Skip Navigation

Receive this page by email each issue: [Sign up for eTOCs]

Cover Image
Other Issues:
Previous Next 		Contents: Volume 22, Number 14, 15 July 2006   [Index by Author] 
       ISMB 2006 CONFERENCE PROCEEDINGS, AUGUST 6-10, FORTALEZA, BRAZIL
                EDITORIALS
                ORIGINAL PAPERS
       ORIGINAL PAPERS
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                STRUCTURAL BIOINFORMATICS
                GENE EXPRESSION
                SYSTEMS BIOLOGY
       APPLICATIONS NOTE
                GENOME ANALYSIS
                SEQUENCE ANALYSIS
                PHYLOGENETICS
                STRUCTURAL BIOINFORMATICS
                SYSTEMS BIOLOGY
Find articles in this issue containing these words:
[Search ALL Issues]

Table of Contents (Print PDF)

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.

ISMB 2006 CONFERENCE PROCEEDINGS, AUGUST 6-10, FORTALEZA, BRAZIL:

EDITORIALS:

Philip E. Bourne and Soren Brunak
ISMB 2006
Bioinformatics 2006 22: e1-e2; doi:10.1093/bioinformatics/btl373 [Print PDF]   OPEN ACCESS ARTICLE  

ISMB 2006 Organization
Bioinformatics 2006 22: e3-e7; doi:10.1093/bioinformatics/btl374 [Print PDF]   OPEN ACCESS ARTICLE  

ORIGINAL PAPERS:

Andrey Alexeyenko, Ivica Tamas, Gang Liu, and Erik L.L. Sonnhammer
Automatic clustering of orthologs and inparalogs shared by multiple proteomes
Bioinformatics 2006 22: e9-e15; doi:10.1093/bioinformatics/btl213 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Iris Antes, Shirley W. I. Siu, and Thomas Lengauer
DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations
Bioinformatics 2006 22: e16-e24; doi:10.1093/bioinformatics/btl216 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Hiroshi Mamitsuka, and Minoru Kanehisa
ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains
Bioinformatics 2006 22: e25-e34; doi:10.1093/bioinformatics/btl244 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Fabrice Armougom, Sébastien Moretti, Vladimir Keduas, and Cedric Notredame
The iRMSD: a local measure of sequence alignment accuracy using structural information
Bioinformatics 2006 22: e35-e39; doi:10.1093/bioinformatics/btl218 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Sitaram Asur, Pichai Raman, Matthew Eric Otey, and Srinivasan Parthasarathy
A model-based approach for mining membrane protein crystallization trials
Bioinformatics 2006 22: e40-e48; doi:10.1093/bioinformatics/btl225 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Karsten M. Borgwardt, Arthur Gretton, Malte J. Rasch, Hans-Peter Kriegel, Bernhard Schölkopf, and Alex J. Smola
Integrating structured biological data by Kernel Maximum Mean Discrepancy
Bioinformatics 2006 22: e49-e57; doi:10.1093/bioinformatics/btl242 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Giovanni Bottegoni, Walter Rocchia, Maurizio Recanatini, and Andrea Cavalli
AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets
Bioinformatics 2006 22: e58-e65; doi:10.1093/bioinformatics/btl212 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Patryk Burek, Robert Hoehndorf, Frank Loebe, Johann Visagie, Heinrich Herre, and Janet Kelso
A top-level ontology of functions and its application in the Open Biomedical Ontologies
Bioinformatics 2006 22: e66-e73; doi:10.1093/bioinformatics/btl266 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Bruno Contreras-Moreira and Julio Collado-Vides
Comparative footprinting of DNA-binding proteins
Bioinformatics 2006 22: e74-e80; doi:10.1093/bioinformatics/btl215 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Frank DiMaio, Jude Shavlik, and George N. Phillips
A probabilistic approach to protein backbone tracing in electron density maps
Bioinformatics 2006 22: e81-e89; doi:10.1093/bioinformatics/btl252 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Chuong B. Do, Daniel A. Woods, and Serafim Batzoglou
CONTRAfold: RNA secondary structure prediction without physics-based models
Bioinformatics 2006 22: e90-e98; doi:10.1093/bioinformatics/btl246 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Timothy M. D. Ebbels, Bernard F. Buxton, and David T. Jones
springScape: visualisation of microarray and contextual bioinformatic data using spring embedding and an ‘information landscape’
Bioinformatics 2006 22: e99-e107; doi:10.1093/bioinformatics/btl205 [Abstract] [Print PDF] [Supplementary material]   OPEN ACCESS ARTICLE  

Elena Edelman, Alessandro Porrello, Justin Guinney, Bala Balakumaran, Andrea Bild, Phillip G. Febbo, and Sayan Mukherjee
Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles
Bioinformatics 2006 22: e108-e116; doi:10.1093/bioinformatics/btl231 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Logan Everett, Li-San Wang, and Sridhar Hannenhalli
Dense subgraph computation via stochastic search: application to detect transcriptional modules
Bioinformatics 2006 22: e117-e123; doi:10.1093/bioinformatics/btl260 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Adrien Fauré, Aurélien Naldi, Claudine Chaouiya, and Denis Thieffry
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
Bioinformatics 2006 22: e124-e131; doi:10.1093/bioinformatics/btl210 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Bernd Fischer, Jonas Grossmann, Volker Roth, Wilhelm Gruissem, Sacha Baginsky, and Joachim M. Buhmann
Semi-supervised LC/MS alignment for differential proteomics
Bioinformatics 2006 22: e132-e140; doi:10.1093/bioinformatics/btl219 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Barrett C. Foat, Alexandre V. Morozov, and Harmen J. Bussemaker
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
Bioinformatics 2006 22: e141-e149; doi:10.1093/bioinformatics/btl223 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Eugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, and Serafim Batzoglou
MotifCut: regulatory motifs finding with maximum density subgraphs
Bioinformatics 2006 22: e150-e157; doi:10.1093/bioinformatics/btl243 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Hendrik Fuß, Werner Dubitzky, Stephen Downes, and Mary Jo Kurth
Bistable switching and excitable behaviour in the activation of Src at mitosis
Bioinformatics 2006 22: e158-e165; doi:10.1093/bioinformatics/btl201 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Benjamin Georgi and Alexander Schliep
Context-specific independence mixture modeling for positional weight matrices
Bioinformatics 2006 22: e166-e173; doi:10.1093/bioinformatics/btl249 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Ivelin Georgiev, Ryan H. Lilien, and Bruce R. Donald
Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design
Bioinformatics 2006 22: e174-e183; doi:10.1093/bioinformatics/btl220 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Olivier Gevaert, Frank De Smet, Dirk Timmerman, Yves Moreau, and Bart De Moor
Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks
Bioinformatics 2006 22: e184-e190; doi:10.1093/bioinformatics/btl230 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Erik Granseth, Håkan Viklund, and Arne Elofsson
ZPRED: Predicting the distance to the membrane center for residues in {alpha}-helical membrane proteins
Bioinformatics 2006 22: e191-e196; doi:10.1093/bioinformatics/btl206 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Jana Hertel and Peter F. Stadler
Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data
Bioinformatics 2006 22: e197-e202; doi:10.1093/bioinformatics/btl257 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Fabien P.E. Huard, Charlotte M. Deane, and Graham R. Wood
Modelling sequential protein folding under kinetic control
Bioinformatics 2006 22: e203-e210; doi:10.1093/bioinformatics/btl248 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Phil Hyoun Lee and Hagit Shatkay
BNTagger: improved tagging SNP selection using Bayesian networks
Bioinformatics 2006 22: e211-e219; doi:10.1093/bioinformatics/btl233 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Hyunchul Jang, Jaesoo Lim, Joon-Ho Lim, Soo-Jun Park, Kyu-Chul Lee, and Seon-Hee Park
Finding the evidence for protein-protein interactions from PubMed abstracts
Bioinformatics 2006 22: e220-e226; doi:10.1093/bioinformatics/btl203 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Nebojsa Jojic, Manuel Reyes-Gomez, David Heckerman, Carl Kadie, and Ora Schueler-Furman
Learning MHC I—peptide binding
Bioinformatics 2006 22: e227-e235; doi:10.1093/bioinformatics/btl255 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Neil C. Jones and Pavel A. Pevzner
Comparative genomics reveals unusually long motifs in mammalian genomes
Bioinformatics 2006 22: e236-e242; doi:10.1093/bioinformatics/btl265 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Emre Karakoc, Artem Cherkasov, and S. Cenk Sahinalp
Distance based algorithms for small biomolecule classification and structural similarity search
