Publications [Google Scholar]:


62. Blischak, P. D., M. E. Mabry, G. C. Conant and J. C. Pires. 2018 Integrating networks, phylogenomics, and population genomics for the study of polyploidy. Annual Review of Ecology, Evolution, and Systematics, 49:253-278. [Reprint from publisher's website]

61. Emery, M., M. M. S. Willis, Y. Hao, K. Barry, K. Oakgrove, Y. Peng, J. Schmutz, E. Lyons, J. C. Pires, P. P. Edger, and G. C. Conant. 2018. 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: e1007267. [Article Online][Reprint].

60. Hao, Y., J. D. Washburn, J. Rosenthal, B. Nielsen, E. Lyons, P. P. Edger, J. C. Pires, and G. C. Conant. 2018. Patterns of population variation in two paleopolyploid eudicot lineages suggest that dosage-based selection on homeologs is long-lived. Genome Biology and Evolution 10: 999-1011. [Reprint].

59. Patil, R. D., M. J. Ellison, S. M. Wolff, C. Shearer, A. M. Wright, R. R. Cockrum, K. J. Austin, W. R. Lamberson, K. M. Cammack, and G. C. Conant. 2018. 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: 2113-2124. [Article Online].

58. Cammack, K. M. K.J. Austin, W.R. Lamberson, G.C. Conant, H.C. Cunningham. (2018) Tiny but mighty: The role of the rumen microbes in livestock production, Journal of Animal Science 96: 752-770.



57. Washburn, J. D., J. C. Schnable, G. C. Conant, T. P. Brutnell, Y. Shao, Y. Zhang, M. Ludwig, G. Davidse and J. C. Pires. (2017) Genome-guided phylo-transcriptomic methods and the nuclear phylogentic tree of the Paniceae grasses, Scientific Reports, 7: 13528.

56. Ellison, M.J., G.C. Conant, W.R. Lamberson, R.R. Cockrum, K.J. Austin, D.C. Rule, and K.M. Cammack. (2017) Diet and feed efficiency status affect rumen microbial profiles of sheep, Small Ruminant Research, 156: 12-19.

55. Wolff, S. M., M. J. Ellison, Y. Hao, R. R. Cockrum, K. J. Austin, M. Baraboo, K. Burch, H. J. Lee, T. Maurer, R. Patil, A. Ravelo, T. M. Tasis, H. Truong, W. R. Lamberson, K. M. Cammack and G. C. Conant. (2017) Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome, Microbiome 5:60. [Reprint][Full-text link]



54. Pires, J. C. and G. C. Conant. (2016) Robust yet fragile: Expression noise, protein misfolding, and gene dosage in the evolution of genomes, Annual Review of Genetics 50: 113-131. [Email for reprint]

53. J. D. Washburn, K. A. Bird, G. C. Conant and J. C. Pires. (2016) Convergent evolution and the origin of complex phenotypes in the age of systems biology, International Journal of Plant Sciences 177:4. [Email for reprint]

52. Mordhorst, B. R., M. L. Wilson and G. C. Conant. (2016) Some assembly required: evolutionary and systems perspectives on the mammalian reproductive system, Cell and Tissue Research 363: 267-278. [Email for reprint]



51. Scienski, K., J. C. Fay, and G. C. Conant. (2015) Patterns of gene conversion in duplicated yeast histones suggests strong selection on a co-adapted macromolecular complex, Genome Biology and Evolution, 7: 3249-3258. [Reprint]

50. Taxis, T. M., S. Wolff, S. J. Gregg, N. O. Minton, C. Zhang, J. Dai, R. D. Schnabel, J. F. Taylor, M. S. Kerley, J. C. Pires, W. R. Lamberson and G. C. Conant. (2015) The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity, Nucleic Acids Research, 43: 9600-9612. [Reprint]

49. Edger, P. P., H. M. Heidel-Fischer, M. Bekaert, J. Rota, G. Glockner, A. E. Platts, D. G. Heckel, J. P. Der, E. K. Wafula, M. Tang, J. A. Hofberger, A. Smithson, J. C. Hall, M. Blanchette, T. E. Bureau, S. I. Wright, M. E. Schranz, M. S. Barker, G. C. Conant, N. Wahlberg, H. Vogel, J. C. Pires and C. W. Wheat. (2015) The butterfly plant arms-race escalated by gene and genome duplications, Proceedings of the National Academy of Sciences, U.S.A., 112: 8362-8366.



