864-889-0519 chg@clemson.edu

Publications

Dr. Trudy Mackay

Gabrawy MM, Campbell S, Carbone MA, Morozova TV, Arya GH, Turlapati LB, Walston JD, Starz-Gaiano M, Everett L, Mackay TFC, Leips J and Abadir PM. 2019. Lisinopril preserves physical resilience and extends life span in a genotype-specific manner in Drosophila melanogaster. J Gerontol A Biol Sci Med Sci 74: 1844-1852. doi: 10.1093/gerona/glz152.

Harbison ST, Kumar S, Huang W, McCoy LJ, Smith KR and Mackay TFC. 2019. Genome wide association study of circadian behavior in Drosophila melanogaster. Behav Genet 49: 60-82. doi: 10.1007/s10519-018-9932-0.

Highfill CA, Baker BM, Stevens SD, Anholt RRH and Mackay TFC. 2019. Genetics of cocaine and methamphetamine consumption and preference in Drosophila melanogaster. PLoS Genet 15: e1007834. doi: 10.1371/journal.pgen.1007834.

Huang W, Campbell T, Carbone MA, Jones WE, Unselt D, Anholt RRH and Mackay TFC. 2020. Context-dependent genetic architecture of Drosophila lifespan. PLoS Biol 18: e3000645. doi: 10.1371/journal.pbio.3000645.

Matute DR, Comeault AA, Earley E, Serrato-Capuchina A, Peede D, Monroy-Eklund A, Huang W, Jones CD, Mackay TFC and Coyne JA. 2020. Rapid and predictable evolution of admixed populations between two Drosophila species pairs. Genetics 214: 211-230. doi: 10.1534/genetics.119.302685.

Morgante F, Huang W, Sørensen P, Maltecca C and Mackay TFC. 2019. Leveraging multiple layers of data to predict Drosophila complex traits. bioRxiv 824896. doi: 10.1101/824896.

Parker GA, Kohn N, Spirina A, McMillen A, Huang W and Mackay TFC. 2020. Genetic basis of increased lifespan and postponed senescence in Drosophila melanogaster. G3 (Bethesda) 10: 1087-1098. doi: 10.1534/g3.120.401041.

Sass TN, MacPherson RA, Mackay TFC and Anholt RRH. 2020. A high-throughput method for measuring alcohol sedation time of individual Drosophila melanogaster. J Vis Exp 158: e61108. doi: 10.3791/61108.

Zhou S, Morgante F, Geisz MS, Ma J, Anholt RRH and Mackay TFC. 2020. Systems genetics of the Drosophila metabolome. Genome Res 30: 392-405. doi: 10.1101/gr.243030.118.

 

Dr. Robert Anholt

Anholt RRH. 2020. Chemosensation and evolution of Drosophila host plant selection. iScience 23: 100799. doi: 10.1016/j.isci.2019.100799.

Anholt RRH. 2020. Evolution of epistatic networks and the genetic basis of innate behaviors. Trends Genet. 36: 24-29. doi: 10.1016/j.tig.2019.10.005.

Anholt RRH, Wolfner MF, O’Grady P and Harbison ST. 2020. Evolution of reproductive behavior. Genetics 214: 49-73. doi: 10.1534/genetics.119.302263.

Everett LJ, Huang W, Zhou S, Carbone MA, Lyman RF, Arya GH, Geisz MS, Ma J, Morgante F, St Armour G, Turlapati L, Anholt RRH and Mackay TFC. 2020. Gene expression networks in the Drosophila Genetic Reference Panel.  Genome Res 30: 485-496. doi: 10.1101/gr.257592.119.

Highfill CA, Baker BM, Stevens SD, Anholt RRH and Mackay TFC. 2019. Genetics of cocaine and methamphetamine consumption and preference in Drosophila melanogaster. PLoS Genet 15: e1007834. doi: 10.1371/journal.pgen.1007834.

Huang W, Campbell T, Carbone MA, Jones WE, Unselt D, Anholt RRH and Mackay TFC. 2020. Context-dependent genetic architecture of Drosophila lifespan. PLoS Biol 18: e3000645. doi: 10.1371/journal.pbio.3000645.

Sass TN, MacPherson RA, Mackay TFC and Anholt RRH. 2020. A high-throughput method for measuring alcohol sedation time of individual Drosophila melanogaster. J Vis Exp 158: e61108. doi: 10.3791/61108.

Zhou S, Morgante F, Geisz MS, Ma J, Anholt RRH and Mackay TFC. 2020. Systems genetics of the Drosophila metabolome. Genome Res 30: 392-405. doi: 10.1101/gr.243030.118.

 

Brandon Baker – graduate student

Highfill CA, Baker BM, Stevens SD, Anholt RRH and Mackay TFC. 2019. Genetics of cocaine and methamphetamine consumption and preference in Drosophila melanogaster. PLoS Genet 15: e1007834. doi: 10.1371/journal.pgen.1007834.

 

Dr. Leigh Anne Clark

Murphy SC, Recio A, de la Fuente C, Guo LT, Shelton GD and Clark LA. 2019. A glycine transporter SLC6A5 frameshift mutation causes startle disease in Spanish greyhounds. Hum Genet 138: 509-513. doi: 10.1007/s00439-019-01986-x.

Tsai KL, Evans JM, Noorai RN, Starr-Moss AN and Clark LA. 2019. Novel Y chromosome retrocopies in canids revealed through a genome-wide association study for sex. Genes (Basel) 10: 320. doi: 10.3390/genes10040320.

 

Dr. Zhana Duren

Duren Z, Chen X, Xin J, Wang Y and Wong WH. 2020. Time course regulatory analysis based on paired expression and chromatin accessibility data. Genome Res 30: 622-634. doi: 10.1101/gr.257063.119.

Lingjie L, Wang Y, Torkelson JL, Shankar G, Pattison JM, Zhen HH, Fang F, Duren Z, Xin J, Gaddam S, Melo SP, Piekos SN, Li J, Liaw EJ, Chen L, Li R, Wernig M, Wong WH, Chang HY and Oro AE. 2019. TFAP2C-and p63-dependent networks sequentially rearrange chromatin landscapes to drive human epidermal lineage commitment. Cell Stem Cell 24: 271-284. doi: 10.1016/j.stem.2018.12.012.

Zeng W, Chen X, Duren Z, Wang Y, Jiang R and Wong WH. 2019. DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data. Nat Commun 10: 4613. doi: 10.1038/s41467-019-12547-1.

Zhang X, Hong D, Ma S, Ward T, Ho M, Pattni R, Duren Z, Stankov A, Bade Shrestha S, Hallmayer J, Wong WH, Reiss AL and Urban AE. 2020. Integrated functional genomic analyses of Klinefelter and Turner syndromes reveal global network effects of altered X chromosome dosage. Proc Natl Acad Sci USA 117: 4864-4873. doi: 10.1073/pnas.1910003117.

Zhu X, Duren Z and Wong WH. Modeling regulatory network topology improves genome-wide analyses of complex human traits. 2020. BioRxiv doi: 10.1101/2020.03.13.990010.

 

Dr. F. Alex Feltus

Casanova EL, Switala AE, Dandamudi S, Hickman AR, Vandenbrink J, Sharp JL, Feltus FA and Casanova MF. 2019. Autism risk genes are evolutionarily ancient and maintain a unique feature landscape that echoes their function. Autism Res 12: 860-869. doi: 10.1002/aur.2112.

Greene MA, Britt JL, Powell RR, Feltus FA, Bridges WC, Bruce T, Klotz JL, Miller MF and Duckett SK. 2019. Ergot alkaloid exposure during gestation alters: 3. Fetal growth, muscle fiber development and miRNA transcriptome. J Anim Sci 97: 3153-3168. doi:10.1093/jas/skz153.

Mills N, Bensman EM, Poehlman WL, Ligon WB 3rd and Feltus FA. 2019. Moving just enough deep sequencing data to get the job done. Bioinform Biol Insights 13: 1177932219856359. doi: 10.1177/1177932219856359.

Paterson AH, Kong W, Johnston RM, Nabukalu P, Wu G, Poehlman WL, Goff VH, Isaacs K, Lee TH, Guo H, Zhang D, Sezen UU, Kennedy M, Bauer D, Feltus FA, Weltzien E, Rattunde HF, Barney JN, Barry K, Cox TS and Scanlon MJ. 2020. The evolution of an invasive plant, Sorghum halepense L. (‘Johnsongrass’). Front Genet 11: 317. doi: 10.3389/fgene.2020.00317.

