Works (90)
Updated: April 8th, 2024 05:20
2024 journal article
Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression
PLOS COMPUTATIONAL BIOLOGY, 20(1).
TL;DR:
It is shown that, even for phenotypically identical diploid progenitors, the inherent kinetics of gene expression give rise to biases between the expression levels of the progenitor genes in the hybrid.
(via Semantic Scholar)
journals.plos.org (publisher PDF)
Sources: Web Of Science, NC State University Libraries
Added: February 12, 2024
2023 article
Complementing model species with model clades
Mabry, M. E., Abrahams, R. S., Al-Shehbaz, I. A., Baker, W. J., Barak, S., Barker, M. S., … Harkess, A. E. (2023, October 12). PLANT CELL, Vol. 10.
TL;DR:
The utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade".
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: January 22, 2024
2023 journal article
Interlocus Gene Conversion, Natural Selection, and Paralog Homogenization
MOLECULAR BIOLOGY AND EVOLUTION, 40(9).
author keywords: interlocus gene conversion; paralog homogenization; teleost genome duplication
Sources: Web Of Science, NC State University Libraries
Added: April 1, 2024
2023 article
POInT: Modeling Polyploidy in the Era of Ubiquitous Genomics
POLYPLOIDY, pp. 77–90.
author keywords: Polyploidy; Evolutionary model; Synteny
TL;DR:
This chapter gives a brief history of the development of POInT as an illustration of the interconnected nature of computational biology research and some of the strengths and drawbacks of its structure.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: November 6, 2023
2023 journal article
POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes
BMC BIOINFORMATICS, 24(1).
author keywords: POInT; Comparative genomics; Browser
MeSH headings : Humans; Synteny; Phylogeny; Genome; Genomics; Polyploidy; Evolution, Molecular
TL;DR:
POInT_browse is described, a web portal that gives access to the orthology inferences made for polyploid genomes with POInT, the Polyploidy Orthology Inference Tool, allowing users to visualize genomic regions produced bypolyploidies and perform batch queries for each polyPLoidy event.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: June 5, 2023
2022 article
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.
author keywords: polyploidy; convergent evolution; reciprocal gene loss; evolutionary model
MeSH headings : Diploidy; Eukaryota; Evolution, Molecular; Humans; Phylogeny; Polyploidy
TL;DR:
By modeling the homoeologous gene losses that occurred in 50 genomes deriving from ten distinct polyploidy events, it is shown that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes, or yeasts.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: May 23, 2022
2022 journal article
Hybridization order is not the driving factor behind biases in duplicate gene losses among the hexaploid Solanaceae
author keywords: Solanaceae; polyploidy; biased fractionation; hexaploidy; repetitive elements
MeSH headings : Genes, Duplicate; Polyploidy; Solanaceae / genetics; Evolution, Molecular; Brassicaceae / genetics; Bias; Genome, Plant
TL;DR:
Whether the distribution of repetitive elements in these genomes can explain the biases in gene losses is explored, but while the signals found are broadly consistent with a role for high RE density in driving gene losses, the REs turn over so quickly that little signal of the RE condition at the time of paleopolyploidy is extant in the modern genomes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: November 14, 2022
2021 journal article
A metagenomic analysis of the effect of antibiotic feed additives on the ovine rumen metabolism
SMALL RUMINANT RESEARCH, 205.
author keywords: Rumen; Antibiotics; Metabolic network; Metagenomics; Vertebrate microbiome
TL;DR:
The addition of antibiotics to ruminant feed alters both the taxonomic and functional structure of their ruminal microbial communities, even if the overall effects of these changes are not fully understood.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: November 8, 2021
2021 journal article
Comparative phylogenetics of repetitive elements in a diverse order of flowering plants (Brassicales)
G3-GENES GENOMES GENETICS, 11(7).
author keywords: Brassicales; repetitive elements; whole-genome duplication; genome size; evolution
MeSH headings : Phylogeny; Magnoliopsida / genetics; Evolution, Molecular; Genome Size; Polyploidy; Genome, Plant; DNA Transposable Elements / genetics; Plants / genetics
TL;DR:
With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, the correlation between genome size and TE content is confirmed, however, it is unable to reconstruct phylogenetic relationships and do not detect any shift in TE abundance associated with WGD.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: January 18, 2022
2021 journal article
Distinct C-4 sub-types and C-3 bundle sheath isolation in the Paniceae grasses
PLANT DIRECT, 5(12).
author keywords: C-4; C-4 sub-types; evolution; photosynthesis
TL;DR:
Using five species from the grass tribe Paniceae, it is shown that, while in some species transcripts encoding multiple C4 acid decarboxylases accumulate, in others, transcript abundance and enzyme activity is almost entirely from one decar boxylase.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: January 10, 2022
2021 journal article
Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa
NEW PHYTOLOGIST, 230(1), 372–386.
author keywords: Brassica; domestication; genetic diversity; genomics; polyploidy; whole genome duplication
MeSH headings : Brassica rapa / genetics; Domestication; Genome, Plant / genetics; Phylogeny; Polyploidy
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: March 22, 2021
2021 journal article
The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
GENOME RESEARCH, 31(5), 799–810.
MeSH headings : Evolution, Molecular; Genome; Genome, Plant; Humans; Hybridization, Genetic; Phylogeny; Polyploidy
TL;DR:
A “mix and match” model of allopolyploidy is proposed, in which subgenome origin drives homoeolog loss propensities but where genes from different subgenomes function together without difficulty.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: June 10, 2021
2020 journal article
A Single, Shared Triploidy in Three Species of Parasitic Nematodes
G3-GENES GENOMES GENETICS, 10(1), 225–233.
Contributors: A. Schoonmaker*, Y. Hao*, D. Bird* & n
author keywords: polyploidy; evolutionary model; root-knot nematode
MeSH headings : Animals; Evolution, Molecular; Genome, Helminth; Phylogeny; Triploidy; Tylenchoidea / classification; Tylenchoidea / genetics
TL;DR:
Three root-knot nematodes of the genus Meloidogyne descend from a single common hybridization event that yielded triplicated genomes with three distinguishable subgenomes, and ancestral loci where two of the three gene copies have been lost are less likely to have orthologs in Caenorhabditis elegans that are lethal when knocked down than are ancestral locu with surviving duplicate copies.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries, ORCID
Added: January 21, 2020
2020 journal article
Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation
GENOME BIOLOGY AND EVOLUTION, 12(3), 35–47.
author keywords: comparative genomics; orthology inference; mammalian pregnancy; placental mammals
MeSH headings : Animals; Evolution, Molecular; Female; Gene Expression Regulation; Genomics; Humans; Immunity, Innate / genetics; Mammals / genetics; Placentation / genetics; Pregnancy; Transcription, Genetic
TL;DR:
It is found that genes that are phylogenetically older are more likely to be implicated in cancer development, and much of the genetic toolkit of mammalian pregnancy evolved through the repurposing of preexisting genes to new roles.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: June 15, 2020
2020 journal article
Phylogeny and multiple independent whole-genome duplication events in the Brassicales
AMERICAN JOURNAL OF BOTANY, 107(8), 1148–1164.
author keywords: Brassicales; Capparaceae; Cleomaceae; phylogeny; phylo-transcriptomics; Resedaceae; whole-genome duplication
MeSH headings : Evolution, Molecular; Gene Duplication; Genome; Genome, Plant / genetics; Humans; Magnoliopsida / genetics; Phylogeny; Polyploidy
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: September 14, 2020
2020 journal article
The lasting after-effects of an ancient polyploidy on the genomes of teleosts
PLOS ONE, 15(4).
