2022
Genome-wide association study of disease resilience traits from a natural polymicrobial disease challenge model in pigs identifies the importance of the major histocompatibility complex region, Jian Cheng, Rohan Fernando, Hao Cheng, Stephen D. Kachman, KyuSang Lim, John C.S. Harding, Michael K. Dyck, Frederic Fortin, Graham S. Plastow, PigGen Canada Research Consortium, and Jack C.M. Dekkers
Seasonal Variation in Terrestrial Invertebrate Subsidies to Tropical Streams and Implications for the Feeding Ecology of Hart’s Rivulus (Anablepsoides hartii), David C. Owens, Thomas N. Heatherly, Kent M. Eskridge, Colden V. Baxter, and Steven A. Thomas
A Survey on the Use of Plastic versus Biodegradable Bottles for Drinking Water Packaging in the United Arab Emirates, Himadri Rajput, Munjed A. Maraqa, Fatima Zraydi, Lina A. Al Khatib, Noor Ameen, Rime Ben ElKaid, Safia S. Al Jaberi, Noura A. Alharbi, Reka Howard, and Ashraf Aly Hassan
Cranberry Polyphenols in Esophageal Cancer Inhibition: New Insights, Katherine M. Weh, Yun Zhang, Connor L. Howard, Amy B. Howell, Jennifer L. Clarke, and Laura A. Kresty
2021
Discussion on “Is group testing ready for prime-time in disease identification”, Christopher R. Bilder, Joshua M. Tebbs, and Christopher S. McMahan
Development of a multiplex real-time PCR assay for predicting macrolide and tetracycline resistance associated with bacterial pathogens of bovine respiratory disease, Enakshy Dutta, John Loy, Caitlyn A. Deal, Emily L. Wynn, Michael L. Clawson, Jennifer Clarke, and Bing Wang
Incorporating Molecular Markers and Causal Structure among Traits Using a Smith-Hazel Index and Structural Equation Models, Juan Valente Hidalgo-Contreras, Josafhat Salinas-Ruiz, Kent M. Eskridge, and Stephen P. Baenziger
Treatment of Inconclusive Results in Firearms Error Rate Studies, Heike Hofmann, Susan VanderPlas, and Alicia L. Carriquiry
A Review of Spatial Causal Inference Methods for Environmental and Epidemiological Applications, Brian J. Reich, Shu Yang, Yawen Guan, Andrew B. Giffin, Matthew J. Miller, and Ana Rappold
Corn residue baling and grazing impacts on corn yield under irrigated conservation tillage systems, Sabrina J. Ruis, Charles Burr, Humberto Blanco-Canqui, Brian Olson, Mark Reiman, Daran Rudnick, Johnna Baller, and Kathryn J. Hanford
Faculty versus Student Repeatability on Evaluating Translucency of the Anterior Dentition, James L. Sheets, David B. Marx, Nina Ariani, Valentim A. R. Barão, and Alvin G. Wee
Fully Bayesian Analysis of Relevance Vector Machine Classification With Probit Link Function for Imbalanced Data Problem, Wenyang Wang, Dongchu Sun, Peng Shao, Haibo Kuang, and Cong Sui
2020
Cost Effectiveness of Sample Pooling to Test for SARS-CoV-2, Baha Abdalhamid, Christopher Richard Bilder, Jodi Louise Garrett, and Peter Charles Iwen
Representation of features as images with neighborhood dependencies for compatibility with convolutional neural networks, Omid Bazgir, Ruibo Zhang, Saugato Rahman Dhruba, Raziur Rahman, Souparno Ghosh, and Ranadip Pal
The role of topography, soil, and remotely sensed vegetation condition towards predicting crop yield, Trenton E. Franz, Sayli Pokal, Justin P. Gibson, Yuzhen Zhou, Hamed Gholizadeh, Fatima Amor Tenorio, Daran Rudnick, Derek M. Heeren, Matthew F. McCabe, Matteo Ziliani, Zhenong Jin, Kaiyu Guan, Ming Pan, John Gates, and Brian Wardlow
