Papers from ISMB are now available for free online at the Journal Bioinformatics. Below is the table of contents.
***************************Announcement*************************
Are you attending the ISMB 2006 Conference in Fortaleza, Brazil?
Visit Oxford Journals at booth # 8 for a chance to win your
choice of an iPod or $250 worth of Oxford University Press books.
Bring a copy of this announcement and receive an additional
entry in our raffle to double your chances to win.
We?ll also have free samples of our journals including
Bioinformatics, which has a recently announced impact factor
of 6.019.* Learn more about our journals at
http://www.oxfordjournals.org*according to 2005 ISI Journal Citation Reports
***************************Announcement*************************
Bioinformatics -- Table of Contents Alert
A new issue of Bioinformatics
has been made available:
15 July 2006; Vol. 22, No. 14
URL:
http://bioinformatics.oxfordjournals.org/content/vol22/issue14/index.dtl?etoc-----------------------------------------------------------------
EDITORIALS
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ISMB 2006
Philip E. Bourne and Soren Brunak
Bioinformatics 2006 22: 1-2.
http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e1?etoc ISMB 2006 Organization
Bioinformatics 2006 22: 3-7.
http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e3?etoc-----------------------------------------------------------------
ORIGINAL PAPERS
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OPEN ACCESS ARTICLE
Automatic clustering of orthologs and inparalogs shared by multiple
proteomes
Andrey Alexeyenko, Ivica Tamas, Gang Liu, and Erik L.L. Sonnhammer
Bioinformatics 2006 22: 9-15.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e9?etoc OPEN ACCESS ARTICLE
DynaPred: A structure and sequence based method for the prediction of MHC
class I binding peptide sequences and conformations
Iris Antes, Shirley W. I. Siu, and Thomas Lengauer
Bioinformatics 2006 22: 16-24.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e16?etoc OPEN ACCESS ARTICLE
ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains
Kiyoko F. Aoki-Kinoshita, Nobuhisa Ueda, Hiroshi Mamitsuka, and Minoru
Kanehisa
Bioinformatics 2006 22: 25-34.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e25?etoc OPEN ACCESS ARTICLE
The iRMSD: a local measure of sequence alignment accuracy using structural
information
Fabrice Armougom, Sebastien Moretti, Vladimir Keduas, and Cedric Notredame
Bioinformatics 2006 22: 35-39.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e35?etoc OPEN ACCESS ARTICLE
A model-based approach for mining membrane protein crystallization trials
Sitaram Asur, Pichai Raman, Matthew Eric Otey, and Srinivasan
Parthasarathy
Bioinformatics 2006 22: 40-48.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e40?etoc OPEN ACCESS ARTICLE
Integrating structured biological data by Kernel Maximum Mean Discrepancy
Karsten M. Borgwardt, Arthur Gretton, Malte J. Rasch, Hans-Peter Kriegel,
Bernhard Scholkopf, and Alex J. Smola
Bioinformatics 2006 22: 49-57.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e49?etoc OPEN ACCESS ARTICLE
AClAP, Autonomous hierarchical agglomerative Cluster Analysis based
protocol to partition conformational datasets
Giovanni Bottegoni, Walter Rocchia, Maurizio Recanatini, and Andrea
Cavalli
Bioinformatics 2006 22: 58-65.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e58?etoc OPEN ACCESS ARTICLE
A top-level ontology of functions and its application in the Open
Biomedical Ontologies
Patryk Burek, Robert Hoehndorf, Frank Loebe, Johann Visagie, Heinrich
Herre, and Janet Kelso
Bioinformatics 2006 22: 66-73.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e66?etoc OPEN ACCESS ARTICLE
Comparative footprinting of DNA-binding proteins
Bruno Contreras-Moreira and Julio Collado-Vides
Bioinformatics 2006 22: 74-80.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e74?etoc OPEN ACCESS ARTICLE
A probabilistic approach to protein backbone tracing in electron density
maps
Frank DiMaio, Jude Shavlik, and George N. Phillips
Bioinformatics 2006 22: 81-89.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e81?etoc OPEN ACCESS ARTICLE
CONTRAfold: RNA secondary structure prediction without physics-based
