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Phylogenomic identification of regulatory sequences in bacteria: an analysis of statistical power and an application to Borrelia burgdorferi sensu lato.
Phylogenomic footprinting is an approach for ab initio identification of genome-wide regulatory elements in bacterial species based on sequence conservation. The statistical power of the phylogenomic approach depends on the degree of sequence conservation, the length of regulatory elements, and the level of phylogenetic divergence among genomes. Building on an earlier model, we propose a binomial model that uses synonymous tree lengths as neutral expectations for determining the statistical...
About Yu “Max” Qian
Dr. Yu “Max” Qian is an associate professor specializing in single cell cytometry informatics. After PhD graduation, he joined the University of Texas Southwestern Medical Center at Dallas (UT Southwestern) as a postdoctoral senior research associate, where he was trained on immunology informatics, bioinformatics, and clinical informatics. He was appointed as an assistant professor of Department of Clinical Sciences and Department of Pathology of UT Southwestern in 2010.
Pathema: a clade-specific bioinformatics resource center for pathogen research.
Pathema (http://pathema.jcvi.org) is one of the eight Bioinformatics Resource Centers (BRCs) funded by the National Institute of Allergy and Infectious Disease (NIAID) designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens;...
TIGR Scientists Complete the First Genome Sequence of an Oral Pathogen Associated with Severe Adult Periodontal Disease
June 12, 2001 ROCKVILLE, MD June 12, 2001 — Biologists at The Institute for Genomic Research (TIGR) in Rockville, MD in collaboration with The Forsyth Institute in Boston, MA, have completed the sequence from Porphyromonas gingivalis, the first oral disease-causing microbe to be completely sequenced. Porphyromonas gingivalis is a bacterium, which may causeadult periodontitis, or gum disease. The Centers for Disease Control estimates that millions of Americans suffer from...
AGBT, Marco Island 2010
I just got back from AGBT in Marco Island, Florida and I am still in awe. As noted in the name, this conference highlights advances in both genome biology and technology. The biology seemed to be very human genome centric. Many of the talks presented full genome sequences of cancer genomes or familial cohorts. Some of the numbers that people threw around were shocking. It was only a short time ago that Craig Venter came out with the first personal genome, and now sequencing centers like...
Sequencing of Human Adenovirus Clinical Isolates From Recent and Reference Genomes
Human adenoviruses (HAdV) are pathogens causing a range of human infectious diseases, including respiratory, ocular, gastrointestinal, renal and metabolic. HAdV infections can be highly contagious, causing high morbidity rate and mortality rates and result in outbreaks. They are also a model organism in the research laboratory for cell and molecular biology. The goal of this project is to understand HAdV biology, especially the evolution and emergence of new and highly pathogenic...
About Marcelo Freire
Marcelo Freire is an associate professor in the Genomic Medicine and Infectious Disease Department at the J. Craig Venter Institute (JCVI). Prior to joining JCVI, Dr. Freire was an assistant faculty member at The Forsyth Institute and Harvard University (Division of Oral Medicine, Infection and Immunity). Early in his career, he worked on tissue biology of infectious diseases, biofilm-induced bone diseases and antibody engineering. As a dual-scientist and clinician, Dr.
About Gene S. Tan
Gene Tan is an associate professor at the J. Craig Venter Institute working in the Infectious Disease group. The focus of his research is on virus-host interactions by defining the immunological, molecular and genetic determinants that govern immunity and disease. The aim is to better understand how viruses manipulate the host machinery to replicate and in turn elucidate the mechanisms by which the host counteracts the pathogen.
Fighting Back Against Flu
The 1918 influenza pandemic, which affected 500 million people globally and caused 50-100 million deaths, was the most severe pandemic in recorded history. Over the course of the last 100 years, advances in science and medicine have provided the tools to address influenza much more successfully. However, despite vaccines and supportive medical interventions such as antivirals and antibiotics, influenza remains a public health problem and can be deadly for the very young, the elderly, and...
DNA Synthesis and Biosecurity:
Lessons Learned and Options for the Future
Synthetic biology promises great scientific advances, but it also has the potential to pose unique biosecurity threats. It now is easier than ever to synthesize very long pieces of DNA from chemicals, potentially enabling a bioterrorist to build a toxin gene or an entire pathogenic virus. In 2007, the JCVI Policy Team released a report titled, “Synthetic Genomics: Options for Governance,” in which we proposed and evaluated a variety of options to address this biosecurity threat. A...