Publications

Greg Gibson  – (Pub Med)

Phantom epistasis between unlinked loci
Hemani G, Powell JE, Wang H et al.  
Nature. 2021 Aug;596(7871) PMID: 34381229

Altered splicing associated with the pathology of inflammatory bowel disease
Berger K, Somineni H, Prince J, Kugathasan S, Gibson G.
Hum Genomics. 2021 Jul 23;15(1):47 PMID: 34301333 

Extrafollicular IgD+ B cells generate IgE antibody secreting cells in the nasal mucosa
Corrado A, Ramonell RP, Woodruff MC, Tipton C, Wise S, Levy J, DelGaudio J, Kuruvilla ME, Magliocca KR, Tomar D, Garimalla S, Scharer CD, Boss JM, Wu H, Gumber S, Fucile C, Gibson G, Rosenberg A, Sanz I, Lee FE.
Mucosal Immunol. 2021 May 28; PMID: 34050324 

Transcriptional firing represses bactericidal activity in cystic fibrosis airway neutrophils
Margaroli C, Moncada-Giraldo D, Gulick DA, Dobosh B, Giacalone VD, Forrest OA, Sun F, Gu C, Gaggar A, Kissick H, Wu R, Gibson G, Tirouvanziam R.
Cell Rep Med. 2021 Apr 8; PMID: 33948572

Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease
Hari K Somineni, Sini Nagpal, Suresh Venkateswaran, David J Cutler, David T Okot et al. 
Am J Hum Genet (2021) 108(3):431-445. PMID: 33600772

Highly elevated polygenic risk scores are better predictors of myocardial infarction risk early in life than later
Monica Isgut, Jimeng Sun, Arshed A Quyyumi, Greg Gibson
Genome Med. (2021) 13(1):13. PMID: 33509272

TreeMap: a structured approach to fine mapping of eQTL variants
Li Liu, Pramod Chandrashekar, Biao Zeng, Maxwell D Sanderford, Sudhir Kumar, Greg Gibson
Bioinformatics. (2020) btaa927. PMID: 33135051

Canalization and Robustness in Human Genetics and Disease
Greg Gibson, Kristine A Lacek
Annu Rev Genet (2020)  54:189-211. PMID: 32867542

Fine-mapping within eQTL credible intervals by expression CROP-seq
Yidan Pan, Ruoyu Tian, Ciaran Lee, Gang Bao, Greg Gibson
Biol Methods Protoc.(2020)  5(1):bpaa008 PMID: 32665975

On the utilization of polygenic risk scores for therapeutic targeting.
Gibson G.
PLoS Genet. (2019) 15:e1008060. PMID: 31022172


King Jordan – (Pub Med)

Socioeconomic deprivation and genetic ancestry interact to modify type 2 diabetes ethnic disparities in the United Kingdom
Nagar SD, Nápoles AM, Jordan IK, Mariño-Ramírez L.
EClinicalMedicine. 2021 Jun 14;37:100960. PMID: 34386746

Genomic Diversity of Azole-Resistant Aspergillus fumigatus in the United States
Etienne KA, Berkow EL, Gade L, Nunnally N, Lockhart SR, Beer K, Jordan IK, Rishishwar L, Litvintseva AP.
mBio. 2021 Aug 10:e0180321. PMID: 34372699

New Histoplasma Diagnostic Assays Designed via Whole Genome Comparisons
Gallo JE, Torres I, Gómez OM, Rishishwar L, Vannberg F, Jordan IK, McEwen JG, Clay OK.
J Fungi (Basel). 2021 Jul 9;7(7):544. PMID: 34356923 

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields
Medina-Cordoba LK, Chande AT, Rishishwar L, Mayer LW, Valderrama-Aguirre LC, Valderrama-Aguirre A, Gaby JC, Kostka JE, Jordan IK.
Sci Rep. (2021) 11(1):9187. PMID: 33911103

Colistin Heteroresistance Is Largely Undetected among Carbapenem-Resistant Enterobacterales in the United States
Band VI, Satola SW, Smith RD et al.
mBio. (2021) 12(1):e02881-20  PMID: 33500343 