Spoor S, Cheng CH, Sanderson LA, Condon B, Almsaeed A, Chen M, Bretaudeau A, Rasche H, Jung S, Main D, Bett K, Staton M, Wegrzyn JL, Feltus FA and Ficklin SP. 2019. Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. Database (Oxford) doi: 10.1093/database/baz077.

 

Dr. Julia George

Yip, P.K., Schmitzberger, M., Al-Hasan, M., George, J., Tripoliti, E., Michael-Titus, A.T., Clayton, D., & Priestley, J.V. (2020) Serotonin Expression in the Song Circuitry of Adult Male Zebra Finches. Neuroscience, 444, 170–182.

Rhie, A. et al (2020) Towards complete and error-free genome assemblies of all vertebrate species. Preprint at https://www.biorxiv.org/content/10.1101/2020.05.22.110833v1.

George, J.M., Bell, Z.W., Condliffe, D., Dohrer, K., Abaurrea, T., Spencer, K., Leitão, A., Gahr, M., Hurd, P.J., & Clayton, D.F. (2020) Acute social isolation alters neurogenomic state in songbird forebrain. Proc. Natl. Acad. Sci. U. S. A., 117, 23311–23316.

Bell, Z.W., Lovell, P., Mello, C.V., Yip, P.K., George, J.M., & Clayton, D.F. (2019) Urotensin-related gene transcripts mark developmental emergence of the male forebrain vocal control system in songbirds. Sci. Rep., 9, 816.

Ysselstein, D., Dehay, B., Costantino, I.M., McCabe, G.P., Frosch, M.P., George, J.M., Bezard, E., & Rochet, J.-C. (2017) Endosulfine-alpha inhibits membrane-induced α-synuclein aggregation and protects against α-synuclein neurotoxicity. Acta Neuropathol Commun, 5, 3.

Tuttle, M.D., Comellas, G., Nieuwkoop, A.J., Covell, D.J., Berthold, D.A., Kloepper, K.D., Courtney, J.M., Kim, J.K., Barclay, A.M., Kendall, A., Wan, W., Stubbs, G., Schwieters, C.D., Lee, V.M.Y., George, J.M., & Rienstra, C.M. (2016) Solid-state NMR structure of a pathogenic fibril of full-length human α-synuclein. Nat. Struct. Mol. Biol., 23, 409–415.

 

Dr. Miriam Konkel

Casanova EL and Konkel MK. 2020. The developmental gene hypothesis for punctuated equilibrium: Combined roles of developmental regulatory genes and transposable elements. Bioessays 42: e1900173. doi: 10.1002/bies.201900173.

Rogers J, Raveendran M, Harris RA, Mailund T, Leppälä K, Athanasiadis G, Schierup MH, Cheng J, Munch K, Walker JA, Konkel MK, Jordan V, Steely CJ, Beckstrom TO, Bergey C, Burrell A, Schrempf D, Noll A, Kothe M, Kopp GH, Liu Y, Murali S, Billis K, Martin FJ, Muffato M, Cox L, Else J, Disotell T, Muzny DM, Phillips-Conroy J, Aken B, Eichler EE, Marques-Bonet T, Kosiol C, Batzer MA, Hahn MW, Tung J, Zinner D, Roos C, Jolly CJ, Gibbs RA and Worley KC. 2019. The comparative genomics and complex population history of Papio baboons. Sci Adv 5: eaau6947. doi: 10.1126/sciadv.aau6947.

Storer JM, Mierl JR, Brantley SA, Threeton B, Sukharutski Y, Rewerts LC, St Romain CP, Foreman MM, Baker JN, Walker JA, Orkin JD, Melin AD, Phillips KA, Konkel MK and Batzer MA. 2019. Amplification dynamics of Platy-1 retrotransposons in the Cebidae Platyrrhine lineage. Genome Biol Evol 4: 1105-1116. doi: 10.1093/gbe/evz062.

Walker JA, Jordan VE, Storer JM, Steely CJ, Gonzalez-Quiroga P, Beckstrom TO, Rewerts LC, St Romain CP, Rockwell CE, Rogers J, Jolly CJ and Konkel MK. 2019. Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry. Mob DNA 10: 46. doi: 10.1186/s13100-019-0187-y.