models
Chuong B. Do, Daniel A. Woods, and Serafim Batzoglou
Bioinformatics 2006 22: 90-98.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e90?etoc OPEN ACCESS ARTICLE
springScape: visualisation of microarray and contextual bioinformatic data
using spring embedding and an 'information landscape'
Timothy M. D. Ebbels, Bernard F. Buxton, and David T. Jones
Bioinformatics 2006 22: 99-107.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e99?etoc OPEN ACCESS ARTICLE
Analysis of sample set enrichment scores: assaying the enrichment of sets
of genes for individual samples in genome-wide expression profiles
Elena Edelman, Alessandro Porrello, Justin Guinney, Bala Balakumaran,
Andrea Bild, Phillip G. Febbo, and Sayan Mukherjee
Bioinformatics 2006 22: 108-116.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e108?etoc OPEN ACCESS ARTICLE
Dense subgraph computation via stochastic search: application to detect
transcriptional modules
Logan Everett, Li-San Wang, and Sridhar Hannenhalli
Bioinformatics 2006 22: 117-123.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e117?etoc OPEN ACCESS ARTICLE
Dynamical analysis of a generic Boolean model for the control of the
mammalian cell cycle
Adrien Faure, Aurelien Naldi, Claudine Chaouiya, and Denis Thieffry
Bioinformatics 2006 22: 124-131.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e124?etoc OPEN ACCESS ARTICLE
Semi-supervised LC/MS alignment for differential proteomics
Bernd Fischer, Jonas Grossmann, Volker Roth, Wilhelm Gruissem, Sacha
Baginsky, and Joachim M. Buhmann
Bioinformatics 2006 22: 132-140.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e132?etoc OPEN ACCESS ARTICLE
Statistical mechanical modeling of genome-wide transcription factor
occupancy data by MatrixREDUCE
Barrett C. Foat, Alexandre V. Morozov, and Harmen J. Bussemaker
Bioinformatics 2006 22: 141-149.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e141?etoc OPEN ACCESS ARTICLE
MotifCut: regulatory motifs finding with maximum density subgraphs
Eugene Fratkin, Brian T. Naughton, Douglas L. Brutlag, and Serafim
Batzoglou
Bioinformatics 2006 22: 150-157.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e150?etoc OPEN ACCESS ARTICLE
Bistable switching and excitable behaviour in the activation of Src at
mitosis
Hendrik Fuss, Werner Dubitzky, Stephen Downes, and Mary Jo Kurth
Bioinformatics 2006 22: 158-165.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e158?etoc OPEN ACCESS ARTICLE
Context-specific independence mixture modeling for positional weight
matrices
Benjamin Georgi and Alexander Schliep
Bioinformatics 2006 22: 166-173.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e166?etoc OPEN ACCESS ARTICLE
Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End
Elimination, with application to protein design
Ivelin Georgiev, Ryan H. Lilien, and Bruce R. Donald
Bioinformatics 2006 22: 174-183.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e174?etoc OPEN ACCESS ARTICLE
Predicting the prognosis of breast cancer by integrating clinical and
microarray data with Bayesian networks
Olivier Gevaert, Frank De Smet, Dirk Timmerman, Yves Moreau, and Bart De
Moor
Bioinformatics 2006 22: 184-190.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e184?etoc OPEN ACCESS ARTICLE
ZPRED: Predicting the distance to the membrane center for residues in
{alpha}-helical membrane proteins
Erik Granseth, Hakan Viklund, and Arne Elofsson
Bioinformatics 2006 22: 191-196.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e191?etoc OPEN ACCESS ARTICLE
Hairpins in a Haystack: recognizing microRNA precursors in comparative
genomics data
Jana Hertel and Peter F. Stadler
Bioinformatics 2006 22: 197-202.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e197?etoc OPEN ACCESS ARTICLE
Modelling sequential protein folding under kinetic control
Fabien P.E. Huard, Charlotte M. Deane, and Graham R. Wood
Bioinformatics 2006 22: 203-210.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e203?etoc OPEN ACCESS ARTICLE
BNTagger: improved tagging SNP selection using Bayesian networks
Phil Hyoun Lee and Hagit Shatkay
Bioinformatics 2006 22: 211-219.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e211?etoc OPEN ACCESS ARTICLE
Finding the evidence for protein-protein interactions from PubMed
abstracts
Hyunchul Jang, Jaesoo Lim, Joon-Ho Lim, Soo-Jun Park, Kyu-Chul Lee, and
Seon-Hee Park
Bioinformatics 2006 22: 220-226.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e220?etoc OPEN ACCESS ARTICLE
Learning MHC I--peptide binding
Nebojsa Jojic, Manuel Reyes-Gomez, David Heckerman, Carl Kadie, and Ora
Schueler-Furman
Bioinformatics 2006 22: 227-235.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e227?etoc OPEN ACCESS ARTICLE
Comparative genomics reveals unusually long motifs in mammalian genomes
Neil C. Jones and Pavel A. Pevzner
Bioinformatics 2006 22: 236-242.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e236?etoc OPEN ACCESS ARTICLE
Distance based algorithms for small biomolecule classification and
structural similarity search
Emre Karakoc, Artem Cherkasov, and S. Cenk Sahinalp
Bioinformatics 2006 22: 243-251.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e243?etoc OPEN ACCESS ARTICLE
Rapid knot detection and application to protein structure prediction
Firas Khatib, Matthew T. Weirauch, and Carol A. Rohl
Bioinformatics 2006 22: 252-259.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e252?etoc OPEN ACCESS ARTICLE
Annotating proteins by mining protein interaction networks
Mustafa Kirac, Gultekin Ozsoyoglu, and Jiong Yang
Bioinformatics 2006 22: 260-270.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e260?etoc OPEN ACCESS ARTICLE
A decompositional approach to parameter estimation in pathway modeling: a
case study of the Akt and MAPK pathways and their crosstalk
Geoffrey Koh, Huey Fern Carol Teong, Marie-Veronique Clement, David Hsu,
and P.S. Thiagarajan
Bioinformatics 2006 22: 271-280.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e271?etoc OPEN ACCESS ARTICLE
Finding novel genes in bacterial communities isolated from the environment
Lutz Krause, Naryttza N. Diaz, Daniela Bartels, Robert A. Edwards, Alfred
Puhler, Forest Rohwer, Folker Meyer, and Jens Stoye
Bioinformatics 2006 22: 281-289.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e281?etoc OPEN ACCESS ARTICLE
A combinatorial pattern discovery approach for the prediction of membrane
dipping (re-entrant) loops
Gorka Lasso, John F. Antoniw, and Jonathan G.L. Mullins
Bioinformatics 2006 22: 290-297.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e290?etoc OPEN ACCESS ARTICLE
Interpreting anonymous DNA samples from mass disasters--probabilistic
forensic inference using genetic markers
Tien-ho Lin, Eugene W. Myers, and Eric P. Xing
Bioinformatics 2006 22: 298-306.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e298?etoc OPEN ACCESS ARTICLE
Peptide sequence tag-based blind identification of post-translational
modifications with point process model
Chunmei Liu, Bo Yan, Yinglei Song, Ying Xu, and Liming Cai
Bioinformatics 2006 22: 307-313.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e307?etoc OPEN ACCESS ARTICLE
Identifying cycling genes by combining sequence homology and expression
data
Yong Lu, Roni Rosenfeld, and Ziv Bar-Joseph
Bioinformatics 2006 22: 314-322.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e314?etoc OPEN ACCESS ARTICLE
Quantification of transcription factor expression from Arabidopsis images
Daniel L. Mace, Ji-Young Lee, Richard W. Twigg, Juliette Colinas, Philip
N. Benfey, and Uwe Ohler
Bioinformatics 2006 22: 323-331.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e323?etoc OPEN ACCESS ARTICLE
Mutation parameters from DNA sequence data using graph theoretic measures
on lineage trees
Reuma Magori-Cohen, Yoram Louzoun, and Steven H. Kleinstein
Bioinformatics 2006 22: 332-340.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e332?etoc OPEN ACCESS ARTICLE
Indel seeds for homology search
Denise Mak, Yevgeniy Gelfand, and Gary Benson
Bioinformatics 2006 22: 341-349.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e341?etoc OPEN ACCESS ARTICLE
Efficient identification of DNA hybridization partners in a sequence
database
Tobias P. Mann and William Stafford Noble
Bioinformatics 2006 22: 350-358.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e350?etoc OPEN ACCESS ARTICLE
An experimental metagenome data management and analysis system
