A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Dana Wyman, Gabriela Balderrama-Gutierrez, Fairlie Reese, +13

GeneticsNovel IsoformsRna SplicingMolecular BiologyTranscriptomics Technology +21

Dynamic Gene Regulatory Networks of Human Myeloid Differentiation

Ricardo N. Ramírez, Nicole El-Ali, Mikayla Anne Mager, +3

Cell Systems

EngineeringGeneticsHuman Myeloid DifferentiationComputational BiologyGene Expression +7

SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads

Alexandre Bolze, Shishi Luo, Simon White, +20

Cell Reports Medicine

Sars-cov-2 Variant DeltaMedicineCovid-19 PandemicImmunologyViral Dynamic +6

The ENCODE Uniform Analysis Pipelines

Benjamin C. Hitz, Jin-Wook Lee, Otto Jolanki, +57

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

Alexandre Bolze, Tracy Basler, Simon White, +27

Med

Emerging Infectious DiseasesViral PathogenesisImmunologyVirologyMedicine +2

TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts

Dana Wyman, A Mortazavi

Bioinformatics

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

Fairlie Reese, Brian A. Williams, Gabriela Balderrama-Gutierrez, +42

EngineeringGeneticsMolecular BiologyTranscriptomics TechnologyMolecular Genetics +19

SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads

Alexandre Bolze, Elizabeth T. Cirulli, Shishi Luo, +19

Sars-cov-2 Variant DeltaVirus EpidemiologyViral PersistenceViral DiagnosticsMedicine +13

The ENCODE Uniform Analysis Pipelines

Benjamin C. Hitz, Jin-Wook Lee, Otto Jolanki, +59

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

Alexandre Bolze, Tracy Basler, Simon White, +26

Viral EvolutionEmerging Infectious DiseasesPathogenesisViral PathogenesisImmunology +12