Irina Pushel
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View article: Integrated multi-omic analysis reveals novel subtype-specific regulatory interactions in pediatric B-cell acute lymphoblastic leukemia
Integrated multi-omic analysis reveals novel subtype-specific regulatory interactions in pediatric B-cell acute lymphoblastic leukemia Open
Molecular subtyping of pediatric B-cell acute lymphoblastic leukemia (B-ALL) has improved patient outcomes through stratification and selection of targeted therapies. Despite extensive genomic and transcriptomic profiling of this cancer, f…
View article: Comparative Analysis of Neural Crest Development in the Chick and Mouse
Comparative Analysis of Neural Crest Development in the Chick and Mouse Open
A core framework of the gene regulatory network (GRN) governing neural crest (NC) cell development has been generated by integrating separate inputs from diverse model organisms rather than direct comparison. This has limited insights into…
View article: Short- and Long-Read RNA Sequencing Improve Molecular Profiling of Pediatric T-Cell Acute Lymphoblastic Leukemia
Short- and Long-Read RNA Sequencing Improve Molecular Profiling of Pediatric T-Cell Acute Lymphoblastic Leukemia Open
Acute lymphoblastic leukemia (ALL) is one of the most common pediatric cancers, accounting for approximately 1/3 of childhood cancer diagnoses. Of these patients, ~15% are diagnosed with T-cell ALL (T-ALL). Pediatric T-ALL is less well-cha…
View article: Evaluation of Hi-C Sequencing for Detection of Gene Fusions in Hematologic and Solid Tumor Pediatric Cancer Samples
Evaluation of Hi-C Sequencing for Detection of Gene Fusions in Hematologic and Solid Tumor Pediatric Cancer Samples Open
Hi-C sequencing is a DNA-based next-generation sequencing method that preserves the 3D genome conformation and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate Hi-C as a potential clinica…
View article: Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples
Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples Open
HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate HiC as a potential cl…
View article: Specification of axial identity by Hoxa2 distinguishes between a phenotypic and molecular ground state in mouse cranial neural crest cells
Specification of axial identity by Hoxa2 distinguishes between a phenotypic and molecular ground state in mouse cranial neural crest cells Open
Hox genes play a key role in head formation by specifying the axial identity of neural crest cells (NCCs) migrating into embryonic pharyngeal arches. In the absence of Hoxa2 , NCC derivatives of the second pharyngeal arch (PA2) undergo a h…
View article: HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets
HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets Open
Hoxa1 has diverse functional roles in differentiation and development. We identify and characterize properties of regions bound by HOXA1 on a genome-wide basis in differentiating mouse ES cells. HOXA1-bound regions are enriched for cluster…
View article: Hoxa1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on Hoxa1 targets
Hoxa1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on Hoxa1 targets Open
Hoxa1 has diverse functional roles in differentiation and development. We have identified and characterized properties of regions bound by Hoxa1 on a genome-wide basis in differentiating mouse ES cells. Hoxa1 bound regions are enriched for…
View article: Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo
Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo Open
Enhancers constitute one of the major components of regulatory machinery of metazoans. Although several genome-wide studies have focused on finding and locating enhancers in the genomes, the fundamental principles governing their internal …
View article: Author response: Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo
Author response: Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo Open
Article Figures and data Abstract eLife digest Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Enhancers constitute one of t…