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
Bioinformatics 2006 22: 359-367.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e359?etoc OPEN ACCESS ARTICLE
An equilibrium partitioning model connecting gene expression and cis-motif
content
Joe Mellor and Charles DeLisi
Bioinformatics 2006 22: 368-374.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e368?etoc OPEN ACCESS ARTICLE
Identification of metabolic units induced by environmental signals
Jose C. Nacher, Jean-Marc Schwartz, Minoru Kanehisa, and Tatsuya Akutsu
Bioinformatics 2006 22: 375-383.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e375?etoc OPEN ACCESS ARTICLE
Informative priors based on transcription factor structural class improve
de novo motif discovery
Leelavati Narlikar, Raluca Gordan, Uwe Ohler, and Alexander J. Hartemink
Bioinformatics 2006 22: 384-392.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e384?etoc OPEN ACCESS ARTICLE
Apples to apples: improving the performance of motif finders and their
significance analysis in the Twilight Zone
Patrick Ng, Niranjan Nagarajan, Neil Jones, and Uri Keich
Bioinformatics 2006 22: 393-401.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e393?etoc OPEN ACCESS ARTICLE
Create and assess protein networks through molecular characteristics of
individual proteins
Yanay Ofran, Guy Yachdav, Eyal Mozes, Ta-tsen Soong, Rajesh Nair, and
Burkhard Rost
Bioinformatics 2006 22: 402-407.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e402?etoc OPEN ACCESS ARTICLE
BaCelLo: a balanced subcellular localization predictor
Andrea Pierleoni, Pier Luigi Martelli, Piero Fariselli, and Rita Casadio
Bioinformatics 2006 22: 408-416.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e408?etoc OPEN ACCESS ARTICLE
Semi-supervised analysis of gene expression profiles for lineage-specific
development in the Caenorhabditis elegans embryo
Yuan Qi, Patrycja E. Missiuro, Ashish Kapoor, Craig P. Hunter, Tommi S.
Jaakkola, David K. Gifford, and Hui Ge
Bioinformatics 2006 22: 417-423.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e417?etoc OPEN ACCESS ARTICLE
Decoding non-unique oligonucleotide hybridization experiments of targets
related by a phylogenetic tree
Alexander Schliep and Sven Rahmann
Bioinformatics 2006 22: 424-430.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e424?etoc OPEN ACCESS ARTICLE
Integrating copy number polymorphisms into array CGH analysis using a
robust HMM
Sohrab P. Shah, Xiang Xuan, Ron J. DeLeeuw, Mehrnoush Khojasteh, Wan L.
Lam, Raymond Ng, and Kevin P. Murphy
Bioinformatics 2006 22: 431-439.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e431?etoc OPEN ACCESS ARTICLE
Relative contributions of structural designability and functional
diversity in molecular evolution of duplicates
Boris E. Shakhnovich
Bioinformatics 2006 22: 440-445.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e440?etoc OPEN ACCESS ARTICLE
Integrating image data into biomedical text categorization
Hagit Shatkay, Nawei Chen, and Dorothea Blostein
Bioinformatics 2006 22: 446-453.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e446?etoc OPEN ACCESS ARTICLE
On counting position weight matrix matches in a sequence, with application
to discriminative motif finding
Saurabh Sinha
Bioinformatics 2006 22: 454-463.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e454?etoc OPEN ACCESS ARTICLE
An ontology for a Robot Scientist
Larisa N. Soldatova, Amanda Clare, Andrew Sparkes, and Ross D. King
Bioinformatics 2006 22: 464-471.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e464?etoc OPEN ACCESS ARTICLE
ARTS: accurate recognition of transcription starts in human
Soren Sonnenburg, Alexander Zien, and Gunnar Ratsch
Bioinformatics 2006 22: 472-480.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e472?etoc OPEN ACCESS ARTICLE
A computational approach toward label-free protein quantification using
predicted peptide detectability
Haixu Tang, Randy J. Arnold, Pedro Alves, Zhiyin Xun, David E. Clemmer,
Milos V. Novotny, James P. Reilly, and Predrag Radivojac
Bioinformatics 2006 22: 481-488.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e481?etoc OPEN ACCESS ARTICLE
An integrative approach for causal gene identification and gene regulatory
pathway inference
Zhidong Tu, Li Wang, Michelle N. Arbeitman, Ting Chen, and Fengzhu Sun
Bioinformatics 2006 22: 489-496.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e489?etoc OPEN ACCESS ARTICLE
Computational inference of the molecular logic for synaptic connectivity
in C. elegans
Vinay Varadan, David M. Miller, III, and Dimitris Anastassiou
Bioinformatics 2006 22: 497-506.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e497?etoc OPEN ACCESS ARTICLE
Novel Unsupervised Feature Filtering of Biological Data
Roy Varshavsky, Assaf Gottlieb, Michal Linial, and David Horn
Bioinformatics 2006 22: 507-513.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e507?etoc OPEN ACCESS ARTICLE
Constructing Near-Perfect Phylogenies with multiple homoplasy events
Ravi Vijaya Satya, Amar Mukherjee, Gabriela Alexe, Laxmi Parida, and Gyan
Bhanot
Bioinformatics 2006 22: 514-522.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e514?etoc OPEN ACCESS ARTICLE
SNP Function Portal: a web database for exploring the function implication
of SNP alleles
Pinglang Wang, Manhong Dai, Weijian Xuan, Richard C. McEachin, Anne U.
Jackson, Laura J. Scott, Brian Athey, Stanley J. Watson, and Fan Meng
Bioinformatics 2006 22: 523-529.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e523?etoc OPEN ACCESS ARTICLE
Protein classification using ontology classification
K. Wolstencroft, P. Lord, L. Tabernero, A. Brass, and R. Stevens
Bioinformatics 2006 22: 530-538.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e530?etoc OPEN ACCESS ARTICLE
Inferring Functional Pathways from Multi-Perturbation Data
Nir Yosef, Alon Kaufman, and Eytan Ruppin
Bioinformatics 2006 22: 539-546.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e539?etoc OPEN ACCESS ARTICLE
Accessing bioscience images from abstract sentences
Hong Yu and Minsuk Lee
Bioinformatics 2006 22: 547-556.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e547?etoc OPEN ACCESS ARTICLE
A sequence-based filtering method for ncRNA identification and its
application to searching for riboswitch elements
Shaojie Zhang, Ilya Borovok, Yair Aharonowitz, Roded Sharan, and Vineet
Bafna
Bioinformatics 2006 22: 557-565.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e557?etoc Author Index
Bioinformatics 2006 22: 567-568.
http://bioinformatics.oxfordjournals.org/cgi/reprint/22/14/e567?etoc-----------------------------------------------------------------
GENOME ANALYSIS
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Method for identifying transcription factor binding sites in yeast
Huai-Kuang Tsai, Grace Tzu-Wei Huang, Meng-Yuan Chou, Henry Horng-Shing
Lu, and Wen-Hsiung Li
Bioinformatics 2006 22: 1675-1681.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1675?etoc Combining multiple microarrays in the presence of controlling variables
Taesung Park, Sung-Gon Yi, Young Kee Shin, and SeungYeoun Lee
Bioinformatics 2006 22: 1682-1689.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1682?etoc Combo: a whole genome comparative browser
Reinhard Engels, Tamara Yu, Chris Burge, Jill P. Mesirov, David DeCaprio,
and James E. Galagan
Bioinformatics 2006 22: 1782-1783.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1782?etoc-----------------------------------------------------------------
SEQUENCE ANALYSIS
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Ribosomal RNA as molecular barcodes: a simple correlation analysis without
sequence alignment
K. H. Chu, C. P. Li, and J. Qi
Bioinformatics 2006 22: 1690-1701.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1690?etoc TSSub: eukaryotic protein subcellular localization by extracting features
from profiles
Jian Guo and Yuanlie Lin
Bioinformatics 2006 22: 1784-1785.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1784?etoc-----------------------------------------------------------------
STRUCTURAL BIOINFORMATICS
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PROXIMO--a new docking algorithm to model protein complexes using data
from radical probe mass spectrometry (RP-MS)
Sebastien K. Gerega and Kevin M. Downard
Bioinformatics 2006 22: 1702-1709.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1702?etoc Molecular complexes at a glance: automated generation of two-dimensional
complex diagrams
