Bioinformatics Resource Centers - AbsoluteAstronomy.com

The Bioinformatics Resource Centers (BRCs) are a group of five Internet-based research centers established in 2004 and funded by NIAID (the National Institute of Allergy and Infectious Diseases

National Institute of Allergy and Infectious Diseases

The National Institute of Allergy and Infectious Diseases is one of the 27 institutes and centers that make up the National Institutes of Health , an agency of the United States Department of Health and Human Services...

.) The BRCs were formed in response to the threats posed by emerging and re-emerging pathogens

Pathogen

A pathogen gignomai "I give birth to") or infectious agent — colloquially, a germ — is a microbe or microorganism such as a virus, bacterium, prion, or fungus that causes disease in its animal or plant host...

, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism

Bioterrorism

Bioterrorism is terrorism involving the intentional release or dissemination of biological agents. These agents are bacteria, viruses, or toxins, and may be in a naturally occurring or a human-modified form. For the use of this method in warfare, see biological warfare.-Definition:According to the...

. The intention of NIAID in funding these bioinformatics

Bioinformatics

Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs

DRUGS

Destroy Rebuild Until God Shows are an American post-hardcore band formed in 2010. They released their debut self-titled album on February 22, 2011.- Formation :...

, vaccines, or diagnostic tools to combat them.

The main goals of the BRCs are as follows:

1) To create comprehensive databases of reliable, up-to-date bioinformatic data (genetic

Genetics

Genetics , a discipline of biology, is the science of genes, heredity, and variation in living organisms....

, proteomic, biochemical, or microbiological) related to the pathogens of interest;

2) To provide researchers with easy access to these data through Internet-based search and data retrieval user interfaces;

3) To provide researchers with relevant, state-of-the art computational tools

Computational biology

Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems...

for bioinformatic analysis of these data.

The five BRCs are supported by various institutions, both publicly and privately owned, throughout the USA and Canada. Each BRC focuses on a different group of pathogens. The Pathogen Portal serves as a common repository and provides summary information about and links into the BRCs.

Bioinformatics Resource Centers
Name	Acrono name	Contributing organization(s)	Number of organisms covered	Organisms covered (CDC Category)
Eukaryotic Pathogen Database Resources	EuPathDB	University of Pennsylvania University of Pennsylvania The University of Pennsylvania is a private, Ivy League university located in Philadelphia, Pennsylvania, United States. Penn is the fourth-oldest institution of higher education in the United States,Penn is the fourth-oldest using the founding dates claimed by each institution... University of Georgia University of Georgia The University of Georgia is a public research university located in Athens, Georgia, United States. Founded in 1785, it is the oldest and largest of the state's institutions of higher learning and is one of multiple schools to claim the title of the oldest public university in the United States...	45 in 13 genera	Crithidia Crithidia Crithidia are members of the trypanosome protozoa. They are parasites that exclusively parasitise arthropods, mainly insects. They pass from host to host as cysts in infective faeces and typically, the parasites develop in the digestive tracts of insects and interact with the intestinal epithelium... (Other) Cryptosporidium Cryptosporidium Cryptosporidium is a protozoan that can cause gastro-intestinal illness with diarrhea in humans.Cryptosporidium is the organism most commonly isolated in HIV positive patients presenting with diarrhea... (B) Encephalitozoon (Group I) Entamoeba Entamoeba Entamoeba is a genus of Amoebozoa found as internal parasites or commensals of animals.In 1875, Fedor Lösch described the first proven case of amoebic dysentery in St Petersburg, Russia. He referred to the amoeba he observed microscopically as 'Amoeba coli'; however it is not clear whether he was... (B) Enterocytozoon (Group I) Giardia Giardia Giardia is a genus of anaerobic flagellated protozoan parasites of the phylum Metamonada in the supergroup "Excavata" that colonise and reproduce in the small intestines of several vertebrates, causing giardiasis, commonly known as Beaver fever... (B) Leishmania Leishmania Leishmania is a genus of Trypanosomatid protozoa, and is the parasite responsible for the disease leishmaniasis. It is spread through sandflies of the genus Phlebotomus in the Old World, and of the genus Lutzomyia in the New World. Their primary hosts are vertebrates; Leishmania commonly infects... (Other) Neospora Neospora Neospora is an important pathogen in cattle and dogs. It was not discovered until 1984 in Norway, where it was found in dogs. It is highly transmissible and some herds can have up to a 90% prevalence. Neospora causes abortions in cattle and up to 33% of pregnancies can result in aborted fetuses on... (Other) Plasmodium Plasmodium Plasmodium is a genus of parasitic protists. Infection by these organisms is known as malaria. The genus Plasmodium was described in 1885 by Ettore Marchiafava and Angelo Celli. Currently over 200 species of this genus are recognized and new species continue to be described.Of the over 200 known... (Other) Theileria Theileria Theileria is a genus of parasitic protozoan that belongs to the phylum Apicomplexa and is closely related to Plasmodium. Two Theileria species, T. annulata and T. parva, are important cattle parasites. T. annulata causes tropical theileriosis and T. parva causes East Coast fever. Theileria are... (Other) Toxoplasma (B) Trichomonas Trichomonas Trichomonas is a genus of anaerobic protists that are parasites of vertebrates. They are included with the parabasalids.Species of Trichomonas include:*Trichomonas vaginalis, an organism generally living inside the vagina of humans... (Other) Trypanosoma Trypanosoma Trypanosoma is a genus of kinetoplastids , a monophyletic group of unicellular parasitic flagellate protozoa. The name is derived from the Greek trypano and soma because of their corkscrew-like motion. All trypanosomes are heteroxenous and are transmitted via a vector... (Other)
Influenza Research Database Influenza Research Database The Influenza Research Database is an integrative and comprehensive publicly-available database and analysis resource to search, analyze, visualize, save and share data for influenza virus research...	IRD	Northrop Grumman Northrop Grumman Northrop Grumman Corporation is an American global aerospace and defense technology company formed by the 1994 purchase of Grumman by Northrop. The company was the fourth-largest defense contractor in the world as of 2010, and the largest builder of naval vessels. Northrop Grumman employs over... Information Technology University of Texas Southwestern Medical Center University of Texas Southwestern Medical Center The University of Texas Southwestern Medical Center is one of the biomedical research institutions of the University of Texas System, incorporating three degree-granting institutions, four affiliated hospitals, including Parkland Memorial, the teaching hospital, and biomedical research... Vecna Technologies Vecna Technologies Vecna is a leading provider of health care IT and robotics solutions. Vecna's health care IT products include QC PathFinder electronic infection surveillance software, patient self-service kiosks and web portal, and QC Bot medication delivery robot. Vecna Robotics is the developer of innovative...	1	Influenza Virus (flu) (C)
PathoSystems Resource Integration Center	PATRIC PATRIC PATRIC, the Pathosystems Resource Integration Center, is one of the four Bioinformatics Resource Centers funded by the National Institutes of Allergy and Infectious Diseases, NIAID a component of the National Institutes of Health , which is an agency of the United States Department of Health and...	Virginia Bioinformatics Institute Virginia Bioinformatics Institute The Virginia Bioinformatics Institute at Virginia Tech is a bioinformatics, computational biology, and systems biology research facility that uses transdisciplinary approaches combining information technology, biology and medicine to interpret and apply vast amounts of biological data generated... University of Chicago University of Chicago The University of Chicago is a private research university in Chicago, Illinois, USA. It was founded by the American Baptist Education Society with a donation from oil magnate and philanthropist John D. Rockefeller and incorporated in 1890... National Centre for Text Mining	22 genera	Bacillus Bacillus Bacillus is a genus of Gram-positive, rod-shaped bacteria and a member of the division Firmicutes. Bacillus species can be obligate aerobes or facultative anaerobes, and test positive for the enzyme catalase. Ubiquitous in nature, Bacillus includes both free-living and pathogenic species... (A) Bartonella Bartonella Bartonella is a genus of Gram-negative bacteria. Facultative intracellular parasites, Bartonella species can infect healthy people but are considered especially important as opportunistic pathogens. Bartonella are transmitted by insect vectors such as ticks, fleas, sand flies and mosquitoes... (Group I) Borrelia Borrelia Borrelia is a genus of bacteria of the spirochete phylum. It causes borreliosis, a zoonotic, vector-borne disease transmitted primarily by ticks and some by lice, depending on the species... (Group I) Brucella Brucella Brucella is a genus of Gram-negative bacteria. They are small , non-motile, non-encapsulated coccobacilli, which function as facultative intracellular parasites.... (B) Burkholderia Burkholderia Burkholderia is a genus of proteobacteria probably best known for its pathogenic members:Burkholderia mallei, responsible for glanders, a disease that occurs mostly in horses and related animals;... (B) Campylobacter Campylobacter Campylobacter is a genus of bacteria that are Gram-negative, spiral, and microaerophilic. Motile, with either unipolar or bipolar flagella, the organisms have a characteristic spiral/corkscrew appearance and are oxidase-positive. Campylobacter jejuni is now recognized as one of the main causes... (B) Chlamydophila Chlamydophila Chlamydophila is a bacterial genus belonging to the family Chlamydiaceae, order Chlamydiales, class/phylum Chlamydiae.-Taxonomy:Chlamydophila was recognized in 1999, with six species in Chlamydophila and three in the original genus, Chlamydia... (B) Clostridium Clostridium Clostridium is a genus of Gram-positive bacteria, belonging to the Firmicutes. They are obligate anaerobes capable of producing endospores. Individual cells are rod-shaped, which gives them their name, from the Greek kloster or spindle... (A) Coxiella Coxiella Coxiella refers to a genus of Gram-negative bacteria in the family Coxiellaceae. It is named after Harold Herald Rea Cox , an American bacteriologist. Coxiella burnetii is the only member of this genus... (B) Ehrlichia Ehrlichia Ehrlichia is a genus of rickettsiales bacteria. They are transmitted by ticks. Several species can cause infection in humans. The genus is named after German microbiologist Paul Ehrlich... (Group I) Escherichia Escherichia Escherichia is a genus of Gram-negative, non-spore forming, facultatively anaerobic, rod-shaped bacteria from the family Enterobacteriaceae. In those species which are inhabitants of the gastrointestinal tracts of warm-blooded animals, Escherichia species provide a portion of the... (B) Francisella Francisella Francisella is a genus of pathogenic, Gram-negative bacteria. They are small coccobacillary or rod-shaped, non-motile organisms, which are also facultative intracellular parasites of macrophages... (A) Helicobacter Helicobacter Helicobacter is a genus of Gram-negative bacteria possessing a characteristic helix shape. They were initially considered to be members of the Campylobacter genus, but since 1989 they have been grouped in their own genus... (Group I) Lysteria (B) Mycobacterium Mycobacterium Mycobacterium is a genus of Actinobacteria, given its own family, the Mycobacteriaceae. The genus includes pathogens known to cause serious diseases in mammals, including tuberculosis and leprosy... (C) Rickettsia Rickettsia Rickettsia is a genus of non-motile, Gram-negative, non-sporeforming, highly pleomorphic bacteria that can present as cocci , rods or thread-like . Being obligate intracellular parasites, the Rickettsia survival depends on entry, growth, and replication within the cytoplasm of eukaryotic host cells... (B, C) Salmonella Salmonella Salmonella is a genus of rod-shaped, Gram-negative, non-spore-forming, predominantly motile enterobacteria with diameters around 0.7 to 1.5 µm, lengths from 2 to 5 µm, and flagella which grade in all directions . They are chemoorganotrophs, obtaining their energy from oxidation and reduction... (B) Shigella Shigella Shigella is a genus of Gram-negative, nonspore forming, non-motile, rod-shaped bacteria closely related to Escherichia coli and Salmonella. The causative agent of human shigellosis, Shigella causes disease in primates, but not in other mammals. It is only naturally found in humans and apes. During... (B) Staphylococcus Staphylococcus Staphylococcus is a genus of Gram-positive bacteria. Under the microscope they appear round , and form in grape-like clusters.... (B) Vibrio Vibrio Vibrio is a genus of Gram-negative bacteria possessing a curved rod shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Typically found in saltwater, Vibrio are facultative anaerobes that test positive for oxidase and do not form... (B) Yersinia Yersinia Yersinia is a genus of bacteria in the family Enterobacteriaceae. Yersinia are Gram-negative rod shaped bacteria, a few micrometers long and fractions of a micrometer in diameter, and are facultative anaerobes. Some members of Yersinia are pathogenic in humans; in particular, Y. pestis is the... (A, B) Other Bacteria Bacteria Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
