Gavin Clay Conant

POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes

BMC BIOINFORMATICS, 24(1).

Convergent evolution of polyploid genomes from across the eukaryotic tree of life

Hao, Y., Fleming, J., Petterson, J., Lyons, E., Edger, P. P., Pires, J. C., … Conant, G. C. (2022, May 10). G3-GENES GENOMES GENETICS, Vol. 5.

Hybridization order is not the driving factor behind biases in duplicate gene losses among the hexaploid Solanaceae

A metagenomic analysis of the effect of antibiotic feed additives on the ovine rumen metabolism

SMALL RUMINANT RESEARCH, 205.

Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)

G3-GENES GENOMES GENETICS, 11(7).

Distinct C-4 sub-types and C-3 bundle sheath isolation in the Paniceae grasses

PLANT DIRECT, 5(12).

Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa

NEW PHYTOLOGIST, 230(1), 372–386.

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

GENOME RESEARCH, 31(5), 799–810.

A Single, Shared Triploidy in Three Species of Parasitic Nematodes

G3-GENES GENOMES GENETICS, 10(1), 225–233.

Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation

GENOME BIOLOGY AND EVOLUTION, 12(3), 35–47.

Phylogeny and multiple independent whole-genome duplication events in the Brassicales

AMERICAN JOURNAL OF BOTANY, 107(8), 1148–1164.

The lasting after-effects of an ancient polyploidy on the genomes of teleosts

PLOS ONE, 15(4).

Functional characterization of SMN evolution in mouse models of SMA

SCIENTIFIC REPORTS, 9.

Predicting residual feed intake status using rumen microbial profiles in ewe lambs

JOURNAL OF ANIMAL SCIENCE, 97(7), 2878–2888.

Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus

NATURE COMMUNICATIONS, 10.

Author Correction: Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses

Scientific Reports, 8(1).

Genome-guided phylo-transcriptomic methods and the nuclear phylogenetic tree of the paniceae grasses (vol 7, 13528, 2017)

Scientific Reports, Vol. 8.

Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy

ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 49, Vol. 49, pp. 253–278.

Patterns of Population Variation in Two Paleopolyploid Eudicot Lineages Suggest That Dosage-Based Selection on Homeologs Is Long-Lived

GENOME BIOLOGY AND EVOLUTION, 10(3), 999–1011.

Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes

JOURNAL OF ANIMAL SCIENCE, 96(6), 2113–2124.

Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization

PLOS GENETICS, 14(3).

RUMINANT NUTRITION SYMPOSIUM: Tiny but mighty: the role of the rumen microbes in livestock production (vol 96, pg 752, 2018)

Cammack, K. M., Austin, K. J., Lamberson, W. R., Conant, G. C., & Cunningham, H. C. (2018, October). JOURNAL OF ANIMAL SCIENCE, Vol. 96, pp. 4481–4481.

Tiny but mighty: The role of the rumen microbes in livestock production

Journal of Animal Science, 1.

Diet and feed efficiency status affect rumen microbial profiles of sheep

SMALL RUMINANT RESEARCH, 156, 12–19.

Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome

MICROBIOME, 5.

Effects of evolutionary pressure on histone modifications

2017 ieee international conference on bioinformatics and biomedicine (bibm), 2267–2267.

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses

SCIENTIFIC REPORTS, 7.

Convergent Evolution and the Origin of Complex Phenotypes in the Age of Systems Biology

International Journal of Plant Sciences, 177(4), 305–318.

Robust Yet Fragile: Expression Noise, Protein Misfolding, and Gene Dosage in the Evolution of Genomes

In Annual Review of Genetics (Vol. 50, pp. 113–131).

Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system

Cell and Tissue Research, 363(1), 267–278.

Patterns of gene conversion in duplicated yeast histones suggest strong selection on a coadapted macromolecular complex

Genome Biology and Evolution, 7(12), 3249–3258.

Structure, interaction, and evolution: Reflections on the natural history of proteins

In Evolutionary Biology: Biodiversification from Genotype to Phenotype (pp. 187–201).

The butterfly plant arms-race escalated by gene and genome duplications

Proceedings of the National Academy of Sciences of the United States of America, 112(27), 8362–8366.

The players may change but the game remains: Network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity

Nucleic Acids Research, 43(20), 9600–9612.

Comparative genomics as a time machine: How relative gene dosage and metabolic requirements shaped the time-dependent resolution of yeast polyploidy

Molecular Biology and Evolution, 31(12), 3184–3193.

Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time

Current Opinion in Plant Biology, 19, 91–98.

Gene duplication and phenotypic changes in the evolution of mammalian metabolic networks

PLoS ONE, 9(1).

Identification and characterization of RING-finger ubiquitin ligase UBR7 in mammalian spermatozoa

Cell and Tissue Research, 356(1), 261–278.

Large-Scale Pairwise Alignments on GPU Clusters: Exploring the Implementation Space

Journal of Signal Processing Systems, 77(1-2), 131–149.

Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the brassicaceae (mustards)

PLoS ONE, 9(7).

The yeast protein interaction network has a capacity for self-organization

FEBS Journal, 281(15), 3420–3432.

A Conserved Mammalian Protein Interaction Network

PLoS ONE, 8(1).

A distributed CPU-GPU framework for pairwise alignments on large-scale sequence datasets

Proceedings of the International Conference on Application-Specific Systems, Architectures and Processors, 329–338.

Diet Alters Both the Structure and Taxonomy of the Ovine Gut Microbial Ecosystem

DNA Research, 21(2), 115–125.

Extreme evolutionary conservation of functionally important regions in H1N1 influenza proteome

PLoS ONE, 8(11).

Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales

Seminars in Cell and Developmental Biology, 24(4), 320–331.

Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy

Genetics, 190(4), 1563–1574.

Cloning and characterization of the peptidoglycan recognition protein genes in the mosquito, Armigeres subalbatus (Diptera: Culicidae)

Journal of Medical Entomology, 49(3), 656–671.

Long identical multispecies elements in plant and animal genomes

Proceedings of the National Academy of Sciences of the United States of America, 109(19).

Metabolic and evolutionary costs of herbivory defense: Systems biology of glucosinolate synthesis

New Phytologist, 196(2), 596–605.

Polyploidy and the Evolution of Complex Traits

International Journal of Evolutionary Biology, 2012, 1–12.

Very low rate of gene conversion in the yeast genome

Molecular Biology and Evolution, 29(12), 3817–3826.

Yeast as a window into changes in genome complexity due to polyploidization

In Polyploidy and Genome Evolution (Vol. 9783642314421, pp. 293–308).

Copy number alterations among mammalian enzymes cluster in the metabolic network

Molecular Biology and Evolution, 28(2), 1111–1121.

Expression level, cellular compartment and metabolic network position all influence the average selective constraint on mammalian enzymes

BMC Evolutionary Biology, 11(1).

Patterns of indirect protein interactions suggest a spatial organization to metabolism

Molecular BioSystems, 7(11), 3056–3064.

Selection for higher gene copy number after different types of plant gene duplications

Genome Biology and Evolution, 3(1), 1369–1380.

The genome of the mesopolyploid crop species Brassica rapa

Nature Genetics, 43(10), 1035–1039.

Transcriptional robustness and protein interactions are associated in yeast

BMC Systems Biology, 5.

Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints

Plant Cell, 23(5), 1719–1728.

Nonrandom survival of gene conversions among yeast ribosomal proteins duplicated through genome doubling.

Genome Biology and Evolution, 2, 826–834. http://www.scopus.com/inward/record.url?eid=2-s2.0-79952199263&partnerID=MN8TOARS

Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast

Proceedings of the Royal Society B: Biological Sciences, 277(1683), 869–876.

The T box regulatory element controlling expression of the class i lysyl-tRNA synthetase of Bacillus cereus strain 14579 is functional and can be partially induced by reduced charging of asparaginyl-tRNA^Asn

BMC Microbiology, 10.

Neutral evolution on mammalian protein surfaces

Trends in Genetics, 25(9), 377–381.

Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics

Proceedings of the National Academy of Sciences of the United States of America, 106(44), 18644–18649.

Solvent exposure imparts similar selective pressures across a range of yeast proteins

Molecular Biology and Evolution, 26(5), 1155–1161.

Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens

BMC GENOMICS, 9.

GenomeVx: Simple web-based creation of editable circular chromosome maps

Bioinformatics, 24(6), 861–862.

Increased glycolytic flux as an outcome of whole-genome duplication in yeast (Molecular Systems Biology (2007) 3 (129) DOI: 10.1038/msb4100170)

Molecular Systems Biology, 4.

Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast

Genetics, 179(3), 1681–1692.

Turning a hobby into a job: How duplicated genes find new functions

Nature Reviews Genetics, 9(12), 938–950.

Increased glycolytic flux as an outcome of whole‐genome duplication in yeast

Molecular Systems Biology, 3(1), 129.

Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication

Proceedings of the National Academy of Sciences of the United States of America, 104(20), 8397–8402.

Modeling amino acid substitution patterns in orthologous and paralogous genes

Molecular Phylogenetics and Evolution, 42(2), 298–307.

Functional Partitioning of Yeast Co-Expression Networks after Genome Duplication

PLoS Biology, 4(4), e109.

The rarity of gene shuffling in conserved genes.

Genome Biology, 6(6). http://www.scopus.com/inward/record.url?eid=2-s2.0-33646556197&partnerID=MN8TOARS

A fast algorithm for determining the best combination of local alignments to a query sequence

BMC Bioinformatics, 5.

A second-generation genome screen for linkage to type 1 diabetes in a Bedouin Arab family

In Annals of the New York Academy of Sciences (Vol. 1037, pp. 157–160).

Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans

Proceedings of the Royal Society of London. Series B: Biological Sciences, 271(1534), 89–96.

Molecular Evolution in Large Genetic Networks: Does Connectivity Equal Constraint?

Journal of Molecular Evolution, 58(2), 203–211.

Asymmetric sequence divergence of duplicate genes

Genome Research, 13(9), 2052–2058.

Convergent evolution of gene circuits

Nature Genetics, 34(3), 264–266.

Parallel genehunter: Implementation of linkage analysis package for distributed-memory architectures

Journal of Parallel and Distributed Computing, 63(7-8), 674–682.

GenomeHistory: A software tool and its application to fully sequenced genomes

Nucleic Acids Research, 30(15), 3378–3386. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036682357&partnerID=MN8TOARS

Parallel genehunter: Implementation of a linkage analysis package for distributed-memory architectures

Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002, 184–191.

Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference

Molecular Biology and Evolution, 18(6), 1024–1033. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034983477&partnerID=MN8TOARS