The local stability of a modified multi-strain SIR model for emerging viral strains, Miguel Fudolig and Reka Howard
Tumor ablation due to inhomogeneous anisotropic diffusion in generic three-dimensional topologies, Erdi Kara, Aminur Rahman, Eugenio Aulisa, and Souparno Ghosh
In praise of partially interpretable predictors, Tri Le and Bertrand S. Clarke
TGCnA: temporal gene coexpression network analysis using a low-rank plus sparse framework, Jinyu Li, Yutong Lai, Chi Zhang, and Qi Zhang
Statistical Downscaling with Spatial Misalignment: Application to Wildland Fire PM2.5 Concentration Forecasting, Suman Majumder, Yawen Guan, Brian J. Reich, Susan O’Neill, and Ana G. Rappold
Association between baseline abundance of Peptoniphilus, a Gram-positive anaerobic coccus, and wound healing outcomes of DFUs, Kyung R. Min, Adriana Galvis, Katherine L. Baquerizo Nole, Rohita Sinha, Jennifer Clarke, Robert S. Kirsner, and Dragana Ajdic
Perceived Neighborhood: Preferences versus Actualities, Saeed Moradi, Ali Nejat, Da Hu, and Souparno Ghosh
Exact Distribution of Linkage Disequilibrium in the Presence of Mutation, Selection, or Minor Allele Frequency Filtering, Jiayi Qu, Stephen D. Kachman, Dorian Garrick, Rohan L. Fernando, and Hao Cheng
Economics of herbicide programs for weed control in conventional, glufosinate, and dicamba/glyphosate-resistant soybean across Nebraska, Adam M. Striegel, Kent M. Eskridge, Nevin C. Lawrence, Stevan Knezevic, Greg R. Kruger, Christopher A. Proctor, Gary Hein, and Amit J. Jhala
A High-Throughput Phenotyping Pipeline for Image Processing and Functional Growth Curve Analysis, Ronghao Wang
2019
Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma, Noah E. Berlow, Rishi Rikhi, Mathew Geltzeiler, Jinu Abraham, Matthew N. Svalina, Lara E. Davis, Erin Wise, Maria Mancini, Jonathan Noujaim, Atiya Mansoor, Michael J. Quist, Kevin L. Matlock, Martin W. Goros, Brian S. Hernandez, Yee C. Doung, Khin Thway, Tomohide Tsukahara, Jun Nishio, Elaine T. Huang, Susan Airhart, Carol J. Bult, Regina Gandour-Edwards, Robert G. Maki, Robin L. Jones, Joel E. Michalek, Milan Milovancev, Souparno Ghosh, Ranadip Pal, and Charles Keller
Informative Group Testing for Multiplex Assays, Christopher R. Bilder, Joshua M. Tebbs, and Christopher S. McMahan
Cost-effective Surveillance for Infectious Diseases Through Specimen Pooling and Multiplex Assays, Christopher Bilder, Joshua Tebbs, and Christopher McMahan
Recursive model for dose-time responses in pharmacological studies, Saugato Rahman Dhruba, Aminur Rahman, Raziur Rahman, Souparno Ghosh, and Ranadip Pal
Soil Fauna Accelerate Dung Pat Decomposition and Nutrient Cycling into Grassland Soil, Kenneth S. Evans, Martha Mamo, Ana Wingeyer, Walter Schacht, Kent Eskridge, Jeff Bradshaw, and Daniel Ginting
Post-ER Stress Biogenesis of Golgi Is Governed by Giantin, Cole P. Frisbie, Alexander Y. Lushnikov, Alexey V. Krasnoslobodtsev, Jean-Jack Riethoven, Jennifer L. Clarke, Elena I. Stepchenkova, and Armen Petrosyan
Genomic Prediction Using Canopy Coverage Image and Genotypic Information in Soybean via a Hybrid Model, Reka Howard and Diego Jarquin
