Recent Publications by CHG Affiliates
2023:
Elise Schnabel, Jacklyn Thomas, Rabia Elhawaz, Yueyao Gao, William Poehlman, Suchitra Chavan, Asher Pasha, Eddi Esteban, Nicholas Provart, F. Alex Feltus, Julia Frugoli. ” A laser capture microdissection transcriptome of M. truncatula roots responding to rhizobia reveals spatiotemporal tissue expression patterns of genes involved in nodule signaling and organogenesis.” Molecular Plant-Microbe Interactions (in press), 2023.
Xusheng Ai, Melissa C. Smith, and F. Alex Feltus. “Generative Adversarial Networks Applied to Gene Expression Analysis: An Interdisciplinary Perspective.” Computational and Systems Oncology (in press), 2023.
Elise Schnabel, Yueyao Gao, William Poehlman, Suchitra Chavan, F. Alex Feltus, and Julia Frugoli. ” A Medicago truncatula Autoregulation of Nodulation Mutant Transcriptome Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2.” Current Issues in Molecular Biology 45(6), 4612-4631, 2023. https://doi.org/10.3390/cimb45060293.
X. Wang, X. Ai, F. A. Feltus and S. Shannigrahi, “GNSGA: A Decentralized Data Replication Algorithm for Big Science Data,” 2023 IFIP Networking Conference (IFIP Networking), Barcelona, Spain, 2023, pp. 1-9, doi: 10.23919/IFIPNetworking57963.2023.10186357.
Arnab Mutsuddy, Cemal Erdem, Jonah R. Huggins, Michael Salim, Daniel Cook, Nicole Hobbs, F. Alex Feltus, and Marc R. Birtwistle. “Computational Speed-Up of Large-Scale, Single-Cell Model Simulations Via a Fully-Integrated SBML-Based Format.” Bioinformatics Advances Volume 3, Issue 1, vbad039, 2023. https://doi.org/10.1093/bioadv/vbad039.
Sankalpa Timilsina, Justin Presley, David Reddick, Susmit Shannigrahi, Xusheng Ai, Coleman Mcknight, and Alex Feltus. “Utilizing NDN DPDK for Kubernetes Genomics Data Lake., Technical Report NDN-0070, 2022.
2022:
Allison R Hickman, Benafsh Husain, Bradley Selee, Rini Pauly, Yuqing Hang, and F. Alex Feltus*. “Discovery of eQTL Alleles Associated with Autism Spectrum Disorder: A Case-Control Study”. Journal of Autism and Developmental Disorders, 2022. https://doi.org/10.1007/s10803-022-05631-x
Nelligan N, Bender MR, and Feltus FA*. “Simulating the Restoration of Normal Gene Expression from Different Thyroid Cancer Stages Using Deep Learning.” BMC Cancer (22)612, 2022 https://doi.org/10.1186/s12885-022-09704-z.
Cemal Erdem, Ethan M. Bensman, Arnab Mutsuddy, Michael M. Saint-Antoine, Mehdi Bouhaddou, Robert C. Blake, Will Dodd, Sean M. Gross, Laura M. Heiser, F. Alex Feltus, Marc R. Birtwistle*. “A Simple and Efficient Pipeline for Construction, Merging, Expansion, and Simulation of Large-Scale, Single-Cell Mechanistic Models.” Nature Communications, 13 (3555), 2022. https://doi.org/10.1038/s41467-022-31138-1.
Yuqing Hang, Josh Burns, Benjamin T. Shealy, Rini Pauly, Stephen P. Ficklin, and Frank A. Feltus*. “Identification of condition-specific regulatory mechanisms in normal and cancerous human lung tissue.” BMC Genomics 23, 350, 2022. https://doi.org/10.1186/s12864-022-08591-92022.
David E. Reddick, Justin Presley, Frank A. Feltus, Susmit Shannigrahi*. “WIP AABAC – Automated Attribute Based Access Control for Genomics Data.” SACMAT ’22: Proceedings of the 27th ACM on Symposium on Access Control Models and Technologies. June 2022 Pages 217-222, 2022. https://doi.org/10.1145/3532105.3535037.
John Hadish, Tyler D. Biggs, Benjamin T. Shealy, M. Reed Bender, Coleman B. McKnight, Connor Wytko, Melissa C. Smith, F. Alex Feltus, Loren A. Honaas, Stephen P. Ficklin*. “GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.” BMC Bioinformatics 23, 156 (2022). https://doi.org/10.1186/s12859-022-04629-7
David Reddick. F. Alex Feltus, Susmit Shannigrahi*. “Case Study of Attribute Based Access Control for Genomics Data Using Named Data Networking.” 2022 IEEE 19th Annual Consumer Communications & Networking Conference (CCNC). 8-11 Jan. 2022. https://doi.org/10.1109/CCNC49033.2022.9700642.
