Applications of deep learning for drug discovery systems with bigdata

Y Matsuzaka, R Yashiro - BioMedInformatics, 2022 - mdpi.com
The adoption of “artificial intelligence (AI) in drug discovery”, where AI is used in the process
of pharmaceutical research and development, is progressing. By using the ability to process …

[HTML][HTML] Waves, patterns, bifurcations: A tutorial review on the vertebrate segmentation clock

P François, V Mochulska - Physics Reports, 2024 - Elsevier
Proper vertebrae formation relies on a tissue-wide oscillator called the segmentation clock.
Individual cellular oscillators in the presomitic mesoderm are modulated by intercellular …

Scale invariance in early embryonic development

M Nikolić, V Antonetti, F Liu, G Muhaxheri… - Proceedings of the …, 2024 - pnas.org
The expression of a few key genes determines the body plan of the fruit fly. We show that the
spatial expression patterns for several of these genes scale precisely with embryo size …

Deriving a genetic regulatory network from an optimization principle

TR Sokolowski, T Gregor, W Bialek, G Tkačik - Proceedings of the …, 2025 - pnas.org
Many biological systems operate near the physical limits to their performance, suggesting
that aspects of their behavior and underlying mechanisms could be derived from …

Waddington landscape for prototype learning in generalized hopfield networks

NE Boukacem, A Leary, R Thériault, F Gottlieb… - Physical Review …, 2024 - APS
Networks in machine learning offer examples of complex high-dimensional dynamical
systems inspired by and reminiscent of biological systems. Here, we study the learning …

Functional analysis of the Drosophila eve locus in response to non-canonical combinations of gap gene expression levels

N Haroush, M Levo, EF Wieschaus, T Gregor - Developmental cell, 2023 - cell.com
Transcription factor combinations play a key role in sha** cellular identity. However, the
precise relationship between specific combinations and downstream effects remains …

Chemical waves in reaction-diffusion networks of small organic molecules

A Paikar, X Li, L Avram, BS Smith, I Sütő, D Horváth… - Chemical …, 2025 - pubs.rsc.org
Chemical waves represent one of the fundamental behaviors that emerge in nonlinear, out-
of-equilibrium chemical systems. They also play a central role in regulating behaviors and …

A phase diagram structure determines the optimal sensitivity-precision trade-off in signaling systems

KK Kong, C Luo, F Liu - Communications Physics, 2024 - nature.com
Signal transduction is crucial for many biological functions. However, it is still unclear how
signaling systems function accurately under noisy situations. More specifically, such systems …

New wave theory

P François - Development, 2023 - journals.biologists.com
There is a long history of theory for biology, initially as a way to provide explanatory and
conceptual frameworks. For example, in evolution, natural selection offers an explanation for …

Stable developmental patterns of gene expression without morphogen gradients

M Majka, NB Becker, PR Ten Wolde… - PLOS Computational …, 2024 - journals.plos.org
Gene expression patterns in develo** organisms are established by groups of cross-
regulating target genes that are driven by morphogen gradients. As development …