Please wait a minute...
Frontiers of Electrical and Electronic Engineering

ISSN 2095-2732

ISSN 2095-2740(Online)

CN 10-1028/TM

Front. Electr. Electron. Eng.  2010, Vol. 5 Issue (3): 391-404   https://doi.org/10.1007/s11460-010-0109-8
  Research articles 本期目录
Bioinformatics — Mining the genome for information
Bioinformatics — Mining the genome for information
Runsheng CHEN,Geir SKOGERBØ - 12-d ,
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China;
 全文: PDF(258 KB)  
Abstract:Since the launching of the human genome sequencing project in the 1990s, genomic research has already achieved definite results. At the beginning of the present century, the complete genomes of several model organisms have already been sequenced, including a number of prokaryote microorganisms and the eukaryotes yeast (Saccharomyces cerevisiae), nematode (C. elegans), fruit fly (Drosophila melanogaster) and thale cress (Arabidopsis thaliana) as well as the major part of the human genome. These achievements signified that a new era of data mining and analysis on the human genome had commenced. The language of human genetics would gradually be read and understood, and the genetic information underlying metabolism, development, differentiation and evolution would progressively become known to mankind. Large amounts of data are already accumulating, but at present many of the rules that should guide the understanding of this information are yet unknown. Bioinformatics research is thus not only becoming more important, but is also faced with severe challenges as well as great opportunities.
Key wordsbioinformatics    genome    algorithm    noncoding RNA    biological network
出版日期: 2010-09-05
 引用本文:   
. Bioinformatics — Mining the genome for information[J]. Front. Electr. Electron. Eng., 2010, 5(3): 391-404.
Runsheng CHEN, Geir SKOGERBØ - 12-d , . Bioinformatics — Mining the genome for information. Front. Electr. Electron. Eng., 2010, 5(3): 391-404.
 链接本文:  
https://academic.hep.com.cn/fee/CN/10.1007/s11460-010-0109-8
https://academic.hep.com.cn/fee/CN/Y2010/V5/I3/391
Benson D A, Boguski M S, Lipman D J, Ostell J, Ouellette B F. GenBank. Nucleic Acids Research, 1998, 26(1): 1―7

doi: 10.1093/nar/26.1.1
Ewing B, Hillier L, Wendl M C, Green P. Base-callingof automated sequencer traces using phred. I. Accuracy assessment. Genome Research, 1998, 8(3): 175―185
Ewing B, Green P. Base-calling of automatedsequencer traces using phred. II. Error probabilities. Genome Research, 1998, 8(3): 186―194
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Ewing </FamilyName><GivenName>B</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Green </FamilyName><GivenName>P</GivenName></NativeName></BibAuthorName>. <BibTitle>Base-calling of automatedsequencer traces using phred. II. Error probabilities</BibTitle>. <BibSourceTitle>Genome Research</BibSourceTitle>, <Year>1998</Year>, <BibVolumeNumber>8</BibVolumeNumber>(<BibIssueNumber>3</BibIssueNumber>): <FirstPage>186</FirstPage>―<LastPage>194</LastPage></BibInfo>
Kent W J, Haussler D. GigAssembler: An algorithmfor the initial assembly of the human genome working draft. Technical Report, UCSC-CRL-00-17, 2000
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Kent </FamilyName><GivenName>W J</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Haussler </FamilyName><GivenName>D</GivenName></NativeName></BibAuthorName>. <BibTitle>GigAssembler: An algorithmfor the initial assembly of the human genome working draft</BibTitle>. <BibPatentNumber>Technical Report, UCSC-CRL-00-17</BibPatentNumber>, <Year>2000</Year></BibInfo>
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Cormen </FamilyName><GivenName>T H</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Leiserson </FamilyName><GivenName>C E</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Rivest </FamilyName><GivenName>R L</GivenName></NativeName></BibAuthorName>. <BibTitle>Introduction to Algorithms</BibTitle>. <PublisherName Language="chs">MIT Press</PublisherName>, <Year>1990</Year></BibInfo>
Cormen T H, Leiserson C E, Rivest R L. Introduction to Algorithms. MIT Press, 1990
Uberbacher E C, Xu Y, Mural R J. Discovering and understanding genes in human DNA sequenceusing GRAIL. Methods in Enzymology, 1996, 266: 259―281

