Comprehensive investigation of pathway enrichment methods for functional interpretation of LC–MS global metabolomics data

Y Lu, Z Pang, J Xia - Briefings in Bioinformatics, 2023 - academic.oup.com
Background: Global or untargeted metabolomics is widely used to comprehensively
investigate metabolic profiles under various pathophysiological conditions such as …

Identifying significantly impacted pathways: a comprehensive review and assessment

TM Nguyen, A Shafi, T Nguyen, S Draghici - Genome biology, 2019 - Springer
Background Many high-throughput experiments compare two phenotypes such as disease
vs. healthy, with the goal of understanding the underlying biological phenomena …

DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)

BT Sherman, M Hao, J Qiu, X Jiao… - Nucleic acids …, 2022 - academic.oup.com
DAVID is a popular bioinformatics resource system including a web server and web service
for functional annotation and enrichment analyses of gene lists. It consists of a …

DIANA-miRPath v3. 0: deciphering microRNA function with experimental support

IS Vlachos, K Zagganas… - Nucleic acids …, 2015 - academic.oup.com
The functional characterization of miRNAs is still an open challenge. Here, we present
DIANA-miRPath v3. 0 (http://www. microrna. gr/miRPathv3) an online software suite …

Correlated gene expression supports synchronous activity in brain networks

J Richiardi, A Altmann, AC Milazzo, C Chang… - Science, 2015 - science.org
During rest, brain activity is synchronized between different regions widely distributed
throughout the brain, forming functional networks. However, the molecular mechanisms …

Phylogenomic analyses provide insights into primate evolution

Y Shao, L Zhou, F Li, L Zhao, BL Zhang, F Shao… - Science, 2023 - science.org
Comparative analysis of primate genomes within a phylogenetic context is essential for
understanding the evolution of human genetic architecture and primate diversity. We present …

An anatomically comprehensive atlas of the adult human brain transcriptome

MJ Hawrylycz, ES Lein, AL Guillozet-Bongaarts… - Nature, 2012 - nature.com
Neuroanatomically precise, genome-wide maps of transcript distributions are critical
resources to complement genomic sequence data and to correlate functional and genetic …

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; …

P Cingolani, A Platts, LL Wang, M Coon, T Nguyen… - fly, 2012 - Taylor & Francis
We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants
in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on …

clusterProfiler: an R package for comparing biological themes among gene clusters

G Yu, LG Wang, Y Han, QY He - Omics: a journal of integrative …, 2012 - liebertpub.com
Increasing quantitative data generated from transcriptomics and proteomics require
integrative strategies for analysis. Here, we present an R package, clusterProfiler that …

Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons

ST Schafer, ACM Paquola, S Stern, D Gosselin… - Nature …, 2019 - nature.com
Autism spectrum disorder (ASD) is thought to emerge during early cortical development.
However, the exact developmental stages and associated molecular networks that prime …