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Baby genomics: tracing the evolutionary changes that gave rise to placentation.

Hao Y, Lee HJ, Baraboo M, Burch K, Maurer T, Somarelli JA, Conant GC.

Genome Biol Evol. 2020 Feb 13. pii: evaa026. doi: 10.1093/gbe/evaa026. [Epub ahead of print]


A Single, Shared Triploidy in Three Species of Parasitic Nematodes.

Schoonmaker A, Hao Y, Bird DM, Conant GC.

G3 (Bethesda). 2020 Jan 7;10(1):225-233. doi: 10.1534/g3.119.400650.


Bovine Genome Database: new annotation tools for a new reference genome.

Shamimuzzaman M, Le Tourneau JJ, Unni DR, Diesh CM, Triant DA, Walsh AT, Tayal A, Conant GC, Hagen DE, Elsik CG.

Nucleic Acids Res. 2020 Jan 8;48(D1):D676-D681. doi: 10.1093/nar/gkz944.


Functional characterization of SMN evolution in mouse models of SMA.

Osman EY, Bolding MR, Villalón E, Kaifer KA, Lorson ZC, Tisdale S, Hao Y, Conant GC, Pires JC, Pellizzoni L, Lorson CL.

Sci Rep. 2019 Jul 1;9(1):9472. doi: 10.1038/s41598-019-45822-8.


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

An H, Qi X, Gaynor ML, Hao Y, Gebken SC, Mabry ME, McAlvay AC, Teakle GR, Conant GC, Barker MS, Fu T, Yi B, Pires JC.

Nat Commun. 2019 Jun 28;10(1):2878. doi: 10.1038/s41467-019-10757-1.


Predicting residual feed intake status using rumen microbial profiles in ewe lambs1.

Ellison MJ, Conant GC, Lamberson WR, Austin KJ, van Kirk E, Cunningham HC, Rule DC, Cammack KM.

J Anim Sci. 2019 Jul 2;97(7):2878-2888. doi: 10.1093/jas/skz170.


RUMINANT NUTRITION SYMPOSIUM: Tiny but mighty: the role of the rumen microbes in livestock production.

Cammack KM, Austin KJ, Lamberson WR, Conant GC, Cunningham HC.

J Anim Sci. 2018 Sep 29;96(10):4481. doi: 10.1093/jas/sky331. No abstract available.


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

Patil RD, Ellison MJ, Wolff SM, Shearer C, Wright AM, Cockrum RR, Austin KJ, Lamberson WR, Cammack KM, Conant GC.

J Anim Sci. 2018 Jun 4;96(6):2113-2124. doi: 10.1093/jas/sky096.


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

Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC.

Sci Rep. 2018 May 2;8(1):7120. doi: 10.1038/s41598-018-25620-4.


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

Hao Y, Washburn JD, Rosenthal J, Nielsen B, Lyons E, Edger PP, Pires JC, Conant GC.

Genome Biol Evol. 2018 Mar 1;10(3):999-1011. doi: 10.1093/gbe/evy061.


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

Emery M, Willis MMS, Hao Y, Barry K, Oakgrove K, Peng Y, Schmutz J, Lyons E, Pires JC, Edger PP, Conant GC.

PLoS Genet. 2018 Mar 28;14(3):e1007267. doi: 10.1371/journal.pgen.1007267. eCollection 2018 Mar.


RUMINANT NUTRITION SYMPOSIUM: Tiny but mighty: the role of the rumen microbes in livestock production.

Cammack KM, Austin KJ, Lamberson WR, Conant GC, Cunningham HC.

J Anim Sci. 2018 Mar 6;96(2):752-770. doi: 10.1093/jas/skx053. Erratum in: J Anim Sci. 2018 Sep 29;96(10):4481.


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

Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC.

Sci Rep. 2017 Oct 19;7(1):13528. doi: 10.1038/s41598-017-13236-z. Erratum in: Sci Rep. 2018 May 2;8(1):7120.


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

Wolff SM, Ellison MJ, Hao Y, Cockrum RR, Austin KJ, Baraboo M, Burch K, Lee HJ, Maurer T, Patil R, Ravelo A, Taxis TM, Truong H, Lamberson WR, Cammack KM, Conant GC.

