Researchers find roadmap to next-generation cancer therapies May 26, 2008
Additional co-authors from the URMC Department of Biomedical Genetics are: Laurel Newman, Bradley Smith and Shaw-Ree Chen; and from the URMC Department of Biostatistics and Computational Biology: Lev Klebanov, Peter Salzman and Andrei Yakovlev. . (EurekAlert!)
Scientist confident of cancer treatment breakthrough May 20, 2008
"In the past decade we've made enormous advances I would say. Most of that has come from advances on the molecular sciences, mainly to do with genetic technology and computational biology," he said. "These advances have allowed us to identify specific defects within particular cancers. "Ultimately these have provided information about drug targets. (ABC Online)
New Tool To Understand Evolution Of Multi-domain Genes Developed May 20, 2008
In a paper published online in Public Library of Science Computational Biology May 15, Durand's team presents a novel method to determine whether a pair of similar genes evolved from a common ancestor, or whether they just look similar because the same domain was inserted into both genes. Their method, called "Neighborhood Correlation," is the first to tackle this problem. (Science Daily)
Geneticists at the American Museum of Natural History trace the evolution of St. Louis encephalitis May 16, 2008
The research was made possible by the U.S. Army Research Laboratory, the U.S. Army Research Office, the Wadsworth Center Media and Tissue Culture facility, and the World Reference Center for Emerging Viruses and Arboviruses through the University of Texas Medical Branch in Galveston, the Computational Biology Service Unit from Cornell University, and CamGrid at the University of Cambridge. No. 56. (EurekAlert!)
Carnegie Mellon engineering researchers automate analysis of protein patterns May 13, 2008
In a research article in the Journal of Proteome Research, Newberg and Murphy, the Ray and Stephanie Lane Professor of Computational Biology and a professor in the departments of Biological Sciences, Biomedical Engineering and Machine Learning at Carnegie Mellon, described how they applied their tools to analyze images of eight major subcellular location patterns with a high degree of accuracy. They pointed to their work as a strong indication that automated analysis of the whole atlas is... (EurekAlert!)
Stem cell group gets its first building block May 8, 2008
Scientists from the four member institutions combine expertise on stem cells as well as bioengineering, computational biology, chemistry and clinical sciences. Seldom are scientists in those disciplines able to work together in one facility with the goals of unleashing the regenerative powers of stem cells and harnessing them for health care. (San Diego Union-Tribune -- Business)
Genetic 'tag team' keeps cells on cycle May 8, 2008
Collaborators on the study include David Orlando, Charles Lin, Allister Bernard, Jean Wang, Joshua Socolar, Edwin Iversen and Alexander Hartemink, representing Dukes biology, computer science, physics and statistical science departments and Duke Universitys Program in Computational Biology and Bioinformatics. . (EurekAlert!)
Stem cell grants awarded May 8, 2008
Scientists from all four member institutions will work there, combining expertise on stem cells as well as bioengineering, computational biology, chemistry and clinical sciences. The idea is that by sharing their resources and different expertise, the four institutes will be better equipped to bring new therapies, diagnostics and research tools to market more quickly and efficiently. (San Diego Union-Tribune)
Lab employees get preview of super-powerful data center May 6, 2008
It will support our strategic goal of building our bioinformatics and computational biology programs. The 200 to 250 servers that ultimately will be housed in the data center will handle virtually all of the lab s information transfer and storage everything from emails to research data to business transactions. (Courier Publications, ME)
DNA Jigsaw Puzzle May 5, 2008
He is a co-author of a study published recently in the scientific journal PLoS Computational Biology, in which the researchers successfully identified the virus strains of four patients infected with the HIV virus. Light signals identify structural elements. (Science Daily)
New Technique Accelerates Biological Image Analysis May 4, 2008
ScienceDaily (May 3, 2008) Researchers in Carnegie Mellon University's Lane Center for Computational Biology have discovered how to significantly speed up critical steps in an automated method for analyzing cell cultures and other biological specimens ... Murphy, director of the Lane Center for Computational Biology, said this technique could improve the performance of belief propagation algorithms in many applications, including text analysis, Web analysis and medical diagnosis. (Science Daily)
Ceres is a pioneer in complex plant genetic mapping May 2, 2008
They also made advances in new scientific disciplines bioinformatics and computational biology. These advances allowed Ceres to build massive databases that made it possible to search and correlate all the sequences, genes, plant types, and expression patterns needed to develop new plant traits. (Minnesota Farm Guide, MN)
