Proteomics: technologies and their applications

B Aslam, M Basit, MA Nisar, M Khurshid… - Journal of …, 2016 - academic.oup.com
Proteomics involves the applications of technologies for the identification and quantification
of overall proteins present content of a cell, tissue or an organism. It supplements the other …

[HTML][HTML] A guide to conquer the biological network era using graph theory

M Koutrouli, E Karatzas, D Paez-Espino… - … in bioengineering and …, 2020 - frontiersin.org
Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …

[HTML][HTML] Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

D Dimitrov, D Türei, M Garrido-Rodriguez… - Nature …, 2022 - nature.com
The growing availability of single-cell data, especially transcriptomics, has sparked an
increased interest in the inference of cell-cell communication. Many computational tools …

WikiPathways: connecting communities

M Martens, A Ammar, A Riutta… - Nucleic acids …, 2021 - academic.oup.com
Abstract WikiPathways (https://www. wikipathways. org) is a biological pathway database
known for its collaborative nature and open science approaches. With the core idea of the …

Pathway enrichment analysis and visualization of omics data using g: Profiler, GSEA, Cytoscape and EnrichmentMap

J Reimand, R Isserlin, V Voisin, M Kucera… - Nature protocols, 2019 - nature.com
Pathway enrichment analysis helps researchers gain mechanistic insight into gene lists
generated from genome-scale (omics) experiments. This method identifies biological …

Association analysis identifies 65 new breast cancer risk loci

K Michailidou, S Lindström, J Dennis, J Beesley, S Hui… - Nature, 2017 - nature.com
Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as
BRCA1, and many common, mostly non-coding variants. However, much of the genetic …

Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci

FR Schumacher, AA Al Olama, SI Berndt, S Benlloch… - Nature …, 2018 - nature.com
Genome-wide association studies (GWAS) and fine-mapping efforts to date have identified
more than 100 prostate cancer (PrCa)-susceptibility loci. We meta-analyzed genotype data …

[HTML][HTML] iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

SX Ge, EW Son, R Yao - BMC bioinformatics, 2018 - Springer
Background RNA-seq is widely used for transcriptomic profiling, but the bioinformatics
analysis of resultant data can be time-consuming and challenging, especially for biologists …

[HTML][HTML] Genome-wide CRISPR screens in primary human T cells reveal key regulators of immune function

E Shifrut, J Carnevale, V Tobin, TL Roth, JM Woo… - Cell, 2018 - cell.com
Human T cells are central effectors of immunity and cancer immunotherapy. CRISPR-based
functional studies in T cells could prioritize novel targets for drug development and improve …

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data

I Rodchenkov, O Babur, A Luna, BA Aksoy… - Nucleic acids …, 2020 - academic.oup.com
Abstract Pathway Commons (https://www. pathwaycommons. org) is an integrated resource
of publicly available information about biological pathways including biochemical reactions …