Bio Saga Blog - A Chronicle of Life Sciences & Informatics

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A new paper written by researchers from the Institute for Systems Biology describes a computational approach for studying regulatory activities in cells that relies on integrated networks of transcriptional and metabolic data. The study, published in PLOS Computational Biology earlier this month, describes software called the Gene Expression and Metabolism Integrated for Network Inference (GEMINI) which uses an integrated model of network and metabolic data to explore growth phenotypes in Saccharomyces cerevisiae . GEMINI builds on work from the same researchers published in 2010 in the Proceedings of the National Academy of Sciences . That paper describes the Probabilistic Regulation of Metabolism (PROM), which provides a mechanism for integrating transcriptional regulatory networks and metabolic networks in a single in silico model and using it to make predictions about phenotypes such as flux and growth rate. While based on PROM, GEMINI is designed to tackle a slightly dif...

Applications are invited for the post of Post Doctoral Fellow for the following time-bound sponsored project as per the details given below: Post :  Post Doctoral Fellow Consolidated fellowship :  As per terms governed by the Wellcome trust DBT India Alliance and National Institute of Immunology (a Minimum of Rs. 40,000/- per month).  Project title :  Exploring the role of a developmental regulator in inflammatory immune response under Wellcome Trust DBT India Alliance Essential Qualification :  a. Must hold a Ph.D Degree (not awarded before 2009), or must already have submitted their thesis towards obtaining a Ph.D degree from a reputed Institute. b. Must have more than Five years of research Experience. c.  Must have proven research expertise/skills in basic biochemistry, cell biology and Molecular Biology, Research Expertise in in vivo animal work is also preferred. d. Must have one publication as first author, in international journal, preferab...

DATES: April 22-24, 2012 LOCALE: Nashville, TN URL:   http://bioinfo.mc.vanderbilt. edu/icibm/index.html Bioinformatics, Systems Biology and Intelligent Computing are synergistic disciplines that hold great promise for the advancement of biomedical research and development through the design of intelligent systems to solve engineering practical problems as well as translational science problems. Research and development in these areas impact science and technology, and synergies among these disciplines provide enormous potential. The International Conference on Intelligent Biology and Medicine (ICIBM) aims to provide a forum for the cross- fertilization of ideas and promotion of interdisciplinary collaborations.

3rd INTERNATIONAL CONFERENCE on BIOINFORMATICS AND SYSTEMS BIOLOGY (INCOBS-2012) 16th -18th February, 2012 ANNOUNCEMENT & CALL FOR PAPER Organised by DEPARTMENT OF ZOOLOGY (DDE) Annamalai University Annmalainagar-608002 Tamilnadu, India Do you wish to know more?

Greetings from Department of Bioinformatics, Alagappa University It gives us immense pleasure to announce that the Department of Bioinformatics, Alagappa University, Karaikudi is organizing 4th National Symposium cum Workshop on “Recent Trends in Structural Bioinformatics and Computer Aided Drug Design [SBCADD’2012]” during Feb 20th – 23rd, 2012. The motive of the National symposium cum workshop is to provide theoretical and practical exposure of Structural Bioinformatics and Computer Aided Drug Design among academicians and technocrats in order to cater the industrial and academic need. We have invited eminent personalities from reputed organizations, who will enlighten the participants in the related fields. Please download the brochure containing information and registration details along with this invitation for your kind perusal. We extend humble invitation to you and your colleagues to participate actively in the workshop and make it a big success. It will be appreciated if you c...

The genome – sequencing and structural genomics efforts worldwide have contributed to huge data on protein sequences and novel protein folds. However, there still remains a wide gap between the number of known protein sequences and three dimensional structures. The conference will deal to protein fold prediction, comparative protein modelling, secondary structure prediction, protein dynamics and simulations, ab-initio prediction and the validation of protein models and various aspects of structure determination and analysis by X – ray crystallography.     Paper submission open December 2, 2010     Paper submission deadline January 20, 2011     Paper acceptance decision January 28, 2011     Poster submission open December 30, 2010     Poster submission deadline January 28, 2011     Poster acceptance decision January 31, 2011     Registratio...

