depend on structure and functional context Wang ZO and Pollock DD
50: BMC Evolutionary Biology, Jul 26;7:123 (2007)
Comparative mitochondrial genomics of snakes:
substitution rate dynamics and functionality of the duplicate
control region Jiang ZJ*, Castoe TA*, Austin CC, Burbrink FT, Herron MD, McGuire JA, Parkinson CL, and Pollock DD
Nature, 447(7141):167-77 (2007).
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA , Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W , Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD , Ray DA , Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA , Waters PD, Webber C, Weidman JR, Xie X, Zody MC; Broad Institute Genome Sequencing Platform, Broad Institute Whole Genome Assembly Team, Broad Institute Whole Genome Assembly Team, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, MacCallum I, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, and Lindblad-Toh K
Genome Research, 17(7):992-1004 (2007). Epub May 10
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, and Jurka J
PLoS Genet, 3(5):e72 (2007) . Epub Mar 21
Regional variation in the density of essential genes in mice Hentges KE, Pollock DD, Liu B, and Justice MJ
Gene, 396(1):46-58 (2007). Epub Mar 19
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica Gu W, Ray DA, Walker JA, Barnes EW, Gentles AJ, Samollow PB, Jurka J, Batzer MA, and Pollock DD
45: in Ancestral Reconstruction , DA Liberles, ed.
(2006)
Dealing with Uncertainty in Ancestral Sequence Reconstruction: Sampling from the Posterior Distribution Pollock DD and Chang BS
44: BMC Bioinformatics, 7 Suppl 2:S7 (2006)
EGenBio : a data management system
for evolutionary genomics and biodiversity Nahum LA, Reynolds MT, Wang ZO, Faith JJ, Jonna R, Jiang ZJ, Meyer TJ, and Pollock DD
43: Public Library of Science Computational Biology, 2(6):e69 (2006). Epub Jun 23
Assessing the accuracy of ancestral protein
reconstruction methods Williams PD, Pollock DD, Blackburne BP, and Goldstein RA
42: Molecular Biology and Evolution, 23(7):1444-9 (2006). Epub May 11
Observations of amino acid gain and loss
during protein evolution are explained by statistical bias Goldstein RA and Pollock DD
International
Journal of Modern Physics C, 17(1): 75-90 (2006)
Selective advantage of recombination in evolving
protein populations: A lattice model study Williams PD, Pollock DD, and Goldstein RA
Evolutionary
Bioinformatics Online, 2 (2006)
Functionality and the evolution of marginal
stability in proteins: inferences from lattice simulations Williams PD, Pollock DD, and Goldstein RA
Human
Genomics, 2(3): 158-67 (2005)
Divergence, recombination,
and retention of functionality during protein evolution Xu YO, Hall RW, Goldstein RA, Pollock DD.
38: Molecular
Biology and Evolution, 23(3): 449-512 (2006) . Epub 2005 Nov 16
Sequences and protein
structures are congruent with functional and fitness differences
among Colias phosphoglucose isomerase genotypes Wheat CW, Watt WB, Pollock DD, Schulte PM
37: NHGRI White Paper 2005
Proposal to sequence the first reptilian
genome: the Green Anole Lizard, Anolis carolinensis J. Losos, E. Braun, D. Brown, S. Clifton, S. Edwards, J.
Gibson-Brown, T. Glenn, L. Guillette, D. Main, P. Minx, W. Modi,
M. Pfrender, D. Pollock, D. Ray, A. Shedlock, and W. Warren
36: Genome
Research, 15(5):665-73 (2005)
Evolution
of base substitution gradients in primate mitochondrial genomes Raina SZ, Faith JJ, Seligmann H, Disotell T, Stewart C-B,
and Pollock DD
35: Mycological
Research, 109:261-5 (2005); Nature 434: 449-450 (2005)
News and Views overview, "Biodiversity:
gut feeling for yeasts" in: The beetle gut: a hyperdiverse
source of novel yeasts Suh S-O, McHugh, JV, Pollock DD, Blackwell M
34: Encyclopedia
of Genomics, Proteomics and Bioinformatics 2005 ; Dunn, Jorde,
Little, and Subramaniam, eds. September 2005
Modeling protein evolution Pollock DD and Goldstein RA
33: Methods
in Enzmology, 395:779-790 (2005)
Context dependence and
coevolution among amino acid residues in proteins Wang ZO and Pollock DD
32: Biological
Procedures Online 2004; 6(1): 180-188
Analysis of among-site
variation in substitution patterns Krishnan NM, Raina SZ, and Pollock DD
31: DNA
and Cell Biology 2004; 23:707-714
Detecting gradients
of asymmetry in site-specific substitutions in mitochondrial
genomes Krishnan NM, Seligmann H, Raina SZ, and Pollock DD
30: DNA