Functional random forest with applications in dose-response predictions, Raziur Rahman, Saugato Rahman Dhruba, Souparno Ghosh, and Ranadip Pal
2018
Application of transfer learning for cancer drug sensitivity prediction, Saugato Rahman Dhruba, Raziur Rahman, Kevin Matlock, Souparno Ghosh, and Ranadip Pal
Characterization of Soybean Protein Adhesives Modified by Xanthan Gum, Chen Feng, Fang Wang, Zheng Xu, Huilin Sui, Yong Fang, Xiaozhi Tang, and Xinchun Shen
Investigation of model stacking for drug sensitivity prediction, Kevin Matlock, Carlos De Niz, Raziur Rahman, Souparno Ghosh, and Ranadip Pal
Development of 11-Plex MOL-PCR Assay for the Rapid Screening of Samples for Shiga Toxin-Producing Escherichia coli, Travis A. Woods, Heather M. Mendez, Sandy Ortega, Xiaorong Shi, David Marx, Jianfa Bai, Rodney A. Moxley, T. G. Nagaraja, Steven W. Graves, and Alina Deshpande
Existing and Potential Statistical and Computational Approaches for the Analysis of 3D CT Images of Plant Roots, Zheng Xu, Camilo Valdes, and Jennifer Clarke
2017
Perennial warm-season grasses for producing biofuel and enhancing soil properties: An alternative to corn residue removal, Humberto Blanco-Canqui, Robert B. Mitchell, Virginia L. Jin, Marty R. Schmer, and Kent M. Eskridge
Trans-ancestry Fine Mapping and Molecular Assays Identify Regulatory Variants at the ANGPTL8 HDL-C GWAS Locus, Maren E. Cannon, Qing Duan, Ying Wu, Monica Zeynalzadeh, Zheng Xu, Antti J. Kangas, Pasi Soininen, Mika Ala-Korpela, Mete Civelek, Aldons J. Lusis, Johanna Kuusisto, Francis S. Collins, Michael Boehnke, Hua Tang, Markku Laakso, Yun Li, and Karen L. Mohlke
Evaluating Current Practices in Shelf Life Estimation, Robert Capen, David Christopher, Patrick Forenzo, Kim Huynh-Ba, David LeBlond, Oscar Liu, John O'Neill, Nate Patterson, Michelle Quinlan, Radhika Rajagopalan, James Schwenke, and Walter W. Stroup
Joint hierarchical models for sparsely sampled high-dimensional LiDAR and forest variables, Andrew O. Finley, Sudipto Banerjee, Yuzhen Zhou, Bruce D. Cook, and Chad Babcock
Application of Response Surface Methods To Determine Conditions for Optimal Genomic Prediction, Reka Howard, Alicia L. Carriquiry, and William D. Beavis
Increasing Genomic-Enabled Prediction Accuracy by Modeling Genotype x Environment Interactions in Kansas Wheat, Diego Jarquin, Cristiano Lemas da Silva, R. Chris Gaynor, Jesse Poland, Allan Fritz, Reka Howard, Sarah Battenfield, and José Crossa
A Bayes Interpretation of Stacking for M-Complete and M-Open Settings, Tri Le and Bertrand S. Clarke
Heterogeneity Aware Random Forest for Drug Sensitivity Prediction, Raziur Rahman, Kevin Matlock, Souparno Ghosh, and Ranadip Pal
Assessing the Impact of Retreat Mechanisms in a Simple Antarctic Ice Sheet Model Using Bayesian Calibration, Kelsey L. Ruckert, Gary Shaffer, David Pollard, Yawen Guan, Tony E. Wong, Chris E. Forest, and Klaus Keller
Generalized Confidence Intervals Compatible with the Min Test for Simultaneous Comparisons of One Subpopulation to Several Other Subpopulations, Julia N. Soulakova
Impact of Menthol Smoking on Nicotine Dependence for Diverse Racial/Ethnic Groups of Daily Smokers, Julia N. Soulakova and Ryan R. Danczak
2016
EnsCat: clustering of categorical data via ensembling, Bertrand S. Clarke, Saeid Amiri, and Jennifer L. Clarke
