Lingling Jin

Quantifying Crop Disease Trait Dynamics through Longitudinal Imaging and Temporal Analytics

The paper presents a pipeline for longitudinal plant disease phenotyping using time-series imaging, enabling objective quantification of disease progression in wheat rusts.

SVPopEx: Population-Wide Visualization and Exploration of Structural Variants

SVPopEx is an interactive tool for visualizing and exploring structural variants across populations, excelling in clear representation and cross-genome comparisons.

Comparative Transcriptome Analysis Unveils Mechanisms of Salt Tolerance in Bluebunch Wheatgrass

This study compares transcriptomes of salt-tolerant and susceptible bluebunch wheatgrass genotypes to identify molecular mechanisms underlying salt tolerance.

Quantum-Classical Reservoir Computing to Predict Influenza A/H3N2 Antigenic Distance

FluQRC predicts influenza A/H3N2 antigenic distance using a hybrid quantum-classical reservoir computing framework, outperforming baselines on large datasets.

Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes

This study uses genome sequences from Cercis canadensis and Chamaecrista fasciculata to infer legume genome structures and histories, including the timing of whole genome duplications and the ancestral karyotype.

Haplotype-resolved Genome Assemblies Reveal Subgenome Origins, Genome Bias and Reticulate Evolution in Wheatgrass Species

This paper presents haplotype-resolved genome assemblies for hybrid wheatgrass and its progenitor, revealing subgenome origins, expression bias, and reticulate evolution.

GNAT: An Interactive Web Tool for Gene Neighbourhood Analysis

GNAT identifies homologues and analyzes genomic neighborhoods to provide interactive visualizations and summary analytics for microbial and viral genomes.

Genomic Analysis Reveals Genetic Diversity, Population Structure and Evolutionary Dynamics in Bluebunch wheatgrass (Pseudoroegneria species)

The paper analyzes genomic variations in seven Bluebunch wheatgrass species to reveal genetic diversity, population structure, and evolutionary dynamics, identifying six genetic clusters and reticulate evolution in Eurasian species.

Exploring The Genome of The Oribatid Mite, Oppia Nitens: Environmental Stress Response and Toxicity Adaptation

This paper presents the draft genome of Oppia nitens, a soil mite model organism, to study its adaptation to environmental stress and toxicity.

From comparative gene content and gene order to ancestral contigs, chromosomes and karyotypes

The paper reconstructs ancestral genomes using a new computational method and finds the monoploid chromosome number x = 9 for rosid and asterid orders.

Predicting Phenotypes From Novel Genomic Markers Using Deep Learning

This paper develops a deep learning model to predict phenotypes using structural variations and transposable elements, showing higher accuracy than SNPs and conventional models.

The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible

The paper confirms a two-step hybridization model for the formation of hexaploidy in Brassiceae and shows subgenomes have distinct loss rates but functionally compatible genes.

High contiguity long read assembly of Brassica nigra allows localization of active centromeres and provides insights into the ancestral Brassica genome.

The paper generates high-contiguity long-read assemblies of Brassica nigra, enabling localization of active centromeres and insights into the ancestral Brassica genome.