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
Applications Note Genome Analysis
Sequence Analysis
Systems Biology
Data and Text Mining
Volume 22,
Number 10,
May 2006
Editorials
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Discovery Note Structural Bioinformatics
Original Papers Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
Applications Note Genome Analysis
Gene Expression
Systems Biology
Data and Text Mining
Databases and Ontologies
- Rasko Leinonen, Francesco Nardone, Weimin Zhu, Rolf Apweiler:
UniSave: the UniProtKB Sequence/Annotation Version database.
1284-1285
Electronic Edition (link) BibTeX
- Ge Gao, Yingfu Zhong, Anyuan Guo, Qihui Zhu, Wen Tang, Weimou Zheng, Xiaocheng Gu, Liping Wei, Jingchu Luo:
DRTF: a database of rice transcription factors.
1286-1287
Electronic Edition (link) BibTeX
Volume 22,
Number 11,
June 2006
Discovery Notes Structural Bioinformatics
Systems Biology
Original Papers Sequence Analysis
- Kira S. Makarova, Eugene V. Koonin, Robert Haselkorn, Michael Y. Galperin:
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion.
1297-1301
Electronic Edition (link) BibTeX
- Florencia G. Leonardi:
A generalization of the PST algorithm: modeling the sparse nature of protein sequences.
1302-1307
Electronic Edition (link) BibTeX
- Stephen McCauley, Jotun Hein:
Using hidden Markov models and observed evolution to annotate viral genomes.
1308-1316
Electronic Edition (link) BibTeX
- Aleksey Y. Ogurtsov, Svetlana A. Shabalina, Alexey S. Kondrashov, Mikhail A. Roytberg:
Analysis of internal loops within the RNA secondary structure in almost quadratic time.
1317-1324
Electronic Edition (link) BibTeX
- Malik Yousef, Michael Nebozhyn, Hagit Shatkay, Stathis Kanterakis, Louise C. Showe, Michael K. Showe:
Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier.
1325-1334
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
Systems Biology
- Xue-wen Chen, Gopalakrishna Anantha, Xinkun Wang:
An effective structure learning method for constructing gene networks.
1367-1374
Electronic Edition (link) BibTeX
- Chao-Ping Hsu, Pei-Hsuan Lee, Ching-Wei Chang, Cheng-Tsung Lee:
Constructing quantitative models from qualitative mutant phenotypes: preferences in selecting sensory organ precursors.
1375-1382
Electronic Edition (link) BibTeX
- Jacob Köhler, Jan Baumbach, Jan Taubert, Michael Specht, Andre Skusa, Alexander Rüegg, Christopher J. Rawlings, Paul Verrier, Stephan Philippi:
Graph-based analysis and visualization of experimental results with ONDEX.
1383-1390
Electronic Edition (link) BibTeX
Data and Text Mining
Applications Note Structural Bioinformatics
Genetics and Population Analysis
Systems Biology
- Rainer Machné, Andrew Finney, Stefan Müller, James Lu, Stefanie Widder, Christoph Flamm:
The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.
1406-1407
Electronic Edition (link) BibTeX
- Vladimir Makarenkov, Dmytro Kevorkov, Pablo Zentilli, Andrei V. Gagarin, Nathalie Malo, Robert Nadon:
HTS-Corrector: software for the statistical analysis and correction of experimental high-throughput screening data.
1408-1409
Electronic Edition (link) BibTeX
Corrigendum
Volume 22,
Number 12,
June 2006
Editorials
Discovery Notes Genome Analysis
Systems Biology
Original Papers Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
- S. E. Ahnert, K. Willbrand, F. C. S. Brown, T. M. A. Fink:
Unbiased pattern detection in microarray data series.
1471-1476
Electronic Edition (link) BibTeX
- Philippe Broët, Vladimir A. Kuznetsov, Jonas Bergh, Edison T. Liu, Lance D. Miller:
Identifying gene expression changes in breast cancer that distinguish early and late relapse among uncured patients.
1477-1485
Electronic Edition (link) BibTeX
- Xin Gao:
Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments.
1486-1494
Electronic Edition (link) BibTeX
- Lars Kaderali, Thomas Zander, Ulrich Faigle, Jürgen Wolf, Joachim L. Schultze, Rainer Schrader:
CASPAR: a hierarchical bayesian approach to predict survival times in cancer from gene expression data.
