Bioinformatics : The importance of gene regulation for common human disease

Source: sanger.ac.uk

Genes and disease? It's what you do with what you haveA new study published in Nature Genetics on Sunday 16 September 2007 show that common, complex diseases are more likely to be due to genetic variation in regions that control activity of genes, rather than in the regions that specify the protein code.

This surprising result comes from a study at the Wellcome Trust Sanger Institute of the activity of almost 14,000 genes in 270 DNA samples collected for the HapMap Project. The authors looked at 2.2 million DNA sequence variants (SNPs) to determine which affected gene activity.

They found that activity of more than 1300 genes was affected by DNA sequence changes in regions predicted to be involved in regulating gene activity, which often lie close to, but outside, the protein-coding regions.

"We predict that variants in regulatory regions make a greater contribution to complex disease than do variants that affect protein sequence," explained Dr Manolis Dermitzakis, senior author from the Wellcome Trust Sanger Institute. "This is the first study on this scale and these results are confirming our intuition about the nature of natural variation in complex traits.

"One of the challenges of large-scale studies that link a DNA variant to a disease is to determine how the variant causes the disease: our analysis will help to develop that understanding, a vital step on the path from genetics to improvements in healthcare.

"Past studies of rare, monogenic disease, such as cystic fibrosis and sickle-cell anaemia, have focused on changes to the protein-coding regions of genes because they have been visible to the tools of human genetics. With the HapMap and large-scale research methods, researchers can inspect the role of regions that regulate activity of many thousands of genes.

The HapMap Project established cell cultures from participants from four populations as well as, for some samples, information from families, which can help to understand inheritance of genetic variation.

The team used these resources to study gene activity in the cell cultures and tie that to DNA sequence variation‘We have generated an information resource readily available to investigators working in the mapping of variants underlying complex traits. Regions of association can be correlated with signatures of regulatory regions affecting gene expression' explained Dr Panos Deloukas, Senior Investigator at the Wellcome Trust Sanger Institute

"We found strong evidence that SNP variation close to genes - where most regulatory regions lie - could have a dramatic effect on gene activity," said Dr Barbara Stranger, post-doctoral fellow at WT Sanger Institute. "Although many effects were shared among all four HapMap populations, we have also shown that a significant number were restricted to one population.

"They also showed that genes required for the basic functions of the cell - so-called housekeeping genes - were less likely to be subject to genetic variation. "This was exactly as we would expect: you can't mess too much with the fundamental life processes and we predicted we would find reduced effects on these genes," said Dr Dermitzakis.

The study also detected SNP variants that affect the activity of genes located a great distance away. Genetic regulation in the human genome is complex and highly variable: a tool to detect such distant effects will expand the search for causative variants. The authors note, however, that the small sample size of 270 HapMap individuals is sensitive enough to detect only the strongest effects.The results of this study are becoming available in public databases such as Ensembl for researchers to use.

The paper is accompanied by two others examining effects of changes to regulatory DNA in samples from asthma and from heart study patients.

Salaries for Jobs in Genetics-amazed!!

An extract from eyeondna.com

According to myDanwei, “a a pioneer of developing the next generation organization, people, salary, and job information searching and data mining platforms,” here are some current genetics salaries in biotechnology companies:

• Microarray Software Engineer - $88,400
• Statistical Genetics Analyst - $85,000
• Senior Scientist - $95,000
• Bioinformatics Research Associate - $68,000
• Bioinformatics Scientist - $88,400
• Cytogenetic Technologist - $50,320
• Molecular Genetics clinical Lab Scientist - $59,987
• Genetic Counselor - $54,600

Here are some more genetics salaries from Indeed.com which pegs the average earnings of someone working in

• genetics at $57,000.
• Genetics Counselor - $53,000
• Research Geneticist - $86,000
• Molecular Biology Research Associate - $45,000
• Biotech Technical Writer - $75,000
• Cytogenetic Technologist - $42,000

What do you think? Do these salaries make you want to join the genetics work force?

