Genomics- The Science and Technology Behind the Human Genome Project. Charles R. Cantor, Cassandra L / genomics11-15 / 15

566

RESULTS AND IMPLICATIONS OF LARGE-SCALE DNA SEQUENCING

Berks, M. The C. elegans genome sequencing project.

C.

elegans

Genome Mapping and

Sequencing Consortium. 1995.

Genome Research

5: 99–104.

Bult, C. J., White, O., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Blake, J. A.,

FitzGerald, L. M., Clayton, R. A., Gocayne, J. D., et al. 1996. Complete genome sequence of the

methanogenic archaeon,

Methanococcus jannaschii. Science

273: 1058–1073

Burland, V., Plunkett III, G., Sofia, H. J., Daniels, D. L., and Blattner, F. R. 1995. Analysis of the

Escherichia coli

genome VI:

DNA sequence of the region from 92.8

through 100

minutes.

Nucleic Acids Research

23: 2105–2119.

Carlock, L., Wisniewski, D., Lorincz, M., Pandrangi, A., and Vo, T. 1992. An estimate of the num-

ber of genes in the Huntington disease gene region and the identification of 13 transcripts in the

4p16.3 segment.

Genomics

13: 1108–1118.

Chothia, C. 1992. One thousand families for the molecular biologist.

Nature

357: 543–544.

Daniels, D. L., Plunkett III, G., Burland, V., and Blattner, F. R. 1992. Analysis of the

Escherichia

coli genome: DNA sequence of the region from 84.5 to 86.5 minutes.

Science

257: 771–778.

Fleischmann, R. D., Adams, M. D., White, O., Clayton, R. A., Kirkness, E. F., Kerlavage, A. R.,

Bult, C. J., Tomb, J. F., Dougherty, B. A., Merrick, J. M., et al. 1995. Whole-genome random se-

quencing and assembly of

Haemophilus influenzae. Science

269: 496–512.

Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult,

C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., et al. 1995. The minimal gene complement of

Mycoplasma genitalium. Science

270: 397–403.

Gardiner, K. 1996. Base composition and gene distribution: Critical patterns in mammalian genome

organization.

Trends in Genetics

12: 519–524.

Goffeau, A. 1995. Life with 482 genes.

Science

270: 445–446.

Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldman, H., Gailbert, F.,

Hoheisel, J. D., Jacq, C., Johnston, M., Louis, E. J., Mewes, H. W., Murakami, Y., Philippsen, P.,

Tettelin, H., and Oliver, S. G. 1996. Life with 6000 genes.

Science

274: 546–567.

Gribskow, M., and Devereaux, J. 1991.

Sequence

Analysis Primer.

Oxford:

Oxford

University

Press.

Harper, R. 1994. Access to DNA and protein databases on the Internet.

Current

Opinion in

Biotechnology

5: 4–18.

Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B.-C., and Herrmann, R. 1996. Complete

sequence analysis of the genome of the bacterium

Mycoplasma

pneumoniae.

Nucleic

Acids

Research

24:4420–4449.

How, G.-F., Venkatesh, B., and Brenner, S. 1996. Conserved linkage between the puffer fish

(Fugu

rubripes)

and human genes for platelet-derived growth factor receptor and macrophage colony-

stimulating factor receptor.

Genome Research

6: 1185–1191.

Johnston, M., Andrews, S., Brinkman, R., Cooper, J., Ding, H., Dover, J., Du, Z., Favello, A.,

Fulton, L., Gattung, S., et al. 1994. Complete nucleotide sequence of

Saccharomyces cerevisiae

chromosome VIII.

Science

265: 2077–2082.

Kaneko, T., et al. 1996. Sequence analysis of the genome of the unicellular cyanobacterium

Synechocystis

sp. strain PCC 6803. II. Sequence determination of the entire genome and assign-

ment of potential protein-coding regions.

DNA Research

3: 109–136.

Karlin, S., and Mrazek, J. 1996. What drives codon choices in human genes?

Journal of Molecular

Biology

262: 459–472.

Lewis, E. B., Knafels, J. D., Mathog, D. R., and Celniker, S. E. 1995. Sequence analysis of the

cis -

regulatory regions of the bithorax complex of

Drosophila. Proceedings of the National Academy

of Sciences USA

92: 8403–8407.

Lopez, R., Larsen, F., and Prydz, H. 1994. Evaluation of the exon predictions of the GRAIL soft-

ware.

Genomics

24: 133–136.

SOURCES

AND

ADDITIONAL READINGS

567

Maier, W. G. 1997. Bonsai genomics: Sequencing the smallest eukaryotic genomes.

Trends in

Genetics

13: 46–49.

Martin, C. H., Mayeda, C. A., Davis, C. A., Ericsson, C. L., Knafels, J. D., Mathog, D. R., Celniker,

S. E., Lewis, E. B., and Palazzolo, M. J. 1995. Complete sequence of the bithorax complex of

Drosophila. Proceedings of the National Academy of Sciences USA

92: 8398–8402.

McCombie, W. R., Martin-Gallardo, A., Gocayne, J. D., FitzGerald, M., et al. 1992. Expressed

genes, Alu repeats and polymorphisms in cosmids sequenced from chromosome 4p16.3.

Nature

Genetics

1: 348–353.

McFadden, G. I., Gilson, P. R., Douglas, S. E., Cavalier-Smith, T., Hofmann, C. J. B., and

Murakami, Y., Naitou, M., Hagiwara, H., Shibata, T., Ozawa, M., Sasanuma, S.-I., Sasanuma,

M., Tsuchiya, Y., Soeda, E., Yokoyama, K., Yamazaki, M., Tashiro, H., and Eki, T. 1995.

Analysis of the nucleotide sequence of chromosome VI from

Saccharomyces cerevisiae. Nature

Genetics

10: 261–264.

Mushegian, A. R., and Koonin, E. V. 1996. A minimal gene set for cellular life derived by compari-

son of complete bacterial genomes.

Proceedings of

the National Academy of

Sciences USA

93:

10268–10273.

Oliver, S. G., van der Aart, Q. J. M., Agostoni-Carbone, M. L., Aigle, M., et al. 1992. The complete

DNA sequence of yeast chromosome III.

Nature

357: 38–46.

Oliver, S. 1995. Size is important, but

. . .

. Nature Genetics

10: 253–256.

Oshima, T., et al. 1996. A 718-kb DNA sequence of the

Escherichia coli

K-12 genome correspond-

ing to the 12.7-28.0 min region on the linkage map.

DNA Research

3: 137–155.

Pearson, W. 1995. Comparison of methods for searching

protein-sequence

databases.

Protein

Science

4: 1145–1160.

Perlin, M. W., Lancia, G., and Ng, S.-K. 1995. Toward

fully

automated

geneotyping:

Geno-

typing microsatellite markers by deconvolution.

American

Journal of

Human Genetics.

57:

1199–1210.

Peters, R., and Sikorski, R. S. 1996. Nucleic acid databases on the Web.

Nature Biotechnology

14:1728–1729.

Posfai, J., and Robert, R. J. 1992. Finding errors in DNA sequences.

Proceedings of the National

Academy of Sciences USA

89: 4698–4702.

Rost, B., and Sander, C. 1996. Bridging the protein sequence-structure gap by structure predictions.

Annual Review of Biophysics and Biomolecular Structure

25: 113–136.

Saccone, S., DeSario, A., Delle Valle, G., and Bernardi, G. 1992. The highest gene concentrations

in the human genome are in telomeric bands of metaphase chromosomes.

Proceedings of

the

National Academy of Sciences USA

89: 4913–4917.

Sharkey, M., Graba, Y., and Scott, M. P. 1997. Hox genes in evolution: Protein surfaces and paralog

groups.

Trends in Genetics

13: 145–151.

Shpaer, E. G., Robinson, M., Yee, D., Candlin, J. D., Mines, R., and Hunkapiller, T. 1996.

Sensitivity and selectivity in protein similarity searchers: A comparison of Smith-Watermanin

hardware to BLAST and FASTA.

Genomics

38: 179–191.

Shevchenko, A., Jensen, O. N., Podtelejnikov, A. V., Sagliocco, F., Wilm, M., Vorm, O., Mortensen,

P., Shevchenko, A., Boucherie, H., and Mann, M. 1996. Linking genome and proteome by mass

spectrometry: Large-scale identification of yeast

proteins

from

two

dimensional

gels.

Proceedings of the National Academy of Sciences USA

93: 14440–14445.

Shoemaker, D. D., Lashkari, D. A., Morris, D., Mittman, M., and Davis, R. W. 1996. Quantitative

phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strat-

egy. Nature Genetics

14: 450–456.

Smith, R. 1996. Perspective: Sequence data base searching in the era of large-scale genomic se-

quencing.

Genome Research

6: 653–660.

568

RESULTS AND IMPLICATIONS OF LARGE-SCALE DNA SEQUENCING

Smith, V., Chou, K. N., Lashkari, D., Botstein, D., and Brown, P. O. 1996. Functional analysis of

the genes of yeast chromosome V by genetic footprinting.

Science

274: 2069–2074.

Sulston, J., Du, Z., Thomas, K., Wilson, R., et al. 1992. The

C. elegans

genome sequencing project:

A beginning.

Nature

356: 37–41.

Strauss, E. J., and Falkow, S. M. 1997. Microbial pathogenesis: Genomics

and beyond.

Science

276: 707–712.

Uberbacher, E. C., and Mural, R. J. 1991. Locating protein-coding regions in human DNA se-

quences by a multiple sensor-neural network approach.

Proceedings of the National Academy of

Sciences USA

88: 4698–4702.

Wilson, R. et al. 1994. 2.2 Mb of contiguous nucleotide sequence from chromosome III of

C. ele-

gans. Nature

363: 32–36.

Wu, R. 1993. Development of enzyme-based methods for DNA sequence analysis and their appli-

cations in the genome proejcts. In A. Meister, ed.,

Advances in Enzymology.

New York: Wiley.

Zhang, M. Q. 1997. Identification of protein coding regions in the human genome by quadratic dis-

criminant analysis.

Proceedings of the National Academy of Sciences USA

94: 565–568.