Bioinformatics - Revision history

Shawndouglas: /* References */ Cats

2022-09-17T19:29:08Z

References: Cats

← Older revision		Revision as of 19:29, 17 September 2022
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	{{Reflist\|colwidth=30em}}		{{Reflist\|colwidth=30em}}

			<!---Place all category tags here-->
	[[Category:Informatics]]		[[Category:Informatics]]
			[[Category:Life sciences industry]]

Shawndouglas: Updated URLs for 2022

2022-01-06T17:05:24Z

Updated URLs for 2022

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Shawndouglas: Tweaks for 2020

2020-03-19T22:50:25Z

Tweaks for 2020

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Shawndouglas: Added attribution.

2014-04-24T20:41:09Z

Added attribution.

← Older revision		Revision as of 20:41, 24 April 2014
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	* [http://www.embnet.org/ Bioinformatics Without Borders]		* [http://www.embnet.org/ Bioinformatics Without Borders]
	* [http://www.open-bio.org/ Open Bioinformatics Foundation]		* [http://www.open-bio.org/ Open Bioinformatics Foundation]

			==Notes==

			Some elements of this article are reused from [http://en.wikipedia.org/wiki/Bioinformatics the Wikipedia article].

	==References==		==References==

Shawndouglas: Typo

2013-11-05T21:42:39Z

Typo

← Older revision		Revision as of 21:42, 5 November 2013
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	[[File:Computer with microarray.jpg\|thumbnail\|right\|300px\|Female laboratory technician sitting at computer that displays a microarray; DNA microarray technology aids in gene expression analysis and ~~other~~ other bioinformatics functions.]]		[[File:Computer with microarray.jpg\|thumbnail\|right\|300px\|Female laboratory technician sitting at computer that displays a microarray; DNA microarray technology aids in gene expression analysis and other bioinformatics functions.]]

	'''Bioinformatics''' is the application of [[computer science]] and information technology to the field of biology, with a primary goal of understanding biological processes. What sets it apart from other approaches, however, is its focus on developing and applying computationally intensive techniques (e.g. pattern recognition, data mining, machine learning algorithms, and visualization) to achieve this goal. Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide association studies, and the modeling of evolution.<ref name="BioInfoPolanski">{{cite book \|url=http://books.google.com/books?id=oZbR3GEdmVMC \|title=Bioinformatics \|chapter=Chapter 1: Introduction \|author=Polanski, Andrzej \|publisher=Springer \|year=2007 \|pages=1–9 \|isbn=3540241663}}</ref><ref name="EssBioInfo">{{cite book \|url=http://books.google.com/books?id=AFsu7_goA8kC \|title=Essential Bioinformatics \|chapter=Chapter 1: Introduction \|author=Xiong, Jin \|publisher=Cambridge University Press \|year=2006 \|pages=3–9 \|isbn=113945062X}}</ref>		'''Bioinformatics''' is the application of [[computer science]] and information technology to the field of biology, with a primary goal of understanding biological processes. What sets it apart from other approaches, however, is its focus on developing and applying computationally intensive techniques (e.g. pattern recognition, data mining, machine learning algorithms, and visualization) to achieve this goal. Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide association studies, and the modeling of evolution.<ref name="BioInfoPolanski">{{cite book \|url=http://books.google.com/books?id=oZbR3GEdmVMC \|title=Bioinformatics \|chapter=Chapter 1: Introduction \|author=Polanski, Andrzej \|publisher=Springer \|year=2007 \|pages=1–9 \|isbn=3540241663}}</ref><ref name="EssBioInfo">{{cite book \|url=http://books.google.com/books?id=AFsu7_goA8kC \|title=Essential Bioinformatics \|chapter=Chapter 1: Introduction \|author=Xiong, Jin \|publisher=Cambridge University Press \|year=2006 \|pages=3–9 \|isbn=113945062X}}</ref>

Shawndouglas: Added content, updated refs.

2013-11-05T21:42:05Z

Added content, updated refs.