Career path in Bioinformatics

When people refer to the field of bioinformatics, they’re usually referring to two overlapping areas. The first is what you would call “bioinformatics”, which is more technical, and examples are creating tools to analyse data for biologists, or specific databases to store and retrieve information. For example if you created a new tool that could analyse microarray data in a way that hasn’t been done previously, then this is bioinformatics. Many journals such as Nature and Bioinformatics, have sections purely for articles about new methods and tools.

The second path is what you might call “computational biology”, which is all about doing biological research, using a computer instead of a pipette. A strong understanding of biology is important, as well as the ability to phrase, then answer a research question. For example, if you believed that duplicate genes were less well conserved compared with non duplicates, and you tested this hypothesis across a set of genomes, then this would be computational biology.

These two fields are not distinct, and overlap a fair amount. Some universities have bioinformatics departments in both the computer science and life science faculties, indicating the type of research carried out in each.

Updates will be SOON!!!

Check for the updates in here soon.. For mean time, why can't u post me some useful info 2 bioinfinite@hotmail.com.. so that i could publish that in the blog... Catch up with the LATEST of BIOINFO and move up with thr trend..

List of Amino Acids

1. alanine - ala - A
2. arginine - arg - R
3. asparagine - asn - N
4. aspartic acid - asp - D
5. cysteine - cys - C
6. glutamine - gln - Q
7. glutamic acid - glu - E
8. glycine - gly - G
9. histidine - his - H
10. isoleucine - ile - I
11. leucine - leu - L
12. lysine - lys - K
13. methionine - met - M
14. phenylalanine - phe - F
15. proline - pro - P
16. serine - ser - S
17. threonine - thr - T
18. tryptophan - trp - W
19. tyrosine - tyr - Y
20. valine - val - V

There are some new amino acids discovered after them, they are

21. selenocysteine

22. pyrrolysine

Red Hat tries spreading open-source idea

source: cnet news

Red Hat is taking a second crack at trying to spread its open-source philosophy beyond the realm of software development.

On Wednesday, the Raleigh, N.C.-based Linux seller announced a partnership with the nearby University of North Carolina to try to encourage use of the open, collaborative model in the fields of health care research, biotechnology, bioinformatics and public policy.

"The history of open source has taught us that the more broadly and transparently information is shared and re-used, the faster and stronger the results," Joanne Rohde, Red Hat's executive vice president of operations, said in a statement.

The move hearkens back to 1999, when the company launched the Red Hat Center for Open Source, with company co-founder Marc Ewing leading the effort. In an interview at the time, Ewing said, "What we want to be able to do is facilitate thinking and discussion about the principles of open source and how they apply in communities other than the software development community--law, medicine, business, governance, scientific research, education."

That earlier effort fizzled. This time, however, the company has a partner.

"We need to know what works faster, better and cheaper than we could do in the past. That means collecting data from more sources, not just in teaching hospitals...but in all settings where new technologies are being used--private practices, health departments, health education centers and walk-in clinics," said Etta Pisano, vice dean for academic affairs at the University of North Carolina's Biomedical Research Imaging Center.

Superbugs-Interesting one!!

Stainless steel door handles and taps at a hospital are being replaced with copper ones in an effort to reduce the presence of superbugs Staphylococcus aureus MRSA and Clostridium difficile.Birmingham's Selly Oak Hospital is swapping steel for copper in an 18-month trial to test the findings. 80% of hospital MRSA transmission is believed to come from contact with surfaces such as door handles, bathroom taps, toilet flush handles and grab rails. To test the theory one general medical ward is having copper installed in preparation for the trial while a similar ward will retain its traditional fittings. Even pens used by staff will be made from copper alloy. Copper reacts with the bacteria and inhibits respiration - the Egyptians may have used copper thousands of years ago to treat infections.

So wat are superbugs?

If a bacterium carries several resistance genes, it is called multiresistant or, informally, a superbug.

Bioinformatics Grad schools!!

hi blog readers,

i've jus made up a summary of all bioinformatics schools in UG/PG category.. May b i'll start posting n a couple of days.. Plz await for them.. If u've any queries, jus comment i'll respond 2 u..

