🧬 Category

genomics

404 papers

Chromosome-level genome sequence of the C4 grass Themeda triandra reveals karyotype orthology with sorghum and genetic variation in accessions adapted to diverse environments

This study presents a chromosome-level genome assembly of the C4 grass *Themeda triandra* that reveals karyotype orthology with sorghum, while comparative analyses of diverse accessions uncover significant genetic variations, including polyploidy and copy number changes in stress-response genes, offering valuable insights for climate-resilient crop improvement.

Butler, J. B., Humphreys, J. L., Allnutt, T. + 8 more2026-03-20🧬 genomics

Patches: A Representation Learning framework for Decoding Shared and Condition-Specific Transcriptional Programs in Wound Healing

Patches is a novel representation learning framework that utilizes conditional subspace learning to effectively disentangle shared and condition-specific transcriptional programs in single-cell RNA sequencing data, enabling robust integration and biological insights in complex experimental designs such as wound healing studies involving aging and drug treatments.

Beker, O., Deursen, S. V., Tarnow, M. + 6 more2026-03-19🧬 genomics

Transcriptional profiling of Pseudomonas aeruginosa biofilm life cycle stages reveals dispersal-specific biomarkers

This study characterizes the stage-specific transcriptional profiles of *Pseudomonas aeruginosa* biofilms, identifying distinct gene expression patterns for attachment, maturation, and dispersal, and utilizes these findings to define fourteen biomarkers that serve as tools for detecting the onset of biofilm dispersal.

Bertran i Forga, X., Fairfull-Smith, K. E., Qin, J. + 1 more2026-03-19🧬 genomics

Atopic Dermatitis and Psoriasis Differ in Lesional DEG Reference Instability and Non-Lesional Spectrum Displacement: Multi-Cohort Geometric Evidence of Individual Homeostatic Boundary Escape

By applying a geometric transcriptomic framework to multi-cohort data, this study reveals that atopic dermatitis exhibits greater reference-dependent instability in lesional gene expression due to smaller effect sizes and demonstrates that a significant subset of non-lesional patients has already crossed a homeostatic boundary into disease-specific states, a phenomenon masked by traditional group-averaged analyses.

Shabana, B.2026-03-19🧬 genomics

Interpretable and predictive models based on high-dimensional data in ecology and evolution

This paper evaluates nine statistical and machine learning methods for handling high-dimensional ecological and evolutionary data, finding that while overfitting is common and accurate variable selection often unattainable under realistic sampling schemes, sparse models can still achieve predictive accuracy and mitigate overfitting when data attributes such as sample size, effect strength, and variable count are favorable.

Jahner, J. P., Buerkle, C. A., Gannon, D. G. + 12 more2026-03-18🧬 genomics

De novo assembly of complete Plasmodium falciparum isolate genomes using PacBio HiFi sequencing technology

This study demonstrates that PacBio HiFi long-read sequencing enables the accurate de novo assembly of complete Plasmodium falciparum genomes, including complex Variant Surface Antigen families, from 43 natural isolates in The Gambia, providing a high-quality genomic resource for studying parasite evolution and antigenic diversity.

Nyarko, P., Quenu, M., Guery, M.-A. + 7 more2026-03-18🧬 genomics

Genome-scale functional mapping of the mammalian whole brain with in vivo Perturb-seq

This study presents a genome-scale functional atlas of the mouse brain by using an enhanced in vivo Perturb-seq platform to profile transcriptome-wide responses to the loss of 1,947 disease-associated genes across 7.7 million cells, revealing cell-type-specific essentiality and opposing transcriptional programs that advance our understanding of neurodevelopmental, psychiatric, and neurodegenerative diseases.

Shi, T., Korshunova, M., Kim, S. + 27 more2026-03-18🧬 genomics

A machine learning approach to infer DNase1L3 activity from plasma cell-free DNA fragmentomics

This study demonstrates that machine learning models trained on cell-free DNA fragmentomics can accurately infer DNase1L3 activity and identify R206C homozygotes, while also revealing that the resulting aberrant fragmentome represents a stable, time-dependent end-state in homozygotes compared to the transient effects observed in wildtype or heterozygote individuals.

Linthorst, J., Sistermans, E. A.2026-03-18🧬 genomics

The impact of low-frequency genetic variants on serum protein levels

By integrating low-frequency genetic variants with serum protein measurements in a large Icelandic cohort, this study reveals that these variants significantly expand the detection of cis-pQTLs, uncovering widespread allelic heterogeneity and distinct biological characteristics—such as enrichment in coding regions and essential pathways—that are often missed when focusing solely on common variants.

Bjarnadottir, H., Jonmundsson, T., Ingvarsdottir, H. K. + 12 more2026-03-18🧬 genomics

Emergence of a novel hypervirulent extensively drug-resistant ST383 Klebsiella pneumoniae lineage carrying ICEKp5 in Lebanon

This study reports the emergence in Lebanon of a novel, monophyletic ST383 *Klebsiella pneumoniae* lineage that uniquely combines extensive drug resistance (carrying *bla*OXA-48, *bla*NDM-5, and *bla*CTX-M variants) with a full spectrum of hypervirulence factors acquired via ICEKp5, marking a concerning convergence of high-risk traits distinct from previously known local clones.

Abboud, M., Chaaya, T. C., Daccache, Y. + 13 more2026-03-18🧬 genomics