Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics
Sign Up to like & getrecommendations! Published in 2017 at "Analytical Chemistry"
DOI: 10.1021/acs.analchem.6b04719
Abstract: As mass spectrometry-based metabolomics becomes more widely used in biomedical research, it is important to revisit existing data analysis paradigms. Existing data preprocessing efforts have largely focused on methods which start by extracting features separately… read more here.
Keywords: differential analysis; mass spectrometry; analysis; based metabolomics ... See more keywords
All ion differential analysis refines the detection of terminal and internal diagnostic fragment ions for the characterization of biologics product-related variants and impurities by middle-down mass spectrometry.
Sign Up to like & getrecommendations! Published in 2019 at "Analytical chemistry"
DOI: 10.1021/acs.analchem.8b05886
Abstract: Characterization and monitoring of post-translational modifications (PTMs) are key analytical requirements during the development of biologics. Top and middle-down (MD) approaches aim at capturing a direct snapshot of all proteoforms with their combinatorial distribution. However,… read more here.
Keywords: methodology; differential analysis; analysis; variants impurities ... See more keywords
HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP
Sign Up to like & getrecommendations! Published in 2021 at "Nature Communications"
DOI: 10.1038/s41467-021-23749-x
Abstract: Recent genome-wide chromosome conformation capture assays such as Hi-C and HiChIP have vastly expanded the resolution and throughput with which we can study 3D genomic architecture and function. Here, we present HiC-DC+, a software tool… read more here.
Keywords: differential analysis; hichip; analysis; enables systematic ... See more keywords
Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis
Sign Up to like & getrecommendations! Published in 2018 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbw092
Abstract: Numerous statistical pipelines are now available for the differential analysis of gene expression measured with RNA-sequencing technology. Most of them are based on similar statistical frameworks after normalization, differing primarily in the choice of data… read more here.
Keywords: data sets; differential analysis; sets identification; key ingredients ... See more keywords
Accurate differential analysis of transcription factor activity from gene expression
Sign Up to like & getrecommendations! Published in 2019 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz398
Abstract: MOTIVATION Activity of transcriptional regulators are crucial in elucidating the mechanism of phenotypes. However regulatory activity hypotheses are difficult to experimentally test. Therefore we need accurate and reliable computational methods for regulator activity inference. There… read more here.
Keywords: differential analysis; analysis transcription; factor activity; transcription factor ... See more keywords
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers.
Sign Up to like & getrecommendations! Published in 2022 at "Nucleic acids research"
DOI: 10.1093/nar/gkac141
Abstract: Super enhancers (SEs) are broad enhancer domains usually containing multiple constituent enhancers that hold elevated activities in gene regulation. Disruption in one or more constituent enhancers causes aberrant SE activities that lead to gene dysregulation… read more here.
Keywords: internal dynamics; differential ses; functional interpretation; differential analysis ... See more keywords
An evaluation of RNA-seq differential analysis methods
Sign Up to like & getrecommendations! Published in 2022 at "PLoS ONE"
DOI: 10.1101/2022.02.09.479723
Abstract: RNA-seq is a high-throughput sequencing technology widely used for gene transcript discovery and quantification under different biological or biomedical conditions. A fundamental research question in most RNA-seq experiments is the identification of differentially expressed genes… read more here.
Keywords: seq differential; seq; analysis methods; rna seq ... See more keywords
Differential analysis of combinatorial protein complexes with CompleXChange
Sign Up to like & getrecommendations! Published in 2019 at "BMC Bioinformatics"
DOI: 10.1186/s12859-019-2852-z
Abstract: BackgroundAlthough a considerable number of proteins operate as multiprotein complexes and not on their own, organism-wide studies so far are only able to quantify individual proteins or protein-coding genes in a condition-specific manner for a… read more here.
Keywords: differential analysis; analysis; protein complexes; analysis combinatorial ... See more keywords
Differential Analysis of Hypertension-Associated Intestinal Microbiota
Sign Up to like & getrecommendations! Published in 2019 at "International Journal of Medical Sciences"
DOI: 10.7150/ijms.29322
Abstract: Hypertension is the main risk factor for cerebral stroke and death resulting from cerebral stroke. Current association studies on hypertension and intestinal microbiota focus on patients with hypertension (HTN); however, no investigations involving patients with… read more here.
Keywords: normal groups; differential analysis; intestinal microbiota; hypertension ... See more keywords