The impact of hair coat color on longevity of Holstein cows in the tropics, C. N. Lee, K. S. Baek, and A. Parkhurst
Genomic Bayesian Prediction Model for Count Data with Genotype x Environment Interaction, Abelardo Montesinos-López, Osval A. Montesinos-López, José Crossa, Juan Burgueño, Kent M. Eskridge, Esteban Falconi-Castillo, Xinyao He, Pawan Singh, and Karen Cichy
A Genomic Bayesian Multi-trait and Multi-environment Model, Osval A. Montesinos-López, Abelardo Montesinos-López, José Crossa, Fernando Toledo, Oscar Pérez-Hernández, Kent M. Eskridge, and Jessica Rutkoski
Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress, Ligia A. Papale, Sisi Li, Andy Madrid, Qi Zhang, Li Chen, Pankaj Chopra, Peng Jin, Sunduz Keles, and Reid S. Alisch
Species discovery and diversity in Lobocriconema (Criconematidae: Nematoda) and related plant-parasitic nematodes from North American ecoregions, Tom Powers, Ernest C. Bernard, T. Harris, Robert Higgins, M. Olson, S. Olson, M. Lodema, Julianne N. Matczyszyn, P. Mullin, L. Sutton, and K.S Powers
Design of Probabilistic Random Forests with Applications to Anticancer Drug Sensitivity Prediction- 2016, Raziur Rahman, Saad Haider, Souparno Ghosh, and Ranadip Pal
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome, Anthony D. Schmitt, Ming Hu, Inkyung Jung, Zheng Xu, Yunjiang Qiu, Catherine L. Tan, Yun Li, Shin Lin, Yiing Lin, Cathy L. Barr, and Bing Ren
How Often Are Antibiotic-Resistant Bacteria Said to “Evolve” in the News?, Nina Singh, Matthew T. Sit, Deanna M. Chung, Ana A. Lopez, Ranil Weerackoon, and Pamela J. Yeh
A BAYESIAN GWAS METHOD UTILIZING HAPLOTYPE CLUSTERS FOR A COMPOSITE BREED POPULATION, Danielle F. Wilson-Wells and Stephen D. Kachman
Optimal Design of Low-Density SNP Arrays for Genomic Prediction: Algorithm and Applications, Xiao-Lin Wu, Jiaqi Xu, Guofei Feng, George R. Wiggans, Jeremy F. Taylor, Jun He, Changsong Qian, Jiansheng Qiu, Barry Simpson, Jeremy Walker, and Stewart Bauck
HiView: an integrative genome browser to leverage Hi‑C results for the interpretation of GWAS variants, Zheng Xu, Guosheng Zhang, Qing Duan, Shengjie Chai, Baqun Zhang, Cong Wu, Fulai Jin, Feng Yue, Yun Li, and Ming Hu
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection, Qi Zhang, Xin Zeng, Sam Younkin, Trupti Kawli, Michael P. Snyder, and Sündüz Kele
2015
Measuring Peer Socialization for Adolescent Substance Use:A Comparison of Perceived and Actual Friends’ Substance Use Effects, Arielle R. Deutsch, Pavel Chernyavskiy, Douglas Steinley, and Wendy S. Slutske
A Copula Based Approach for Design of Multivariate Random Forests for Drug Sensitivity Prediction, Saad Haider, Raziur Rahman, Souparno Ghosh, and Ranadip Pal
S1: Supplementary Information for Article: A copula based approach for design of multivariate random forests for drug sensitivity prediction, Saad Haider, Raziur Rahman, Souparno Ghosh, and Ranadip Pal
Effect of dexamethasone prodrug on inflamed temporomandibular joints in juvenile rats, Mitchell Knudsen, Matthew Bury, Callie Holwegner, Adam L. Reinhardt, Fang Yuan, Yijia Zhang, Peter Giannini, D. B. Marx, Dong Wang, and Richard A. Reinhardt