48. G. C. Conant. (2014) 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: 3184-3193. [Reprint]

47. Dhroso, A., D. Korkin and G. C. Conant. (2014) The yeast protein interaction network has a capacity for self-organization, The FEBS Journal 281: 3420-3432. [Email for reprint]

46. Edger, P. P., M. Tang, K. A. Bird, D. R. Mayfield, G. Conant, K. Mummenhoff, M. A. Koch, and J. C. Pires. (2014) "Secondary structure analyses of the nuclear rRNA internal transcribed spacers and assessment Of its phylogenetic utility across the Brassicaceae (mustards)," PLoS ONE, 9: e101341. [Reprint]

45. Conant, G. C., J. A. Birchler, and J. C. Pires. (2014) Dosage, Duplication, and Diploidization: Clarifying the interplay of multiple models for duplicate gene evolution over time, Current Opinion in Plant Biology, 19: 91-98. [Email for reprint]

44. H. Truong, D. Li, K. Sajjapongse, G. Conant and M. Becchi. (2014) Large-Scale pairwise alignments on GPU clusters: Exploring the implementation space, Journal of Signal Processing Systems 77: 131-149.

43. Bekaert, M. and G. C. Conant. (2014) Gene duplication and phenotypic changes in the evolution of mammalian metabolic networks, PLoS ONE 9: e87115. [Reprint]

42. Zimmerman, S. W. Y.-J. Yi, M. Sutovsky, F. W. van Leeuwen, G. Conant and P. Sutovsky. (2014)Identification and characterization of RING-finger ubiquitin 5 ligase UBR7 in mammalian spermatozoa, Cell and Tissue Research, 356:261-278.

41. Ellison, M., G. C. Conant, R. Cockrum, K. Austin, M. Becchi, H. Truong, W. Lamberson, and K. Cammack. (2014) Diet alters both the structure and taxonomy of the ovine gut microbial ecosystem, DNA Research, 21: 115-125. [Reprint]



40. Warren, S., X. F. Wan, G. Conant and D. Korkin. (2013) Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome, PLoS ONE, 8: e81027. [Reprint]

##. Li, D. K. Sajjapongse, H. Truong, G. Conant and Michela Becchi. (2013)A Distributed CPU-GPU Framework for Pairwise Alignments on Large-Scale Sequence Datasets Proceedings of the 24th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP), Ashburn, VA, June 2013. [Reprint]

39. Pérez-Bercoff, Å., C. M. Hudson and G. C. Conant, (2013) A Conserved Mammalian Protein Interaction Network, PLoS ONE, 8: e52581. [Reprint]

38. Mayfield-Jones, D. J. D. Washburn, T. Arias, P. P. Edger, J. C. Pires and G. C. Conant, (2013) Watching the grin fade: Tracing the effects of polyploidy on different evolutionary time scales, Seminars in Cell and Developmental Biology, in press. [Email for pre-print]



37. Reneker, J., E. Lyons, G. C. Conant, J. C. Pires, M. Freeling, C.-R. Shyu, and D. Korkin, (2012) Long identical multispecies elements in plant and animal genomes, Proceedings of the National Academy of Sciences, U.S.A., 109: E1183-E1191. [Reprint]

36. Wang, S., G. C. Conant, R. Ou, B. T. Beerntsen (2012) Cloning and characterization of the peptidoglycan recognition protein genes in the mosquito, Armigeres subalbatus (Diptera: Culicidae), Journal of Medical Entomology, 49: 656-671.

35. Tang, H., M. R. Woodhouse, F. Cheng, J. C. Schnable, B. S. Pedersen, G. C. Conant, X. Wang, M. Freeling and J. Chris Pires, (2012) Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy, Genetics, 190 1563-1574.

34. Huminiecki, L. and G. C. Conant, (2012) Polyploidy and the evolution of complex traits, International Journal of Evolutionary Biology, 2012: 292068. [Reprint]

33. Casola, C., G. C. Conant and M. W. Hahn, (2012) Very low rate of gene conversion in the yeast genome, Molecular Biology and Evolution, 29: 3817-3826. [Reprint]

32. Bekaert, M., P. P. Edger, C. M. Hudson, J. C. Pires, and G. C. Conant, (2012) Metabolic and evolutionary costs of herbivory defense: Systems biology of glucosinolate synthesis, The New Phytologist 196: 596-605. [Reprint]



31. Hudson, C. M. E. E. Puckett, M. Bekaert, J. C. Pires and G. C. Conant, (2011) Selection for higher gene copy number after different types of plant gene duplications, Genome Biology and Evolution, 3: 1369-1380. [Reprint]

30. Pérez-Bercoff, Å., A. McLysaght and G. C. Conant, (2011) Patterns of indirect protein interactions suggest a spatial organization to metabolism, Molecular BioSystems, 7: 3056-3064. [Reprint]

29. Wang, X., H. Wang, J. Wang, R. Sun, J. Wu, S. Liu, Y. Bai, J. H. Mun, I. Bancroft, F. Cheng, S. Huang, X. Li, W. Hua, M. Freeling, J. C. Pires, A. H. Paterson, B. Chalhoub, B. Wang, A. Hayward, A. G. Sharpe, B. S. Park, B. Weisshaar, B. Liu, B. Li, C. Tong, C. Song, C. Duran, C. Peng, C. Geng, C. Koh, C. Lin, D. Edwards, D. Mu, D. Shen, E. Soumpourou, F. Li, F. Fraser, G. Conant, G. Lassalle, G. J. King, G. Bonnema, H. Tang, H. Belcram, H. Zhou, H. Hirakawa, H. Abe, H. Guo, H. Jin, I. A. Parkin, J. Batley, J. S. Kim, J. Just, J. Li, J. Xu, J. Deng, J. A. Kim, J. Yu, J. Meng, J. Min, J. Poulain, K. Hatakeyama, K. Wu, L. Wang, L. Fang, M. Trick, M. G. Links, M. Zhao, M. Jin, N. Ramchiary, N. Drou, P. J. Berkman, Q. Cai, Q. Huang, R. Li, S. Tabata, S. Cheng, S. Zhang, S. Sato, S. Sun, S. J. Kwon, S. R. Choi, T. H. Lee, W. Fan, X. Zhao, X. Tan, X. Xu, Y. Wang, Y. Qiu, Y. Yin, Y. Li, Y. Du, Y. Liao, Y. Lim, Y. Narusaka, Z. Wang, Z. Li, Z. Xiong, and Z. Zhang, (2011) The genome of the mesopolyploid crop species Brassica rapa, Nature Genetics, 43: 1035-1039.

28. Bekaert, M. and G. C. Conant, (2011) Copy number alterations among mammalian enzymes cluster in the metabolic network, Molecular Biology and Evolution 28: 1111-1121. [Reprint]

27. Hudson, C. M. and G. C. Conant. (2011) Expression level, cellular compartment and metabolic network position all influence the average selective constraint on mammalian enzymes, BMC Evolutionary Biology, 11: 89. [Reprint]

26. Bekaert, M., P. P. Edger, J. C. Pires and G. C. Conant, (2011) Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints, The Plant Cell, 23: 1719-1728. [Reprint]

25. Bekaert, M. and G. C. Conant, (2011) Transcriptional robustness and protein interactions are associated in yeast, BMC Systems Biology, 5: 62. [Reprint]



24. Evangelisti, A. M. and G. C. Conant, (2010) Non-random survival of gene conversions among yeast ribosomal proteins duplicated through genome doubling, Genome Biology and Evolution 2: 826-834. [Reprint]

23. Foy, N., B. Jester, G. C. Conant and K. M. Devine, (2010) 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-tRNAAsn, BMC Microbiology 10: 196. [Reprint]  

22. Conant, G. C., (2010) Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast, Proceedings of the Royal Society, Biological Sciences 277: 869:876. [Reprint]



21. Decker, J. E., J. C. Pires, G. C. Conant, S, D. McKay, M. P. Heaton, K. Chen, A. Cooper, J. Vilkki, C. M. Seabury, A. R. Caetano, G. S. Johnson, R. A. Brenneman, O. Hanotte, L. S. Eggert, P. Wiener, J.-J. Kim, K. Suk Kim, T. S. Sonstegard, C. P. Van Tassell, H. L. Neibergs, J. C. McEwan, R. Brauning, L. L. Coutinho, M. E. Babar, G. A. Wilson, M. C. McClure, M. M. Rolf, J. Kim, R. D. Schnabel, and J. F. Taylor, (2009) Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics, Proceedings of the National Academy of Sciences, U.S.A. 106:18644-18649.

20. Conant, G. C. (2009)  Neutral evolution on mammalian protein surfaces, Trends in Genetics 25: 377-381. [Email for reprint]

19. Conant, G. C. and P. F. Stadler. (2009)  Solvent exposure imparts similar selective pressures across a range of yeast proteins, Molecular Biology and Evolution 26:1155-1161. [Reprint]



18. Conant, G. C. and K. H. Wolfe. (2008)  GenomeVx: Simple web-based creation of editable circular chromosome maps, Bioinformatics 24: 861-862. [Reprint]

17. Powell, A. J., G. C. Conant, D. E. Brown, I. Carbone and R. A. Dean. (2008)  Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens, BMC Genomics 9: 147. [Reprint]

16. Conant, G. C. and K. H. Wolfe. (2008) Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast, Genetics 179: 1681-1692. [Reprint]

15. Conant, G. C. and K. H. Wolfe. (2008) Turning a hobby into a job: How duplicated genes find new functions, Nature Reviews Genetics, 9: 938-950. [Email for reprint]



14. Conant, G. C., G. P. Wagner and P. F. Stadler. (2007)  Modeling amino acid substitution patterns in orthologous and paralogous genes, Molecular Phylogenetics and Evolution, 42: 298-307. [Email for reprint]

13. Scannell, D. R., A. C. Frank, G. C. Conant, K. P. Byrne, M. Woolfit and K. H. Wolfe. (2007)  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, U.S.A., 104: 8397-8402. [Reprint

12. Conant, G. C., and K. H. Wolfe. (2007)  Increased glycolytic flux as an outcome of whole-genome duplication in yeast, Molecular Systems Biology, 3: 129. [Reprint]



11. Conant, G. C., and K. H. Wolfe. (2006)  Functional partitioning of yeast co-expression networks after genome duplication, PLoS Biology,4: e109. [Reprint



10. Conant, G. C., and A. Wagner. (2005)  The rarity of gene shuffling in conserved genes, Genome Biology, 6: R50 [Reprint]



9. Conant, G. C. and A. Wagner. (2004) Duplicate genes and robustness to transient gene knockouts in Caenorhabditis elegans, Proceedings of the Royal Society, Biological Sciences, 271: 89-96 [Reprint]

8. Hahn, M. H., G. C. Conant and A. Wagner. (2004) Molecular evolution in large genetic networks: Does connectivity equal constraint?  Journal of Molecular Evolution, 58: 203-211.  [Reprint][Original Article available at] Copyright retained by Springer-Verlag, NY.

7. Conant, G. C., and A. Wagner. (2004)  A fast algorithm for determining the best combination of local alignments to a query sequence, BMC Bioinformatics, 5: 62 [Reprint]

6. Babu, S. R., G. C. Conant, E. Eller, C. M. Roberts, K. Gowan, G. S. Eisenbarth, P. R. Fain, and P. Vardi. (2004)  A Second-generation genome screen for linkage to Type 1 diabetes in a Bedouin Arab family, Annals of the New York Academy of Sciences,1037: 157-160  



5. Conant, G. C. and A. Wagner. (2003) Convergent evolution of gene circuits, Nature Genetics, 34: 264-266 [Reprint][Supplemental Methods][Nature Genetics Online]

4. Conant, G. C., S. J. Plimpton, W. Old, A.Wagner, P. R. Fain, T. R. Pacheco and G. Heffelfinger. (2003)  Parallel Genehunter: Implementation of a linkage analysis package for distributed-memory architectures, Journal of Parallel and Distributed Computing, 63: 674-682.[Corrected Pre-Print][Email for reprint]

3. Conant, G. C. and A. Wagner. (2003) Asymmetric sequence divergence of duplicate genes, Genome Research, 13: 2052-2058. [Reprint]



2. Conant, G. C. and A. Wagner. (2002)  GenomeHistory: A software tool and its application to fully sequenced genomes, Nucleic Acids Research, 30: 3378-3386 [Reprint]



1. Conant, G. C. and P. O. Lewis.  (2001)  Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference, Molecular Biology and Evolution, 18: 1024-1033 [Reprint]


Conference Papers and Presentations:

Parallel Genehunter: Implementation of a Linkage Analysis Package for Distributed-Memory Architectures, First IEEE Workshop on High Performance Computational Biology, at the International Parallel and Distributed Computing Symposium,  Ft. Lauderdale, FL, April 2002  [Paper Reprint: old version of JDPC paper]


Non-peer reviewed

Op-Ed Debate in the Irish Times on teaching creationism.