 

Dr. Richard Lyman

Everett LJ, Huang W, Zhou S, Carbone MA, Lyman RF, Arya GH, Geisz MS, Ma J, Morgante F, St Armour G, Turlapati L, Anholt RRH and Mackay TFC. 2020. Gene expression networks in the Drosophila Genetic Reference Panel.  Genome Res 30: 485-496. doi: 10.1101/gr.257592.119.

 

Roberta Lyman – Staff Scientist

Anderson KL, Kearns R, Lyman RL, and Correa MT. 2019. Staphylococci in dairy goats and human milkers, and the relationship with herd management practices. Small Ruminant Research 171: 13-22 doi: 10.1016/j.smallrumres.2018.11.021.

 

Rebecca MacPherson – graduate student

Sass TN, MacPherson RA, Mackay TFC and Anholt RRH. 2020. A high-throughput method for measuring alcohol sedation time of individual Drosophila melanogaster. J Vis Exp 158: e61108. doi: 10.3791/61108.

 

Dr. C. Steven McMahan

Bilder C, Tebbs J and McMahan C. 2019. Informative group testing for multiplex assays. Biometrics 75: 278-288. doi: 10.1111/biom.12988.

Gettings JR, Self SCW, McMahan CS, Brown DA, Nordone SK and Yabsley MJ. 2020. Local and regional temporal trends (2013-2019) of canine Ehrlichia spp. seroprevalence in the USA. Parasites and Vectors 13: 153. doi: 10.1186/s13071-020-04022-4.

Gregory K, Wang D and McMahan C. 2019. Adaptive elastic net regression with group testing data. Biometrics 75: 13-23. doi: 10.1111/biom.12973.

Hou P, Tebbs J, Wang D, McMahan C and Bilder C. 2020. Array testing with multiplex assays. Biostatistics 21: 417-431. doi: 10.1093/biostatistics/kxy058.

Joyner C, McMahan C, Baurley J and Pardamean B. 2020. A two-phase Bayesian methodology for the analysis of binary phenotypes in genome-wide association studies. Biom J 62: 191-201. doi: 10.1002/bimj.201900050

Sekhon R, Joyner C, Ackerman A, McMahan C, Cook D and Robertson D. 2020. Stalk bending strength is strongly associated with maize stalk lodging incidence across multiple Environments. Field Crops 249: e107737. doi: 10.1016/j.fcr.2020.107737.

Self SCW, Liu Y, Nordone SK, Yabsley MJ, Walden HS, Lund RB, Bowman DD, Carpenter C, McMahan CS and Gettings JR. 2019. Canine vector-borne disease: mapping and the accuracy of forecasting using big data from the veterinary community. Anim Health Res Rev 20: 47-60. doi: 10.1017/S1466252319000045.

Withana Gamage PW, Chaudari M, McMahan CS, Kim EH and Kosorok MR. 2020. An extended proportional hazards model for interval-censored data subject to instantaneous failures. Lifetime Data Anal 26: 158-182. doi: 10.1007/s10985-019-09467-z.

Yang T, Gallagher CM and McMahan CS. 2019. A robust regression methodology via M-estimation. Communications in Statistics 48: 1092-1107. doi: 10.1080/03610926.2018.1423698.

 

Dr. Fabio Morgante

Everett LJ, Huang W, Zhou S, Carbone MA, Lyman RF, Arya GH, Geisz MS, Ma J, Morgante F, St Armour G, Turlapati L, Anholt RRH and Mackay TFC. 2020. Gene expression networks in the Drosophila Genetic Reference Panel.  Genome Res 30: 485-496. doi: 10.1101/gr.257592.119.

Morgante F, Huang W, Sørensen P, Maltecca C and Mackay TFC. 2019. Leveraging multiple layers of data to predict Drosophila complex traits. bioRxiv 824896. doi: 10.1101/824896.

Zhou S, Morgante F, Geisz MS, Ma J, Anholt RRH and Mackay TFC. 2020. Systems genetics of the Drosophila metabolome. Genome Res 30: 392-405. doi: 10.1101/gr.243030.118.

 

Dr. Nestor Octavio Nazario-Yepiz

Mateus RP, Nazario-Yepiz NO, Ibarra-Laclette E, Ramirez Loustalot-Laclette M, Markow TA. 2019. Developmental and transcriptomal responses to seasonal dietary shifts in the cactophilic Drosophila mojavensis of North America. J Hered 110: 58-67. doi: 10.1093/jhered/esy056.