Population structure and pharmacogenomic risk stratification in the United States.
Nagar SD, Conley AB, Jordan IK.
BMC Biol.(2020) 18(1):140. PMID:33050895 

STing: accurate and ultrafast genomic profiling with exact sequence matches
Espitia-Navarro HF, Chande AT, Nagar SD, Smith H, Jordan IK, Rishishwar L.
Nucleic Acids Res. (2020) 48(14):7681-7689. PMID: 32619234 

Admixture-enabled selection for rapid adaptive evolution in the Americas
Norris ET, Rishishwar L, Chande AT, Conley AB, Ye K, Valderrama-Aguirre A, Jordan IK.
Genome Biol. (2020) 21(1):29. PMID: 32028992 

Native American admixture recapitulates population-specific migration and settlement of the continental United States
Jordan IK, Rishishwar L, Conley AB.
PLoS Genet. (2019) 15(9):e1008225. PMID: 31545791 

Population Pharmacogenomics for Precision Public Health in Colombia
Nagar SD, Moreno AM, Norris ET, Rishishwar L, Conley AB, O’Neal KL, Vélez-Gómez S, Montes-Rodríguez C, Jaraba-Álvarez WV, Torres I, Medina-Rivas MA, Valderrama-Aguirre A, Jordan IK, Gallo JE.
Front Genet. (2019) 10:241. PMID: 30967898 

Genetic ancestry, admixture and health determinants in Latin America
Norris ET, Wang L, Conley AB, Rishishwar L, Mariño-Ramírez L, Valderrama-Aguirre A, Jordan IK.
BMC Genomics. (2018) 19(Suppl 8):861. PMID: 30537949 


Joseph Lachance – (Pub Med)

Beyond Stamp Collecting: Evolutionary and Functional Genomics Advance Our Understanding of Cancer Biology
Lachance J.
Cancer Res. (2021) 81(7):1637-1638. PMID: 34003790

Large sample spaces do not imply biological systems are ‘fine-tuned’
Lachance J, Simonti CN, Weitz JS.
J Theor Biol. (2020) 507:110457. PMID: 32828844 

A Custom Genotyping Array Reveals Population-Level Heterogeneity for the Genetic Risks of Prostate Cancer and Other Cancers in Africa
Harlemon M, Ajayi O, Kachambwa P, Kim MS, Simonti CN et al. 
Cancer Res. (2020) 80(13):2956-2966. PMID: 32393663 

Genetic disease risks can be misestimated across global populations
Kim MS, Patel KP, Teng AK, Berens AJ, Lachance J.
Genome Biol. (2018) 19(1):179. PMID: 30424772 

Genetic Hitchhiking and Population Bottlenecks Contribute to Prostate Cancer Disparities in Men of African Descent
Lachance J, Berens AJ, Hansen MEB, Teng AK, Tishkoff SA, Rebbeck TR.
Cancer Res. (2018) 78(9):2432-2443. PMID: 29438991 

The Genomic Health of Ancient Hominins
Berens AJ, Cooper TL, Lachance J.
Hum Biol. (2017) 89(1):7-19. PMID: 29285967


Patrick McGrath – (Pub Med)

From QTL to gene: C. elegans facilitates discoveries of the genetic mechanisms underlying natural variation
Evans KS, van Wijk MH, McGrath PT, Andersen EC, Sterken MG.
Trends Genet. 2021 Jul 3:S0168-9525(21)00146-3. PMID: 34229867  

Genome-enabled discovery of evolutionary divergence in brains and behavior
Patil C, Sylvester JB, Abdilleh K, Norsworthy MW, Pottin K, Malinsky M, Bloomquist RF, Johnson ZV, McGrath PT, Streelman JT.
Sci Rep. 2021 Jun 21;11(1):13016. PMID: 34155279

Automated measurement of long-term bower behaviors in Lake Malawi cichlids using depth sensing and action recognition
Johnson ZV, Arrojwala MTS, Aljapur V, Lee T, Lancaster TJ, Lowder MC, Gu K, Stockert JI, Lecesne RL, Moorman JM, Streelman JT, McGrath PT.
Sci Rep. (2020) 10(1):20573. PMID: 33239639

