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silico in Biological News

Application of Genomatix in silico methods reveals novel cancer associated genes

Genomatix Software GmbH, an in silico systems biology company with headquarter in Munich (Germany), released today that researcher in Dublin, Ireland and Boston, U.S.A. identified novel cancer associated genes, based on strategies and products developed and promoted by Genomatix. Experimental verif...

New e-science service could accelerate cancer research

... at The University of Manchester provides access to over 3,500 Web Services that can be composed by scientists for constructing and enacting their in silico experiments. But one of the main issues that hinders the wide adoption and use of Web Services is the difficulty in locating those that perform th...

Malfunction of the respiratory epithelium is a cause of allergy?

...xpensive and produce much more raw data than hypothesis-derived approaches thus generating an overflow of data. However, the urgent need to develop in silico data managing and analysis environments has been recognized by several research groups and biocompanies. ...

Researchers iron out new role for serotonin

...ues also demonstrates the utility of a powerful in silico approach for discovering novel traits linked to su...linked with the low functioning SERT. From this in silico approach, Blakely and colleagues identified multip...d. The study also demonstrates the power of an in silico approach combined with traditional experimentatio...

Research-based undergraduate course expands beyond Washington University

...enewed in 2006. With that support, she set out to make the course available to undergraduates at institutions across the country. Researching in silico Biology majors at Washington University often begin their research by spending a summer in the laboratory under the guidance of a faculty, gradua...

Researchers apply systems biology and glycomics to study human inflammatory diseases

...he glycome reaction network that controls the final glycan structure that appears on cells," Neelamegham explained. "This approach then provides an in silico tool that can be applied to perturb the system of interest, such as the glycosylation network." Those studies, in turn, he continued, can then gener...

New lab manual focuses on essential methods for purifying and characterizing proteins

...new manual, Basic Methods in Protein Purification and Analysis , integrates established in vitro and in vivo molecular techniques with more modern in silico methods. It takes the user from the initial steps of obtaining cellular and subcellular extracts, through the purification and isolation steps approp...

Work with power grids leads to cell biology discovery

...utational scientists now are beginning to develop quantitative models of biological systems that allow them to predict cellular behavior. In one in silico experiment (via computer simulation) with E. coli, the researchers found that the deletion of one gene is lethal to the cell but when that same gene i...

Researchers discover the structural alphabet of RNA

...arisien, a graduate student in his laboratory, to propose a radically different approach to model RNA structure. Their idea: assemble the structure in silico starting from motifs that combine all the possible interactions between a nucleotide and its neighbors. The researchers implemented a first algori...

From stem cells to organs: The bioengineering challenge

..., you have a much better understanding of it than if you just observe it," he says. "And it's also a powerful way to test many different hypotheses in silico before going into the lab and doing the much more difficult experiments in vitro." Dr. Zandstra, the Canada Research Chair in Stem Cell Bioenginee...

Biophysical Society announces winners of 2008 Student Travel Awards

... in Live Cell Membranes Quantified by Fluorescence Photoactivation Localization Microscopy. Pia Guinto, Albert Einstein College of Medicine, in silico and in vitro Characterization of Cardiac Troponin T Mutations Known to Cause Familial Hypertrophic Cardiomyopathy. Nicholas R. Guydosh, Stanfor...

Proteins pack tighter in crowded native state

...rotein's structure where compaction was occurring and secondary structures improved," Cheung said. "This offers the first observed evidence -- both in silico and in vitro -- for structural effects on proteins in the native state." To find out how crowded environments affect the stability, structure and fo...

Executable biology -- Computer science sheds light on animal development

...kes place in order to determine the fates of individual cells. The novel in silico model is described in a paper appearing May 18, 2007 in the open-access jou...n use the model to test hypotheses that would fill in the missing pieces in silico before performing actual lab experiments. By running their model with ...

NYU algorithm enhances ability to detect cancer genes

... order to validate their algorithm, the authors produced a high fidelity in silico model of cancer, and checked how well they can detect the right genes, as t...f the model in an adversarial manner. Encouraged by the success of their in silico study, they applied the algorithm to currently available patient data, and ...

When the going gets tough, slime molds start synthesizing

...tic evidence that would suggest the existence of a type III PKS in Dictyostelium." Using various computer programs to find, assemble, and translate in silico the relevant raw DNA sequencing fragments first into genes then into the proteins these genes encode, Austin reconstructed two type III PKS-like gene ...

Picking particles faster than one at a time

...h a low error rate, future refinement of the segmentation algorithm aims higher. By concentrating on the highest quality particles, crystallization in silico may need far fewer than hundreds of thousands of particles. "Jacqueline Milne of the National Cancer Institute has demonstrated that high-quality ...

The synapse is a shotgun

...tic function. The simulation combines 3-D electron microscope maps with computer simulation and physiological measurements from real neurons. Their in silico modeling indicates that the synapse may behave more like a shotgun than a rifle when it comes to firing the neurotransmitters involved in neuronal com...

Researchers rein in regulatory RNAs

...e been documented in all life forms ?from viruses and prokaryotes to plants and animals. To date, most studies on SAT pairs have utilized purely in silico approaches; very few have experimentally validated the existence of overlapping RNA molecules in vivo. With this in mind, Dr. Hidenori Kiyosawa, the l...
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