U can also review some universities, colleges, certificate programs n send it 2 bioinfinite@hotmail.com... Any contributions u wanna do to bioinfinite (may be some articles, descriptors of any topics, link,etc..) , send n urs to above mail_id.. Keep urself updated..

Phenomics

Phenomics describes the state of an organism as it changes with time. It is a word he coined at a guest lecture he gave at the University of Waterloo in 1996 by Steven A. Garan, Director of the Aging Research Centre (ARC).

Then what s meant by phenome??

Answer is right down..

A phenome is the set of all phenotypes expressed by a cell, tissue, organ, organism, or species. A phenome includes phenotypic traits due to either genetic or environmental influences.

Just as the genome and proteome signify all of an organism's genes and proteins, the phenome represents the sum total of its phenotypic traits. Some examples of human phenotypes are skin color, eye color, height, or specific personality characteristics. Phenotypic differences between individuals can be due to environmental influences, genetic variation such as single nucleotide polymorphisms (SNPs), or a combination of the two.

Phenomics is the study of the nature of phenotypes and how they are determined, particularly when studied in relation to the set of all genes (genomics) or all proteins (proteomics).

SMD : Stanford Microarray Database

SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. SMD provides interfaces for data retrieval, analysis and visualization.

SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization.

Link: http://genome-www5.stanford.edu/

Junk DNA

"Junk" DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. About 97% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA. While much of this sequence may be an evolutionary artifact that serves no present-day purpose, some is believed to function in ways that are not currently understood.

Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function.

8% of human junk DNA has been shown to be formed by retrotransposons of Human Endogenous Retroviruses (HERVs).

Junk DNA may act as a protective buffer against genetic damage and harmful mutations.Junk DNA may have no function.

For example, recent experiments removed 1% of the mouse genome and were unable to detect any effect on the phenotype. This result suggests that the DNA is, in fact, non-functional.

Research Nuggets:
A 2006 study by the McKusick-Nathans Institute of Genetic Medicine (Johns Hopkins) stated that "Junk DNA may not be so junky after all."
Researchers at the University of Illinois Society for Experimental Biology found an antifreeze-protein gene in a species of fish which "evolved" from junk DNA.
A mathematical analysis of the genetic code by IBM identified patterns that suggested junk DNA had an important role after all.
In 2006, University of Iowa researchers documented segments of RNA (previously considered "junk") that regulated protein production, and could generate microRNAs.

BLAST Beta

NCBI is holding a beta test for a new BLAST interface design.

One major improvement is a new "Recent Results" feature that provideslinks to all of your recent BLAST search results.

Another is "SavedStrategies", which allows you to save BLAST forms with their parameters and use them later. Saved Strategies requires a free MyNCBI account, andis compatible with existing accounts. Signing in to MyNCBI also makesyour Recent Results available from any browser.

Other improvements include:-

-Easier navigation

- Simplified BLAST program selection

- Easy access to genome searches

- Improved Organism selection with species name auto-complete

- Automatic parameter adjustment to optimize for short queries

- A user-specifiable title for each BLAST job

The Beta test is available HERE

Folding @ Home - Distributed Computing

To my reviewer's request, i've posted this,

Folding @ Home is an initiative started by Stanford University to have a distributed computing environment, where each online user can contibute a share of his/her computer process to the folding program( we've to download the program and install it to be a part of the Project). Folding@Home uses novel computational methods coupled to distributed computing, to simulate problems thousands to millions of times more challenging than previously achieved.

Since October 1, 2000, over 1,000,000 CPUs throughout the world have participated in Folding@Home. Each additional CPU gives them an added boost in performance, allowing them to tackle more difficult problems or solve existing research faster or more accurately.

you can access this at http://folding.stanford.edu/

One more project is also available, named Genome@Home (Pande Lab) at http://genomeathome.stanford.edu

Mathematician Probes Geometric Route To Combat Viruses

source: Science Daily

A mathematician at the University of York has been awarded a Research Leadership Award of more than £700,000 by the Leverhulme Trust to study the geometry of viruses.

