Recent developments and future directions in computational genomics

被引:45
作者
Tsoka, S [1 ]
Ouzounis, CA [1 ]
机构
[1] EMBL, European Bioinformat Inst, Computat Gen Grp, Res Programme,Cambridge Outstn, Cambridge CB10 1SD, England
基金
英国医学研究理事会;
关键词
genomics; bioinformatics; algorithm; molecular biology database; genomic context; systems modelling; knowledge representation;
D O I
10.1016/S0014-5793(00)01776-2
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Computational genomics is a subfield of computational biology that deals with the analysis of entire genome sequences. Transcending the boundaries of classical sequence analysis, computational genomics exploits the inherent properties of entire genomes by modelling them as systems. We review recent developments in the field, discuss in some detail a number of novel approaches that take into account the genomic context and argue that progress will be made by novel knowledge representation and simulation technologies. (C) 2000 Federation of European Biochemical Societies. Published by Elsevier Science B.V. All rights reserved.
引用
收藏
页码:42 / 48
页数:7
相关论文
共 107 条
[1]   Sophia: A flexible, Web-based knowledge server [J].
Abernethy, NF ;
Wu, JJ ;
Hewett, M ;
Altman, RB .
IEEE INTELLIGENT SYSTEMS & THEIR APPLICATIONS, 1999, 14 (04) :79-85
[2]   ISSUES IN SEARCHING MOLECULAR SEQUENCE DATABASES [J].
ALTSCHUL, SF ;
BOGUSKI, MS ;
GISH, W ;
WOOTTON, JC .
NATURE GENETICS, 1994, 6 (02) :119-129
[3]  
Andrade M, 1997, COMPUT APPL BIOSCI, V13, P481
[4]   Functional classes in the three domains of life [J].
Andrade, MA ;
Ouzounis, C ;
Sander, C ;
Tamames, J ;
Valencia, A .
JOURNAL OF MOLECULAR EVOLUTION, 1999, 49 (05) :551-557
[5]   Bioinformatics: From genome data to biological knowledge [J].
Andrade, MA ;
Sander, C .
CURRENT OPINION IN BIOTECHNOLOGY, 1997, 8 (06) :675-683
[6]   Automated genome sequence analysis and annotation [J].
Andrade, MA ;
Brown, NP ;
Leroy, C ;
Hoersch, S ;
de Daruvar, A ;
Reich, C ;
Franchini, A ;
Tamames, J ;
Valencia, A ;
Ouzounis, C ;
Sander, C .
BIOINFORMATICS, 1999, 15 (05) :391-412
[7]   Gene Ontology: tool for the unification of biology [J].
Ashburner, M ;
Ball, CA ;
Blake, JA ;
Botstein, D ;
Butler, H ;
Cherry, JM ;
Davis, AP ;
Dolinski, K ;
Dwight, SS ;
Eppig, JT ;
Harris, MA ;
Hill, DP ;
Issel-Tarver, L ;
Kasarskis, A ;
Lewis, S ;
Matese, JC ;
Richardson, JE ;
Ringwald, M ;
Rubin, GM ;
Sherlock, G .
NATURE GENETICS, 2000, 25 (01) :25-29
[8]   GAIA: Framework annotation of genomic sequence [J].
Bailey, LC ;
Fischer, S ;
Schug, J ;
Crabtree, J ;
Gibson, M ;
Overton, GC .
GENOME RESEARCH, 1998, 8 (03) :234-250
[9]   Methods and statistics for combining motif match scores [J].
Bailey, TL ;
Gribskov, M .
JOURNAL OF COMPUTATIONAL BIOLOGY, 1998, 5 (02) :211-221
[10]   Gene expression informatics - it's all in your mine [J].
Bassett, DE ;
Eisen, MB ;
Boguski, MS .
NATURE GENETICS, 1999, 21 (Suppl 1) :51-55