EmbryoNet: using deep learning to link embryonic phenotypes to signaling pathways

D Čapek, M Safroshkin, H Morales-Navarrete… - Nature …, 2023‏ - nature.com
Evolutionarily conserved signaling pathways are essential for early embryogenesis, and
reducing or abolishing their activity leads to characteristic developmental defects …

Modelling human genetic disorders in Xenopus tropicalis

HR Willsey, EG Seaby, A Godwin… - Disease Models & …, 2024‏ - journals.biologists.com
Recent progress in human disease genetics is leading to rapid advances in understanding
pathobiological mechanisms. However, the sheer number of risk-conveying genetic variants …

A review on deep learning-driven drug discovery: Strategies, tools and applications

S Sumathi, K Suganya, K Swathi… - Current …, 2023‏ - benthamdirect.com
It takes an average of 10-15 years to uncover and develop a new drug, and the process is
incredibly time-consuming, expensive, difficult, and ineffective. In recent years the dramatic …

Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for cleared samples

N Vladimirov, FF Voigt, T Naert, GR Araujo… - Nature …, 2024‏ - nature.com
In 2015, we launched the mesoSPIM initiative, an open-source project for making light-sheet
microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging …

Uncovering developmental time and tempo using deep learning

N Toulany, H Morales-Navarrete, D Čapek… - Nature …, 2023‏ - nature.com
During animal development, embryos undergo complex morphological changes over time.
Differences in developmental tempo between species are emerging as principal drivers of …

Reflective multi-immersion microscope objectives inspired by the Schmidt telescope

FF Voigt, AM Reuss, T Naert, S Hildebrand… - Nature …, 2024‏ - nature.com
Imaging large, cleared samples requires microscope objectives that combine a large field of
view (FOV) with a long working distance (WD) and a high numerical aperture (NA). Ideally …

Open problems in mathematical biology

ST Vittadello, MPH Stumpf - Mathematical Biosciences, 2022‏ - Elsevier
Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to
understand biological processes and systems is therefore to confront our ideas and …

HNF1B alters an evolutionarily conserved nephrogenic program of target genes

K Grand, M Stoltz, L Rizzo, R Röck… - Journal of the …, 2023‏ - journals.lww.com
Background Hepatocyte nuclear factor-1 β (HNF1B) is an essential transcription factor
during embryogenesis. Mutations in HNF1B are the most common monogenic causes of …

Virtual tissue microstructure reconstruction across species using generative deep learning

N Bettancourt, C Pérez-Gallardo, V Candia, P Guevara… - Plos one, 2024‏ - journals.plos.org
Analyzing tissue microstructure is essential for understanding complex biological systems in
different species. Tissue functions largely depend on their intrinsic tissue architecture …

Deletion upstream of MAB21L2 highlights the importance of evolutionarily conserved non-coding sequences for eye development

F Ceroni, MB Cicekdal, R Holt, E Sorokina… - Nature …, 2024‏ - nature.com
Anophthalmia, microphthalmia and coloboma (AMC) comprise a spectrum of developmental
eye disorders, accounting for approximately 20% of childhood visual impairment. While non …