☆ 4.7 Review

Omics and Multi-Omics in IBD: No Integration, No Breakthroughs

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

Related references

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

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023

Yongbiao Xue et al.

Summary: The National Genomics Data Center (NGDC) of the China National Center for Bioinformation (CNCB) provides database resources to support global academic and industrial communities. The NGDC constantly expands and updates core database resources by archiving big data, conducting integrative analysis, and providing value-added curation. New database resources have been developed for infectious diseases and microbiology, cancer-trait association, and tropical plants. Additionally, resources for the monkeypox virus and SARS-CoV-2 have been newly constructed and regularly updated. All resources and services are publicly accessible at https://ngdc.cncb.ac.cn.

NUCLEIC ACIDS RESEARCH (2023)

Add to Collection
Review Gastroenterology & Hepatology

Advancing the precision management of inflammatory bowel disease in the era of omics approaches and new technology

Xin-Yu Liu et al.

Summary: There is a great diversity in pathogenesis, clinical presentation, treatment response, and prognosis among inflammatory bowel disease (IBD) patients, necessitating individualized and precise management. Numerous studies have focused on predicting disease type, activity, severity, and prognosis using biomarkers and models. In the era of biologics, predicting treatment response, side effects, and loss of response has become important. Multiomics, combined with artificial intelligence, is a promising approach for understanding the complex network of IBD pathogenesis.

WORLD JOURNAL OF GASTROENTEROLOGY (2023)

Add to Collection
Article Biochemistry & Molecular Biology

The enteric nervous system relays psychological stress to intestinal inflammation

Kai Markus Schneider et al.

CELL (2023)

Add to Collection
Article Gastroenterology & Hepatology

Distinct blood protein profiles associated with the risk of short-term and mid/long-term clinical relapse in patients with Crohn's disease stopping infliximab: when the remission state hides different types of residual disease activity

Nicolas Pierre et al.

Summary: Distinct blood protein profiles were identified and associated with the risk of short-term and mid/long-term clinical relapse in patients with Crohn's disease (CD) stopping infliximab. High serum levels of proteins mainly expressed in lymphocytes (LAG3, SH2B3, SIT1), low serum levels of anti-inflammatory effectors (IL-10, HSD11B1), and cellular junction proteins (CDSN, CNTNAP2, CXADR, ITGA11) were specifically associated with mid/long-term relapse risk. On the other hand, high serum levels of pro-inflammatory effectors (IL-6, IL12RB1) and low or high serum levels of proteins mainly expressed in antigen presenting cells (CLEC4A, CLEC4C, CLEC7A, LAMP3) were specifically associated with short-term relapse risk.

GUT (2023)

Add to Collection
Article Biochemistry & Molecular Biology

Systems biology approach delineates critical pathways associated with disease progression in rheumatoid arthritis

Sai Krishna Srimadh Bhagavatham et al.

Summary: Rheumatoid Arthritis (RA) is a chronic systemic autoimmune disease. This study aimed to identify the critical pathways involved in RA pathophysiology through the analysis of transcriptomics, proteomics, and metabolomics datasets. The analysis revealed that SNPs associated with RA were categorized into pathways driving immune response and cytokine production. Further analysis identified gene expression and metabolic pathways with potential implications for RA.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2023)

Add to Collection
Article Gastroenterology & Hepatology

Analysis of Systemic Epigenetic Alterations in Inflammatory Bowel Disease: Defining Geographical, Genetic and Immune-Inflammatory influences on the Circulating Methylome

R. Kalla et al.

Summary: This study identified consistent epigenetic alterations in European patients with IBD at diagnosis, providing insights into gene-environment interactions and immune system activation. Furthermore, significant correlations were observed between methylation at specific loci and gene expression. These findings offer important clues for understanding the pathogenesis of IBD and developing new treatment strategies.

JOURNAL OF CROHNS & COLITIS (2023)

Add to Collection
Article Gastroenterology & Hepatology

Multiomics-empowered Deep Phenotyping of Ulcerative Colitis Identifies Biomarker Signatures Reporting Functional Remission States

Lukas Janker et al.

Summary: Ulcerative colitis (UC) is a chronic disease with unknown causes and increasing incidence. This study analyzed the proteome of human tissue samples from UC patients and found activation of various immune cells, as well as downregulation of mitochondrial proteins. The systemic analysis of plasma proteins and metabolites revealed chronic inflammation and deregulation of gut-derived metabolites in UC patients. Some molecular biomarkers recovered to normal levels during remission, but microvascular damage and platelet deregulation may persist as disease-associated molecular signatures.

JOURNAL OF CROHNS & COLITIS (2023)

Add to Collection
Review Medicine, General & Internal

Precision medicine in complex diseases-Molecular subgrouping for improved prediction and treatment stratification

Asa Johansson et al.

Summary: Complex diseases result from a combination of genetic, lifestyle, and environmental factors and include common noncommunicable diseases. Precision medicine, using genomic and molecular data, has been successful for certain diseases but faces challenges due to heterogeneity and high number of risk factors in complex diseases. Subclassifying patients based on molecular or phenotypic data holds promise for improving diagnosis, treatment, and prognosis.

JOURNAL OF INTERNAL MEDICINE (2023)

Add to Collection
Review Biochemical Research Methods

Multi-Omics Profiling for Health

Mohan Babu et al.

