An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

M. Ryan Corces, Alexandro E. Trevino, Emily G. Hamilton, +19

Nature Methods

EngineeringFrozen TissuesBiosignal ProcessingBiomedical ImagingBiomedical Analysis +3

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

Jeffrey M. Granja, Sandy Klemm, Lisa McGinnis, +10

Nature Biotechnology

BioinformaticsFunctional GenomicsSingle Cell SequencingMedicineMixed-phenotype Acute Leukemia +9

Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

Alexandro E. Trevino, Fabian Müller, Jimena Andersen, +9

Cell

ChromatinDevelopmental BiologyChromatin StructureNeurogenomicsBrain Development +10

Landscape of stimulation-responsive chromatin across diverse human immune cells

Diego Calderon, Michelle Nguyen, Anja Mezger, +17

Nature Genetics

ChromatinChromatin RemodelingImmunologyStimulation-responsive ChromatinCellular Immune Response +3

Single-cell transcriptomic analysis of the adult mouse spinal cord reveals molecular diversity of autonomic and skeletal motor neurons

Jacob A. Blum, Sandy Klemm, Jennifer L. Shadrach, +8

Nature Neuroscience

Spinal Cord InjuryMolecular NeuroscienceSingle Cell SequencingNeuroanatomyMedicine +9

NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells

Amy F. Chen, Benjamin Parks, Arwa S. Kathiria, +3

Nature Methods

ChromatinChromatin AccessibilityFunctional GenomicsChromatin RemodelingSingle Cell Sequencing +8

Single-cell epigenomic variability reveals functional cancer heterogeneity

Ulrike Litzenburger, Jason D. Buenrostro, Beijing Wu, +5

Genome biology

ChromBPNet: bias factorized, base-resolution deep learning models of chromatin accessibility reveal cis-regulatory sequence syntax, transcription factor footprints and regulatory variants

Anusri Pampari, Anna Shcherbina, Evgeny Z. Kvon, +10

EngineeringCis-regulatory Sequence SyntaxGeneticsGene Regulatory NetworkChromatin Accessibility +16

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks

Jacob W. Freimer, Oren Shaked, Sahin Naqvi, +8

Nature Genetics

Immune NetworksAutoimmune DiseaseSystematic DiscoveryMedicineT-regulatory Cell +9

The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

Daniel Seung Kim, Viviana I. Risca, David L. Reynolds, +17

Nature Genetics

Signal TransductionCombinatorial Cis-regulatory LexiconMorphogenesisGene Regulatory NetworkDermatology +2