1495-1502
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
Data and Text Mining
- Chuen Seng Tan, Alexander Ploner, Andreas Quandt, Janne Lehtiö, Yudi Pawitan:
Finding regions of significance in SELDI measurements for identifying protein biomarkers.
1515-1523
Electronic Edition (link) BibTeX
- Smriti R. Ramakrishnan, Rui Mao, Aleksey A. Nakorchevskiy, John T. Prince, Willard S. Willard, Weijia Xu, Edward M. Marcotte, Daniel P. Miranker:
A fast coarse filtering method for peptide identification by mass spectrometry.
1524-1531
Electronic Edition (link) BibTeX
Applications Note Genome Analysis
Sequence Analysis
Gene Expression
Data and Text Mining
Volume 22,
Number 13,
July 2006
Editorials
Discovery Note Sequence Analysis
Original Papers Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
Applications Note Sequence Analysis
Structural Bioinformatics
Gene Expression
- Hiro Takahashi, Hiroyuki Honda:
Modified signal-to-noise: a new simple and practical gene filtering approach based on the concept of projective adaptive resonance theory (PART) filtering method.
1662-1664
Electronic Edition (link) BibTeX
- Fei Pan, Kiran Kamath, Kangyu Zhang, Sudip Pulapura, Avinash Achar, Juan Nunez-Iglesias, Yu Huang, Xifeng Yan, Jiawei Han, Haiyan Hu, Min Xu, Jianjun Hu, Xianghong Jasmine Zhou:
Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data.
1665-1667
Electronic Edition (link) BibTeX
Data and Text Mining
Corrigendum
Volume 22,
Number 14,
July 2006
Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, Fortaleza, Brazil, August 6-10, 2006.
2006
Contents BibTeX
Original Papers - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Sin-Ho Jung, Woncheol Jang:
How accurately can we control the FDR in analyzing microarray data?
1730-1736
Electronic Edition (link) BibTeX
- X. Liu, Siva Sivaganesan, Ka Yee Yeung, Junhai Guo, Roger Eugene Bumgarner, Mario Medvedovic:
Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset.
1737-1744
Electronic Edition (link) BibTeX
- Shu-Kay Ng, Geoffrey J. McLachlan, Kui Wang, Liat Ben-Tovim Jones, S.-W. Ng:
A Mixture model with random-effects components for clustering correlated gene-expression profiles.
1745-1752
Electronic Edition (link) BibTeX
- Guido Sanguinetti, Magnus Rattray, Neil D. Lawrence:
A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription.
1753-1759
Electronic Edition (link) BibTeX
- Suman Sundaresh, Denise L. Doolan, Siddiqua Hirst, Yunxiang Mu, Berkay Unal, D. Huw Davies, Philip L. Felgner, Pierre Baldi:
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques.
1760-1766
Electronic Edition (link) BibTeX
Systems Biology
Applications Note - Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
- Isabel K. Darcy, Robert G. Scharein:
TopoICE-R: 3D visualization modeling the topology of DNA recombination.
1790-1791
Electronic Edition (link) BibTeX
- Ricard García-Serna, Lulla Opatowski, Jordi Mestres:
FCP: functional coverage of the proteome by structures.
1792-1793
Electronic Edition (link) BibTeX
- Yoichi Murakami, Susan Jones:
SHARP2: protein-protein interaction predictions using patch analysis.
1794-1795
Electronic Edition (link) BibTeX
- Frank Mueller, Daniel J. Muller, Dirk Labudde:
Analysis assistant for single-molecule force spectroscopy data on membrane proteins - MPTV.
1796-1799
Electronic Edition (link) BibTeX
- Jean Marc Kwasigroch, Marianne Rooman:
Prelude&Fugue, predicting local protein structure, early folding regions and structural weaknesses.
1800-1802
Electronic Edition (link) BibTeX
- Montserrat Vaqué, Anna Arola, Carles Aliagas, Gerard Pujadas:
BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock.
1803-1804
Electronic Edition (link) BibTeX
Systems Biology
Volume 22,
Number 15,
August 2006
Original Papers - Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
Data and Text Mining
- Matthew Bellew, Marc Coram, Matthew Fitzgibbon, Mark Igra, Tim Randolph, Pei Wang, Damon May, Jimmy K. Eng, Ruihua Fang, ChenWei Lin, Jinzhi Chen, David Goodlett, Jeffrey Whiteaker, Amanda G. Paulovich, Martin McIntosh:
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.
1902-1909
Electronic Edition (link) BibTeX
Databases and Ontologies
Applications Note - Genome Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Systems Biology
Volume 22,
Number 16,
August 2006
Discovery Note - Genetics and Population Analysis
Original Papers - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
Systems Biology
- Jin Chen, Wynne Hsu, Mong-Li Lee, See-Kiong Ng:
Increasing confidence of protein interactomes using network topological metrics.
1998-2004
Electronic Edition (link) BibTeX
- Je-Gun Joung, Dong-Ho Shin, Rho Hyun Seong, Byoung-Tak Zhang:
Identification of regulatory modules by co-clustering latent variable models: stem cell differentiation.
2005-2011
Electronic Edition (link) BibTeX
- Julie L. Morrison, Rainer Breitling, Desmond J. Higham, David R. Gilbert:
A lock-and-key model for protein-protein interactions.
2012-2019
Electronic Edition (link) BibTeX
- Simen Myhre, Henrik Tveit, Torulf Mollestad, Astrid Lægreid:
Additional Gene Ontology structure for improved biological reasoning.
2020-2027
Electronic Edition (link) BibTeX
- Herbert Pang, Aiping Lin, Matthew Holford, Bradley E. Enerson, Bin Lu, Michael P. Lawton, Eugenia Floyd, Hongyu Zhao:
Pathway analysis using random forests classification and regression.
2028-2036
Electronic Edition (link) BibTeX
Data and Text Mining
Applications Note - Genome Analysis
Phylogenetics
Structural Bioinformatics
Systems Biology
Data and Text Mining
Volume 22,
Number 17,
September 2006
Original Papers - Genome Analysis
- Pan Du, Warren A. Kibbe, Simon M. Lin:
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.
2059-2065
Electronic Edition (link) BibTeX
- Philippe La Rosa, Eric Viara, Philippe Hupé, Gaëlle Pierron, Stéphane Liva, Pierre Neuvial, Isabel Brito, Séverine Lair, Nicolas Servant, Nicolas Robine, Elodie Manié, Caroline Brennetot, Isabelle Janoueix-Lerosey, Virginie Raynal, Nadège Gruel, Céline Rouveirol, Nicolas Stransky, Marc-Henri Stern, Olivier Delattre, Alain Aurias, François Radvanyi, Emmanuel Barillot:
VAMP: Visualization and analysis of array-CGH, transcriptome and other molecular profiles.
2066-2073
Electronic Edition (link) BibTeX
- P. Thébault, Simon de Givry, Thomas Schiex, Christine Gaspin:
Searching RNA motifs and their intermolecular contacts with constraint networks.
2074-2080
Electronic Edition (link) BibTeX
Sequence Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
- Chun Zhang, Dione K. Bailey, Tarif Awad, Guoying Liu, Guoliang Xing, Manqiu Cao, Venu Valmeekam, Jacques Retief, Hajime Matsuzaki, Margaret Taub, Mark Seielstad, Giulia C. Kennedy:
A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations.
2122-2128
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
Applications Note - Sequence Analysis
Phylogenetics
- Joshua Wing Kei Ho, Cameron E. Adams, Jie Bin Lew, Timothy J. Matthews, Chiu Chin Ng, Arash Shahabi-Sirjani, Leng Hong Tan, Yu Zhao, Simon Easteal, Susan R. Wilson, Lars S. Jermiin:
SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides.
2162-2163
Electronic Edition (link) BibTeX
Structural Bioinformatics
- Nicolas Garnier, A. Friedrich, Raphael Bolze, Emmanuel Bettler, Luc Moulinier, Christophe Geourjon, Julie Dawn Thompson, Gilbert Deléage, Olivier Poch:
MAGOS: multiple alignment and modelling server.
2164-2165
Electronic Edition (link) BibTeX
- Rachel Kolodny, Barry Honig:
VISTAL - a new 2D visualization tool of protein 3D structural alignments.
2166-2167
Electronic Edition (link) BibTeX
- Ali Mokdad, Neocles Leontis:
Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities.
2168-2170
Electronic Edition (link) BibTeX
- Douglas L. Theobald, Deborah S. Wuttke:
THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.
2171-2172
Electronic Edition (link) BibTeX
Genetics and Population Analysis
Systems Biology
Databases and Ontologies
Volume 22,
Number 18,
September 2006
Editorials
Discovery Note - Sequence Analysis
Structural Bioinformatics
Original Papers - Genome Analysis
Sequence Analysis
- Fang Fang, Shicai Fan, Xuegong Zhang, Michael Q. Zhang:
Predicting methylation status of CpG islands in the human brain.
2204-2209
Electronic Edition (link) BibTeX
- Lang Li, Alfred S. L. Cheng, Victor X. Jin, Henry H. Paik, Meiyun Fan, Xiaoman Li, Wei Zhang, Jason Robarge, Curtis Balch, Ramana V. Davuluri, Sun Kim, Tim Hui-Ming Huang, Kenneth P. Nephew:
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha.
2210-2216
Electronic Edition (link) BibTeX
- Henry C. M. Leung, Francis Y. L. Chin:
Finding motifs from all sequences with and without binding sites.
2217-2223
Electronic Edition (link) BibTeX
- Thomas Lingner, Peter Meinicke:
Remote homology detection based on oligomer distances.
2224-2231
Electronic Edition (link) BibTeX
- Ketil Malde, Korbinian Schneeberger, Eivind Coward, Inge Jonassen:
RBR: library-less repeat detection for ESTs.
2232-2236
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
- Yifan Huang, Haiyan Xu, Violeta Calian, Jason C. Hsu:
To permute or not to permute.
2244-2248
Electronic Edition (link) BibTeX
- Dougu Nam, Sang-Bae Kim, Seon-Kyu Kim, Sungjin Yang, Seon-Young Kim, In-Sun Chu:
ADGO: analysis of differentially expressed gene sets using composite GO annotation.
2249-2253
Electronic Edition (link) BibTeX
- Ariadni Papana, Hemant Ishwaran:
CART variance stabilization and regularization for high-throughput genomic data.
2254-2261
Electronic Edition (link) BibTeX
- Naijun Sha, Mahlet G. Tadesse, Marina Vannucci:
Bayesian variable selection for the analysis of microarray data with censored outcomes.
2262-2268
Electronic Edition (link) BibTeX
- Andrew E. Teschendorff, Ali Naderi, Nuno L. Barbosa-Morais, Carlos H. Caldas:
PACK: Profile Analysis using Clustering and Kurtosis to find molecular classifiers in cancer.
2269-2275
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
Applications Note - Genome Analysis
Sequence Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Volume 22,
Number 19,
October 2006
Editorials
Original Articles - Genome Analysis
Sequence Analysis
Structural Bioinformatics
Gene Expression
- Gavin C. Cawley, Nicola L. C. Talbot:
Gene selection in cancer classification using sparse logistic regression with Bayesian regularization.
2348-2355
Electronic Edition (link) BibTeX
- Chad A. Davis, Fabian Gerick, Volker Hintermair, Caroline C. Friedel, Katrin Fundel, Robert Küffner, Ralf Zimmer:
Reliable gene signatures for microarray classification: assessment of stability and performance.
2356-2363
Electronic Edition (link) BibTeX
- Darlene R. Goldstein:
Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays.
2364-2372
Electronic Edition (link) BibTeX
- Sek Won Kong, William T. Pu, Peter J. Park:
A multivariate approach for integrating genome-wide expression data and biological knowledge.
2373-2380
Electronic Edition (link) BibTeX
- Ann L. Oberg, Douglas W. Mahoney, Karla V. Ballman, Terry M. Therneau:
Joint estimation of calibration and expression for high-density oligonucleotide arrays.
2381-2387
Electronic Edition (link) BibTeX
- Wei Pan, Xiaotong Shen, Aixiang Jiang, Robert P. Hebbel:
Semi-supervised learning via penalized mixture model with application to microarray sample classification.
2388-2395
Electronic Edition (link) BibTeX
- Antonio Reverter, Aaron Ingham, Sigrid A. Lehnert, Siok-Hwee Tan, Yonghong Wang, Abhirami Ratnakumar, Brian P. Dalrymple:
Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer.
2396-2404
Electronic Edition (link) BibTeX
- Anbupalam Thalamuthu, Indranil Mukhopadhyay, Xiaojing Zheng, George C. Tseng:
Evaluation and comparison of gene clustering methods in microarray analysis.
2405-2412
Electronic Edition (link) BibTeX
- Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, Luonan Chen:
Inferring gene regulatory networks from multiple microarray datasets.
