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List of works by David D. Pollock

A call for benchmarking transposable element annotation methods

scientific article published on 4 August 2015

A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

scientific article

A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus) ⬇️

scientific article (publication date: 25 August 2011)

A proposal to sequence the genome of a garter snake (Thamnophis sirtalis) ⬇️

scientific article

Adaptive evolution and functional redesign of core metabolic proteins in snakes

scientific article

Adaptive molecular convergence: Molecular evolution versus molecular phylogenetics.

scientific article

Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution

scientific article published on 08 September 2020

Amino acid coevolution induces an evolutionary Stokes shift.

scientific article

Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.

scientific article

Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition.

scientific article

Assessing the accuracy of ancestral protein reconstruction methods

scientific article

Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions

scientific article published on November 2011

Chinese alligator genome illustrates molecular adaptations

scientific article published on 24 September 2013

Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context

scientific article published on 01 November 2007

Coevolving protein residues: maximum likelihood identification and relationship to structure.

scientific article

Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region

scientific article

Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing

scientific article

Context dependence and coevolution among amino acid residues in proteins.

scientific article

Correction: Rapid Microsatellite Identification from Illumina Paired-End Genomic Sequencing in Two Birds and a Snake

scientific article published on 20 August 2015

Detecting gradients of asymmetry in site-specific substitutions in mitochondrial genomes

scientific article

Divergence, recombination and retention of functionality during protein evolution.

scientific article

Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes

scientific article (publication date: 2009)

EGenBio: a data management system for evolutionary genomics and biodiversity

scientific article

Editorial

Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution

scientific article published in June 1997

Estimating the degree of saturation in mutant screens

scientific article

Evidence for an ancient adaptive episode of convergent molecular evolution.

scholarly article

Evolution of base-substitution gradients in primate mitochondrial genomes

scientific article

Evolution of functionality in lattice proteins

scientific article published on January 2001

Finding and extending ancient simple sequence repeat-derived regions in the human genome

scientific article published on 17 February 2020

From DNA to fitness differences: sequences and structures of adaptive variants of Colias phosphoglucose isomerase (PGI).

scientific article

Gene-specific RNA polymerase II phosphorylation and the CTD code

scientific article

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

scientific article

Germline TRAV5D-4 T-cell receptor sequence targets a primary insulin peptide of NOD mice

scientific article published on 7 February 2012

Identification of repeat structure in large genomes using repeat probability clouds

scientific article published on 20 May 2008

Increased Accuracy in Analytical Molecular Distance Estimation ⬇️

scientific article published on August 1, 1998

Increased taxon sampling is advantageous for phylogenetic inference

scientific article

Inference of transposable element ancestry

scientific article

Intrinsic amino acid side-chain hydrophilicity/hydrophobicity coefficients determined by reversed-phase high-performance liquid chromatography of model peptides: comparison with other hydrophilicity/hydrophobicity scales

scientific article published on January 2009

Is sparse taxon sampling a problem for phylogenetic inference?

scientific article published on February 2003

LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders

scientific article (publication date: 2012)

Launching microsatellites: a review of mutation processes and methods of phylogenetic interference

scientific article published on September 1997

Least squares estimation of molecular distance--noise abatement in phylogenetic reconstruction

scientific article published in June 1994

Microsatellite behavior with range constraints: parameter estimation and improved distances for use in phylogenetic reconstruction

scientific article published on June 1998

Nonadaptive Amino Acid Convergence Rates Decrease over Time.

scientific article

Observations of amino acid gain and loss during protein evolution are explained by statistical bias.

scientific article

Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum)

scientific article published on 06 January 2021

Phylogenetics, likelihood, evolution and complexity

scientific article

Platform technology to generate broadly cross-reactive antibodies to α-helical epitopes in hemagglutinin proteins from influenza a viruses.

scientific article published on 21 January 2016

Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding

scientific article published on 10 February 2015

Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence

scientific article published on 30 July 2009

Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories

scientific article

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake

scientific article

Regional variation in the density of essential genes in mice

scientific article

Repetitive elements may comprise over two-thirds of the human genome

scientific article

Report from the first snake genomics and integrative biology meeting

scientific article published on 24 September 2012

SELECTIVE ADVANTAGE OF RECOMBINATION IN EVOLVING PROTEIN POPULATIONS: A LATTICE MODEL STUDY.

scientific article

SINEs, evolution and genome structure in the opossum

scientific article published on 19 March 2007

SP transcription factor paralogs and DNA-binding sites coevolve and adaptively converge in mammals and birds

scientific article

Sequence entropy of folding and the absolute rate of amino acid substitutions.

scientific article published on 23 October 2017

Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes

scientific article published on 28 July 2011

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

scientific article

Strong evidence for protein epistasis, weak evidence against it.

scientific article published on 20 March 2014

Structural, Biochemical, and in Vivo Characterization of the First Virally Encoded Cyclophilin from the Mimivirus

scientific article

The Ambush Hypothesis: Hidden Stop Codons Prevent Off-Frame Gene Reading

article

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

scientific article

The ambush hypothesis: hidden stop codons prevent off-frame gene reading

scientific article

The beetle gut: a hyperdiverse source of novel yeasts

scientific article

The genome of a songbird

scientific article

The genome of the green anole lizard and a comparative analysis with birds and mammals ⬇️

scientific article

The interface of protein structure, protein biophysics, and molecular evolution

scientific article

The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

scientific article

The tangled bank of amino acids

scientific article

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

scientific article

Thousands of microsatellite loci from the venomous coralsnake Micrurus fulvius and variability of select loci across populations and related species.

scientific article

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

scientific article

Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development

scientific article

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment

scientific article

Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia.

scientific article

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