Establishment and Persistence of Yellow-Flowered Alfalfa No-Till Interseeded into Crested Wheatgrass Stands, Christopher G. Misar, Lan Xu, Roger N. Gates, Arvid Boe, Patricia S. Johnson, Christopher S. Schauer, John R. Rickertsen, and Walter Stroup
Genomic-Enabled Prediction of Ordinal Data with Bayesian Logistic Ordinal Regression, Osval A. Montesinos-López, Abelardo Montesinos-López, José Crossa, Juan Burgueño, and Kent M. Eskridge
Threshold Models for Genome-Enabled Prediction of Ordinal Categorical Traits in Plant Breeding, Osval A. Montesinos-López, Abelardo Montesinos-López, Paulino Pérez-Rodríguez, Gustavo de los Campos, Kent M. Eskridge, and José Crossa
Design of Probabilistic Random Forests with Applications to Anticancer Drug Sensitivity Prediction, Raziur Rahman, Saad Haider, Souparno Gosh, and Ranadip Pal
VOC emissions from beef feedlot pen surfaces as affected by within-pen location, moisture and temperature, Bryan L. Woodbury, John E. Gilley, David B. Parker, David B. Marx, and Roger A. Eigenberg
2014
Cytological and Transcriptional Dynamics Analysis of Host Plant Revealed Stage-Specific Biological Processes Related to Compatible Rice-Ustilaginoidea virens Interaction, Jinquan Chao, Jie Jin, Dong Wang, Ran Han, Renshan Zhu, Yingguo Zhu, and Shaoqing Li
Parametric and Nonparametric Statistical Methods for Genomic Selection of Traits with Additive and Epistatic Genetic Architectures, Reka Howard, Alicia L. Carriquiry, and William D. Beavis
Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis, Vasileios Stathias, Chiara Pastori, Tess Z. Griffin, Ricardo Komotar, Jennifer L. Clarke, Ming Zhang, and Nagi G. Ayad
Confidence intervals for ranks of age-adjusted rates across states or counties, Shunpu Zhang, Jun Luo, Li Zhu, David G. Stinchcomb, Dave Campbell, Ginger Carter, Scott Gilkeson, and Eric J. Feuer
2013
Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data, Timonthy Bailey, Pawel Krajewski, Istvan Ladunga, Celine Lefebvre, Qunhua Li, Tao Liu, Pedro Madrigal, Cenny Taslim, and Jie Zhang
Prediction in M-complete Problems with Limited Sample Size, Jennifer Lynn Clarke, Bertrand Clarke, and Chi-Wai Yu
Comparison of molecular breeding values based on within- and across-breed training in beef cattle, Stephen D. Kachman, Matthew L. Spangler, Gary L. Bennett, Kathryn J. Hanford, Larry A. Kuehn, Warren M. Snelling, Mark Thallman, Mahdi Saatchi, Dorian J. Garrick, Robert D. Schnabel, Jeremy F. Taylor, and E John Pollak
The change in differing leukocyte populations during vaccination to bovine respiratory disease and their correlations with lung scores, health records, and average daily gain, R. J. Leach, C. G. Chitko-McKown, G. L. Bennett, S. A. Jones, Stephen D. Kachman, J. W. Keele, K. A. Leymaster, R. M. Thallman, and L. A. Kuehn
Drosophila melanogaster Selection for Survival after Infection with Bacillus cereus Spores: Evolutionary Genetic and Phenotypic Investigations of Respiration and Movement, Junjie Ma, Andrew K. Benson, Stephen D. Kachman, Deidra J. Jacobsen, and Lawrence G. Harshman
Atrazine and Nitrate in Public Drinking Water Supplies and non-Hodgkin Lymphoma in Nebraska, USA, Martha G. Rhoades, Jane L. Meza, Cheryl L. Beseler, Patrick J. Shea, Andy Kahle, Julie M. Vose, Kent M. Eskridge, and Roy F. Spalding
2012
Comment on Article by Sancetta, Bertrand Clarke