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Shawndouglas: Saved progress

2013-11-05T20:00:08Z

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Shawndouglas: /* History */

2013-11-05T00:51:16Z

History

← Older revision		Revision as of 00:51, 5 November 2013
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	==History==		==History==

	Arguably one of the first "bioinformatics" projects — though the concept didn't yet exist — involved the 1965 creation and maintenance of a protein sequence database called the ''Atlas of Protein Sequence and Structure'' by Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley. The work grew out of their "biochemical investigation of the relations between the structures and function of proteins and the theoretical attempt to decipher the genetic code."<ref name="EssBioInfo" /><ref name="CCCAtlas">{{cite journal \|url=http://www.ncbi.nlm.nih.gov/pubmed/20665074 \|journal=Journal of the History of Biology \|title=Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s ''Atlas of Protein Sequence and Structure'', 1954–1965 \|author=Strasser, Bruno J. \|volume=43 \|issue=4 \|pages=623–660 \|date=December 2010 \|pmid=20665074 \|doi=10.1007/s10739-009-9221-0}}</ref> Six years later the Brookhaven National Laboratory and the Cambridge Crystallographic Data Centre jointly created the Protein Data Bank, intended as a public database of three-dimensional protein structures. The work at Brookhaven would go on to influence others in the field to contribute, with 23 structures contributed in 1976, breaking 5,000 by the end of 1996 and 40,000 in 2006.<ref name="EssBioInfo" /><ref name="PDBHist">{{cite journal \|url=http://www.ebi.ac.uk/msd/embo08/pdf/pdb_history.pdf‎ \|format=PDF \|journal=Acta crystallographica. Section A, Foundations of crystallography \|title=The Protein Data Bank: a historical perspective \|author=Berman, Helen M. \|volume=64 \|issue=1 \|date=January 2008 \|pages=88–95 \|pmid=18156675}}</ref> The significant growth in contributions was fueled by several events, including: Peter Y. Chou and Gerald D. Fasman's 1974 creation (and later, refinement) of a protein structure prediction algorithm<ref name="ChouPred1">{{cite journal \|author=Chou, Peter Y,; Fasman, Gerald D. \|year=1974 \|title=Prediction of protein conformation \|journal=Biochemistry \|volume=13 \|issue=2 \|pages=222–245 \|doi=10.1021/bi00699a002 \|pmid=4358940}}</ref><ref name="ChouPred2">{{cite journal \|author=Chou, Peter Y,; Fasman, Gerald D. \|year=1978 \|title=Empirical predictions of protein conformation \|journal=Annu Rev Biochem \|volume=47 \|pages=251–276 \|doi=10.1146/annurev.bi.47.070178.001343 \|pmid=354496}}</ref><ref name="ChouPred3">{{cite journal \|author=Chou, Peter Y,; Fasman, Gerald D. \|year=1978 \|title=Prediction of the secondary structure of proteins from their amino acid sequence \|journal=Adv Enzymol Relat Areas Mol Biol \|volume=47 \|pages=45–148 \|pmid=364941}}</ref>; David J. Lipman and William R. Pearson's 1985 development (and later, refinement) of FASTP (later FASTA)<ref name="RapSenProt">{{cite journal \|pmid=2983426 \|year=1985 \|title=Rapid and sensitive protein similarity searches \|volume=227 \|issue=4693 \|pages=1435–41 \|journal=Science \|doi=10.1126/science.2983426 \|author=Lipman, David J.; Pearson, William R.}}</ref><ref name="ImpToolBio">{{cite journal \|pmid=3162770 \|year=1988 \|title=Improved tools for biological sequence comparison \|volume=85 \|issue=8 \|pages=2444–8 \|pmc=280013 \|journal=Proceedings of the National Academy of Sciences of the United States of America \|doi=10.1073/pnas.85.8.2444 \|author=Lipman, David J.; Pearson, William R.}}</ref> as well as Stephen Altschul and company's 1990 development and refinement of BLAST<ref name="BLAST">{{cite journal \|author=Altschul, Stephen; Gish, Warren; Miller, Webb; Myers, Eugene; Lipman, David \|title=Basic local alignment search tool \|doi=10.1016/S0022-2836(05)80360-2 \|journal=Journal of Molecular Biology \|volume=215 \|issue=3 \|pages=403–410 \|year=1990 \|pmid=2231712}}</ref>, both database sequence searching algorithms and programs; and the formal start of the Human Genome Project in 1990.<ref name="EssBioInfo" />		Arguably one of the first "bioinformatics" projects — though the concept didn't yet exist — involved the 1965 creation and maintenance of a protein sequence database called the ''Atlas of Protein Sequence and Structure'' by Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley. The work grew out of their "biochemical investigation of the relations between the structures and function of proteins and the theoretical attempt to decipher the genetic code."<ref name="EssBioInfo" /><ref name="CCCAtlas">{{cite journal \|url=http://www.ncbi.nlm.nih.gov/pubmed/20665074 \|journal=Journal of the History of Biology \|title=Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s ''Atlas of Protein Sequence and Structure'', 1954–1965 \|author=Strasser, Bruno J. \|volume=43 \|issue=4 \|pages=623–660 \|date=December 2010 \|pmid=20665074 \|doi=10.1007/s10739-009-9221-0}}</ref> Six years later the Brookhaven National Laboratory and the Cambridge Crystallographic Data Centre jointly created the Protein Data Bank, intended as a public database of three-dimensional protein structures.