Microbiome. 2017 Jun 8;5(1):60. doi: 10.1186/s40168-017-0274-6.


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

Pires JC, Conant GC.

Annu Rev Genet. 2016 Nov 23;50:113-131. Epub 2016 Sep 12. Review.


Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex.

Scienski K, Fay JC, Conant GC.

Genome Biol Evol. 2015 Nov 11;7(12):3249-58. doi: 10.1093/gbe/evv216.


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

Taxis TM, Wolff S, Gregg SJ, Minton NO, Zhang C, Dai J, Schnabel RD, Taylor JF, Kerley MS, Pires JC, Lamberson WR, Conant GC.

Nucleic Acids Res. 2015 Nov 16;43(20):9600-12. doi: 10.1093/nar/gkv973. Epub 2015 Sep 29.


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

Mordhorst BR, Wilson ML, Conant GC.

Cell Tissue Res. 2016 Jan;363(1):267-278. doi: 10.1007/s00441-015-2257-x. Epub 2015 Aug 8. Review.


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

Edger PP, Heidel-Fischer HM, Bekaert M, Rota J, Glöckner G, Platts AE, Heckel DG, Der JP, Wafula EK, Tang M, Hofberger JA, Smithson A, Hall JC, Blanchette M, Bureau TE, Wright SI, dePamphilis CW, Eric Schranz M, Barker MS, Conant GC, Wahlberg N, Vogel H, Pires JC, Wheat CW.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8362-6. doi: 10.1073/pnas.1503926112. Epub 2015 Jun 22.


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

Conant GC.

Mol Biol Evol. 2014 Dec;31(12):3184-93. doi: 10.1093/molbev/msu250. Epub 2014 Aug 25.


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

Dhroso A, Korkin D, Conant GC.

FEBS J. 2014 Aug;281(15):3420-32. doi: 10.1111/febs.12870. Epub 2014 Jul 1.


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

Conant GC, Birchler JA, Pires JC.

Curr Opin Plant Biol. 2014 Jun;19:91-8. doi: 10.1016/j.pbi.2014.05.008. Epub 2014 Jun 5. Review.


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

Bekaert M, Conant GC.

PLoS One. 2014 Jan 28;9(1):e87115. doi: 10.1371/journal.pone.0087115. eCollection 2014.


Diet alters both the structure and taxonomy of the ovine gut microbial ecosystem.

Ellison MJ, Conant GC, Cockrum RR, Austin KJ, Truong H, Becchi M, Lamberson WR, Cammack KM.

DNA Res. 2014;21(2):115-25. doi: 10.1093/dnares/dst044. Epub 2013 Oct 29.


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

Mayfield-Jones D, Washburn JD, Arias T, Edger PP, Pires JC, Conant GC.

Semin Cell Dev Biol. 2013 Apr;24(4):320-31. doi: 10.1016/j.semcdb.2013.02.002. Epub 2013 Mar 1. Review.


A conserved mammalian protein interaction network.

Pérez-Bercoff Å, Hudson CM, Conant GC.

PLoS One. 2013;8(1):e52581. doi: 10.1371/journal.pone.0052581. Epub 2013 Jan 2.


Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinolate synthesis.

Bekaert M, Edger PP, Hudson CM, Pires JC, Conant GC.

New Phytol. 2012 Oct;196(2):596-605. doi: 10.1111/j.1469-8137.2012.04302.x. Epub 2012 Sep 4.


Polyploidy and the evolution of complex traits.

Huminiecki L, Conant GC.

Int J Evol Biol. 2012;2012:292068. doi: 10.1155/2012/292068. Epub 2012 Jul 30.


Very low rate of gene conversion in the yeast genome.

Casola C, Conant GC, Hahn MW.

Mol Biol Evol. 2012 Dec;29(12):3817-26. doi: 10.1093/molbev/mss192. Epub 2012 Jul 27.


Long identical multispecies elements in plant and animal genomes.

Reneker J, Lyons E, Conant GC, Pires JC, Freeling M, Shyu CR, Korkin D.