Automatic Classification of Cichlid Behaviors Using 3D Convolutional Residual Networks
Long L, Johnson ZV, Li J, Lancaster TJ, Aljapur V, Streelman JT, McGrath PT.
iScience. (2020 Sep) 23(10):101591. PMID: 33083750 

Quantitative benzimidazole resistance and fitness effects of parasitic nematode beta-tubulin alleles
Dilks CM, Hahnel SR, Sheng Q, Long L, McGrath PT, Andersen EC.
Int J Parasitol Drugs Drug Resist. (2020) 14:28-36. PMID: 32858477 

Evolution of Yin and Yang isoforms of a chromatin remodeling subunit precedes the creation of two genes.
Xu W, Long L, Zhao Y, Stevens L, Felipe I, Munoz J, Ellis RE, McGrath PT.
Elife. (2019) 8: e48119. PMID: 31498079

A primer on pheromone signaling in Caenorhabditis elegans for systems biologists.
McGrath PT, Ruvinsky I.
Curr Opin Syst Biol. (2019) 13:23-30. PMID: 30984890

Changes to social feeding behaviors are not sufficient for fitness gains of the Caenorhabditis elegans N2 reference strain.
Zhao Y, Long L, Xu W, Campbell RF, Large EE, Greene JS, McGrath PT.
Elife. (2018) 7: e38675. PMID: 30328811


Annalise Paaby – (Pub Med)

High-Temporal-Resolution smFISH Method for Gene Expression Studies in Caenorhabditis elegans Embryos
Charles S, Aubry G, Chou HT, Paaby AB, Lu H.
Anal Chem. (2021) 93(3):1369-1376. PMID: 33355449

Extent and context dependence of pleiotropy revealed by high-throughput single-cell phenotyping
Geiler-Samerotte KA, Li S, Lazaris C, Taylor A, Ziv N, Ramjeawan C, Paaby AB, Siegal ML.
PLoS Biol. (2020) 18(8):e3000836. PMID: 32804946


A portable, low-cost device for precise control of specimen temperature under stereomicroscopes
Testa ND, Kaul S, Le KN, Zhan M, Lu H, Paaby AB.
PLoS One. (2020) 15(3):e0230241. PMID: 32160236 Free PMC article.

Analysis of Epistasis in Natural Traits Using Model Organisms
Campbell RF, McGrath PT, Paaby AB.
Trends Genet. (2018) 34(11):883-898. PMID: 30166071

Cryptic Genetic Variation in Evolutionary Developmental Genetics
Paaby AB, Gibson G.
Biology (Basel). (2016) 5(2):28. PMID: 27304973   


Peng Qiu

Correction to: Aging progression of human gut microbiota
Xu C, Zhu H, Qiu P.
BMC Microbiol. 2021 Apr 28;21(1):129.PMID: 33910508 

Identifying gene expression patterns associated with drug-specific survival in cancer patients
Neary B, Zhou J, Qiu P.
Sci Rep. (2021) 11(1):5004. PMID: 33654134 

Dual delivery of IL-10 and AT-RvD1 from PEG hydrogels polarize immune cells towards pro-regenerative phenotypes
Sok MCP, Baker N, McClain C, Lim HS, Turner T, Hymel L, Ogle M, Olingy C, Palacios JI, Garcia JR, Srithar K, García AJ, Qiu P, Botchwey EA.
Biomaterials. (2021) 268:120475. PMID: 33321293

Leveraging TCGA gene expression data to build predictive models for cancer drug response
Clayton EA, Pujol TA, McDonald JF, Qiu P.
BMC Bioinformatics. (2020) 21(Suppl 14):364. PMID: 32998700

GLaMST: grow lineages along minimum spanning tree for b cell receptor sequencing data
Yang X, Tipton CM, Woodruff MC, Zhou E, Lee FE, Sanz I, Qiu P.
BMC Genomics. (2020) 21(Suppl 9):583. PMID: 32900378  

Embracing the dropouts in single-cell RNA-seq analysis
Qiu P.
Nat Commun. (2020) 11(1):1169. PMID: 32127540 

GDISC: a web portal for integrative analysis of gene-drug interaction for survival in cancer
Spainhour JCG, Lim J, Qiu P
Bioinformatics. (2017) 33(9):1426-1428. PMID: 28453687 