			The work at Brookhaven would go on to influence others in the field to contribute, with 23 structures contributed in 1976, breaking 5,000 by the end of 1996 and 40,000 in 2006.<ref name="EssBioInfo" /><ref name="PDBHist">{{cite journal \|url=http://www.ebi.ac.uk/msd/embo08/pdf/pdb_history.pdf‎ \|format=PDF \|journal=Acta crystallographica. Section A, Foundations of crystallography \|title=The Protein Data Bank: a historical perspective \|author=Berman, Helen M. \|volume=64 \|issue=1 \|date=January 2008 \|pages=88–95 \|pmid=18156675}}</ref> The significant growth in contributions was fueled by several events, including: Peter Y. Chou and Gerald D. Fasman's 1974 creation (and later, refinement) of a protein structure prediction algorithm<ref name="ChouPred1">{{cite journal \|author=Chou, Peter Y,; Fasman, Gerald D. \|year=1974 \|title=Prediction of protein conformation \|journal=Biochemistry \|volume=13 \|issue=2 \|pages=222–245 \|doi=10.1021/bi00699a002 \|pmid=4358940}}</ref><ref name="ChouPred2">{{cite journal \|author=Chou, Peter Y,; Fasman, Gerald D. \|year=1978 \|title=Empirical predictions of protein conformation \|journal=Annu Rev Biochem \|volume=47 \|pages=251–276 \|doi=10.1146/annurev.bi.47.070178.001343 \|pmid=354496}}</ref><ref name="ChouPred3">{{cite journal \|author=Chou, Peter Y,; Fasman, Gerald D. \|year=1978 \|title=Prediction of the secondary structure of proteins from their amino acid sequence \|journal=Adv Enzymol Relat Areas Mol Biol \|volume=47 \|pages=45–148 \|pmid=364941}}</ref>; David J. Lipman and William R. Pearson's 1985 development (and later, refinement) of FASTP (later FASTA)<ref name="RapSenProt">{{cite journal \|pmid=2983426 \|year=1985 \|title=Rapid and sensitive protein similarity searches \|volume=227 \|issue=4693 \|pages=1435–41 \|journal=Science \|doi=10.1126/science.2983426 \|author=Lipman, David J.; Pearson, William R.}}</ref><ref name="ImpToolBio">{{cite journal \|pmid=3162770 \|year=1988 \|title=Improved tools for biological sequence comparison \|volume=85 \|issue=8 \|pages=2444–8 \|pmc=280013 \|journal=Proceedings of the National Academy of Sciences of the United States of America \|doi=10.1073/pnas.85.8.2444 \|author=Lipman, David J.; Pearson, William R.}}</ref> as well as Stephen Altschul and company's 1990 development and refinement of BLAST<ref name="BLAST">{{cite journal \|author=Altschul, Stephen; Gish, Warren; Miller, Webb; Myers, Eugene; Lipman, David \|title=Basic local alignment search tool \|doi=10.1016/S0022-2836(05)80360-2 \|journal=Journal of Molecular Biology \|volume=215 \|issue=3 \|pages=403–410 \|year=1990 \|pmid=2231712}}</ref>, both database sequence searching algorithms and programs; and the formal start of the Human Genome Project in 1990.<ref name="EssBioInfo" />

