Carnegie Mellon University’s Justin Y. Newberg and Robert F. Murphy have developed a software toolbox that is intended to help bioscience researchers characterize protein patterns in human tissues.

Researchers from the United States and Switzerland have developed mathematical and statistical tools for reconstructing viral populations using pyrosequencing, a novel and effective technique for sequencing DNA. They describe their findings in an article published May 9th in the open-access journal PLoS Computational Biology.

Genome Research is publishing several papers related to analyses of the duck-billed platypus (Ornithorhynchus anatinus) genome sequence. The place of (egg-laying) monotremes, such as the platypus, in mammalian evolutionary history has remained controversial. Now, researchers are finding that the distinctive anatomical and physiological properties of the platypus are reflected in the newly sequenced platypus genome. Through comparative genomics, the platypus genome is providing remarkable insights into the evolution of venom components, the sex-determination system, testicular descent, and small RNA pathways. Primary research reports describing these novel insights will appear online May 8, concurrent with publication of the platypus genome sequence report in the journal Nature.

The genome of a newly-emerging superbug, commonly known as Steno, has just been sequenced. The results reveal an organism with a remarkable capacity for drug resistance. The research was carried out by scientists at the Wellcome Trust Sanger Institute near Cambridge and the University of Bristol.

A nationwide team of researchers, funded in part by the National Human Genome Research Institute (NHGRI), one of the National Institutes of Health (NIH), has produced the first sequence-based map of large-scale structural variation across the human genome. The work, published today in the journal Nature, provides a starting point to examine how such DNA variation contributes to human health and disease.

The papaya ringspot virus (PRSV) interferes with the plant's ability to photosynthesize. The transgenic papaya at the center of this field (darker, rectangular patch of green) are surrounded by non-transgenic... A broad collaboration of research institutions in the U.S. and China has produced a first draft of the papaya genome. This draft, which spells out more than 90 percent of the plant’s gene coding sequence, sheds new light on the evolution of flowering plants. And because it involves a genetically modified plant, the newly sequenced papaya genome offers the most detailed picture yet of the genetic changes that make the plant resistant to the papaya ringspot virus.

The availability of new genome sequencing technology has prompted a Virginia Tech plant scientist to test an intriguing hypothesis about how agriculture’s early beginnings may have impacted the evolution of plant pathogens.

Hemoglobin (PDB ID 4hhb), one of the earliest structures deposited in the archive. Today, there are dozens of structures of hemoglobin in the PDB, showing the process of oxygen binding and revealing the molecular details of sickle cell anemia. Credit: Protein Data Bank and David Goodsell The Protein Data Bank (PDB) based at Rutgers, The State University of New Jersey, and the University of California-San Diego (UCSD) this month reached a significant milestone in its 37-year history. The 50,000th molecule structure was released into its archive, joining other structures vital to pharmacology, bioinformatics and education.

For a quarter century, GenBank has helped advance scientific discovery worldwide. Established by the National Institutes of Health (NIH) in 1982, the database of nucleic acid sequences is one of the key tools that scientists use to conduct biomedical and biologic research. Since its creation, GenBank has grown at an exponential rate, doubling in size every 18 months. In celebration of this vital resource and its contribution to science over the last 25 years, the National Center for Biotechnology Information, National Library of Medicine (NLM), NIH, is holding a two-day conference on GenBank.

Giant panda. Cardiff University is contributing to the first genome project to assist conservation efforts for an endangered species.

Scientists have discovered two key proteins that guide one of the two groups of pathogenic bacteria to make their hardy outer shells -- their defense against the world.

75% of all animal species in the world are insects. The largest group within insects are beetles (400,000 species). Beetles can be very beautiful and colorful, but many beetle species are also serious agricultural pests that can destroy food plants like potatoes (the Colorado potato beetle) and threaten large areas of forest. Altogether, insect pests cause U.S. $ 26 billion in losses to U.S. agriculture yearly and beetles are responsible for a substantial part of this.

Human diseases and social networks would seem to have little in common. However, at the crux of these two lies a network, communities within the network, and farther even, substructures of the communities. In a recent paper in Physical Review E 77:016104 (2008), Weixiong Zhang, Ph.D., Washington University associate professor of computer science and engineering and of genetics, and his Ph.D. student, Jianhua Ruan, published an algorithm, a recipe of computer instructions, to automatically discover communities and their subtle structures in various networks.

In 2005, NSF, DOE, and USDA funded the sequencing of the corn genome. A consortium of researchers led by the Genome Sequencing Center (GSC) at Washington University in St. Louis, Mo., announced today the completion of a draft sequence of the corn genome.

Scientists may gain a new insight into the relationship between viruses and their environments thanks to a new computational technology developed by researchers at the U.S. Department of Energy’s (DOE) Argonne National Laboratory. This technology has already been used to identify subtle differences in the metabolic processes of microbial communities.

By using computer simulations and modeling, an international group of researchers including scientists from the Virginia Bioinformatics Institute (VBI) at Virginia Tech’s Network Dynamics and Simulation Science Laboratory (NDSSL) have determined how a pandemic influenza outbreak might travel through a city similar in size to Chicago, Ill. This information helped them to determine the preferred intervention strategy to contain a potential flu pandemic, including what people should do to decrease the likelihood of disease transmission.

BGI-Shenzhen is pleased to announce the launch of the International Giant Panda Genome Project. This announcement follows on the heels of the Panda Genome workshop held on January 21–22, 2008, in Shenzhen, China. Dr. Hongmei Zhu, a scientist from BGI-Shenzhen, stated that, "The goal of this project is to finish the sequencing and assembling of the draft sequence within six months."

A study led by Brown University biologist Casey Dunn uses new genomics tools to answer old questions about animal evolution. The study is the most comprehensive animal phylogenomic research project to date, involving 40 million base pairs of new DNA data taken from 29 animal species.

Genomatix Software with businesses in Munich, Germany and Ann Arbor, Michigan released today that the group of Kenneth R. Boheler at the National Institute on Aging, National Institutes of Health, Baltimore, Md published some remarkable work on embryonic stem (ES) cells.

Researchers from the University of North Carolina at Chapel Hill have identified a key molecular mechanism that may account for the development of cystic fibrosis, which about 1 in 3000 children are born with in the US every year. 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.

The pea is one of many important crop species that is unsuited to the Agrobacterium-based genetic modification techniques that are commonly used to work with crops. Researchers, reporting in the open access journal Genome Biology have now discovered the first high-throughput forward and reverse genetics tool for the pea (Pisum sativum), could have major benefits for crop breeders around the world..

Genomatix Software GmbH, a Systems Biology company focussed on high quality annotation and the understanding of gene regulation, has begun showcasing its abilities in the analysis of data generated by Next Generation Sequencing (NGS) technology.

A team of scientists led by Washington University in St. Louis has begun to unlock the genetic secrets of corn, a crop vital to U.S. agriculture. The researchers have completed a working draft of the corn genome, an accomplishment that should accelerate efforts to develop better crop varieties to meet society's growing demands for food, livestock feed and fuel.

University of Michigan scientists and their colleagues at the National Institute on Aging have produced the largest and most detailed worldwide study of human genetic variation, a treasure trove offering new insights into early migrations out of Africa and across the globe.

To meet the demands of biologists who work with the model worm C. elegans in the laboratory, a new anatomical atlas has just been published. It is the most detailed and comprehensive atlas of C. elegans in print to date and will be an essential laboratory reference tool for all working worm biologists.

In order for meat producers and retailers to satisfy anticipated consumer desires to avoid meat and milk from cloned animals, access to DNA from every unique clone should be made public so that DNA traceability technology can be used, according to Patrick Cunningham of Dublin's Trinity College and Chief Scientific Adviser to the Government of Ireland, who will speak at the American Association for the Advancement of Science (AAAS) conference in Boston tomorrow.

Choanoflagellates are aquatic microbial eukaryotes that are distinguished by an apical flagellum (green), which is used for swimming and feeding, surrounded by a collar of microvilli or tentacles (red) against which bacterial prey are trapped. The nucleus is highlighted in blue. Credit: Nicole King laboratory, UC Berkeley The newly sequenced genome of a one-celled, planktonic marine organism, reported today (Thursday, Feb. 14) in the journal Nature, is already telling scientists about the evolutionary changes that accompanied the jump from one-celled life forms to multicellular animals like ourselves.

The study, published today in Proceedings of the National Academy of Sciences, USA, claims to have solved this scientific riddle by analysing the genomics of primitive living fishes such as sharks and lampreys and their spineless relatives, such as the sea squirts.

Genomatix is a company with a renowned track record in the analysis of genomic data generated by high throughput technologies. Genomatix algorithms include optimized fast mapping strategies and Genomatix already provides the most complete genome annotation in terms of transcriptome and promoters available in its ElDorado database surpassing alternative databases in this specific content by a factor of 2 to 4.

More than 99 percent of all modern potato varieties planted today are the direct descendents of varieties that once grew in the lowlands of south-central Chile. How Chilean germplasm came to dominate the modern potato-which spread worldwide from Europe-has been the subject of a long, contentious debate among scientists.