Bioinformatics 2006 22: e243-e251; doi:10.1093/bioinformatics/btl259 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Firas Khatib, Matthew T. Weirauch, and Carol A. Rohl
Rapid knot detection and application to protein structure prediction
Bioinformatics 2006 22: e252-e259; doi:10.1093/bioinformatics/btl236 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Mustafa Kirac, Gultekin Ozsoyoglu, and Jiong Yang
Annotating proteins by mining protein interaction networks
Bioinformatics 2006 22: e260-e270; doi:10.1093/bioinformatics/btl221 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Geoffrey Koh, Huey Fern Carol Teong, Marie-Véronique Clément, David Hsu, and P.S. Thiagarajan
A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk
Bioinformatics 2006 22: e271-e280; doi:10.1093/bioinformatics/btl264 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred Pühler, Forest Rohwer, Folker Meyer, and Jens Stoye
Finding novel genes in bacterial communities isolated from the environment
Bioinformatics 2006 22: e281-e289; doi:10.1093/bioinformatics/btl247 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Gorka Lasso, John F. Antoniw, and Jonathan G.L. Mullins
A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops
Bioinformatics 2006 22: e290-e297; doi:10.1093/bioinformatics/btl209 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Tien-ho Lin, Eugene W. Myers, and Eric P. Xing
Interpreting anonymous DNA samples from mass disasters—probabilistic forensic inference using genetic markers
Bioinformatics 2006 22: e298-e306; doi:10.1093/bioinformatics/btl200 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, and Liming Cai
Peptide sequence tag-based blind identification of post-translational modifications with point process model
Bioinformatics 2006 22: e307-e313; doi:10.1093/bioinformatics/btl226 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Yong Lu, Roni Rosenfeld, and Ziv Bar-Joseph
Identifying cycling genes by combining sequence homology and expression data
Bioinformatics 2006 22: e314-e322; doi:10.1093/bioinformatics/btl229 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Daniel L. Mace, Ji-Young Lee, Richard W. Twigg, Juliette Colinas, Philip N. Benfey, and Uwe Ohler
Quantification of transcription factor expression from Arabidopsis images
Bioinformatics 2006 22: e323-e331; doi:10.1093/bioinformatics/btl228 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Reuma Magori-Cohen, Yoram Louzoun, and Steven H. Kleinstein
Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees
Bioinformatics 2006 22: e332-e340; doi:10.1093/bioinformatics/btl239 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Denise Mak, Yevgeniy Gelfand, and Gary Benson
Indel seeds for homology search
Bioinformatics 2006 22: e341-e349; doi:10.1093/bioinformatics/btl263 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Tobias P. Mann and William Stafford Noble
Efficient identification of DNA hybridization partners in a sequence database
Bioinformatics 2006 22: e350-e358; doi:10.1093/bioinformatics/btl240 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Victor M. Markowitz, Natalia Ivanova, Krishna Palaniappan, Ernest Szeto, Frank Korzeniewski, Athanasios Lykidis, Iain Anderson, Konstantinos Mavrommatis, Victor Kunin, Hector Garcia Martin, Inna Dubchak, Phil Hugenholtz, and Nikos C. Kyrpides
An experimental metagenome data management and analysis system
Bioinformatics 2006 22: e359-e367; doi:10.1093/bioinformatics/btl217 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Joe Mellor and Charles DeLisi
An equilibrium partitioning model connecting gene expression and cis-motif content
Bioinformatics 2006 22: e368-e374; doi:10.1093/bioinformatics/btl253 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Jose C. Nacher, Jean-Marc Schwartz, Minoru Kanehisa, and Tatsuya Akutsu
Identification of metabolic units induced by environmental signals
Bioinformatics 2006 22: e375-e383; doi:10.1093/bioinformatics/btl202 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Leelavati Narlikar, Raluca Gordân, Uwe Ohler, and Alexander J. Hartemink
Informative priors based on transcription factor structural class improve de novo motif discovery
Bioinformatics 2006 22: e384-e392; doi:10.1093/bioinformatics/btl251 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Patrick Ng, Niranjan Nagarajan, Neil Jones, and Uri Keich
Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone
Bioinformatics 2006 22: e393-e401; doi:10.1093/bioinformatics/btl245 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Yanay Ofran, Guy Yachdav, Eyal Mozes, Ta-tsen Soong, Rajesh Nair, and Burkhard Rost
Create and assess protein networks through molecular characteristics of individual proteins
Bioinformatics 2006 22: e402-e407; doi:10.1093/bioinformatics/btl258 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, and Rita Casadio
BaCelLo: a balanced subcellular localization predictor
Bioinformatics 2006 22: e408-e416; doi:10.1093/bioinformatics/btl222 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Yuan Qi, Patrycja E. Missiuro, Ashish Kapoor, Craig P. Hunter, Tommi S. Jaakkola, David K. Gifford, and Hui Ge
Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo
Bioinformatics 2006 22: e417-e423; doi:10.1093/bioinformatics/btl256 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Alexander Schliep and Sven Rahmann
Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree
Bioinformatics 2006 22: e424-e430; doi:10.1093/bioinformatics/btl254 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Sohrab P. Shah, Xiang Xuan, Ron J. DeLeeuw, Mehrnoush Khojasteh, Wan L. Lam, Raymond Ng, and Kevin P. Murphy
Integrating copy number polymorphisms into array CGH analysis using a robust HMM
Bioinformatics 2006 22: e431-e439; doi:10.1093/bioinformatics/btl238 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Boris E. Shakhnovich
Relative contributions of structural designability and functional diversity in molecular evolution of duplicates
Bioinformatics 2006 22: e440-e445; doi:10.1093/bioinformatics/btl211 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Hagit Shatkay, Nawei Chen, and Dorothea Blostein
Integrating image data into biomedical text categorization
Bioinformatics 2006 22: e446-e453; doi:10.1093/bioinformatics/btl235 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Saurabh Sinha
On counting position weight matrix matches in a sequence, with application to discriminative motif finding
Bioinformatics 2006 22: e454-e463; doi:10.1093/bioinformatics/btl227 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Larisa N. Soldatova, Amanda Clare, Andrew Sparkes, and Ross D. King
An ontology for a Robot Scientist
Bioinformatics 2006 22: e464-e471; doi:10.1093/bioinformatics/btl207 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Sören Sonnenburg, Alexander Zien, and Gunnar Rätsch
ARTS: accurate recognition of transcription starts in human
Bioinformatics 2006 22: e472-e480; doi:10.1093/bioinformatics/btl250 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Haixu Tang, Randy J. Arnold, Pedro Alves, Zhiyin Xun, David E. Clemmer, Milos V. Novotny, James P. Reilly, and Predrag Radivojac
A computational approach toward label-free protein quantification using predicted peptide detectability
Bioinformatics 2006 22: e481-e488; doi:10.1093/bioinformatics/btl237 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Zhidong Tu, Li Wang, Michelle N. Arbeitman, Ting Chen, and Fengzhu Sun
An integrative approach for causal gene identification and gene regulatory pathway inference
Bioinformatics 2006 22: e489-e496; doi:10.1093/bioinformatics/btl234 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Vinay Varadan, David M. Miller, III, and Dimitris Anastassiou
Computational inference of the molecular logic for synaptic connectivity in C. elegans
Bioinformatics 2006 22: e497-e506; doi:10.1093/bioinformatics/btl224 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Roy Varshavsky, Assaf Gottlieb, Michal Linial, and David Horn
Novel Unsupervised Feature Filtering of Biological Data
Bioinformatics 2006 22: e507-e513; doi:10.1093/bioinformatics/btl214 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Ravi Vijaya Satya, Amar Mukherjee, Gabriela Alexe, Laxmi Parida, and Gyan Bhanot
Constructing Near-Perfect Phylogenies with multiple homoplasy events
Bioinformatics 2006 22: e514-e522; doi:10.1093/bioinformatics/btl262 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Pinglang Wang, Manhong Dai, Weijian Xuan, Richard C. McEachin, Anne U. Jackson, Laura J. Scott, Brian Athey, Stanley J. Watson, and Fan Meng
SNP Function Portal: a web database for exploring the function implication of SNP alleles
Bioinformatics 2006 22: e523-e529; doi:10.1093/bioinformatics/btl241 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