Todd Streelman – (Pub Med)

Convergent Evolution of Cichlid Fish Pharyngeal Jaw Dentitions in Mollusk-Crushing Predators: Comparative X-Ray Computed Tomography of Tooth Sizes, Numbers, and Replacement
Hulsey CD, Meyer A, Streelman JT.
Integr Comp Biol. (2020) 60(3):656-664. PMID: 32584994

Ecotype differences in aggression, neural activity and behaviorally relevant gene expression in cichlid fish
Baran NM, Streelman JT.
Genes Brain Behav. (2020) 19(6):e12657. PMID: 32323443 

Behavioral evolution contributes to hindbrain diversification among Lake Malawi cichlid fish
York RA, Byrne A, Abdilleh K, Patil C, Streelman T, Finger TE, Fernald RD.
Sci Rep. (2019) 9(1):19994. PMID: 31882605 

Developmental plasticity of epithelial stem cells in tooth and taste bud renewal.
Bloomquist RF, Fowler TE, An Z, Yu TY, Abdilleh K, Fraser GJ, Sharpe PT, Streelman JT.
Proc Natl Acad Sci U S A. (2019) 116:17858-17866. PMID: 31427537

Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes.
York RA, Patil C, Abdilleh K, Johnson ZV, Conte MA, Genner MJ, McGrath PT, Fraser HB, Fernald RD, Streelman JT.
Proc Natl Acad Sci U S A. (2018) 115:E11081-E11090. PMID: 30397142

A quiescent cell population replenishes mesenchymal stem cells to drive accelerated growth in mouse incisors.
An Z, Sabalic M, Bloomquist RF, Fowler TE, Streelman T, Sharpe PT.
Nat Commun. (2018) 9:378. PMID: 29371677

Genome-wide protein phylogenies for four African cichlid species.
Ramakrishnan Varadarajan A, Mopuri R, Streelman JT, McGrath PT./br> BMC Evol Biol. (2018) 18:1. PMID: 29368592


Eberhard Voit

A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression
Dalvi-Garcia F, Fonseca LL, Vasconcelos ATR, Hedin-Pereira C, Voit EO.
PLoS Comput Biol. (2021) 17(5):e1008956. PMID: 33970902 

Mechanistic Model of Signaling Dynamics Across an Epithelial Mesenchymal Transition
Wade JD, Lun XK, Zivanovic N, Voit EO, Bodenmiller B.
Front Physiol. (2020) 11:579117. PMID: 33329028 

ENaC regulation by phospholipids and DGK explained through mathematical modeling
Olivença DV, Voit EO, Pinto FR.
Sci Rep. (2020) 10(1):13952. PMID: 32811866 

Agent-Based Modeling and Simulation in Mathematics and Biology Education
Bodine EN, Panoff RM, Voit EO, Weisstein AE.
Bull Math Biol. (2020) 82(8):101. PMID: 32725363

Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes
Dam P, Rodriguez-R LM, Luo C, Hatt J, Tsementzi D, Konstantinidis KT, Voit EO.
Sci Rep. (2020) 10(1):2423. PMID: 32051429

Perspective: Dimensions of the scientific method
Voit EO.
PLoS Comput Biol. (2019) 15(9):e1007279. PMID: 31513575 

Dynamical systems approaches to personalized medicine
Davis JD, Kumbale CM, Zhang Q, Voit EO.
Curr Opin Biotechnol. (2019) 58:168-174. PMID: 30978644 Free PMC article.

Agent-based modeling of morphogenetic systems: Advantages and challenges
Glen CM, Kemp ML, Voit EO.
PLoS Comput Biol. (2019) 15(3):e1006577. PMID: 30921323 

Metrics for regulated biochemical pathway systems
Davis JD, Voit EO.
Bioinformatics. (2019) 35(12):2118-2124. PMID: 30428007


May Wang

Models for Predicting Stage in Head and Neck Squamous Cell Carcinoma using Proteomic and Transcriptomic Data
C Kaddi, M Wang
IEEE

A Semi-Supervised Method for Predicting Cancer Survival Using Incomplete Clinical Data
HR Hassanzadeh, JH Phan, MD Wang
arXiv