July 15, 2008
Pfizer Inks Global License to Genomatix Software and Databases
Ann Arbor, MI - July 15, 2008 - Genomatix Software, Inc. the US branch of Munich (Germany) based Genomatix Software GmbH, announced that it has reached an agreement with Pfizer Pharmaceuticals to provide Genomatix software and data content to Pfizer sites across the globe. The Genomatix tools licensed by Pfizer are designed to show how genes are regulated at a molecular level, and Pfizer scientists will use the software and data content to help understand the molecular basis of how their potential drug targets may be co-regulated with other important targets, producing potential desirable or unwanted side-effects.
"Adding Genomatix to Pfizer's existing genomics software capabilities was a natural choice." said Peter Grant, CEO of Genomatix Software, Inc. "Our broad set of capabilities are a good compliment to those that Pfizer already has in house. We are pleased to be a part of Pfizer's significant effort in molecular genomics. We believe our tools will provide a great value to their research effort, but the proof is always in the results. Now the fun really begins!" he concluded.
July 8, 2008
Deep Sequencing Study Reveals New Insights into Human Transcriptome
Joint project of the Max-Planck-Institute for Molecular Genetics and Genomatix takes the first step towards a new picture of the mammalian genome annotation
Munich, Germany - July 8, 2008 - In a collaborative project scientists from the Max-Planck-Institute for Molecular Genetics in Berlin (MPI MolGen), Germany and Genomatix with a business in Munich, Germany and Ann Arbor, MI, USA, applied next generation sequencing and analysis methods to generate an unprecedented view at the human transcriptome.
Deep sequencing of transcripts from two human cell lines revealed so far unrecognized complexity and variability of the human transcriptome. They found that 34% of the polyadenylated transcriptome mapped to previously non-annotated genomic regions. Obviously a large number of novel gene candidates are active in the cell lines under study.
In addition, a global survey of mRNA splicing events identified 94,241 splice junctions, of which 4,096 are novel, and showed that exon skipping is the most prevalent form of alternative splicing.
Details are presented in the Science report of Sultan et al.: "A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome", published online at Science Express (www.scienceexpress.org). Annotation and data visualization is publicly available at http://www.genomatix.de/MPI.html .
Dr. Marie-Laure Yaspo, Group Leader at the MPI MolGen and head scientist of the study states: "Deep sequencing allows for the first time to explore directly the complexity and dynamics of the human transcriptome with a reasonable effort. This will lead to a new picture of the mammalian genome annotation far beyond the current state of the art. We provide here global features of alternative splicing events in human cell lines. Such a comparison of within-cell and between-cell alternative splicing events, combined with the simultaneous analysis of gene expression has never been presented before. It becomes clear that the so far available methods only delivered a part of the transcriptional landscape of mammalian cells, especially if gene regulation analysis is considered."
Dr. Martin Seifert, Vice President Business Development and Consulting at Genomatix says: "The main biological impact is the observation of a new dimension in complexity and variability. Based on the method we could find a significant number of new transcriptional units and splice variants. Our analyses clearly show that transcription is a highly dynamic and variable process. We learned a lot by having access to such high quality data and co-developed necessary new analysis strategies with the MPI MolGen. Especially users of our brand new Genomatix Genome Analyzer will benefit from our experiences along the project, since they have access to all developed strategies."
For more information please contact:
Dr. Martin Seifert, seifert@genomatix.de
Genomatix Software GmbH
Bayerstr. 85a
80335 Munich
Germany
phone +49-89-599 766 0
fax +49-89-599 766 55
July 2, 2008
Next Generation Data Analysis for Next Generation Sequencing Data
Genomatix Genome Analyzer released
Munich, Germany and Ann Arbor, MI
- July 2, 2008 - Genomatix Software, a company with an outstanding track record in the analysis of genomic data generated by high throughput technologies, announced availability of the Genomatix Genome Analyzer today. The Genomatix Genome Analyzer (GGA) is the first integrated hardware/software solution for in-depth analysis of data generated by next generation sequencing (NGS) devices as provided by Illumina™, 454 Life Sciences™ (Roche), Applied Biosystems™ (SOLiD™) and Helicos™.
Terabytes of locally installed data integrated with Genomatix powerful analysis technology facilitate easy extraction of relevant biological knowledge from mammalian ChIP-seq and transcriptome studies.
A typical analysis of a ChIP-seq experiment with 10 million reads takes only 2 hours. Results contain all important information: clustered and classified enriched regions, transcription factor (TF) over-representation and TF associations. In addition, genome-wide correlations with genomic features as well as meta-analysis with genome-wide chromatin modification, methylation state, expression levels or any data derived by other NGS experiments can be added with a few mouse clicks. Identification of phylogenetically conserved functional elements add another dimension of analytic power.
Transcriptome studies result in normalized and quantified expression values and allow for immediate identification of new transcriptional units and splice variants, all integrated and visualized in today‘s most complete genome annotation ElDorado, which is built into the GGA.
The GGA is driven by an easy-to-use, integrated browser based interface. Alternatively all database structures, scripts and tools are open and accessible to the bio-informatics specialist for re-arrangement or integration of own procedures.
"I am really excited about the power and possibilities arriving with all this new technology!", says Klaus May, Chief Business Officer of Genomatix. "All this flood of data arriving from NGS now reinforce our developments over the last decade. We have a unique knowledge base which together with our leading technology lifts biological understanding to the next level. Further proof comes from a multitude of projects and a series of scientific publications to be out shortly. The GGA empowers the researcher beyond comparison. All you need, in one box on your desk." he concludes.
March 3, 2008
NIA uses Genomatix software in Stem Cell Research,
Suggests Novel Transcription Factors for "Stemness"
Linkage of Pluripotent Stem Cell-Associated Transcripts to Regulatory Gene Networks
Munich, Germany and Ann Arbor, MI
- March 3, 2008 - Genomatix Software with businesses in Munich, Germany and Ann Arbor, Michigan released today that the group of Kenneth R. Boheler at the National Institute on Aging, National Institutes of Health, Baltimore, Md published some remarkable work on embryonic stem (ES) cells.
In their work they first identified and validated ES cell predominant transcripts by SAGE and qRT-PCR methods. Then they employed extensive DNA promoter analysis based on the integrated Genomatix system in order to identify conserved cis-elements and putative trans-regulators. Framework analysis for promoter organization, as introduced by Genomatix, increased likeliness for functional significance of the candidate transcription factors.
Predictions were experimentally verified by Chromosomal Immunoprecipitation assays.
The study led to the novel identification of two transcription factors, B-Myb and Maz which are implicated either in the maintenance of the undifferentiated stem cell state or in early steps of differentiation.
The work was e-published ahead of print on Feb. 27, 2008 in
- Tarasov KV, Testa G, Tarasova YS, Kania G, Riordon DR, Volkova M, Anisimov SV, Wobus AM, Boheler KR
Linkage of Pluripotent Stem Cell- Associated Transcripts to Regulatory Gene Networks
Cells Tissues Organs, Pubmed ID: 18303244
Read the abstract at http://www.karger.com
Genomatix Software GmbH is a Systems Biology company focused on high quality annotation and the understanding of eukaryotic gene regulation.
Core competences at Genomatix are annotation driven microarray analysis, ChIP on chip, next generation sequencing data analysis, regulatory network/pathway mining and promoter analysis. Genomatix has published more than 170 peer reviewed scientific papers that have been cited in more than 4,000 papers.
February 26, 2008
Genomatix Integrates Genome-Wide Open Chromatin from Next Generation Sequencing.
Correlation studies confirm quality of Genomatix Promoter Annotations.
Munich, Germany and Ann Arbor, MI
- February 26, 2008 - Genomatix Software GmbH, a Systems Biology company focussed on high quality annotation and the understanding of gene regulation, has begun showcasing its abilities in the analysis of data generated by Next Generation Sequencing (NGS) technology.
In the January 2008 issue of Cell Allan P. Boyle et al published some remarkable work on "High-Resolution Mapping and Characterization of Open Chromatin across the Genome" where they identified DNase I hypersensitive sites from primary human CD4+ Cells. Those samples were sequenced using both the Illumina Solexa and Roche 454 NGS platforms.
Genomatix applied its NGS analysis pipeline to the Illumina Solexa data as deposited at the Gene Expression Omnibus and made the results publicly available.
Out of the roughly 15 million 20mer sequence tags, the Genomatix proprietary ultra fast mapping capability delivered over 11 million (75%) unique positions in less than two hours, allowing up to three point mutations and two insertions/deletions.
Effective noise filtering was performed by sequence tag clustering at different levels of stringency. Genome wide correlation studies show that the majority of open chromatin is located in intergenic and intronic regions.
Additionally a strong correlation is shown between open chromatin and the Genomatix promoter annotation. Distance correlations of sequence tags and transcriptional start sites give further experimental confirmation to the longstanding Genomatix definition of a proximal promoter, spanning from -500 base pairs from TSS to +100 base pairs downstream of TSS. The analyses show the frequent use of alternative promoters for alternative transcripts within the same gene locus, as postulated by Genomatix since its first genome wide promoter annotations in 2000.
Genomic localization of identified sequences in context with other genomic annotations like transcripts, promoters, TSS, microRNAs, etc. can be accessed by all Genomatix customers and subscribers to a no charge evaluation account to the ElDorado extended genome annotation database.
Dr. Martin Seifert, Vice President Business Development and Consulting at Genomatix says: "We are excited about the power and wealth of all the new data being delivered by NGS technology. We have everything in place to analyze all these data and integrate them into our ElDorado annotation database today... something we can do within hours of starting an analysis. The real value is realized by overlaying and correlating all this data that has been derived by different approaches, for example, the open chromatin data correlated with chromatinIP tags for several nuclear receptors, expression profiles, microRNAs and all the wealth of other information in our databases that give an excellent handle on localizing and elucidating the role of enhancers/repressors in intergenic regions."
Dr. Seifert continues: "Several in-house projects which we conducted for customers demonstrate the clear superiority of our rich data content, our proprietary approaches, and open and modular architecture. With the emergence of NGS, the outstanding value of our technology is now more evident than ever!"
Open chromatin results: http://www.genomatix.de/open_chromatin.html
Original data set: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM252783
January 31, 2008
Genomatix takes a lead in Next Generation Sequencing.
Powerful analysis services available today
Munich, Germany and Ann Arbor, MI
- January 31, 2008 - Genomatix is a company with a renowned track record in the analysis of genomic data generated by high throughput technologies. Genomatix algorithms include optimized fast mapping strategies and Genomatix already provides the most complete genome annotation in terms of transcriptome and promoters available in its ElDorado database surpassing alternative databases in this specific content by a factor of 2 to 4.
Pilot studies in collaboration with customers, successfully analyzing Next Generation Sequencing data (from 454 and Solexa) have firmly established that ElDorado brings a dramatic advantage to NGS data processing and interpretation, providing additional information about the transcriptome and its regulation. Result data can be visualized by ElDorado in the full genomic annotation context and a variety of correlation studies and further downstream analyses are possible using other established Genomatix services.
Genomatix announces today that services for NGS studies are available within our consulting model, effective immediately, including Digital Gene Expression (DGE) Studies as well as ChIP Sequencing (ChIPSeq) Assays. Inquiries are welcome.
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