Summary: The rise in chronic diseases has led to a cross-disciplinary approach in understanding and treating disease. Current medical care focuses on treating patients rather than preventing illness, resulting in high costs. The advancement of omics technologies and computational capabilities has allowed for precision health approaches. This review discusses the applications and challenges of multi-omics in precision health.

MOLECULAR & CELLULAR PROTEOMICS (2023)

Add to Collection
News Item Multidisciplinary Sciences

First human 'pangenome' aims to catalogue genetic diversity

Layal Liverpool

NATURE (2023)

Add to Collection
Review Genetics & Heredity

Methods and applications for single-cell and spatial multi-omics

Katy Vandereyken et al.

Summary: The joint analysis of multiple molecular modalities from single cells, such as the genome, epigenome, transcriptome, proteome, and metabolome, is transforming our understanding of cell biology in health and disease. This review discusses the advances in single-cell and spatial multi-omics technologies and the computational strategies for integrating information across these molecular layers. It also highlights their impact on fundamental cell biology and translational research, current challenges, and future prospects.

NATURE REVIEWS GENETICS (2023)

Add to Collection
Article Gastroenterology & Hepatology

Genome-Wide Methylation Profiling in 229 Patients With Crohn's Disease Requiring Intestinal Resection: Epigenetic Analysis of the Trial of Prevention of Post-operative Crohn's Disease (TOPPIC)

Nicholas T. Ventham et al.

Summary: This study aimed to investigate the DNA methylation alterations associated with Crohn's disease (CD) recurrence following surgery. The results showed differentially methylated positions and differentially variable positions in patients with CD recurrence. The study also validated the previously reported CD-associated methylome.

CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY (2023)

Add to Collection
Review Microbiology

Targeting the gut microbiota in inflammatory bowel diseases: where are we?

Nicolas Benech et al.

CURRENT OPINION IN MICROBIOLOGY (2023)

Add to Collection
Article Gastroenterology & Hepatology

630 SINGLE-CELL AND SPATIAL MULTI-OMICS IDENTIFY INNATE AND STROMAL MODULES TARGETED BY ANTI-INTEGRIN THERAPY IN ULCERATIVE COLITIS

Elvira Mennillo et al.

Gastroenterology (2023)

Add to Collection
Review Gastroenterology & Hepatology

Defining Interactions Between the Genome, Epigenome, and the Environment in Inflammatory Bowel Disease: Progress and Prospects

Alexandra J. Noble et al.

Summary: Recent advances in understanding the pathogenesis of IBD have shown the complex interplay between the genome, the epigenome, and the environment. Gene-environment interactions, especially through epigenetic mechanisms, may contribute to the missing heritability and alter disease susceptibility. Environmental factors, such as the microbiome, nutrition, and tobacco smoking, can induce changes in the epigenome that impact disease development. Understanding GxE interactions may lead to new therapeutic targets or preventative strategies for IBD.

GASTROENTEROLOGY (2023)

Add to Collection
Article Gastroenterology & Hepatology

Stricturing Crohn's Disease Single-Cell RNA Sequencing Reveals Fibroblast Heterogeneity and Intercellular Interactions

Pranab K. Mukherjee et al.

Summary: By performing single-cell RNA sequencing on tissue samples from patients with Crohn's disease, the study reveals the heterogeneity and interactions of fibroblasts in the affected areas, and confirms CDH11 as a potential therapeutic target.

GASTROENTEROLOGY (2023)

Add to Collection
Editorial Material Multidisciplinary Sciences

Reference maps for the human body

Roser Vento-Tormo et al.

Summary: The HuBMAP consortium has created spatially resolved cell atlases for the human intestine, kidney, and placenta, providing unprecedented detail for analyzing tissue organization.

NATURE (2023)

Add to Collection
Article Multidisciplinary Sciences

Organization of the human intestine at single-cell resolution

John W. Hickey et al.

Summary: The intestine is a complex organ with various functions including digestion, immune surveillance, and maintaining symbiotic relationships with microbiota. It has differences in structure and function along its over nine-meter length. Through multiplexed imaging and single-cell assays, this study reveals substantial differences in cell compositions across different regions of the intestine, highlighting distinct immunological niches. The findings also suggest a regulatory differentiation cascade and associate specific cell types with intestinal disease heritability. This research provides an important reference map for understanding human biology and disease.

NATURE (2023)

Add to Collection
Editorial Material Medical Informatics

Multimodal prognostic models and recent therapeutic advances

Andrea Minervini et al.

LANCET DIGITAL HEALTH (2023)

Add to Collection
Review Gastroenterology & Hepatology

Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All

Padhmanand Sudhakar et al.

Summary: Inflammatory bowel disease (IBD) has a complex and largely unknown etiology, and obtaining multi-omic datasets from IBD patients is necessary for further understanding its biology. However, there are barriers and gaps in the availability of multi-omic data in the field of IBD that need to be addressed. The utility and interpretability of multi-omic datasets, as well as the study design of research projects generating such datasets, are influenced by various technical and non-technical factors.

JOURNAL OF CROHNS & COLITIS (2022)

Add to Collection
Review Oncology

The Essentials of Multiomics

John L. Marshall et al.

Summary: This paper discusses the development and importance of multiomics in clinical practice, highlighting the knowledge gap within the medical community and urging physicians to actively adapt and prepare for this new era.

ONCOLOGIST (2022)

Add to Collection
Article Gastroenterology & Hepatology

The Effect of Phenotype and Genotype on the Plasma Proteome in Patients with Inflammatory Bowel Disease

Arno R. Bourgonje et al.

