High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes

Noah Fahlgren, Miya D. Howell, Kristin D. Kasschau, +8

PLoS ONE

BiologyMirna GenesHigh-throughput SequencingGeneticsEvolutionary Biology +13

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Kristin D. Kasschau, Noah Fahlgren, Elisabeth J. Chapman, +4

PLoS Biology

Transcriptional RegulationFunctional Genomics24-Nt SirnasNatural SciencesGenetics +13

Genome-Wide Analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 Pathway in<i>Arabidopsis</i>Reveals Dependency on miRNA- and tasiRNA-Directed Targeting

Miya D. Howell, Noah Fahlgren, Elisabeth J. Chapman, +5

The Plant Cell

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

Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis

Sergei A. Filichkin, Jason S. Cumbie, Palitha Dharmawardhana, +6

Molecular Plant

BiologyPlant Circadian ClockPlant Molecular BiologyChronobiologyPlant Stress +8

Computational and analytical framework for small RNA profiling by high-throughput sequencing

Noah Fahlgren, Christopher M. Sullivan, Kristin D. Kasschau, +8

RNA

Distinct Expression Patterns of Natural Antisense Transcripts in Arabidopsis

Stefan R. Henz, Jason S. Cumbie, Kristin D. Kasschau, +4

PLANT PHYSIOLOGY

Update of ASRP: the Arabidopsis Small RNA Project database

Tyler W. H. Backman, Christopher M. Sullivan, Jason S. Cumbie, +6

Nucleic Acids Research

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