Slight Of Hand Is Not So Slight, Motor Development Research Shows Apr 21, 2008
On both accounts, the answer is no." Zelaznik was part of research team led by Viktor Jirsa, director of research at the Centre National de la Recherche Scientifique (CNRS) and a professor of movement sciences at the University of the Mediterranean in Marseilles, France, and Raoul Huys, a research associate at the Centre National de la Recherche Scientifique as well as at the University of the Mediterranean. Purdue graduate students Breanna Studenka and Nicole Rheaume also were part of the team.... (Science Daily)
Fittest Males Don't Always Get The Girl Apr 17, 2008
The other member of the research team were Larry Cabral of Cal State Sacramento (co-corresponding author with Foley), and Foley's supervisor Sergey Nuzhdin, professor of molecular and computational biology at USC. The paper was written at USC based on experiments conducted at the University of California, Davis, where Foley and Nuzhdin worked previously. Funding for the study came from the National Science Foundation. (Science Daily)
Mechanism That Helps Fruit Flies Lock-in Memories Identified Apr 1, 2008
appears in PLoS Computational Biology on February 29, 2008. Authors include: Gengxin Chen, Wanhe Li, Qing-Shuo Zhang, Michael Regulski, Nishi Sinha, Jody Barditch, Tim Tully, Adrian R. Krainer, Michael Q. Zhang, and Josh Dubnau. (Science Daily)
You might not be all that you eat Mar 29, 2008
Findings of the study have been published in the open-access journal PLoS Computational Biology. The work also shows, however, that another class of models directly refutes this assumption, predicting that food intake and energy expenditure rates uniquely determine body weight. (India Times, India -- Health/Science)
Reason For Almost Two Billion Year Delay In Animal Evolution On Earth Discovered Mar 27, 2008
9, 2006) Researchers in computational biology and marine science have combined their diverse expertise and found that trace-metal usage by present-day organisms probably derives from major changes in ocean. (Aug. (Science Daily)
Model offers new understanding of cell signaling Mar 25, 2008
She is the senior author of a study about the new model published online March 21 in Plos Computational Biology. Around the world, researchers scrutinize the pathways inside cells where signals travel and activate or suppress thousands of cell functions. (EurekAlert!)
Algorithm Finds The Network -- For Genes Or The Internet Mar 20, 2008
One impact of having such a computational biology tool is found in the genomics field ... Zhang began his computer science career as a specialist in artificial intelligence, but in recent years he has focused more on computational biology ... The results were published in PLoS Computational Biology, 3(3):e37 (2007). (Science Daily)
Genes That Reduce 'Bad Cholesterol' And Protect Against Atherosclerosis Identified Mar 18, 2008
It is on account of years of network algorithm development under Jesper Tegn;r, professor of computational biology, that the discovery of gene networks has been made possible. "The time when individual genes or gene pathways were thought to explain the development of complex common diseases, such as atherosclerosis, is past," says Dr Bj. (Science Daily)
Buck Institute partners on graduate program Mar 17, 2008
That is Buck's focus on the intersection of the processes of aging, diseases of aging -- Alzheimer's and Parkinson's disease, cancer and arthritis, for example -- and technology like computational biology, mass spectrometry and bioenergetics. Buck, which started its research program in 1999, is the only independent research facility in the United States to focus solely on aging and age-related conditions. (San Francisco Business Times, CA)
History Of Life Seen In The Structure Of Transfer RNA Mar 10, 2008
The study, co-written by Gustavo Caetano-Anoll;s,* a professor of crop sciences, and postdoctoral researcher Feng-Jie Sun, appears March 7 in PLoS Computational Biology. Of the thousands of RNAs so far identified, transfer RNA (tRNA) is the most direct intermediary between genes and proteins. (Science Daily)
Microsoft Struts Its Latest Research Innovations at TechFest Mar 8, 2008
"I mean, we're working in things like vaccine design and computational biology, quantum computing.". WWT is actually a nifty new PC program that stitches together imagery from the most advanced ground- and space-based telescopes to provide a seamless digital view of the universe in much the same way as , which debuted in August. (Scientific American)
Computers explain why pears may become brown during commercial storage Mar 8, 2008
Internal browning of pears stored under low oxygen conditions is related to restricted gas exchange inside the fruit, according to a study published March 7th in the open-access journal PLoS Computational Biology ... This press release refers to an upcoming article in PLoS Computational Biology ... About PLoS Computational Biology. (EurekAlert!)
Language of a fly proves surprising Mar 8, 2008
In an article published in the Public Library of Science Computational Biology Journal, Los Alamos physicist Ilya Nemenman joins Geoffrey Lewen, William Bialek and Rob de Ruyter van Steveninck of the Hun School of Princeton, Princeton University and Indiana University, respectively, in describing the research. The team used tiny electrodes to tap into motion-sensitive neurons in the visual system of a common blowfly. (EurekAlert!)
Viruses Evolve To Play By Host Rules Mar 7, 2008
The study, appearing in the current issue of the journal Public Library of Science Computational Biology, was performed by Plotkin and Grzegorz Kudla of the Department of Biology in the School of Afrts and Sciences at Penn and Julius Lucks and David Nelson of Harvard University. The study was supported by grants from the Burroughs Wellcome Fund and the National Science Foundation. (Science Daily)
Faculty Position Mar 7, 2008
Areas of particular interests include structural biology, neuroscience and cell biology, computational biology, systems biology, microbial pathogenesis, molecular, cellular and nanobioengineering, and blood diseases. The Schools of Natural Sciences and Mathematics, Behavioral and Brain Science, and Engineering and Computer Science are expanding, with an emphasis on recruiting faculty who can foster interdisciplinary interactions. (Nature News Service)
Mathematicians Prove New Way To Build A Better Estimate Mar 3, 2008
Their work shows that these centroid estimators allow for better statistical predictions and, as a result, better ways to extract information from the immense data sets used in computational biology, information technology, banking and finance, medicine and engineering. What s exciting about this work what makes it every scientist s dream is that it s so fundamental, Lawrence said. (Science Daily)
Computer simulations point to key molecular basis of cystic fibrosis Mar 1, 2008
The findings, published February 29 in the open-access journal PLoS Computational Biology, add new knowledge to understanding the development of this disease and may also point the way to new corrective treatments ... This press release refers to an upcoming article in PLoS Computational Biology ... About PLoS Computational Biology. (EurekAlert!)
Whites an Inferior Race? Feb 23, 2008
"Since we tend to think of European populations as quite large, we did not expect to see a significant difference in the distribution of neutral and deleterious variation between the two populations," said senior co-author Carlos Bustamante, an assistant professor of biological statistics and computational biology at Cornell. Related. (Fox News)
Ancient Impact Seen In Modern European Diversity Feb 22, 2008
"What we may be seeing is a 'population genetic echo' of the founding of Europe," said Carlos Bustamante, assistant professor of biological statistics and computational biology at Cornell and senior co-author with Andrew Clark, a professor of molecular biology and genetics. "Since we tend to think of European populations as quite large, we did not expect to see a significant difference in the distribution of neutral and deleterious variation between the two populations," said Bustamante. (Science Daily)
DNA Findings Reveal Genetic History of Humans Feb 22, 2008
In the second report, Carlos Bustamante, an assistant professor of biological statistics and computational biology at Cornell University, looked at DNA from European-Americans and black Americans. The researchers looked at 10,000 genes in 15 black Americans and 20 European-Americans, all of whom were healthy. (MEDLINEplus)
DNA findings confirm "out of Africa" theories Feb 21, 2008
In another study, Carlos Bustamante, an assistant professor of biological statistics and computational biology at Cornell University, looked at 10,000 genes in 15 black Americans and 20 European-Americans, all of whom were healthy. "Across all the individuals, we found almost 40,000 DNA sites that varied. The African-American sample [had] more variations than the European-American sample, which is consistent with previous work showing higher levels of overall genetic diversity in... (Xinhuanet, China)
How Believing Can Be Seeing: Context Dictates What We Believe We See Feb 20, 2008
19, 2008) Scientists at UCL (University College London) have found the link between what we expect to see, and what our brain tells us we actually saw. The study reveals that the context surrounding what we see is all important -- sometimes overriding the evidence gathered by our eyes and even causing us to imagine things which aren't really there. (Science Daily)
Defining Cancer's Genetic 'Support Network' Feb 20, 2008
The team reported its findings in PLoS Computational Biology on Feb. 15, 2008. Collaborators on the study include Elena Edelman and Justin Guinney, both graduate students in the Computational Biology and Bioinformatics Program, Jen-Tsan Chi, assistant professor of molecular genetics and microbiology and Phillip Febbo, assistant professor in the department of medicine. (Science Daily)