doi: 10.1016/S0076-6879(96)66018-2
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Uberbacher </FamilyName><GivenName>E C</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Xu </FamilyName><GivenName>Y</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Mural </FamilyName><GivenName>R J</GivenName></NativeName></BibAuthorName>. <BibTitle>Discovering and understanding genes in human DNA sequenceusing GRAIL</BibTitle>. <BibSourceTitle>Methods in Enzymology</BibSourceTitle>, <Year>1996</Year>, <BibVolumeNumber>266</BibVolumeNumber>: <FirstPage>259</FirstPage>―<LastPage>281</LastPage><DOI>10.1016/S0076-6879(96)66018-2</DOI></BibInfo>
Uberbacher E C, Mural R J. Locating protein-coding regionsin human DNA sequences by a multiple sensor-neural network approach. Proceedings of the National Academy of Sciencesof the United States of America, 1991, 88(24): 11261―11265

doi: 10.1073/pnas.88.24.11261
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Uberbacher </FamilyName><GivenName>E C</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Mural </FamilyName><GivenName>R J</GivenName></NativeName></BibAuthorName>. <BibTitle>Locating protein-coding regionsin human DNA sequences by a multiple sensor-neural network approach</BibTitle>. <BibSourceTitle>Proceedings of the National Academy of Sciencesof the United States of America</BibSourceTitle>, <Year>1991</Year>, <BibVolumeNumber>88</BibVolumeNumber>(<BibIssueNumber>24</BibIssueNumber>): <FirstPage>11261</FirstPage>―<LastPage>11265</LastPage><DOI>10.1073/pnas.88.24.11261</DOI></BibInfo>
Synder E E, Stormo G D. Identification of codingregions in genomic DNA sequences: An application of dynamic programmingand neural networks. Nucleic Acids Research, 1993, 21(3): 607―613

doi: 10.1093/nar/21.3.607
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Synder </FamilyName><GivenName>E E</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Stormo </FamilyName><GivenName>G D</GivenName></NativeName></BibAuthorName>. <BibTitle>Identification of codingregions in genomic DNA sequences: An application of dynamic programmingand neural networks</BibTitle>. <BibSourceTitle>Nucleic Acids Research</BibSourceTitle>, <Year>1993</Year>, <BibVolumeNumber>21</BibVolumeNumber>(<BibIssueNumber>3</BibIssueNumber>): <FirstPage>607</FirstPage>―<LastPage>613</LastPage><DOI>10.1093/nar/21.3.607</DOI></BibInfo>
Guigó R, Knudsen S, Drake N, Smith T. Predictionof gene structure. Journal of MolecularBiology, 1992, 226(1): 141―157

doi: 10.1016/0022-2836(92)90130-C
Pesole G, Attimonelli M, Saccone C. Linguistic analysis of nucleotide sequences: Algorithmsfor pattern recognition and analysis of codon strategy. Method in Enzymology, 1996, 266: 281―294

doi: 10.1016/S0076-6879(96)66019-4
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Pesole </FamilyName><GivenName>G</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Attimonelli </FamilyName><GivenName>M</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Saccone </FamilyName><GivenName>C</GivenName></NativeName></BibAuthorName>. <BibTitle>Linguistic analysis of nucleotide sequences: Algorithmsfor pattern recognition and analysis of codon strategy</BibTitle>. <BibSourceTitle>Method in Enzymology</BibSourceTitle>, <Year>1996</Year>, <BibVolumeNumber>266</BibVolumeNumber>: <FirstPage>281</FirstPage>―<LastPage>294</LastPage><DOI>10.1016/S0076-6879(96)66019-4</DOI></BibInfo>
Girbal L, Soucaille P. Regulation of solvent productionin Clostridium acetobutylicum. Trends in Biotechnology, 1998, 16(1): 11―16

doi: 10.1016/S0167-7799(97)01141-4
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Girbal </FamilyName><GivenName>L</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Soucaille </FamilyName><GivenName>P</GivenName></NativeName></BibAuthorName>. <BibTitle>Regulation of solvent productionin <Emphasis Type="Italic" Font="0" Color="000000">Clostridium acetobutylicum</Emphasis></BibTitle>. <BibSourceTitle>Trends in Biotechnology</BibSourceTitle>, <Year>1998</Year>, <BibVolumeNumber>16</BibVolumeNumber>(<BibIssueNumber>1</BibIssueNumber>): <FirstPage>11</FirstPage>―<LastPage>16</LastPage><DOI>10.1016/S0167-7799(97)01141-4</DOI></BibInfo>
Henderson J, Salzberg S, Fasman K H. Finding genes in DNA with a hidden Markov model. Journal of Computational Biology, 1997, 4(2): 127―141

doi: 10.1089/cmb.1997.4.127
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Henderson </FamilyName><GivenName>J</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Salzberg </FamilyName><GivenName>S</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Fasman </FamilyName><GivenName>K H</GivenName></NativeName></BibAuthorName>. <BibTitle>Finding genes in DNA with a hidden Markov model</BibTitle>. <BibSourceTitle>Journal of Computational Biology</BibSourceTitle>, <Year>1997</Year>, <BibVolumeNumber>4</BibVolumeNumber>(<BibIssueNumber>2</BibIssueNumber>): <FirstPage>127</FirstPage>―<LastPage>141</LastPage><DOI>10.1089/cmb.1997.4.127</DOI></BibInfo>
Xiao Y, Chen R S, Shen R Q, Sun J, Xu J. Fractal dimension of exon and intron sequences. Journal of Theoretical Biology, 1995, 175(1): 23―26

doi: 10.1006/jtbi.1995.0117
Shen R Q, Chen R S, Ling L J, Sun J, Xiao Y, Xu J. Thecomplexity of different regions of protein coding genes. Chinese Science Bulletin, 1993, 38(21): 1995―1997 (in Chinese)
Xu J, Chen R S, Ling L J, Shen R, Sun J. Coincident indices of exons and introns. Computers in Biology and Medicine, 1993, 23(4): 333―343

doi: 10.1016/0010-4825(93)90088-I
Miller G, Fuchs R, Lai E. IMAGE cDNA clones, UniGene clustering, and ACeDB: Anintegrated resource for expressed sequence information. Genome Research, 1997, 7(10): 1027―1032
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Miller </FamilyName><GivenName>G</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Fuchs </FamilyName><GivenName>R</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Lai </FamilyName><GivenName>E</GivenName></NativeName></BibAuthorName>. <BibTitle>IMAGE cDNA clones, UniGene clustering, and ACeDB: Anintegrated resource for expressed sequence information</BibTitle>. <BibSourceTitle>Genome Research</BibSourceTitle>, <Year>1997</Year>, <BibVolumeNumber>7</BibVolumeNumber>(<BibIssueNumber>10</BibIssueNumber>): <FirstPage>1027</FirstPage>―<LastPage>1032</LastPage></BibInfo>
Eckman B A, Aaronson J S, Borkowski J A, Bailey W J, Elliston K O, Williamson A R, Blevins R A. The Merck Gene Index browser: An extensible data integration systemfor gene finding, gene characterization and EST data mining. Bioinformatics, 1998, 14(1): 2―13

doi: 10.1093/bioinformatics/14.1.2
Ho7ulgatte R, Mariage-Samson R, Duprat S, Tessier A, Bentolila S, Lamy B, Auffray C. Thegenexpress index: A resource for gene discovery and the genic mapof the human genome. Genome Research, 1995, 5(3): 272―304

doi: 10.1101/gr.5.3.272
Girard A, Sachidanandam R, Hannon G J, Carmell M A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature, 2006, 442(7099): 199―202
Deng W, Zhu X P, Skogerb? G, Zhao Y, Fu Z, Wang Y D, He H S, Cai L, Sun H, Liu C N, Li B, Bai B Y, Wang J, Jia D, Sun S W, He H, Cui Y, Wang Y, Bu D B, Chen R S. Organization of the Caenorhabditis elegans small non-coding transcriptome:Genomic features, biogenesis and expression. Genome Research, 2006, 16(1): 20―29

