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Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease

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TLDR
This work defines how the colonic mesenchyme remodels to fuel inflammation and barrier dysfunction in IBD.
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This article is published in Cell.The article was published on 2018-10-04 and is currently open access. It has received 380 citations till now. The article focuses on the topics: Mesenchyme & Population.

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Fibrosis: from mechanisms to medicines

TL;DR: The transformative experimental strategies that are being leveraged to dissect the key cellular and molecular mechanisms that regulate fibrosis, and the translational approaches that are enabling the emergence of precision medicine-based therapies for patients with fibrosis are discussed.
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Diversity and Biology of Cancer-Associated Fibroblasts.

TL;DR: The body of work on CAFs is summarized, with a particular focus on the most recent discoveries about fibroblast heterogeneity, plasticity and functions, and the commonalities of fibroblasts present across different cancer types, and in normal and inflammatory states are highlighted.
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Cytokine Networks in the Pathophysiology of Inflammatory Bowel Disease.

TL;DR: The progression of IBD from the perspective of remodeling of cytokine networks is discussed, placing well-established and under-studied cytokine modules in the context of cellular interactions, their dynamic regulation in late stages of disease and their current and potential use in the clinic.
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Pathway paradigms revealed from the genetics of inflammatory bowel disease.

TL;DR: IBD is described as a model disease in the context of leveraging human genetics to dissect interactions in cellular and molecular pathways that regulate homeostasis of the mucosal immune system and future prospects for disease-subtype classification and therapeutic intervention are discussed.
References
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Journal ArticleDOI

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

TL;DR: An R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters and can be easily extended to other species and ontologies is presented.

Classification and Regression by randomForest

TL;DR: random forests are proposed, which add an additional layer of randomness to bagging and are robust against overfitting, and the randomForest package provides an R interface to the Fortran programs by Breiman and Cutler.
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WGCNA: an R package for weighted correlation network analysis.

TL;DR: The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software.
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featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features

TL;DR: FeatureCounts as discussed by the authors is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments, which implements highly efficient chromosome hashing and feature blocking techniques.
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HISAT: a fast spliced aligner with low memory requirements

TL;DR: Tests showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method, and requires only 4.3 gigabytes of memory.
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