A pan-grass transcriptome reveals patterns of cellular divergence in crops

B Guillotin, R Rahni, M Passalacqua, MA Mohammed… - Nature, 2023 - nature.com
Different plant species within the grasses were parallel targets of domestication, giving rise
to crops with distinct evolutionary histories and traits. Key traits that distinguish these species …

Convergent evolution of plant prickles by repeated gene co-option over deep time

JW Satterlee, D Alonso, P Gramazio, KM Jenike, J He… - Science, 2024 - science.org
An enduring question in evolutionary biology concerns the degree to which episodes of
convergent trait evolution depend on the same genetic programs, particularly over long …

Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution

H Suresh, M Crow, N Jorstad, R Hodge… - Nature Ecology & …, 2023 - nature.com
Enhanced cognitive function in humans is hypothesized to result from cortical expansion
and increased cellular diversity. However, the mechanisms that drive these phenotypic …

Cell types as species: Exploring a metaphor

JJ Doyle - Frontiers in Plant Science, 2022 - frontiersin.org
The concept of “cell type,” though fundamental to cell biology, is controversial. Cells have
historically been classified into types based on morphology, physiology, or location. More …

Reimagining Cortical Connectivity by Deconstructing Its Molecular Logic into Building Blocks

X Chen - Cold Spring Harbor Perspectives in Biology, 2024 - cshperspectives.cshlp.org
Comprehensive maps of neuronal connectivity provide a foundation for understanding the
structure of neural circuits. In a circuit, neurons are diverse in morphology …

Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator

D Ciren, S Zebell, ZB Lippman - PLoS Genetics, 2024 - journals.plos.org
A striking paradox is that genes with conserved protein sequence, function and expression
pattern over deep time often exhibit extremely divergent cis-regulatory sequences. It remains …

Coexpression enhances cross-species integration of single-cell RNA sequencing across diverse plant species

MJ Passalacqua, J Gillis - Nature Plants, 2024 - nature.com
Single-cell RNA sequencing is increasingly used to investigate cross-species differences
driven by gene expression and cell-type composition in plants. However, the frequent …

A neural algorithm for computing bipartite matchings

S Dasgupta, Y Meirovitch, X Zheng, I Bush… - Proceedings of the …, 2024 - pnas.org
Finding optimal bipartite matchings—eg, matching medical students to hospitals for
residency, items to buyers in an auction, or papers to reviewers for peer review—is a …

Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes

Y Liu, I Hoskins, M Geng, Q Zhao, J Chacko, K Qi… - …, 2024 - pmc.ncbi.nlm.nih.gov
Characterization of shared patterns of RNA expression between genes across conditions
has led to the discovery of regulatory networks and novel biological functions. However, it is …

Predictive biomarkers for embryotoxicity: a machine learning approach to mitigating multicollinearity in RNA-Seq

Y Quah, S Jung, JYL Chan, O Ham, JS Jeong… - Archives of …, 2024 - Springer
Multicollinearity, characterized by significant co-expression patterns among genes, often
occurs in high-throughput expression data, potentially impacting the predictive model's …