Viruses have highly symmetrical external shells formed from proteins that encapsulate the viral genome. Dr Twarock has developed a method for encoding the structures of these protein shells that pinpoint the locations of the proteins and the bonds between them. With collaborators Professor Cristian Micheletti, from the International School for Advanced Studies (SISSA) in Trieste, Italy, and Professor Anne Taormina, from the University of Durham, she has used these results to model the assembly of viruses.

Subsequent work with collaborators Professor Peter Stockley, Dr Neil Ranson and their groups at the Astbury Centre for Structural Molecular Biology at the University of Leeds suggests that not only the geometry of the viral capsids themselves but also the full three-dimensional structures of the particles are constrained. The implications of this discovery on virus assembly are currently being investigated.

Database of incorrect Protein conformations

Decoys ‘R’Us database contains a wide variety of decoys generated by different methods with the aim of fooling scoring functions.

Decoys are computergenerated conformations of protein sequences that possess some characteristics of native proteins, but are not biologically real.

Decoys have been based on discrete-state models, molecular dynamics trajectories, crystal structures of different resolutions ,conformations with different loops, and amino acid sequences mounted on radically different folds.In other words, this database provide incorrect conformations data in order to improve the protein structure prediciton.

Organisation of decoy sets

1.The multiple decoy sets

2.The single decoy sets

3.The loop decoy sets

The current version of the entire decoy set is only available as a single tar and gzipped file to download.

Link: Decoys 'R' Us database

Human Protein Reference Database

Human Protein Reference Database (HPRD) that integrates information relevant to the function of human proteins in health and disease.Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization for each protein in the human proteome.

Go to Human Protein Reference Database

STRING - Search Tool for the Retrieval of Interacting Proteins

STRING is a database of known and predicted protein-protein interactions.The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources:

• Genomic Context
• High-throughput Experiments
• (Conserved) Coexpression
• Previous Knowledge

STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently contains 1,513,782 proteins in 373 species.

Access STRING.

RNA Interference and Gene silencing

RNA interference, or RNAi, is a way for cells to regulate which genes would be expressed. This amazing phenomenon was first observed in petunias, when a scientist called Rich Jorgensen introduced a pigment-producing gene under the control of a powerful promoter. Instead of the expected deep purple color in the petunia, the result was a mixture of variegated and white petunias.RNAi was named the breakthrough of the year in 2002, yielding a new potential for disease treatment and unraveling the mysteries of the functioning of human genes.

So, why do we need to shutdown the production of some genes?

• Scientists have been interested in the ability to shut down genes, so that observing the effect of turning down a gene can be observed on an organism, giving clues about the function of the gene.
• The ability to shut off the genes, may also result in developing new treatments for diseases by turning down the harmful protein producing gene.

A very beautiful article about RNA Interference, or RNAi appeared on pbs.org, and can be found at http://www.pbs.org/wgbh/nova/sciencenow/3210/02.html.

Putting Playstation to work for science

A network of Playstation computers might help Danish scientists to solve themystery of prostate cancer.

A team of scientists has enlisted the help of Playstation 3 owners to help themcrack the code for prostate cancer.

Brian Vest, a professor in computer science at the University of Copenhagen,realised that the lightning fast processor in Playstation 3 can double as ahome computer. Together with specialists at the Bioinformation Research Centreat Aarhus University, he developed a method for applying the gaming machine'sprocessor to help crunch data about prostate cancer.
'The machine is ten times faster than a normal computer so by using its enormouscalculating powers we can lighten our work considerably,' Vest told Nyhedsavisennewspaper.

Playstation owners involved in the project simply install a program, link theirconsole to the scientists' network via the internet and then let the machine dothe work. While the owners rest their hands and fingers for the next round ofArmored Core, the machine searches a DNA chip that contains genetic materialfrom 2000 people. The goal is to locate the gene that causes prostate cancer.

Some 100 Playstation owners have participated in the project since January.

Dr Jørgen Kvist Kristensen at State Hospital's Urology Department is hopeful theproject can give insight into who develops prostate cancer, which is the secondmost fatal form of cancer among Danish men.

'That would give us the possibility to manipulate the disease so it neverdevelops,' Kristensen said.

