Nicoletta Bobola

A cell atlas of the developing human outflow tract of the heart and its adult aortic valve derivatives

This study presents a transcriptomic atlas of the developing human outflow tract and its adult aortic valve derivatives, revealing persistent embryonic signatures and key regulatory factors in valve development.

The level of HAND1 controls the specification of multipotent cardiac and extraembryonic progenitors

This study identifies HAND1's concentration-dependent role in specifying cardiac and extraembryonic progenitors from human pluripotent stem cells.

MicroRNA miR-92b-3p regulation of a cardiovascular gene regulatory network in the developing branchial arches

The paper identifies miR-92b-3p as a regulator of cardiovascular gene regulatory networks in mouse branchial arches, showing its role in downregulating cardiac transcription factors during development.

The evolutionary ancient MEIS transcription factors actuate lineage-specific transcription to establish cardiac fate

The paper shows MEIS transcription factors are essential for activating cardiac-specific gene expression by working with lineage-restricted TFs to drive cardiac differentiation.

Systematic analysis of transcription factor combinatorial binding uncovers TEAD1 as an antagonist of tissue-specific transcription factors in human organogenesis

The paper identifies TEAD1 as a repressor of tissue-specific transcription factors in human organ development by analyzing combinatorial TF binding in enhancers.

A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2

The paper reconstructs a gene regulatory network directed by PBX1/2 and HAND2 in mouse limb development, showing their genetic interaction and tissue-specific function.

A spatial map of human liver cirrhosis reveals the patho-architecture and gene signatures associated with cell state transitions during liver disease

The paper maps the spatial transcriptional changes in human liver cirrhosis, identifying gene signatures and cell state transitions linked to disease progression.

Motif2Site: a Bioconductor package to detect accurate transcription factor binding sites from ChIP-seq

Motif2Site improves TF binding site detection by recentering motifs based on ChIP-seq signal, enhancing accuracy in mouse embryonic stem cells and heart tissues.

HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation

The paper investigates how HOX paralogs interact with TALE TFs to generate tissue-specific enhancer activation patterns in mouse embryos.

Uncovering tissue-specific binding features from differential deep learning

The paper uses deep learning to identify tissue-specific TF binding sites by analyzing ChIP-seq data from MEIS and HOXA2 in mouse branchial arches.

TALE and NF-Y co-occupancy marks enhancers of developmental control genes during zygotic genome activation in zebrafish

The paper identifies NF-Y and TALE co-occupancy at enhancers of developmental control genes during zebrafish zygotic genome activation, showing distinct gene regulatory roles for each TF.

The epigenomic landscape regulating organogenesis in human embryos linked to developmental disorders

The paper maps histone modifications across thirteen human tissues during organogenesis to understand gene regulation and link noncoding mutations to developmental disorders.