2413-2420
Electronic Edition (link) BibTeX
Data and Text Mining
Applications Note - Genome Analysis
- Nicholas Navin, Vladimir Grubor, Jim Hicks, Evan Leibu, Elizabeth Thomas, Jennifer Troge, Michael Riggs, Pär Lundin, Susanne Månér, Jonathan Sebat, Anders Zetterberg, Michael Wigler:
PROBER: oligonucleotide FISH probe design software.
2437-2438
Electronic Edition (link) BibTeX
Sequence Analysis
- Fabrice Armougom, Olivier Poirot, Sébastien Moretti, Desmond G. Higgins, Phillip Bucher, Vladimir Keduas, Cédric Notredame:
APDB: a web server to evaluate the accuracy of sequence alignments using structural information.
2439-2440
Electronic Edition (link) BibTeX
- Karsten Hiller, Andreas Grote, Matthias Maneck, Richard Münch, Dieter Jahn:
JVirGel 2.0: computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins.
2441-2443
Electronic Edition (link) BibTeX
Data and Text Mining
Letter To Editor - Gene Expression
Corrigendum
Volume 22,
Number 20,
October 2006
Discovery Note - Sequence Analysis
Original Papers - Genome Analysis
Sequence Analysis
- Pekka Marttinen, Jukka Corander, Petri Törönen, Liisa Holm:
Bayesian search of functionally divergent protein subgroups and their function specific residues.
2466-2474
Electronic Edition (link) BibTeX
- Xijin Ge, Qingfa Wu, Yong-Chul Jung, Jun Chen, San Ming Wang:
A large quantity of novel human antisense transcripts detected by LongSAGE.
2475-2479
Electronic Edition (link) BibTeX
- Michiaki Hamada, Koji Tsuda, Taku Kudo, Taishin Kin, Kiyoshi Asai:
Mining frequent stem patterns from unaligned RNA sequences.
2480-2487
Electronic Edition (link) BibTeX
- Tetsuya Sato, Yoshihiro Yamanishi, Katsuhisa Horimoto, Minoru Kanehisa, Hiroyuki Toh:
Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions.
2488-2492
Electronic Edition (link) BibTeX
Phylogenetics
Gene Expression
Systems Biology
- Adriano V. Werhli, Marco Grzegorczyk, Dirk Husmeier:
Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical gaussian models and bayesian networks.
2523-2531
Electronic Edition (link) BibTeX
- Quansong Ruan, Debojyoti Dutta, Michael S. Schwalbach, Joshua A. Steele, Jed A. Fuhrman, Fengzhu Sun:
Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors.
2532-2538
Electronic Edition (link) BibTeX
- Gautier Stoll, Jacques Rougemont, Felix Naef:
Few crucial links assure checkpoint efficiency in the yeast cell-cycle network.
2539-2546
Electronic Edition (link) BibTeX
Data and Text Mining
Applications Note - Gene Expression
Genetics and Population Analysis
Systems Biology
Data and Text Mining
- Roger M. Jarvis, David Broadhurst, Helen E. Johnson, Noel M. O'Boyle, Royston Goodacre:
PYCHEM: a multivariate analysis package for python.
2565-2566
Electronic Edition (link) BibTeX
- Julio Bonis, Laura Inés Furlong, Ferran Sanz:
OSIRIS: a tool for retrieving literature about sequence variants.
2567-2569
Electronic Edition (link) BibTeX
- Luca Lenzi, Flavia Frabetti, Federica Facchin, Raffaella Casadei, Lorenza Vitale, Silvia Canaider, Paolo Carinci, Maria Zannotti, Pierluigi Strippoli:
UniGene Tabulator: a full parser for the UniGene format.
2570-2571
Electronic Edition (link) BibTeX
Databases and Ontologies
Corrigendum
Volume 22,
Number 21,
November 2006
Discovery Note - Genome Analysis
Sequence Analysis
Original Papers - Genome Analysis
Sequence Analysis
Phylogenetics
Structural Bioinformatics
Gene Expression
- Ronglai Shen, Debashis Ghosh, Arul M. Chinnaiyan, Zhaoling Meng:
Eigengene-based linear discriminant model for tumor classification using gene expression microarray data.
2635-2642
Electronic Edition (link) BibTeX
- Natasa Rajicic, Dianne M. Finkelstein, David A. Schoenfeld:
Survival analysis of longitudinal microarrays.
2643-2649
Electronic Edition (link) BibTeX
- Chao Cheng, Xiaotu Ma, Xiting Yan, Fengzhu Sun, Lei M. Li:
MARD: a new method to detect differential gene expression in treatment-control time courses.
2650-2657
Electronic Edition (link) BibTeX
- A. Callegaro, Dario Basso, Silvio Bicciato:
A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions.
2658-2666
Electronic Edition (link) BibTeX
- Joe Faith, Robert Mintram, Maia Angelova:
Targeted projection pursuit for visualizing gene expression data classifications.
2667-2673
Electronic Edition (link) BibTeX
Systems Biology
Applications Note - Phylogenetics
Structural Bioinformatics
- Brajesh Kumar Rai, Carlos J. Madrid-Aliste, J. Eduardo Fajardo, András Fiser:
MMM: a sequence-to-structure alignment protocol.
2691-2692
Electronic Edition (link) BibTeX
- Shantanu Sharma, Feng Ding, Huifen Nie, Daniel Watson, Aditya Unnithan, Jameson Lopp, Diane Pozefsky, Nikolay V. Dokholyan:
iFold: a platform for interactive folding simulations of proteins.
2693-2694
Electronic Edition (link) BibTeX
- Barry J. Grant, Ana P. C. Rodrigues, Karim M. ElSawy, J. Andrew McCammon, Leo S. D. Caves:
Bio3d: an R package for the comparative analysis of protein structures.
2695-2696
Electronic Edition (link) BibTeX
Gene Expression
Genetics and Population Analysis
Systems Biology
Volume 22,
Number 22,
November 2006
Discovery Note - Sequence Analysis
Original Papers - Sequence Analysis
Structural Bioinformatics
- Anne E. Counterman Burba, Ursula Lehnert, Eric Z. Yu, Mark Gerstein:
Helix Interaction Tool (HIT): a web-based tool for analysis of helix-helix interactions in proteins.
2735-2738
Electronic Edition (link) BibTeX
- J. E. Ecker-Passow, Ann L. Oberg, Terry M. Therneau, C. J. Mason, Douglas W. Mahoney, K. L. Johnson, J. E. Olson, H. R. Bergen III:
Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass spectrometry.
2739-2745
Electronic Edition (link) BibTeX
- N. Morozova, J. Allers, J. Myers, Y. Shamoo:
Protein-RNA interactions: exploring binding patterns with a three-dimensional superposition analysis of high resolution structures.
2746-2752
Electronic Edition (link) BibTeX
- Darrin P. Lewis, Tony Jebara, William Stafford Noble:
Support vector machine learning from heterogeneous data: an empirical analysis using protein sequence and structure.
2753-2760
Electronic Edition (link) BibTeX
- Stewart T. Chang, Debashis Ghosh, Denise E. Kirschner, Jennifer J. Linderman:
Peptide length-based prediction of peptide-MHC class II binding.
2761-2767
Electronic Edition (link) BibTeX
- Yong Zhao, Daniel Stoffler, Michel F. Sanner:
Hierarchical and multi-resolution representation of protein flexibility.
2768-2774
Electronic Edition (link) BibTeX
Gene Expression
Systems Biology
Databases and Ontologies
Applications Note - Sequence Analysis
Phylogenetics
Gene Expression
Genetics and Population Analysis
Data and Text Mining
Databases and Ontologies
- Eric J. Vallender, Justin E. Paschall, Christine M. Malcom, Bruce T. Lahn, Gerald J. Wyckoff:
SPEED: a molecular-evolution-based database of mammalian orthologous groups.
2835-2837
Electronic Edition (link) BibTeX
- Kris Laukens, Rune Matthiesen, Filip Lemière, Eddy Esmans, Harry Van Onckelen, Ole Nørregaard Jensen, Erwin Witters:
Integration of gel-based proteome data with pProRep.
2838-2840
Electronic Edition (link) BibTeX
Volume 22,
Number 23,
December 2006
Discovery Note - Sequence Analysis
Structural Bioinformatics
Original Papers - Sequence Analysis
- Torben Friedrich, Birgit Pils, Thomas Dandekar, Jörg Schultz, Tobias Müller:
Modelling interaction sites in protein domains with interaction profile hidden Markov models.
2851-2857
Electronic Edition (link) BibTeX
- Nora Pierstorff, Casey M. Bergman, Thomas Wiehe:
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.
2858-2864
Electronic Edition (link) BibTeX
- László Kaján, Attila Kertész-Farkas, Dino Franklin, Neli Ivanova, András Kocsor, Sándor Pongor:
Application of a simple likelihood ratio approximant to protein sequence classification.
