864-889-0519 chg@clemson.edu

Recent Publications by CHG Affiliates

2021:

2020:

Abrams SR, Hawks AL, Evans JM, Famula TR, Mahaffey M, Johnson GS, Mason JM and Clark LA. 2020. Variants in FtsJ RNA 2′-O-Methyltransferase 3 and Growth Hormone 1 are associated with small body size and a dental anomaly in dogs. Proc Natl Acad Sci USA. 117: 24929-24935. doi: 10.1073/pnas.2009500117.

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.

Borem R, Walters J, Madeline A, Madeline L, Gill S, Easley J, Mercuri J. 2020. Characterization of chondroitinase‐induced lumbar intervertebral disc degeneration in a sheep model intended for assessing biomaterials. J Biomedl Mater Res A. doi: 10.1002/jbm.a.37117.

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.

Cho H, Zitkovsky J, Li X, Lu M, Shah K, Sperger J, Tsilimigras MCB, and Kosorok MR. 2020. Comment: Diagnostics and kernel-based extensions for linear mixed effects models with endogenous covariates. Stat Sci. 35: 396–399. doi:10.1214/20-STS782.

Cutcher-Gershenfeld J, Baker KS, Berente N, Berkman PA, Canavan P, Feltus FA, Garmulewicz A, Hutchins R, King JL, Kirkpatrick C, Lenhardt C, Lewis S, Maffe M, Mittleman B, Sampath R, Shin N, Stall S, Winter S, Veazey P. 2020. Negotiated sharing of pandemic data, models, and resources. Negotiation Journal. 36. doi: doi.org/10.1111/nejo.12340.

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.

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.

George JM, Bell ZW, Condliffe D, Dohrer K, Abaurrea T, Spencer K, Leitao A, Gahr M, Hurd PJ, Clayton DF. 2020. Acute social isolation alters neurogenomic state in songbird forebrain. Proc Natl Acad Sci. 38: 23311-23316. doi 10.1073/pnas.1820841116. 

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.

Gettings JR, Self SCW, McMahan CS, Brown DA, Nordone SK and Yabsley MJ. 2020. Regional and local temporal trends of Borrelia burgdorferi and Anaplasma spp. seroprevalence in domestic dogs: Contiguous United States 2013-2019. Front. Vet. Sci. 7: 561592. doi: 10.3389/fvets.2020.561592.

Hang Y, Aburidi M, Poehlman WL, Husain B, Hickman A, Feltus FA. 2020. Tissue specific brain gene co-expression networks reveal genes that sub-type human tumors.  Sci Rep. 10. doi: 10.1038/s41598-020-73611-1.

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.

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.

Huang W, Carbone MA, Lyman RF, Anholt RRH and Mackay TFC. 2020. Genotype by environment interaction for gene expression in Drosophila melanogaster. Nat Commun. 11: 5451. doi: 10.1038/s41467-020-19131-y.

Husain B, Hickman AR, Hang Y, Shealy BT, Sapra K and Feltus FA. 2020. NetExtractor: Extracting a cerebellar tissue gene regulatory network using differentially expressed high mutual information binary RNA profiles. G3 (Bethesda) 10: 2953-2963. doi: 10.1534/g3.120.401067.

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

Joyner CN, McMahan CS, Tebbs JM and Bilder CR. From mixed effects modeling to spike and slab variable selection: A Bayesian regression model for group testing data. Biometrics 76: 913-923. doi: 10.1111/biom.13176.

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.

Li W, Duren Z, Jiang R, Wong WH. 2020. A method for scoring the cell type-specific impacts of noncoding variants in personal genomes. Proc Natl Acad Sci. 35: 21364-72. doi: 10.1073/pnas.1922703117.

Li X, Wang L, and Wang H. 2020. Sparse learning and structure identification for ultra-high-dimensional image-on-scalar regression. J Amer Stat Assoc. doi: 10.1080/01621459.2020.1753523.

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. 2020. Leveraging multiple layers of data to predict Drosophila complex traits. G3 (Bethesda) 10: 4599-4613. doi: 10.1534/g3.120.401847.

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.

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.

Pauly R, Ogle C, Mcknight C, Reddick D, Presley J, Shannigrahi S, Feltus FA. 2020. NDN-TR68: Utilizing NDN for domain science applications – a genomics example.  NDN Technical Report.