and Cell Biology 2004; 23:701-705
The ambush hypothesis:
Hidden stop codons prevent off-frame gene reading Seligmann H and Pollock DD
29: Molecular
Biology and Evolution 2004; 21(10): 1871-1883
Ancestral sequence reconstruction
in primate mitochondrial DNA: compositional bias and effect
on functional inference Krishnan NM, Seligmann H, Stewart, C-B, de Koning APJ, and Pollock
DD
28: Genetics
2004; 168(1): 489-502
Estimating the degree
of saturation in mutant screens Pollock DD and Larkin J
27: Human Genomics 2004; 1(2): 85
Human genomics and the
role of evolutionary genomics Pollock DD
26: Genetics
2003; 165(2): 735-745
Likelihood analysis of
asymmetrical mutation bias gradients in vertebrate mitochondrial
genomes Faith JJ and Pollock DD
25: NHGRI White Paper 2003
Proposal for complete sequencing of the genome
of a Marsupial, the gray, short-tailed opossum, Monodelphis
domestica Amemiya CT, Greally JM, Jirtle RL, Lander ES, Lindblad-Toh
K, Miller RD, Pollock DD, Samallow PB, Springer MS, and Wilson RK
24: Journal of Molecular Evolution 2003; 56(4): 375-376
The Zuckerkandl Prize:
Structure and Evolution Pollock DD
23: Systematic
Biology 2003; 52(1):124-6
Is sparse taxon sampling
a problem for phylogenetic inference? Hillis, DM, Pollock DD, McGuire JA, and Zwickl DJ
22: Systematic
Biology 2002; 51(4):664-71
Increased taxon sampling
is advantageous for phylogenetic inference Pollock DD, Zwickl DJ, McGuire JA, and Hillis DM
21: Applied
Bioinformatics 2002; 1(2): 81-92
Genomic biodiversity,
phylogenetics, and coevolution in proteins Pollock DD
20: Pac
Symp Biocomp 2002 ; tutorial
Molecular evolution and phylogenetic analysis Pollock DD and Goldstein RA
19:
J
Mol Graph Model 2001;19(1):150-6
Evolution of functionality
in lattice Williams PD, Pollock DD, and Goldstein RA
18: Pac
Symp Biocomp 2001 13:164-166
Structures, phylogenies, and genomes: The integrated
study of protein evolution Goldstein RA, Pollock DD, and Thorne JL
17: Mol
Biol Evol 2000 Dec;17(12):1854-8
Assessing an unknown Pollock DD, Bruno WJ.
16: Mol
Biol Evol 2000 Dec;17(12):1776-88
A case Pollock DD, Eisen JA, Doggett NA, Cummings MP.
15: Pac
Symp Biocomp 2000; 12:3-5
Protein Evolution and Structural Genomics Frishman D, Goldstein RA, Pollock DD.
14: Comp
Chem 2000; 24(1):133-134
RECOMB98: Computational molecular biology:
pre- and post-genomics Pollock DD and Heringa J
13: J
Mol Biol 1999 Mar; 19;287(1):187-98
Coevolving Pollock DD, Taylor WR, and Goldman N
Myoglobin data from
12: Theor
Popul Biol 1998 Aug; 54(1):78-90
Increased accuracy Pollock DD
11: Theor
Popul Biol 1998 Jun; 53(3):256-71
Microsatellite behavior with range Pollock DD, Bergman A, Feldman MW, and Goldstein DB
10: Annals
Ent Soc America 1998; 91(5):524-531.
Molecular phylogeny for Colias Pollock DD, Watt WB, Rashbrook VK, and Iyengar EV
9: J
Hered 1997 Sep-Oct; 88(5):335-42
Launching Goldstein DB and Pollock DD
8: Protein
Eng 1997 Jun; 10(6):647-57
Effectiveness of correlation Pollock DD and Taylor WR
7: Genetics
1997 Jan; 145(1):207-16
Microsatellite genetic distances
with range constraints Feldman MW, Bergman A, Pollock DD, Goldstein DB
6: Mol
Biol Evol 1995 Jul; 12(4):713-7
A comparison Pollock DD, Goldstein DB
5: Mol
Mar Biol Biotechnol 1995 Sep; 4(3):224-31
Evolutionary relations among vertebrate muscle-type
lactate Quattro JM, Pollock DD, Powell M, Woods HA, Powers DA
4:
Theor
Popul Biol 1994 Jun; 45(3):219-26
Least squares Goldstein DB, Pollock DD
3: Cytog. Cell. Genet 1991; 58(1-4): 1930
Chromosomal localization of the calbindin gene Modi, W. S., M. Dean, D. D. Pollock, H. N. Suanez, and S. Christakos
2: Cytog. Cell. Genet 1991; 58(1-4): 1870
Regional localization of the human glutaminase
gls and interleukin-9 il9 genes by in situ hybridization Modi WS, Pollock DD, Mock BA, Banner C, Renauld JC, Van Snick
J
1: Cytog.
Cell. Genet 1991; 57(2-3):114-116
Regional localization of the human glutaminase
GLS and interferon Modi WS, Pollock DD, Mock BA, Banner C, Renauld JC, and Van Snick
J
53: in review
Adaptive evolution and functional redesign of core metabolic proteins in snakes Castoe TA, Jiang ZJ, Gu W. O., Wang ZO, and Pollock DD
54: in revision
Dissection of the human genome using repeat
probability clouds
Gu W, Hedges D, Batzer MA, and Pollock DD
55: in revision
Reconciling the biochemical and genetic data
on replication of mitochondrial genomes Pollock DD