MeSH headings : Animals; Evolution, Molecular; Fishes / classification; Fishes / genetics; Genome; Phylogeny; Polyploidy
TL;DR:
It is found that duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy at some point in this species’ history.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: June 15, 2020
2019 journal article
Functional characterization of SMN evolution in mouse models of SMA
SCIENTIFIC REPORTS, 9.
MeSH headings : Animals; Caenorhabditis elegans; Disease Models, Animal; Drosophila melanogaster; Evolution, Molecular; Mice; Mice, Knockout; Muscular Atrophy, Spinal / genetics; Muscular Atrophy, Spinal / metabolism; Schizosaccharomyces; Survival of Motor Neuron 1 Protein / genetics; Survival of Motor Neuron 1 Protein / metabolism; Xenopus Proteins / genetics; Xenopus Proteins / metabolism; Xenopus laevis; Zebrafish / genetics; Zebrafish Proteins / genetics; Zebrafish Proteins / metabolism
TL;DR:
A minimal SMN construct was designed consisting of exons 2, 3, and 6, which showed a partial rescue of the SMA phenotype, which suggests that while the core conserved region is essential, additional sequences contribute to the overall ability of the SMN protein to rescue disease pathology.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: July 22, 2019
2019 journal article
Predicting residual feed intake status using rumen microbial profiles in ewe lambs
JOURNAL OF ANIMAL SCIENCE, 97(7), 2878–2888.
author keywords: feed efficiency; RFI prediction; rumen microbiome; sheep
MeSH headings : Animal Feed / analysis; Animals; Diet / veterinary; Eating; Female; Microbiota; Phenotype; Rumen / microbiology; Sheep / microbiology; Sheep / physiology
TL;DR:
Results indicate that specific rumen microbial species may play a role in feed efficiency, and that a microbial profile could be used to rank sheep for feed efficiency.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: July 22, 2019
2019 journal article
Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus
NATURE COMMUNICATIONS, 10.
MeSH headings : Brassica napus / genetics; Brassica napus / metabolism; Gene Expression Regulation, Plant; Genomics; Organelles; Phylogeny; Plant Leaves / growth & development; Plant Tubers; Ploidies; Polymorphism, Single Nucleotide; RNA, Plant / genetics; Sequence Analysis, RNA; Transcriptome
TL;DR:
The authors show the complex origin and diversification of Brassica napus by analyzing transcriptome and organellar sequencing data and discern regions with signatures of selective sweeps and detect 8,187 differentially expressed genes with implications for B. napus diversification.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: July 22, 2019
2018 journal article
Author Correction: Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses
Scientific Reports, 8(1).
TL;DR:
A correction to this article has been published and is linked from the HTML and PDF versions of this paper.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Crossref, NC State University Libraries
Added: February 12, 2020
2018 article
Genome-guided phylo-transcriptomic methods and the nuclear phylogenetic tree of the paniceae grasses (vol 7, 13528, 2017)
Scientific Reports, Vol. 8.
Source: NC State University Libraries
Added: August 6, 2018
2018 article
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.
author keywords: dosage; genome evolution; network biology; phylogenomics; polyploidy; population genomics
TL;DR:
The prevalence of polyploidy across the tree of life is discussed, followed by an overview of studies investigating genome evolution and gene expression and the need for models that can accommodate polyploids is highlighted.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 10, 2018
2018 journal article
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.
author keywords: whole genome duplication; Arabidopsis thaliana; Brassica; dosage balance; metabolic network
MeSH headings : Arabidopsis / genetics; Brassica / genetics; Evolution, Molecular; Gene Dosage / genetics; Gene Duplication; Genes, Plant / genetics; Genome, Plant / genetics; Phylogeny; Polyploidy; Selection, Genetic / genetics
TL;DR:
The results paint a picture of the long-lived effects of polyploidy on plant genomes, suggesting that even yesterday’s polyploids still have distinct evolutionary trajectories.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2018 journal article
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.
author keywords: feed efficiency; metabolic network; metagenomics; rumen; vertebrate microbiome
MeSH headings : Animal Feed / analysis; Animals; Female; Gastrointestinal Microbiome; Metabolic Networks and Pathways; Metagenomics; Rumen / metabolism; Rumen / microbiology; Sheep / microbiology; Sheep / physiology
TL;DR:
System approach to the ruminal microbiome identified differences attributable to feed efficiency in the structure of the microbes' community metabolic network that were undetected at the level of individual microbial taxa or reactions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2018 journal article
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).
MeSH headings : Brassicaceae / genetics; Evolution, Molecular; Genes, Plant; Genomic Imprinting; Hybridization, Genetic; Models, Genetic; Polyploidy
TL;DR:
It is suggested that, after allopolyploidy, there are functional conflicts between interacting genes encoded in different subgenomes that are ultimately resolved through preferential duplicate loss.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2018 article
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.
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 16, 2018
2018 journal article
Tiny but mighty: The role of the rumen microbes in livestock production
Journal of Animal Science, 1.
author keywords: metagenomics; microbes; performance; production; rumen
MeSH headings : Animals; Archaea / genetics; Archaea / physiology; Bacteria / genetics; Bacteria / metabolism; Fungi / genetics; Fungi / physiology; Livestock / microbiology; Microbiota / genetics; Nutritional Status; Rumen / microbiology; Ruminants / microbiology; Ruminants / physiology; Virus Physiological Phenomena; Viruses / genetics
TL;DR:
In conclusion, elucidation of maternal, genetic, and environmental factors that influence rumen microbiome establishment and development may provide novel insights into possible mechanisms for manipulating the rumen microbial composition to enhance long-term host health and performance.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
Sources: Crossref, NC State University Libraries
Added: September 28, 2019
2017 journal article
Diet and feed efficiency status affect rumen microbial profiles of sheep
SMALL RUMINANT RESEARCH, 156, 12–19.
author keywords: Diet; Feed efficiency; Microbes; Rumen; Sheep
TL;DR:
It is confirmed that diet is a major influence on composition of the rumen microbiome and key microbial species may play important roles in the regulation of feed efficiency, and those species may differ according to diet composition.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2017 journal article
Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome
MICROBIOME, 5.
author keywords: metagenomics; vertebrate microbiome; metabolic network
MeSH headings : Animal Feed / analysis; Animals; Diet; Digestion / physiology; Edible Grain; Feeding Behavior; Gastrointestinal Microbiome / physiology; Metabolic Networks and Pathways; Metagenomics; Rumen / microbiology; Rumen / physiology; Sheep / microbiology; Sheep / physiology
TL;DR:
It is argued that network approaches, particularly those that link the microbial network with that of the host, illuminate aspects of the structure of the microbiome not seen from a strictly taxonomic perspective.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2017 conference paper
Effects of evolutionary pressure on histone modifications
2017 ieee international conference on bioinformatics and biomedicine (bibm), 2267–2267.
