Machine learning approaches on high throughput NGS data to unveil mechanisms of function in biology and disease

VC Pezoulas, O Hazapis, N Lagopati… - Cancer genomics & …, 2021 - cgp.iiarjournals.org
In this review, the fundamental basis of machine learning (ML) and data mining (DM) are
summarized together with the techniques for distilling knowledge from state-of-the-art omics …

Brain Sensory Organs of the Ascidian Ciona robusta: Structure, Function and Developmental Mechanisms

P Olivo, A Palladino, F Ristoratore… - Frontiers in Cell and …, 2021 - frontiersin.org
During evolution, new characters are designed by modifying pre-existing structures already
present in ancient organisms. In this perspective, the Central Nervous System (CNS) of …

Conservation of cis-Regulatory Syntax Underlying Deuterostome Gastrulation

L Buono, G Annona, MS Magri, S Negueruela… - Cells, 2024 - mdpi.com
Throughout embryonic development, the shaping of the functional and morphological
characteristics of embryos is orchestrated by an intricate interaction between transcription …

An amphioxus neurula stage cell atlas supports a complex scenario for the emergence of vertebrate head mesoderm

X Grau-Bové, L Subirana, L Meister… - Nature …, 2024 - nature.com
The emergence of new structures can often be linked to the evolution of novel cell types that
follows the rewiring of developmental gene regulatory subnetworks. Vertebrates are …

Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish

L Buono, J Corbacho, S Naranjo… - Nature …, 2021 - nature.com
Sight depends on the tight cooperation between photoreceptors and pigmented cells, which
derive from common progenitors through the bifurcation of a single gene regulatory network …

Dynamics of Chromatin Opening across Larval Development in the Urochordate Ascidian Ciona savignyi

M He, Y Li, Y Li, B Dong, H Yu - International Journal of Molecular …, 2024 - mdpi.com
Ascidian larvae undergo tail elongation and notochord lumenogenesis, making them an
ideal model for investigating tissue morphogenesis in embryogenesis. The cellular and …

Chromatin accessibility profile and the role of PeAtf1 transcription factor in the postharvest pathogen Penicillium expansum

Y Wang, K Wang, Q Yang, Z Wang, Y Su… - Horticulture …, 2025 - academic.oup.com
Gene transcription is governed by a complex regulatory system involving changes in
chromatin structure, the action of transcription factors, and the activation of cis-regulatory …

Mutation of vsx genes in zebrafish highlights the robustness of the retinal specification network

J Letelier, L Buono, M Almuedo-Castillo, J Zang… - Elife, 2023 - elifesciences.org
Genetic studies in human and mice have established a dual role for Vsx genes in retina
development: an early function in progenitors' specification, and a later requirement for …

[HTML][HTML] Dynamic Chromatin Accessibility and Gene Expression Regulation During Maize Leaf Development

Y Wang, S Wang, Y Wu, J Cheng, H Wang - Genes, 2024 - mdpi.com
Background/Objectives: Chromatin accessibility is closely associated with transcriptional
regulation during maize (Zea mays) leaf development. However, its precise role in …

Gene regulatory networks of epidermal and neural fate choice in a chordate

A Leon, L Subirana, K Magre, I Cases… - Molecular Biology …, 2022 - academic.oup.com
Neurons are a highly specialized cell type only found in metazoans. They can be scattered
throughout the body or grouped together, forming ganglia or nerve cords. During …