4.4 Article

Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Expression Atlas update: gene and protein expression in multiple species

Pablo Moreno et al.

Summary: EMBL-EBI Expression Atlas is a knowledge base that integrates data from over 4500 expression studies across different species, enabling researchers to explore the expression patterns of genes or proteins under various biological conditions. The data are curated by experts, re-analyzed, and visualized in an easily accessible form, aiming to reproduce the original conclusions of the experiments.

NUCLEIC ACIDS RESEARCH (2022)

Article Genetics & Heredity

Zebrafish information network, the knowledgebase for Danio rerio research

Yvonne M. Bradford et al.

Summary: The Zebrafish Information Network is a central repository for genetic and genomic data of Danio rerio, providing services for the zebrafish research community. It makes zebrafish research data accessible and integrable through various activities and tools, and collaborates with other model organism knowledgebases for data integration.

GENETICS (2022)

Article Genetics & Heredity

FlyBase: a guided tour of highlighted features

L. Sian Gramates et al.

Summary: As FlyBase celebrates its fourth decade, it highlights its unique aspects and expresses its commitment to collaborate with other research communities. They emphasize the reports and tools dedicated to fly researchers' needs and provide multiple avenues for researchers to interact with FlyBase.

GENETICS (2022)

Review Oncology

Single-cell RNA sequencing technologies and applications: A brief overview

Dragomirka Jovic et al.

Summary: Single-cell RNA sequencing technology is an advanced method for studying the diversity and complexity of RNA transcripts within individual cells, and for understanding the composition and functions of different cell types in highly organized tissues/ organs/ organisms. This technology has made significant contributions to various fields, providing unique insights into health and diseases. It can be used to construct high-resolution atlases of cells in all living organisms, and has the potential to transform current protocols in disease diagnosis and treatment.

CLINICAL AND TRANSLATIONAL MEDICINE (2022)

Article Multidisciplinary Sciences

Multi-species single-cell transcriptomic analysis of ocular compartment regulons

Pradeep Gautam et al.

Summary: This study presents a multi-species single-cell transcriptomic atlas of the eye, highlighting inter-species differences in the retina and identifying putative adult stem cells in the iris tissue. The research also includes the creation of a disease map of genes involved in eye disorders across different compartments of the eye, as well as the study of conservation of regulons across vertebrates and zebrafish to identify common core factors. Additionally, the perturbation of KLF7 gene expression during retinal ganglion cell differentiation and its role in the maturation process is demonstrated.

NATURE COMMUNICATIONS (2021)

Article Neurosciences

Single-cell atlas of early human brain development highlights heterogeneity of human neuroepithelial cells and early radial glia

Ugomma C. Eze et al.

Summary: Through single-cell RNA sequencing, nine progenitor populations at the earliest stages of human brain development were identified, including a highly prevalent mesenchymal-like population that disappears once neurogenesis begins. Comparison with mouse progenitor populations revealed two clusters enriched in the early stages of human cortical development. Organoid systems displayed low fidelity to neuroepithelial and early radial glia cell types, but improved as neurogenesis progressed.

NATURE NEUROSCIENCE (2021)

Article Gastroenterology & Hepatology

Regular Use of Proton Pump Inhibitor and the Risk of Inflammatory Bowel Disease: Pooled Analysis of 3 Prospective Cohorts

Bin Xia et al.

Summary: The study found that regular use of PPIs was associated with an increased risk of IBD and its subtypes, highlighting the potential impact of PPIs on gut microbiome and immune function.

GASTROENTEROLOGY (2021)

Article Multidisciplinary Sciences

Cells of the human intestinal tract mapped across space and time

Rasa Elmentaite et al.

Summary: The study analyzes cells from various stages of human development along the intestinal tract, revealing transcriptionally distinct BEST4 epithelial cells and implicating IgG sensing as a function of tuft cells. It also describes neural cell populations in the developing enteric nervous system and identifies key players in the formation of lymphoid tissue in early human development and inflammatory bowel disease.

NATURE (2021)

Article Medicine, General & Internal

Association of ultra-processed food intake with risk of inflammatory bowel disease: prospective cohort study

Neeraj Narula et al.

Summary: The study evaluated the association between intake of ultra-processed food and risk of inflammatory bowel disease (IBD). The results showed a positive association between higher intake of ultra-processed food and risk of IBD, with different subgroups of ultra-processed food associated with higher hazard ratios for IBD.

BMJ-BRITISH MEDICAL JOURNAL (2021)

Review Immunology

Mechanism of fibrosis and stricture formation in Crohn's disease

Johannes Alfredsson et al.

SCANDINAVIAN JOURNAL OF IMMUNOLOGY (2020)

Article Cardiac & Cardiovascular Systems

Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body

Griffin M. Weber et al.

FRONTIERS IN CARDIOVASCULAR MEDICINE (2020)

Article Gastroenterology & Hepatology

IBD prevalence in Lothian, Scotland, derived by capture-recapture methodology

Gareth-Rhys Jones et al.

Article Multidisciplinary Sciences

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

Michael P. Snyder et al.

NATURE (2019)

Review Biochemistry & Molecular Biology

Toward a Common Coordinate Framework for the Human Body

Jennifer E. Rood et al.

Review Medicine, General & Internal

A comprehensive review and update on Crohn's disease

Mahesh Gajendran et al.

DM DISEASE-A-MONTH (2018)

Article Biology

The Human Cell Atlas

Aviv Regev et al.

ELIFE (2017)

Review Physiology

LungMAP: The Molecular Atlas of Lung Development Program

Maryanne E. Ardini-Poleske et al.

AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY (2017)

Article Gastroenterology & Hepatology

Dietary Patterns and Risk of Inflammatory Bowel Disease in Europe: Results from the EPIC Study

Antoine Racine et al.

INFLAMMATORY BOWEL DISEASES (2016)

Article Mathematical & Computational Biology

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

Alexander D. Diehl et al.

JOURNAL OF BIOMEDICAL SEMANTICS (2016)

Review Biochemistry & Molecular Biology

eMouseAtlas informatics: embryo atlas and gene expression database

Chris Armit et al.

MAMMALIAN GENOME (2015)

Article Mathematical & Computational Biology

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology

Wasila M. Dahdul et al.

JOURNAL OF BIOMEDICAL SEMANTICS (2014)

Article Mathematical & Computational Biology

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Melissa A. Haendel et al.

JOURNAL OF BIOMEDICAL SEMANTICS (2014)

Article Developmental Biology

eChickAtlas: An introduction to the database

Frances Wong et al.

GENESIS (2013)

Article Mathematical & Computational Biology

Functional tissue units and their primary tissue motifs in multi-scale physiology

Bernard de Bono et al.

JOURNAL OF BIOMEDICAL SEMANTICS (2013)

Article Multidisciplinary Sciences

An anatomically comprehensive atlas of the adult human brain transcriptome

Michael J. Hawrylycz et al.

NATURE (2012)

Article Computer Science, Interdisciplinary Applications

A reference ontology for biomedical informatics: the Foundational Model of Anatomy

C Rosse et al.

JOURNAL OF BIOMEDICAL INFORMATICS (2003)