TL;DR:
This simulation indicates that evolutionary selection pressure of an orthologous pair (Ka/Ks ratio) is more strongly correlated with its histone modification than any other similarity measure.
(via Semantic Scholar)
Sources: NC State University Libraries, NC State University Libraries
Added: August 6, 2018
2017 journal article
Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses
SCIENTIFIC REPORTS, 7.
MeSH headings : Gene Expression Profiling; Genome, Plant; Phylogeny; Poaceae / classification; Poaceae / genetics; RNA, Plant / chemistry; RNA, Plant / isolation & purification; RNA, Plant / metabolism; Sequence Analysis, RNA
TL;DR:
This method, which the authors call “genome-guided phylo-transcriptomics”, is compared to other recently published orthology inference pipelines, and benchmarked using a set of sequenced genomes from across the grasses to provide a framework for future researchers to evaluate the costs and benefits of adding sequences to transcriptome data sets.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
Convergent Evolution and the Origin of Complex Phenotypes in the Age of Systems Biology
International Journal of Plant Sciences, 177(4), 305–318.
Contributors: J. Washburn *, K. Bird *, * & J. Pires *
author keywords: convergent evolution; parallel evolution; systems biology; comparative genomics; yeast; cancer; polyploidy; domestication; heterosis; C-4 photosynthesis
TL;DR:
Although examples of convergence are known from many domains of life, green plants in particular have remarkable promise for the study of convergence because they are experimentally tractable, have considerable “-omics” and systems biology resources available, and show convergence in a number of important and complex traits.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 12, 2019
2016 book
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).
author keywords: dosage balance; gene expression noise; polyploidy; robustness; aneuploidy; gene duplication
MeSH headings : Aneuploidy; Animals; Biological Evolution; Gene Dosage; Gene Duplication; Gene Expression; Genome; Phenotype; Protein Folding
TL;DR:
It is proposed that noise in gene expression and evolutionary strategies for its suppression play a role in generating dosage phenotypes, and an unappreciated mechanism for the preservation of duplicate genes, namely preservation to limit expression noise is outlined, arguing that it is particularly relevant in polyploid organisms.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2016 journal article
Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system
Cell and Tissue Research, 363(1), 267–278.
Contributors: B. Mordhorst*, M. Wilson * & *
author keywords: Evolution; Reproduction; Systems biology; Metabolic modeling; Selection
MeSH headings : Animals; Biological Evolution; Genitalia / physiology; Genomics; Humans; Reproduction; Sex Chromosomes / genetics; Systems Biology
TL;DR:
The way that insights from evolutionary theory and systems biology shed light on form and function in mammalian reproductive systems is discussed, including the Warburg effect, whereby glucose is fermented to lactate and alanine rather than respired to carbon dioxide.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2015 journal article
Patterns of gene conversion in duplicated yeast histones suggest strong selection on a coadapted macromolecular complex
Genome Biology and Evolution, 7(12), 3249–3258.
author keywords: genome duplication; gene conversion; histones
MeSH headings : Evolution, Molecular; Gene Conversion; Gene Duplication; Histones / genetics; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae Proteins / genetics; Selection, Genetic
TL;DR:
Evidence for interlocus gene conversion is found in five duplicated histone genes from six yeast species and it is speculated that in cases where duplicated genes code for proteins that are a part of tightly interacting complexes, selection may favor the fixation of gene conversion events in order to maintain high protein identities between duplicated copies.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2015 book
Structure, interaction, and evolution: Reflections on the natural history of proteins
In Evolutionary Biology: Biodiversification from Genotype to Phenotype (pp. 187–201).
TL;DR:
This work discusses the effect of structure, expression, and protein interactions on the rate of protein evolution, the interplay of gene duplication and protein interaction, neutral and selective forces that may shape interaction evolution, and what is known about how conserved protein interactions are over evolutionary time.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2015 journal article
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.
Contributors: P. Edger *, H. Heidel-Fischer*, M. Bekaert *, J. Rota *, G. Glöckner*, A. Platts *, D. Heckel *, J. Der*
author keywords: coevolution; phylogenomics; evolutionary novelty; chemical defenses; diversification
MeSH headings : Animals; Bayes Theorem; Biodiversity; Brassicaceae / classification; Brassicaceae / genetics; Brassicaceae / parasitology; Butterflies / classification; Butterflies / genetics; Butterflies / physiology; Evolution, Molecular; Gene Duplication; Gene Expression; Genes, Insect / genetics; Genes, Plant / genetics; Genetic Variation; Genome, Insect / genetics; Genome, Plant / genetics; Host-Parasite Interactions / genetics; Insect Proteins / genetics; Phylogeny; Plant Proteins / genetics; Species Specificity
TL;DR:
The coevolutionary interactions between plants and butterflies are examined, and evidence for an escalating evolutionary arms-race is uncovered, providing an important connection between the origins of biodiversity, coev evolution, and the role of gene and genome duplications as a substrate for novel traits.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2015 journal article
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.
Contributors: T. Taxis *, S. Wolff*, S. Gregg*, N. Minton*, C. Zhang *, J. Dai*, R. Schnabel*, J. Taylor*
MeSH headings : Animals; Cattle; DNA, Ribosomal / chemistry; Enzymes / genetics; Fatty Acids, Volatile / metabolism; Male; Metabolic Networks and Pathways; Metagenome; Metagenomics; Microbiota / genetics; Phylogeny; RNA, Ribosomal, 16S / genetics; Rumen / metabolism; Rumen / microbiology
TL;DR:
By mapping translated metagenomic reads to a microbial metabolic network, it is shown that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2014 journal article
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.
author keywords: protein interaction network; metabolic flux; gene dosage; transcriptional regulatory network; polyploidy; Saccharomyces cerevisiae
MeSH headings : Evolution, Molecular; Gene Dosage; Gene Duplication; Gene Expression Regulation, Fungal; Genes, Duplicate; Genes, Fungal; Models, Genetic; Phylogeny; Polyploidy; Protein Interaction Maps; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae Proteins / genetics
TL;DR:
Using a phylogenetic model of evolution after genome duplication (i.e., polyploidy) and 12 yeast genomes with a shared genome duplication, it is shown that the loss of duplicate genes after that duplication occurred in three phases.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2014 journal article
Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time
Current Opinion in Plant Biology, 19, 91–98.
