It has been suggested that full genome sequencing be merged into this article or section. (Discuss) Proposed since January 2012.

Genomics is a discipline in genetics concerned with the study of the genomes of organisms. The field includes efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping. The field also includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy and other interactions between loci and alleles within the genome. In contrast, the investigation of the roles and functions of single genes is a primary focus of molecular biology or genetics and is a common topic of modern medical and biological research. Research of single genes does not fall into the definition of genomics unless the aim of this genetic, pathway, and functional information analysis is to elucidate its effect on, place in, and response to the entire genome's networks.^[1]

For the United States Environmental Protection Agency, "the term "genomics" encompasses a broader scope of scientific inquiry associated technologies than when genomics was initially considered. A genome is the sum total of all an individual organism's genes. Thus, genomics is the study of all the genes of a cell, or tissue, at the DNA (genotype), mRNA (transcriptome), or protein (proteome) levels."^[2]

History[link]

The first genomes to be sequenced were those of a virus and a mitochondrion, and were done by Fred Sanger. His group established techniques of sequencing, genome mapping, data storage, and bioinformatic analyses in the 1970-1980s. A major branch of genomics is still concerned with sequencing the genomes of various organisms, but the knowledge of full genomes has created the possibility for the field of functional genomics, mainly concerned with patterns of gene expression during various conditions. The most important tools here are microarrays and bioinformatics. Study of the full set of proteins in a cell type or tissue, and the changes during various conditions, is called proteomics. A related concept is materiomics, which is defined as the study of the material properties of biological materials (e.g. hierarchical protein structures and materials, mineralized biological tissues, etc.) and their effect on the macroscopic function and failure in their biological context, linking processes, structure and properties at multiple scales through a materials science approach. The actual term 'genomics' is thought to have been coined by Dr. Tom Roderick, a geneticist at the Jackson Laboratory (Bar Harbor, ME) over beer at a meeting held in Maryland on the mapping of the human genome in 1986^[3]. The Genomic Science Program (formerly Genomes to Life) uses microbial and plants.

In 1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent (Ghent, Belgium) were the first to determine the sequence of a gene: the gene for Bacteriophage MS2 coat protein.^[4] In 1976, the team determined the complete nucleotide-sequence of bacteriophage MS2-RNA.^[5] The first DNA-based genome to be sequenced in its entirety was that of bacteriophage Φ-X174; (5,368 bp), sequenced by Frederick Sanger in 1977.^[6]

The first free-living organism to be sequenced was that of Haemophilus influenzae (1.8 Mb) in 1995^[7], and since then genomes are being sequenced at a rapid pace. As of October 2011, the complete sequences are available for: 2719 viruses,^[8] 1115 archaea and bacteria, and 36 eukaryotes, of which about half are fungi. ^[9]

Most of the bacteria whose genomes have been completely sequenced are problematic disease-causing agents, such as Haemophilus influenzae.^[10] Of the other sequenced species, most were chosen because they were well-studied model organisms or promised to become good models. Yeast (Saccharomyces cerevisiae) has long been an important model organism for the eukaryotic cell, while the fruit fly Drosophila melanogaster has been a very important tool (notably in early pre-molecular genetics). The worm Caenorhabditis elegans is an often used simple model for multicellular organisms. The zebrafish Brachydanio rerio is used for many developmental studies on the molecular level and the flower Arabidopsis thaliana is a model organism for flowering plants. The Japanese pufferfish (Takifugu rubripes) and the spotted green pufferfish (Tetraodon nigroviridis) are interesting because of their small and compact genomes, containing very little non-coding DNA compared to most species. ^{[11] [12]} The mammals dog (Canis familiaris), ^[13] brown rat (Rattus norvegicus), mouse (Mus musculus), and chimpanzee (Pan troglodytes) are all important model animals in medical research.

Major research areas[link]

Bacteriophage genomics[link]

Bacteriophages have played and continue to play a key role in bacterial genetics and molecular biology. Historically, they were used to define gene structure and gene regulation. Also the first genome to be sequenced was a bacteriophage. However, bacteriophage research did not lead the genomics revolution, which is clearly dominated by bacterial genomics. Only very recently has the study of bacteriophage genomes become prominent, thereby enabling researchers to understand the mechanisms underlying phage evolution. Bacteriophage genome sequences can be obtained through direct sequencing of isolated bacteriophages, but can also be derived as part of microbial genomes. Analysis of bacterial genomes has shown that a substantial amount of microbial DNA consists of prophage sequences and prophage-like elements. A detailed database mining of these sequences offers insights into the role of prophages in shaping the bacterial genome.^[14]

Cyanobacteria genomics[link]

At present there are 24 cyanobacteria for which a total genome sequence is available. 15 of these cyanobacteria come from the marine environment. These are six Prochlorococcus strains, seven marine Synechococcus strains, Trichodesmium erythraeum IMS101 and Crocosphaera watsonii WH8501. Several studies have demonstrated how these sequences could be used very successfully to infer important ecological and physiological characteristics of marine cyanobacteria. However, there are many more genome projects currently in progress, amongst those there are further Prochlorococcus and marine Synechococcus isolates, Acaryochloris and Prochloron, the N₂-fixing filamentous cyanobacteria Nodularia spumigena, Lyngbya aestuarii and Lyngbya majuscula, as well as bacteriophages infecting marine cyanobaceria. Thus, the growing body of genome information can also be tapped in a more general way to address global problems by applying a comparative approach. Some new and exciting examples of progress in this field are the identification of genes for regulatory RNAs, insights into the evolutionary origin of photosynthesis, or estimation of the contribution of horizontal gene transfer to the genomes that have been analyzed.^[15]

Human genomics[link]

A rough draft of the human genome was completed by the Human Genome Project in early 2001, creating much fanfare. By 2007 the human sequence was declared "finished" (less than one error in 20,000 bases and all chromosomes assembled).^[16] Display of the results of the project required significant bioinformatics resources. The sequence of the human reference assembly can be explored using the UCSC Genome Browser or Ensembl.

Metagenomics[link]

Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods.^[17] Recent studies use "shotgun" Sanger sequencing or massively parallel pyrosequencing to get largely unbiased samples of all genes from all the members of the sampled communities.^[18] Because of its power to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world.^[19][20]

Pharmacogenomics[link]

Pharmacogenomics is the branch of pharmacology which deals with the influence of genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms with a drug's efficacy or toxicity.^[21] By doing so, pharmacogenomics aims to develop rational means to optimize drug therapy, with respect to the patients' genotype, to ensure maximum efficacy with minimal adverse effects.^[22] Such approaches promise the advent of "personalized medicine"; in which drugs and drug combinations are optimized for each individual's unique genetic makeup.^[23][24] Pharmacogenomics is the whole genome application of pharmacogenetics, which examines the single gene interactions with drugs.

See also[link]

• Computational genomics
• Epigenomics
• Full Genome Sequencing
• Functional genomics
• Genomics of domestication
• Immunomics
• Metagenomics
• Nitrogenomics
• Personal genomics
• Proteomics
• Psychogenomics

References[link]

External links[link]

• Genomics Directory: A one-stop biotechnology resource center for bioentrepreneurs, scientists, and students
• Annual Review of Genomics and Human Genetics
• BMC Genomics: A BMC journal on Genomics
• Center for Applied Genomics: Genomics Research - a specialized Center of Emphasis at the Children’s Hospital of Philadelphia
• Genomics: UK companies and laboratories* Genomics journal
• Genomics and Quantitative Genetics: An international electronic, open access journal publishing, inter alia, genomics research.
• Genomics.org: An openfree wiki based Genomics portal
• NHGRI: US government's genome institute
• Pharmacogenomics in Drug Discovery and Development, a book on pharmacogenomics, diseases, personalized medicine, and therapeutics
• Tishchenko P. D. Genomics: New Science in the New Cultural Situation
• Undergraduate program on Genomic Sciences (spanish): One of the first undergraduate programs in the world
• JCVI Comprehensive Microbial Resource
• Pathema: A Clade Specific Bioinformatics Resource Center
• KoreaGenome.org: The first Korean Genome published and the sequence is available freely.
• GenomicsNetwork: Looks at the development and use of the science and technologies of genomics.
• Institute for Genome Sciences: Genomics research.
• MIT OpenCourseWare HST.512 Genomic Medicine A free, self-study course in genomic medicine. Resources include audio lectures and selected lecture notes.
• The Plant Breeding and Genomics Community of Practice on eXtension - provides education and training materials for plant breeders and allied professionals

Barry Martin Schuler (born September 7, 1953 in Jersey City, New Jersey) is an American Internet entrepreneur and former chairman and CEO of America Online Inc. He is best known for leading the AOL team that simplified the online service provider’s user interface, making it possible for millions of consumers to gain easy access to the Internet.