Stub from http://www.cphpost.dk/get/101009.html

Biophysics

Biophysics (also biological physics) is an interdisciplinary science that applies the theories and methods of physics, to questions of biology. Biophysics research today comprises a number of specific biological studies, which do not share a unique identifying factor, nor subject themselves to clear and concise definitions. The studies included under the umbrella of biophysics range from sequence analysis to neural networks. In the recent past, biophysics included creating mechanical limbs and nanomachines to regulate biological functions. Today, these are more commonly referred to as belonging to the fields of bioengineering and nanotechnology respectively.

> read full article at Wikipedia.org

Best of Bioinformatics' Book: Hand Picked

Hi 2 all,

I recently browsed through the available books, magazines for bioinformatics for the convenience of my blog readers . I hand picked some books that all bioinformaticists must need that u may not aware of.. So u can find the books that i've picked in the following page..

BIOINFLUX STORE

Language created for describing genes

source: ScienceDaily

A U.S.-led international group of scientists has expanded a lingua franca used to describe the activities of genes in living organisms.

The expansion is part of the unified language called Gene Ontology, which provides terms that scientists can use to describe the complex events that occur when a pathogenic or beneficial microbe encounters its host.

The initiative is part of the Plant-Associated Microbe Gene Ontology project, a recently-established interest group of the worldwide Gene Ontology Consortium, supported in part by the U.S. National Science Foundation.

Professor Brett Tyler of the Virginia Bioinformatics Institute, located at Virginia Tech, said, "By providing a precise vocabulary for the functions of these genes, scientists can compare among microbes the many processes that make up the interplay between a microbe and its host."
The PAMGO consortium is a collaboration of the Virginia Bioinformatics Institute, Cornell University, North Carolina State University, the University of Wisconsin-Madison, The Institute of Genomic Research and Wells College.

Molecular Biology : The molecular post office inside the cell

For most proteins, there is a particular place inside a cell where they carry out their function. But how do they get there? Scientists from the Charité Berlin, the University of Heidelberg, and the Max Planck Institute for Molecular Genetics in Berlin have now been able to visualize the structure of a "molecular machine" involved in protein sorting using cryo-electron microscopy and single particle analysis. This "machine" is made up of a single active ribosome, plus a special signal recognition protein and a matching receptor. The scientists have shown that when the three proteins interact, certain areas open up on the ribosome, which allows the ribosome to dock onto another complex. The later complex, which is called translocon complex, takes over the job of transferring a newly produced protein through the membrane. Knowing the structure of the molecular machine helps scientists to understand how secretory and membrane proteins in a cell are expressed and sorted (Science, May 5, 2006).

Sorting proteins is fundamental to the gene expression of every organism - from bacteria to humans. Particularly important during biosynthesis is sorting secretory and membrane proteins, which have to find the way to their final destination inside or outside the cell. Secretory proteins are those that later on leave the cell, like anti-bodies. Membrane proteins are proteins embedded into the cell's membranes - for example, signalling receptors. One particular molecular complex is important in protein sorting. It is made from an active ribosome - that is, the protein synthesis machine in the cell - called the signal recognition particle (SRP), and its corresponding receptor. It is the structure of this complex that the scientific team is now able to describe.

The key element to this machine's functioning is a signal sequence located at the N-terminal end of the protein to be sorted. The sequence acts as a kind of "postal code" in the cell. The SRP reads the sequence as soon as the newly built protein chain leaves the ribosome. The SRP binds to the ribosome and directs it, together with the SRP receptor, to what is called the "translocon complex" in the membrane of the endoplasmic reticulum. The translocon complex is made of a "protein conducting channel" and other membrane proteins. The ribosome is anchored at the translocon and continues with protein biosynthesis.Notable is that the ribosome can no longer bind to the translocon as soon as the SRP has bound to the ribosome. The ribosome needs additional support from the SRP receptor, which it transfers from the SRP to the translocon. Now that scientists understand the structure of the complex, they can see how the receptor interacts with ribosome and SRP and replaces parts of the SRP molecule. In this way, specific sites are made available for the translocon, which allows it to bind to the ribosome. Understanding this key event during protein sorting is essential to understanding how secretory and membrane proteins are expressed in a cell.

--http://www.mpg.de

Sorry! No updates!!

