An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics
RC Taylor - BMC bioinformatics, 2010 - Springer
Background Bioinformatics researchers are now confronted with analysis of ultra large-scale
data sets, a problem that will only increase at an alarming rate in coming years. Recent …
data sets, a problem that will only increase at an alarming rate in coming years. Recent …
A proteomics sample metadata representation for multiomics integration and big data analysis
C Dai, A Füllgrabe, J Pfeuffer, EM Solovyeva… - Nature …, 2021 - nature.com
The amount of public proteomics data is rapidly increasing but there is no standardized
format to describe the sample metadata and their relationship with the dataset files in a way …
format to describe the sample metadata and their relationship with the dataset files in a way …
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
Y Perez-Riverol, J Bai, C Bandla… - Nucleic acids …, 2022 - academic.oup.com
Abstract The PRoteomics IDEntifications (PRIDE) database (https://www. ebi. ac. uk/pride/) is
the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is …
the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is …
ArrayExpress update–from bulk to single-cell expression data
Abstract ArrayExpress (https://www. ebi. ac. uk/arrayexpress) is an archive of functional
genomics data from a variety of technologies assaying functional modalities of a genome …
genomics data from a variety of technologies assaying functional modalities of a genome …
ArrayExpress update—simplifying data submissions
N Kolesnikov, E Hastings, M Keays… - Nucleic acids …, 2015 - academic.oup.com
Abstract The ArrayExpress Archive of Functional Genomics Data (http://www. ebi. ac.
uk/arrayexpress) is an international functional genomics database at the European …
uk/arrayexpress) is an international functional genomics database at the European …
A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor
S Gadd, V Huff, AL Walz, AHAG Ooms, AE Armstrong… - Nature …, 2017 - nature.com
We performed genome-wide sequencing and analyzed mRNA and miRNA expression, DNA
copy number, and DNA methylation in 117 Wilms tumors, followed by targeted sequencing …
copy number, and DNA methylation in 117 Wilms tumors, followed by targeted sequencing …
The ontology for biomedical investigations
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with
precisely defined meanings to describe all aspects of how investigations in the biological …
precisely defined meanings to describe all aspects of how investigations in the biological …
Gateways to the FANTOM5 promoter level mammalian expression atlas
M Lizio, J Harshbarger, H Shimoji, J Severin… - Genome biology, 2015 - Springer
The FANTOM5 project investigates transcription initiation activities in more than 1,000
human and mouse primary cells, cell lines and tissues using CAGE. Based on manual …
human and mouse primary cells, cell lines and tissues using CAGE. Based on manual …
FANTOM5 CAGE profiles of human and mouse samples
S Noguchi, T Arakawa, S Fukuda, M Furuno… - Scientific data, 2017 - nature.com
In the FANTOM5 project, transcription initiation events across the human and mouse
genomes were mapped at a single base-pair resolution and their frequencies were …
genomes were mapped at a single base-pair resolution and their frequencies were …
Image Data Resource: a bioimage data integration and publication platform
E Williams, J Moore, SW Li, G Rustici, A Tarkowska… - Nature …, 2017 - nature.com
Access to primary research data is vital for the advancement of science. To extend the data
types supported by community repositories, we built a prototype Image Data Resource …
types supported by community repositories, we built a prototype Image Data Resource …