Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis

Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development

(2014) V. R. Paralkar et al.   BLOOD

Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis

(2014) Maxim Pimkin et al.   GENOME RESEARCH

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

GATA factor switching from GATA2 to GATA1 contributes to erythroid differentiation

(2013) Mikiko Suzuki et al.   GENES TO CELLS

Platelet-biased stem cells reside at the apex of the haematopoietic stem-cell hierarchy

(2013) Alejandra Sanjuan-Pla et al.   NATURE

Structural Basis for LMO2-Driven Recruitment of the SCL:E47bHLH Heterodimer to Hematopoietic-Specific Transcriptional Targets

(2013) Kamel El Omari et al.   Cell Reports

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

The role of Tal2 and Tal1 in the differentiation of midbrain GABAergic neuron precursors

(2013) K. Achim et al.   Biology Open

Chromatin occupancy analysis reveals genome-wide GATA factor switching during hematopoiesis

(2012) L. C. Dore et al.   BLOOD

Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis

(2012) Jian Xu et al.   DEVELOPMENTAL CELL

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq

(2012) M. R. Tallack et al.   GENOME RESEARCH

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje et al.   GENOME RESEARCH

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Intragenic Enhancers Act as Alternative Promoters

(2012) Monika S. Kowalczyk et al.   MOLECULAR CELL

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Inferring rules of lineage commitment in haematopoiesis

(2012) Cristina Pina et al.   NATURE CELL BIOLOGY

Genome-wide analyses reveal the extent of opportunistic STAT5 binding that does not yield transcriptional activation of neighboring genes

(2012) Bing-Mei Zhu et al.   NUCLEIC ACIDS RESEARCH

An encyclopedia of mouse DNA elements (Mouse ENCODE)

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Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes

(2011) P. Wong et al.   BLOOD

Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation

(2011) A. M. Pilon et al.   BLOOD

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

(2011) Eirini Trompouki et al.   CELL

Genome-wide Analysis of Simultaneous GATA1/2, RUNX1, FLI1, and SCL Binding in Megakaryocytes Identifies Hematopoietic Regulators

(2011) Marloes R. Tijssen et al.   DEVELOPMENTAL CELL

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

(2011) A. Ozdemir et al.   GENOME RESEARCH

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

(2011) G. Hu et al.   GENOME RESEARCH

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

(2011) W. Wu et al.   GENOME RESEARCH

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes

(2011) J. M. Lamonica et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combinatorial Transcriptional Control In Blood Stem/Progenitor Cells: Genome-wide Analysis of Ten Major Transcriptional Regulators

(2010) Nicola K. Wilson et al.   Cell Stem Cell

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages

(2010) Carmen G Palii et al.   EMBO JOURNAL

The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation

(2010) E. Soler et al.   GENES & DEVELOPMENT

A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells

(2010) M. R. Tallack et al.   GENOME RESEARCH

Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells

(2010) M. T. Kassouf et al.   GENOME RESEARCH

GATA Switches as Developmental Drivers

(2010) Emery H. Bresnick et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development

(2009) N. K. Wilson et al.   BLOOD

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

(2009) Y. Cheng et al.   GENOME RESEARCH

Definitive hematopoiesis requires Runx1 C-terminal-mediated subnuclear targeting and transactivation

(2009) Christopher R. Dowdy et al.   HUMAN MOLECULAR GENETICS

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1

(2009) Ying Zhang et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Differential use of SCL/TAL-1 DNA-binding domain in developmental hematopoiesis

(2008) M. T. Kassouf et al.   BLOOD

SCL and associated proteins distinguish active from repressive GATA transcription factor complexes

(2008) T. Tripic et al.   BLOOD

Molecular Hallmarks of Endogenous Chromatin Complexes Containing Master Regulators of Hematopoiesis

(2008) R. J. Wozniak et al.   MOLECULAR AND CELLULAR BIOLOGY

Exchange of GATA Factors Mediates Transitions in Looped Chromatin Organization at a Developmentally Regulated Gene Locus

(2008) Huie Jing et al.   MOLECULAR CELL

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY