Classical Articles in Bioinformatics and Genomics

 

 

Last updated:2003-10-22

 

Bioinformatics: Alogrithm

 

Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 48(3):443-53

Staden R. Sequence data handling by computer. Nucleic Acids Res. 1977 4(11):4037-51

Smith TF, Waterman MS. Identification of common molecular subsequences. J Mol Biol. 198125;147(1):195-7

Doolittle RF. Similar amino acid sequences: chance or common ancestry? Science. 1981214(4517):149-59

Wilbur WJ, Lipman DJ. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 198380(3):726-30

Lipman DJ, Pearson WR. Rapid and sensitive protein similarity searches. Science. 1985227(4693):1435-41

Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA, 1990, 87:2264-2268

 

                                

Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. Basic Local Alignment Search Tool. J. Mol. Biol., 215, pp. 403-410, 1990.

Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs. Nucleic Acids Research, 25(17), pp. 3389-3402, 1997.

Bowie, J.U., Luthy, R., and Eisenberg, D. A Method to Identify Protein Sequences that Fold into a Known Three-Dimensional Structure. Science, 253, pp. 164-170, 1991.

Burge, C. and Karlin, S. Prediction of Complete Gene Structures in Human Genomic DNA. J. Mol. Biol., 268, pp. 78-94, 1997.

Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. A Model of Evolutionary Change in Proteins. Atlas of Protein Sequence and Structure, v. 5 suppl. 3, pp. 345-352, 1978.

Doolittle, R.F., Feng, D-F, Tsang, S., Cho, G., and Little, E. Determining Divergence Times of the Major Kingdoms of Living Organisms with a Protein Clock. Science, 271, pp. 470-477, 1996.

Henikoff, S. and Henikoff, Jorja G. Amino Acid Substitution Matrices from Protein Blocks. Proc. Natl. Acad. Sci. USA, 89, pp. 10915-10919, 1992.

Krogh, A., Brown, M., Mian, I.S., Sjolander, K., and Haussler, D. Hidden Markov Models in Computational Biology. J. Mol. Biol., 235. pp. 1501-1531, 1994.

Lipman, D.J., Altschul, S.F., and Kececioglu, J.D. A Tool for Multiple Sequence Alignment. Proc. Natl. Acad. Sci. USA, Vol. 86, pp. 4412-4415, 1989.

Eugene W. Myers, Granger G. Sutton, Art L. Delcher, et al. A Whole-Genome Assembly of Drosophila. Science Mar 24 2000: 2196-2204. [Abstract] [Full Text]

 

 

Genomics: A collection of publications on sequenced genome

 

 

1977 First biology: Phage φX174 (5.386kb)

Sanger F, Air G M, Barrell B G, et al. Nucleotide sequence of bacteriophage phi X174 DNA. Nature, 1977, 265:687-695

 

1982 Phage lambda genome

Sanger F, Coulson AR, Hong GF, Hill DF, Petersen GB. Nucleotide sequence of bacteriophage lambda DNA. J Mol Biol. 1982, Dec 25;162(4):729-73

 

1983 Phage T7 genome (39.937kb)

Dunn,J.J. and Studier,F.W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 1983, 166 (4), 477-535

 

1995 First bacterial genomes (1.8 Mb)

Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496-512

 

1996 Yeast genome completely sequenced

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

Overview of the yeast genome

H. W. MEWES et al. Nature 387, suppl. 7-8 (29 May 1997) | PDF (46 K) |

The nucleotide sequence of Saccharomyces cerevisiae chromosome IV
C. JACQ et al.
Nature 387, suppl. 75-78 (29 May 1997)
| PDF (186 K) |

The nucleotide sequence of Saccharomyces cerevisiae chromosome V
F. S. DIETRICH et al.
Nature
387, suppl. 78-81 (29 May 1997)
| PDF (76 K) |

The nucleotide sequence of Saccharomyces cerevisiae chromosome VII
H. TETTELIN et al.
Nature
387, suppl. 81-84 (29 May 1997)
| PDF (72 K) |

The nucleotide sequence of Saccharomyces cerevisiae chromosome IX
C. CHURCHER et al.
Nature
387, suppl. 84-87 (29 May 1997)
| PDF (229 K) |

The nucleotide sequence of Saccharomyces cerevisiae chromosome XII
M. JOHNSTON et al.
Nature
387, suppl. 87-90 (29 May 1997)
| PDF (81 K) |

The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII
S. BOWMAN et al.
Nature
387, suppl. 90-93 (29 May 1997)
| PDF (220 K) |

The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications
P. PHILIPPSEN et al.
Nature
387, suppl. 93-97 (29 May 1997)
| PDF (141 K) |

The nucleotide sequence of Saccharomyces cerevisiae chromosome XV
B. DUJON et al.
Nature
387, suppl. 98-102 (29 May 1997)
| PDF (184 K) |

The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI
H. BUSSEY et al.

Nature 387, suppl. 103-105 (29 May 1997)
| PDF (101 K) |

 

1997 E. coli genome

The Complete Genome Sequence of Escherichia coli K-12

Frederick R. Blattner, et al. Science, Volume 277, Number 5331, Issue of 5 Sep 1997, pp. 1453-1462.

 

1998 Worm (multicellular) genome completely sequenced

Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology

The C. elegans Sequencing Consortium. Science Dec 11 1998: 2012-2018. [Abstract] [Full Text]

 

1999 Fly genome completely sequenced

The Genome Sequence of Drosophila melanogaster

Mark D. Adams, et al. Science Mar 24 2000: 2185-2195. [Abstract] [Full Text]

 

2000 First plant genome: Arabidopsis thaliana

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
THE ARABIDOPSIS GENOME INITIATIVE
Nature 408, 796-815 (14 December 2000)
| Summary | Full Text | PDF (403 K) |

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana
K. MAYER et al.
Nature 402, 769-777 (16 December 1999)
| Summary | Full Text | PDF (815 K) |

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana
XIAOYING LIN, et al. Nature 402, 761-768 (16 December 1999)
| Summary | Full Text | PDF (1.1 M) |

Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana
ATHANASIOS THEOLOGIS et al.
Nature 408, 816-820 (14 December 2000)
| First Paragraph | Full Text | PDF (279 K) |

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana
EUROPEAN UNION CHROMOSOME 3 ARABIDOPSIS GENOME SEQUENCING CONSORTIUM , THE INSTITUTE FOR GENOMIC RESEARCH & KAZUSA DNA RESEARCH INSTITUTE
Nature 408, 820-823 (14 December 2000)
| First Paragraph | Full Text | PDF (120 K) |

Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana
KAZUSA DNA RESEARCH INSTITUTE, THE COLD SPRING HARBOR AND WASHINGTON UNIVERSITY SEQUENCING CONSORTIUM , THE EUROPEAN UNION ARABIDOPSIS GENOME SEQUENCING CONSORTIUM & INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH (IPK)
Nature 408, 823-826 (14 December 2000)
| First Paragraph | Full Text | PDF (176 K) |

 

 

2001 Human genome

The Sequence of the Human Genome

J. Craig Venter, et al. Science Feb 16 2001: 1304-1351. [Abstract] [Full Text] [Supplemental Data] [Web Fig. 1]

Initial sequencing and analysis of the human genome
THE GENOME INTERNATIONAL SEQUENCING CONSORTIUM
Nature 409, 860-921 (15 February 2001)
| Summary | Full Text | PDF |

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

 

 

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

A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica)

Jun Yu, et al. Science Apr 5 2002: 79-92. [Abstract] [Full Text] [Supplemental Data]

A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)

Stephen A. Goff, et al. Science Apr 5 2002: 92-100. [Abstract] [Full Text] [Supplemental Data]

Sequence and analysis of rice chromosome 4

Qi Feng, et al. Nature420, 316 - 320 (21 Nov 2002) Letters to Nature Abstract | Full Text | PDF

The genome sequence and structure of rice chromosome 1

Takuji Sasaki, et al. Nature420, 312 - 316 (21 Nov 2002) Letters to Nature Abstract | Full Text | PDF

In-Depth View of Structure, Activity, and Evolution of Rice Chromosome 10

The Rice Chromosome 10 Sequencing Consortium. Science Jun 6 2003: 1566-1569. [Abstract] [Full Text] [PDF] [Supporting Online Material]

 

2002 The Japanese pufferfish genome

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

Samuel Aparicio, et al. Science Aug 23 2002: 1301-1310. [Abstract] [Full Text] [Supporting Online Material] [Notes and Corrections]

 

2002 Malaria mosquito genome

 

The Genome Sequence of the Malaria Mosquito Anopheles gambiae
R. A. Holt et al.; Science 298, 129 (2002) [Abstract] [Full Text]

Genome sequence of the human malaria parasite Plasmodium falciparum
MALCOLM J. GARDNER et al. Nature 419, 498–511 (2002);| Summary | Full Text (HTML / PDF) |

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

JANE M. CARLTON et al. Nature 419, 512–519 (2002); | Summary | Full Text (HTML / PDF)

 

2002 Mouse genome

Initial sequencing and comparative analysis of the mouse genome

Asif T., et al. Nature420, 520 - 562 (05 Dec 2002) The Mouse Genome Abstract | Full Text | PDF

 

2003 Dog genome

The Dog Genome: Survey Sequencing and Comparative Analysis

Kirkness et al. Science, Volume 301, Number 5641, Issue of 26 Sep 2003, pp. 1898-1903

 

2004 Rat genome

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Rat Genome Sequencing Project Consortium. Nature 428, 493-521 (1 Apr 2004) [Full text link] [PDF]