Classical Articles in Bioinformatics and Genomics

 

 

Last updated:2018-6-22

 

Bioinformatics: Alogrithm

 

Needleman S B, Wunsch C D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of molecular biology. 1970 , doi: 10.1016/0022-2836(70)90057-4 PDF

Dayhoff M O, Schwartz R M, Orcutt B C. A model of evolutionary change in proteins. Atlas of protein sequence and structure. 1972 PDF

Staden R. Sequence data handling by computer. Nucleic Acids Research. 1977 , doi: 10.1093/nar/4.11.4037 PDF

Smith T F, Waterman M S. Identification of common molecular subsequences. Journal of molecular biology. 1981 , doi: 10.1016/0022-2836(81)90087-5 PDF

Doolittle R F. Similar amino acid sequences: chance or common ancestry? Science. 1981 , doi: 10.1126/science.7280687 PDF

Wilbur W J, Lipman D J. Rapid similarity searches of nucleic acid and protein data banks. PNAS. 1983 , doi: 10.1073/pnas.80.3.726 PDF

Devereux J, Haeberli P, Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic acids research. 1984 , doi: 10.1093/nar/12.1Part1.387 PDF

Lipman D J, Pearson W R. Rapid and sensitive protein similarity searches. Science. 1985 , doi: 10.1126/science.2983426 PDF

Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Science. 1985 , doi: 10.1111/j.1558-5646.1985.tb00420.x PDF

Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution. 1987 , doi: 10.1093/oxfordjournals.molbev.a040454 PDF

Lander E S, Waterman M S. Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics. 1988 , doi: 10.1016/0888-7543(88)90007-9 PDF

Lipman D J, Altschul S F, Kececioglu J D. A tool for multiple sequence alignment. PNAS. 1989 , doi: 10.1073/pnas.86.12.4412 PDF

Karlin S, Altschul S F. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. PNAS. 1990 , doi: 87 (6) 2264-2268 PDF

Altschul S F, Gish W, Miller W, et al. Basic local alignment search tool. Journal of molecular biology. 1990 , doi: 10.1016/S0022-2836(05)80360-2 PDF

Bowie J U, Luthy R, Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 1991 , doi: 10.1126/science.1853201 PDF

Henikoff S, Henikoff J G. Amino acid substitution matrices from protein blocks. PNAS. 1992 , doi: 10.1073/pnas.89.22.10915 PDF

Krogh A, Brown M, Mian I S. Hidden markov models in computational biology: applications to protein modeling. Journal of molecular biology. 1992 , doi: 10.1006/jmbi.1994.1104 PDF

Thompson J D, Higgins D G, Gibson T J. CLUSTAL W: improving the sensitivity of progressive weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research. 1994 , doi: 10.1093/nar/22.22.4673 PDF

Doolittle R F, Feng D F, Tsang S. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science. 1996 , doi: 10.1126/science.271.5248.470 PDF

Altschul S F, Madden T L, Schaffer A A. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research. 1997 , doi: 10.1093/nar/25.17.3389 PDF

Thompson J D, Gibson T J, Plewniak F. The CLUSTAL_X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools. Nucleic Acids Research. 1997 , doi: 10.1093/nar/25.24.4876 PDF

Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. Journal of molecular biology. 1997 , doi: 10.1006/jmbi.1997.0951 PDF

Posada D, Crandall K A. MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998 , doi: 10.1093/bioinformatics/14.9.817 PDF

Myers E W, Sutton G G, Delcher A L. A whole-genome assembly of Drosophila. Science. 2000 , doi: 10.1126/science.287.5461.2196 PDF

Pevzner P A, Tang H X, Waterman M S. An Eulerian path approach to DNA fragment assembly. PNAS. 2001 , doi: 10.1073/pnas.171285098 PDF

Li X M, Waterman M S. Estimating the repeat structure and length of DNA sequences using l-tuples. Genome research. 2003 , doi: 10.1101/gr.1251803 PDF

Ronquist F, Huelsenbeck J P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003 , doi: 10.1093/bioinformatics/btg180 PDF

Koichiro T, Joel D, Masatoshi N. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular biology and evolution. 2007 , doi: 10.1093/molbev/msm092 PDF

Li R, Zhu H, Ruan J. De novo assembly of human genomes with massively parallel short read sequencing. Genome research. 2010 , doi: 10.1101/gr.097261.109 PDF

 

 

Genomics: A collection of publications on early sequenced genomes (1977-2004)

 

 

1977 First biology: Phage φX174 (5.386kb)

Sanger F, Air G M, Barrell, B G. Nucleotide sequence of bacteriophage phi X174 DNA. Nature. 1977 , doi: 10.1038/265687a0 PDF

 

1982 Phage lambda genome

Sanger F, Coulson A R, Hong G F. Nucleotide sequence of bacteriophage lambda DNA. Journal of molecular biology. 1982 , doi: 10.1016/0022-2836(82)90546-0

 

1983 Phage T7 genome (39.937kb)

Dunn J J, Studier, F W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. Journal of molecular biology. 1983 , doi: 10.1016/S0022-2836(83)80282-4

 

1995 First bacterial genomes (1.8 Mb)

Fleischmann R D, Adams M D, White O. Whole-genome random sequencing and assembly of Haemophilus influenzae. Science. 1995 , doi: 10.1126/science.7542800