Summary: This study reveals a strong association between genotype and multiple disease phenotypes with the plasma inflammatory proteome in patients with IBD, identifying disease-associated pathways that may help improve disease management in the future.

JOURNAL OF CROHNS & COLITIS (2022)

Add to Collection
Article Multidisciplinary Sciences

Discovery of bioactive microbial gene products in inflammatory bowel disease

Yancong Zhang et al.

Summary: This article investigates the role of microbial communities and their associated bioactive compounds in inflammatory bowel diseases (IBD). It systematically identifies potentially bioactive protein families involved in gut inflammation during IBD and validates their bioactivity using a combination of metagenomics, metatranscriptomics, and metaproteomics. The results provide candidate microbial proteins that interact with the host immune system in IBD, expanding our understanding of potentially bioactive gene products in chronic diseases.

NATURE (2022)

Add to Collection
Article Gastroenterology & Hepatology

Multiomics to elucidate inflammatory bowel disease risk factors and pathways

Manasi Agrawal et al.

Summary: This article discusses the current knowledge and applications of omics platforms in the diagnosis of inflammatory bowel disease and identification of risk factors, emphasizing the granular high-throughput data provided by multiomics platforms for characterizing molecular pathways and risk factors in chronic diseases like IBD. It also highlights the knowledge gaps in IBD risk factors and pathways, and stresses the importance of birth, at-risk, and pre-diagnostic cohorts, as well as neonatal blood spots in omics analyses. Moreover, the article touches upon the use of network analysis as a powerful bioinformatics tool to extract clinical relevance from high-throughput data.

NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2022)

Add to Collection
Article Multidisciplinary Sciences

Combining explainable machine learning, demographic and multi-omic data to inform precision medicine strategies for inflammatory bowel disease

Laura-Jayne Gardiner et al.

Summary: This study proposes an explainable machine learning approach that integrates bioinformatics and domain insights to predict inter-patient variation in drug response for inflammatory bowel diseases (IBDs). The researchers identified important predictive features, including genomic, transcriptomic, demographic, medicinal, and pharmacological data. The study showed that patient characteristics and genetic polymorphisms are associated with variations in drug effectiveness for anti-inflammatory treatment.

PLOS ONE (2022)

Add to Collection
Review Cell Biology

Immune Cell Plasticity in Inflammation: Insights into Description and Regulation of Immune Cell Phenotypes

Andreas Margraf et al.

Summary: This article discusses the importance of inflammation for immune response and its potential role in chronic diseases and organ damage. The mechanisms triggering, hindering, or resolving inflammation have been studied, but precise therapeutic interventions are not yet fully understood. The article highlights the role of cellular phenotypes, particularly neutrophils, macrophages, and platelets, in inflammation research and suggests implications for diagnostics and therapeutics.

CELLS (2022)

Add to Collection
Article Immunology

ImmUniverse Consortium: Multi-omics integrative approach in personalized medicine for immune-mediated inflammatory diseases

Stefania Vetrano et al.

Summary: Immune mediated inflammatory diseases (IMIDs) are a group of heterogeneous and destructive conditions characterized by dysregulated immune responses. The lack of reliable disease progression and therapy response biomarkers makes it difficult to predict disease development and treatment effectiveness. ImmUniverse, a consortium of 27 partners, aims to advance the understanding of two IMIDs and identify new biomarkers through a multi-omics approach.

FRONTIERS IN IMMUNOLOGY (2022)

Add to Collection
Editorial Material Biochemistry & Molecular Biology

Omics and AI advance biomarker discovery for liver disease

Tiffany Wu et al.

Summary: The new technologies enable noninvasive detection and staging of asymptomatic alcohol-associated liver disease, potentially improving patient outcomes through better clinical management.

NATURE MEDICINE (2022)

Add to Collection
Review Biochemistry & Molecular Biology

Computational approaches for network-based integrative multi-omics analysis

Francis E. Agamah et al.

Summary: Advances in omics technologies have enabled the holistic study of biological systems. Network-based integrative approaches have revolutionized multi-omics analysis by capturing interactions between different layers of omics data. These approaches can identify biomarkers, disease subtypes, crosstalk, causality, and molecular drivers, providing insights into the understanding and treatment of diseases like COVID-19. However, challenges remain in terms of reproducibility, heterogeneity, and interpretability of results in multi-omics network-based analysis.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

Add to Collection
Article Genetics & Heredity

Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility

Aleksejs Sazonovs et al.

Summary: Genome-wide association studies have identified new risk variants and susceptibility genes for Crohn's disease. These studies highlight the crucial role of immune cells and autophagy in the development of Crohn's disease, and also emphasize the importance of mesenchymal cells in intestinal inflammation.

NATURE GENETICS (2022)

Add to Collection
Article Genetics & Heredity

Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

Neha Mishra et al.

Summary: This study investigated the dynamics of gene expression and DNA methylation in blood samples of IBD patients treated with TNF antagonist infliximab. The results showed that early shifts in gene expression and DNA methylation could predict the response to anti-TNF treatment. This finding can help identify IBD patients who are unlikely to benefit from TNF antagonists.

GENOME MEDICINE (2022)

Add to Collection
Article Microbiology

Location-specific signatures of Crohn's disease at a multi-omics scale

Carlos G. Gonzalez et al.

Summary: By utilizing a multi-omics approach, this study identified distinct molecular profiles between colonic and ileal Crohn's disease (CD) subtypes, suggesting separate pathologies associated with the two disease locations. Colonic CD displayed similarities to ulcerative colitis, while ileal CD showed a unique profile characterized by bile acid-driven changes. These findings highlight the power of multi-omics in discovering biomarkers and understanding the underlying biology of inflammatory bowel diseases.

MICROBIOME (2022)

Add to Collection
Review Biochemistry & Molecular Biology

Interpretable machine learning methods for predictions in systems biology from omics data

David Sidak et al.

Summary: Machine learning has become a powerful tool in systems biology, allowing for tasks such as cancer diagnosis, kinetic model optimization, and cell state or growth dynamics prediction. This paper aims to familiarize systems biologists with the concept of model interpretability in machine learning, and discusses relevant topics such as data sets, data preparation, machine learning methods, and software tools in omics research.

FRONTIERS IN MOLECULAR BIOSCIENCES (2022)

Add to Collection
Article Gastroenterology & Hepatology

Transcription and DNA Methylation Patterns of Blood-Derived CD8+ T Cells Are Associated With Age and Inflammatory Bowel Disease But Do Not Predict Prognosis

Marco Gasparetto et al.

Summary: The study aimed to validate the correlation between CD8(+) T-cell gene expression and disease outcome in IBD patients, but failed to reproduce the previously reported findings. It highlights the challenges of developing prognostic biomarkers for IBD patients and stresses the importance of validation in large, independent cohorts before clinical application.

GASTROENTEROLOGY (2021)

Add to Collection
Editorial Material Gastroenterology & Hepatology

Validation of Predictive Models in Inflammatory Bowel Diseases

Richard Kellermayer et al.

GASTROENTEROLOGY (2021)

Add to Collection
Article Gastroenterology & Hepatology

Understanding the Molecular Drivers of Disease Heterogeneity in Crohn's Disease Using Multi-omic Data Integration and Network Analysis

Padhmanand Sudhakar et al.

Summary: This study investigated the contribution of CD susceptibility variants and gene expression in different immune cell subsets to CD heterogeneity, revealing potential molecular features driving the diversity of clinical traits. Identification of contextual hub proteins offers the possibility for more individualized treatment approaches for specific subtypes of CD patients based on underlying biology.

INFLAMMATORY BOWEL DISEASES (2021)

Add to Collection
Review Immunology

Trained Immunity: Reprogramming Innate Immunity in Health and Disease

Siroon Bekkering et al.

Summary: Trained immunity is a newly recognized phenomenon where cells of the innate immune system exhibit memory characteristics and enhanced responses upon secondary challenge. It explains the heterologous effects of vaccines, but can also lead to maladaptive effects in chronic inflammatory conditions.

ANNUAL REVIEW OF IMMUNOLOGY, VOL 39 (2021)

Add to Collection
Review Biochemistry & Molecular Biology

Hallmarks of environmental insults

Annette Peters et al.

Summary: Environmental insults such as contaminated air, water, and food expose human beings to a plethora of chemicals and stressors, impacting health at all stages of life. The proposed eight hallmarks of environmental insults encompass oxidative stress, genomic alterations, epigenetic changes, and disruptions to various bodily functions, offering insight into the severe health effects induced by complex mixtures of environmental exposures.

CELL (2021)

Add to Collection
Article Gastroenterology & Hepatology

Tissue Proteomic Approaches to Understand the Pathogenesis of Inflammatory Bowel Disease

Montserrat Baldan-Martin et al.

Summary: Inflammatory bowel disease is a global disease with challenges in understanding its complex pathogenesis and progression, leading to limited progress in diagnosis and treatment. Future studies are needed to comprehensively characterize the disease biology for early detection and monitoring of clinical outcomes.

INFLAMMATORY BOWEL DISEASES (2021)

Add to Collection
Review Obstetrics & Gynecology

Multi 'omic data integration: A review of concepts, considerations, and approaches

Tasha M. Santiago-Rodriguez et al.

Summary: The application of various 'omic techniques on a single sample can generate multiple datasets to identify biological, molecular, and ecological functions, as well as associations. However, numerous challenges must be addressed in the successful design and execution of a multi-omics study, including considerations for sample collection, processing, data storage, and analysis. Case studies provide examples of how multi-omic approaches can offer novel insights and a more holistic understanding of biological processes.

SEMINARS IN PERINATOLOGY (2021)

Add to Collection
Article Multidisciplinary Sciences

Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease

Shixian Hu et al.

Summary: The study investigated intestinal biopsies from 171 IBD patients and identified inflammation-dependent intestinal cis-eQTLs that mainly interact with prevalence of immune cell types. This genetic susceptibility under inflammatory conditions may guide future drug development and precision medicine in IBD patients.

NATURE COMMUNICATIONS (2021)

Add to Collection
Correction Biochemistry & Molecular Biology

Hallmarks of health (vol 184, pg 33, 2021)

Carlos Lopez-Otin et al.

CELL (2021)

Add to Collection
Article Gastroenterology & Hepatology

Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome

Laura A. Bolte et al.

Summary: The study revealed correlations between dietary patterns and microbial clusters, as well as associations between individual foods and nutrients with bacterial species and metabolic pathways. Processed and animal-derived foods were linked to certain bacteria and endotoxin synthesis pathways, while plant foods and fish were associated with different bacteria and pathways related to nutrient metabolism. These findings provide insights into how diet affects gut inflammation and suggest directions for future intervention studies.

GUT (2021)

Add to Collection
Review Genetics & Heredity

Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease

John P. Thomas et al.

Summary: Inflammatory bowel disease is a complex immune-mediated condition with unclear pathogenesis, leading to suboptimal clinical outcomes for patients. Researchers are increasingly using network biology to better understand the disease from multi-omics datasets, but translating these findings into clinically relevant endpoints remains challenging. Incorporating other data sources and developing more robust network integration and analysis frameworks could help achieve the goal of precision medicine in IBD.

FRONTIERS IN GENETICS (2021)

Add to Collection
Article Gastroenterology & Hepatology

Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD-Prediction and Prevention of Inflammatory Bowel Disease

Joana Torres et al.

Summary: Inflammatory bowel disease is a complex chronic disorder with no known cure, causing substantial burden to patients. New strategies for preventing the global increase of IBD are urgently needed. Data on the preclinical period preceding disease diagnosis may hold the key to disease triggers and early intervention, potentially leading to improved understanding, prediction and prevention of the disease.

JOURNAL OF CROHNS & COLITIS (2021)

Add to Collection
Article Gastroenterology & Hepatology

Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD-What, Why, and How

Claudio Fiocchi et al.

Summary: Many common diseases in modern humans are complex diseases that require precision medicine for personalized treatment. Precision medicine plays a vital role in the field of inflammatory bowel disease, contributing to prediction, prevention, prognosis, and treatment.

JOURNAL OF CROHNS & COLITIS (2021)

Add to Collection
Article Gastroenterology & Hepatology

Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD-Disease Outcome and Response to Therapy

Bram Verstockt et al.

Summary: The ECCO workshop aims to provide a state-of-the-art overview on prognostic and predictive markers in IBD, shed light on key questions in biomarker development, and discuss the potential for multi-omic data integration to make precision medicine a reality in IBD.

JOURNAL OF CROHNS & COLITIS (2021)

Add to Collection
Editorial Material Gastroenterology & Hepatology

Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD - Challenges and Future Directions

Robin J. Dart et al.

JOURNAL OF CROHNS & COLITIS (2021)

Add to Collection
Article Health Care Sciences & Services

Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma

Marianthi Logotheti et al.

Summary: Asthma is a multifactorial inflammatory disorder with diverse clinical manifestations. Microbiota dysbiosis may lead to chronic inflammation, including in conditions like asthma. By integrating microbiome analysis, there is potential for a better understanding of asthma complexity and improving treatment options.

JOURNAL OF PERSONALIZED MEDICINE (2021)

Add to Collection
Article Microbiology

Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease

Jonathan Wei Jie Lee et al.

Summary: The intestinal microbiome plays a key role in determining responses to biologic therapy in inflammatory bowel disease. Microbial profiles can help predict clinical therapeutic success and guide the selection of optimal treatments for patients.

CELL HOST & MICROBE (2021)

Add to Collection
Editorial Material Multidisciplinary Sciences

Personalized profiles for disease risk must capture all facets of health

Mark McCarthy et al.

NATURE (2021)

Add to Collection
Article Immunology

Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity

Susan N. Christo et al.

Summary: Tissue-resident memory T (T-RM) cells are non-recirculating cells distributed throughout the body, and their properties, durability, and malleability are influenced by the tissue in which they are generated. Unequal responsiveness to TGF beta plays a major role in driving diversity in T-RM cell function.

NATURE IMMUNOLOGY (2021)

Add to Collection
Review Urology & Nephrology

Multi-omics integration in the age of million single-cell data

Zhen Miao et al.

Summary: The explosion of single-cell technologies has highlighted the heterogeneity of cell types and their associations with sex, disease, and development. The integration of multimodal data into biological models presents a challenge, but has the potential to provide new insights into complex biological processes. Understanding the principles of data integration and visualization methods is crucial for achieving various biological goals.

NATURE REVIEWS NEPHROLOGY (2021)

Add to Collection
Review Gastroenterology & Hepatology

Protein Glycosylation as a Diagnostic and Prognostic Marker of Chronic Inflammatory Gastrointestinal and Liver Diseases

Xavier Verhelst et al.

GASTROENTEROLOGY (2020)

Add to Collection
Article Gastroenterology & Hepatology

Big data in IBD: big progress for clinical practice

Nasim Sadat Seyed Tabib et al.

GUT (2020)

Add to Collection
Article Biochemistry & Molecular Biology

Personal aging markers and ageotypes revealed by deep longitudinal profiling

Sara Ahadi et al.

NATURE MEDICINE (2020)

Add to Collection
Review Multidisciplinary Sciences

The exposome and health: Where chemistry meets biology

Roel Vermeulen et al.

SCIENCE (2020)

Add to Collection
Article Multidisciplinary Sciences

Impact of commonly used drugs on the composition and metabolic function of the gut microbiota

Arnau Vich Vila et al.

NATURE COMMUNICATIONS (2020)

Add to Collection
Review Gastroenterology & Hepatology

Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features

Mirazul Islam et al.

GASTROENTEROLOGY (2020)

Add to Collection
Article Gastroenterology & Hepatology

Multi--Omics Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse

Nienke Z. Borren et al.

INFLAMMATORY BOWEL DISEASES (2020)

Add to Collection
Article Gastroenterology & Hepatology

Identification of Environmental Risk Factors Associated With the Development of Inflammatory Bowel Disease

Kimberley W. J. van der Sloot et al.

JOURNAL OF CROHNS & COLITIS (2020)

Add to Collection
Review Gastroenterology & Hepatology

Single-cell genomics and spatial transcriptomics: Discovery of novel cell states and cellular interactions in liver physiology and disease biology

Antonio Saviano et al.

JOURNAL OF HEPATOLOGY (2020)

Add to Collection
Article Biochemistry & Molecular Biology

Single-cell atlas of colonic CD8+T cells in ulcerative colitis

Daniele Corridoni et al.

NATURE MEDICINE (2020)

Add to Collection
Review Immunology

Environmental pollutants and the immune response

Takafumi Suzuki et al.

NATURE IMMUNOLOGY (2020)

Add to Collection
Article Multidisciplinary Sciences

The impact of sex on gene expression across human tissues

Meritxell Oliva et al.

SCIENCE (2020)

Add to Collection
Review Biochemistry & Molecular Biology

A Customizable Analysis Flow in Integrative Multi-Omics

Samuel M. Lancaster et al.

BIOMOLECULES (2020)

Add to Collection
Correction Biochemistry & Molecular Biology

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome (vol 182, pg 1460, 2020)

Ruben A. T. Mars et al.

CELL (2020)

Add to Collection
Article Gastroenterology & Hepatology

Multi--Omics Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse

Nienke Z. Borren et al.

INFLAMMATORY BOWEL DISEASES (2020)

Add to Collection
Review Gastroenterology & Hepatology

You are what you eat: diet, health and the gut microbiota

Niv Zmora et al.

NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2019)

Add to Collection
Review Biochemical Research Methods

Multi-omics at single-cell resolution: comparison of experimental and data fusion approaches

Karolis Leonavicius et al.

CURRENT OPINION IN BIOTECHNOLOGY (2019)

Add to Collection
Article Multidisciplinary Sciences

Colonic epithelial cell diversity in health and inflammatory bowel disease

Kaushal Parikh et al.

NATURE (2019)

Add to Collection
Article Gastroenterology & Hepatology

Challenges in IBD Research: Precision Medicine

Lee A. Denson et al.

INFLAMMATORY BOWEL DISEASES (2019)

Add to Collection
Article Multidisciplinary Sciences

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

Jason Lloyd-Price et al.

NATURE (2019)

Add to Collection
Article Biochemistry & Molecular Biology

A longitudinal big data approach for precision health

Sophia Miryam Schussler-Fiorenza Rose et al.

NATURE MEDICINE (2019)

Add to Collection
Review Multidisciplinary Sciences

Advances in epigenetics link genetics to the environment and disease

Giacomo Cavalli et al.

NATURE (2019)

Add to Collection
Article Biochemistry & Molecular Biology

Single-Cell Analysis of Crohn's Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

Jerome C. Martin et al.

CELL (2019)

Add to Collection
Article Gastroenterology & Hepatology

The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1

Floris Imhann et al.

BMC GASTROENTEROLOGY (2019)

Add to Collection
Article Biochemical Research Methods

Best Practices for Preparing a Single Cell Suspension from Solid Tissues for Flow Cytometry

Andrew Reichard et al.

CYTOMETRY PART A (2019)

Add to Collection
Review Biochemistry & Molecular Biology

High-performance medicine: the convergence of human and artificial intelligence

Eric J. Topol

NATURE MEDICINE (2019)

Add to Collection
Article Multidisciplinary Sciences

Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics

Konstantin Carlberg et al.

SCIENTIFIC REPORTS (2019)

Add to Collection
Review Gastroenterology & Hepatology

Environmental triggers in IBD: a review of progress and evidence

Ashwin N. Ananthakrishnan et al.

NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2018)

Add to Collection
Article Respiratory System

Integration of multi-omics datasets enables molecular classification of COPD

Chuan-Xing Li et al.

EUROPEAN RESPIRATORY JOURNAL (2018)

Add to Collection
Article Gastroenterology & Hepatology

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome

Kate Joanne Howell et al.

GASTROENTEROLOGY (2018)

Add to Collection
Review Genetics & Heredity

Integrative omics for health and disease

Konrad J. Karczewski et al.

NATURE REVIEWS GENETICS (2018)

Add to Collection
Article Multidisciplinary Sciences

Metabolic control of T cell immune response through glycans in inflammatory bowel disease

Ana M. Dias et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

Add to Collection
Review Biochemistry & Molecular Biology

Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification

Bjoern Titz et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2018)

Add to Collection
Article Multidisciplinary Sciences

Extensive impact of non-antibiotic drugs on human gut bacteria

Lisa Maier et al.

NATURE (2018)

Add to Collection
Article Multidisciplinary Sciences

Environment dominates over host genetics in shaping human gut microbiota

Daphna Rothschild et al.

NATURE (2018)

Add to Collection
Article Gastroenterology & Hepatology

Multiomics Analyses to Deliver the Most Effective Treatment to Every Patient With Inflammatory Bowel Disease

Rinse K. Weersma et al.

GASTROENTEROLOGY (2018)

Add to Collection
Article Medicine, General & Internal

Inflammatory Bowel Disease: Complexity and Variability Need Integration

Claudio Fiocchi

FRONTIERS IN MEDICINE (2018)

Add to Collection
Article Gastroenterology & Hepatology

Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches

R. Balfour Sartor et al.

GASTROENTEROLOGY (2017)

Add to Collection
Article Oncology

Integration of multiple OMIC biomarkers: A precision medicine strategy for lung cancer

Ana I. Robles et al.

LUNG CANCER (2017)

Add to Collection
Article Multidisciplinary Sciences

A single-cell survey of the small intestinal epithelium

Adam L. Haber et al.

NATURE (2017)

Add to Collection
Article Gastroenterology & Hepatology

The IBD interactome: an integrated view of aetiology, pathogenesis and therapy

Heitor S. P. de Souza et al.

NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY (2017)

Add to Collection
Article Multidisciplinary Sciences

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

Alexandra-Chloe Villani et al.

SCIENCE (2017)

Add to Collection
Review Genetics & Heredity

Single-Cell Multiomics: Multiple Measurements from Single Cells

Iain C. Macaulay et al.

TRENDS IN GENETICS (2017)

Add to Collection
Article Genetics & Heredity

More Is Better: Recent Progress in Multi-Omics Data Integration Methods

Sijia Huang et al.

Frontiers in Genetics (2017)

Add to Collection
Review Biochemistry & Molecular Biology

High-Definition Medicine

Ali Torkamani et al.

CELL (2017)

Add to Collection
Review Biotechnology & Applied Microbiology

Multi-omics approaches to disease

Yehudit Hasin et al.

GENOME BIOLOGY (2017)

Add to Collection
Article Biochemistry & Molecular Biology

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity

Melanie Schirmer et al.

CELL (2016)

Add to Collection
Article Biochemistry & Molecular Biology

Personalized Immunomonitoring Uncovers Molecular Networks that Stratify Lupus Patients

Romain Banchereau et al.

CELL (2016)

Add to Collection
Article Gastroenterology & Hepatology

Novel CD8+T-Cell Subsets Demonstrating Plasticity in Patients with Inflammatory Bowel Disease

Michael R. Tom et al.

INFLAMMATORY BOWEL DISEASES (2016)

Add to Collection
Article Immunology

The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing

Asa K. Bjorklund et al.

NATURE IMMUNOLOGY (2016)

Add to Collection
Article Biochemical Research Methods

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

Daniel Marbach et al.

NATURE METHODS (2016)

Add to Collection
Review Neurosciences

Disentangling neural cell diversity using single-cell transcriptomics

Jean-Francois Poulin et al.

NATURE NEUROSCIENCE (2016)

Add to Collection
Review Biochemical Research Methods

Integrative methods for analyzing big data in precision medicine

Vladimir Gligorijevic et al.

PROTEOMICS (2016)

Add to Collection
Article Multidisciplinary Sciences

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease

Hiutung Chu et al.

SCIENCE (2016)

Add to Collection
Article Genetics & Heredity

Making sense of big data in health research: Towards an EU action plan

Charles Auffray et al.

GENOME MEDICINE (2016)

Add to Collection
Article Multidisciplinary Sciences

Endophenotype Network Models: Common Core of Complex Diseases

Susan Dina Ghiassian et al.

SCIENTIFIC REPORTS (2016)

Add to Collection
Review Genetics & Heredity

From big data analysis to personalized medicine for all: challenges and opportunities

Akram Alyass et al.

BMC MEDICAL GENOMICS (2015)

Add to Collection
Article Gastroenterology & Hepatology

Biomarkers of Inflammation in Inflammatory Bowel Disease

Bruce E. Sands

GASTROENTEROLOGY (2015)

Add to Collection
Article Genetics & Heredity

What Do You Mean, Epigenetic?

Carrie Deans et al.

GENETICS (2015)

Add to Collection
Article Gastroenterology & Hepatology

Lipidomic Profiling in Inflammatory Bowel Disease: Comparison Between Ulcerative Colitis and Crohn's Disease

Fenling Fan et al.

INFLAMMATORY BOWEL DISEASES (2015)

Add to Collection
Article Biochemistry & Molecular Biology

Quantitative variability of 342 plasma proteins in a human twin population

Yansheng Liu et al.

MOLECULAR SYSTEMS BIOLOGY (2015)

Add to Collection
Article Multidisciplinary Sciences

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Dominic Grun et al.

NATURE (2015)

Add to Collection
Editorial Material Biochemical Research Methods

Association, correlation and causation

Naomi Altman et al.

NATURE METHODS (2015)

Add to Collection
Article Gastroenterology & Hepatology

Immunopathogenesis of IBD: current state of the art

Heitor S. P. de Souza et al.

Nature Reviews Gastroenterology & Hepatology (2015)

Add to Collection
Review Biotechnology & Applied Microbiology

The Promise of Multi-Omics and Clinical Data Integration to Identify and Target Personalized Healthcare Approaches in Autism Spectrum Disorders

Roger Higdon et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2015)

Add to Collection
Article Biotechnology & Applied Microbiology

Computational Systems Biology of Psoriasis: Are We Ready for the Age of Omics and Systems Biomarkers?

Tuba Sevimoglu et al.

OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY (2015)

Add to Collection
Article Multidisciplinary Sciences

Identifying personal microbiomes using metagenomic codes

Eric A. Franzosa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Add to Collection
Article Genetics & Heredity

What Do You Mean, Epigenetic?

Carrie Deans et al.

GENETICS (2015)

Add to Collection
Editorial Material Gastroenterology & Hepatology

Western lifestyle: a 'master' manipulator of the intestinal microbiota?

Georgina L. Hold

GUT (2014)

Add to Collection
Review Immunology

Multi-omics analysis of inflammatory bowel disease

Hu Huang et al.

IMMUNOLOGY LETTERS (2014)

Add to Collection
Article Gastroenterology & Hepatology

High C-reactive protein in Crohn's disease patients predicts nonresponse to infliximab treatment

Fernando Magro et al.

