Steven J.M. Jones

The paper develops EpiSignaLR, a resource for genome-wide episignature analysis using methylation-aware sequencing data, identifying DMRs and classifiers for three neurodevelopmental disorders.

This study identifies CYB-4 as a meiosis-specific cyclin that coordinates meiotic entry, chromosome structure, and oocyte maturation with CDK-1 in C. elegans.

This study identifies a role for the TRiC/CCT chaperonin in folding meiotic HORMAD proteins into chromosome axes necessary for crossing over.

The paper presents the genome sequence of the hemlock woolly adelgid, including chromosome assembly, gene annotation, and mitogenome data.

CIViC-Fact evaluates AI models for verifying cancer variant interpretations using full-text evidence, showing abstracts are insufficient for accurate validation.

This paper develops and characterizes small-molecule inhibitors of LAG-3, a protein that suppresses antitumor immunity, using a novel semi-allosteric mechanism.

The paper identifies gene expression signatures related to neutrophil extracellular traps (NETs) in pancreatic ductal adenocarcinoma (PDAC) and shows they correlate with patient survival and metastasis, with potential therapeutic targets.

The paper uses long-read sequencing to analyze HPV integration sites in cervical cancer genomes, identifying structural and epigenetic impacts of integration.

This paper presents a long-read sequencing dataset of cancer samples, showing its ability to resolve structural variants, haplotypes, and methylation patterns in precision medicine.

This study uses nanopore sequencing to analyze RNA modifications and their correlations with other RNA features in human cells, revealing negative associations and pathway-specific responses.

This paper shows that using a complete reference genome improves the accuracy and reduces false positives in detecting structural variants in cancer genomes.

The paper develops accurate 6mA base calling to profile chromatin accessibility and detect CpG methylation in humans using long-read sequencing.

IMPALA detects allele-specific expression in cancer samples and identifies potential regulatory mechanisms influencing ASE.

The paper uses genome-wide data to infer isolation-by-distance and population size history in coho salmon, identifying genes associated with latitude and potential osmoregulation roles.

This paper uses long-read DNA methylation sequencing and Strand-seq to detect parent-of-origin and haplotype chromosomes, achieving high accuracy in five trios.

The paper uses nanopore sequencing to detect imprinted differentially methylated regions in human B-lymphocyte cell lines, identifying known and novel DMRs and showing conservation across species.

cSurvival is a web resource that enables biomarker interaction analysis and integrates clinical and experimental cancer data to improve prognosis and drug resistance insights.

PORI is an open-source platform for interpreting somatic variants in cancer, demonstrating that 88.2% of TCGA tumors have at least one potentially targetable alteration.

The paper analyzes the pink salmon genome to identify genomic consequences of a two-year life-cycle, finding Fst peaks and gene regions associated with temporal isolation and selection.

The paper optimizes a magnetic bead-based nucleic acid extraction protocol for SARS-CoV-2 testing to reduce cross-well contamination while maintaining sensitivity.

Copy-scAT deconvolutes single-cell chromatin accessibility to infer genetic subclones in cancer, revealing how genetics influence chromatin profiles and subclonal phenotypes.

The paper describes the evolution of the CIViC knowledgebase to meet the needs of the cancer variant interpretation community by expanding its functionality and data types.

The paper investigates the association of rare loss-of-function variants in type I IFN immunity genes with severe COVID-19 and finds no significant association.

CanDIG enables secure, federated genomic and health data analysis across jurisdictions while maintaining data locality and privacy.

The paper sequences and assembles the largest complete mitochondrial genome of a gymnosperm, Sitka spruce, revealing a complex multipartite structure.

The paper investigates rare ACE2 coding variants as potential X-linked risk factors for COVID-19, showing their frequency and impact on SARS-CoV-2 binding in different populations.

This study uses GANs to synthesize high-resolution cancer pathology images, showing they are visually indistinguishable from real images and perform as well as real images in diagnostic tasks.

The paper describes the development of CIViCmine, a text-mining tool that extracts clinically relevant cancer biomarkers from literature to aid curation into the CIViC database.

The paper identifies nhj-1 as a fourth cNHEJ factor in C. elegans, showing its role in DNA repair and IR sensitivity through genetic and localization studies.