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History of Bioinformatics

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Jong ~~Park~~Bhak

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~~<a href="mailto:~~j@bio.cc~~">j@bio.cc</a>~~, BiO Centre, Cambridge, UK, +44 1223 524889

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Results:

1843: Richard Owen elaborated the distinction of homology and analogy.

1850-1855: </font~~><a href="http://bio.cc/Bioinformatics/dates_1800.html#Boussingault"~~>Jean-Baptiste Boussingault</font~~></a~~>, who had proved that the carbon in plants came from atmospheric CO2, proposes that plant nitrogen comes from the soil. demonstrates that higher plants cannot utilize atmospheric nitrogen, but only nitrates from the soil. He also demonstrates the necessity of nitrogen for plants and animals. His experimental results were not conclusive, however, and conflicting data were soon published by another Parisian chemist, Ville, and popularized by Liebig. The question he resolved was whether the nitrogen that plants need to grow came from the soil or from the air. Joseph Priestley had argued, in the 18th century, in favor of the air, and his opinion was seconded in the early 19th century, by Liebig, then the world's most famous chemist.

1855: Alfred Russell Wallace publishes On the Law Which Has Regulated the Introduction of New Species

1858: Charles Darwin and Alfred Wallace publish papers on theory of evolution.

1859: Charles Darwin, Cambridge, UK, publishes The Origin of Species, vastly strengthening the adaptationist hypothesis.

1864: Ernst Haeckel (Häckel) outlines the essential elements of modern zoological classification

1865: Gregory Mendel (1823-1884), Austria,  <img height="44" alt="img1.gif" src="http://bio.cc/Bioinformatics/img1.gif" width="52" border="0" /> established the genetic inheritance. The theoretical study of genetics. Experiments in Plant Hybridisation. Cambridge, MA: Harvard University Press. His work, in German, was first published in 1865 in the Proceedings of the Brünn Society for Natural History, Brünn, Austria (</font~~><a href="http://bio.cc/Bioinformatics/history_of_bioinformatics.html#Hewlett"~~>Hewlett, 1998</font~~></a~~>). It was ignored for a generation.1868: Friedrich </font~~><a href="http://biopeople.net/Biologists/Friedrich_Miescher"~~>Miescher</font~~></a~~> - discovery of nuclein found in cell nucleus, acidic, rich in PO4,  lacks S (characteristic of protein). Now know this as nucleic acid

1902: The chromosome theory of heredity is proposed by Sutton and Boveri, working independently.

1905: The word "genetics" is coined by William Bateson.

1930s: Chemical nature of nuclei acid  investigated. It was thought to be a tetranucleotide composed of one unit each of adenylic, guanylic, thymidylic and cytidylic acids

1936: Alan Turing, Cambridge University, The Turing machine, computability, universal machine

1941: Beadle and Tatum. ~~<a href="http://www.mun.ca/biology/scarr/Beadle_&_Tatum_experiment.htm">~~Genetic Control of Biochemical Reactions~~</a>~~ in Neurospora: First sound scientific evidence for one-gene-one-enzyme hypothesis 1944: </font~~><a href="http://biopeople.net/Biologists/Oswald_Avery"~~>Oswald Avery</font~~></a~~> identifies nucleic acids as the active principle in bacterial transformation. Avery, O. T., C. M. MacLeod, and M. McCarty (1944). Studies on the Chemical Nature of Substance Inducing Transformation of Pneumococcal Typoes.  Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III.  Journal of Experimental Medicine 79: 137-158. Also in Peters (1959).  Oswald Avery (1877-1955) was a bacteriologist whose research on pneumococcus bacteria made him one of the founders of immunochemistry and laid the foundation for later discoveries that launched the science of molecular genetics.

1945: John von Neumann, Princeton University, USA, First Draft of a Report on the EDVAC, Contract No. W-670-ORD-492, Moore School of Electrical Engineering, Univ. of Penn., Philadelphia. Reprinted (in part) in Randell, Brian. 1982. Origins of Digital Computers: Selected Papers, Springer-Verlag, Berlin Heidelberg, pp. 383-392.

1946: Genetic material can be transferred laterally between bacterial cells, as shown by ~~<a href="http://profiles.nlm.nih.gov/BB/">~~Lederberg~~</a>~~ and Tatum.

