Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry

N Verbeeck, RM Caprioli… - Mass spectrometry …, 2020 - Wiley Online Library
Imaging mass spectrometry (IMS) is a rapidly advancing molecular imaging modality that
can map the spatial distribution of molecules with high chemical specificity. IMS does not …

The dynamic control of signal transduction networks in cancer cells

W Kolch, M Halasz, M Granovskaya… - Nature Reviews …, 2015 - nature.com
Cancer is often considered a genetic disease. However, much of the enormous plasticity of
cancer cells to evolve different phenotypes, to adapt to challenging microenvironments and …

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

KD Korthauer, LF Chu, MA Newton, Y Li, J Thomson… - Genome biology, 2016 - Springer
The ability to quantify cellular heterogeneity is a major advantage of single-cell
technologies. However, statistical methods often treat cellular heterogeneity as a nuisance …

[HTML][HTML] Bistability in the Rac1, PAK, and RhoA signaling network drives actin cytoskeleton dynamics and cell motility switches

KM Byrne, N Monsefi, JC Dawson, A Degasperi… - Cell systems, 2016 - cell.com
Dynamic interactions between RhoA and Rac1, members of the Rho small GTPase family,
play a vital role in the control of cell migration. Using predictive mathematical modeling …

Differential expression analysis of single-cell rna-seq data: current statistical approaches and outstanding challenges

S Das, A Rai, SN Rai - Entropy, 2022 - mdpi.com
With the advent of single-cell RNA-sequencing (scRNA-seq), it is possible to measure the
expression dynamics of genes at the single-cell level. Through scRNA-seq, a huge amount …

MarcoPolo: a method to discover differentially expressed genes in single-cell RNA-seq data without depending on prior clustering

C Kim, H Lee, J Jeong, K Jung, B Han - Nucleic acids research, 2022 - academic.oup.com
The standard analysis pipeline for single-cell RNA-seq data consists of sequential steps
initiated by clustering the cells. An innate limitation of this pipeline is that an imperfect …

Dynamic hydrogen peroxide levels reveal a rate-dependent sensitivity in B-cell lymphoma signaling

M Witmond, E Keizer, B Kiffen, WTS Huck… - Scientific Reports, 2024 - nature.com
Although in vivo extracellular microenvironments are dynamic, most in vitro studies are
conducted under static conditions. Here, we exposed diffuse large B-cell lymphoma …

Microfluidic single-cell measurements of oxidative stress as a function of cell cycle position

TJ Allcroft, JT Duong, PS Skardal… - Analytical and Bioanalytical …, 2023 - Springer
Single-cell measurements routinely demonstrate high levels of variation between cells, but
fewer studies provide insight into the analytical and biological sources of this variation. This …

Multiplicity of mathematical modeling strategies to search for molecular and cellular insights into bacteria lung infection

M Cantone, G Santos, P Wentker, X Lai… - Frontiers in physiology, 2017 - frontiersin.org
Even today two bacterial lung infections, namely pneumonia and tuberculosis, are among
the 10 most frequent causes of death worldwide. These infections still lack effective …

DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks

LK Nguyen, A Degasperi, P Cotter, BN Kholodenko - Scientific reports, 2015 - nature.com
Biochemical networks are dynamic and multi-dimensional systems, consisting of tens or
hundreds of molecular components. Diseases such as cancer commonly arise due to …