2865-2869
Electronic Edition (link) BibTeX
- Nak-Kyeong Kim, Kannan Tharakaraman, John L. Spouge:
Adding sequence context to a Markov background model improves the identification of regulatory elements.
2870-2875
Electronic Edition (link) BibTeX
Structural Bioinformatics
Gene Expression
- Dong Wang, Yingli Lv, Zheng Guo, Xia Li, Yanhui Li, Jing Zhu, Da Yang, Jianzhen Xu, Chenguang Wang, Shaoqi Rao, Baofeng Yang:
Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules.
2883-2889
Electronic Edition (link) BibTeX
- Curtis Huttenhower, Matthew A. Hibbs, Chad L. Myers, Olga G. Troyanskaya:
A scalable method for integration and functional analysis of multiple microarray datasets.
2890-2897
Electronic Edition (link) BibTeX
- Sukjoon Yoon, Young Yang, Jiwon Choi, Jeeweon Seong:
Large scale data mining approach for gene-specific standardization of microarray gene expression data.
2898-2904
Electronic Edition (link) BibTeX
- Alexander Begun:
Robust method for detecting differential gene expression in twin studies.
2905-2909
Electronic Edition (link) BibTeX
- Antti Lehmussola, Pekka Ruusuvuori, Olli Yli-Harja:
Evaluating the performance of microarray segmentation algorithms.
2910-2917
Electronic Edition (link) BibTeX
Systems Biology
Data and Text Mining
Databases and Ontologies
Applications Note - Genome Analysis
Structural Bioinformatics
Gene Expression
Genetics and Population Analysis
Systems Biology
- Boyke Bunk, Martin Kucklick, Rochus Jonas, Richard Münch, Max Schobert, Dieter Jahn, Karsten Hiller:
MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data.
2962-2965
Electronic Edition (link) BibTeX
- Anastasia Deckard, Frank T. Bergmann, Herbert M. Sauro:
Supporting the SBML layout extension.
2966-2967
Electronic Edition (link) BibTeX
- Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin H. Schultz, Mark Gerstein:
The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks.
2968-2970
Electronic Edition (link) BibTeX
Databases and Ontologies
Volume 22,
Number 24,
December 2006
Editorials
Discovery Note - Sequence Analysis
Original Papers - Sequence Analysis
Structural Bioinformatics
Gene Expression
- Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, Martin H. Schultz, Michael Snyder, Mark Gerstein:
A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge.
3016-3024
Electronic Edition (link) BibTeX
- Yudi Pawitan, Stefano Calza, Alexander Ploner:
Estimation of false discovery proportion under general dependence.
3025-3031
Electronic Edition (link) BibTeX
- Cathal Seoighe, Victoria Nembaware, Konrad Scheffler:
Maximum likelihood inference of imprinting and allele-specific expression from EST data.
3032-3039
Electronic Edition (link) BibTeX
- Mark P. Brynildsen, Linh M. Tran, James C. Liao:
A Gibbs sampler for the identification of gene expression and network connectivity consistency.
3040-3046
Electronic Edition (link) BibTeX
- János Z. Kelemen, Attila Kertész-Farkas, András Kocsor, László G. Puskás:
Kalman filtering for disease-state estimation from microarray data.
3047-3053
Electronic Edition (link) BibTeX
- Daniel S. Yuan, Rafael A. Irizarry:
High-resolution spatial normalization for microarrays containing embedded technical replicates.
3054-3060
Electronic Edition (link) BibTeX
Genetics and Populations Analysis
Systems Biology
- Stefan Hoops, Sven Sahle, Ralph Gauges, Christine Lee, Jürgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer:
COPASI - a COmplex PAthway SImulator.
3067-3074
Electronic Edition (link) BibTeX
- Claudio Eccher, Corrado Priami:
Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus.
3075-3081
Electronic Edition (link) BibTeX
- Fangping Mu, Pat J. Unkefer, Clifford J. Unkefer, William S. Hlavacek:
Prediction of oxidoreductase-catalyzed reactions based on atomic properties of metabolites.
3082-3088
Electronic Edition (link) BibTeX
Data and Text Mining
Applications Note - Sequence Analysis
Structural Bioinformatics
Genetics and Population Analysis
Systems Biology
Copyright © Sat May 16 23:51:32 2009
by Michael Ley (ley@uni-trier.de)