1948: Information Theory Claude Shannon

1950: </font~~><a href="http://biopeople.net/Biologists/Erwin_Chargaff"~~>Erwin Chargaff</font~~></a~~> shows that the four nucleotides are not present in nucleic acids in stable proportions, and that the nucleotide composition differs according to its biological source. Chargaff, Erwin, ed. (1955-60). The Nucleic Acids: Chemistry and Biology. New York, Academic Press.

1951: Pauling and Corey propose the structure for the alpha-helix and beta-sheet (Proc. Natl. Acad. Sci. USA, 27: 205-211, 1951; Proc. Natl. Acad. Sci. USA, 37: 729-740, 1951).

1952: Alfred Day Hershey and Martha Chase proved, on the basis of their bacteriophage research, that DNA alone carries genetic information.

1957: Seymour Benzer introduced the concept of the cistron: the smallest unit of function of the gene.

1958: The first integrated circuit is constructed by Jack Kilby at Texas Instruments.

1958: The Advanced Research Projects Agency (</font~~><a href="http://www.dei.isep.ipp.pt/docs/arpa.html"~~>ARPA</font~~></a~~>) is formed in the US.

1958: Francis Harry Compton Crick, Cambridge, UK, enunciated the central dogma of molecular genetics: information flows from DNA to RNA to protein.

1960: Fran?is Jacob and Jacques Lucien Monod proposed the operon hypothesis for the regulation of enzyme synthesis.

1974: Chou PY, Fasman GD. Conformational parameters for amino acids in helical, beta-sheet, and random coil regions calculated from proteins. Biochemistry. 1974 Jan 15;13(2):211-22.

1975: Microsoft Corporation is founded by Bill Gates and Paul Allen.

1975: Cesar Milstein group's </font~~><a href="http://bio.cc/IE/Monoclonal_Antibody.html"~~>Monoclonal antibodies~~</a>~~ are produced

1975: King and Wilson, suggests the difference between Chimpanzee and humans is small. King, M.C. and A.C. Wilson (1975). Evolution at two levels in Humans and Chimpanzees. Science 188: 107-116.

For an update on the topic, see </font~~><a href="http://bio.cc/Abstracts/Gibbons_98.html"~~>Gibbons 1998</font~~></a~~>; for recent work on multiple transcriptional controls, see </font~~><a href="http://bio.cc/Bioinformatics/history_of_bioinformatics.html#Tijan"~~>Tijan and Holmes 2000</font~~></a~~>.

1975: Two-dimensional electrophoresis, where separation of proteins on SDS polyacrylamide gel is combined with separation according to isoelectric points, is announced by P. H. O'Farrell (J. Biol. Chem., 250: 4007-4021, 1975).

1975: E. M. Southern published the experimental details for the Southern Blot technique of specific sequences of DNA (J. Mol. Biol., 98: 503-517, 1975).

1986: The SWISS-PROT database is created by the Department of Medical Biochemistry of the University of Geneva and the European Molecular Biology Laboratory (EMBL).

1987: The use of yeast artifical chromosomes (YAC) is described (David T. Burke, et. al., Science, 236: 806-812).

1987: McClintock, Barbara (1987). The Discovery and Characterization of Transposable Elements: The Collected Papers of Barbara McClintock. New York: Garland, 1987.  In her 1983 Nobel lecture, McClintock said the genome is "a highly sensitive organ of the cell, that in times of stress could initiate its own restructuring and renovation." See the </font~~><a href="http://www.mbl.edu/html/WOMEN/mcclintock.html"~~>biography</font~~></a~~> at the Cold Springs Harbor site (external). For a current discussion, see </font~~><a href="http://bio.cc/Abstracts/Pennisi_98.html"~~>Pennisi 1998</font~~></a~~>.

1987: The physical map of e. coli is published (Y. Kohara, et. al., Cell 51: 319-337).

1987: Perl (Practical Extraction Report Language) is released by Larry Wall.

1990: The BLAST program (Altschul, et. al.) is implemented. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10.