Pfeiler E and Nazario-Yepiz NO. 2020. DNA-based taxonomy and potential suppression of long-established names: the case of Telegonus fulgerator (Lepidoptera: Hesperiidae). Syst Biodivers 18: 338–346. doi: 10.1080/14772000.2020.1758825.

Pfeiler E, Nazario-Yepiz NO, Hernández-Cervantes PL and Markow TA. 2020. Mitochondrial DNA barcodes provide insight into the phylogeography and subspecies controversy in the widespread neotropical White Peacock butterfly, Anartia jatrophae (Nymphalidae: Nymphalinae). Biol J Linn Soc 130: 700–714. doi: 10.1093/biolinnean/blaa080.

Vanderlinde T, Guimarães DE, Nazario-Yepiz NO and Carvalho AB. 2019. An improved genome assembly for Drosophila navojoa, the basal species in the mojavensis cluster. J Hered 110: 118-123. doi: 10.1093/jhered/esy059.

 

Dr. Vijay Shankar

Krombeen SK, Shankar V, Noorai RE, Saski CA, Sharp JL, Wilson ME and Wilmoth TA. 2019. The identification of differentially expressed genes between extremes of placental efficiency in maternal line gilts on day 95 of gestation. BMC Genomics 20: 254. doi: 10.1186/s12864-019-5626-0.

Nayduch D, Shankar V, Mills MK, Robl T, Drolet BS, Ruder MG, Scully ED and Saski CA. 2019. Transcriptome response of female Culicoides sonorensis biting midges (Diptera: Ceratopogonidae) to early infection with Epizootic Hemorrhagic Disease Virus (EHDV-2). Viruses 11: 473. doi: 10.3390/v11050473.

Noorai RE, Shankar V, Freese NH, Gregorski CM and Chapman SC. 2019. Discovery of genomic variants by whole-genome resequencing of the North American Araucana chicken. PLoS One 14: e0225834. doi: 10.1371/journal.pone.0225834.

Zhebentyayeva T, Shankar V, Scorza R, Callahan A, Ravelonandro M, Castro S, DeJong T, Saski CA, Dardick C. 2019. Genetic characterization of world-wide Prunus domestica (plum) germplasm using sequence-based genotyping. Hortic Res 6: 12. doi: 10.1038/s41438-018-0090-6.

 

Dr. Lakshmi Sunkara

Sunkara LT, Ahmad SM and Heidari M. 2019. RNA-seq analysis of viral gene expression in the skin of Marek’s disease virus infected chicken. Vet Immunol Immunopathol 213: 109882. doi: 10.1016/j.vetimm.2019.109882.

 

Dr. Joshua Walters

Walters JD, Gill SS and Mercuri JJ. 2019. Ethanol-mediated compaction and cross-linking enhance mechanical properties and degradation resistance while maintaining cytocompatibility of a nucleus pulposus scaffold. J Biomed Mater Res B Appl Biomater 8: 2488-2499. doi: 10.1002/jbm.b.34339.

 

Dr. Lianjiang (LJ) Wang

Ang CE, Ma Q, Wapinski OL, Fan S, Flynn RA, Lee QY, Coe B, Onoguchi M, Olmos VH, Do BT, Dukes-Rimsky L, Xu J, Tanabe K, Wang L, Elling U, Penninger JM, Zhao Y, Qu K, Eichler EE, Srivastava A, Wernig M and Chang HY. 2019. The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders. Elife 8: 41770. doi: 10.7554/eLife.41770.

Gudenas BL, Wang J, Kuang SZ, Wei AQ, Cogill SB and Wang LJ. 2019. Genomic data mining for functional annotation of human long noncoding RNAs.  J Zhejiang Univ Sci 20: 476-487. doi:10.1631/jzus.B1900162.

Kuang S and Wang L. 2020. Identification and analysis of consensus RNA motifs binding to the genome regulator CTCF. NAR Genomics and Bioinformatics 2: lqaa031. doi: 10.1093/nargab/lqaa031.

Wang J and Wang L. 2020. Deep analysis of RNA N6-adenosine methylation (m6A) patterns in human cells. NAR Genomics and Bioinformatics 2: lqaa007. doi: 10.1093/nargab/lqaa007.

Wang J and Wang L. 2019. Deep learning of the back-splicing code for circular RNA formation. Bioinformatics 35: 5235-5242. doi: 10.1093/bioinformatics/btz382.