doi: 10.1101/gr.4139206
Chureau C, Prissette M, Bourdet A, Barbe B, Cattolico L, Jones L, Eggen A, Avner P, Duret L. Comparativesequence analysis of the X-inactivation center region in mouse, human,and bovine. Genome Research, 2002, 12(6): 894―908
Petrovics G, Zhang W, Makarem M, Street J P, Connelly R, Sun L, Sesterhenn I A, Srikantan V, Moul J W, Srivastava S. Elevatedexpression of PCGEM1, a prostatespecificgene with cell growth-promoting function, is associated with high-riskprostate cancer patients. Oncogene, 2004, 23(2): 605―611

doi: 10.1038/sj.onc.1207069
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Xu </FamilyName><GivenName>F</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>McFarland </FamilyName><GivenName>M</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Askew </FamilyName><GivenName>D S</GivenName></NativeName></BibAuthorName>. <BibTitle>His-1: A noncoding RNA implicated in mouse leukemogenesis</BibTitle>. <BibSourceTitle>Current Science</BibSourceTitle>, <Year>1999</Year>, <BibVolumeNumber>77</BibVolumeNumber>(<BibIssueNumber>4</BibIssueNumber>): <FirstPage>545</FirstPage>―<LastPage>549</LastPage></BibInfo>
Xu F, McFarland M, Askew D S. His-1: A noncoding RNA implicated in mouse leukemogenesis. Current Science, 1999, 77(4): 545―549
Ji P, Diederichs S, Wang W, B?ing S, Metzger R, Schneider P M, Tidow N, Brandt B, Buerger H, Bulk E, Thomas M, Berdel W E, Serve H, Müller-Tidow C. MALAT-1,a novel noncoding RNA, and thymosin beta4 predict metastasis and survivalin early-stage non-small cell lung cancer. Oncogene, 2003, 22(39): 8031―8041

doi: 10.1038/sj.onc.1206928
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Li </FamilyName><GivenName>W H</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Graur </FamilyName><GivenName>D</GivenName></NativeName></BibAuthorName>. <BibTitle>Fundamentals of MolecularEvolution</BibTitle>. <BibSourceTitle>Sinauer Associates</BibSourceTitle>, <Year>1991</Year></BibInfo>
Li W H, Graur D. Fundamentals of MolecularEvolution. Sinauer Associates, 1991
Pearon WR. Rapid and sensitive sequence comparison with FASTP and FASTA. Methods in Enzymology, 1990, 183: 63―98

doi: 10.1016/0076-6879(90)83007-V
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Pearon </FamilyName><GivenName>WR</GivenName></NativeName></BibAuthorName>. <BibTitle>Rapid and sensitive sequence comparison with FASTP and FASTA</BibTitle>. <BibSourceTitle>Methods in Enzymology</BibSourceTitle>, <Year>1990</Year>, <BibVolumeNumber>183</BibVolumeNumber>: <FirstPage>63</FirstPage>―<LastPage>98</LastPage><DOI>10.1016/0076-6879(90)83007-V</DOI></BibInfo>
Altschul S F, Madden T L, Sch?ffer A A, Zhang J, Zhang Z, Miller W, Lipman D J. Gapped BLAST and PSI-BLAST: A new generation of protein databasesearch programs. Nucleic Acids Research, 1997, 25(17): 3389―3402

