Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features. The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences.

The Human Genome Project was a landmark genome project that is already having a major impact on research across the life sciences, with potential for spurring numerous medical and commercial developments.

==Genome assembly== Genome assembly refers to the process of taking a large number of short DNA sequences and putting them back together to create a representation of the original chromosomes from which the DNA originated. In a shotgun sequencing project, all the DNA from a source (usually a single organism, anything from a bacterium to a mammal) is first fractured into millions of small pieces. These pieces are then "read" by automated sequencing machines, which can read up to 900 nucleotides or bases at a time. (The four bases are adenine, guanine, cytosine, and thymine, represented as AGCT.) A genome assembly algorithm works by taking all the pieces and aligning them to one another, and detecting all places where two of the short sequences, or ''reads'', overlap. These overlapping reads can be merged together, and the process continues.

Genome assembly is a very difficult computational problem, made more difficult because many genomes contain large numbers of identical sequences, known as ''repeats''. These repeats can be thousands of nucleotides long, and some occur in thousands of different locations, especially in the large genomes of plants and animals.

The resulting (draft) genome sequence is produced by combining the information sequenced contigs and then employing linking information to create scaffolds. Scaffolds are positioned along the physical map of the chromosomes creating a "golden path".

Assembly Software

Originally, most large-scale DNA sequencing centers developed their own software for assembling the sequences that they produced. However, this has changed as the software has grown more complex and as the number of sequencing centers has increased. An example of such assembler ''Short Oligonucleotide Analysis Package'' developed by BGI for de novo assembly of human-sized genomes, alignment, SNP detection, resequencing, indel finding, and structural variation analysis.

Genome annotation

Genome annotation is the process of attaching biological information to sequences. It consists of two main steps: # identifying elements on the genome, a process called gene prediction, and # attaching biological information to these elements. Automatic annotation tools try to perform all this by computer analysis, as opposed to manual annotation (a.k.a. curation) which involves human expertise. Ideally, these approaches co-exist and complement each other in the same annotation pipeline.

The basic level of annotation is using BLAST for finding similarities, and then annotating genomes based on that. However, nowadays more and more additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. Some databases use genome context information, similarity scores, experimental data, and integrations of other resources to provide genome annotations through their Subsystems approach. Other databases (e.g Ensembl) rely on both curated data sources as well as a range of different software tools in their automated genome annotation pipeline.

''Structural annotation'' consists of the identification of genomic elements.

ORFs and their localisation

gene structure

coding regions

location of regulatory motifs

''Functional annotation'' consists of attaching biological information to genomic elements.

biochemical function

biological function

involved regulation and interactions

expression

These steps may involve both biological experiments and ''in silico'' analysis.

A variety of software tools have been developed to permit scientists to view and share genome annotations.

Genome annotation is the next major challenge for the Human Genome Project, now that the genome sequences of human and several model organisms are largely complete. Identifying the locations of genes and other genetic control elements is often described as defining the biological "parts list" for the assembly and normal operation of an organism. Scientists are still at an early stage in the process of delineating this parts list and in understanding how all the parts "fit together".

Genome annotation is an active area of investigation and involves a number of different organizations in the life science community which publish the results of their efforts in publicly available biological databases accessible via the web and other electronic means. Here is an alphabetical listing of on-going projects relevant to genome annotation:

ENCyclopedia Of DNA Elements (ENCODE)

Entrez Gene

Ensembl

GENCODE

Gene Ontology Consortium

GeneRIF

RefSeq

Uniprot

Vertebrate and Genome Annotation Project (Vega)

At Wikipedia, genome annotation has started to become automated under the auspices of the Gene Wiki portal which operates a bot that harvests gene data from research databases and creates gene stubs on that basis.

When is a genome project finished?

When sequencing a genome, there are usually regions that are difficult to sequence (often regions with highly repetitive DNA). Thus, 'completed' genome sequences are rarely ever complete, and terms such as 'working draft' or 'essentially complete' have been used to more accurately describe the status of such genome projects. Even when every base pair of a genome sequence has been determined, there are still likely to be errors present because DNA sequencing is not a completely accurate process. It could also be argued that a complete genome project should include the sequences of mitochondria and (for plants) chloroplasts as these organelles have their own genomes.

It is often reported that the goal of sequencing a genome is to obtain information about the complete set of genes in that particular genome sequence. The proportion of a genome that encodes for genes may be very small (particularly in eukaryotes such as humans, where coding DNA may only account for a few percent of the entire sequence). However, it is not always possible (or desirable) to only sequence the coding regions separately. Also, as scientists understand more about the role of this noncoding DNA (often referred to as junk DNA), it will become more important to have a complete genome sequence as a background to understanding the genetics and biology of any given organism.

In many ways genome projects do not confine themselves to only determining a DNA sequence of an organism. Such projects may also include gene prediction to find out where the genes are in a genome, and what those genes do. There may also be related projects to sequence ESTs or mRNAs to help find out where the genes actually are.

Historical and technological perspectives

Historically, when sequencing eukaryotic genomes (such as the worm ''Caenorhabditis elegans'') it was common to first map the genome to provide a series of landmarks across the genome. Rather than sequence a chromosome in one go, it would be sequenced piece by piece (with the prior knowledge of approximately where that piece is located on the larger chromosome). Changes in technology and in particular improvements to the processing power of computers, means that genomes can now be 'shotgun sequenced' in one go (there are caveats to this approach though when compared to the traditional approach).

Improvements in DNA sequencing technology has meant that the cost of sequencing a new genome sequence has steadily fallen (in terms of cost per base pair) and newer technology has also meant that genomes can be sequenced far more quickly.

When research agencies decide what new genomes to sequence, the emphasis has been on species which are either high importance as model organism or have a relevance to human health (e.g. pathogenic bacteria or vectors of disease such as mosquitos) or species which have commercial importance (e.g. livestock and crop plants). Secondary emphasis is placed on species whose genomes will help answer important questions in molecular evolution (e.g. the common chimpanzee).

In the future, it is likely that it will become even cheaper and quicker to sequence a genome. This will allow for complete genome sequences to be determined from many different individuals of the same species. For humans, this will allow us to better understand aspects of human genetic diversity.

Example genome projects

Many organisms have genome projects that have either been completed or will be completed shortly, including:

Humans, ''Homo sapiens''; see Human genome project

Palaeo-Eskimo, an ancient-human

Neanderthal, "''Homo neanderthalensis''" (partial); see Neanderthal Genome Project

Common Chimpanzee ''Pan troglodytes''; see Chimpanzee Genome Project

Domestic Cow

Bovine Genome

Honey Bee Genome Sequencing Consortium

Human microbiome project

International Grape Genome Program

International HapMap Project

See also

Joint Genome Institute

Model organism

National Center for Biotechnology Information

Illumina, private company involved in genome sequencing

Knome, private company offering genome analysis & sequencing

References

External links

GOLD:Genomes OnLine Database

Genome Project Database

The Protein Naming Utility

SUPERFAMILY

The sea urchin genome database

*

fr:Projet de séquençage de génome hi:जीनोम परियोजना nl:Genoomproject ja:ゲノムプロジェクト pt:Projeto Genoma zh:基因组作图

name	Sid Meier
birth date	February 24, 1954
birth place	Sarnia, Ontario, Canada
occupation	Game designer
years active	1982—present
employer	Firaxis Games
known for	''Civilization'' series
spouse	Susan Meier
children	Ryan Meier }}

Sidney K. "Sid" Meier (born February 24, 1954) is a Canadian programmer and designer of several popular computer strategy games, most notably ''Civilization''. He has won accolades for his contributions to the computer games industry. Meier is a Director of Creative Development for computer game developer Firaxis Games, which he co-founded with Jeff Briggs and Brian Reynolds in 1996.

Biography

Meier was born in Sarnia, Ontario, Canada. A graduate of the University of Michigan, Meier founded MicroProse together with Bill Stealey in 1982. MicroProse initially developed flight simulator video games, such as ''F-15 Strike Eagle'' and ''F-19 Stealth Fighter''. In 1987, the company released ''Sid Meier's Pirates!'', which also began a trend of placing Meier's name in the titles of his games. Meier later explained that the inclusion of his name was because of the dramatic departure in the design of ''Pirates!'' compared to the company's earlier games. Stealey decided that it would improve the company's branding, believing that it would make those who purchased the flight simulators more likely to play ''Pirates!''. After the release of ''F-19 Stealth Fighter'', Meier decided to focus on developing strategy games. He later said, "Everything I thought was cool about a flight simulator had gone into that game." Inspired by ''SimCity'' and ''Empire!'', Meier created ''Railroad Tycoon'' and later the game series for which he is most widely recognized, ''Civilization'', although he designed only the first installment. Meier eventually left MicroProse and in 1996 founded Firaxis Games along with veteran designer and gaming executive Jeff Briggs. Today Firaxis makes strategy games, many of which are follow-ups to Meier titles, such as ''Civilization V'' and ''Pirates!''. In 1996 he was awarded US Patent 5,496,962 for a "System for Real-Time Music Composition and Synthesis" used in a product called "CPU Bach".

In 1999, Meier became the second person to be inducted into the Academy of Interactive Arts and Sciences' Hall of Fame. The first to receive that honor was Shigeru Miyamoto from Nintendo.

Meier is not always the main designer on titles that carry his name. For instance, Brian Reynolds has been credited as the primary designer behind ''Sid Meier's Civilization II'', ''Sid Meier's Alpha Centauri'', and ''Sid Meier's Colonization'', while Jeff Briggs designed ''Sid Meier's Civilization III'', Soren Johnson led ''Sid Meier's Civilization IV'' and Jon Shafer ''Sid Meier's Civilization V''. Currently Meier's role appears to be that of a creative director, simultaneously contributing to multiple projects.

Meier worked with a team on a dinosaur themed game starting early 2000, but announced in an online development diary on January 24, 2001 that the game had been shelved. Despite trying various approaches, including turn-based and real-time gameplay, he said he found no way to make the concept fun enough. In August 2005, Meier said, "We've been nonstop busy making other games over the past several years, so the dinosaur game remains on the shelf. However, I do love the idea of a dinosaur game and would like to revisit it when I have some time."

In January 2008, CMP Game Group announced that Meier would receive a Lifetime Achievement Award at the 2008 Game Developer's Conference.

Meier has been ranked 2nd in IGN's list of Top 100 Game Creators of All Time.

Meier currently lives in Hunt Valley, Maryland with his wife, Susan, and son, Ryan. He met his wife at Faith Evangelical Lutheran Church in Cockeysville, where they both sing in the choir.

Games

1980s

''Spitfire Ace'' (1982) — The first project in which Sid played a major role in the game creation stage.

''HellCat Ace'' (1982)

''Floyd of the Jungle'' (1982)

''NATO Commander'' (1984)

''Solo Flight'' (1984)

''Kennedy Approach'' (1985)

''F-15 Strike Eagle'' (1985) — one of the first combat flight simulators

''Silent Service'' (1985), a World War II submarine simulation game, and Meier's first foray out of flight sims.

''Crusade in Europe'' (1985)

''Decision in the Desert'' (1985)

''Conflict in Vietnam'' (1986)

''Gunship'' (1986)

''Sid Meier's Pirates!'' (1987)

''F-19 Stealth Fighter'' (1988)

''F-15 Strike Eagle II'' (1989)

''Sword of the Samurai'' (1989)

1990s

''Covert Action'' (1990)

''Sid Meier's Railroad Tycoon'' (1990), a business simulation game that paints the early development of railroads in the United States and Europe, a time when competition between railroad companies was very fierce. With the release of ''Sid Meier's Railroads!'', this series now has four installments.

''Sid Meier's Civilization'' (1991), Meier's most successful game franchise to date. It has lived through several versions (see below) and sold over 6 million copies. This game is a turn-based strategy game.

''Pirates! Gold'' (1993)

C.P.U. Bach (1993), 3DO Console exclusive interactive music-generating program.

''Sid Meier's Colonization'' (1994), a turn-based strategy game themed on the early European colonization of the New World, starting in 1492 and lasting until the age of independence in 1850. To achieve victory in this game, the player must declare independence, and win in a revolutionary war against their mother country in Europe (France, England, Netherlands, or Spain).

''Sid Meier's Civilization II'' (1996) Follow-up to Sid Meier's successful ''Civilization''; Brian Reynolds was lead designer on the game.

''Magic: The Gathering'' (1997) This would be the last game that Sid Meier worked on for MicroProse.

''Sid Meier's Gettysburg!'' (1997) Sid Meier's first real-time tactical game.

''Sid Meier's Antietam!'' (1998) ''Sid Meier's Gettysburg'' and ''Antietam'' are part of his Civil War set.

''Sid Meier's Alpha Centauri'' (1999) Brian Reynolds was lead designer on this adaptation of ''Civilization'' to an outer space theme. ''Alpha Centauri'' is set in a futuristic setting on an alien world, with ideological factions substituting for civilizations. This is a much more versatile version of ''Civilization'', featuring economics and unique military customization, as well as diplomacy.

2000s

''Sid Meier's Civilization III'' (2001), Jeff Briggs designed the third installment of the series, with more complex rules, graphics and gameplay. New features include expanded diplomacy (much like ''Alpha Centauri''); the introduction of "culture" as a tool for domination; and "strategic resources" required for trade and to produce certain units. Sales of this installment made the ''Civilization'' series the best selling PC series to date.

''Sid Meier's SimGolf'' (2002) A golfing simulation in which the player built their own golf course and played it, against computer players, co-created by Maxis. Not to be confused with Maxis' 1996 title ''SimGolf''.

''Sid Meier's Pirates!'' (2004), follow-up to the acclaimed ''Pirates!'' game from 1987, updating the graphics and featuring some entirely new gameplay elements and an all new ballroom dancing segment.

''Sid Meier's Civilization IV'', Designed by Soren Johnson and released October 25, 2005. A full 3D engine replaces the isometric maps of ''Civilization II'' and ''III''. This installment makes "Religion" (present in earlier versions only as a means of population pacification and control) a tool of domination, alongside the Culture and Diplomacy elements from previous incarnations.

''Sid Meier's Railroads!'', released October 17, 2006. When Take 2 shut down PopTop Software and folded it into Firaxis, Meier once again became responsible for the ''Railroad Tycoon'' series, and this is billed as the sequel to ''Railroad Tycoon 3''.

''Sid Meier's Civilization Revolution'', announced on June 28, 2007 and released on June 13, 2008. A seventh generation console edition of ''Civilization''. This is the only Civilization title available for seventh generation consoles.

''Sid Meier's Civilization IV: War of Two Cities''. One of three Sid Meier properties to be launched by Oasys Mobile, this Sid Meier property takes the major civilizations and pits them against one another in a real time one on one battle to take over the opponent's major city. The game was developed by Floodgate Entertainment.

''Sid Meier's Pirates! Mobile''. The game was developed and published by Oasys Mobile and was led by one of the original programmers for Pirates! Gold.

''Sid Meier's Railroad Tycoon Mobile''. Developed by Blue Heat and published by Oasys Mobile. This version is based on the Sid Meier classic game series; the mobile version allows players to build their own transportation empire.

''Sid Meier's Civilization IV: Colonization'', is a 2008 remake of the 1994 ''Colonization'', and is a standalone game based on the ''Civilization IV'' engine.

2010s

''Sid Meier's Civilization V'', released on September 21, 2010 for North America and on September 24, 2010 for the rest of the world. Jon Shafer was the lead designer of the game. New features include Social Policy (which replaces "Civics" system), unit stacking change, City-States and fully animated leaders.

See Also

Civilization (series)

External links

Sid Meier's biography and his games history at Firaxis.com

"The Sid Meier Legacy" from ''GameSpot''

References

Category:1954 births Category:Canadian Lutherans Category:Canadian video game designers Category:Canadian expatriates in the United States Category:Living people Category:MicroProse Category:People from Detroit, Michigan Category:People from Sarnia, Ontario Category:University of Michigan alumni Category:Video game producers Category:Video game programmers

bar:Sid Meier ca:Sid Meier da:Sid Meier de:Sid Meier el:Σιντ Μάιερ es:Sid Meier fa:سید میر fr:Sid Meier ko:시드 마이어 is:Sid Meier it:Sid Meier he:סיד מאייר lv:Sids Maijers lt:Sid Meier hu:Sid Meier nl:Sid Meier ja:シド・マイヤー pl:Sid Meier pt:Sid Meier ru:Мейер, Сид simple:Sid Meier sh:Sid Meier fi:Sid Meier sv:Sid Meier tr:Sid Meier uk:Сід Мейєр zh:席德·梅爾

Name	John Quackenbush
Birth date	January 04, 1962
Birth place	Kingston, Pennsylvania, United States
Alma mater	California Institute of Technology (B.S.)University of California, Los Angeles (Ph.D.)
Work institutions	Harvard UniversityDana-Farber Cancer InstituteInstitute for Molecular Bioscience, (University of Queensland)
Known for	bioinformatics, computational biology, microarray analysis, genomics, functional genomics }}

John Quackenbush (born January 4, 1962) is an American computational biologist and genome scientist. He is the Professor of Biostatistics and Computational Biology, Professor of Cancer Biology at the Dana-Farber Cancer Institute (DFCI), as well as the director of its Center for Cancer Computational Biology (CCCB). Quackenbush also holds an appointment as Professor of Computational Biology and Bioinformatics in the Department of Biostatistics at the Harvard School of Public Health (HSPH).

Biography

A native of Mountain Top, Pennsylvania, Quackenbush attended Bishop Hoban High School in Wilkes Barre, graduating in 1979, after which he attended the California Institute of Technology, where he earned a bachelor’s degree in physics. He went on to earn a doctorate in theoretical particle physics from the University of California, Los Angeles (UCLA) in 1990.

After working two years as a postdoctoral fellow in physics, Quackenbush was awarded a Special Emphasis Research Career Award from the National Center for Human Genome Research (the predecessor of the National Human Genome Research Institute), and subsequently spent the next two years at the Salk Institute working on physical maps of human chromosome 11, followed by another two years at Stanford University developing new laboratory and computational strategies for sequencing the human genome.

In 1997, Quackenbush joined the faculty of The Institute for Genomic Research (TIGR) in Rockville, Maryland, where his focus began to shift to post-genomic applications, with an emphasis on microarray analysis. Using a combination of laboratory and computational approaches, Quackenbush and his group developed analytical methods based on the integration of data across domains to derive biological meaning from high-dimensional data.

In 2005, Quackenbush was appointed to his current positions at the Dana-Farber Cancer Institute (DFCI) and the Harvard School of Public Health. Four years later, he launched the DFCI’s Center for Cancer Computational Biology (CCCB), which he directs and which provides broad-based bioinformatics and computational biology support to the research community through a collaborative consulting model, and which also performs and analyzes large-scale second-generation DNA sequencing.

A leader in the fields of genomics and computational biology, Quackenbush’s current research focuses on the analysis of human cancer using systems biology-based approaches to understanding and modeling the biological networks that underlie disease. This has led him and his colleagues to make fundamental discoveries about the role that variation in gene expression plays in defining biological phenotypes.

In 2010, Quackenbush and his colleagues at DFCI's CCCB, together with investigators at National Jewish Health's Center for Genes, Environment and Health, University of Pittsburgh's, Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Boston University's, Section for Computational Biomedicine and the Pulmonary Center, and the University of Colorado Denver, Genomics Core Facility received an $11 million grant under the American Recovery and Reinvestment Act of 2009 to launch the Lung Genomics Research Consortium. This project, funded by the National Heart Lung and Blood Institute (NHLBI), will add genetic, genomic, and epigenetic data to a collection of clinical biological samples developed by the NHLBI's Lung Tissue Research Consortium. The consortium aims to use genomic technologies and advanced data-analysis tools on available patient lung-tissue samples to gain new insights into pulmonary disease and thus develop more effective, personalized treatments.

In 2011, Quackenbush published ''The Human Genome: Book of Essential Knowledge'' (Imagine Publishing, U.S.), which outlines the history, science, and implications behind the Human Genome Project. He was also awarded with a $4 million-dollar fellowship bestowed by Australia's National Health and Medical Research Council to study chemotherapy resistant ovarian cancers in collaboration with colleagues at the University of Queensland's Institute for Molecular Bioscience.

Quackenbush currently serves on the editorial boards of five major journals and is editor-in-chief at ''Genomics''. He has served on several committees at the National Academies and the Institute of Medicine, including the Panel on Emerging Issues in Toxicogenomics, the Panel on Collecting, Storing, and Distributing Biodata linked to Social Science Surveys, and the Committee Review of Omics-Based Predictive Tests. He is currently a member of scientific advisory boards at St. Jude Children’s Research Hospital, at the Lovelace Respiratory Research Institute, The Hope Funds for Cancer Research. and for the National Institute for Health's Roadmap Epigenomics Project. Quackenbush is also a member of the scientific advisory boards of a number of biotech start-up companies, including Exosome Diagnostics, Karyopharm Therapeutics, and NABsys.

Awards and Honors

Jun John Sakurai Scholarship, 24th International School of Subnuclear Physics, Ettore Majorana Foundation and Centre for Scientific Culture, Erice, Italy, 1986

Prize for Best Student and Prize for Best Scientific Secretary, 25th International School of Subnuclear Physics, Ettore Majorana Foundation and Centre for Scientific Culture, Erice, Italy, 1987

SERCA Fellow, National Human Genome Research Institute, 1992

Myra Samuels Memorial Lecture, Perdue University, Lafayette, Indiana USA, 2002

George D. Wilbanks Lectureship in Gynecological Oncology, University of South Florida College of Medicine, Tampa, Florida, USA, 2006

President’s Distinguished Lectureship, American Society of Reproductive Medicine, 2007

Leopold G. Koss Lectureship, Universität Bern, Switzerland, 2007

Distinguished Lecture in Computer Science, Wayne State University, Detroit, Michigan, USA, 2008

Institute for Personalized, Medicine, Distinguished Lecture, Mount Sinai Medical School, New York, New York, USA, 2010

The Ian Lawson Van Toch Memorial Seminar in Computational Biology, Ontario Cancer Institute, Toronto, Ontario, Canada, 2010

Harvard-Australia Foundation Fellowship, 2010

Bancroft Fellow-in-Residence, Queensland Institute of Medical Research, Queensland, Australia, 2010

Jackson Memorial Fellowship, Griffith University, Queensland, Australia, 2010

National Health and Medical Research Council (NHMRC), Australia Fellowship 2011

Publications

Books

Author, ''The Human Genome: Book of Essential Knowledge'' (Imagine Publishing, U.S., 2011)

Contributor, ''Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins'' (Wiley Interscience, 2004)

Coauthor, ''Microarray Gene Expression Data Analysis: A Beginner's Guide'' (Wiley-Blackwell, 2003)

Select Papers

References

1.

External links

Harvard School of Public Health Bio

Dana-Farber Cancer Institute Bio

Center for Cancer Computational Biology, Dana-Farber Cancer Institute

Lung Genomics Research Consortium Investigator Bio

See also

genomics

bioinformatics

Human Genome Project

sequencing

DNA microarrays

Category:1962 births Category:University of California, Los Angeles alumni Category:Harvard School of Public Health faculty Category:California Institute of Technology people Category:Molecular genetics Category:Genomics Category:Bioinformaticians Category:Bioinformatics Category:Molecular biology Category:Biotechnology Category:Living people