Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation

Explore, edit and leverage genomic annotations using Python GTF toolkit

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Programming for T-lymphocyte fates: modularity and mechanisms

(2019) Ellen V. Rothenberg   GENES & DEVELOPMENT

OLOGRAM: Determining significance of total overlap length between genomic regions sets

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Gene length corrected trimmed mean of M-values (GeTMM) processing of RNA-seq data performs similarly in intersample analyses while improving intrasample comparisons

(2018) Marcel Smid et al.   BMC BIOINFORMATICS

Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells

(2018) Gangqing Hu et al.   IMMUNITY

A Single-Cell Transcriptomic Atlas of Thymus Organogenesis Resolves Cell Types and Developmental Maturation

(2018) Eric M. Kernfeld et al.   IMMUNITY

Pluripotency factors functionally premark cell-type-restricted enhancers in ES cells

(2018) Hong Sook Kim et al.   NATURE

Human thymopoiesis is influenced by a common genetic variant within the TCRA-TCRD locus

(2018) Emmanuel Clave et al.   Science Translational Medicine

TCRα rearrangements identify a subgroup of NKL-deregulated adult T-ALLs associated with favorable outcome

(2017) P Villarese et al.   LEUKEMIA

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

Automatic identification of informative regions with epigenomic changes associated to hematopoiesis

(2017) Enrique Carrillo-de-Santa-Pau et al.   NUCLEIC ACIDS RESEARCH

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

Triggering the TCR Developmental Checkpoint Activates a Therapeutically Targetable Tumor Suppressive Pathway in T-cell Leukemia

(2016) A. Trinquand et al.   Cancer Discovery

Transcription-Dependent Generation of a Specialized Chromatin Structure at the TCRβ Locus

(2015) Joaquin Zacarías-Cabeza et al.   JOURNAL OF IMMUNOLOGY

Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages

(2015) David Casero et al.   NATURE IMMUNOLOGY

Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation

(2015) Pierre Cauchy et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Ikaros mediates gene silencing in T cells through Polycomb repressive complex 2

(2015) Attila Oravecz et al.   Nature Communications

High-throughput and quantitative assessment of enhancer activity in mammals by CapStarr-seq

(2015) Laurent Vanhille et al.   Nature Communications

Divergent transcription is associated with promoters of transcriptional regulators

(2013) Cyrille Lepoivre et al.   BMC GENOMICS

TLX Homeodomain Oncogenes Mediate T Cell Maturation Arrest in T-ALL via Interaction with ETS1 and Suppression of TCRα Gene Expression

(2012) Saïda Dadi et al.   CANCER CELL

The role of HOX genes in normal hematopoiesis and acute leukemia

(2012) R A Alharbi et al.   LEUKEMIA

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia

(2012) Jinghui Zhang et al.   NATURE

Icy: an open bioimage informatics platform for extended reproducible research

(2012) Fabrice de Chaumont et al.   NATURE METHODS

Identification and characterization of Hoxa9 binding sites in hematopoietic cells

(2011) Y. Huang et al.   BLOOD

Cytokines and culture medium have a major impact on human in vitro T-cell differentiation

(2011) Emmanuelle M. Six et al.   BLOOD CELLS MOLECULES AND DISEASES

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

H3K4 tri-methylation provides an epigenetic signature of active enhancers

(2011) Aleksandra Pekowska et al.   EMBO JOURNAL

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types

(2011) Gang Wei et al.   IMMUNITY

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-Wide Analysis of the Binding of the Hox Protein Ultrabithorax and the Hox Cofactor Homothorax in Drosophila

(2011) Siew Woh Choo et al.   PLoS One

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

DNA Specificity Determinants Associate with Distinct Transcription Factor Functions

(2009) Peter C. Hollenhorst et al.   PLoS Genetics

The recurrent SET-NUP214 fusion as a new HOXA activation mechanism in pediatric T-cell acute lymphoblastic leukemia

(2008) P. Van Vlierberghe et al.   BLOOD

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL