A5088040720- Inflammatory Bowel Disease
- Bioinformatics and Genomic Networks
- Microscopic Colitis
- Machine Learning in Bioinformatics
- Helicobacter pylori-related gastroenterology studies
- Algorithms and Data Compression
- Genomics and Phylogenetic Studies
- IL-33, ST2, and ILC Pathways
- Colorectal Cancer Screening and Detection
- Advanced Proteomics Techniques and Applications
- Mycobacterium research and diagnosis
- Data Management and Algorithms
- Protein Structure and Dynamics
- Complex Network Analysis Techniques
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Advanced Image and Video Retrieval Techniques
- Gastrointestinal Bleeding Diagnosis and Treatment
- Computational Drug Discovery Methods
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Metabolic Engineering and Bioproduction
- Immunodeficiency and Autoimmune Disorders
- Genetic factors in colorectal cancer
- RNA and protein synthesis mechanisms
- COVID-19 Clinical Research Studies
Johnson & Johnson (United States)
2019-2024
Janssen (United States)
2014-2023
National Center for Biotechnology Information
2006-2015
Imperial College London
2015
University of California, Irvine
2015
National Institutes of Health
2006-2014
Center for Human Genetics
2014
Vanderbilt University
2014
University of Ottawa
2002-2007
Sophisticated methods for analysing complex networks promise to be of great benefit almost all scientific disciplines, yet they elude us. In this work, we make fundamental methodological advances rectify this. We discover that the interaction between a small number roles, played by nodes in network, can characterize network's structure and also provide clear real-world interpretation. Given insight, develop framework comparing networks, which outperforms existing ones. demonstrate its...
Objective IBD therapies and treatments are evolving to deeper levels of remission. Molecular measures disease may augment current endpoints including the potential for less invasive assessments. Design Transcriptome analysis on 712 endoscopically defined inflamed (Inf) 1778 non-inflamed (Non-Inf) intestinal biopsies (n=498 Crohn’s disease, n=421 UC 243 controls) in Mount Sinai Colitis Registry were used identify genes differentially expressed between Inf Non-Inf generate a molecular...
Background & AimsEndoscopic assessment of ulcerative colitis (UC) typically reports only the maximum severity observed. Computer vision methods may better quantify mucosal injury detail, which varies among patients.MethodsEndoscopic video from UNIFI clinical trial (A Study to Evaluate Safety and Efficacy Ustekinumab Induction Maintenance Therapy in Participants With Moderately Severely Active Ulcerative Colitis) comparing ustekinumab placebo for UC were processed a computer analysis that...
Abstract Motivation: Proteins underlay the functioning of a cell and wiring proteins in protein–protein interaction network (PIN) relates to their biological functions. with similar PIN (topology around them) have been shown This property has successfully exploited for predicting protein Topological similarity is also used guide alignment algorithms that find similarly wired between PINs different species; these similarities are transfer annotation across PINs, e.g. from model organisms...
SERPINE1/PAI-1 is elevated in the colon tissue of most difficult-to-treat patients with IBD and leads to worsening experimental colitis.
Histological disease activity in inflammatory bowel [IBD] is associated with clinical outcomes and an important endpoint drug development. We developed deep learning models for automating histological assessments IBD.
Genome-wide association studies (GWAS) have identified loci reproducibly associated with inflammatory bowel disease (IBD) and other immune-mediated diseases; however, the molecular mechanisms underlying most of genetic susceptibility remain undefined. Expressional quantitative trait (eQTL) disease-relevant tissue can be employed in order to elucidate genes pathways affected by disease-specific variance.In this study, we derived eQTLs for human whole blood intestine tissues anti-tumor...
The role of long noncoding RNAs (lncRNAs) in disease is incompletely understood, but their regulation inflammation increasingly appreciated. We addressed the extent lncRNA involvement inflammatory bowel (IBD) using biopsy-derived RNA-sequencing data from a large cohort deeply phenotyped patients with IBD. Weighted gene correlation network analysis revealed modules lncRNAs coexpressed protein-coding genes enriched for biological pathways, correlated epithelial and immune cell signatures, or...
BackgroundInflammatory bowel disease (IBD) is a complex with variable presentation, progression, and response to therapies. Current classification based on subjective clinical phenotypes. The peripheral blood immunophenome can reflect local inflammation, thus we measured 39 circulating immune cell types in large cohort of IBD control subjects performed immunotype:phenotype associations.MethodsWe fluorescence-activated sorting or CyTOF analysis from 728 Crohn's disease, 464 ulcerative...
Interaction networks, consisting of agents linked by their interactions, are ubiquitous across many disciplines modern science. Many methods analysis interaction networks have been proposed, mainly concentrating on node degree distribution or aiming to discover clusters that very strongly connected between themselves. These principally based graph-theory machine learning. We present a mathematically simple formalism for modelling context-specific information propagation in random walks. The...
Founded upon diffusion with damping, ITM Probe is an application for modeling information flow in protein interaction networks without prior restriction to the sub-network of interest. Given a context consisting desired origins and destinations information, returns set most relevant proteins weights graphical representation corresponding sub-network. With click, user may send resulting list enrichment analysis facilitate hypothesis formation or confirmation.ITM web service documentation can...
We suggest a variation of the Hellerstein – Koutsoupias Papadimitriou indexability model for datasets equipped with similarity measure, aim better understanding structure indexing schemes similarity-based search and geometry workloads. This in particular provides unified approach to great variety used index into metric spaces facilitates their transfer more general measures such as quasi-metrics. discuss links between performance high-dimensional geometry. The concepts results are...
We introduce a geometric framework suitable for studying the relationships among biological sequences. In contrast to previous works, our formulation allows asymmetric distances (quasi-metrics), originating from uneven weighting of strings, which may induce non-trivial partial orders on sets biosequences. The considered are more general than traditional generalized string edit distances. particular, enables conversion between sequence similarities, both local and global, Our constructions...
Abstract Motivation: Term-enrichment analysis facilitates biological interpretation by assigning to experimentally/computationally obtained data annotation associated with terms from controlled vocabularies. This process usually involves obtaining statistical significance for each vocabulary term and using the most significant describe a given set of entities, often weights. Many existing enrichment methods require selections (arbitrary number of) entities and/or do not account weights...
Abstract Immune dysregulation and cytokine release syndrome have emerged as pathological hallmarks of severe Coronavirus Disease 2019 (COVID-19), leading to the evaluation antagonists therapeutic agents. A number immune-directed therapies being considered for COVID-19 patients are already in clinical use chronic inflammatory conditions like bowel disease (IBD). These considerations led us systematically examine intersections between GI tract during health intestinal inflammation. We observed...
Abstract Previous studies have conducted time course characterization of murine colitis models through transcriptional profiling differential expression. We characterize the landscape acute and chronic dextran sodium sulfate (DSS) adoptive transfer (AT) to derive temporal gene expression splicing signatures in blood colonic tissue order capture dynamics remission relapse. identify sub networks patient-derived causal that are enriched these distinguish disease components within broader...
In our previous publication, a framework for information flow in interaction networks based on random walks with damping was formulated two fundamental modes: emitting and absorbing. While many other network analysis methods or equivalent notions have been developed before after earlier work, one can show that they all be mapped to of the modes. addition these modes, major strength formalism its accommodation context-specific directed yielded plausible meaningful biological interpretation...