JOURNAL OF CROHNS & COLITIS (2014)

Add to Collection
Review Biochemistry & Molecular Biology

iPOP Goes the World: Integrated Personalized Omics Profiling and the Road toward Improved Health Care

Jennifer Li-Pock-Than et al.

CHEMISTRY & BIOLOGY (2013)

Add to Collection
Editorial Material Biochemistry & Molecular Biology

Complex diseases require complex therapies - Science & Society series on drugs and science

Ravi Iyengar

EMBO REPORTS (2013)

Add to Collection
Review Gastroenterology & Hepatology

Beyond Gene Discovery in Inflammatory Bowel Disease: The Emerging Role of Epigenetics

Nicholas T. Ventham et al.

GASTROENTEROLOGY (2013)

Add to Collection
Review Biochemistry & Molecular Biology

Lifestyle and nutritional imbalances associated with Western diseases: causes and consequences of chronic systemic low-grade inflammation in an evolutionary context

Begona Ruiz-Nunez et al.

JOURNAL OF NUTRITIONAL BIOCHEMISTRY (2013)

Add to Collection
Article Multidisciplinary Sciences

Variation and genetic control of protein abundance in humans

Linfeng Wu et al.

NATURE (2013)

Add to Collection
Editorial Material Genetics & Heredity

The Cancer Genome Atlas Pan-Cancer analysis project

John N. Weinstein et al.

NATURE GENETICS (2013)

Add to Collection
Article Oncology

OPINION Reproducibility of research and preclinical validation: problems and solutions

Lajos Pusztai et al.

NATURE REVIEWS CLINICAL ONCOLOGY (2013)

Add to Collection
Article Biochemistry & Molecular Biology

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

Rui Chen et al.

CELL (2012)

Add to Collection
Article Gastroenterology & Hepatology

Genetics in Diagnosing and Managing Inflammatory Bowel Disease

Jacob L. McCauley et al.

GASTROENTEROLOGY CLINICS OF NORTH AMERICA (2012)

Add to Collection
Review Gastroenterology & Hepatology

Serological antibodies in inflammatory bowel disease: A systematic review

Lani Prideaux et al.

INFLAMMATORY BOWEL DISEASES (2012)

Add to Collection
Article Multidisciplinary Sciences

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease

Luke Jostins et al.

NATURE (2012)

Add to Collection
Article Multidisciplinary Sciences

Selective Loss of Chemokine Receptor Expression on Leukocytes after Cell Isolation

Juan C. Nieto et al.

PLOS ONE (2012)

Add to Collection
Review Multidisciplinary Sciences

Interactions Between the Microbiota and the Immune System

Lora V. Hooper et al.

SCIENCE (2012)

Add to Collection
Article Pathology

Immunotoxicity of Perfluorinated Compounds: Recent Developments

Jamie C. DeWitt et al.

TOXICOLOGIC PATHOLOGY (2012)

Add to Collection
Article Medicine, Research & Experimental

Gene expression profiling of CD8+ T cells predicts prognosis in patients with Crohn disease and ulcerative colitis

James C. Lee et al.

JOURNAL OF CLINICAL INVESTIGATION (2011)

Add to Collection
Article Biochemical Research Methods

mRNA-Seq whole-transcriptome analysis of a single cell

Fuchou Tang et al.

NATURE METHODS (2009)

Add to Collection
Article Medical Laboratory Technology

Proteomics for prediction and characterization of response to infliximab in Crohn's disease:: A pilot study

Marie-Alice Meuwis et al.

CLINICAL BIOCHEMISTRY (2008)

Add to Collection
Article Genetics & Heredity

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

Jeffrey C. Barrett et al.

NATURE GENETICS (2008)

Add to Collection
Article Pharmacology & Pharmacy

Biomarker discovery for inflammatory bowel disease, using proteomic serum profiling

Marie-Alice Meuwis et al.

BIOCHEMICAL PHARMACOLOGY (2007)

Add to Collection
Article Gastroenterology & Hepatology

Antibody blockade of CCL25/CCR9 ameliorates early but not late chronic murine ileitis

Jesus Rivera-Nieves et al.

GASTROENTEROLOGY (2006)

Add to Collection
Article Gastroenterology & Hepatology

Proinflammatory effects of TH2 cytokines in a murine model of chronic small intestinal inflammation

G Bamias et al.

GASTROENTEROLOGY (2005)

Add to Collection
Article Gastroenterology & Hepatology

Mutations in NOD2 are associated with fibrostenosing disease in patients with Crohn's disease

MT Abreu et al.

GASTROENTEROLOGY (2002)

Add to Collection
Article Multidisciplinary Sciences

Single-cell gene expression profiling

JM Levsky et al.

SCIENCE (2002)

Add to Collection
Article Gastroenterology & Hepatology

NOD2/CARD15 does not influence response to infliximab in Crohn's disease

S Vermeire et al.

GASTROENTEROLOGY (2002)

Add to Collection
Article Gastroenterology & Hepatology

Distinct inflammatory mechanisms mediate early versus late colitis in mice

DM Spencer et al.

GASTROENTEROLOGY (2002)

Add to Collection
Review Multidisciplinary Sciences

Glycosylation and the immune system

PM Rudd et al.

SCIENCE (2001)

Add to Collection
Webinars Posters Questions Hubs Funding Journals Papers Connect Collections Reviewers About Us FAQs Mobile App Privacy Policy Terms of Use
© Peeref 2019-2024. All rights reserved.