The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq

Yanming Di, Daniel W. Schafer, Jason S. Cumbie, +1

Statistical Applications in Genetics and Molecular Biology

EngineeringGeneticsMolecular BiologyGene CharacterizationGenomics +17

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

Kathryn E. Bushley, Rajani Raja, Pankaj Jaiswal, +10

PLoS Genetics

Comparative GenomicsGeneticsMolecular BiologyTolypocladium InflatumMolecular Genetics +21

A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries

Satyanarayana Gouthu, Shawn T. O’Neil, Yanming Di, +3

Journal of Experimental Botany

GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences

Jason S. Cumbie, Jeffrey A. Kimbrel, Yanming Di, +8

PLoS ONE

Gene CountsStatistics PackagesEngineeringGeneticsTranscriptomics Technology +20

Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa

Kelly Vining, Kyle Pomraning, Larry Wilhelm, +6

BMC Plant Biology

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Gu Mi, Yanming Di, Sarah Emerson, +2

PLoS ONE

EngineeringGeneticsGenomicsGene Ontology MembershipGene Recognition +22

Identifying stably expressed genes from multiple RNA-Seq data sets

Bin Zhuo, Sarah Emerson, Jeff H. Chang, +1

PeerJ

EngineeringGeneticsTranscriptomics TechnologyGene CharacterizationGenomics +14

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite <i>Tolypocladium ophioglossoides</i>

C. Alisha Quandt, Yanming Di, Justin Elser, +2

G3 Genes Genomes Genetics

Model-Based Clustering with Measurement or Estimation Errors

Wanli Zhang, Yanming Di

Genes

Cluster ComputingEngineeringUnsupervised Machine LearningData ScienceData Mining +14

Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of RNA Sequencing Data

Gu Mi, Yanming Di, Daniel W. Schafer

PLoS ONE

EngineeringGeneticsTranscriptomics TechnologyGenomicsGene Expression Profiling +23