Virus Pathogen Database and Analysis Resource Virus Pathogen Database and Analysis Resource The Virus Pathogen Database and Analysis Resource is an integrative and comprehensive publicly available database and analysis resource to search, analyze, visualize, save and share data for viral pathogens in the U.S...	ViPR	Northrop Grumman Northrop Grumman Northrop Grumman Corporation is an American global aerospace and defense technology company formed by the 1994 purchase of Grumman by Northrop. The company was the fourth-largest defense contractor in the world as of 2010, and the largest builder of naval vessels. Northrop Grumman employs over... Information Technology University of Texas Southwestern Medical Center University of Texas Southwestern Medical Center The University of Texas Southwestern Medical Center is one of the biomedical research institutions of the University of Texas System, incorporating three degree-granting institutions, four affiliated hospitals, including Parkland Memorial, the teaching hospital, and biomedical research... Vecna Technologies Vecna Technologies Vecna is a leading provider of health care IT and robotics solutions. Vecna's health care IT products include QC PathFinder electronic infection surveillance software, patient self-service kiosks and web portal, and QC Bot medication delivery robot. Vecna Robotics is the developer of innovative...	13 families	Arenaviridae (A) Bunyaviridae Bunyaviridae Bunyaviridae is a family of negative-stranded RNA viruses. Though generally found in arthropods or rodents, certain viruses in this family occasionally infect humans. Some of them also infect plants.... (A) Filoviridae Filoviridae The family Filoviridae is the taxonomic home of several related viruses that form filamentous virions. Two members of the family that are commonly known are Ebola virus and Marburg virus. Both viruses, and some of their lesser known relatives, cause severe disease in humans and nonhuman primates in... (A) Flaviviridae Flaviviridae The Flaviviridae are a family of viruses that are primarily spread through arthropod vectors . The family gets its name from Yellow Fever virus, a type virus of Flaviviridae; flavus means yellow in Latin... (A) Poxviridae Poxviridae Poxviruses are viruses that can, as a family, infect both vertebrate and invertebrate animals.Four genera of poxviruses may infect humans: orthopox, parapox, yatapox, molluscipox.... (A) Caliciviridae Caliciviridae The Caliciviridae family are a family of viruses, members of Class IV of the Baltimore scheme. They are positive-sense, single stranded RNA which is non-segmented. The caliciviruses have been found in a number of organisms such as humans, cattle, pigs, cats, chickens, reptiles, dolphins and... (B) Togaviridae Togaviridae The Togaviridae are a family of viruses, including the following genera:* Genus Alphavirus; type species: Sindbis virus, Eastern equine encephalitis virus, Western equine encephalitis virus, Venezuelan equine encephalitis virus, Ross River virus, O'nyong'nyong virus, Chikungunya* Genus Rubivirus;... (B) Hepatitis A Hepatitis A Hepatitis A is an acute infectious disease of the liver caused by the hepatitis A virus , an RNA virus, usually spread the fecal-oral route; transmitted person-to-person by ingestion of contaminated food or water or through direct contact with an infectious person... virus (B) Coronaviridae Coronaviridae Coronaviruses are enveloped, single-stranded, positive-sense RNA viruses with club-shaped surface about 120-160 nm in diameter that resemble a “corona”.-Virology:... (C) Paramyxoviridae (C) Lyssavirus Lyssavirus Lyssavirus is a genus of viruses belonging to the family Rhabdoviridae, in the order Mononegavirales. This group of RNA viruses includes the Rabies virus traditionally associated with the disease.-Structure:Viruses typically have either helical or cubic symmetry... (C) Hepatitis E Hepatitis E Hepatitis E is a viral hepatitis caused by infection with a virus called hepatitis E virus . HEV is a positive-sense single-stranded RNA icosahedral virus with a 7.5 kilobase genome. HEV has a fecal-oral transmission route. It is one of five known hepatitis viruses: A, B, C, D, and E... Herpesviridae Herpesviridae The Herpesviridae are a large family of DNA viruses that cause diseases in animals, including humans. The members of this family are also known as herpesviruses. The family name is derived from the Greek word herpein , referring to the latent, recurring infections typical of this group of viruses... Reoviridae Reoviridae Reoviridae is a family of viruses that can affect the gastrointestinal system and respiratory tract. Viruses in the family Reoviridae have genomes consisting of segmented, double-stranded RNA...
VectorBase VectorBase is one of the five Bioinformatics Resource Centers funded by the National Institutes of Allergy and Infectious Diseases, NIAID a component of the National Institutes of Health , which is an agency of the United States Department of Health and Human Services...	VB	University of Notre Dame University of Notre Dame The University of Notre Dame du Lac is a Catholic research university located in Notre Dame, an unincorporated community north of the city of South Bend, in St. Joseph County, Indiana, United States... European Bioinformatics Institute European Bioinformatics Institute The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory... Imperial College London Imperial College London Imperial College London is a public research university located in London, United Kingdom, specialising in science, engineering, business and medicine... Institute of Molecular Biology and Biotechnology Harvard University Harvard University Harvard University is a private Ivy League university located in Cambridge, Massachusetts, United States, established in 1636 by the Massachusetts legislature. Harvard is the oldest institution of higher learning in the United States and the first corporation chartered in the country... University of New Mexico University of New Mexico The University of New Mexico at Albuquerque is a public research university located in Albuquerque, New Mexico, in the United States. It is the state's flagship research institution...	5	Anopheles gambiae Anopheles gambiae Anopheles gambiae is a complex of at least seven morphologically distinguishable species of mosquitoes in the genus Anopheles. This complex was recognised in the 1960s and includes the most important vectors of malaria in sub-Saharan Africa and the most efficient malaria vectors known.This species... (Other) Aedes aegypti Aedes aegypti The yellow fever mosquito, Aedes aegypti is a mosquito that can spread the dengue fever, Chikungunya and yellow fever viruses, and other diseases. The mosquito can be recognized by white markings on legs and a marking in the form of a lyre on the thorax... (Other) Ixodes scapularis Ixodes scapularis Ixodes scapularis is commonly known as the deer tick or blacklegged tick , and in some parts of the USA as the bear tick. It is a hard-bodied tick of the eastern and northern Midwestern United States... (Other) Culex quinquefasciatus Culex Culex is a genus of mosquito, and is important in that several species serve as vectors of important diseases, such as West Nile virus, filariasis, Japanese encephalitis, St. Louis encephalitis and avian malaria.... (Other) Pediculus humanus Pediculus humanus Pediculus humanus is a species of lice that infects humans. It comprises two subspecies:Pediculus humanus humanus Linnaeus, 1758 – the body lousePediculus humanus capitis De Geer, 1767 – the head louse... (Other)
Pathogen Portal	none	Virginia Bioinformatics Institute Virginia Bioinformatics Institute The Virginia Bioinformatics Institute at Virginia Tech is a bioinformatics, computational biology, and systems biology research facility that uses transdisciplinary approaches combining information technology, biology and medicine to interpret and apply vast amounts of biological data generated...	Data for 13 species: Gene expression Gene expression Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA... , proteomics Proteomics Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...	Vaccinia Vaccinia Vaccinia virus is a large, complex, enveloped virus belonging to the poxvirus family. It has a linear, double-stranded DNA genome approximately 190 kbp in length, and which encodes for approximately 250 genes. The dimensions of the virion are roughly 360 × 270 × 250 nm, with a mass of... (Other) Variola (A) Monkeypox Monkeypox Monkeypox also known as cockpox is an exotic infectious disease caused by the monkeypox virus. The disease was first identified in laboratory monkeys, hence its name, but in its natural state it seems to infect rodents more often than primates... (A) Coronavirus Coronavirus Coronaviruses are species in the genera of virus belonging to the subfamily Coronavirinae in the family Coronaviridae. Coronaviruses are enveloped viruses with a positive-sense single-stranded RNA genome and a helical symmetry. The genomic size of coronaviruses ranges from approximately 16 to 31... (C) Brucella abortus (B) Bacillus anthracis Bacillus anthracis Bacillus anthracis is the pathogen of the Anthrax acute disease. It is a Gram-positive, spore-forming, rod-shaped bacterium, with a width of 1-1.2µm and a length of 3-5µm. It can be grown in an ordinary nutrient medium under aerobic or anaerobic conditions.It is one of few bacteria known to... (A) Salmonella typhimurium (B) Yersinia pestis Yersinia pestis Yersinia pestis is a Gram-negative rod-shaped bacterium. It is a facultative anaerobe that can infect humans and other animals.... (A) Vibrio cholerae Vibrio cholerae Vibrio cholerae is a Gram-negative, comma-shaped bacterium. Some strains of V. cholerae cause the disease cholera. V. cholerae is facultatively anaerobic and has a flagella at one cell pole. V... (B) Cryptosporidium parvum Cryptosporidium parvum Cryptosporidium parvum is one of several protozoal species that cause cryptosporidiosis, a parasitic disease of the mammalian intestinal tract.... (B) Toxoplasma gondii Toxoplasma gondii Toxoplasma gondii is a species of parasitic protozoa in the genus Toxoplasma. The definitive host of T. gondii is the cat, but the parasite can be carried by many warm-blooded animals . Toxoplasmosis, the disease of which T... (B) Homo sapiens (Other) Mus musculus (Other)

External links

NIAID home page
Bioinformatics Resource Centers The NIAID page describing the goals and activities of the BRCs
PathogenPortal Hub site for the BRCs; provides summary information
EuPathDB Eukaryotic Pathogens BRC
IRD Influenza Research Database BRC
ViPR Virus Database and Analysis Resource BRC
PATRIC PathoSystems Resource Integration Center
VectorBase VectorBase BRC

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See also

External links