Human-pathogen Protein Interactions Illuminated With Bioinformatics Feb 18, 2008
Matt Dyer, a bioinformatician at VBI and a graduate student in Virginia Tech's Genetics, Bioinformatics, and Computational Biology Program, remarked: "Infectious diseases result in millions of deaths each year. Although much effort has been directed towards the study of how infection by a pathogen causes disease in humans, only recently have large data sets for protein interactions become publicly available. We have leveraged this opportunity to compare protein interactions between human and... (Science Daily)
How believing can be seeing: Study shows how context dictates what we believe we see Feb 16, 2008
The study, published in this weeks PLoS Journal of Computational Biology, reveals that the context surrounding what we see is all important sometimes overriding the evidence gathered by our eyes and even causing us to imagine things which arent really there ... Filling-in and suppression of visual perception from context a Bayesian account of perceptual biases by contextual influences, by Professor Li Zhaoping and Dr Li Jingling appears in the 15 February issue of the journal PLoS... (EurekAlert!)
Pathway To Turn Off Immune System Cells Discovered Feb 2, 2008
D., research associate in Bohjanen's molecular biology laboratory, who received training in computational biology through a Minnesota Supercomputing Institute fellowship. The research is published in the February 1 issue of Molecular Cell. (Science Daily)
Computer Vision May Not Be As Good As Thought Feb 1, 2008
"The ease with which we recognize visual objects belies the computational difficulty of this feat," explains DiCarlo, senior author of the study in the online Jan. 25 PLoS Computational Biology. "The core challenge is image variation. Any given object can cast innumerable images onto the retina depending on its position, distance, orientation, lighting and background.". (Science Daily)
Biologists Use Computers To Study Bacterial Cell Division Jan 31, 2008
The research, published in the January issue of PLoS Computational Biology, looks at the molecular machinery that governs replication of DNA and cell division in Caulobacter crescentus, an easily studied bacterium that is closely related to the bacteria that fix nitrogen in legumes and to the bacteria that cause brucellosis in cattle and Rocky Mountain spotted fever in humans ... "Computational biology is not much different from experimental biology -- you learn, publish, and keep working. There... (Science Daily)
How Some Plants And Animals Appear To Defy The Aging Process Jan 18, 2008
The research paper 'Density Dependence Triggers Runaway Selection of Reduced Senescence' is published in PLoS Computational Biology. Adapted from materials provided by. (Science Daily)
Postdoctoral Appointee Metabolic Network Modeling Jan 18, 2008
Department Description: The Computational Bioscience department, based in Albuquerque, New Mexico, collaboratively develops computational biology tools for application to biology and biotechnology S&T challenges relevant to Sandia s National Security missions ... The department is thus the focal point of our efforts to grow computational biology programs at Sandia to support the objectives of Sandia s Strategic Management Units. (Nature News Service)
UK's largest ever illegal coral seizure Jan 16, 2008
"Posted by: - 14 hours, 43 minutes agoDate: Tuesday January 15th, 2008, 5:40 pmPlease login to leave a comment Login Please login using your current username and password. If you have forgotten your details you can get a . Username Password Keep me signed in About the author: Matt Clarke Website Editor, Matt Clarke, writes the regular Interesting Imports column on rare and unusual fish in the UK aquarium trade. He's kept fish for over 20 years and holds a degree, two higher degrees and two... (Practical Fishkeeping)
Drug Addiction Genes Identified Jan 10, 2008
The researchers focused on four addictive substances -- cocaine, opiate, alcohol and nicotine -- and mapped out five main routes, or "molecular pathways", that lead to addiction, they wrote in the journal PLoS Computational Biology. Figuring out the molecular pathways of complex diseases is important as the genes and proteins involved are narrowed down. (MEDLINEplus)
* World News Quick Take Jan 9, 2008
The researchers focused on four addictive substances -- cocaine, opiates, alcohol and nicotine -- and mapped out five main routes, or "molecular pathways," that lead to addiction, they wrote in the journal PLoS Computational Biology. JAPAN. (Taipei Times, Taiwan -- World)
480 Genes That Control Human Cell Division Identified Jan 9, 2008
8, 2008) A team of U.S., Israeli and German scientists used computational biology techniques to discover 480 genes that play a role in human cell division and to identify more than 100 of those genes that have an abnormal pattern of activation in cancer cells ... "Some of the mutations may be caused by the non-cycling genes, rather than the other way around," said Bar-Joseph, an assistant professor of computer science and machine learning in the School of Computer Science and a member of... (Science Daily)
China experts identify drug addiction genes Jan 8, 2008
The researchers focused on four addictive substances -- cocaine, opiate, alcohol and nicotine -- and mapped out five main routes, or "molecular pathways," that lead to addiction, they wrote in the journal PLoS Computational Biology. Figuring out pathways are important in the study of complex diseases as they narrow down the genes and proteins involved. (Scientific American)
Assembling the jigsaw puzzle of drug addiction Jan 5, 2008
This novel paper appears in PLoS Computational Biology on January 4, 2008 ... This press release refers to an upcoming article in PLoS Computational Biology ... About PLoS Computational Biology. (EurekAlert!)
New Gene Prediction Method Capitalizes On Multiple Genomes Dec 21, 2007
Subjects covered include any aspect of molecular, cellular, organismal or population biology studied from a genomic perspective, as well as genomics, proteomics, bioinformatics, genomic methods (including structure prediction), computational biology, sequence analysis (including large-scale and cross-genome analyses), comparative biology and evolution. Genome Biology has an impact factor of 7. (Science Daily)
Why don't we get cancer all the time? Dec 20, 2007
Pepper and his colleagues published their paper, "Animal Cell Differentiation Patterns Suppress Somatic Evolution," in the current issue of PLoS Computational Biology. Pepper's co-authors are Kathleen Sprouffske of the University of Pennsylvania in Philadelphia and the Wistar Institute in Philadelphia and Carlo C. Maley of the Wistar Institute. (EurekAlert!)
Human Evolution May Be Spurred By Gene Loss Dec 15, 2007
Their findings appear in the December 14 issue of PLoS Computational Biology. This research was funded by the National Human Genome Research Institute, the National Institutes of Health, the National Cancer Institute, and the Howard Hughes Medical Institute. (Science Daily)
Bodily breakdown explained: How cell differentiation patterns suppress somatic evolution Dec 14, 2007
Fortunately it is normally controlled by a well-known pattern of ongoing cell differentiation in the mature tissues of animals, according to a new study published December 14 in PLoS Computational Biology ... This press release refers to an upcoming article in PLoS Computational Biology ... About PLoS Computational Biology. (EurekAlert!)
New computational technique can predict drug side effects Dec 12, 2007
Their study is currently available on line at PLoS Computational Biology. Conventional test methods screen compounds in animal studies in advance of human trials in the hope of identifying the side effects of promising therapeutics. (EurekAlert!)
Malaria Parasite In Patient Blood Finds Distinct Physiological States Dec 5, 2007
"This work illustrates the true power that comes from developing the right computational methods and applying them to important biomedical problems," said co-senior author Jill Mesirov, director of Computational Biology and Bioinformatics at the Broad Institute of MIT and Harvard. "Even more importantly, it reflects scientific research at its best -- a global effort that brings together clinicians and researchers with diverse expertise, working directly with patients in areas hardest hit by... (Science Daily)
Gene Research Has Implications For Huntington's Disease Nov 26, 2007
These findings were recently presented in PLoS Computational Biology. Adapted from materials provided by. (Science Daily)
Evolutionary Comparison Finds New Human Genes Nov 24, 2007
The research is reported by Adam Siepel, Cornell assistant professor of biological statistics and computational biology, Cornell postdoctoral researcher Brona Brejova and colleagues at several other institutions in the online version of the journal Genome Research, and it will appear in the December print edition. The complete human genome was sequenced several years ago, but that simply means that the order of the 3 billion or so chemical units, called bases, that make up the genetic code is... (Science Daily)
Rebuilding the evolutionary history of HIV-1 unravels a complex loop Nov 24, 2007
An essential component of the human immunodeficiency virus (HIV-1) molecular machinery responsible for infecting cells consists of functionally-specialized layers, according to a study by investigators at the University of California San Diego (UCSD) Antiviral Research Center (AVRC), published November 23 in PLoS Computational Biology ... This press release refers to an upcoming article in PLoS Computational Biology ... About PLoS Computational Biology. (EurekAlert!)
Are There Rearrangement Hot Spots In The Human Genome? Nov 14, 2007
The study, published on November 9 in PLoS Computational Biology, holds that there are indeed rearrangement hotspots in the human genome. See also. (Science Daily)
Role Of Hemoglobin In Oxygen Transport Modeled At Atomic Level Nov 13, 2007
The investigation led by V;ctor Guallar, ICREA researcher with the Life Sciences department of the Barcelona Supecomputing Center (BSC) and group leader of the Joint Computational Biology Programme between the Institute for Research in Biomedicine (IRB Barcelona) and the BSC, has allowed the definition at atomic level of the mechanism that regulates the exchange of lung oxygen to hemoglobin and from hemoglobin to tissue. More than a hundred years of study have led to the knowledge that... (Science Daily)
Genome study charts genetic landscape of lung cancer Nov 5, 2007
11Departments of Medicine, Surgery, Pathology, and Computational Biology, 12Human Oncology and Pathogenesis Program, 13Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA 10065. 14Section of Thoracic Surgery, Department of Surgery and 15Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA 48109. (EurekAlert!)
Unravelling The Secrets Of Cancer Cells Oct 30, 2007
Professor Soto, Professor of Anatomy and Cellular Biology at Tufts, is working alongside UU s Professor Vyvyan Howard, Professor of Bio-Imaging, Dr George McKerr, Director of the Centre for Advanced Imaging and Dr Kurt Saetzler, a lecturer in computational biology. Professor Soto says: We think the 3-D model will allow us to study cancer as it occurs. (Science Daily)
DNA pioneer retires after comment on blacks Oct 27, 2007
Under Watson's direction, the laboratory has investigated the genetic causes of cancer, plant biology, neuroscience and computational biology, according to a statement the lab issued Thursday about Watson's retirement. In his own statement, which amounted to a professional biography, Watson described coming to the lab 49 years ago to give his first course, and he noted the contributions to scientific understanding that the research center has made since then. (San Francisco Chronicle)
DNA pioneer steps down as lab chief after racial remark Oct 26, 2007
After he left Harvard to direct the laboratory, Watson transformed it from a small facility into a world-class institution prominent in research on cancer, plant biology, neuroscience, and computational biology, the board said in announcing his retirement. Bruce Stillman, who succeeded him as president, said that Watson had created an unparalleled research environment at the lab. (Boston Globe)
Emergence of recombinant forms of HIV: dynamics and scaling Oct 26, 2007
In a study publishing in PLoS Computational Biology on October 26, 2007, researchers Suryavanshi and Dixit from the Indian Institute of Science, Bangalore, India present a new model of HIV dynamics that provides a detailed account of the emergence and growth of recombinant forms of HIV following infection with diverse viral genomes ... PLEASE MENTION THE OPEN ACCESS JOURNAL PLoS COMPUTATIONAL BIOLOGY () AS THE SOURCE FOR THIS ARTICLE AND PROVIDE A LINK TO THE FREELY AVAILABLE TEXT. THANK YOU.... (EurekAlert!)
CMU given big grant for Life Sciences Oct 23, 2007
The latest gift will establish a Life Sciences Competitiveness Fund to support faculty, new labs and a Presidential Scholars Fund for graduate students focusing on life science fields, such as computational biology, medical robotics and biomedical engineering. "The world is seeing phenomenal breakthroughs in biological sciences, and the implications of that for human health and business are tremendous," said CMU President Jared Cohon. (Pittsburgh Post-Gazette, PA)