Proc Natl Acad Sci U S A. 2012 May 8;109(19):E1183-91. doi: 10.1073/pnas.1121356109. Epub 2012 Apr 10.


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

Hudson CM, Puckett EE, Bekaert M, Pires JC, Conant GC.

Genome Biol Evol. 2011;3:1369-80. doi: 10.1093/gbe/evr115. Epub 2011 Nov 4.


Patterns of indirect protein interactions suggest a spatial organization to metabolism.

Pérez-Bercoff Å, McLysaght A, Conant GC.

Mol Biosyst. 2011 Nov;7(11):3056-64. doi: 10.1039/c1mb05168g. Epub 2011 Aug 31.


Transcriptional robustness and protein interactions are associated in yeast.

Bekaert M, Conant GC.

BMC Syst Biol. 2011 May 5;5:62. doi: 10.1186/1752-0509-5-62.


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

Bekaert M, Edger PP, Pires JC, Conant GC.

Plant Cell. 2011 May;23(5):1719-28. doi: 10.1105/tpc.110.081281. Epub 2011 May 3.


Copy number alterations among mammalian enzymes cluster in the metabolic network.

Bekaert M, Conant GC.

Mol Biol Evol. 2011 Feb;28(2):1111-21. doi: 10.1093/molbev/msq296. Epub 2010 Nov 3.


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

Evangelisti AM, Conant GC.

Genome Biol Evol. 2010;2:826-34. doi: 10.1093/gbe/evq067. Epub 2010 Oct 21.


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

Conant GC.

Proc Biol Sci. 2010 Mar 22;277(1683):869-76. doi: 10.1098/rspb.2009.1592. Epub 2009 Nov 18.


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

Decker JE, Pires JC, Conant GC, McKay SD, Heaton MP, Chen K, Cooper A, Vilkki J, Seabury CM, Caetano AR, Johnson GS, Brenneman RA, Hanotte O, Eggert LS, Wiener P, Kim JJ, Kim KS, Sonstegard TS, Van Tassell CP, Neibergs HL, McEwan JC, Brauning R, Coutinho LL, Babar ME, Wilson GA, McClure MC, Rolf MM, Kim J, Schnabel RD, Taylor JF.

Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18644-9. doi: 10.1073/pnas.0904691106. Epub 2009 Oct 21.


Neutral evolution on mammalian protein surfaces.

Conant GC.

Trends Genet. 2009 Sep;25(9):377-81. doi: 10.1016/j.tig.2009.07.004. Epub 2009 Aug 26.


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

Conant GC, Stadler PF.

Mol Biol Evol. 2009 May;26(5):1155-61. doi: 10.1093/molbev/msp031. Epub 2009 Feb 20.


Turning a hobby into a job: how duplicated genes find new functions.

Conant GC, Wolfe KH.

Nat Rev Genet. 2008 Dec;9(12):938-50. doi: 10.1038/nrg2482. Review.


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

Conant GC, Wolfe KH.

Genetics. 2008 Jul;179(3):1681-92. doi: 10.1534/genetics.107.074450. Epub 2008 Jun 18.


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

Powell AJ, Conant GC, Brown DE, Carbone I, Dean RA.

BMC Genomics. 2008 Mar 28;9:147. doi: 10.1186/1471-2164-9-147.


GenomeVx: simple web-based creation of editable circular chromosome maps.

Conant GC, Wolfe KH.

Bioinformatics. 2008 Mar 15;24(6):861-2. doi: 10.1093/bioinformatics/btm598. Epub 2008 Jan 28.


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

Conant GC, Wolfe KH.

Mol Syst Biol. 2007;3:129. Epub 2007 Jul 31. Erratum in: Mol Syst Biol. 2008;4():204.


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

Scannell DR, Frank AC, Conant GC, Byrne KP, Woolfit M, Wolfe KH.

Proc Natl Acad Sci U S A. 2007 May 15;104(20):8397-402. Epub 2007 May 9.


Modeling amino acid substitution patterns in orthologous and paralogous genes.

Conant GC, Wagner GP, Stadler PF.

Mol Phylogenet Evol. 2007 Feb;42(2):298-307. Epub 2006 Jul 26.


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