Classical Articles in Bioinformatics and Genomics

 

 

Last updated:2018-6-22

 

Bioinformatics: Alogrithm

 

Saul B.Needleman, Christian D.Wunsch. 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)90057-4PDF

MO Dayhoff. A model of evolutionary change in proteins. Atlas of protein sequence and structure. 1972 PDF

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

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

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

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

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

DJ Lipman, WR Pearson. Rapid and sensitive protein similarity searches. Science. 1985 , doi: 10.1126/science.2983426 PDF

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

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

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

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

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

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

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

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

Krogh et al. Hidden markov models in computational biology: applications to protein modeling. Journal of molecular biology. 1992 , doi: 10.1006/jmbi.1994.1104 PDF

Julie D.Thompson, Desmond G.Higgins and Toby J.Gibson. 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 et al. 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 et al. 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 et al. 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

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

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

Myers et al. A whole-genome assembly of Drosophila. Science. 2000 , doi: 10.1126/science.287.5461.2196 PDF

Pavel A. Pevzner, Haixu Tang, and Michael S. Waterman. An Eulerian path approach to DNA fragment assembly. PNAS. 2001 , doi: 10.1073/pnas.171285098 PDF

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

Fredrik Ronquist, John P. Huelsenbeck. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003 , doi: 10.1093/bioinformatics/btg180PDF

Koichiro Tamura, Joel Dudley, Masatoshi Nei, Sudhir Kumar. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular biology and evolution. 2007 , doi: 10.1093/molbev/msm092PDF

Li et al. 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 early publications on sequenced genomes (1977-2004)

 

 

1977 First biology: Phage φX174 (5.386kb)

Sanger et al. Nucleotide sequence of bacteriophage phi X174 DNA. Nature. 1977 , doi: 10.1038/265687a0 PDF

 

1982 Phage lambda genome

Sanger et al. 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)

John J.Dunn, F. William Studier and M.Gottesman. 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)

Richard et al. 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 et al. Overview of the yeast genome. Nature. 387, suppl. 7-8 (29 May 1997) | PDF (46 K) |

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

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

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

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

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

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

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

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

Bussey et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature. 387, suppl. 103-105 (29 May 1997) | PDF (101 K) |

 

1997 E. coli genome

Blattner et al. 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 et al. The Genome Sequence of Drosophila melanogaster. Science. 2000 ,doi: 10.1126/science.287.5461.2185 PDF

 

2000 First plant genome: Arabidopsis thaliana

Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 ,408, 796–815 PDF

Mayer et al. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature. 1999 ,402, 769-777 PDF

Lin et al. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature. 1999 , doi: 10.1038/45471 PDF

Theologis et al. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature. 2000 , doi: 10.1038/35048500 PDF

Salanoubat et al. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature. 2000 , doi: 408, 820–823 PDF

Tabata et al. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature. 2000 , doi: 408, 823–826 PDF

 

2001 Human genome

Venter et al. The Sequence of the Human Genome. Science. 2001 , doi: 10.1126/science.1058040 PDF

International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001 , 409, 860–921PDF

(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

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

Goff et al. A draft sequence of the rice genome (Oryza sativa L. ssp japonica). Science. 2002 , doi: 10.1126/science.1068275 PDF

Feng et al. Sequence and analysis of rice chromosome 4. Nature. 2002 , doi: 10.1038/nature01183 PDF

Sasaki et al. The genome sequence and structure of rice chromosome 1. Nature. 2002 , doi: 10.1038/nature01184 PDF

Yu et al. 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 et al. 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 et al. The Genome Sequence of the Malaria Mosquito Anopheles gambiae. Science. 2002 , doi: 10.1126/science.1076181 PDF

Gardner et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature. 2002 , doi: 10.1038/nature01097 PDF

Carlton et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature. 2002 , doi: 10.1038/nature01099 PDF

 

2002 Mouse genome

Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002 , doi: 10.1038/nature01262 PDF

 

2003 Dog genome

Kirkness et al. The Dog Genome: Survey Sequencing and Comparative Analysis. Science. 2003 , doi: 10.1126/science.1086432 PDF

 

2004 Rat genome

Rat Genome Sequencing Project Consortium. 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