Hi to all my BLOG subscribers,

Sorry, i cudn't post blog posts 4 the recent time due 2 server running low on fuel in our research lab.. But anyway, am still striving hard 2 put forward the information watever i get.. Thanks 2 one and all 4 regularly turning 2 my blog...

Various Structure Prediction Methods

Structure Prediction in 1D

• Limited computing resources and experimental inaccurices prevent prediction of protein structure from first principles. Therefore, the only succesful structure prediction tools are knowledge-based, using a combination of statistical theory and empirical rules.
  

Secondary Structure Prediction Methods

• Basic concept: segments of consecutive residues have preferences for certain secondary structure states: a pattern recognition problem (helix, strand or coil or loop). Physicochemical principles, rule-based devices, expert systems, graph theory, linear and multilinear statistics, nearest-neighbor algorithms, molecular dynamics, neural networks. The main limitation is the use of only local information, which is estimated to play for roughly 65% of secondary structure formation. To improve predictions, it is key the use of evolutionary information.
  

•  Programs: PHD, JPred2 (JNet, NSSP, PREDATOR, PHD), PSIRED, SSPro2, HMMSTR/I, etc.
  

• Specialized methods: coiled-coil predictions. A coiled coil is a bundle of several helices assuming a side-chain packing geometry ("knob-into-holes"). COILS.
  

Solvent Accesibility Prediction Methods

• Basic concept: try different arrangements and assess them by predicting the extent to which a residue embedded in a protein structure is accesible to the solvent. PDH, PROFphd, JPred2 server.
  

Transmembrane Helix Prediction Methods

• Transmembrane proteins still represent a challenge. They do not crystalize, and are hardly tractable by NMR spectroscopy. Prediction is simplified by the fat of the lipid bilayer of the membrane, which reduced the degrees of freedom making the prediction almost a 2D problem.
  

• Basic concept: TM helices are predominantly apolar and between 12 and 35 residues long, globular regions between membrane helices are typically shorter than 60 residues, most TMH proteins have a specific distribution of the positively charged amino acids Arginine and Lysine (the "positive-inside-rule").
  

• Programs: ToPred2, MEMSAT, TMAP, PHD, TMHMM, HMMTOP
  

Public Servers

PHDsec,PROFsec  : neural-network based prediction of secondary structure, accessibility                                            and TMH.
JPred, Jpred2       : neural networks, evolutionary information. Version 2 evaluates results                                         from 4 different neural networks (JNet, NSSP, Predator, PHD).
PROF                         : multiple alignments and other characteristic from databases.
PSIpred                    : based on profiles created by psi-blast and neural networks.
SAM-T99                  : neural network and HMM.
SCRATCH                 : uses SSPro (recursive bidirectional neural networks).

Wkicamp '07- jus got over

Wikicamp '07 was all about harnessing and understanding the power of Wikis. It was a one day event aimed to bring together the best minds from the Wiki/Internet space to talk about issues, opportunities and what the future and evolution of this valuable tool. It jus got over yesterday that had a huge number of participants registering and the highlight of the camp was the presence of Jimmy Wales, founder of Wikipedia Organisation.

I was very lucky to take a snap with Jimmy Wales, founder of Wikipedia. Thanks to the generous man.

Seminar on Protein Engineering @ VIT,Vellore

About the Seminar:

The Seminar aims at inviting eminent speakers from national and foreign institutes, research laboratories and industries working in the related aspects of protein engineering.

Sessions include:

• Protein and Peptide design
• Macromolecular Recognition
• Protein folding & Dynamics
• Production and analysis of recombinant protiens
• Directed Evolution of Proteins &
• Protein Bioinformatics

Scheduled on : 27 - 28th February, 2007

For more information, log on to

http://www.vit.ac.in/Seminars/sbtche/Biotechnology_PE_Seminar/seminar.html

Reliance Life sciences gets 36 patents

Reliance Life Sciences, the Mukesh Ambani-controlled biotechnology-driven life sciences company, has received 36 patents from applications filed for 200 rights. The valuation of these patents could not be ascertained. Of the accepted patents, six are design patents, seven product patents and 23 process patents.