Contributors: * , J. Birchler * & J. Pires *
MeSH headings : Diploidy; Evolution, Molecular; Gene Dosage; Gene Duplication; Plants / genetics
TL;DR:
It is argued that dosage effects represent one aspect of an emerging pluralistic framework, a framework that will use biophysics, genomic technologies, and systems-level models of cells to broaden the view of how genomes evolve.
(via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: September 12, 2019
2014 journal article
Gene duplication and phenotypic changes in the evolution of mammalian metabolic networks
PLoS ONE, 9(1).
Contributors: M. Bekaert * & *
MeSH headings : Algorithms; Animals; Cluster Analysis; Gene Dosage; Gene Duplication; Genomics; Humans; Isoenzymes / chemistry; Mammals / genetics; Metabolic Networks and Pathways / genetics; Mice; Phenotype; Principal Component Analysis; Selection, Genetic
TL;DR:
This work infer enzyme orthology networks for sixteen mammals as well as for their common ancestors using a phylogenetically-aware comparative genomics approach, and finds that the pattern of isoenzymes copy-number alterations (CNAs) in these networks is suggestive of natural selection acting on the retention of certain gene duplications.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2014 journal article
Identification and characterization of RING-finger ubiquitin ligase UBR7 in mammalian spermatozoa
Cell and Tissue Research, 356(1), 261–278.
Contributors: S. Zimmerman*, Y. Yi *, M. Sutovsky*, F. Van Leeuwen*, * & P. Sutovsky *
author keywords: Ubiquitin; Proteasome; UBR7; C14ORF130; Spermatozoa; Fertilization; Zona pellucida; Pig; Mouse
MeSH headings : Acrosome / drug effects; Acrosome / metabolism; Animals; Antibodies, Blocking / pharmacology; Blotting, Western; Fertilization in Vitro; Fluorescent Antibody Technique; Humans; Male; Mice; Phylogeny; Protein Transport / drug effects; RNA, Messenger / genetics; RNA, Messenger / metabolism; Spermatids / cytology; Spermatids / drug effects; Spermatids / metabolism; Spermatozoa / cytology; Spermatozoa / drug effects; Spermatozoa / enzymology; Swine; Testis / drug effects; Testis / metabolism; Ubiquitin-Protein Ligases / genetics; Ubiquitin-Protein Ligases / metabolism
TL;DR:
Genomic analysis indicated a high degree of evolutionary conservation, remarkably constant purifying selection and conserved testis expression of the UBR7 gene, which provides the first evidence of ubiquitin ligase activity in mammalian spermatozoa and indicate U BR7 involvement in spermiogenesis.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2014 journal article
Large-Scale Pairwise Alignments on GPU Clusters: Exploring the Implementation Space
Journal of Signal Processing Systems, 77(1-2), 131–149.
author keywords: Heterogeneous system; Sequence alignment; GPU
TL;DR:
This work presents four GPU implementations for large-scale pairwise sequence alignment, and suggests that LazyRScan-mNW is the preferred solution for applications that require performing the trace-back operation only on a subset of the considered sequence pairs.
(via Semantic Scholar)
Sources: ORCID, Crossref
Added: July 20, 2019
2014 journal article
Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment of its phylogenetic utility across the brassicaceae (mustards)
PLoS ONE, 9(7).
Contributors: P. Edger *, M. Tang *, K. Bird *, D. Mayfield*, * , K. Mummenhoff *, M. Koch *, J. Pires *
MeSH headings : Brassicaceae / genetics; DNA, Ribosomal Spacer / chemistry; Genes, rRNA; Nucleic Acid Conformation; Phylogeny
TL;DR:
These analyses of ITS1 and ITS2 for 50 species suggest that both sequences are instead under selective constraints to preserve proper secondary structure, likely to maintain complete self-splicing functions, and thus are not neutrally-evolving phylogenetic markers.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2014 journal article
The yeast protein interaction network has a capacity for self-organization
FEBS Journal, 281(15), 3420–3432.
Contributors: A. Dhroso*, D. Korkin * & *
author keywords: metabolic channeling; protein interaction network; robustness; self-assembly
MeSH headings : Computer Simulation; Fungal Proteins / chemistry; Fungal Proteins / physiology; Models, Molecular; Phosphorylation; Protein Interaction Maps; Protein Processing, Post-Translational; Saccharomyces / metabolism
TL;DR:
A lattice model of molecular crowding is used, together with literature‐derived protein interactions and abundances, to describe the molecular organization and stoichiometry of local cellular regions, showing that physical protein–protein interactions induce emergent structures not seen when random interaction networks are modeled.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2013 journal article
A Conserved Mammalian Protein Interaction Network
PLoS ONE, 8(1).
Contributors: Å. Pérez-Bercoff*, C. Hudson * & *
MeSH headings : Animals; Conserved Sequence / genetics; Evolution, Molecular; Humans; Mammals / classification; Mammals / genetics; Models, Genetic; Phylogeny; Primates / genetics; Protein Interaction Maps / genetics; Time Factors
TL;DR:
Paired alignments of orthologous and putatively interacting protein-coding genes from eight mammals are analyzed to suggest that, on the whole, protein interactions in mammals are under selective constraint, presumably due to their functional roles.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2013 conference paper
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.
Contributors: D. Li *, K. Sajjapongse*, H. Truong*, * & M. Becchi *
TL;DR:
This paper presents a parallel version of the Needleman-Wunsch alignment algorithm for graphics processing units (GPUs), which can be used for all-against-all pairwise comparisons on large datasets.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2013 journal article
Diet Alters Both the Structure and Taxonomy of the Ovine Gut Microbial Ecosystem
DNA Research, 21(2), 115–125.
Contributors: M. Ellison *, * , R. Cockrum *, K. Austin*, H. Truong*, M. Becchi*, W. Lamberson *, K. Cammack*
author keywords: Ovis aries; microbiome; 16S subunit
MeSH headings : Animals; Bacteria / classification; Bacteria / genetics; DNA, Ribosomal / genetics; Diet; Ecosystem; Metagenome; Rumen / microbiology; Sequence Analysis, DNA; Sheep / microbiology
TL;DR:
Differences in taxonomic distributions appear to be grounded in an underlying common input of new microbial individuals into the rumen environment, with common organisms from one feed group being present in the other, but at much lower abundance.