Prediction in several conventional contexts, Bertrand Clarke and Jennifer clarke
Transcriptome-Wide Changes in Chlamydomonas reinhardtii Gene Expression Regulated by Carbon Dioxide and the CO2-Concentrating Mechanism Regulator CIA5/CCM1, Wei Fang, Yaqing Si, Stephen Douglass, David Casero, Sabeeha S. Merchant, Matteo Pellegrini, Istvan Ladunga, Peng Liu, and Martin H. Spalding
Learning Interdisciplinary Pedagogies, Alison J. Friedow, Erin E. Blankenship, Jennifer L. Green, and Walter Stroup
Drosophila melanogaster Selection for Survival of Bacillus cereus Infection: Life History Trait Indirect Responses, Junjie Ma, Andrew K. Benson, Stephen D. Kachman, Zhen Hu, and Lawrence G. Harshman
Murine Gut Microbiota Is Defined by Host Genetics and Modulates Variation of Metabolic Traits, Autumn M. McKnite, Maria Elisa Perez-Munoz, Lu Lu, Evan G. Williams, Simon Brewer, Penelope A. Andreux, John W. M. Bastiaansen, Xusheng Wang, Stephen D. Kachman, Johan Auwerx, Robert W. Williams, Andrew K. Benson, Daniel A. Peterson, and Daniel C. Ciobanu
Sample Size under Inverse Negative Binomial Group Testing for Accuracy in Parameter Estimation, Osval Antonio Montesinos-López, Abelardo Montesinos-López, Jose Crossa, and Kent M. Eskridge
Muscle Organization in Individuals with and without Pain and Joint Dysfunction, J. C. Nickel, Y. M. Gonzalez, W. D. McCall, R. Ohrbach, D. B. Marx, H. Liu, and L. R. Iwasaki
Anticancer Peptidylarginine Deiminase (PAD) Inhibitors Regulate the Autophagy Flux and the Mammalian Target of Rapamycin Complex 1 Activity, Yuji Wang, Pingxin Li, Shu Wang, Jing Hu, Xiangyun Amy Chen, Jianhui Wu, Megan Fisher, Kira Oshaben, Na Zhao, Ying Gu, Dong Wang, Gong Chen, and Yanming Wang
2011
Effects of Animal Diet, Manure Application Rate, and Tillage on Transport of Microorganisms from Manure-Amended Fields, Lisa M. Durso, John Gilley, David B. Marx, and Bryan Woodbury
Variation in Sclerotinia sclerotiorum Bean Isolates from Multisite Resistance Screening Locations, Lindsey Otto-Hanson; James R, Steadman; Rebecca Higgins; and Kent M. Eskridge
Development of an internet based system for modeling biotin metabolism using Bayesian networks, Jinglei Zhou, Dong Wang, Vicki L. Schlegel, and Janos Zempleni
2010
Weakly Positioned Nucleosomes Enhance the Transcriptional Competency of Chromatin, Yaakov Belch, Jingyi Yang, Yang Liu, Sridhar A. Malkaram, Rong Liu, Jean-Jack M. Riethoven, and Istvan Ladunga
Desiderata for a Predictive Theory of Statistics, Bertrand Clarke
Reference priors for exponential families with increasing dimension, Bertrand Clarke and Subhashis Ghosal
Reference priors for exponential families with increasing dimension, Bertrand S. Clarke and Subhashis Ghosal
Principal component analysis and biochemical characterization of protein and starch reveal primary targets for improving sorghum grain, Joshua H. Wong, D. B. Marx, Jeff D. Wilson, Bob B. Buchanan, Peggy G. Lemaux, and Jeffrey F. Pedersen
2009
The EM algorithm for group testing regression models under matrix pooling, Christopher R. Bilder and Boan Zhang
Pattern Recognition of Longitudinal Trial Data with Nonignorable Missingness: An Empirical Case Study, Julia Hua Fang, Kimberly A. Espy, Maria L. Rizzo, Christian Stopp, Sandra A. Wiebe, and Walter W. Stroup