These patents have been filed in 16 countries, including India and the US. "We are in the process of making assessment," said a top executive of the company. Experts said the depth and diversity of the company's patent portfolio were significant for a start-up company with just four years of active research.Reliance Life Sciences is growing its intellectual property portfolio across the medical, plant and industrial biotechnology areas.


Reliance Life Sciences is the *biggest intellectual property holder* in the country in the field of *stem cells*. some of the important patents the company holds include process for* isolation of inner cell mass using laser ablation technique for establishment of human embryonic stem cell lines; growth of human mesenchymal stem cells using cord blood serum; three dimensional dermal construct and diagnostic test to detect low-grade genetic abnormalities of ovaries in follicular fluid, which are usually not reflected in blood test or other biological samples. *

Apply For Bioinformatics Jobs in the following companies

Hello to all my blog readers,

I got this very good informative links of career sites of Bioinformatics, Pharmaceutical companies on searching through the web. I thought this could be useful for everyone... Add this to your favourites for late references...

STRAND GENOMICShttp://www.strandgenomics.com/
Careershttp://www.strandgenomics.com/careers.html

METAHELIX LIFE SCIENCEShttp://www.meta-helix.com/
Careershttp://www.meta-helix.com/jobs.html

BIGTEChttp://bigtec.co.in/

Careershttp://bigtec.co.in/careers.html

WIPROhttp://www.wipro.in/

Mphasishttp://www.mphasis.com/offerings/lifescience.asp

careershttp://www.mphasis.com/careers/overview.asp

bioWORLDwww.gene-pixels.com

Careershttp://www.gene-pixels.com/career.htm

ZENSARhttp://www.zensar.com/

Careershttp://zensar.com/careers.html

AVESTHA GENGRAINE TECHNOLOGIESwww.avesthagen.com/

Careershttp://database.avesthagen.com/jobapp/careers_new.php

IBM INDIA RESEARCH LABS (IRL),http://www.research.ibm.com/irl/

Careershttp://www.research.ibm.com/irl/jobs/

SUN MICROSYSTEMShttp://www.sun.com/products-n-solutions/edu/commofinterest/compbio/

Dr Reddy\'s Laboratories Limitedhttp://www.drreddys.com/

Careershttp://www.drreddys.com/careers/careers.htm

TATA CONSULTANCY SERVICES (TCS)-Advanced TechnologyCentre (ATC)http://www.atc.tcs.co.in/
Careershttp://www.atc.tcs.co.in/careers.html

Ranbaxyhttp://www.ranbaxy.com/

Careershttp://www.ranbaxy.com/humanresources.htm

Nicholas piramalhttp://www.nicholaspiramal.com/

careershttp://www.nicholaspiramal.com/career_opportunities.htm

Biocon/syngene/clingenehttp://www.biocon.com/

careershttp://www.biocon.com/biocon_careers.asp

Institute of Bioinformaticshttp://www.ibioinformatics.org/

careershttp://www.ibioinformatics.org/careers.htm

Jubilant Biosys Ltd. (JBL)http://www.jubilantbiosys.com/

Careershttp://www.jubilantbiosys.com/car.htm

Molecular Connectionshttp://www.molecularconnections.com/home.html

Careershttp://www.molecularconnections.com/openings.html

Accelryshttp://www.accelrys.com/

Careershttp://www.accelrys.com/about/careers/

Ocimum biohttp://www.ocimumbio.com/web/default.asp

careerhttp://www.ocimumbio.com/web/careers/careers.aspx

Bioinformatics Institute of Indiahttp://www.bii.in/page/index.asp

SATYAMCOMPUTER SERVICEShttp://www.satyam.com/

Careershttp://careers.satyam.com/c_introduction.html

BrainWavehttp://www.brainwave.in/

Becton Dickinson India Pvt. Ltd.www.bd.com/india

Bhat Bio-Tech India (P) Ltd.http://www.bhatbiotech.com

Reliance Life Scienceshttp://www.relbio.com/

Careerhttp://www.relbio.com/html/careers.html

Labvantagehttp://www.labvantage.com/companyinfo/contactus/index.html

A complete Bioinformatics package from CSIR-TCS team

Bio-Suite is an end-to-end software tool for BioInformatics developed at the Life Sciences division of Advanced Technology Center of Tata Consultancy Services Ltd. Bio-Suite is developed in collaboration with Council of Scientific and Industrial Research (CSIR) and several leading Indian academic institutes under the Government of India funded New Millennium Indian Technology Leadership Initiative (NMITLI) program. Bio-Suite is versatile, portable and comprehensive software catering to the needs of academics and the research community as well as Pharmaceutical and Biotech companies. The product was launched by His Excellency, The President of India, Dr. A. P. J. Abdul Kalam.

Bio-Suite package is a tool that covers all the major functional areas of Bioinformatics. This package can be used to analyze, formulate, predict and provide solutions to specific areas in computational biology. The package comprises of four focus areas: Genomics, Protein modeling & Structural analysis, Simulation and Drug Design.The state of the art Bio-Suite package combines in itself TCS’ best software engineering practices and implements well-established algorithms. The entire package is well documented and comes with easy to use Tutorials, which reduce the learning curve and increase efficiency.

The salient features of the package are:

• Robust Graphical User Interface
• Modular in nature
• Highly user-friendly
• Well documented
• Ease of installation and customization
• Secure system
  

What makes a good biological database?

In the 2007 Database Issue of Nucleic Acids Research (A series dedicated to databases in the field of molecular biology) , Alex Batemen has wriiten about the qualities of a good biological database. He pointed the data and web interference condiderations which make a good database. According to him, The quality, quantity and originality of data as well as the quality of the web interface are the most important. He stressed on comprehensive nature of web database and database should not be overspecialized . He ask to have flat files for huge database. He also added the necessity of having high speed and secure access of database to public domain.

Read more: http://nar.oxfordjournals.org/cgi/content/full/35/suppl_1/D1

Info obtained from: http://b4bioinfo.blogspot.com/search/label/Database%20Designing

New Web Site Features For Viewing Ligand, SNP, and Pfam Data- PDB

The RCSB PDB website now offers improved access to ligand, Single Nucleotide Polymorphism (SNP), and Pfam information.

Improved Access to Ligand Data

The PDB chemical components dictionary (formally the HET dictionary) has been remediated to better describe the components that interact with macromolecular structures. This new dictionary has been incorporated with the RCSB PDB database. Options available after a search now includes a tab called 'Ligand Hits'. This page lists the ligands known to interact with the structures that match the query.

For example, a search for 'protein kinase' returns 2051 structures and 678 ligands. From the 'Ligand Hits' page, users can find all of the structures that contain that ligand or access information from the 'Ligand Summary' page. This page offers summary information, downloads (definitions and coordinates), and interactive and static views.

Ligand Explorer Tool for Viewing Protein-Ligand Interactions.....

Access to Single Nucleotide Polymorphism (SNP), Pfam, and more .....

Bioinformatics Interview Questions and Answers

To all my Blog Readers,

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Site Address: http://biotech.fyicenter.com/interview/Bioinformatics_Interview_Questions_and_Answers.html

Spanish scientists reveal dynamic map of proteins

January 10, 2007 - This work provides important basic information on the flexibility of proteins and their ability to link with other molecules, an area of study which opens enormous possibilities for the design of new drugs.

Scientists from the Institute for Research in Biomedicine (IRB Barcelona), the Life Sciences Programme at the Barcelona Supercomputing Center (BSC) and the National Institute for Bioinformatics (INB) have published a provisional “atlas” of the dynamic behaviour of proteins in the prestigious scientific journal, Proceedings of the National Academy of Sciences USA. Proteins determine the shape and structure of cells and drive nearly all of a cell’s vital processes.All proteins carry out their functions according to the same process – by binding with other molecules. Now, the scientists have compiled a map that shows them how proteins can move and form complexes, a valuable tool that will help them understand the basic functions of the molecules, but also what happens when they function incorrectly. Such a map opens vast possibilities for the design of new drugs.

The goal of this study is to define a map of the dynamic properties of a very representative group of proteins....

click on the link above(title) for more info..