Volume 21, Number 1, January 2005 Editorials
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journals/bioinformatics/ValenciaB05
Original Papers - Genome Analysis
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journals/bioinformatics/Roos05 Albert D. G. de Roos :
Origins of introns based on the definition of exon modules and their conserved interfaces. 2-9
Sequence Analysis
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journals/bioinformatics/Chou05 Kuo-Chen Chou :
Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. 10-19
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journals/bioinformatics/ChenZT05
Gene Expression
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journals/bioinformatics/ZouC05 Min Zou ,
Suzanne D. Conzen :
A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. 71-79
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journals/bioinformatics/Reverter-GomezMBD05
Genetics And Population Analysis
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Applications Notes - Sequence Analysis
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journals/bioinformatics/VuceticOVRPICLBSND05 Slobodan Vucetic ,
Zoran Obradovic ,
Vladimir Vacic ,
Predrag Radivojac ,
Kang Peng ,
Lilia M. Iakoucheva ,
Marc S. Cortese ,
J. David Lawson ,
Celeste J. Brown ,
Jason G. Sikes ,
Crystal D. Newton ,
A. Keith Dunker :
DisProt: a database of protein disorder. 137-140
Volume 21, Number 2, January 2005 Original Papers - Genome Analysis
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journals/bioinformatics/YiuWLMKLC05
Sequence Analysis
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journals/bioinformatics/LinSTH05 export record as
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journals/bioinformatics/ShinK05 Sung W. Shin ,
Sam Kim :
A new algorithm for detecting low-complexity regions in protein sequences. 160-170
Gene Expression
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Applications Notes - Sequence Analysis
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journals/bioinformatics/YoungWCS05 Volume 21, Number 3, February 2005 Editorials
Genome Analysis
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journals/bioinformatics/EtheringtonDR05 export record as
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Sequence Analysis
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Structural Bioinformatics
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journals/bioinformatics/LiL05 Haiquan Li ,
Jinyan Li :
Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets. 314-324
Gene Expression
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journals/bioinformatics/KahramanANPTPW05 Volume 21, Number 4, February 2005 SAC 2004 Papers
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journals/bioinformatics/VinciottiKDLCHBJRSKW05 Veronica Vinciotti ,
Raya Khanin ,
Davide D'Alimonte ,
Xiaohui Liu ,
N. Cattini ,
G. Hotchkiss ,
G. Bucca ,
O. de Jesus ,
J. Rasaiyaah ,
Colin P. Smith ,
Paul Kellam ,
Ernst Wit :
An experimental evaluation of a loop versus a reference design for two-channel microarrays. 492-501
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journals/bioinformatics/GuanZ05 Zhong Guan ,
Hongyu Zhao :
A semiparametric approach for marker gene selection based on gene expression data. 529-536
Genome Analysis
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journals/bioinformatics/StothardW05
Sequence Analysis
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Structural Bioinformatics
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journals/bioinformatics/KongM05
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journals/bioinformatics/OlivierRH05 Volume 21, Number 5, March 2005 Genome Analysis
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journals/bioinformatics/YanPOHX05 export record as
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journals/bioinformatics/ChenX05 Yu Chen ,
Dong Xu :
Understanding protein dispensability through machine-learning analysis of high-throughput data. 575-581
Sequence Analysis
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journals/bioinformatics/BurdenLZ05 S. Burden ,
Y.-X. Lin ,
R. Zhang :
Improving promoter prediction Improving promoter prediction for the NNPP2.2 algorithm: a case study using Escherichia coli DNA sequences. 601-607
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journals/bioinformatics/Costa05 Luciano da Fontoura Costa :
Biological sequence analysis through the one-dimensional percolation transform and its enhanced version. 608-616
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journals/bioinformatics/GardyLCRWEB05
Structural Bioinformatics
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Gene Expression
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journals/bioinformatics/StatnikovATHL05 export record as
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journals/bioinformatics/AsyaliA05 Musa H. Asyali ,
Musa Alci :
Reliability analysis of microarray data using fuzzy c-means and normal mixture modeling based classification methods. 644-649
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journals/bioinformatics/YanaiBSCSOBHSDLS05 Itai Yanai ,
Hila Benjamin-Rodrig ,
Michael Shmoish ,
Vered Chalifa-Caspi ,
Maxim Shklar ,
Ron Ophir ,
Arren Bar-Even ,
Shirley Horn-Saban ,
Marilyn Safran ,
Eytan Domany ,
Doron Lancet ,
Orit Shmueli :
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. 650-659
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journals/bioinformatics/DalmassoBM05
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journals/bioinformatics/HuangPG05
Sequence Analysis
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Data And Text Mining
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journals/bioinformatics/DingB05
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journals/bioinformatics/FelderSLENPG05 Volume 21, Number 6, March 2005 Sequence Analysis
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journals/bioinformatics/CallebautM05
Genome Analysis
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journals/bioinformatics/ZhengLWZHM05
Structural Bioinformatics
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Gene Expression
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journals/bioinformatics/BakewellW05 export record as
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journals/bioinformatics/TaguchiO05 Y.-h. Taguchi ,
Y. Oono :
Relational patterns of gene expression via non-metric multidimensional scaling analysis. 730-740
Systems Biology
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journals/bioinformatics/YangSMH05
Data And Text Mining
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journals/bioinformatics/Lin05 D. Y. Lin :
An efficient Monte Carlo approach to assessing statistical significance in genomic studies. 781-787
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journals/bioinformatics/RajagopalanA05
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Genome Analysis
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Genetics And Population Analysis
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journals/bioinformatics/WellockCS05
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journals/bioinformatics/PagelKOBDFMMSMRF05 Philipp Pagel ,
Stefan Kovac ,
Matthias Oesterheld ,
Barbara Brauner ,
Irmtraud Dunger-Kaltenbach ,
Goar Frishman ,
Corinna Montrone ,
Pekka Mark ,
Volker Stümpflen ,
Hans-Werner Mewes ,
Andreas Ruepp ,
Dmitrij Frishman :
The MIPS mammalian protein?Cprotein interaction database. 832-834
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journals/bioinformatics/PalaniswamyJSD05 Volume 21, Number 7, April 2005 Genome Analysis
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journals/bioinformatics/Kochetov05 Alexey V. Kochetov :
AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon context. 837-840
Sequence Analysis
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journals/bioinformatics/LegendreLG05
Genome Analysis
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journals/bioinformatics/PaarPRGBPZ05 export record as
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journals/bioinformatics/BartelsKADGHKPPRSMS05 Daniela Bartels ,
Sebastian Kespohl ,
Stefan P. Albaum ,
Tanja Drüke ,
Alexander Goesmann ,
Julia Herold ,
Olaf Kaiser ,
Alfred Pühler ,
Friedhelm Pfeiffer ,
Günter Raddatz ,
Jens Stoye ,
Folker Meyer ,
Stephan C. Schuster :
BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. 853-859
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journals/bioinformatics/DrorSS05
Sequence Analysis
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journals/bioinformatics/YuA05 Yi-Kuo Yu ,
Stephen F. Altschul :
The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions. 902-911
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journals/bioinformatics/Zheng05 Wei-Mou Zheng :
Relation between weight matrix and substitution matrix: motif search by similarity. 938-943
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journals/bioinformatics/Soding05 Johannes Söding :
Protein homology detection by HMM?CHMM comparison. 951-960
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journals/bioinformatics/GromihaS05
Phylogenetics
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journals/bioinformatics/CrooksB05
Structural Bioinformatics
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journals/bioinformatics/Sandelin05 Erik Sandelin :
Extracting multiple structural alignments from pairwise alignments: a comparison of a rigorous and a heuristic approach. 1002-1009
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journals/bioinformatics/YuanB05 Xin Yuan ,
Christopher Bystroff :
Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. 1010-1019
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journals/bioinformatics/KingsfordCS05
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journals/bioinformatics/Bickel05 David R. Bickel :
Probabilities of spurious connections in gene networks: application to expression time series. 1121-1128
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journals/bioinformatics/Ben-ShaulBS05
Genetics And Population Analysis
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Genome Analysis
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journals/bioinformatics/XuG05 Jian Xu ,
Jeffrey I. Gordon :
MapLinker: a software tool that aids physical map-linked whole genome shotgun assembly. 1265-1266
Sequence Analysis
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journals/bioinformatics/GerthV05 Victor E. Gerth ,
Peter D. Vize :
A Java tool for dynamic web-based 3D visualization of anatomy and overlapping gene or protein expression patterns. 1278-1279
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journals/bioinformatics/CarauxP05 Gilles Caraux ,
Sylvie Pinloche :
PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order. 1280-1281
Genetics And Population Analysis
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journals/bioinformatics/ReicheltDKSH05 Volume 21, Number 8, April 2005 Sequence Analysis
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Systems Biology
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Genome Analysis
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journals/bioinformatics/LianG05 Yun Lian ,
Harold R. Garner :
Evidence for the regulation of alternative splicing via complementary DNA sequence repeats. 1358-1364
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journals/bioinformatics/BoW05 Xiaochen Bo ,
Shengqi Wang :
TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA. 1401-1402
Sequence Analysis
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journals/bioinformatics/NozakiB05 Yasuyuki Nozaki ,
Matthew I. Bellgard :
Statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties. 1421-1428
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Structural Bioinformatics
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journals/bioinformatics/Gough05 Julian Gough :
Convergent evolution of domain architectures (is rare). 1464-1471
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journals/bioinformatics/BradfordW05
Gene Expression
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journals/bioinformatics/SarkansPLOSACHRMSKSFRB05 Ugis Sarkans ,
Helen E. Parkinson ,
Gonzalo Garcia Lara ,
Ahmet Oezcimen ,
Anjan Sharma ,
Niran Abeygunawardena ,
Sergio Contrino ,
Ele Holloway ,
Philippe Rocca-Serra ,
Gaurab Mukherjee ,
Mohammadreza Shojatalab ,
Misha Kapushesky ,
Susanna-Assunta Sansone ,
Anna Farne ,
Tim F. Rayner ,
Alvis Brazma :
The ArrayExpress gene expression database: a software engineering and implementation perspective. 1495-1501
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journals/bioinformatics/CuiLJM05 Qinghua Cui ,
Bing Liu ,
Tianzi Jiang ,
Songde Ma :
Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression data. 1538-1541
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journals/bioinformatics/ZhouM05 Xin Zhou ,
K. Z. Mao :
LS Bound based gene selection for DNA microarray data. 1559-1564
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journals/bioinformatics/Wu05 Baolin Wu :
Differential gene expression detection using penalized linear regression models: the improved SAM statistics. 1565-1571
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Genetics And Population Analysis
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journals/bioinformatics/KopkaSKBUBDWGSWFS05 Joachim Kopka ,
Nicolas Schauer ,
Stephan Krueger ,
Claudia Birkemeyer ,
Björn Usadel ,
Eveline Bergmüller ,
Peter Dörmann ,
Wolfram Weckwerth ,
Yves Gibon ,
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Lothar Willmitzer ,
Alisdair R. Fernie ,
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GMD@CSB.DB: the Golm Metabolome Database. 1635-1638
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journals/bioinformatics/SantosES05 Carlos Santos ,
Daniela Eggle ,
David J. States :
Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction. 1653-1658
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journals/bioinformatics/BergmanCC05 Volume 21, Number 9, May 1 2005 Databases And Ontologies
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journals/bioinformatics/KitagawaWKYHYHSOSMMKCHKT05 Noriyuki Kitagawa ,
Takanori Washio ,
Shunichi Kosugi ,
Tomoya Yamashita ,
Kenji Higashi ,
Hiroshi Yanagawa ,
Kenichi Higo ,
Koji Satoh ,
Yasuhiro Ohtomo ,
Tomomi Sunako ,
Kazuo Murakami ,
Kenichi Matsubara ,
Jun Kawai ,
Piero Carninci ,
Yoshihide Hayashizaki ,
Shoshi Kikuchi ,
Masaru Tomita :
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). 1758-1763
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journals/bioinformatics/CameronHR05 J. M. Cameron ,
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Computational identification of human mitochondrial proteins based on homology to yeast mitochondrially targeted proteins. 1825-1830
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journals/bioinformatics/Yang05 Zheng Rong Yang :
Prediction of caspase cleavage sites using Bayesian bio-basis function neural networks. 1831-1837
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journals/bioinformatics/LiF05 Han-Lin Li ,
Chang-Jui Fu :
A linear programming approach for identifying a consensus sequence on DNA sequences. 1838-1845
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journals/bioinformatics/KahsayGL05 Robel Y. Kahsay ,
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An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. 1853-1858
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journals/bioinformatics/CoeytauxP05 Karen Coeytaux ,
Anne Poupon :
Prediction of unfolded segments in a protein sequence based on amino acid composition. 1891-1900
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journals/bioinformatics/DiMWHLDBHCYSKKMJC05 Xiaojun Di ,
Hajime Matsuzaki ,
Teresa A. Webster ,
Earl Hubbell ,
Guoying Liu ,
Shoulian Dong ,
Dan Bartell ,
Jing Huang ,
Richard Chiles ,
Geoffrey Yang ,
Mei-mei Shen ,
David Kulp ,
Giulia C. Kennedy ,
Rui Mei ,
Keith W. Jones ,
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Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays. 1958-1963
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journals/bioinformatics/LottazS05 Claudio Lottaz ,
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Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data. 1971-1978
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journals/bioinformatics/Azuaje05 Francisco Azuaje :
Integrative data analysis for functional prediction: a multi-objective optimization approach. 2099-2100
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Albert D. G. de Roos: Origins of introns based on the definition of exon modules and their conserved interfaces. 2-9