 

1996 Yeast genome completely sequenced

An international consortium publicly releases the complete genome sequence of the yeast S. cerevisiae

Mewes H W, Albermann K, Bahr M. Overview of the yeast genome. Nature. 1997PDF

Jacq C, AltMorbe J, Andre B. The nucleotide sequence of Saccharomyces cerevisiae chromosome IV. Nature. 1997PDF

Dietrich F S, Mulligan J, Hennessy K. The nucleotide sequence of Saccharomyces cerevisiae chromosome V. Nature. 1997PDF

Tettelin H, Carbone MLA, Albermann K. The nucleotide sequence of Saccharomyces cerevisiae chromosome VII. Nature. 1997PDF

Churcher C, Bowman S, Badcock K. The nucleotide sequence of Saccharomyces cerevisiae chromosome IX. Nature. 1997PDF

Johnston M, Hillier L, Riles L. The nucleotide sequence of Saccharomyces cerevisiae chromosome XII. Nature. 1997PDF

Bowman S, Churcher C, Badcock K. The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII. Nature. 1997PDF

Philippsen P, Kleine K, Pohlmann R. The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications. Nature. 1997PDF

Dujon B, Albermann K, Aldea M. The nucleotide sequence of Saccharomyces cerevisiae chromosome XV. Nature. 1997PDF

Bussey H, Storms R K, Ahmed A. The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature. 1997PDF

 

1997 E. coli genome

Blattner F R, Plunkett G, Bloch C A. The Complete Genome Sequence of Escherichia coli K-12. Science. 1997 , doi: 10.1126/science.277.5331.1453 PDF

 

1998 Worm (multicellular) genome completely sequenced

The C.elegans Sequencing Consortium. Genome Sequence of the Nematode C.elegans: A Platform for Investigating Biology. Science. 1998 , doi: 10.1126/science.282.5396.2012 PDF

 

1999 Fly genome completely sequenced

Adams M D, Celniker S E, Holt R A. The Genome Sequence of Drosophila melanogaster. Science. 2000 ,doi: 10.1126/science.287.5461.2185 PDF

 

2000 First plant genome: Arabidopsis thaliana

Kaul S, Koo H L, Jenkins J. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 , doi: 408, 796–815 PDF

Mayer K, Schuller C, Wambutt R. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature. 1999 , doi: 402, 769-777 PDF

Lin XY, Kaul SS, Rounsley S. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature. 1999 , doi: 10.1038/45471 PDF

Theologis A, Ecker J R, Palm C J. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature. 2000 , doi: 10.1038/35048500 PDF

Salanoubat M, Lemcke K, Rieger, M. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature. 2000 , doi: 408, 820–823 PDF

Tabata S, Kaneko T, Nakamura Y. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature. 2000 , doi: 408, 823–826 PDF

 

2001 Human genome

Venter J C, Adams M D, Myers E W. The Sequence of the Human Genome. Science. 2001 , doi: 10.1126/science.1058040 PDF

Lander E S, Int Human Genome Sequencing Consortium, Linton L M, et al. Initial sequencing and analysis of the human genome. Nature. 2001 , doi: 409, 860–921PDF

British, Japanese, and U.S. researchers complete the first sequence of a human chromosome, number 22. Nature. 1999.

 

2002 First crop genome: Rice (ssp. indica and japonica) genomes

Yu J, Hu SN, Wang J. A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science. 2002 , doi: 10.1126/science.1068037 PDF

Goff SA, Ricke D, Lan TH. A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science. 2002 , doi: 10.1126/science.1068275 PDF

Feng Q, Zhang YJ, Hao P. Sequence and analysis of rice chromosome 4. Nature. 2002 , doi: 10.1038/nature01183 PDF

Sasaki T, Matsumoto T, Yamamoto K. The genome sequence and structure of rice chromosome 1. Nature. 2002 , doi: 10.1038/nature01184 PDF

Yu Y S, Rambo T, Currie J. In-Depth View of Structure, Activity, and Evolution of Rice Chromosome 10. Science. 2003 , doi: 10.1126/science.1083523 PDF

 

2002 The Japanese pufferfish genome

Aparicio S, Chapman J, Stupka E. Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes. Science. 2002 , doi: 10.1126/science.1072104 PDF

 

2002 Malaria mosquito genome

Holt R A, Subramanian G M, Halpern A. The Genome Sequence of the Malaria Mosquito Anopheles gambiae. Science. 2002 , doi: 10.1126/science.1076181 PDF

Gardner M J, Hall N, Fung E. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 2002 , doi: 10.1038/nature01097 PDF

Carlton J M, Angiuoli S V, Suh B B. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 2002 , doi: 10.1038/nature01099 PDF

 

2002 Mouse genome

Waterston R H, Lindblad-Toh K, Birney E. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 , doi: 10.1038/nature01262 PDF

 

2003 Dog genome

Kirkness E F, Bafna V, Halpern A L. The Dog Genome: Survey Sequencing and Comparative Analysis. Science. 2003 , doi: 10.1126/science.1086432 PDF

 

2004 Rat genome

Gibbs R A, Weinstock G M, Metzker M L. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 , doi: 10.1038/nature02426 PDF

 

 

Genomics: A collection of publications on sequenced plant genomes (2000-2017) PDF