(via Semantic Scholar)
Sources: ORCID, Crossref
Added: July 20, 2019
2013 journal article
Extreme evolutionary conservation of functionally important regions in H1N1 influenza proteome
PLoS ONE, 8(11).
Contributors: S. Warren*, X. Wan *, * & D. Korkin *
MeSH headings : Biological Evolution; Influenza A Virus, H1N1 Subtype / classification; Influenza A Virus, H1N1 Subtype / genetics; Influenza A Virus, H1N1 Subtype / metabolism; Phylogeny; Viral Proteins / genetics; Viral Proteins / metabolism
TL;DR:
A single coherent pattern of faster evolution on the protein surfaces that characterizes all influenza proteins is found, consistent with the events of inter-species reassortment, the worldwide introduction of the flu vaccine in the early 80’s, as well as the differences caused by the geographic origins of the virus.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2013 journal article
Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales
Seminars in Cell and Developmental Biology, 24(4), 320–331.
Contributors: D. Mayfield-Jones*, J. Washburn *, T. Arias *, P. Edger *, J. Pires * & *
author keywords: Polyploidy; WGD; Network evolution; Meiosis; Mitosis; Cancer; Warburg effect; Crabtree effect
MeSH headings : Animals; Biological Evolution; Evolution, Molecular; Genome; Humans; Plants / genetics; Polyploidy
TL;DR:
It is argued that the study of polyploidy across organisms, cell types, and time scales serves not only as a window into basic cell biology, but also as a basis for a predictive biology with applications ranging from crop improvement to treating cancer.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2012 journal article
Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy
Genetics, 190(4), 1563–1574.
Contributors: H. Tang *, M. Woodhouse *, F. Cheng *, J. Schnable *, B. Pedersen *, * , X. Wang *, M. Freeling *, J. Pires *
MeSH headings : Arabidopsis / genetics; Brassica rapa / classification; Brassica rapa / genetics; Cell Nucleus / genetics; Chromosomes, Plant / genetics; Computer Simulation; DNA, Plant / genetics; Evolution, Molecular; Exons; Genome, Plant; Models, Genetic; Molecular Sequence Data; Phylogeny; Polyploidy; Recombination, Genetic; Repetitive Sequences, Nucleic Acid; Sequence Deletion
TL;DR:
It is concluded that the observed patterns of the triplicated regions in the Brassica genome are best explained by a two-step fractionation model, which could influence the potential to generate morphological diversity—a hallmark of the Brassicas genus.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2012 journal article
Cloning and characterization of the peptidoglycan recognition protein genes in the mosquito, Armigeres subalbatus (Diptera: Culicidae)
Journal of Medical Entomology, 49(3), 656–671.
Contributors: S. Wang *, * , R. Ou* & B. Beerntsen *
author keywords: peptidoglycan recognition protein; Armigeres subalbatus; mosquito; AsPGRP; immune response
MeSH headings : Animals; Carrier Proteins / genetics; Carrier Proteins / metabolism; Cloning, Molecular; Culicidae / genetics; Culicidae / physiology; Evolution, Molecular; Female; Insect Proteins / genetics; Insect Proteins / metabolism; Life Cycle Stages; Male; Phylogeny; Protein Isoforms / genetics; Protein Isoforms / metabolism; Sequence Alignment; Sequence Analysis, DNA
TL;DR:
Phylogenetic analysis indicated that PGRPs represent an ancient gene family that has primarily diverged through speciation events among these Dipterans, with only a limited number of lineage specific gene duplications.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2012 journal article
Long identical multispecies elements in plant and animal genomes
Proceedings of the National Academy of Sciences of the United States of America, 109(19).
Contributors: J. Reneker*, E. Lyons *, * , J. Pires *, M. Freeling *, C. Shyu*, D. Korkin *
author keywords: extreme conservation; repetitive elements
MeSH headings : Amino Acid Sequence; Animals; Arabidopsis / genetics; Base Sequence; Cell Nucleus / genetics; Chromosome Mapping; Chromosomes, Mammalian / genetics; Chromosomes, Plant / genetics; Conserved Sequence / genetics; Evolution, Molecular; Gene Regulatory Networks; Genome / genetics; Genome, Mitochondrial / genetics; Genome, Plant / genetics; Humans; Mice; Models, Genetic; Molecular Sequence Data; Rats; Species Specificity; Synteny
TL;DR:
Despite the common presence of LIMEs in both animal and plant lineages, the evolutionary processes involved in the creation and maintenance of these elements differ in the two groups and are likely attributable to several mechanisms, including transfer of genetic material from organellar to nuclear genomes, de novo sequence manufacturing, and purifying selection.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2012 journal article
Metabolic and evolutionary costs of herbivory defense: Systems biology of glucosinolate synthesis
New Phytologist, 196(2), 596–605.
Contributors: M. Bekaert *, P. Edger *, C. Hudson *, J. Pires * & *
author keywords: adaptation; Arabidopsis thaliana; costly traits; flux balance analysis; metabolic network
MeSH headings : Amino Acids / metabolism; Arabidopsis / genetics; Arabidopsis / immunology; Arabidopsis / metabolism; Biological Evolution; Biomass; Biosynthetic Pathways / genetics; Gene Duplication; Gene Expression Regulation, Plant; Glucosinolates / biosynthesis; Herbivory / genetics; Metabolome / genetics; Models, Biological; Photons; Systems Biology
TL;DR:
It is found that glucosinolate production can increase photosynthetic requirements by at least 15% and that this cost is specific to the suite of glucos inolates found in A. thaliana, with other combinations of glucOSinolates being even more costly.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2012 journal article
Polyploidy and the Evolution of Complex Traits
International Journal of Evolutionary Biology, 2012, 1–12.
TL;DR:
It is argued that the evolutionary importance of WGD may require updating certain aspects of modern evolutionary theory, perhaps helping to synthesize a new evolutionary systems biology.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: November 17, 2019
2012 journal article
Very low rate of gene conversion in the yeast genome
Molecular Biology and Evolution, 29(12), 3817–3826.
Contributors: C. Casola *, * & M. Hahn*
author keywords: gene duplication; Saccharomyces cerevisiae; interlocus gene conversion
MeSH headings : Base Sequence; Computational Biology; Evolution, Molecular; Gene Conversion / genetics; Gene Duplication / genetics; Genome, Fungal / genetics; Likelihood Functions; Models, Genetic; Molecular Sequence Data; Phylogeny; Saccharomyces cerevisiae / genetics; Sequence Alignment; Species Specificity
TL;DR:
This work applies four different methodologies-including one approach that closely mirrors Gao and Innan's method-to estimate the level of interlocus gene conversion in Scer, and points to a maximum conversion level of 13% between paralogs in this species, in close agreement with most estimates of IGC in eukaryotes.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2012 book
Yeast as a window into changes in genome complexity due to polyploidization
In Polyploidy and Genome Evolution (Vol. 9783642314421, pp. 293–308).
Contributors: C. Hudson * & *
TL;DR:
The role of the WGD in shaping several complex metabolic and regulatory phenotypes is explored, including the dosage balance hypothesis as it applies to the yeast WGD and the selective forces that act on the W GD-produced paralogs and shape their patterns of loss and retention.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2011 journal article
Copy number alterations among mammalian enzymes cluster in the metabolic network
Molecular Biology and Evolution, 28(2), 1111–1121.
Contributors: M. Bekaert * & *
author keywords: comparative genomic; gene duplication; gene dosage; mammals; metabolic networks and pathways; milk
MeSH headings : Animals; Cattle; Gene Dosage; Humans; Mammals / metabolism; Membrane Transport Proteins / genetics; Metabolic Networks and Pathways; Milk / metabolism
TL;DR:
An excess of transporter genes in cattle involved in the milk production, secretion, and regulation is found and a potential role for dosage selection in the evolution of mammalian metabolic networks is suggested.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2011 journal article
Expression level, cellular compartment and metabolic network position all influence the average selective constraint on mammalian enzymes
BMC Evolutionary Biology, 11(1).
Contributors: C. Hudson * & *
MeSH headings : Animals; Enzymes / genetics; Enzymes / metabolism; Gene Expression; Humans; Mammals / genetics; Mammals / metabolism; Metabolic Networks and Pathways; Protein Transport; Selection, Genetic
TL;DR:
The results imply that the relationship between selective constraint and enzyme centrality is complex: the strength of selective constraint acting on mammalian genes is quite variable and does not appear to exclusively follow patterns seen in other organisms.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 12, 2019
2011 journal article
Patterns of indirect protein interactions suggest a spatial organization to metabolism
Molecular BioSystems, 7(11), 3056–3064.
Contributors: A. Pérez-Bercoff*, A. McLysaght * & *
MeSH headings : Binding Sites; Escherichia coli / metabolism; Escherichia coli Proteins / chemistry; Escherichia coli Proteins / metabolism; Fungal Proteins / chemistry; Fungal Proteins / metabolism; Humans; Mediator Complex / metabolism; Metabolic Networks and Pathways; Protein Interaction Maps; Proteins / chemistry; Proteins / metabolism; Species Specificity; Yeasts / metabolism
TL;DR:
Analysis of the metabolic and protein-protein interactions networks of Escherichia coli, yeast and humans is able to show that all three species have many more indirect protein interactions linking enzymes that share metabolites than would be expected by chance.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2011 journal article
Selection for higher gene copy number after different types of plant gene duplications
Genome Biology and Evolution, 3(1), 1369–1380.
Contributors: C. Hudson *, E. Puckett *, M. Bekaert *, J. Pires * & *
author keywords: dosage selection; genome duplication; gene duplication
MeSH headings : Arabidopsis / genetics; Evolution, Molecular; Gene Dosage; Gene Duplication; Genes, Plant; Ion Pumps / genetics; Multigene Family; Phylogeny; Plant Proteins / genetics; Plants / genetics; Sorghum / genetics
TL;DR:
It is found that the different duplication mechanisms give rise to differing selective constraints, and the exact nature of this pattern varies between the gene families, and is argued that the duplication mechanism alone does not define a duplicated gene's subsequent evolutionary trajectory.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2011 journal article
The genome of the mesopolyploid crop species Brassica rapa
Nature Genetics, 43(10), 1035–1039.
Contributors: X. Wang, H. Wang, J. Wang, R. Sun, J. Wu, S. Liu, Y. Bai, J. Mun
MeSH headings : Arabidopsis / genetics; Brassica rapa / genetics; Chromosomes, Artificial, Bacterial / genetics; Chromosomes, Plant / genetics; Contig Mapping; Evolution, Molecular; Gene Duplication; Genes, Plant; Genome, Plant; Molecular Sequence Annotation; Molecular Sequence Data; Phylogeny; Polyploidy; Sequence Analysis, DNA
TL;DR:
The annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage, and used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 12, 2019
2011 journal article
Transcriptional robustness and protein interactions are associated in yeast
BMC Systems Biology, 5.
Contributors: M. Bekaert * & *
author keywords: Aneuploidy Dosage balance; Epistasis; Protein-Protein Interactions; Saccharomyces cerevisiae
MeSH headings : Aneuploidy; Epistasis, Genetic; Fungal Proteins / chemistry; Gene Expression Profiling; Gene Expression Regulation, Fungal; Genes, Fungal; Models, Biological; Protein Interaction Mapping; RNA, Messenger / metabolism; Regression Analysis; Saccharomyces cerevisiae / metabolism; Systems Biology / methods; Transcription, Genetic
TL;DR:
This work shows a general association between the degree to which yeast cells have evolved mechanisms to buffer changes in gene expression and whether they possess protein-protein interactions, and suggests that these observations can be best understood as resulting from the higher fitness cost of misexpression in epistatic genes and a commensurate greater regulatory control of them.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2011 journal article
Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints
Plant Cell, 23(5), 1719–1728.
Contributors: M. Bekaert *, P. Edger *, J. Chris Pires * & *
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Computational Biology; Evolution, Molecular; Gene Dosage / genetics; Gene Duplication; Genome, Plant / genetics; Logistic Models; Models, Genetic; Multigene Family; Polyploidy
TL;DR:
It is argued for an interplay of relative and absolute dosage constraints, such that the relative constraints imposed by the recent WGD are still being resolved by evolution, while they have been essentially fully resolved for the ancient event.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2010 journal article
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
Source: ORCID
Added: September 12, 2019
2010 journal article
Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast
Proceedings of the Royal Society B: Biological Sciences, 277(1683), 869–876.
author keywords: whole-genome duplication; network evolution; regulatory evolution
MeSH headings : Computational Biology; Evolution, Molecular; Gene Duplication; Gene Regulatory Networks / genetics; Gene Regulatory Networks / physiology; Genome, Fungal / genetics; Genome, Fungal / physiology; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / physiology
TL;DR:
The reorganization of the yeast transcriptional regulatory network after whole-genome duplication is studied, and it is found that genes targeted by many TFs appear to be preferentially retained in duplicate after WGD, an effect I attribute to selection to maintain dosage balance in the regulatory networkAfter WGD.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2010 journal article
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<sup>Asn</sup>
BMC Microbiology, 10.
