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TranscriptomicsGenetic regulators of large-scale transcriptional signatures in cancer
Gene expression signatures encompassing dozens to hundreds of genes have been associated with many important parameters of cancer, but mechanisms of their control are largely unknown. Here we present a method based on genetic linkage that can prospectively identify functional regulators driving larg...
ORGANISM(S): Homo sapiens 
2006-03-09 | E-GEOD-4433 | biostudies-arrayexpress
MetabolomicsData processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

Systems biology is the study of complex living organisms, and as such, analysis on a systems-wide scale involves the collection of information-dense data sets that are representative of an entire phenotype. To uncover dynamic biological mechanisms, bioinformatics tools have become essential to fa...

2017-11-23 | MTBLS572 | MetaboLights
ProteomicsApplication of de novo sequencing to large-scale complex proteomics datasets
Dependent on concise, pre-defined protein sequence databases, traditional search algorithms perform poorly when analyzing mass spectra derived from wholly uncharacterized protein products. Conversely, de novo peptide sequencing algorithms can interpret mass spectra without relying on reference datab...
ORGANISM(S): Bos taurus (Bovine) Saccharomyces cerevisiae (Baker's yeast) 
2016-01-12 | PXD003317 | Pride
De novo peptide sequencing Ms/ms Large-scale computational analysis Yeast Bos Mass spectrometry Proteomics 
UnknownMetHoS: a platform for large-scale processing, storage and analysis of metabolomics data.
Not available
S-EPMC9270834 | biostudies-literature
Transcriptomics8-chip high-resolution aCGH experiment NA15510 vs. NA18505
We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome sequencing method to identify SVs 3 kb or larger that combines the rescue and capture of paired-ends of 3 kb fragments, massive 454 Sequencing, and a computational approach to map DNA reads onto a reference genom...
ORGANISM(S): Homo sapiens 
2007-09-28 | E-GEOD-9002 | biostudies-arrayexpress
MetabolomicsMetabolic phenotyping of urine from a dementia research cohort
To better understand the molecular mechanisms underpinning physiological variation in human populations, metabolic phenotyping approaches are increasingly being applied to studies involving hundreds and thousands of biofluid samples. Hyphenated ultra-performance liquid chromatography-mass spectromet...
2022-03-01 | MTBLS719 | MetaboLights
ProteomicsQuantitative Single-Cell Proteomics as a Tool to Characterize Cellular Hierarchies
Large-scale single-cell analyses are of fundamental importance in order to capture biological heterogeneity within complex cell systems, but have largely been limited to RNA-based technologies. Here we present a comprehensive benchmarked experimental and computational workflow, which establishes glo...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2022-10-21 | MSV000090570 | MassIVE
TranscriptomicsIdentification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis
This study provides a first large-scale cloning and characterization of Porphyra miRNAs and their predicted targets. These miRNAs belong to 224 conserved miRNA families and 7 are novel in Porphyra. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding...
ORGANISM(S): Pyropia yezoensis 
2010-06-04 | E-GEOD-20534 | biostudies-arrayexpress
UnknownMeasuring diversity in Hollywood through the large-scale computational analysis of film.
Not available
S-EPMC11573682 | biostudies-literature
UnknownA parallel computational framework for ultra-large-scale sequence clustering analysis.
Not available
S-EPMC6931356 | biostudies-literature
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