Katrin Stierand, Patrick C. Maass, and Matthias Rarey
Bioinformatics 2006 22: 1710-1716.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1710?etoc Ensemble classifier for protein fold pattern recognition
Hong-Bin Shen and Kuo-Chen Chou
Bioinformatics 2006 22: 1717-1722.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1717?etoc SCARNA: fast and accurate structural alignment of RNA sequences by
matching fixed-length stem fragments
Yasuo Tabei, Koji Tsuda, Taishin Kin, and Kiyoshi Asai
Bioinformatics 2006 22: 1723-1729.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1723?etoc TopoICE-R: 3D visualization modeling the topology of DNA recombination
Isabel K. Darcy and Robert G. Scharein
Bioinformatics 2006 22: 1790-1791.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1790?etoc FCP: functional coverage of the proteome by structures
Ricard Garcia-Serna, Lulla Opatowski, and Jordi Mestres
Bioinformatics 2006 22: 1792-1793.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1792?etoc SHARP2: protein-protein interaction predictions using patch analysis
Yoichi Murakami and Susan Jones
Bioinformatics 2006 22: 1794-1795.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1794?etoc Analysis assistant for single-molecule force spectroscopy data on membrane
proteins--MPTV
Frank Mueller, Daniel J. Muller, and Dirk Labudde
Bioinformatics 2006 22: 1796-1799.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1796?etoc OPEN ACCESS ARTICLE
Prelude&Fugue, predicting local protein structure, early folding regions
and structural weaknesses
Jean Marc Kwasigroch and Marianne Rooman
Bioinformatics 2006 22: 1800-1802.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1800?etoc BDT: an easy-to-use front-end application for automation of massive
docking tasks and complex docking strategies with AutoDock
Montserrat Vaque, Anna Arola, Carles Aliagas, and Gerard Pujadas
Bioinformatics 2006 22: 1803-1804.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1803?etoc-----------------------------------------------------------------
GENE EXPRESSION
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How accurately can we control the FDR in analyzing microarray data?
Sin-Ho Jung and Woncheol Jang
Bioinformatics 2006 22: 1730-1736.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1730?etoc Context-specific infinite mixtures for clustering gene expression profiles
across diverse microarray dataset
X. Liu, S. Sivaganesan, K. Y. Yeung, J. Guo, R. E. Bumgarner, and Mario
Medvedovic
Bioinformatics 2006 22: 1737-1744.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1737?etoc A Mixture model with random-effects components for clustering correlated
gene-expression profiles
S. K. Ng, G. J. McLachlan, K. Wang, L. Ben-Tovim Jones, and S.-W. Ng
Bioinformatics 2006 22: 1745-1752.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1745?etoc A probabilistic dynamical model for quantitative inference of the
regulatory mechanism of transcription
Guido Sanguinetti, Magnus Rattray, and Neil D. Lawrence
Bioinformatics 2006 22: 1753-1759.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1753?etoc Identification of humoral immune responses in protein microarrays using
DNA microarray data analysis techniques
Suman Sundaresh, Denise L. Doolan, Siddiqua Hirst, Yunxiang Mu, Berkay
Unal, D. Huw Davies, Philip L. Felgner, and Pierre Baldi
Bioinformatics 2006 22: 1760-1766.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1760?etoc-----------------------------------------------------------------
SYSTEMS BIOLOGY
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Observing local and global properties of metabolic pathways: 'load points'
and 'choke points' in the metabolic networks
Syed Asad Rahman and Dietmar Schomburg
Bioinformatics 2006 22: 1767-1774.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1767?etoc Synchronizing a multicellular system by external input: an artificial
control strategy
Ruiqi Wang, Luonan Chen, and Kazuyuki Aihara
Bioinformatics 2006 22: 1775-1781.
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/1775?etoc BIOCHAM: an environment for modeling biological systems and formalizing
experimental knowledge
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