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 and Markow TA. 2020. Additional species records and nomenclature updates of butterflies from a threatened coastal habitat in southern Sonora, Mexico. Journal Lepid Soc. 74:197–200. doi: 10.18473/lepi.74i3.a8.

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.

Phan IQ, Rice CA, Craig J, Noorai RE, McDonald J, Subramanian S, Tillery L, Barrett LK, Shankar V, Morris JC and Van Voorhis WC. 2020. The transcriptome of Balamuthia mandrillaris trophozoites for structure based drug design. bioRxiv. doi: 10.1101/2020.06.29.178905.

Ren L, Gao C, Duren Z, and Wang Y. 2020. GuidingNet: revealing transcriptional cofactor and predicting binding for DNA methyltransferase by network regularization. Brief Bioinform. doi: 10.1093/bib/bbaa245.

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.

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.

Spoor S, Wytko C, Soto B, Chen M, Almsaeed A, Condon B, Herndon N, Hough H, Staton M, Wegrzyn J, Main D, Feltus FA, Ficklin S. 2020. Tripal and Galaxy: supporting reproducible scientific workflows for community biological databases. Database. doi: 10.1093/database/baaa032.

Targonski C, Bender MR, Shealy BT, Husain B, Smith MC, Paseman B, Feltus FA. 2020. Cellular state transformations using deep learning for precision medicine applications. Patterns. 1:6. doi: 10.1016/j.patter.2020.100087.

Tsai KL, Vernau KM, Winger K, Zwueste DM, Sturges BK, Knipe M, Williams DC, Anderson KJ, Evans JM, Guo LT, Clark LA, Shelton GD. 2020. Congenital myasthenic syndrome in Golden Retrievers is associated with a novel COLQ mutation. J Vet Intern Med. 34: 258-265. doi: 10.1111/jvim.15667.

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. 2020. Prediction and prioritization of autism-associated long non-coding RNAs using gene expression and sequence features. BMC Bioinformatics 21: 505. doi: 10.1186/s12859-020-03843-5.

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.

Xin J, Zhang H, He Y, Duren Z, Bai C, Chen L, Luo X, Yan DS, Zhang C, Zhu X, Yuan Q, Feng Z, Cui C, Qi X, Ouzhuluobu, Wong WH, Wang Y and Su B. 2020. Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation. Nat. Commun. 11: 4928. doi: 10.1038/s41467-020-18638-8. 

Yanagawa A, Huang W, Yamamoto A, Wada-Katsumata A, Schal C and Mackay TFC. 2020. Genetic basis of natural variation in spontaneous grooming in Drosophila melanogaster. G3 (Bethesda) 10: 3453-3460. doi: 10.1534/g3.120.401360.

Yip PK, Schmitzberger M, Al-Hasan M, George J, Tripoliti E, Michael-Titus AT, Clayton D, and Priestley JV. 2020. Serotonin expression in the song circuitry of adult male zebra finches. Neuroscience. 444: 170-182. doi: 10.1016/j.neuroscience.2020.06.018.

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.

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.

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.

 

2019:

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.

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.

Bell ZW, Lovell P, Mello CV, Yip P, George JM, Clayton DF. 2019. Urotensin-related gene transcripts mark developmental emergence of the male forebrain vocal control system in songbirds. Sci Rep 9: 816. doi 10.1038/s41598-018-37057-w.

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

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.

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.

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.

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.

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.

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.

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.

Li X, Wang L, and Nettleton D. 2019. Additive partially linear models for ultra-high-dimensional regression. Stat. 8: e223. doi: 10.1002/sta4.223.

Li X, Wang L, and Nettleton D. 2019. Simultaneous sparse model identification and learning for ultra-high-dimensional additive partially linear models. J Multivar Anal. 173: 204-228. doi: 10.1016/j.jmva.2019.02.010.

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.

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.

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.

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.

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.

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.

Poehlman WL, Hsieh JJ and Feltus FA. 2019. Linking binary gene relationships to drivers of renal cell carcinoma reveals convergent function in alternate tumor progression paths. Sci Rep 9: 2899. doi: 10.1038/s41598-019-39875-y.

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.

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.

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.

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.

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.

Targonski C, Shearer CA, Shealy BT, Smith MC and Feltus FA. 2019. Uncovering biomarker genes with enriched classification potential from Hallmark gene sets. Sci Rep 9: 9747. doi: 10.1038/s41598-019-46059-1.

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.

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.

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.

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.

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.

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.

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.

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.