Courtesy Bioclues Are you a skilled bioinformatician? Do you have experience with analysis and integration  of large data sets? Would you like to work with leading experts and constantly improve  your skills? Then you may be Intomics’ next bioinformatician. We are expanding our bioinformatics team and are seeking a skilled bioinformatician to  help the team provide innovative solutions for our clients in the pharmaceutical industry.  You will play an important role in implementing data mining strategies for projects in  areas such as target identification, biomarker identification, disease systems biology, and  translation research. Our preferred candidate has the following profile: Bioinformatics or computational biology background Experience with large-scale data mining Strong experience with programming (e.g.  Perl,  Python,  Java),  databases (e.g.  MySQL, PostgreSQL), and Unix Excellent communication skills and the abi...

This something really interesting to PPI, Systems biology  and molecular networks people, I just recently came across, Cellular processes and pathways, whose deregulation may contribute to the development of cancers, are often represented as cascades of proteins transmitting a signal from the cell surface to the nucleus. However, recent functional genomic experiments have identified thousands of interactions for the signalling canonical proteins, challenging the traditional view of pathways as independent functional entities. Combining information from pathway databases and interaction networks obtained from functional genomic experiments is therefore a promising strategy to obtain more robust pathway and process representations, facilitating the study of cancer-related pathways.  Results: We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them t...

Thomson Reuters today announced that it has acquired GeneGo, a leading provider of biology and disease information, analytics, and decision support solutions for pharmaceutical research and development. Effective immediately, GeneGo will become part of the Healthcare & Science business of Thomson Reuters. Financial terms of the transaction were not disclosed. The acquisition enables Thomson Reuters to provide the pharmaceutical, biotechnology, and academic research communities with solutions that provide better understanding of the underlying mechanism of disease and potential therapies. GeneGo’s scientific expertise and assets in biology-driven drug discovery complement the Thomson Reuters life sciences portfolio that covers drug pipeline competitive intelligence, patents, and chemistry. do you wish to know more?

Under the auspices of the University of Tübingen, approximately 120 students from all over the world are working on their PhDs at the Max Planck Institute for Developmental Biology and the Friedrich Miescher Laboratory. Here, they profit from an interdisciplinary environment and first-rate scientific resources. Dedicated support and educational programs foster the scientific growth of doctoral students. The program offers cutting edge training in Bioinformatics Structural Biology Plant & Animal Development  Molecular & Cellular Biology/ Biochemistry Developmental & Quantitative Genetics Evolutionary Biology & Ecological Genetics The  application deadline is November 24, 2010. Do you wish to know more?

The Computational Systems Biology group led by Harri Lähdesmäki in the Department of Information and Computer Science at Aalto University School of Science and Technology (formerly Helsinki University of Technology) uses computational and statistical modeling techniques to study molecular regulatory mechanisms and biomolecular networks, and their role in health and disease. We have interest in statistics, computational science and molecular biology, and how modern computational methods can be applied to experimental data to understand biological systems. 1.   Post-doc/Ph.D. studentship in computational systems biology 2.   Ph.D. studentship in computational systems biology 3.   Ph.D. studentship in statistical modeling and machine learning for next-generation sequencing data in systems biology 4.   Part-time research assistant (MSc student level) in bioinformatics/computational systems biology Do you wish to know more?

The 4th Asian Young Researchers Conference on Computational and Omics Biology is jointly organized by the Joint-International Society for Computational Biology Student Council ISCB-SC Regional Student Group RSG Japan, Korea and Singapore; young researchers in Taiwan and the GCOE program “Genome BigBang” of The University of Tokyo, Japan. The 4th AYRCOB aims to achieve a 2-fold objective: 1) To provide an avenue of exposure for students who are interested in the areas Computational and Omics Biology to participate in lectures of current topics from leading scientists of the field. 2) To establish international collaboration through interaction and discussion with fellow participants. ** Travel expenses of selected ORAL presenters will be FULLY COVERED by the conference sponsors! **   Key Dates Wednessday, 25th August 2010:  Call for Abstract Opens Monday, 13th September 2010:  Website Registration open Monday, 25th October 2010:  Abstract Submission Deadline Fri...

Centre for Systems and Synthetic Biology  &  Centre for Bioinformatics University of Kerala, Thiruvananthapuram, Kerala Welcome to India's First Symposium on Synthetic Biology                       The event will address several strategic issues: 1. How to design organisms from scratch ? 2. Are we ready for the Computer Aided Design of organisms ? 3. Can we design stable genetic circuits for useful applications ? 4. Have we entered the era of ordering genomes by email ? 5. Is the emergence of biohacking, the next big thing in biology ? Invite you to this first synthetic biology meeting in India . The evolving synthetic biology community in our country needs to discuss unique ideas, interest groups, synergies, funding avenues and useful applications. The key goal will be to identify areas where India has potential to take global leadership.     Welcome to BIODESIGN INDIA 1.0   Share | ...

