gene recognition papers (1994)

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1994

D. Barrick, K. Villanueba, J. Childs, R. Kalil, T.D. Schneider, C.E. Lawrence, L. Gold, and G.D. Stormo, G.D. (1994),
"Quantitative analysis of ribosome binding sites in E. coli",
Nucleic Acids Research, 22, 1287-1295.
M.S. Boguski, C.M.Tolstoshev, D.E. Bassett Jr. (1994),
"Gene discovery in dbEST",
Science, 265, 1993
[dbEST is at http://www.ncbi.nlm.nih.gov/dbEST/ ].
M. Borodovsky, E.V. Koonin and K.E. Rudd (1994),
"New genes in old sequence: a strategy for finding genes in the bacterial genome",
Trends in Biochemical Sciences 19, 309-313.
M. Borodovsky, K.E. Rudd and E.V. Koonin (1994),
"Intrinsic and extrinsic approaches for detecting genes in a bacterial genome",
Nucleic Acids Research, 22, 4756-4767.
[ abstract]
D.M. Church, C.J. Stotler, J.L. Rutter, J.R. Murrell, J.A. Trofatter and A.J. Buckler (1994),
"Isolation of genes from complex sources of mammalian genomic DNA using exon amplification",
Nature Genetics, 6: 98-105.
J.-M. Claverie (1994),
"Some useful statistical properties of position-weight matrices",
Computer & Chemistry, 18(3), 287-294 (OPCB94).
[ abstract]
J.-M. Claverie (1994) ,
"Large scale sequence analysis",
in Automated DNA Sequencing and Analysis , eds. M.D. Adams, C. Fields, and J.C. Venter, pages 267-279 (Academic Press. San Diego, CA).
J.-M. Claverie (1994),
"A streamlined random sequencing strategy for finding coding exons",
Genomics, 23, 575-581.
[abstract]
S. Dong, D.B. Searls (1994),
"Gene structure prediction by linguistic methods",
Genomics, 23, 540-551.
[abstract]
[the GenLang service is provided at http://cbil.humgen.upenn.edu/~sdong/genlang_home.html ]
J.W. Fickett (1994),
"Inferring genes from open reading frames",
Computer & Chemistry, 18(3), 203-205.
[ abstract] [ Medline entry] (OPCB94).
C.A. Fields (1994),
"Integrating computational and experimental methods for gene discovery",
in Automated DNA Sequencing and Analysis eds. M.D. Adams, C. Fields, and J.C. Venter, pages 321-325, (Academic Press. San Diego, CA).
C. Fondat, A. Kalogeropoulos (1994),
"Approaching the function of new genes by the detection of their potential upstream activation sequences in Saccharomyces cerevisiae: application to chromosome III",
Current Genetics, 25, 396-406.
P. Green (1994),
"Ancient conserved regions in gene sequences",
Current Opinions in Structural Biology, 4, 404-412.
A. Griffin and H.G. Griffin (1994),
Computer Analysis of Sequence Data (2 vol)
(Humana Press. Totwa, NJ).
S. Henikoff (1994),
"Comparative sequence analysis: finding genes",
in Biocomputing: Informatics and Genome Projects ed. D.W. Smith (Academic Press)
R. Knueppel, P. Dietze, W. Lehnberg, K. Frech, E. Wingender (1994),
"TRANSFAC retrieval program: A network model database of eukaryotic transcription regulating sequences and proteins",
Journal of Computational Biology, 1, 191-198.
Y. Kondrakhin, V. Shamir, N. Kolchanov (1994)
"Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3' terminal processing sites",
Computer Applications in Biosciences, 10, 597-603.
A.K. Konopka (1994),
"Sequences and codes: fundamentals of biomolecular cryptography",
in Biocomputing: Informatics and Genome Projects , ed. D.W. Smith (Academic Press)
A Krogh, IS Mian, D Haussler (1994),
"A hidden Markov model that finds genes in E. coli DNA",
Nucleic Acids Research, 22, 4768-4778.
(and in a slightly expanded version: UCSC Report CRL-93-33.)
R. Lopez, F. Larsen, H. Prydz (1994),
"Evaluation of the exon predictions of the GRAIL software",
Genomics, 24, 133-136.
H. Mizushima, K. Hayashi (1994),
"Establishment of transcription factor database and human mutation database",
in Proceedings of Genome Informatics Workshop 1994 , eds. Miyano, S., Akutsu, T., Imai, H., Gotoh, O., Takagi, T. (Universal Academy Press, Tokyo).
S.M. Ossadnik, S.V. Buldyrev, A.L. Goldberger, S. Havlin, R.N. Mantegna, V.-K. Peng, M. Simons and H.E. Stanley (1994),
"Correlation approach to identify coding regions in DNA sequences",
Biophysical Journal, 67, 64-70.
J.J. Puthukattukaran, S. Chalasani and P. Senapathy (1994),
"Serial and parallel algorithms for gene finding",
in Proceedings of the Third International Symposium on High Performance Distributed Computing, pages 186-193 (San Francisco, CA)
K. Robison, W. Gilbert, G.M. Church (1994),
"Large scale bacterial gene discovery by similarity search",
Nature Genetics, 7: 205-214.
P. Senapathy (1994),
Independent Birth of Organisms ,
(Genome Press, Madison, WI).
J.W. Shavlik (1994),
"Finding frameshift errors in anonymous DNA",
in Automated DNA Sequencing and Analysis eds. M.D. Adams, C. Fields, and J.C. Venter, eds. pages 280-288, (Academic Press. San Diego, CA).
G.B. Singh S.A. Krawetz (1994),
"Computer based exon detection: an evaluation metric for comparison",
International Journal of Genome Research, 1, 321-338.
VV Solovyev, AA Salamov, CB Lawrence (1994),
"The prediction of human exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames",
in ISMB94, 354-362.
[ Medline entry]
[the Genefinder service is provided at http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html ]
VV Solovyev, AA Salamov, CB Lawrence (1994)
"Predicting internal exons by oligonucleotide composition and discriminant analysis of spliceable open reading frames",
Nucleic Acids Research, 22:5156-5163.
[ abstract] [ Medline entry]
S Stamm, MQ Zhang, TG Marr, DM Helfman (1994),
"A sequence compilation and comparison of exons that are alternatively spliced in neurons",
Nucleic Acids Research, 22(9):1515-1526.
[ Medline entry]
D.J. States and W. Gish (1994),
"Combined use of sequence similarity and codon bias for coding region identification",
Journal of Computational Biology, 1, 39-50.
G.D. Stormo and D. Haussler (1994),
"Optimally parsing a sequence into different classes based on multiple types of evidence",
in ISMB94, 369-375.
A. Thomas and M.H. Skolnick (1994),
"A probabilistic model for detecting coding regions in DNA sequences",
IMA Journal of Mathematics Applied in Medicine and Biology, 11, 149-160.
P.H. von Hippel (1994),
"Protein-DNA recognition: new perspectives and underlying themes",
Science, 263, 769-770.
Y. Xu, J.R. Einstein, R.J. Mural, M. Shah, E.C. Uberbacher (1994),
"An improved system for exon recognition and gene modeling in human DNA sequences",
in ISMB94, 376-383.
T. Yada, M. Ishikawa, Y. Totoki and K. Okubo (1994) ,
"Statistical analysis of human DNA sequences in the vicinity of poly(A) signal",
Institute for New Generation Computer Technology, Technical Report TR-876.
MQ Zhang, TG Marr (1994),
"Fission yeast gene structure and recognition",
Nucleic Acids Research, 22(9):1750-1759.
[ Medline entry]