Generalizable machine learning methods for network inference in systems biology

G Rabadam - 2024 - escholarship.org
Tissues comprise a multiplicity of specialized cell types that must coordinate state changes
in order to function collectively. These state changes are orchestrated by coordinated direct …

Learning cell-specific networks from dynamics and geometry of single cells

SY Zhang, MPH Stumpf - bioRxiv, 2023 - biorxiv.org
Cell dynamics and biological function are governed by intricate networks of molecular
interactions. Inferring these interactions from data is a notoriously difficult inverse problem …

[HTML][HTML] Machine Learning and Network-Driven Integrative Genomics

M Pirooznia, S Han, RS Lee - Frontiers in Genetics, 2021 - frontiersin.org
Rapid advances in high-throughput technologies have produced distinct biomedical data
sets that can be analyzed using mathematical and statistical models including network …

From genotype to phenotype: augmenting deep learning with networks and systems biology

VH Gazestani, NE Lewis - Current opinion in systems biology, 2019 - Elsevier
Cells, as complex systems, consist of diverse interacting biomolecules arranged in dynamic
hierarchical modules. Recent advances in deep learning methods now allow one to encode …

Enabling precision medicine through integrative network models

V Yao, AK Wong, OG Troyanskaya - Journal of molecular biology, 2018 - Elsevier
A key challenge in precision medicine lies in understanding molecular-level underpinnings
of complex human disease. Biological networks in multicellular organisms can generate …

Network-based approaches for analysis of complex biological systems

D Chasman, AF Siahpirani, S Roy - Current opinion in biotechnology, 2016 - Elsevier
Cells function and respond to changes in their environment by the coordinated activity of
their molecular components, including mRNAs, proteins and metabolites. At the heart of …

Current and future directions in network biology

M Zitnik, MM Li, A Wells, K Glass, DM Gysi… - arXiv preprint arXiv …, 2023 - arxiv.org
Network biology, an interdisciplinary field at the intersection of computational and biological
sciences, is critical for deepening understanding of cellular functioning and disease. While …

Unraveling Single-Cell Heterogeneity Through Graph Neural Networks and Multiplexed Imaging

JA Shahir - 2023 - search.proquest.com
Cells are the basic building blocks of life, and understanding how they transition from one
state to another is a fundamental question in cell biology. Advances in single-cell genomics …

[HTML][HTML] Learning to encode cellular responses to systematic perturbations with deep generative models

Y Xue, MQ Ding, X Lu - NPJ systems biology and applications, 2020 - nature.com
Cellular signaling systems play a vital role in maintaining homeostasis when a cell is
exposed to different perturbations. Components of the systems are organized as hierarchical …

Reverse-engineering biological networks from large data sets

JL Natale, D Hofmann, DG Hernández… - arXiv preprint arXiv …, 2017 - arxiv.org
Much of contemporary systems biology owes its success to the abstraction of a network, the
idea that diverse kinds of molecular, cellular, and organismal species and interactions can …