			A flurry of genome studies went on to produce unprecedented amounts of biological data, creating a sudden demand for rapid and efficient computational tools to manage and analyze the data. "The development of these computational tools depended on knowledge generated from a wide range of disciplines including mathematics, statistics, computer science, information technology, and molecular biology."<ref name="EssBioInfo" /> The merger of these disciplines largely went on to form what is now known as bioinformatics.


	In order to study how normal cellular activities are altered in different disease states, the biological data must be combined to form a comprehensive picture of these activities. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. The actual process of analyzing and interpreting data is referred to as computational biology. Important sub-disciplines within bioinformatics and computational biology include:		In order to study how normal cellular activities are altered in different disease states, the biological data must be combined to form a comprehensive picture of these activities. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. The actual process of analyzing and interpreting data is referred to as computational biology. Important sub-disciplines within bioinformatics and computational biology include:

Shawndouglas: Added more history.

2013-11-05T00:22:06Z

Added more history.

← Older revision		Revision as of 00:22, 5 November 2013
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	==History==		==History==

	Arguably one of the first "bioinformatics" projects — though the concept didn't yet exist — involved the 1965 creation and maintenance of a protein sequence database called the ''Atlas of Protein Sequence and Structure'' by Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley. The work grew out of their "biochemical investigation of the relations between the structures and function of proteins and the theoretical attempt to decipher the genetic code."<ref name="EssBioInfo" /><ref name="CCCAtlas">{{cite journal \|url=http://www.ncbi.nlm.nih.gov/pubmed/20665074 \|journal=Journal of the History of Biology \|title=Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s ''Atlas of Protein Sequence and Structure'', 1954–1965 \|author=Strasser, Bruno J. \|volume=43 \|issue=4 \|pages=623–660 \|date=December 2010 \|pmid=20665074 \|doi=10.1007/s10739-009-9221-0}}</ref> Six years later the Brookhaven National Laboratory and the Cambridge Crystallographic Data Centre jointly created the Protein Data Bank, intended as a public database of three-dimensional protein structures. The work at Brookhaven would go on to influence others in the field to contribute, with 23 structures contributed in 1976, breaking 5,000 by the end of 1996 and 40,000 in 2006.<ref name="EssBioInfo" /><ref name="PDBHist">{{cite journal \|url=http://www.ebi.ac.uk/msd/embo08/pdf/pdb_history.pdf‎ \|format=PDF \|journal=Acta crystallographica. Section A, Foundations of crystallography \|title=The Protein Data Bank: a historical perspective \|author=Berman, Helen M. \|volume=64 \|issue=1 \|date=January 2008 \|pages=88–95 \|pmid=18156675}}</ref> The significant growth in contributions was ~~partially~~ fueled by		Arguably one of the first "bioinformatics" projects — though the concept didn't yet exist — involved the 1965 creation and maintenance of a protein sequence database called the ''Atlas of Protein Sequence and Structure'' by Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley. The work grew out of their "biochemical investigation of the relations between the structures and function of proteins and the theoretical attempt to decipher the genetic code."<ref name="EssBioInfo" /><ref name="CCCAtlas">{{cite journal \|url=http://www.ncbi.nlm.nih.gov/pubmed/20665074 \|journal=Journal of the History of Biology \|title=Collecting, Comparing, and Computing Sequences: The Making of Margaret O. Dayhoff’s ''Atlas of Protein Sequence and Structure'', 1954–1965 \|author=Strasser, Bruno J. \|volume=43 \|issue=4 \|pages=623–660 \|date=December 2010 \|pmid=20665074 \|doi=10.1007/s10739-009-9221-0}}</ref> Six years later the Brookhaven National Laboratory and the Cambridge Crystallographic Data Centre jointly created the Protein Data Bank, intended as a public database of three-dimensional protein structures. The work at Brookhaven would go on to influence others in the field to contribute, with 23 structures contributed in 1976, breaking 5,000 by the end of 1996 and 40,000 in 2006.<ref name="EssBioInfo" /><ref name="PDBHist">{{cite journal \|url=http://www.ebi.ac.uk/msd/embo08/pdf/pdb_history.pdf‎ \|format=PDF \|journal=Acta crystallographica. Section A, Foundations of crystallography \|title=The Protein Data Bank: a historical perspective \|author=Berman, Helen M. \|volume=64 \|issue=1 \|date=January 2008 \|pages=88–95 \|pmid=18156675}}</ref> The significant growth in contributions was fueled by several events, including: Peter Y. Chou and Gerald D. Fasman's 1974 creation (and later, refinement) of a protein structure prediction algorithm<ref name="ChouPred1">{{cite journal \|author=Chou, Peter Y,; Fasman, Gerald D. \|year=1974 \|title=Prediction of protein conformation \|journal=Biochemistry \|volume=13 \|issue=2 \|pages=222–245 \|doi=10.1021/bi00699a002 \|pmid=4358940}}</ref><ref name="ChouPred2">{{cite journal \|author=Chou, Peter Y,; Fasman, Gerald D. \|year=1978 \|title=Empirical predictions of protein conformation \|journal=Annu Rev Biochem \|volume=47 \|pages=251–276 \|doi=10.1146/annurev.bi.47.070178.001343 \|pmid=354496}}</ref><ref name="ChouPred3">{{cite journal \|author=Chou, Peter Y,; Fasman, Gerald D. \|year=1978 \|title=Prediction of the secondary structure of proteins from their amino acid sequence \|journal=Adv Enzymol Relat Areas Mol Biol \|volume=47 \|pages=45–148 \|pmid=364941}}</ref>; David J. Lipman and William R. Pearson's 1985 development (and later, refinement) of FASTP (later FASTA)<ref name="RapSenProt">{{cite journal \|pmid=2983426 \|year=1985 \|title=Rapid and sensitive protein similarity searches \|volume=227 \|issue=4693 \|pages=1435–41 \|journal=Science \|doi=10.1126/science.2983426 \|author=Lipman, David J.; Pearson, William R.}}</ref><ref name="ImpToolBio">{{cite journal \|pmid=3162770 \|year=1988 \|title=Improved tools for biological sequence comparison \|volume=85 \|issue=8 \|pages=2444–8 \|pmc=280013 \|journal=Proceedings of the National Academy of Sciences of the United States of America \|doi=10.1073/pnas.85.8.2444 \|author=Lipman, David J.; Pearson, William R.}}</ref> as well as Stephen Altschul and company's 1990 development and refinement of BLAST<ref name="BLAST">{{cite journal \|author=Altschul, Stephen; Gish, Warren; Miller, Webb; Myers, Eugene; Lipman, David \|title=Basic local alignment search tool \|doi=10.1016/S0022-2836(05)80360-2 \|journal=Journal of Molecular Biology \|volume=215 \|issue=3 \|pages=403–410 \|year=1990 \|pmid=2231712}}</ref>, both database sequence searching algorithms and programs; and the formal start of the Human Genome Project in 1990.<ref name="EssBioInfo" />






	In order to study how normal cellular activities are altered in different disease states, the biological data must be combined to form a comprehensive picture of these activities. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. The actual process of analyzing and interpreting data is referred to as computational biology. Important sub-disciplines within bioinformatics and computational biology include:		In order to study how normal cellular activities are altered in different disease states, the biological data must be combined to form a comprehensive picture of these activities. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. The actual process of analyzing and interpreting data is referred to as computational biology. Important sub-disciplines within bioinformatics and computational biology include:

Shawndouglas: Made some updates. Saving changes and adding more.

2013-11-04T23:48:05Z

Made some updates. Saving changes and adding more.

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