1990: The HTTP 1.0 specification is published. Tim Berners-Lee publishes the first HTML document. Merit, IBM and MCI formed a not for profit corporation called ANS, Advanced Network & Services, which was to conduct research into high speed networking. It soon came up with the concept of the T3, a 45 Mbps line. NSF quickly adopted the new network and by the end of 1991 all of its sites were connected by this new backbone. While the T3 lines were being constructed, the Department of Defense disbanded the ARPANET and it was replaced by the NSFNET backbone. The original 50Kbs lines of ARPANET were taken out of service. Tim Berners-Lee and CERN in Geneva implements a hypertext system to provide efficient information access to the members of the international high-energy physics community.

1991: Linus Torvalds announces a Unix-Like operating system which later </font~~><a href="http://bio.cc/Bioinformatics/history_of_linux.htm"~~>becomes Linux.</font~~></a~~>

1991: The creation and use of expressed sequence tags (ESTs) is described (J. Craig Venter, et. al., Science, 252: 1651-1656).

1992: FSSP the global protein structural family database published by Liisa Holm et al., Protein Sci 1992 Dec;1(12):1691-1698 A database of protein structure families with common folding motifs. Holm L, Ouzounis C, Sander C, Tuparev G, Vriend G

1992: Cyrus Chothia, Cambridge UK, suggests approximate number of protein families to be 1000. Nature, 1992, June, 357, 543-544 Proteins. One thousand families for the molecular biologist.

1992: Jones DT, Taylor WR, Thornton JM. A new approach to protein fold recognition. Nature. 1992 Jul 2;358(6381):86-9, </font~~><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1614539&dopt=Abstract"~~>PubMed</font~~></a~~>

1993: Dali was published in JMB by Liisa Holm and Christ Sander. J Mol Biol 1993 Sep 5;233(1):123-138 Protein structure comparison by alignment of distance matrices. Holm L, Sander C.

1993: Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol. 1993 Jul 20;232(2):584-99, </font~~><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8345525&dopt=Abstract"~~>PubMed</font~~></a~~>.

1993: InterNIC created by NSF to provide specific Internet services: directory and database services (by AT&T), registration services (by Network Solutions Inc.), and information services (by General Atomics/CERFnet). Marc Andreessen and NCSA and the University of Illinois develops a graphical user interface to the WWW, called "Mosaic for X".

1993: Hidden Markov Model based algorithm popularized.

1993: Affymetrix begins independent operations in Santa Clara, California

1993: Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F., & Wootton, J. C. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 1993, 262(5131), 208-14. </font~~><a href="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=8211139&form=6&db=m&Dopt=b"~~>PubMed</font~~></a~~>

1994: The first CASP (protein structure prediction meeting) held at Asilomar, California. Hidden Markov Model, Interative search method, Threading method were successful in predicting protein structures.

1994: DNA computer Leonard Adelman

1995: SCOP data base published. (structural classification of proteins).

1995: The smallest free-living organism Mycoplasma genitalium genome is sequenced.

1995: The first open-community ~~<a href="http://bioperl.net/">~~BioPerl~~</a>~~ project (with other sister projects BioJava, BioLinux, etc) in bioinformatics initiated by Jong Park and Steve Brenner, Cambridge, MRC Centre, UK (~~<a href="http://bioperl.net/history_of_bioperl.html">~~history_of_bioperl.html~~</a>~~)

1996: The genome for Saccharomyces cerevisiae (baker's yeast, 12.1 Mb) is sequenced.

1996-1997: The first cloning of a mammal (Dolly the sheep) is performed by Ian Wilmut and colleagues, from the Roslin institute in Scotland.

1996: Affymetrix produces the first commercial DNA chips.

1997: The genome for E. coli (4.7 Mbp) is published.

1997: Intermediate Sequence Search method by J. Park, et al., proving the validity of homology transitivity in sequence searches by using structural homology benchmark set that was based on </font~~><a href="http://scop.mrc-lmb.cam.ac.uk/"~~>SCOP</font~~></a~~>.1997: Dahiyat BI, Mayo SL. De novo protein design: fully automated sequence selection. Science. 1997 Oct 3;278(5335):82-7. </font~~><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9311930&dopt=Abstract"~~>PubMed</font~~></a~~> 1997: PSI-BLAST algorithm was published. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Domains Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. </font~~><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9254694&dopt=Abstract"~~>PubMed</font~~></a~~>

1998: The genomes for Caenorhabditis elegans and baker's yeast are published.