MeSH headings : Amino Acid Sequence; Bacillus cereus / chemistry; Bacillus cereus / enzymology; Bacillus cereus / genetics; Bacillus cereus / metabolism; Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Gene Expression Regulation, Enzymologic; Lysine-tRNA Ligase / chemistry; Lysine-tRNA Ligase / genetics; Lysine-tRNA Ligase / metabolism; Molecular Sequence Data; RNA, Transfer, Amino Acyl / metabolism; RNA, Transfer, Asn / metabolism; Regulatory Elements, Transcriptional; Sequence Alignment
TL;DR:
The T box element controlling lysK (encoding LysRS1) expression in B. cereus strain 14579 is functional, but unusually responds to depletion of charged tRNALys and tRNAAsn.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2009 journal article
MeSH headings : Amino Acid Substitution / genetics; Animals; Evolution, Molecular; Genetic Variation; Humans; Membrane Proteins / chemistry; Membrane Proteins / genetics; Models, Genetic; Mutation; Selection, Genetic
TL;DR:
It is suggested that natural selection can function to preserve protein interactions without requiring strict conservation of the individual residue contacts that impart those interactions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2009 journal article
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.
Contributors: J. Decker, J. Pires, * , S. McKay, M. Heaton *, K. Chen *, A. Cooper *, J. Vilkki *
author keywords: ancient DNA; Pecorans; domestication
MeSH headings : Animals; Biological Evolution; Breeding; Cattle; DNA / analysis; DNA / genetics; Extinction, Biological; Fossils; Genomics / methods; Genotype; Phylogeny; Ruminants / genetics
TL;DR:
It is demonstrated that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species diverged up to 29 million years ago and that the produced genotypes can beused to resolve the phylogeny for this rapidly radiated infraorder.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2009 journal article
Solvent exposure imparts similar selective pressures across a range of yeast proteins
Molecular Biology and Evolution, 26(5), 1155–1161.
Contributors: * & P. Stadler *
author keywords: amino acid substitution; evolutionary models; protein structure
MeSH headings : Amino Acid Substitution / genetics; Amino Acids; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae Proteins / chemistry; Saccharomyces cerevisiae Proteins / genetics; Selection, Genetic; Solvents / chemistry; Structural Homology, Protein; Surface Properties
TL;DR:
It is shown that although residue volume and hydropathy are strongly conserved across most alignments, there is little variation in interior versus surface conservation for these two properties.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2008 journal article
Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens
BMC GENOMICS, 9.
Contributors: A. Powell*, * , D. Brown n, I. Carbone n & R. Dean n
MeSH headings : Computational Biology; Evolution, Molecular; Fungi / genetics; Fungi / pathogenicity; Gene Duplication; Genomics; Multigene Family / genetics; Sequence Homology
TL;DR:
Differences in the overall levels of gene duplication in phytopathogenic species versus non-pathogenic relatives implicate gene inventory flux as an important virulence-associated process in fungi.
(via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: August 6, 2018
2008 journal article
GenomeVx: Simple web-based creation of editable circular chromosome maps
Bioinformatics, 24(6), 861–862.
Contributors: * & K. Wolfe *
MeSH headings : Chromosome Mapping / methods; Computer Graphics; Documentation / methods; Internet; Software; User-Computer Interface; Word Processing / methods
TL;DR:
GenomeVx is a web-based tool for making editable, publication-quality, maps of mitochondrial and chloroplast genomes and of large plasmids that show the location of genes and chromosomal features as well as a position scale.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2008 journal article
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.
Source: ORCID
Added: September 12, 2019
2008 journal article
Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast
Genetics, 179(3), 1681–1692.
Contributors: * & K. Wolfe *
MeSH headings : Candida glabrata / genetics; Gene Duplication; Genes, Fungal; Genome, Fungal / genetics; Models, Genetic; Phylogeny; Saccharomyces cerevisiae / genetics; Sequence Homology, Nucleic Acid; Species Specificity; Time Factors; Yeasts / genetics
TL;DR:
It is suggested that while duplicate copies of some genes may be lost neutrally after WGD, another set of genes May be initially preserved in duplicate by natural selection for reasons including dosage.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2008 journal article
Turning a hobby into a job: How duplicated genes find new functions
Nature Reviews Genetics, 9(12), 938–950.
Contributors: * & K. Wolfe *
MeSH headings : Animals; Galactokinase / genetics; Gene Dosage; Gene Duplication; Gene Expression; Genome; Humans; Mutation; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae Proteins / genetics; Selection, Genetic; Transcription Factors / genetics
TL;DR:
Genomic data suggest that different gene classes tend to be retained after single-gene and whole-genome duplications, and in many cases the 'new' function of one copy is a secondary property that was always present, but that has been co-opted to a primary role after the duplication.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2007 journal article
Increased glycolytic flux as an outcome of whole‐genome duplication in yeast
Molecular Systems Biology, 3(1), 129.
Contributors: * & K. Wolfe *
author keywords: evolution; genome duplication; metabolism
MeSH headings : Cell Compartmentation; Ecology; Fermentation; Gene Duplication; Genes, Duplicate; Genes, Fungal; Genome, Fungal / genetics; Glycolysis / genetics; Models, Biological; Monosaccharide Transport Proteins / genetics; Respiration / genetics; Saccharomyces cerevisiae / enzymology; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Selection, Genetic
TL;DR:
It is proposed that the loss of other redundant genes throughout the genome resulted in incremental dosage increases for the surviving duplicated glycolytic genes, which gave post‐WGD yeasts a growth advantage through rapid glucose fermentation; one of this lineage's many adaptations to glucose‐rich environments.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 12, 2019
2007 journal article
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.
Contributors: D. Scannell*, A. Frank *, * , K. Byrne *, M. Woolfit* & K. Wolfe *
author keywords: genomics; polyploidy; reciprocal gene loss; Vanderwaltozyma polyspora
MeSH headings : Base Sequence; Conserved Sequence; Evolution, Molecular; Gene Duplication; Gene Order; Genes, Duplicate; Genome, Fungal / genetics; Kluyveromyces / genetics; Likelihood Functions; Models, Genetic; Molecular Sequence Data; Saccharomyces cerevisiae / genetics; Sequence Homology, Nucleic Acid; Time Factors
TL;DR:
It is proposed that the yeast WGD was probably an autopolyploidization, and the patterns of gene loss changed over time, parallels an increasing restriction of reciprocal gene loss to more slowly evolving gene pairs over time and suggests that, as duplicate genes diverged, one gene copy became favored over the other.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2007 journal article
Modeling amino acid substitution patterns in orthologous and paralogous genes
Molecular Phylogenetics and Evolution, 42(2), 298–307.
Contributors: * , G. Wagner * & P. Stadler *
author keywords: amino acid substitution; evolutionary models; protein evolution
MeSH headings : Actins / genetics; Amino Acid Substitution / genetics; Amino Acids / chemistry; Amino Acids / genetics; Animals; Databases, Nucleic Acid; Evolution, Molecular; Hemoglobins / genetics; Humans; Hydrophobic and Hydrophilic Interactions; Isoelectric Point; Models, Genetic; Myosins / genetics; Phylogeny; Rhodopsin / genetics; Rod Opsins / genetics
TL;DR:
It is found that, although patterns of amino acid substitution vary temporally within the history of a gene, variation is not greater in paralogous than in orthologous genes, and improved understanding of such gene-specific variation in substitution patterns may have implications for applications such as sequence alignment and phylogenetic inference.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2006 journal article
Functional Partitioning of Yeast Co-Expression Networks after Genome Duplication
PLoS Biology, 4(4), e109.
Contributors: * & K. Wolfe *
Ed(s): L. Hurst
MeSH headings : Base Sequence; Biological Evolution; Databases, Genetic; Fungal Proteins / genetics; Fungal Proteins / metabolism; Gene Duplication; Gene Expression Regulation, Fungal / genetics; Genome, Fungal / genetics; Models, Biological; Phenotype; Protein Binding; Yeasts / genetics; Yeasts / metabolism
TL;DR:
It is proposed that the rationalization of network structure through the loss of pair-wise gene interactions after genome duplication provides a mechanism for the creation of semi-independent daughter networks through the division of ancestral functions between these daughter networks.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 12, 2019
2005 journal article
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
Source: ORCID
Added: September 12, 2019
2004 journal article
A fast algorithm for determining the best combination of local alignments to a query sequence
BMC Bioinformatics, 5.
Contributors: * & A. Wagner *
MeSH headings : Algorithms; Animals; Caenorhabditis elegans / genetics; Computational Biology / methods; Computational Biology / statistics & numerical data; Computer Graphics / statistics & numerical data; DNA, Helminth / genetics; DNA, Mitochondrial / genetics; Drosophila melanogaster / genetics; Genome; Genome, Human; Hagfishes / genetics; Humans; Mitochondria / genetics; Sequence Alignment / methods; Sequence Alignment / statistics & numerical data
TL;DR:
A graph-based algorithm for combining multiple local alignments to a query sequence into the single combination of alignments that either covers the maximal portion of the query or results in the single highest alignment score to the query is proposed.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2004 book
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).
Contributors: S. Babu*, * , E. Eller*, C. Roberts *, K. Gowan*, G. Eisenbarth*, P. Fain*, P. Vardi*
author keywords: IDDM17; genome screen; genehunter; type 1 diabetes
MeSH headings : Arabs / genetics; Chromosomes, Human, Pair 10; Diabetes Mellitus, Type 1 / genetics; Female; Genetic Linkage; Genetic Markers; Genetic Predisposition to Disease; Genetic Testing; Genome, Human; Humans; Lod Score; Male; Statistics, Nonparametric
TL;DR:
The results demonstrate the strong potential of genetically homogenous, extended families for mapping genes that contribute to a complex disease.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2004 journal article
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.
Contributors: * & A. Wagner *
author keywords: Caenorhabditis elegans; gene duplication; mutational robustness
MeSH headings : Animals; Caenorhabditis elegans / genetics; Databases, Genetic; Evolution, Molecular; Genes, Duplicate / genetics; Multigene Family; Mutation / genetics; Oligonucleotide Array Sequence Analysis; Phenotype; RNA Interference
TL;DR:
It is found that mutational robustness is greatest for closely related gene duplicates, large gene families and similarly expressed genes.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: September 12, 2019
2004 journal article
Molecular Evolution in Large Genetic Networks: Does Connectivity Equal Constraint?
Journal of Molecular Evolution, 58(2), 203–211.
Contributors: M. Hahn*, * & A. Wagner *
author keywords: power-law; mutational robustness; selective constraint; genetic network
MeSH headings : Energy Metabolism / genetics; Escherichia coli; Escherichia coli Proteins / genetics; Escherichia coli Proteins / metabolism; Evolution, Molecular; Likelihood Functions; Point Mutation / genetics; Protein Interaction Mapping; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins / genetics; Saccharomyces cerevisiae Proteins / metabolism; Selection, Genetic; Two-Hybrid System Techniques
TL;DR:
The finding that highly connected proteins can tolerate just as many amino acid substitutions as other proteins leads us to conclude that power-laws in cellular networks do not reflect selection for mutational robustness.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: ORCID
Added: September 12, 2019
2003 journal article
Asymmetric sequence divergence of duplicate genes
Genome Research, 13(9), 2052–2058.
MeSH headings : Amino Acid Substitution / genetics; Animals; Caenorhabditis elegans / genetics; Computational Biology / methods; Computational Biology / statistics & numerical data; Drosophila melanogaster / genetics; Evolution, Molecular; Gene Expression Profiling / methods; Gene Expression Profiling / statistics & numerical data; Gene Expression Regulation / genetics; Gene Expression Regulation, Fungal / genetics; Genes, Duplicate; Genetic Variation / genetics; Saccharomyces cerevisiae / genetics; Schizosaccharomyces / genetics
Source: ORCID
Added: September 12, 2019
2003 journal article
Convergent evolution of gene circuits
Nature Genetics, 34(3), 264–266.
Contributors: * & A. Wagner *
MeSH headings : Escherichia coli / genetics; Evolution, Molecular; Feedback / physiology; Gene Duplication; Gene Expression Regulation / genetics; Genes, Bacterial / physiology; Genes, Fungal / physiology; Genome, Bacterial; Genome, Fungal; Models, Genetic; Saccharomyces cerevisiae / genetics; Schizosaccharomyces / genetics; Transcription, Genetic / genetics
TL;DR:
It is shown that multiple types of transcriptional regulation circuitry in Escherichia coli and the yeast Saccharomyces cerevisiae have evolved independently and not by duplication of one or a few ancestral circuits.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2003 journal article
Parallel genehunter: Implementation of linkage analysis package for distributed-memory architectures
Journal of Parallel and Distributed Computing, 63(7-8), 674–682.
Contributors: * , S. Plimpton*, W. Old*, A. Wagner *, P. Fain, T. Pacheco, G. Heffelfinger*
TL;DR:
Preliminary benchmarks indicate reasonable scalability of the algorithm even for fixed-size problems, with parallel efficiencies of 75% or more on up to 128 processors.
(via Semantic Scholar)
Source: ORCID
Added: September 12, 2019
2002 journal article
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
Source: ORCID
Added: September 12, 2019
2002 conference paper
Parallel genehunter: Implementation of a linkage analysis package for distributed-memory architectures
Proceedings - International Parallel and Distributed Processing Symposium, IPDPS 2002, 184–191.
Contributors: * , S. Plimpton*, W. Old*, A. Wagner *, P. Fain* & G. Heffelfinger*
Source: ORCID
Added: September 12, 2019
2001 journal article
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
Source: ORCID
Added: September 12, 2019
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