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2022

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Comparative antiplatelet effects of chlorthalidone and hydrochlorothiazide, Khalid Bashir, Tammy Burns, Samuel J. Pirruccello, and Sarah J. Aurit

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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

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Bayesian analysis for the Lomax model using noninformative priors, Daojiang He, Dongchu Sun, and Qing Zhu

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Kryging: Geostatistical analysis of large-scale datasets using Krylov subspace methods, Suman Majumder, Yawen Guan, Brian J. Reich, and Arvind K. Saibaba

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Evaluating dimensionality reduction for genomic prediction, Vamsi Manthena, Diego Jarquín, Rajeev K. Varshney, Manish Roorkiwal, Girish Prasad Dixit, Chellapilla Bharadwaj, and Reka Howard

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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

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Spatio-temporal models of infectious disease with high rates of asymptomatic transmission, Aminur Rahman, Angela Peace, Ramesh Kesawan, and Souparno Ghosh

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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

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Genomic Prediction Accuracy of Stripe Rust in Six Spring Wheat Populations by Modeling Genotype by Environment Interaction, Kassa Semagn, Muhammad Iqbal, Diego Jarquin, Harpinder Randhawa, Reem Aboukhaddour, Reka Howard, Izabela Ciechanowska, Momna Farzand, Raman Dhariwal, Colin W. Hiebert, Amidou N’Diaye, Curtis Pozniak, and Dean Spaner

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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

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Discussion on “Is group testing ready for prime-time in disease identification”, Christopher R. Bilder, Joshua M. Tebbs, and Christopher S. McMahan

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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

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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

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Treatment of Inconclusive Results in Firearms Error Rate Studies, Heike Hofmann, Susan VanderPlas, and Alicia L. Carriquiry

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Posterior propriety of an objective prior for generalized hierarchical normal linear models, Cong Lin, Dongchu Sun, and Chengyuan Song

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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

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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

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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

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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

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Cost Effectiveness of Sample Pooling to Test for SARS-CoV-2, Baha Abdalhamid, Christopher Richard Bilder, Jodi Louise Garrett, and Peter Charles Iwen

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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

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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

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The local stability of a modified multi-strain SIR model for emerging viral strains, Miguel Fudolig and Reka Howard

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Tumor ablation due to inhomogeneous anisotropic diffusion in generic three-dimensional topologies, Erdi Kara, Aminur Rahman, Eugenio Aulisa, and Souparno Ghosh

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In praise of partially interpretable predictors, Tri Le and Bertrand S. Clarke

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TGCnA: temporal gene coexpression network analysis using a low-rank plus sparse framework, Jinyu Li, Yutong Lai, Chi Zhang, and Qi Zhang

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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

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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

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Perceived Neighborhood: Preferences versus Actualities, Saeed Moradi, Ali Nejat, Da Hu, and Souparno Ghosh

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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

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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

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A High-Throughput Phenotyping Pipeline for Image Processing and Functional Growth Curve Analysis, Ronghao Wang

2019

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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

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Informative Group Testing for Multiplex Assays, Christopher R. Bilder, Joshua M. Tebbs, and Christopher S. McMahan

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Cost-effective Surveillance for Infectious Diseases Through Specimen Pooling and Multiplex Assays, Christopher Bilder, Joshua Tebbs, and Christopher McMahan

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Recursive model for dose-time responses in pharmacological studies, Saugato Rahman Dhruba, Aminur Rahman, Raziur Rahman, Souparno Ghosh, and Ranadip Pal

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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

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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

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Genomic Prediction Using Canopy Coverage Image and Genotypic Information in Soybean via a Hybrid Model, Reka Howard and Diego Jarquin

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Functional random forest with applications in dose-response predictions, Raziur Rahman, Saugato Rahman Dhruba, Souparno Ghosh, and Ranadip Pal

2018

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Application of transfer learning for cancer drug sensitivity prediction, Saugato Rahman Dhruba, Raziur Rahman, Kevin Matlock, Souparno Ghosh, and Ranadip Pal

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Characterization of Soybean Protein Adhesives Modified by Xanthan Gum, Chen Feng, Fang Wang, Zheng Xu, Huilin Sui, Yong Fang, Xiaozhi Tang, and Xinchun Shen

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Investigation of model stacking for drug sensitivity prediction, Kevin Matlock, Carlos De Niz, Raziur Rahman, Souparno Ghosh, and Ranadip Pal

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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

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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

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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

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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

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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

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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

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Application of Response Surface Methods To Determine Conditions for Optimal Genomic Prediction, Reka Howard, Alicia L. Carriquiry, and William D. Beavis

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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

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A Bayes Interpretation of Stacking for M-Complete and M-Open Settings, Tri Le and Bertrand S. Clarke

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Heterogeneity Aware Random Forest for Drug Sensitivity Prediction, Raziur Rahman, Kevin Matlock, Souparno Ghosh, and Ranadip Pal

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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

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Generalized Confidence Intervals Compatible with the Min Test for Simultaneous Comparisons of One Subpopulation to Several Other Subpopulations, Julia N. Soulakova

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Impact of Menthol Smoking on Nicotine Dependence for Diverse Racial/Ethnic Groups of Daily Smokers, Julia N. Soulakova and Ryan R. Danczak

2016

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EnsCat: clustering of categorical data via ensembling, Bertrand S. Clarke, Saeid Amiri, and Jennifer L. Clarke

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The impact of hair coat color on longevity of Holstein cows in the tropics, C. N. Lee, K. S. Baek, and A. Parkhurst

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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

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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

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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

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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

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Design of Probabilistic Random Forests with Applications to Anticancer Drug Sensitivity Prediction- 2016, Raziur Rahman, Saad Haider, Souparno Ghosh, and Ranadip Pal

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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

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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

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A BAYESIAN GWAS METHOD UTILIZING HAPLOTYPE CLUSTERS FOR A COMPOSITE BREED POPULATION, Danielle F. Wilson-Wells and Stephen D. Kachman

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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

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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

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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

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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

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A Copula Based Approach for Design of Multivariate Random Forests for Drug Sensitivity Prediction, Saad Haider, Raziur Rahman, Souparno Ghosh, and Ranadip Pal

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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

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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

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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

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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

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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

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Design of Probabilistic Random Forests with Applications to Anticancer Drug Sensitivity Prediction, Raziur Rahman, Saad Haider, Souparno Gosh, and Ranadip Pal

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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

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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

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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

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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

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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

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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

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Prediction in M-complete Problems with Limited Sample Size, Jennifer Lynn Clarke, Bertrand Clarke, and Chi-Wai Yu

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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

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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

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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

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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

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Comment on Article by Sancetta, Bertrand Clarke

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Prediction in several conventional contexts, Bertrand Clarke and Jennifer clarke

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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

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Learning Interdisciplinary Pedagogies, Alison J. Friedow, Erin E. Blankenship, Jennifer L. Green, and Walter Stroup

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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

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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

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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

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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

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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

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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

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Variation in Sclerotinia sclerotiorum Bean Isolates from Multisite Resistance Screening Locations, Lindsey Otto-Hanson; James R, Steadman; Rebecca Higgins; and Kent M. Eskridge

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Development of an internet based system for modeling biotin metabolism using Bayesian networks, Jinglei Zhou, Dong Wang, Vicki L. Schlegel, and Janos Zempleni