Nathan C. Sheffield

Taming the reference genome jungle: the refget sequence collection standard

The paper introduces a standard for unambiguously representing, retrieving, and comparing reference genomes and transcriptomes, revealing inconsistencies across 60 human and 36 mouse references.

Atacformer: A transformer-based foundation model for analysis and interpretation of ATAC-seq data

Atacformer is a transformer-based model for scATAC-seq data analysis that improves clustering, cell-type annotation, and cross-modal alignment with RNA-seq data.

The FAIRSCAPE AI-readiness Framework for Biomedical Research

The paper introduces FAIRSCAPE, a framework for packaging biomedical datasets with metadata to enhance AI-readiness, explainability, and FAIR compliance.

AI-readiness criteria for biomedical data

The paper defines AI-readiness criteria for biomedical data, encompassing seven dimensions, and evaluates them across flagship datasets to ensure ethical and explainable AI practices.

BEDMS: A metadata standardizer for genomic regionattributes

BEDMS standardizes genomic interval metadata by predicting standardized attributes using trained models and supports custom schemas for improved data interoperability.

Methods for constructing and evaluating consensus genomic interval sets

The paper introduces methods to construct and evaluate consensus genomic interval sets, showing how to minimize loss of resolution while enabling interoperability of interval data.

Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings

The paper introduces scEmbed, a framework for fast clustering and cell-type annotation of scATAC-seq data using pre-trained embeddings, showing improved performance and transferability.

Methods for evaluating unsupervised vector representations of genomic regions

The paper introduces four metrics to evaluate unsupervised embeddings of genomic regions and provides guidelines for reliable embedding learning.

DeepGSEA: Explainable Deep Gene Set Enrichment Analysis for Single-cell Transcriptomic Data

DeepGSEA provides an explainable deep learning approach for gene set enrichment analysis in single-cell RNA sequencing data, improving sensitivity and specificity over traditional methods.

Joint representation learning for retrieval and annotation of genomic interval sets

The paper develops a system for fast and flexible genomic interval retrieval using joint representation learning of region sets and metadata.

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata

PEPhub is a database and web interface for sharing, editing, and validating biological sample metadata, enabling fast semantic search and interoperability.

Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis

This study performs a meta-analysis of scRNA-seq datasets to map human atherosclerosis cell diversity and identifies disease-relevant vascular cell states and markers.

Protein Kinase A Inhibition Epigenetically Silences Ren1

The paper investigates how PKA inhibition affects renin expression by altering epigenetic marks and gene regulation at the renin locus.

Determinants of renin cell differentiation: a single cell epi-transcriptomics approach

The paper uses single-cell epi-transcriptomics to map the developmental trajectory of renin cell differentiation and identifies key transcription factors involved in their formation.

excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies

The paper provides exclusion region sets for T2T-CHM13, GRCm39, and other genomes through an R/Bioconductor package and API, offering unified access to curated genomic ranges.

Single-cell Transcriptome and Accessible Chromatin Dynamics During Endocrine Pancreas Development

The paper analyzes single-cell transcriptome and chromatin accessibility data to uncover transcription factor networks governing pancreatic endocrine cell lineage specification.

Expanding the Galaxy's reference data

The paper describes integrating refgenie into Galaxy to manage and share reference datasets, with tools for retrieval and a global repository for easy access.

Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects

The paper introduces PEP, a metadata standard for biological projects, to improve data portability and tool compatibility across bioinformatics workflows.

PEPATAC: An optimized pipeline for ATAC-seq data analysis with serial alignments

PEPATAC is an ATAC-seq analysis pipeline that improves speed and accuracy through serial mitochondrial genome alignment, providing standardized outputs for downstream analysis.

Bedshift: perturbation of genomic interval sets

Bedshift generates perturbed BED files to benchmark region set similarity metrics, showing differences in their sensitivity to added, dropped, or shifted regions.

Embeddings of genomic region sets capture rich biological associations in lower dimensions

The paper introduces a method to represent genomic region sets as embeddings using a modified word2vec approach, showing it effectively captures biological associations in lower dimensions.

DNA Methyltransferase 1 and 3a Expression in the Frontal Cortex Regulates Palatable Food Consumption

This study shows that deleting DNA methyltransferase 1 and 3a in the mouse prefrontal cortex reduces palatable food consumption without affecting chow intake, with effects on neuron excitability and DNA methylation patterns.

Quality control and processing of nascent RNA profiling data

The paper introduces PEPPRO, a workflow for processing nascent RNA profiling data, providing standardized output and quality assessments.

Identity and compatibility of reference genome resources

The paper establishes identity and compatibility of genome reference resources using unique identifiers, parent-child relationships, and recursive identifiers.

Chromatin conformation capture (Hi-C) sequencing of patient-derived xenografts: analysis guidelines

This study evaluates the impact of mouse read removal and library preparation on Hi-C data quality in patient-derived xenografts, finding that library strategy has the largest effect.

Refget: standardised access to reference sequences

The paper introduces refget, an API for standardized access to reference sequences using identifiers derived from the sequences themselves.

IGD: high-performance search for large-scale genomic interval datasets

IGD provides a high-performance tool for searching large-scale genomic interval datasets, achieving faster speed and lower memory usage than existing methods.

COCOA: Coordinate covariation analysis of epigenetic heterogeneity

COCOA analyzes epigenetic variation by examining covariation across individuals and annotates heterogeneity using genomic region sets.

Data Integration with SUMO Detects Latent Relationships Between Patients in Lower-Grade Gliomas

The paper integrates multi-omic data to identify a prognostic subtype in lower-grade gliomas with genomic features similar to Grade IV gliomas.

Seqpare: a self-consistent metric of similarity between genomic interval sets

The paper introduces Seqpare, a self-consistent metric for comparing genomic interval sets by calculating the ratio of effective overlap over the union.