The National Institutes of Health has awarded 970 stimulus grants worth more than $625 million — around 14 percent of total NIH stimulus grant funding to date — to projects that fall within the broad family of 'omics disciplines, according to a preliminary analysis of the NIH funding database conducted by GenomeWeb Daily News . As of Sept. 30, the close of the fiscal year, the National Institutes of Health had awarded a total of $5 billion in stimulus funding — nearly half of the $10 billion appropriation that NIH will disburse over two years under the American Recovery and Reinvestment Act of 2009 . The $5 billion figure includes both grants and contracts, however. For grants alone, NIH had awarded approximately $4.4 billion via 12,789 ARRA grants as of Oct. 7, according to the database. The 970 grants awarded to 'omics projects comprise 7.5 percent of the stimulus grants awarded so far, but the total funding awarded to these projects makes up 14 percent of NIH ARRA grant ...

This Pathways Compendium provides an index of Alzheimer disease pathway models contributed by researchers and companies. Probable Interaction Networks Involved in Pathology of Alzheimer Disease: Predicting Targets and Therapeutic Agents - NetPro™ based Study . Developed by researchers at Molecular Connections Private Limited, an in silico discovery services company. Users can click on a specific node (molecule) to get information on all interactions of the molecule in the given network. Click on the interaction arrows for information on the specific interaction. The Alzheimer Research Forum is a Pioneering Biomedical Web Community . Founded 13 years ago when the Web was still in its infancy, the "Alzforum" has more than 5,000 registered members and is familiar to most Alzheimer scientists in the world. XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "manu...

A team of American and French researchers used systems biology to identify gene signatures predicting human immune responses to the yellow fever vaccine, YF-17D. The work appeared in an advanced online publication in Nature Immunology yesterday. Using high-throughput gene expression measurements, multiplex analysis of cytokines and chemokines, and multi-parameter flow cytometry, investigators tested samples taken from more than a dozen individuals in the days and weeks following their yellow fever vaccination. Computational modeling allowed them to come up with signatures predicting CD8+ T-cell and neutralizing antibody responses to YF-17D — insights into vaccine immunogenicity that may inform future vaccine research and development. “The identification of gene signatures that correlate with, and are capable of predicting, the magnitudes of the antigen-specific CD8+ T-cell and neutralizing antibody responses provides the first methodological evidence that vaccine-induced immune r...

The Computational Biology Unit (CBU) has been established to conduct top-level European research in bioinformatics, and to serve functional genomics research in Norway with relevant training and services. CBU is searching for an additional group leader. The group leader will carry out research in the field of computational biology/bioinformat ics and contribute to the overall objectives of CBU. The group leader should have a PhD and post-doctoral experience including a solid publication record in a relevant subject. Candidates will be evaluated with emphasis on their ability to raise external funding and to supervise and carry out research projects. The research profile of the candidate should be within a relevant area for CBU. Candidates with profiles in direction of systems biology will be preferred. The group leader will direct a research group consisting of Ph.D. and post-doctoral scientists. The CBU and its partners currently have bioinformatics research activities in the fields ...

The emergence of “Systems Biology” in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper , dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function. Satisfactory and insightful results are achieved. Owing to the generality of this methodology, dual descriptor method has wide application perspective for many problems of pattern recognition, especially those involved in “Systems Biology”. Be a part of ...

DNA is pretty straight forward. With its simple composition and linear structure, it easily lends itself to mathematical models. Not so with proteins. In fact, proteins are an order of magnitude more complex than DNA. It is proteins, not DNA, that carry out the cell's heavy lifting. However, with their intricately folded three-dimensional shapes determining a seemingly endless range of possible functions and their manifold interactions with other proteins and with DNA, the leg-work required to mathematically capture the protein universe seems absurd. That is why a team of Harvard Medical School researchers have decided to attack this issue from an entirely new angle. Rather than build a mountain range of proteomic data one grain of dirt at a time, they have developed a computer program that can take on the responsibility of assembling such a gargantuan model. "Through incorporating principles of engineering, we've developed a language that can describe biology in the same ...