K. Wolstencroft, P. Lord, L. Tabernero, A. Brass, and R. Stevens
Protein classification using ontology classification
Bioinformatics 2006 22: e530-e538; doi:10.1093/bioinformatics/btl208 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Nir Yosef, Alon Kaufman, and Eytan Ruppin
Inferring Functional Pathways from Multi-Perturbation Data
Bioinformatics 2006 22: e539-e546; doi:10.1093/bioinformatics/btl204 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Hong Yu and Minsuk Lee
Accessing bioscience images from abstract sentences
Bioinformatics 2006 22: e547-e556; doi:10.1093/bioinformatics/btl261 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, and Vineet Bafna
A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements
Bioinformatics 2006 22: e557-e565; doi:10.1093/bioinformatics/btl232 [Abstract] [Print PDF]   OPEN ACCESS ARTICLE  

Author Index
Bioinformatics 2006 22: e567-e568; doi:10.1093/bioinformatics/btl375 [Print PDF] [Request Permissions]  

ORIGINAL PAPERS:

GENOME ANALYSIS:

Huai-Kuang Tsai, Grace Tzu-Wei Huang, Meng-Yuan Chou, Henry Horng-Shing Lu, and Wen-Hsiung Li
Method for identifying transcription factor binding sites in yeast
Bioinformatics Advance Access published on April 27, 2006
Bioinformatics 2006 22: 1675-1681; doi:10.1093/bioinformatics/btl160 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Taesung Park, Sung-Gon Yi, Young Kee Shin, and SeungYeoun Lee
Combining multiple microarrays in the presence of controlling variables
Bioinformatics Advance Access published on May 16, 2006
Bioinformatics 2006 22: 1682-1689; doi:10.1093/bioinformatics/btl183 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

K. H. Chu, C. P. Li, and J. Qi
Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment
Bioinformatics Advance Access published on April 13, 2006
Bioinformatics 2006 22: 1690-1701; doi:10.1093/bioinformatics/btl146 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Sebastien K. Gerega and Kevin M. Downard
PROXIMO—a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS)
Bioinformatics Advance Access published on May 5, 2006
Bioinformatics 2006 22: 1702-1709; doi:10.1093/bioinformatics/btl178 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Katrin Stierand, Patrick C. Maaß, and Matthias Rarey
Molecular complexes at a glance: automated generation of two-dimensional complex diagrams
Bioinformatics Advance Access published on April 21, 2006
Bioinformatics 2006 22: 1710-1716; doi:10.1093/bioinformatics/btl150 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Hong-Bin Shen and Kuo-Chen Chou
Ensemble classifier for protein fold pattern recognition
Bioinformatics Advance Access published on May 3, 2006
Bioinformatics 2006 22: 1717-1722; doi:10.1093/bioinformatics/btl170 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Yasuo Tabei, Koji Tsuda, Taishin Kin, and Kiyoshi Asai
SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments
Bioinformatics Advance Access published on May 11, 2006
Bioinformatics 2006 22: 1723-1729; doi:10.1093/bioinformatics/btl177 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

GENE EXPRESSION:

Sin-Ho Jung and Woncheol Jang
How accurately can we control the FDR in analyzing microarray data?
Bioinformatics Advance Access published on April 27, 2006
Bioinformatics 2006 22: 1730-1736; doi:10.1093/bioinformatics/btl161 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

X. Liu, S. Sivaganesan, K. Y. Yeung, J. Guo, R. E. Bumgarner, and Mario Medvedovic
Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset
Bioinformatics Advance Access published on May 18, 2006
Bioinformatics 2006 22: 1737-1744; doi:10.1093/bioinformatics/btl184 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

S. K. Ng, G. J. McLachlan, K. Wang, L. Ben-Tovim Jones, and S.-W. Ng
A Mixture model with random-effects components for clustering correlated gene-expression profiles
Bioinformatics Advance Access published on May 3, 2006
Bioinformatics 2006 22: 1745-1752; doi:10.1093/bioinformatics/btl165 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Guido Sanguinetti, Magnus Rattray, and Neil D. Lawrence
A probabilistic dynamical model for quantitative inference of the regulatory mechanism of transcription
Bioinformatics Advance Access published on April 21, 2006
Bioinformatics 2006 22: 1753-1759; doi:10.1093/bioinformatics/btl154 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Suman Sundaresh, Denise L. Doolan, Siddiqua Hirst, Yunxiang Mu, Berkay Unal, D. Huw Davies, Philip L. Felgner, and Pierre Baldi
Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques
Bioinformatics Advance Access published on April 27, 2006
Bioinformatics 2006 22: 1760-1766; doi:10.1093/bioinformatics/btl162 [Abstract] [Full Text] [Print PDF] [Supplementary material] [Request Permissions]  

SYSTEMS BIOLOGY:

Syed Asad Rahman and Dietmar Schomburg
Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks
Bioinformatics Advance Access published on May 8, 2006
Bioinformatics 2006 22: 1767-1774; doi:10.1093/bioinformatics/btl181 [Abstract] [Full Text] [Print PDF] [Supplementary Data] [Request Permissions]  

Ruiqi Wang, Luonan Chen, and Kazuyuki Aihara
Synchronizing a multicellular system by external input: an artificial control strategy
Bioinformatics Advance Access published on May 11, 2006
Bioinformatics 2006 22: 1775-1781; doi:10.1093/bioinformatics/btl182 [Abstract] [Full Text] [Print PDF] [Supplementary] [Request Permissions]  

APPLICATIONS NOTE:

GENOME ANALYSIS:

Reinhard Engels, Tamara Yu, Chris Burge, Jill P. Mesirov, David DeCaprio, and James E. Galagan
Combo: a whole genome comparative browser
Bioinformatics Advance Access published on May 18, 2006
Bioinformatics 2006 22: 1782-1783; doi:10.1093/bioinformatics/btl193 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SEQUENCE ANALYSIS:

Jian Guo and Yuanlie Lin
TSSub: eukaryotic protein subcellular localization by extracting features from profiles
Bioinformatics Advance Access published on June 20, 2006
Bioinformatics 2006 22: 1784-1785; doi:10.1093/bioinformatics/btl180 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

PHYLOGENETICS:

Anne-Muriel Arigon, Guy Perrière, and Manolo Gouy
HoSeqI: automated homologous sequence identification in gene family databases
Bioinformatics Advance Access published on May 8, 2006
Bioinformatics 2006 22: 1786-1787; doi:10.1093/bioinformatics/btl179 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Yoshio Nakano, Toru Takeshita, and Yoshihisa Yamashita
TRFMA: a web-based tool for terminal restriction fragment length polymorphism analysis based on molecular weight
Bioinformatics Advance Access published on May 18, 2006
Bioinformatics 2006 22: 1788-1789; doi:10.1093/bioinformatics/btl186 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

STRUCTURAL BIOINFORMATICS:

Isabel K. Darcy and Robert G. Scharein
TopoICE-R: 3D visualization modeling the topology of DNA recombination
Bioinformatics Advance Access published on May 3, 2006
Bioinformatics 2006 22: 1790-1791; doi:10.1093/bioinformatics/btl164 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Ricard García-Serna, Lulla Opatowski, and Jordi Mestres
FCP: functional coverage of the proteome by structures
Bioinformatics Advance Access published on May 16, 2006
Bioinformatics 2006 22: 1792-1793; doi:10.1093/bioinformatics/btl188 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Yoichi Murakami and Susan Jones
SHARP2: protein–protein interaction predictions using patch analysis
Bioinformatics Advance Access published on May 3, 2006
Bioinformatics 2006 22: 1794-1795; doi:10.1093/bioinformatics/btl171 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Frank Mueller, Daniel J. Muller, and Dirk Labudde
Analysis assistant for single-molecule force spectroscopy data on membrane proteins—MPTV
Bioinformatics Advance Access published on April 10, 2006
Bioinformatics 2006 22: 1796-1799; doi:10.1093/bioinformatics/btl138 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

Jean Marc Kwasigroch and Marianne Rooman
Prelude&Fugue, predicting local protein structure, early folding regions and structural weaknesses
Bioinformatics Advance Access published on May 8, 2006
Bioinformatics 2006 22: 1800-1802; doi:10.1093/bioinformatics/btl176 [Abstract] [FREE Full Text] [Print PDF]   OPEN ACCESS ARTICLE  

Montserrat Vaqué, Anna Arola, Carles Aliagas, and Gerard Pujadas
BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock
Bioinformatics Advance Access published on May 23, 2006
Bioinformatics 2006 22: 1803-1804; doi:10.1093/bioinformatics/btl197 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

SYSTEMS BIOLOGY:

Laurence Calzone, François Fages, and Sylvain Soliman
BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
Bioinformatics Advance Access published on May 3, 2006
Bioinformatics 2006 22: 1805-1807; doi:10.1093/bioinformatics/btl172 [Abstract] [Full Text] [Print PDF] [Request Permissions]  

To see an article, click its [Full Text] link. To review many abstracts, check the boxes to the left of the titles you want, and click the 'Get All Checked Abstract(s)' button. To see one abstract at a time, click its [Abstract] link.