Early years[link]

Barry Schuler grew up in West New York, New Jersey. As a suburban youth, Schuler was encouraged early on by his parents to explore the arts (photography, painting and sculpture) as well as electronics. He turned his family’s basement into a darkroom while helping his father, a warehouse owner and part-time repair man, tinker with television sets and other gadgetry.^[1]

In the mid-1970s, while completing a Bachelor’s degree in psychology at Rutgers University, Schuler became captivated by filmmaking. In 1976, he left the university to produce and direct commercial and industrial films. An avid computer hobbyist and reader of Popular Electronics, Schuler befriended a group of technical enthusiasts who were developing software applications for microcomputers. After assembling a do-it-yourself IMSAI computer and experiencing first hand the potential of at-home computing, Schuler saw the technology’s ability to positively disrupt and enhance the way people lived and worked.^[2] In 1978, he established CMP Communications, an advertising and marketing company devoted to helping high tech entrepreneurs spread the word about the impending revolution in microcomputing.

Schuler quit CMP in 1988 and took a position as president and CEO of Cricket Software, overseeing the development and marketing of color desktop applications for Apple Computer’s Macintosh, including a Postscript driven drawing program.^[3] Cricket also developed the first color, graphical desktop presentation software, “Cricket Presents.” Cricket was ultimately sold to Computer Associates International in 1991.

Schuler was President of San Francisco-based Jasmine Technologies from 1989 to 1990. Jasmine was a leading Macintosh peripherals developer that buckled under the weight of bitter lawsuits and mounting customer dissatisfaction. Jasmine declared bankruptcy in March 1990 and Schuler resigned shortly thereafter.

Looking to take advantage of the opportunities that a new ‘Interactive” medium would bring, Schuler teamed up with (present day) wife Tracy and David Goldman shortly after and established Medior Inc., a multimedia development company, Medior Inc. In 1994, the company entered into a joint venture with, Apple Computer Inc., and Redgate Communications and launched 2Market, considered to be the first rich media online shopping service.^[4] That same year, AOL (America Online) also enlisted Medior’s help designing its product to give consumers with little or no computing expertise easy access to its online information services. While at Medior, Schuler and company co-developed a music creation game with Nick Tenbrock and Gary Levenberg of San Francisco-based Interactive Audio. The software, called Rock, Rap and Roll, allowed Macintosh users to quickly build soundtracks in a variety of musical styles.^[5] Medior also collaborated with Time Warner, one of its clients, on the building of the world’s first digital, switched, interactive broadband communications network delivering a range of services. The service was launched in December 1994 in Orlando, Fla.^[6]

AOL years[link]

In 1995, Medior was acquired by AOL. Schuler, brought over from Medior by AOL founder and CEO Steve Case, was charged with helping him and then president Ted Leonsis to transform the online service provider into a broad based, consumer-driven medium. Schuler worked his way up the ranks at AOL becoming president of its Interactive Services group in 1998. During this time, he led the design team that integrated an Internet browser directly in AOL’s proprietary user interface (version 5.0) making it possible for millions of computer users to access the Internet through a Web-based portal. He also advocated the opening up of AOL’s proprietary message service known as IM, a key development that allowed its subscriber base to “chat” electronically over the Internet with non-AOL computer users free of charge.^[7] By January 2001, the same month that AOL announced its merger with Time-Warner, the company’s 26 million subscribers were sending an estimated 660 million instant messages daily.^[8]

It was on the heels of the Time Warner merger that Schuler was appointed chairman and CEO of the AOL unit. He was charged with finding ways to turn AOL into an interactive outlet for Time-Warner’s various media divisions, which included film, music, television and publishing. The goal was to transform AOL into a high-speed, Internet-based,” one-stop shop for movies, music, interactive video games, phone service, and more.” ^[9]

In a July 2, 2001 article, BusinessWeek reporter Amy Borrus wrote that Schuler, “deserves just as much credit for AOL’s explosive success” as then AOL Time Warner Inc. Chairman Steve Case or co-Chief Operating Officer Robert Pittman. The reporter pointed to the three years Schuler spent running AOL’s Interactive Services group, “putting his stamp on much of the design that makes it so simple to use and features that make it so popular with families.” Schuler’s objective of converging a souped-up version of AOL’s online distribution platform with Time Warner’s various media outlets hit several roadblocks one being reluctance on the part of cable companies to open up their network to Internet service providers such as AOL. Likewise, internal dissent over the best ways to merge AOL’s distribution channels with Time Warner’s more traditional media content plagued the online unit.^[10] Against this backdrop, AOL was struggling with declining advertising sales due to an economic downturn as well as a leveling out of its still dial-up driven subscriber growth. The unit took a further hit when its parent was forced to restate its earnings forecast in January 2002, in part due to the slowdown in AOL’s business.^[11] Schuler stepped down as head of the unit in April 2002, taking over a newly created digital development unit charged with overseeing the formation of interactive digital products and services for all of AOL Time Warner.^[12] He officially resigned from AOL-Time Warner in 2003.

After AOL[link]

Shortly after his departure from AOL, Schuler found himself invited to invest in a start up Ablation Industries, Inc. Ablation Industries, Inc was commercializing (Ultrashort pulse laser) USP laser technology funded by the U.S. government’s Defense Advanced Research Projects Agency, also known as DARPA. When Mr Schuler invested in the company, the name of the company was changed to Raydiance, where he raised a significant amount of venture capital funding to help commercialize new technologies of national interest, among them ultrashort pulse lasers. A form of optoelectronics, the lasers emits short pulses of highly concentrated energy that can be used to break down atoms.^[13] In 2004, Schuler joined Raydiance Inc. to develop commercial applications for ultra-short pulse lasers. In July 2007, Wired Magazine reported that Raydiance had signed a deal with the U.S. Federal Drug Administration (FDA) to explore laser therapies, ranging from common laser eye treatments to the cell-by-cell tumor ablation.^[14]

In addition to serving as CEO of Raydiance, Schuler is managing director of the Draper Fisher Jurvetson Growth Fund and serves on the boards of UBMatrix, Hands On Mobile, UU See, Synthetic Genomics, and Visto. Schuler is an investor in Adirondack Pictures. He also co-produced and helped finance the film Look, a drama shot entirely from the point of view of surveillance cameras. Written and directed by Adam Rifkin with Brad Wyman as his fellow producer. The film was digitally shot in high-definition with all the special effects, post production and music done on Apple’s Macintosh computers in a “virtual studio” setting. Look, released in December 2007, is distributed by Liberated Artists, another Schuler venture. It won the Grand Jury Prize at the 2007 CineVegas Film Festival.^[15] It also won Special Jury Prize at The Lone Star International Film Festival and was an official selection in both AFI Fest and The Chicago International Film Festival.

Schuler lives in Napa, California. A vocal proponent of public education reform,^[16] He co-founded the Blue Oak School, an independent, not-for-profit entity for students, kindergarten through eighth grade. Schuler is a national advisory member for the New Technology Foundation (NTF), a non-profit organization established in 1999 with the objective of achieving national education reform.^[17] Using the New Technology High School in Napa as a prototype for encouraging innovative academic objectives, NTF provides interested schools with training, tools and access to expertise developed through the NTHS school site. Through his affiliation with the foundation, Schuler has helped drive and co-funded the implementation of Internet-based technology to establish a project-based learning methodology consistent with the implementation of the 21st Century Learning Initiative.

He and wife Tracy co-own Meteor Vineyard, located in the Coombsville region of the Napa Valley, with winemakers Bill and Dawnine Dyer.

Schuler is a member of the Rutgers Hall of Distinguished Alumni.

Meteor Vineyard[link]

Meteor Vineyard is a 22-acre (89,000 m²) property located in the Coombsville agricultural area of the Napa Valley AVA. It was established in 1998 by former America Online Inc. Chairman and Chief Executive Barry M. Schuler and his wife, Tracy Strong Schuler. Meteor Vineyard is located at the southeast end of the Napa Valley, near the San Francisco Bay.

Through 2004, Meteor Vineyard’s grapes were sold in bulk to a handful of Napa Valley properties including Dyer, Arietta, Etude and Vineyard 29. In 2005, the Schulers entered into a partnership with winemakers Dawnine Dyer and Bill Dyer to produce a single-vineyard Cabernet Sauvignon bottled under the Meteor Vineyard. The team bottled their first vintage later that year, and the wine was released beginning 2008.^[18]

Soil conditions in the Coombsville area are a mix of well-draining river rock and mineral-rich volcanic ash, both of which are considered suitable for Bordeaux varietals, including Cabernet Sauvignon.^[19]

References[link]

External links[link]

• Barry Schuler - IMDb Profile
• Barry Schuler - LOOK-the Movie
• Barry Schuler - Speech by Schuler, sc21 21st Century Education
• Barry Schuler - Meteor Vineyard
• Barry Schuler - Draper Fisher Jurvetson Growth Fund
• Barry Schuler - Synthetic Genomics
• Barry Schuler - Raydiance, Inc. Bio
• Barry Schuler - Visto Biography
• Barry Schuler - UU See
• Barry Schuler - Hands on Mobile
• Barry Schuler - UBMatrix
• Barry Schuler - New Tech Foundation