doi: 10.1093/nar/25.17.3389
Higgins D G, Bleasby A J, Fuchs R. CLUSTAL V: Improved software for multiple sequence alignment. Computer Applications in the Biosciences, 1992, 8(2): 189―191
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Higgins </FamilyName><GivenName>D G</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Bleasby </FamilyName><GivenName>A J</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Fuchs </FamilyName><GivenName>R</GivenName></NativeName></BibAuthorName>. <BibTitle>CLUSTAL V: Improved software for multiple sequence alignment</BibTitle>. <BibSourceTitle>Computer Applications in the Biosciences</BibSourceTitle>, <Year>1992</Year>, <BibVolumeNumber>8</BibVolumeNumber>(<BibIssueNumber>2</BibIssueNumber>): <FirstPage>189</FirstPage>―<LastPage>191</LastPage></BibInfo>
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Kumar </FamilyName><GivenName>S</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Tamura </FamilyName><GivenName>K</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Nei </FamilyName><GivenName>M</GivenName></NativeName></BibAuthorName>. <BibTitle>MEGA: Molecular evolutionary genetic analysis</BibTitle>. <BibSourceTitle>University Park: Pennsylvania State University</BibSourceTitle>, <Year>1993</Year></BibInfo>
Kumar S, Tamura K, Nei M. MEGA: Molecular evolutionary genetic analysis. University Park: Pennsylvania State University, 1993
Felsenstein J. Confidencelimits on phylogenies: An approach using the bootstrap. Evolution, 1985, 39(4): 783―791

doi: 10.2307/2408678
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Felsenstein </FamilyName><GivenName>J</GivenName></NativeName></BibAuthorName>. <BibTitle>Confidencelimits on phylogenies: An approach using the bootstrap</BibTitle>. <BibSourceTitle>Evolution</BibSourceTitle>, <Year>1985</Year>, <BibVolumeNumber>39</BibVolumeNumber>(<BibIssueNumber>4</BibIssueNumber>): <FirstPage>783</FirstPage>―<LastPage>791</LastPage><DOI>10.2307/2408678</DOI></BibInfo>
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Kimura </FamilyName><GivenName>M</GivenName></NativeName></BibAuthorName>. <BibTitle>TheNeutral Theory of Molecular Evolution</BibTitle>. <PublisherLocation>Cambridge</PublisherLocation>: <PublisherName Language="chs">Cambridge UniversityPress</PublisherName>, <Year>1983</Year><DOI>10.1017/CBO9780511623486</DOI></BibInfo>
Kimura M. TheNeutral Theory of Molecular Evolution. Cambridge: Cambridge UniversityPress, 1983

doi: 10.1017/CBO9780511623486
Wang N, Chen R S. Comparison between phylogenyof introns and exons in primates. ChineseScience Bulletin, 1999, 44(21): 1940―1946

doi: 10.1007/BF02887113
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Wang </FamilyName><GivenName>N</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Chen </FamilyName><GivenName>R S</GivenName></NativeName></BibAuthorName>. <BibTitle>Comparison between phylogenyof introns and exons in primates</BibTitle>. <BibSourceTitle>ChineseScience Bulletin</BibSourceTitle>, <Year>1999</Year>, <BibVolumeNumber>44</BibVolumeNumber>(<BibIssueNumber>21</BibIssueNumber>): <FirstPage>1940</FirstPage>―<LastPage>1946</LastPage><DOI>10.1007/BF02887113</DOI></BibInfo>
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Koonin </FamilyName><GivenName>E V</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Tatusov </FamilyName><GivenName>R L</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Galperin </FamilyName><GivenName>M Y</GivenName></NativeName></BibAuthorName>. <BibTitle>Beyond complete genomes: From sequence to structure andfunction</BibTitle>. <BibSourceTitle>Current Opinion Structural Biology</BibSourceTitle>, <Year>1998</Year>, <BibVolumeNumber>8</BibVolumeNumber>(<BibIssueNumber>3</BibIssueNumber>): <FirstPage>355</FirstPage>―<LastPage>363</LastPage><DOI>10.1016/S0959-440X(98)80070-5</DOI></BibInfo>
Koonin E V, Tatusov R L, Galperin M Y. Beyond complete genomes: From sequence to structure andfunction. Current Opinion Structural Biology, 1998, 8(3): 355―363

doi: 10.1016/S0959-440X(98)80070-5
Somogyi R, Sniegoski C. Modeling the complexity ofgene networks: Understanding multigenic and pleiotropic regulation. Complexity, 1996, 1(6): 45―63
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Somogyi </FamilyName><GivenName>R</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Sniegoski </FamilyName><GivenName>C</GivenName></NativeName></BibAuthorName>. <BibTitle>Modeling the complexity ofgene networks: Understanding multigenic and pleiotropic regulation</BibTitle>. <BibSourceTitle>Complexity</BibSourceTitle>, <Year>1996</Year>, <BibVolumeNumber>1</BibVolumeNumber>(<BibIssueNumber>6</BibIssueNumber>): <FirstPage>45</FirstPage>―<LastPage>63</LastPage></BibInfo>
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Vidal </FamilyName><GivenName>M</GivenName></NativeName></BibAuthorName>. <BibTitle>Abiological atlas of functional maps</BibTitle>. <BibSourceTitle>Cell</BibSourceTitle>, <Year>2001</Year>, <BibVolumeNumber>104</BibVolumeNumber>(<BibIssueNumber>1</BibIssueNumber>): <FirstPage>333</FirstPage>―<LastPage>339</LastPage></BibInfo>
Vidal M. Abiological atlas of functional maps. Cell, 2001, 104(1): 333―339
Bu D B, Zhao Y, Cai L, Xue H, Zhu X P, Lu H C, Zhang J F, Sun S W, Ling L J, Zhang N, Li G J, Chen R S. Topological structure analysisof the protein-protein interaction network in budding yeast. Nucleic Acids Research, 2003, 31(9): 2443―2450

doi: 10.1093/nar/gkg340
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Gibson </FamilyName><GivenName>D</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Kleinberg </FamilyName><GivenName>J</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Raghavan </FamilyName><GivenName>P</GivenName></NativeName></BibAuthorName>. <BibTitle>InferringWeb communities from link topology</BibTitle>. In: <BibSourceTitle>Preceedings of the 9th ACM Conference on Hypertextand Hypermedia</BibSourceTitle>. <Year>1998</Year>, <FirstPage>225</FirstPage>―<LastPage>234</LastPage></BibInfo>
Gibson D, Kleinberg J, Raghavan P. InferringWeb communities from link topology. In: Preceedings of the 9th ACM Conference on Hypertextand Hypermedia. 1998, 225―234
Kleinberg J M. Authoritative sources in a hyper-linked environment. In: Proceedings of the 9th Annual ACM-SIAM Symposium on Discrete Algorithms. 1998, 668―677
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Kleinberg </FamilyName><GivenName>J M</GivenName></NativeName></BibAuthorName>. <BibTitle>Authoritative sources in a hyper-linked environment</BibTitle>. In: <BibSourceTitle>Proceedings of the 9th Annual ACM-SIAM Symposium on Discrete Algorithms</BibSourceTitle>. <Year>1998</Year>, <FirstPage>668</FirstPage>―<LastPage>677</LastPage></BibInfo>
Zhang Z H, Liu C N, Skogerb? G, Zhu X P, Lu H C, Chen L, Shi B C, Zhang Y, Wang J, Wu T, Chen R S. Dynamic changes in subgraph preference profiles of crucialtranscription factors. PLoS ComputationalBiology, 2006, 2(5): e47

doi: 10.1371/journal.pcbi.0020047
Lee T I, Rinaldi N J, Robert F, Odom D T, Bar-Joseph Z, Gerber G K, Hannett N M, Harbison C T, Thompson C M, Simon I, Zeitlinger J, Jennings E G, Murray H L, Gordon D B, Ren B, Wyrick J J, Tagne J B, Volkert T L, Fraenkel E, Gifford D K, Young R A. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 2002, 298(5594): 799―804

doi: 10.1126/science.1075090
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chclovskii D, Alon U. Network motifs: Simple building blocks of complex networks. Science, 2002, 298(5594): 824―827

doi: 10.1126/science.298.5594.824
Vázquez A, Dobrin R, Sergi D, Eckmann J P, Oltvai Z N, Barabási A L. The topological relationship betweenthe large-scale attributes and local interaction patterns of complexnetworks. Proceedings of the National Academyof Sciences of United States of America, 2004, 101(52): 17940―17945

doi: 10.1073/pnas.0406024101
Guelzim N, Bottani S, Bourgnie P, Képès F. Topologicaland causal structure of theyeast transcriptional regulatory network. Nature Genetics, 2002, 31(1): 60―63

doi: 10.1038/ng873
Bray D. Proteinmolecules as computational elements in living cells. Nature, 1995, 376(6538): 307―312

doi: 10.1038/376307a0
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Bray </FamilyName><GivenName>D</GivenName></NativeName></BibAuthorName>. <BibTitle>Proteinmolecules as computational elements in living cells</BibTitle>. <BibSourceTitle>Nature</BibSourceTitle>, <Year>1995</Year>, <BibVolumeNumber>376</BibVolumeNumber>(<BibIssueNumber>6538</BibIssueNumber>): <FirstPage>307</FirstPage>―<LastPage>312</LastPage><DOI>10.1038/376307a0</DOI></BibInfo>
Luscombe N M, Babu M M, Yu H, Snyder M, Teichmann S A, Gerstein M. Genomic analysis of regulatory network dynamics revealslarge topological changes. Nature, 2004, 431(7006): 308―312

doi: 10.1038/nature02782
Zhao Y, He S M, Liu C N, Ru SW, Zhao H T, Yang Z, Yang P C, Yuan X Y, Sun S W, Bu D B, Huang J F, Skogerb? G, Chen R S. MicroRNA regulation of messenger-like noncoding RNAs:A network of mutual microRNA control. Trendsin Genetics, 2008, 24(7): 323―327

doi: 10.1016/j.tig.2008.04.004
Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, Sementchenko V, Piccolboni A, Bekiranov S, Bailey D K, Ganesh M, Ghosh S, Bell I, Gerhard D S, Gingeras T R. Transcriptional maps of 10human chromosomes at 5-nucleotide resolution. Science, 2005, 308(5725): 1149―1154

doi: 10.1126/science.1108625
Bartel D P. MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 2004, 116(2): 281―297
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Bartel </FamilyName><GivenName>D P</GivenName></NativeName></BibAuthorName>. <BibTitle>MicroRNAs: Genomics, biogenesis, mechanism, and function</BibTitle>. <BibSourceTitle>Cell</BibSourceTitle>, <Year>2004</Year>, <BibVolumeNumber>116</BibVolumeNumber>(<BibIssueNumber>2</BibIssueNumber>): <FirstPage>281</FirstPage>―<LastPage>297</LastPage></BibInfo>
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Will </FamilyName><GivenName>C L</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Lührmann </FamilyName><GivenName>R</GivenName></NativeName></BibAuthorName>. <BibTitle>Spliceosomal UsnRNP biogenesis,structure and function</BibTitle>. <BibSourceTitle>Current Opinionin Cell Biology</BibSourceTitle>, <Year>2001</Year>, <BibVolumeNumber>13</BibVolumeNumber>(<BibIssueNumber>3</BibIssueNumber>): <FirstPage>290</FirstPage>―<LastPage>301</LastPage><DOI>10.1016/S0955-0674(00)00211-8</DOI></BibInfo>
Will C L, Lührmann R. Spliceosomal UsnRNP biogenesis,structure and function. Current Opinionin Cell Biology, 2001, 13(3): 290―301

doi: 10.1016/S0955-0674(00)00211-8
Willingham A T, Orth A P, Batalov S, Peters E C, Wen B G, Aza-Blanc P, Hogenesch J B, Schultz P G. A strategy for probing thefunction of noncoding RNAs finds a repressor of NFAT. Science, 2005, 309(5740): 1570―1573

doi: 10.1126/science.1115901
Chen C L, Liang D, Zhou H, Zhuo M, Chen Y Q, Qu L H. The high diversity of snoRNAs in plants: Identification and comparativestudy of 120 snoRNA genes from Oryza sativa. Nucleic Acids Research, 2003, 31(10): 2601―2613

doi: 10.1093/nar/gkg373
Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming L G, Hume D A, RIKEN GER Group, GSLMembers, Hayashizaki Y, Tomita M. Identification of putativenoncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Research, 2003, 13(6B): 1301―1306

doi: 10.1101/gr.1011603
Sood P, Krek A, Zavolan M, Macino G, Rajewsky N. Celltype- specific signaturesof microRNAs on target mRNA expression. Proceedings of the National Academy of Sciences of the United Statesof America, 2006, 103(8): 2746―2751

doi: 10.1073/pnas.0511045103
Ho S P, DeGrado W F. Design of a 4-helix bundleprotein: Synthesis of peptides which self-associate into a helicalprotein. Journal of the American ChemicalSociety, 1987, 109(22): 6751―6758

doi: 10.1021/ja00256a032
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Ho </FamilyName><GivenName>S P</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>DeGrado </FamilyName><GivenName>W F</GivenName></NativeName></BibAuthorName>. <BibTitle>Design of a 4-helix bundleprotein: Synthesis of peptides which self-associate into a helicalprotein</BibTitle>. <BibSourceTitle>Journal of the American ChemicalSociety</BibSourceTitle>, <Year>1987</Year>, <BibVolumeNumber>109</BibVolumeNumber>(<BibIssueNumber>22</BibIssueNumber>): <FirstPage>6751</FirstPage>―<LastPage>6758</LastPage><DOI>10.1021/ja00256a032</DOI></BibInfo>
Riechmann L, Clark M, Waldmann H, Winter G. Reshapinghuman antibodies for therapy. Nature, 1988, 332(6162): 323―327

doi: 10.1038/332323a0
Liu X F, Xiao S, Gu Z, Wang Y, Chen A, Lin Q, Zhang W G, Huang H L, Sun J, Chen R S, Shen B F, Chen X. The expression of CD3 singlechain and reshaping singledomain antibody. Science in China (Series C), 1996, 26(5): 428―435 (in Chinese)
Greer J, Erickson J W, Baldwin J J, Varney M D. Application of the three-dimensional structures of protein targetmolecules in structure-based drug design. Journal of Medicinal Chemistry, 1994, 37(8): 1035―1054

doi: 10.1021/jm00034a001
Lam P Y, Jadhav P K, Eyermann C J, Hodge C N, Ru Y, Bacheler L T, Meek J L, Otto M J, Rayner M M, Wong Y N, Chang C H, Weber P C, Jackson D A, Sharpe T R, Erickson-Viitanen S. Rational designof potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science, 1994, 263(5145): 380―384

doi: 10.1126/science.8278812
Blundell T L, Johnson M S. Catching a common fold. Protein Science, 1993, 2(6): 877―883

doi: 10.1002/pro.5560020602
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Blundell </FamilyName><GivenName>T L</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Johnson </FamilyName><GivenName>M S</GivenName></NativeName></BibAuthorName>. <BibTitle>Catching a common fold</BibTitle>. <BibSourceTitle>Protein Science</BibSourceTitle>, <Year>1993</Year>, <BibVolumeNumber>2</BibVolumeNumber>(<BibIssueNumber>6</BibIssueNumber>): <FirstPage>877</FirstPage>―<LastPage>883</LastPage><DOI>10.1002/pro.5560020602</DOI></BibInfo>
Orengo C A, Jones D T, Thornton J M. Protein superfamilies and domain superfolds. Nature, 1994, 372(6507): 631―634S

doi: 10.1038/372631a0
<BibInfo BibType="Journal" Style="1"><BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Orengo </FamilyName><GivenName>C A</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Jones </FamilyName><GivenName>D T</GivenName></NativeName></BibAuthorName>, <BibAuthorName><NativeName DisplayOrder="Western" Language="chs"><FamilyName>Thornton </FamilyName><GivenName>J M</GivenName></NativeName></BibAuthorName>. <BibTitle>Protein superfamilies and domain superfolds</BibTitle>. <BibSourceTitle>Nature</BibSourceTitle>, <Year>1994</Year>, <BibVolumeNumber>372</BibVolumeNumber>(<BibIssueNumber>6507</BibIssueNumber>): <FirstPage>631</FirstPage>―<LastPage>634S</LastPage><DOI>10.1038/372631a0</DOI></BibInfo>
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed