Antonio J. Giráldez

The paper identifies codon pairs and amino acid pairs as regulators of mRNA stability in zebrafish, showing context-dependent decay mechanisms involving deadenylation and decapping.

The paper investigates how Lamin A/C influences chromatin structure during early mammalian lineage segregation, showing its role in maintaining trophectoderm identity.

This paper introduces nanogold probes for identifying proteins in live cells and cryo-ET tomograms, enhancing proteome accessibility for electron microscopy.

RNAdecayCafe provides a uniformly processed atlas of RNA half-life estimates across 11 human cell lines, revealing RNA stability's role in gene expression.

The paper introduces NaP-TRAP, a new MPRA method to measure mRNA translation, and uses it to analyze cis-regulatory elements in zebrafish and human cells.

The paper investigates the developmental fate of zebrafish embryos lacking the reprogramming factors Nanog, Pou5f3, and Sox19b, finding that cells can acquire novel cell states or primordial germ cell-like states.

This paper introduces GEARs, a toolkit for visualizing and manipulating endogenous proteins in vivo, demonstrating its use with Nanog and Vangl2 in zebrafish.

This paper identifies maternal-effect mutants in zebrafish that reveal molecular mechanisms controlling the oocyte-to-egg transition, focusing on yolk globule formation and protein processing.

The paper identifies two micropeptides encoded by lincRNAs that regulate chromatin accessibility in vertebrate-specific neural cells and show their role in brain development.

Nano3P-seq quantifies RNA abundance, tail composition, and tail length dynamics at single-read resolution without PCR or adapters.

This study demonstrates the use of SpG and SpRY CRISPR-Cas9 variants in zebrafish and C. elegans for genome editing, showing improved accessibility to previously uneditable sites.

The paper investigates the role of Satb2 in regulating zygotic genome activation and developmental transitions during vertebrate embryogenesis, showing distinct maternal and zygotic functions.

The paper identifies Bicc1 and Dicer1 as regulators of left-right patterning by posttranscriptionally repressing Dand5, a Nodal inhibitor, downstream of flow sensing.

This paper introduces a method to quantify perturbation effects at single-cell resolution using manifold-based likelihood estimation and vertex frequency clustering, achieving higher accuracy than existing methods.

This study shows that Nanog, Pou5f3, and Sox19b work together in a context-dependent way to establish chromatin accessibility and developmental competence in zebrafish embryos.

The paper identifies a functional non-coding RNA derived from xbp-1 mRNA cleavage in C. elegans neurons, showing it is essential for axon regeneration independent of the protein-coding function of xbp-1.

This paper shows that combining mutational profiles and drop-off information improves RNA structure analysis by capturing complementary structural information and reducing false positives.

The paper identifies cis-regulatory elements and trans-factors governing mRNA stability during zebrafish MZT and develops a model to predict mRNA stability.

The paper shows that mutant mRNA degradation triggers transcriptional adaptation in zebrafish and mouse, leading to upregulation of related genes.

The paper characterizes mRNA structure dynamics during zebrafish development and identifies ribosome-mediated RNA remodeling and 3-UTR structures as key regulators of gene expression and decay.

This study shows that Brd4 and P300 regulate zygotic genome activation through histone acetylation in zebrafish embryos.

The study shows the RES complex is essential for zebrafish early development and intron splicing, with specific intronic features associated with its activity.

This study shows that LbCpf1 enables efficient homology-directed repair and temperature-controlled genome editing in zebrafish, improving targeted DNA integration.