Gao Y, Selee B, Schnabel EL, Poehlman WL, Chavan SA, Frugoli JA and Feltus FA*. “Time Series Transcriptome Analysis in Medicago truncatula Shoot and Root Tissue During Early Nodulation.” Frontiers in Plant Science. 13:861639, 2022. doi: https://doi.org/10.3389/fpls.2022.861639
Benafsh Husain, M. Reed Bender, and F. Alex Feltus.” EdgeCrafting: Mining embedded, latent, non-linear patterns to construct Gene Relationship Networks.” G3:Genes|Genetics|Genomes. 12-4, jkac042, 2022 https://doi.org/10.1093/g3journal/jkac042
Joel Gershenfeld, Karen S. Baker, Nicholas Berente, Pat Canavan, F. Alex Feltus, Alysia Garmulewicz, Ron Hutchins, John Leslie King, Christine Kirkpatrick, Chris Lenhardt, Spencer Lewis, Michael Maffie, Matthew Mayernik, Barbara Mittleman, Beth Plale, Rahesh Sampath, Namchul Shin, Shelley Stall, John Towns, Susan Winter, Pips Veazey. “When Launching a Collaboration, Keep it Agile.” Stanford Social Innovation Review. 20(2), 2022.
Allison R. Hickman, Yuqing Hang, Rini Pauly, and Frank A. Feltus*. “Identification of Condition-Specific Biomarker Systems in Uterine Cancer.” G3:Genes|Genetics|Genomes. 12-1, January 2022, jkab392, 2021. https://doi.org/10.1093/g3journal/jkab392
2021:
Feltus FA and Clarke DJ. “ISO digital learning solutions (DLS) Toolkit.” https://capacity.iso.org/home/iso-digital-learning-solutions.html, 2021.
Joshua J.R. Burns, Benjamin T. Shealy, Mitchell S. Greer, John A. Hadish, Matthew T. McGowan, Tyler Biggs, Melissa C. Smith, F. Alex Feltus, Stephen P. Ficklin. “Addressing Noise in Co-Expression Network Construction.” Briefings in Bioinformatics bbab495, 2021. https://doi.org/10.1093/bib/bbab495
Siqi Liu, Varun Patil, Tianyuan Yu, Alexander Afanasyev, Frank Alex Feltus, Susmit Shannigrahi, and Lixia Zhang. “Designing Hydra with Centralized versus Decentralized Control: A Comparative Study.” ACM CoNEXT 2021 Interdisciplinary Workshop on (de)Centralization in the Internet (ACM IWCI 2021). P4-10, 2021. https://doi.org/10.1145/3488663.3493690
Shealy BT, Feltus FA, and Smith MC*. “Intelligent Resource Provisioning for Scientific Workflows and HPC”. IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS). 15 Nov. 2021. https://doi.org/10.1109/WORKS54523.2021.00007
Cameron Ogle, Susmit Shannigrahi, David Riddick, Coleman McKnight, Rini Pauly, Tyler Biggs, Stephen Ficklin, F. Alex Feltus*. “Information Centric Networking for Genomics Data Management and Integrated Workflows” Frontiers in Big Data. Volume 4, 2021.
Baker BM, Mokashi SS, Shankar V, Hatfield JS, Hannah RC, Mackay TFC and Anholt RRH. 2021. The Drosophila brain on cocaine at single cell resolution. Genome Res, in press. doi: 10.1101/gr.268037.120.
Baker BM, Carbone MA, Huang W, Anholt RRH and Mackay TFC. 2021. Genetic basis of variation in cocaine and methamphetamine consumption in outbred populations of Drosophila melanogaster. Proc Natl Acad Sci USA, in press. BioRxiv 2021. doi: https://doi.org/10.1101/2021.o3.o1.433403.
Herbert A, Wang H, Saski C, and Turechek W. 2021. Draft Genome Sequences of Two Xanthomonas fragariae Strains. Microbiol. resour 10: 16. doi: 10.1128/MRA.00138-21.
Huggett SB, Hatfield JS, Walters JD, McGeary J, Welsh J, Mackay TFC, Anholt RRH and Palmer RHC. 2021. Ibrutinib as a potential therapeutic for cocaine use disorder. Biol Psychiatry, submitted. MedRxiv 2021. https//www.medrxiv.org/content/10.1101/2021.02.05.21251228v1
Johnstun JA, Shankar V, Mokashi SS, Sunkara LT, Ihearahu UE, Lyman RL, Mackay TFC and Anholt RRH. 2021. Functional diversification, redundancy and epistasis among paralogs of the Drosophila melanogaster Obp50a-d gene cluster. Mol Biol Evol 38, 2030-2044. https://doi.org/10.1093/molbev/msab004.
Mokashi SS, Shankar V, MacPherson RA, Hannah RC, Mackay TFC and Anholt RRH. 2021. Developmental alcohol exposure in Drosophila: Effects on adult phenotypes and gene expression in the brain. Front Psychiatry, submitted. BioRXiv https://biorxiv.org/cgi/content/short/2021.04.22.440913v1.
Morozova TV, Shankar V, MacPherson RA, Zhou S, Mackay TFC and Anholt RRH. 2021. Modulation of the Drosophila transcriptome by developmental exposure to alcohol. In preparation.
Nazario-Yepiz NO, Fernández Sobaberas J, Lyman R, Campbell MR III, Shankar V, Anholt RRH and Mackay TFC. 2021. A Drosophila model for metabolic syndrome: Physiological and metabolomic consequences of reduced expression of the brummer triglyceride lipase. Sci Rep, submitted.
Özsoy ED, Yılmaz M, Patlar B, Emecen G, Durmaz E, Magwire MM, Zhou S, Huang W, Anholt RRH and Mackay TFC. 2021. Epistasis for head morphology in Drosophila melanogaster. Genetics, submitted.
Walters JD, Hatfield JS, Baker BB, Mackay TFCand Anholt RRH. 2021. A high-throughput microplate feeder assay for the quantification of consumption in Drosophila. J Vis Exp, submitted.
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.
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