Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

C Manzoni, DA Kia, J Vandrovcova… - Briefings in …, 2018 - academic.oup.com
Advances in the technologies and informatics used to generate and process large biological
data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While …

Emerging trends and new developments in information science: A document co-citation analysis (2009–2016)

J Hou, X Yang, C Chen - Scientometrics, 2018 - Springer
Characterizing the structure of knowledge, the evolution of research topics, and the
emergence of topics has always been an important part of information science (IS). Our …

WebGestalt 2024: faster gene set analysis and new support for metabolomics and multi-omics

JM Elizarraras, Y Liao, Z Shi, Q Zhu… - Nucleic Acids …, 2024 - academic.oup.com
Enrichment analysis, crucial for interpreting genomic, transcriptomic, and proteomic data, is
expanding into metabolomics. Furthermore, there is a rising demand for integrated …

WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

Y Liao, J Wang, EJ Jaehnig, Z Shi… - Nucleic acids …, 2019 - academic.oup.com
WebGestalt is a popular tool for the interpretation of gene lists derived from large scale-
omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers …

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 …

Co-regulatory networks of human serum proteins link genetics to disease

V Emilsson, M Ilkov, JR Lamb, N Finkel… - Science, 2018 - science.org
Proteins circulating in the blood are critical for age-related disease processes; however, the
serum proteome has remained largely unexplored. To this end, 4137 proteins covering most …

m6A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways

HB Li, J Tong, S Zhu, PJ Batista, EE Duffy, J Zhao… - Nature, 2017 - nature.com
Abstract N 6-methyladenosine (m6A) is the most common and abundant messenger RNA
modification, modulated by 'writers','erasers' and 'readers' of this mark,. In vitro data have …

WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit

J Wang, S Vasaikar, Z Shi, M Greer… - Nucleic acids …, 2017 - academic.oup.com
Functional enrichment analysis has played a key role in the biological interpretation of high-
throughput omics data. As a long-standing and widely used web application for functional …

Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation

J Li, MK Jaiswal, JF Chien, A Kozlenkov, J Jung… - Nature …, 2023 - nature.com
A repeat expansion in the C9orf72 (C9) gene is the most common genetic cause of
amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Here we investigate …

The human phenotype ontology in 2017

S Köhler, NA Vasilevsky, M Engelstad… - Nucleic acids …, 2017 - academic.oup.com
Deep phenoty** has been defined as the precise and comprehensive analysis of
phenotypic abnormalities in which the individual components of the phenotype are observed …