John Marshall

Taming the reference genome jungle: the refget sequence collection standard

Donald R. Campbell, Timothée Cezard, Sveinung Gundersen, Andrew Yates et autres

MOTIVATION: Reference genomes are foundational to genomics but suffer from widespread ambiguity and incompatibility due to inconsistent naming, undocumented differences, and lack of formal mechanisms for comparison. RESULTS: To address this, we introduce the GA4GH refget Sequence Collections (seqcol) standard. Refget seqcol …

us, gb, no, au (code pays fourni par la source)

Data from: Tandem repeat variation shapes immune cell type-specific gene expression

Hope A. Tanudisastro, Anna Cuomo, Ben Weisburd, Matthew Welland et autres

This dataset contains the polymorphic catalog and association summary statistics (v1.0) for genome-wide tandem repeat (TR) expression quantitative trait loci (eQTL) analysis of TenK10K Phase 1 (https://doi.org/10.1101/2024.11.02.621562). Please access the respective README files for a detailed description of file contents. caQTL summary …

au, us, gb (code pays fourni par la source)

Impact of rare and common genetic variation on cell type-specific gene expression in human blood

Anna Cuomo, Eleanor Spenceley, Hope A. Tanudisastro, Blake Bowen et autres

Abstract Understanding the genetic basis of gene expression can shed light on the regulatory mechanisms underlying complex traits and diseases. Single cell-resolved measures of RNA levels and single-cell expression quantitative trait loci (sc-eQTLs) have revealed genetic regulation that drives sub-tissue cell states …

au, us (code pays fourni par la source)

Tofacitinib for Hospitalized Acute Severe Ulcerative Colitis Management (The TRIUMPH Study)

Neeraj Narula, Cara Pray, Hasan Hamam, Farhad Peerani et autres

Background: Tofacitinib is a rapidly acting Janus kinase (JAK) inhibitor with increasing evidence of effectiveness in patients with acute severe ulcerative colitis (ASUC). However, there are scarce prospective data analyzing the efficacy and rapidity of action in hospitalized ASUC. Methods: The TRIUMPH …

ca (code pays fourni par la source)

902 TOFACITINIB FOR HOSPITALIZED ACUTE SEVERE ULCERATIVE COLITIS - THE TRIUMPH STUDY

Neeraj Narula, Farhad Peerani, Tawnya Hansen, Talat Bessissow et autres

The Impact of Self Scheduling on Intern Wellness

John Marshall, David Jones

B residents who did not receive targeted simulations.

Dysregulated DNA methylation in the pathogenesis of Fabry disease

Jin‐Song Shen, Uthra Balaji, Kunitoshi Shigeyasu, Yoshinaga Okugawa et autres

Fabry disease is an X-linked lysosomal storage disorder caused by a deficiency of α-galactosidase A and subsequent accumulation of glycosphingolipids with terminal α-D-galactosyl residues. The molecular process through which this abnormal metabolism of glycosphingolipids causes multisystem dysfunction in Fabry disease is not …

us, fr (code pays fourni par la source)

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Heidi L. Rehm, Angela Page, Lindsay Smith, Jeremy Adams et autres

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular …

us, ca, ch, gb, es, au, qa, hk, cz, at, tw, sg, jp (code pays fourni par la source)

Crypt4GH: a file format standard enabling native access to encrypted data

Alexander Senf, Robert M. Davies, Frédéric Haziza, John Marshall et autres

MOTIVATION: The majority of genome analysis tools and pipelines require data to be decrypted for access. This potentially leaves sensitive genetic data exposed, either because the unencrypted data is not removed after analysis, or because the data leaves traces on the permanent …

gb, us, es, ch, au (code pays fourni par la source)

Twelve years of SAMtools and BCFtools

Petr Danecek, James Bonfield, Jennifer Liddle, John Marshall et autres

BACKGROUND: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS: The first version appeared online 12 …

gb, us (code pays fourni par la source)

HTSlib: C library for reading/writing high-throughput sequencing data

James Bonfield, John Marshall, Petr Danecek, Heng Li et autres

BACKGROUND: Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files. To facilitate this a library was produced out of the original SAMtools implementation, with a focus on performance …

gb, us (code pays fourni par la source)

Twelve years of SAMtools and BCFtools

Petr Danecek, James Bonfield, Jennifer Liddle, John Marshall et autres

BACKGROUND: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS: The first version appeared online 12 …

gb, us (code pays fourni par la source)