Mechanistic models versus machine learning, a fight worth fighting for the biological community?

RE Baker, JM Pena, J Jayamohan… - Biology …, 2018 - royalsocietypublishing.org
Ninety per cent of the world's data have been generated in the last 5 years (Machine
learning: the power and promise of computers that learn by example. Report no. DES4702 …

Studying stochastic systems biology of the cell with single-cell genomics data

G Gorin, JJ Vastola, L Pachter - Cell Systems, 2023 - cell.com
Recent experimental developments in genome-wide RNA quantification hold considerable
promise for systems biology. However, rigorously probing the biology of living cells requires …

RNA velocity unraveled

G Gorin, M Fang, T Chari, L Pachter - PLOS Computational …, 2022 - journals.plos.org
We perform a thorough analysis of RNA velocity methods, with a view towards
understanding the suitability of the various assumptions underlying popular …

A single-cell analysis of the Arabidopsis vegetative shoot apex

TQ Zhang, Y Chen, JW Wang - Developmental Cell, 2021 - cell.com
The shoot apical meristem allows for reiterative formation of new aerial structures throughout
the life cycle of a plant. We use single-cell RNA sequencing to define the cellular taxonomy …

Gene regulatory network inference from single-cell data using multivariate information measures

TE Chan, MPH Stumpf, AC Babtie - Cell systems, 2017 - cell.com
While single-cell gene expression experiments present new challenges for data processing,
the cell-to-cell variability observed also reveals statistical relationships that can be used by …

Julia for biologists

E Roesch, JG Greener, AL MacLean, H Nassar… - Nature …, 2023 - nature.com
Major computational challenges exist in relation to the collection, curation, processing and
analysis of large genomic and imaging datasets, as well as the simulation of larger and …

Statistical mechanics meets single-cell biology

AE Teschendorff, AP Feinberg - Nature Reviews Genetics, 2021 - nature.com
Single-cell omics is transforming our understanding of cell biology and disease, yet the
systems-level analysis and interpretation of single-cell data faces many challenges. In this …

Phylodynamics for cell biologists

T Stadler, OG Pybus, MPH Stumpf - Science, 2021 - science.org
BACKGROUND The birth, death, and diversification of individuals are events that drive
biological processes across all scales. This is true whether the individuals in question …

Cell competition during reprogramming gives rise to dominant clones

N Shakiba, A Fahmy, G Jayakumaran, S McGibbon… - Science, 2019 - science.org
INTRODUCTION Recent advances in lineage tracking using DNA-based barcoding
technologies have provided new insights into the developmental dynamics of cell …

[HTML][HTML] Noise distorts the epigenetic landscape and shapes cell-fate decisions

MA Coomer, L Ham, MPH Stumpf - Cell Systems, 2022 - cell.com
The Waddington epigenetic landscape has become an iconic representation of the cellular
differentiation process. Recent single-cell transcriptomic data provide new opportunities for …