All the single cells: single-cell transcriptomics/epigenomics experimental design and analysis considerations for glial biologists
KE Prater, KZ Lin - arXiv preprint arXiv:2408.06521, 2024 - arxiv.org
Single-cell transcriptomics, epigenomics, and other'omics applied at single-cell resolution
can significantly advance hypotheses and understanding of glial biology. Omics …
can significantly advance hypotheses and understanding of glial biology. Omics …
Network Modeling and Control of Dynamic Disease Pathways, Review and Perspectives
Dynamic disease pathways are a combination of complex dynamical processes among bio-
molecules in a cell that leads to diseases. Network modeling of disease pathways considers …
molecules in a cell that leads to diseases. Network modeling of disease pathways considers …
Contextualized Networks Reveal Heterogeneous Transcriptomic Regulation in Tumors at Sample-Specific Resolution
CN Ellington, BJ Lengerich, TBK Watkins, J Yang… - bioRxiv, 2023 - biorxiv.org
Cancers are shaped by somatic mutations, microenvironment, and patient background, each
altering gene expression and regulation in complex ways, resulting in heterogeneous …
altering gene expression and regulation in complex ways, resulting in heterogeneous …
Joint trajectory and network inference via reference fitting
SY Zhang - arXiv preprint arXiv:2409.06879, 2024 - arxiv.org
Network inference, the task of reconstructing interactions in a complex system from
experimental observables, is a central yet extremely challenging problem in systems …
experimental observables, is a central yet extremely challenging problem in systems …
scPRINT: pre-training on 50 million cells allows robust gene network predictions
A cell is governed by the interaction of myriads of macromolecules. Such a network of
interaction has remained an elusive milestone in cellular biology. Building on recent …
interaction has remained an elusive milestone in cellular biology. Building on recent …
Logical Modelling, Some Recent Methodological Advances Illustrated
C Chaouiya, PT Monteiro, E Remy - International Workshop on Cellular …, 2024 - Springer
Logical modelling is a popular mathematical framework for assessing the behaviour of
regulatory and signalling networks. Despite its qualitative nature, it allows disclosing crucial …
regulatory and signalling networks. Despite its qualitative nature, it allows disclosing crucial …
ctQC improves biological inferences from single cell and spatial transcriptomics data
V Lakshmanan, M Kahraman, DC Macalinao, N Gunn… - bioRxiv, 2024 - biorxiv.org
Quality control (QC) is the first critical step in single cell and spatial data analysis pipelines.
QC is particularly important when analysing data from primary human samples, since …
QC is particularly important when analysing data from primary human samples, since …
Trans-eQTLs Can Be Used to Identify Tissue-Specific Gene Regulatory Networks
M Nikpay - 2024 - preprints.org
Previous high throughput screening studies indicated trans-eQTLs tend to be tissue specific.
In this study, I probed if this feature can be used to identify tissue-specific gene regulatory …
In this study, I probed if this feature can be used to identify tissue-specific gene regulatory …
The Regulatory Logic of Planarian Stem Cell Differentiation
A Pérez-Posada, H García-Castro, E Emili, V Vanni… - bioRxiv, 2024 - biorxiv.org
Cell type identity is determined by gene regulatory networks (GRNs), comprising the
expression of specific transcription factors (TFs) regulating target genes (TGs) via binding to …
expression of specific transcription factors (TFs) regulating target genes (TGs) via binding to …
scDirect: key transcription factor identification for directing cell state transitions based on single-cell multi-omics data
Cell state transitions are complicated processes that occur in various life activities.
Understanding and artificially manipulating them have been longstanding challenges …
Understanding and artificially manipulating them have been longstanding challenges …