1998: Complete genomes show extensive gene/protein sequence/structure duplication. Teichmann etc. al. PNAS.

1998: Proving that multiple sequence based sequence search algorithms (use much more homology information than pairwise methods. J. Park, et al.

1998: Inpharmatica, a new Genomics and Bioinformatics company, is established by University College London, the Wolfson Institute for Biomedical Research, five leading scientists from major British academic centers and Unibio Limited.

1999: Protein Structural Interactome Map: </font~~><a href="http://interactome.org/PSIMAP"~~>PSIMAP</font~~></a~~> including the first full genome interaction network using PDB and yeast two hybrid system was created by Liisa Holm group members, EBI, Cambridge, UK ( ~~<a href="http://jongpark.net/">~~J Park~~</a>~~, Liisa Holm, Michael Lappe) and ~~<a href="http://www.mrc-lmb.cam.ac.uk/genomes/Sarah/">~~S Teichmann~~</a>~~. It is the first phylogenetic interaction network. The first map using protein Domains. The first global interaction network.1999: Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 1999 Jul 30;285(5428):751-3. </font~~><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10427000&dopt=Abstract"~~>PubMed</font~~></a~~>

1999: Bush, R. M., Bender, C. A., Subbarao, K., Cox, N. J., and Fitch, W. M. Predicting the evolution of human influenza A. Science (1999) 286:1921-1925.

1999: Barabasi AL, Albert R. Emergence of scaling in random networks. Science 1999 Oct 15;286(5439):509-12, </font~~><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10521342&dopt=Abstract"~~>PubMed</font~~></a~~> 2000: Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. The large-scale organization of metabolic networks. Nature 2000 Oct 5;407(6804):651-4, </font~~><a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11034217&dopt=Abstract"~~>PubMed</font~~></a~~>

2000:  The genome for Pseudomonas aeruginosa (6.3 Mbp) is published.

2000: The A. thaliana genome (100 Mb) is secquenced.

Online References:

The hisotyr of internet: </font~~><a href="http://www.davesite.com/webstation/net-history.shtml"~~>http://www.davesite.com/webstation/net-history.shtml</font~~></a~~>Allen B. Richon, <em~~><a href="mailto:arichon@www.netsci.org"~~>E-mail: arichon@netsci.org</font~~></a~~> http://www.netsci.org/Science/Bioinform/feature06.htmlInternet hisotyr: </font~~><a href="http://members.magnet.at/dmayr/history.htm"~~>http://members.magnet.at/dmayr/history.htm</font~~></a~~><p~~><a href="http://www.mun.ca/biology/scarr/2250_History.htm"~~>Biological hisotory to 1953: http://www.mun.ca/biology/scarr/2250_History.htm</font~~></a~~>Long history of biology: ~~<a href="http://www.crevola.com/laurent/sitelolo/histoire/historybc.html">~~http://www.crevola.com/laurent/sitelolo/histoire/historybc.html~~</a>~~<p~~><a href="http://cumicro2.cpmc.columbia.edu/icb/:"~~>http://cumicro2.cpmc.columbia.edu/icb/:~~</a> <a href="~~http://cumicro2.cpmc.columbia.edu/icb/Lecture~~">http://cumicro2.cpmc.columbia.edu/icb/Lecture</a>~~%201.pdf, jovanovic@cancercenter.columbia.edu <jovanovic@cancercenter.columbia.edu>Classical papers in bioinformatics: ~~<a href="http://www.sbc.su.se/~per/classics-bioinfo/">~~http://www.sbc.su.se/~per/classics-bioinfo/~~</a>~~About Darwinism: ~~<a href="~~http://www.aboutdarwin.com/literature/Pre_Dar.html~~">http://www.aboutdarwin.com/literature/Pre_Dar.html</a>~~Theoretical Biology: ~~<a href="~~http://www.zbi.ee/~uexkull/theor.htm~~">http://www.zbi.ee/~uexkull/theor.htm</a>~~

John Blamire: http://www.brooklyn.cuny.edu/bc/ahp/MBG/MBG3/MBG.C3.Question.html

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