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Integromics is a global bioinformatics company headquartered in Granada, Spain, with a second office in Madrid and subsidiaries in the US and UK and distributors in 10 countries. Integromics S.L. provides bioinformatics software for data management and data analysis in genomics and proteomics. The company provides a line of products that serve the gene expression, sequencing and proteomics markets. Customers include genomic research centers, pharmaceutical companies, academic institutions, clinical research organizations and biotechnology companies. Wikipedia.

Ozsolak F.,Helicos BioSciences | Kapranov P.,Helicos BioSciences | Foissac S.,Integromics | Kim S.W.,University of Pittsburgh | And 4 more authors.
Cell | Year: 2010

The emerging discoveries on the link between polyadenylation and disease states underline the need to fully characterize genome-wide polyadenylation states. Here, we report comprehensive maps of global polyadenylation events in human and yeast generated using refinements to the Direct RNA Sequencing technology. This direct approach provides a quantitative view of genome-wide polyadenylation states in a strand-specific manner and requires only attomole RNA quantities. The polyadenylation profiles revealed an abundance of unannotated polyadenylation sites, alternative polyadenylation patterns, and regulatory element-associated poly(A)+ RNAs. We observed differences in sequence composition surrounding canonical and noncanonical human polyadenylation sites, suggesting novel noncoding RNA-specific polyadenylation mechanisms in humans. Furthermore, we observed the correlation level between sense and antisense transcripts to depend on gene expression levels, supporting the view that overlapping transcription from opposite strands may play a regulatory role. Our data provide a comprehensive view of the polyadenylation state and overlapping transcription. © 2010 Elsevier Inc.

Kapranov P.,Helicos BioSciences | Ozsolak F.,Helicos BioSciences | Kim S.W.,University of Pittsburgh | Foissac S.,Integromics | And 8 more authors.
Nature | Year: 2010

Small (<200 nucleotide) RNA (sRNA) profiling of human cells using various technologies demonstrates unexpected complexity of sRNAs with hundreds of thousands of sRNA species present. Genetic and in vitro studies show that these RNAs are not merely degradation products of longer transcripts but could indeed have a function. Furthermore, profiling of RNAs, including the sRNAs, can reveal not only novel transcripts, but also make clear predictions about the existence and properties of novel biochemical pathways operating in a cell. For example, sRNA profiling in human cells indicated the existence of an unknown capping mechanism operating on cleaved RNA, a biochemical component of which was later identified. Here we show that human cells contain a novel type of sRNA that has non-genomically encoded 5ĝ€2 poly(U) tails. The presence of these RNAs at the termini of genes, specifically at the very 3ĝ€2 ends of known mRNAs, strongly argues for the presence of a yet uncharacterized endogenous biochemical pathway in cells that can copy RNA. We show that this pathway can operate on multiple genes, with specific enrichment towards transcript-encoding components of the translational machinery. Finally, we show that genes are also flanked by sense, 3ĝ€2 polyadenylated sRNAs that are likely to be capped. © 2010 Macmillan Publishers Limited. All rights reserved.

Gonzalez-Couto E.,Integromics
Briefings in Functional Genomics | Year: 2011

Huntington's disease (HD) is a hereditary, progressively degenerative and fatal brain disorder classified as a rare, or 'orphan', disease. HD is caused by the extension of trinucleotide repeats encoding a stretch of glutamine residues at the amino-terminal end of the large huntingtin (HTT) protein. Since the discovery of the mutated HTT gene in 1993, the mechanisms by which the mutant HTT protein induces neurodegeneration remain poorly understood and no disease-modifying therapy is currently available. Several functional approaches combining different experimental models and experimental technologies have been used to shed some light on the mechanisms underlying this disease. This review presents these functional approaches, highlights their potential and limitations. © The Author 2011. Published by Oxford University Press. All rights reserved.

Integromics | Date: 2012-07-24

Computer software database application for use in data management and integration to collect, analyze, and annotate experimental data in fields of genomics, proteomics and drug discovery.

Integromics | Date: 2012-07-24

Computer software database application for use in data management and integration to collect, analyze, and annotate experimental data in fields of genomics, proteomics and drug discovery.

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