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.
Agency: European Commission | Branch: FP7 | Program: CSA-CA | Phase: HEALTH.2010.2.1.1-2 | Award Amount: 2.20M | Year: 2011
Over the last few years the field of proteomics has evolved into a prolific data producer. As a result, various databases that collect and redistribute the acquired data have been established. While data format standards for quantitative proteomics have now been defined and implemented with significant contribution from the recently completed EU ProDaC grant, standards for quantitative proteomics are still lacking. This simultaneous creation of multiple repositories and databases, and lack of standards for quantitative proteomics result in a fragmentation of data, and cause confusion for data submitters and users alike. Based on consortium expertise in the operation of large scale proteomics repositories (PRIDE, PeptideAtlas, Tranche, Peptidome) we aim to implement the next step, regular data exchange between major international proteomics resources. In parallel, we will further develop standards (mzQuantML) for the dynamic field of quantitative mass spectrometry. The main objectives of ProteomExchange are user-oriented: (i) to provide a single point of data submission to the user; (ii) to ensure data availability in all of the different member databases; (iii) to use community standard formats to represent the data, so it becomes accessible to all regardless of data origin; (iv) to provide added value through different views on the same data, from repositories to derived search tools. With an international consortium and support from large scale data producers (ISAS (Germany), U. Cambridge (UK), Karolinska Institute (Sweden)), industry (Pfizer, Philips, Waters), and journals (Nature Biotechnology, MCP, JPR), we here propose a Coordination Action project to solidify an emerging informal collaboration between major repositories into a production-quality data deposition and dissemination consortium on par with the systems so successfully employed by three-dimensional structure databases and nucleotide sequence databases, amongst others.
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: HEALTH-2007-2.1.1-6 | Award Amount: 16.02M | Year: 2008
Lipids are central to the regulation and control of cellular processes by acting as basic building units for biomembranes, the platforms for the vast majority of cellular functions. Recent developments in lipid mass spectrometry have set the scene for a completely new way to understand the composition of membranes, cells and tissues in space and time by allowing the precise identification and quantification of alterations of the total lipid profile after specific perturbations. In combination with advanced proteome and transcriptome analysis tools and novel imaging techniques using RNA interference, it is now possible to unravel the complex network between lipids, genes and proteins in an integrated lipidomics approach. This project application of the European Lipidomics Initiative (ELife; www.lipidomics.net) will address lipid droplets (LD) as dynamic organelles with regard to composition, metabolism and regulation. LD are the hallmark of energy overload diseases with a major health care impact in Europe. The project will exploit recent advances in lipidomics to establish high-throughput methods to define drugable targets and novel biomarkers related to LD lipid and protein species, their interaction and regulation during assembly, disassembly and storage. Translational research from mouse to man applied to LD pathology is a cornerstone of this project at the interface between research and development. To maximize the value of the assembled data generated throughout the project, LipidomicNet as a detailed special purpose Wiki formate data base will be developed and integrated into the existing Lipidomics Expertise Platform (LEP) established through the SSA ELife project (www.lipidomics-expertise.de). ELife collaborates with the NIH initiative LIPID MAPS (www.lipidmaps.org) and the Japanese pendant Lipidbank (www.lipidbank.jp) and is connected to the Danubian Biobank consortium (SSA DanuBiobank, www.danubianbiobank.de) for clinical lipidomics.
Agency: European Commission | Branch: FP7 | Program: MC-IAPP | Phase: FP7-PEOPLE-2012-IAPP | Award Amount: 2.62M | Year: 2013
Large scale genomics projects exploiting high throughput leading technology have produced and continue to produce massive data sets with exponential growing rates. So far, only a small part of this data can be abstracted, managed and processed, giving an incomplete understanding of the biological process being observed. The lack of processing power is a bottle neck in acquiring results. Comparative genomics is a good example since it includes all the ingredients: huge and ever growing datasets, complex applications that demands large computational resources and new mathematical and statistical models for analysing and synthetizing genomic information. A promising approach to address such massive data sets is the creation of new computer software that makes effective use of parallel processing. This proposal pursues the linking of different research domains to come up with a coordinated multi-disciplinary approach in the development of tools targeting Big-Data and computationally intensive scientific applications. Generic solutions for Big-Data storage, management, distribution, processing and final analysis will be developed. These solutions will target a broad range of scientific applications, in concrete, as proof-of-concept they will be implemented in the Comparative Genomics field of bioinformatics and biomedical domains. Applications such as the detection of main evolutionary events, new comparative genomics models that can be evaluated experimentally, for inter-species evolutionary distance, the composition of the k-mers dictionaries for each specie, or customising symbolic computing methods to determine the consensus tree from a sequence of trees with application in multiple sequence alignments, phylogenetic studies, clustering algorithms, etc. present in diverse fields of bioinformatics, from NGS-DNA assembly to gene-expression, all of them well suited applications to apply HPC-CC approaches and with high and attractive potential for commercialization.
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: HEALTH-2007-2.2.2-2 | Award Amount: 14.17M | Year: 2008
RESOLVE has been outlined to better understand the regulatory networks that control the devel-opmental processes in organ repair and to identify mechanisms which cause the termination of regu-lar organ development leading to fibroproliferative wound healing. Fibroproliferative wound healing represents a major pathology in elderly people shifting regular organ development into progressive organ fibrosis with complete loss of organ function. Based on the identification of valuated molecu-lar targets of fibroproliferative repair, RESOLVE aims to create suitable treatment strategies to achieve healthy ageing in the elderly. In doing so, RESOLVE will create a significant impact on life quality of elderly people. RESOLVEs outcomes will strengthen the competitiveness of European science and biotechnology industry and contribute to cost saving strategies in the health care sector. RESOLVEs structured scientific approach combines as yet fragmented fields of research using model organisms which represent (a) different forms of wound healing, (b) different human diseases and (c) different genetic backgrounds, guaranteeing social and scientific relevance, modularity of re-search and the integration of existing biological knowledge, technical expertise and medical experi-ence. In addition, sequential generation of data during improvement or worsening ensures clinical relevance and leads to a stringent exploitation strategy. The sustainable outcomes of RESOLVEs efforts will be: (A) the urgently needed diagnostic tool for fibroproliferative wound healing in various organs, (B) highly valuable transgenic animals offering test systems for fibroproliferative wound healing, and (C) a characterization of compounds capable of interfering with targets involved in fibroprolifera-tive repair.
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.
Agency: European Commission | Branch: FP7 | Program: CP-TP | Phase: HEALTH-2007-1.1-4 | Award Amount: 3.95M | Year: 2008
The PROACTIVE consortium will through research and innovation develop the multiplexed proximity ligation assay into a high throughput protein detection and quantification technology along with novel data management and analysis tools. Hundreds of putative biomarkers of the plasma proteome can then be assayed with high sensitivity in minute sample volumes, far surpassing any current capabilities. This consortium combines three SMEs across Europe with synergistic competences in technology development, reagent manufacturing, and software development for data management and analysis. Together with clinical cancer scientists, biostatisticians, and diagnostics industry, these high capacity tools will be evaluated in pilot projects for cancer biomarkers using biobanked samples. Preliminary data in the literature claim improved diagnostics with the use of multiple complementary protein markers. However, there is a lack of suitable high throughput procedures for finding new markers and discovering which markers complement each other into effective diagnostic panels. Better capabilities to diagnose cancer at the early and most curable stages will greatly improve human health and reduce health care costs. Patient stratification is also in need of better diagnostics to facilitate the selection of appropriate patient care. Many clinically used immunoassays capable of diagnosing cancer have been in use for many years as single markers but with limited sensitivity and specificity. No marker can today single-handedly diagnose all cases with desired accuracy for a certain cancer type. Also, the performance of these markers is decreased for the earliest stages of the disease. At the conclusion of this collaborative project, the research and innovation conducted within the consortium will enable the partners to position themselves at the very fore-front of high-throughput biomarker research strengthening their competitiveness in the international arena.
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.
Integromics | Date: 2012-11-13
Computer software for use in data management, integration, data analysis and data mining in the field of genomics, proteomics and drug discovery.