Volume 22,
Number 1,
January 2006
Editorials
Discovery Note Sequence Analysis
Original Papers Genome Analysis
Sequence Analysis
Phylogenetics
Gene Expression
- Marta Blangiardo, Simona Toti, Betti Giusti, Rosanna Abbate, Alberto Magi, Filippo Poggi, Luciana Rossi, Francesca Torricelli, Annibale Biggeri:
Using a calibration experiment to assess gene-specific information: full Bayesian and empirical Bayesian models for two-channel microarray data.
50-57
Electronic Edition (link) BibTeX
- Thomas Grotkjær, Ole Winther, Birgitte Regenberg, Jens Nielsen, Lars Kai Hansen:
Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm.
58-67
Electronic Edition (link) BibTeX
- Xiaoyan Leng, Hans-Georg Müller:
Classification using functional data analysis for temporal gene expression data.
68-76
Electronic Edition (link) BibTeX
- Yongxi Tan, Leming M. Shi, Saber M. Hussain, Jun Xu, Weida Tong, John M. Frazier, Charles Wang:
Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium.
77-87
Electronic Edition (link) BibTeX
- Hao Helen Zhang, Jeongyoun Ahn, Xiaodong Lin, Cheolwoo Park:
Gene selection using support vector machines with non-convex penalty.
88-95
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
Databases and Ontologies
Applications Note Sequence Analysis
Phylogenetics
Gene Expression
Systems Biology
Volume 22,
Number 2,
January 2006
Editorials
Discovery Note Structural Bioinformatics
Original Papers Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Applications Note Genome Analysis
Gene Expression
Systems Biology
Databases and Ontologies
Volume 22,
Number 3,
February 2006
Discovery Note Sequence Analysis
Structural Bioinformatics
Data and Text Mining
Original Papers Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Applications Note Genome Analysis
Sequence Analysis
- A. V. McDonnell, T. Jiang, A. E. Keating, B. Berger:
Paircoil2: improved prediction of coiled coils from sequence.
356-358
Electronic Edition (link) BibTeX
- Tobias Dezulian, Michael Remmert, Javier F. Palatnik, Detlef Weigel, Daniel H. Huson:
Identification of plant microRNA homologs.
359-360
Electronic Edition (link) BibTeX
- Tiago José P. Sobreira, Alan M. Durham, Arthur Gruber:
TRAP: automated classification, quantification and annotation of tandemly repeated sequences.
361-362
Electronic Edition (link) BibTeX
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
Volume 22,
Number 4,
February 2006
Original Papers Genome Analysis
- Jiexin Zhang, Li Zhang, Kevin R. Coombes:
Gene sequence signatures revealed by mining the UniGene affiliation network.
385-391
Electronic Edition (link) BibTeX
- Xiang Guo, Kay Tatsuoka, Rongxiang Liu:
Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae.
392-399
Electronic Edition (link) BibTeX
- Jussi Salmi, Robert Moulder, Jan-Jonas Filén, Olli Nevalainen, Tuula A. Nyman, Riitta Lahesmaa, Tero Aittokallio:
Quality classification of tandem mass spectrometry data.
400-406
Electronic Edition (link) BibTeX
Sequence Analysis
- András Kocsor, Attila Kertész-Farkas, László Kaján, Sándor Pongor:
Application of compression-based distance measures to protein sequence classification: a methodological study.
407-412
Electronic Edition (link) BibTeX
- Yao-ming Huang, Christopher Bystroff:
Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions.
413-422
Electronic Edition (link) BibTeX
- Kenzie D. MacIsaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, Richard A. Young, Ernest Fraenkel:
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.
423-429
Electronic Edition (link) BibTeX
- Tilman Sauer, Ekaterina Shelest, Edgar Wingender:
Evaluating phylogenetic footprinting for human-rodent comparisons.
430-437
Electronic Edition (link) BibTeX
- Joseph M. Volpe, Lindsay G. Cowell, Thomas B. Kepler:
SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations.
438-444
Electronic Edition (link) BibTeX
- Zizhen Yao, Zasha Weinberg, Walter L. Ruzzo:
CMfinder - a covariance model based RNA motif finding algorithm.
445-452
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Systems Biology
Databases and Ontologies
Applications Note - Sequence Analysis
- Jörg Rothgänger, Markus Weniger, Thomas Weniger, Alexander Mellmann, Dag Harmsen:
Ridom TraceEdit: a DNA trace editor and viewer.
493-494
Electronic Edition (link) BibTeX
- Derek Huntley, Angela Baldo, Saurabh Johri, Marek J. Sergot:
SEAN: SNP prediction and display program utilizing EST sequence clusters.
495-496
Electronic Edition (link) BibTeX
- Tiziana Castrignanò, Paolo D'Onorio De Meo, Giorgio Grillo, Sabino Liuni, Flavio Mignone, Ivano Giuseppe Talamo, Graziano Pesole:
GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags.
497-499
Electronic Edition (link) BibTeX
- Peter Steffen, Björn Voß, Marc Rehmsmeier, Jens Reeder, Robert Giegerich:
RNAshapes: an integrated RNA analysis package based on abstract shapes.
500-503
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Volume 22,
Number 5,
March 2006
Original Papers Genome Analysis
Sequence Analysis
- Giuseppe D'Auria, Ravindra Pushker, Francisco Rodríguez-Valera:
IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships.
527-531
Electronic Edition (link) BibTeX
- Wolfgang P. Lehrach, Dirk Husmeier, Christopher K. I. Williams:
A regularized discriminative model for the prediction of protein-peptide interactions.
532-540
Electronic Edition (link) BibTeX
- Matthew Rabinowitz, Lance Myers, Milena Banjevic, Albert Chan, Joshua Sweetkind-Singer, Jessica Haberer, Kelly McCann, Roland Wolkowicz:
Accurate prediction of HIV-1 drug response from the reverse transcriptase and protease amino acid sequences using sparse models created by convex optimization.
541-549
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
- Roberto Amato, Angelo Ciaramella, N. Deniskina, Carmine Del Mondo, Diego di Bernardo, Ciro Donalek, Giuseppe Longo, Giuseppe Mangano, Gennaro Miele, Giancarlo Raiconi, Antonino Staiano, Roberto Tagliaferri:
A multi-step approach to time series analysis and gene expression clustering.
589-596
Electronic Edition (link) BibTeX
- Jung-jae Kim, Zhuo Zhang, Jong C. Park, See-Kiong Ng:
BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature.
597-605
Electronic Edition (link) BibTeX
- Ofer Shai, Quaid Morris, Benjamin J. Blencowe, Brendan J. Frey:
Inferring global levels of alternative splicing isoforms using a generative model of microarray data.
606-613
Electronic Edition (link) BibTeX
Applications Note Genome Analysis
Sequence Analysis
Structural Bioinformatics
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
- Stephen Montgomery, Obi L. Griffith, Monica C. Sleumer, Casey M. Bergman, Misha Bilenky, Erin Pleasance, Y. Prychyna, X. Zhang, Steven J. M. Jones:
ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.
637-640
Electronic Edition (link) BibTeX
- M. Dennis Prickett, Matt Page, Angela E. Douglas, Gavin H. Thomas:
BuchneraBASE: a post-genomic resource for Buchnera sp. APS.
641-642
Electronic Edition (link) BibTeX
Volume 22,
Number 6,
March 2006
Editorials
Data and Text Mining
Discovery Note - Sequence Analysis
Original Papers - Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Applications Note Sequence Analysis
Gene Expression
Genetics and Population Analysis
Data and Text Mining
Volume 22,
Number 7,
April 2006
Discovery Note - Sequence Analysis
Original Papers Genome Analysis
Gene Expression
Systems Biology
Data and Text Mining
- Ashish Choudhary, Marcel Brun, Jianping Hua, James Lowey, Edward Suh, Edward R. Dougherty:
Genetic test bed for feature selection.
837-842
Electronic Edition (link) BibTeX
- Kazumi Hakamada, Masahiro Okamoto, Taizo Hanai:
Novel technique for preprocessing high dimensional time-course data from DNA microarray: mathematical model-based clustering.
843-848
Electronic Edition (link) BibTeX
- Céline Rouveirol, Nicolas Stransky, Philippe Hupé, Philippe La Rosa, Eric Viara, Emmanuel Barillot, François Radvanyi:
Computation of recurrent minimal genomic alterations from array-CGH data.
849-856
Electronic Edition (link) BibTeX
Databases and Ontologies
- Parantu K. Shah, Peer Bork:
LSAT: learning about alternative transcripts in MEDLINE.
857-865
Electronic Edition (link) BibTeX
- Patricia L. Whetzel, Helen E. Parkinson, Helen C. Causton, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Laurence Game, Mervi Heiskanen, Norman Morrison, Philippe Rocca-Serra, Susanna-Assunta Sansone, Chris J. Taylor, Joseph White, Christian J. Stoeckert Jr.:
The MGED Ontology: a resource for semantics-based description of microarray experiments.
866-873
Electronic Edition (link) BibTeX
- Sandhya Xirasagar, Scott F. Gustafson, Cheng-Cheng Huang, Qinyan Pan, Jennifer Fostel, Paul Boyer, B. Alex Merrick, Kenneth B. Tomer, Denny D. Chan, Kenneth J. Yost III, Danielle Choi, Nianqing Xiao, Stanley Stasiewicz, Pierre R. Bushel, Michael D. Waters:
Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.
874-882
Electronic Edition (link) BibTeX
Applications Note Genome Analysis
Sequence Analysis
- Payan Canaran, Lincoln Stein, Doreen Ware:
Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support.
885-886
Electronic Edition (link) BibTeX
- Weizhong Li, Adam Godzik:
VISSA: a program to visualize structural features from structure sequence alignment.
887-888
Electronic Edition (link) BibTeX
- Michael Sammeth, Thasso Griebel, Felix Tille, Jens Stoye:
Panta rhei (QAlign2): an open graphical environment for sequence analysis.
889-890
Electronic Edition (link) BibTeX
- Avner Schlessinger, Guy Yachdav, Burkhard Rost:
PROFbval: predict flexible and rigid residues in proteins.
891-893
Electronic Edition (link) BibTeX
- Fengfeng Zhou, Yu Xue, Xuebiao Yao, Ying Xu:
CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS).
894-896
Electronic Edition (link) BibTeX
Gene Expression
Databases and Ontologies
Volume 22,
Number 8,
April 2006
Discovery Note Sequence Analysis
Original Papers Genome Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Applications Note Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
Databases and Ontologies
- Adam Ameur, Vladimir Yankovski, Stefan Enroth, Ola Spjuth, Henryk Jan Komorowski:
The LCB Data Warehouse.
1024-1026
Electronic Edition (link) BibTeX
- Yongliang Ren, Wuming Gong, Qiqi Xu, Xin Zheng, Dong Lin, Yejun Wang, Tongbin Li:
siRecords: an extensive database of mammalian siRNAs with efficacy ratings.
1027-1028
Electronic Edition (link) BibTeX
Corrigendum
Volume 22,
Number 9,
May 2006
Discovery Note Sequence Analysis
Original Papers Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
- Ana Conesa, María José Nueda, Alberto Ferrer, Manuel Talón:
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments.
1096-1102
Electronic Edition (link) BibTeX
- Carlos Prieto, M. J. Rivas, J. M. Sánchez, J. López-Fidalgo, Javier De Las Rivas:
Algorithm to find gene expression profiles of deregulation and identify families of disease-altered genes.
1103-1110
Electronic Edition (link) BibTeX
- Lee Weng, Hongyue Dai, Yihui Zhan, Yudong D. He, Sergey B. Stepaniants, Douglas E. Bassett:
Rosetta error model for gene expression analysis.
1111-1121
Electronic Edition (link) BibTeX
- Amela Prelic, Stefan Bleuler, Philip Zimmermann, Anja Wille, Peter Bühlmann, Wilhelm Gruissem, Lars Hennig, Lothar Thiele, Eckart Zitzler:
A systematic comparison and evaluation of biclustering methods for gene expression data.
1122-1129
Electronic Edition (link) BibTeX
Data and Text Mining
Databases and Ontologies
