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BMC Bioinformatics, Volume 10

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Volume 10, 2009

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Shuangge Ma, Jian Huang:
Regularized gene selection in cancer microarray meta-analysis.
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  - journals/bmcbi/DurinckBSD09
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Steffen Durinck, James H. Bullard, Paul T. Spellman, Sandrine Dudoit:
GenomeGraphs: integrated genomic data visualization with R.
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  - journals/bmcbi/FerrantiniAHC09
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Alessandro Ferrantini, Joke Allemeersch, Paul van Hummelen, Enrico Carlon:
Thermodynamic scaling behavior in genechips.
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  - journals/bmcbi/YangHY09
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Chao Yang, Zengyou He, Weichuan Yu:
Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis.
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  - journals/bmcbi/CaoXZWW09
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Jing Cao, Xian-Jin Xie, Song Zhang, Angelique Whitehurst, Michael A. White:
Bayesian optimal discovery procedure for simultaneous significance testing.
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  - journals/bmcbi/BacarditSHVSK09
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Jaume Bacardit, Michael Stout, Jonathan D. Hirst, Alfonso Valencia, Robert Elliott Smith, Natalio Krasnogor:
Automated Alphabet Reduction for Protein Datasets.
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  - journals/bmcbi/HackenbergLM09
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Michael Hackenberg, Gorka Lasso, Rune Matthiesen:
ContDist: a tool for the analysis of quantitative gene and promoter properties.
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  - journals/bmcbi/HanZNF09
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Pengfei Han, Xiuzhen Zhang, Raymond S. Norton, Zhi-Ping Feng:
Large-scale prediction of long disordered regions in proteins using random forests.
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  - journals/bmcbi/YoneyaN09
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Takashi Yoneya, Reina Nishida:
TCP: a tool for designing chimera proteins based on the tertiary structure information.
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  - journals/bmcbi/RancoitaHBK09
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Paola M. V. Rancoita, Marcus Hutter, Francesco Bertoni, Ivo Kwee:
Bayesian DNA copy number analysis.
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  - journals/bmcbi/HackstadtH09
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Amber J. Hackstadt, Ann M. Hess:
Filtering for increased power for microarray data analysis.
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  - journals/bmcbi/WangLLBW09
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Kai Wang, Jian Li, Shengting Li, Lars Bolund, Carsten Wiuf:
Estimation of tumor heterogeneity using CGH array data.
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  - journals/bmcbi/WanYYXTY09
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Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson L. S. Tang, Weichuan Yu:
MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study.
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  - journals/bmcbi/XuWLZX09
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Yun Xu, ZhiHao Wang, YiMing Lei, YuZhong Zhao, Yu Xue:
MBA: a literature mining system for extracting biomedical abbreviations.
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  - journals/bmcbi/LiangWL09
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Kuo-ching Liang, Xiaodong Wang, Ta-Hsin Li:
Robust discovery of periodically expressed genes using the laplace periodogram.
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  - journals/bmcbi/Martin-RequenaMCT09
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Victoria Martin-Requena, Antonio Muñoz-Merida, M. Gonzalo Claros, Oswaldo Trelles:
PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data.
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  - journals/bmcbi/ChipmanS09
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Kyle C. Chipman, Ambuj K. Singh:
Predicting genetic interactions with random walks on biological networks.
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  - journals/bmcbi/BinderS09
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Harald Binder, Martin Schumacher:
Incorporating pathway information into boosting estimation of high-dimensional risk prediction models.
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  - journals/bmcbi/HashimotoNKM09
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Tatsunori B. Hashimoto, Masao Nagasaki, Kaname Kojima, Satoru Miyano:
BFL: a node and edge betweenness based fast layout algorithm for large scale networks.
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  - journals/bmcbi/HuQGKY09
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Rui Hu, Xing Qiu, Galina V. Glazko, Lev Klebanov, Andrei Yakovlev:
Detecting intergene correlation changes in microarray analysis: a new approach to gene selection.
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  - journals/bmcbi/FrechKDKHBO09
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Christian Frech, Michael Kommenda, Viktoria Dorfer, Thomas Kern, Helmut Hintner, Johann W. Bauer, Kamil Önder:
Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis.
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  - journals/bmcbi/KumarR09
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Manish Kumar, Gajendra P. S. Raghava:
Prediction of nuclear proteins using SVM and HMM models.
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  - journals/bmcbi/DattaZ09
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Debayan Datta, Hongyu Zhao:
Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data.
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Tsong Yueh Chen, Joshua W. K. Ho, Huai Liu, Xiaoyuan Xie:
An innovative approach for testing bioinformatics programs using metamorphic testing.
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  - journals/bmcbi/BrownA09
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J. B. Brown, Tatsuya Akutsu:
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology.
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Sonia H. Shah, Jacqueline A. Pallas:
Identifying differential exon splicing using linear models and correlation coefficients.
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  - journals/bmcbi/MaulikMB09
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Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay:
Combining Pareto-optimal clusters using supervised learning for identifying co-expressed genes.
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  - journals/bmcbi/AlexopoulouADDGHKSW09
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Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien L. Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder, Thomas Wächter:
Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy.
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  - journals/bmcbi/LiuFR09
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Yu-Shen Liu, Yi Fang, Karthik Ramani:
Using least median of squares for structural superposition of flexible proteins.
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  - journals/bmcbi/BergKMB09
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Bart H. J. van den Berg, Jay H. Konieczka, Fiona M. McCarthy, Shane C. Burgess:
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.
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  - journals/bmcbi/ArakawaTKKIOT09
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Kazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa, Masaru Tomita:
Genome Projector: zoomable genome map with multiple views.
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  - journals/bmcbi/SteinkellnerRTKG09
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Georg Steinkellner, Robert Rader, Gerhard G. Thallinger, Christoph Kratky, Karl Gruber:
VASCo: computation and visualization of annotated protein surface contacts.
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  - journals/bmcbi/ArrigoTEGA09
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Nils Arrigo, Jarek W. Tuszynski, Dorothee Ehrich, Tommy Gerdes, Nadir Alvarez:
Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring.
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  - journals/bmcbi/CaoMRB09
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Kim-Anh Lê Cao, Pascal G. P. Martin, Christèle Robert-Granié, Philippe Besse:
Sparse canonical methods for biological data integration: application to a cross-platform study.
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  - journals/bmcbi/WarrenS09
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Andrew S. Warren, João Carlos Setubal:
The Genome Reverse Compiler: an explorative annotation tool.
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  - journals/bmcbi/ParkRGKK09
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Sung-Hee Park, José A. Reyes, David R. Gilbert, Ji Woong Kim, Sangsoo Kim:
Prediction of protein-protein interaction types using association rule based classification.
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  - journals/bmcbi/Glez-PenaADF09
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Daniel Glez-Peña, Rodrigo Álvarez, Fernando Díaz, Florentino Fdez-Riverola:
DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data.
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  - journals/bmcbi/NilssonBT09
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Roland Nilsson, Johan Björkegren, Jesper Tegnér:
On reliable discovery of molecular signatures.
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  - journals/bmcbi/KummerfeldT09
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Sarah K. Kummerfeld, Sarah A. Teichmann:
Protein domain organisation: adding order.
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  - journals/bmcbi/JonnalagaddaS09
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Sudhakar Jonnalagadda, Rajagopalan Srinivasan:
NIFTI: An evolutionary approach for finding number of clusters in microarray data.
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  - journals/bmcbi/KraemerBGHLMPF09
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Lars Kraemer, Bánk Beszteri, Steffi Gäbler-Schwarz, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Stephan Frickenhaus:
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
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  - journals/bmcbi/PopoviciGAJDW09
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Vlad Popovici, Darlene R. Goldstein, Janine Antonov, Rolf Jaggi, Mauro Delorenzi, Pratyaksha Wirapati:
Selecting control genes for RT-QPCR using public microarray data.
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  - journals/bmcbi/LiR09
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Qingbo Li, Bryan A. P. Roxas:
An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters.
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  - journals/bmcbi/ChenHCH09
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Pei-Chun Chen, Su-Yun Huang, Wei J. Chen, Chuhsing Kate Hsiao:
A new regularized least squares support vector regression for gene selection.
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  - journals/bmcbi/MurieWLN09
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Carl Murie, Owen Z. Woody, Anna Y. Lee, Robert Nadon:
Comparison of small n statistical tests of differential expression applied to microarrays.
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  - journals/bmcbi/Lin09
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Jimmy J. Lin:
Is searching full text more effective than searching abstracts?
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  - journals/bmcbi/AckermannS09
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Marit Ackermann, Korbinian Strimmer:
A general modular framework for gene set enrichment analysis.
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  - journals/bmcbi/EdenNSLY09
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Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini:
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.
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  - journals/bmcbi/BarlatiCM09
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Sergio Barlati, Sergio Chiesa, Chiara Magri:
"GenotypeColour^TM": colour visualisation of SNPs and CNVs.
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  - journals/bmcbi/DondrupAGHJKKKLMMNRTTPG09
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Michael Dondrup, Stefan P. Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K. Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J. Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann:
EMMA 2 - A MAGE-compliant system for the collaborative analysis and integration of microarray data.
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  - journals/bmcbi/ClementeIVG09
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José Carlos Clemente, Kazuho Ikeo, Gabriel Valiente, Takashi Gojobori:
Optimized ancestral state reconstruction using Sankoff parsimony.
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  - journals/bmcbi/ThissenWBBKKDOS09
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Uwe Thissen, Suzan Wopereis, Sjoerd A. A. van den Berg, Ivana Bobeldijk, Robert Kleemann, Teake Kooistra, Ko Willems van Dijk, Ben van Ommen, Age K. Smilde:
Improving the analysis of designed studies by combining statistical modelling with study design information.
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  - journals/bmcbi/ZervakisBTDTK09
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Michalis E. Zervakis, Michalis E. Blazadonakis, Georgia Tsiliki, Vasiliki Danilatou, Manolis Tsiknakis, Dimitris Kafetzopoulos:
Outcome prediction based on microarray analysis: a critical perspective on methods.
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  - journals/bmcbi/FischerENBSM09
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André Fischer, Nils Enkler, Gerd Neudert, Marco Bocola, Reinhard Sterner, Rainer Merkl:
TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis.
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  - journals/bmcbi/YangA09
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Eric Yang, Ioannis P. Androulakis:
Assessing and selecting gene expression signals based upon the quality of the measured dynamics.
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  - journals/bmcbi/DiazKGNN09
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Naryttza N. Diaz, Lutz Krause, Alexander Goesmann, Karsten Niehaus, Tim W. Nattkemper:
TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach.
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  - journals/bmcbi/ErillO09
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Ivan Erill, Michael C. O'Neill:
A reexamination of information theory-based methods for DNA-binding site identification.
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  - journals/bmcbi/LiZZLKLWJ09
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Honglin Li, Hailei Zhang, Mingyue Zheng, Jie Luo, Ling Kang, Xiaofeng Liu, Xicheng Wang, Hualiang Jiang:
An effective docking strategy for virtual screening based on multi-objective optimization algorithm.
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  - journals/bmcbi/LoevenichBKDSAH09
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Sandra N. Loevenich, Erich Brunner, Nichole L. King, Eric W. Deutsch, Stephen E. Stein, Ruedi Aebersold, Ernst Hafen:
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation.
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  - journals/bmcbi/LeaderM09
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David P. Leader, E. James Milner-White:
Motivated Proteins: A web application for studying small three-dimensional protein motifs.
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  - journals/bmcbi/ChiognaMRR09
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Monica Chiogna, Maria Sofia Massa, Davide Risso, Chiara Romualdi:
A comparison on effects of normalisations in the detection of differentially expressed genes.
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  - journals/bmcbi/PihurDD09
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Vasyl Pihur, Susmita Datta, Somnath Datta:
RankAggreg, an R package for weighted rank aggregation.
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  - journals/bmcbi/YuGZAS09
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Zhaoxia Yu, Chad Garner, Argyrios Ziogas, Hoda Anton-Culver, Daniel J. Schaid:
Genotype determination for polymorphisms in linkage disequilibrium.
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  - journals/bmcbi/MuldersBC09
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Geert C. W. M. Mulders, Gerard T. Barkema, Enrico Carlon:
Inverse Langmuir method for oligonucleotide microarray analysis.
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  - journals/bmcbi/HanZ09
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Leng Han, Zhongming Zhao:
CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome?
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  - journals/bmcbi/BottingTBSD09
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Shaleen K. Botting, Jerome P. Trzeciakowski, Michelle F. Benoit, Salama A. Salama, Concepcion R. Diaz-Arrastia:
Sample entropy analysis of cervical neoplasia gene-expression signatures.
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Karen Eilbeck, Barry Moore, Carson Holt, Mark Yandell:
Quantitative measures for the management and comparison of annotated genomes.
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  - journals/bmcbi/SampsonZ09
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Joshua N. Sampson, Hongyu Zhao:
Genotyping and inflated type I error rate in genome-wide association case/control studies.
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Douglas W. Bryant Jr., Weng-Keen Wong, Todd C. Mockler:
QSRA - a quality-value guided de novo short read assembler.
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Anna Maria Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Lieberman, Chris Mungall, Richard H. Scheuermann, Barry Smith, Lindsay G. Cowell:
An improved ontological representation of dendritic cells as a paradigm for all cell types.
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Atsushi Niida, Andrew D. Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama:
Gene set-based module discovery in the breast cancer transcriptome.
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Amalia Annest, Roger Eugene Bumgarner, Adrian E. Raftery, Ka Yee Yeung:
Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data.
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Jing Chen, Bruce J. Aronow, Anil G. Jegga:
Disease candidate gene identification and prioritization using protein interaction networks.
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  - journals/bmcbi/VisneDVLYWNLK09
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Ilhami Visne, Erkan Dilaveroglu, Klemens Vierlinger, Martin Lauss, Ahmet Yildiz, Andreas Weinhäusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner:
RGG: A general GUI Framework for R scripts.
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Tobias Gebäck, Petros Koumoutsakos:
Edge detection in microscopy images using curvelets.
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Yair Horesh, Ydo Wexler, Ilana Lebenthal, Michal Ziv-Ukelson, Ron Unger:
RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry.
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Donna M. Toleno, Gabriel Renaud, Tyra G. Wolfsberg, Munirul Islam, Derek E. Wildman, Kimberly D. Siegmund, Joseph G. Hacia:
Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees.
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Yan A. Meng, Yi Yu, L. Adrienne Cupples, Lindsay A. Farrer, Kathryn L. Lunetta:
Performance of random forest when SNPs are in linkage disequilibrium.
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  - journals/bmcbi/BoyleRCBKS09
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John Boyle, Hector Rovira, Christopher C. Cavnor, David B. Burdick, Sarah A. Killcoyne, Ilya Shmulevich:
Adaptable data management for systems biology investigations.
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Chao Xie, Martti T. Tammi:
CNV-seq, a new method to detect copy number variation using high-throughput sequencing.
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  - journals/bmcbi/TeuberWSF09
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Markus Teuber, Michael H. Wenz, Stefan Schreiber, Andre Franke:
GMFilter and SXTestPlate: software tools for improving the SNPlex^TM genotyping system.
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  - journals/bmcbi/WilczynskiDPT09
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Bartek Wilczynski, Norbert Dojer, Mateusz Patelak, Jerzy Tiuryn:
Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs.
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  - journals/bmcbi/WangSCRMQHJX09
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Tao Wang, Kang Shao, Qinying Chu, Yanfei Ren, Yiming Mu, Lijia Qu, Jie He, Changwen Jin, Bin Xia:
Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis.
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Mickaël Guedj, Stéphane Robin, Alain Celisse, Grégory Nuel:
Kerfdr: a semi-parametric kernel-based approach to local false discovery rate estimation.
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  - journals/bmcbi/LiuCCTLPCKHLJLCH09
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Li-Yu D. Liu, Chien-Yu Chen, Mei-Ju May Chen, Ming-Shian Tsai, Cho-Han S. Lee, Tzu L. Phang, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Huang-Chun Lien, Shih-Ming Jung, Yi-Shing Lin, King-Jen Chang, Fon-Jou Hsieh:
Statistical identification of gene association by CID in application of constructing ER regulatory network.
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  - journals/bmcbi/LinCLS09
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Frank P. Y. Lin, Enrico W. Coiera, Ruiting Lan, Vitali Sintchenko:
In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles.
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Navdeep Jaitly, Anoop M. Mayampurath, Kyle Littlefield, Joshua N. Adkins, Gordon A. Anderson, Richard D. Smith:
Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.
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Qi Liu, Jinling Huang, Huiqing Liu, Ping Wan, Xiuzi Ye, Ying Xu:
Analyses of domains and domain fusions in human proto-oncogenes.
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  - journals/bmcbi/KnollHWMP09
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Michael Knoll, Thomas M. Hamm, Florian Wagner, Virginia Martinez, Jürgen Pleiss:
The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases.
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  - journals/bmcbi/MarttinenMC09
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Pekka Marttinen, Samuel Myllykangas, Jukka Corander:
Bayesian clustering and feature selection for cancer tissue samples.
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  - journals/bmcbi/SnipenNSAN09
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Lars Snipen, Otto L. Nyquist, Margrete Solheim, Ågot Aakra, Ingolf F. Nes:
Improved analysis of bacterial CGH data beyond the log-ratio paradigm.
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  - journals/bmcbi/KaeverLFGFM09
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Alexander Kaever, Thomas Lingner, Kirstin Feussner, Cornelia Göbel, Ivo Feussner, Peter Meinicke:
MarVis: a tool for clustering and visualization of metabolic biomarkers.
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  - journals/bmcbi/Zare-MirakabadASNG09
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Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdi Sadeghi, Abbas Nowzari-Dalini, Bahram Goliaei:
New scoring schema for finding motifs in DNA Sequences.
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  - journals/bmcbi/HamiltonWKT09
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Nicholas A. Hamilton, Jack T. H. Wang, Markus C. Kerr, Rohan D. Teasdale:
Statistical and visual differentiation of subcellular imaging.
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  - journals/bmcbi/MacPhersonPR09
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Jamie I. MacPherson, John W. Pinney, David L. Robertson:
JNets: Exploring networks by integrating annotation.
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  - journals/bmcbi/BillupsNRPS09
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Stephen C. Billups, Margaret C. Neville, Michael Rudolph, Weston Porter, Pepper Schedin:
Identifying significant temporal variation in time course microarray data without replicates.
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  - journals/bmcbi/BuschW09
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Norbert Busch, Gero Wedemann:
Modeling genomic data with type attributes, balancing stability and maintainability.
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  - journals/bmcbi/GlatignyDTFAM09
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Annie Glatigny, Hervé Delacroix, Thomas Tang, Nicolas François, Lawrence Aggerbeck, Marie-Hélène Mucchielli-Giorgi:
Characterisation and correction of signal fluctuations in successive acquisitions of microarray images.
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  - journals/bmcbi/VlasblomW09
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James Vlasblom, Shoshana J. Wodak:
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs.
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  - journals/bmcbi/AlmeidaV09
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Jonas S. Almeida, Susana Vinga:
Biological sequences as pictures - a generic two dimensional solution for iterated maps.
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  - journals/bmcbi/LiuBOWLJ09
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Xiaofeng Liu, Fang Bai, Sisheng Ouyang, Xicheng Wang, Honglin Li, Hualiang Jiang:
Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation.
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  - journals/bmcbi/ChaiSBTAK09
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High-Seng Chai, Hugues Sicotte, Kent R. Bailey, Stephen T. Turner, Yan W. Asmann, Jean-Pierre A. Kocher:
GLOSSI: a method to assess the association of genetic loci-sets with complex diseases.
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  - journals/bmcbi/PalBRC09
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Arumay Pal, Ranjit Prasad Bahadur, Partha Sarathi Ray, Pinak Chakrabarti:
Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display.
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  - journals/bmcbi/EstradaBBS09
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Jorge Estrada, Pau Bernadó, Martin Blackledge, Javier Sancho:
ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble.
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  - journals/bmcbi/AhmedAR09
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Firoz Ahmed, Hifzur Rahman Ansari, Gajendra P. S. Raghava:
Prediction of guide strand of microRNAs from its sequence and secondary structure.
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  - journals/bmcbi/HahneLBEHSSSG09
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Florian Hahne, Nolwenn LeMeur, Ryan R. Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, Robert Gentleman:
flowCore: a Bioconductor package for high throughput flow cytometry.
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  - journals/bmcbi/ArakakiHS09
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Adrian K. Arakaki, Ying Huang, Jeffrey Skolnick:
EFICAz²: enzyme function inference by a combined approach enhanced by machine learning.
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  - journals/bmcbi/HariharanSB09
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Manoj Hariharan, Vinod Scaria, Samir K. Brahmachari:
dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation.
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  - journals/bmcbi/ChoKK09
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Sung-Bum Cho, Jihun Kim, Ju Han Kim:
Identifying set-wise differential co-expression in gene expression microarray data.
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  - journals/bmcbi/MarKSIHSHQ09
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Jessica C. Mar, Yasumasa Kimura, Kate Schroder, Katharine M. Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David A. Hume, John Quackenbush:
Data-driven normalization strategies for high-throughput quantitative RT-PCR.
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  - journals/bmcbi/RileyYSL09
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Todd Riley, Xin Yu, Eduardo Sontag, Arnold Levine:
The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes.
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  - journals/bmcbi/Poleksic09
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Aleksandar Poleksic:
Island method for estimating the statistical significance of profile-profile alignment scores.
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  - journals/bmcbi/ExarchosEPTF09
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Costas P. Exarchos, Themis P. Exarchos, Costas Papaloukas, Anastassios N. Troganis, Dimitrios I. Fotiadis:
Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation.
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  - journals/bmcbi/LeeCCYHTLWKH09
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Sheng-An Lee, Chen-hsiung Chan, Tzu-Chi Chen, Chia-Ying Yang, Kuo-Chuan Huang, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, Chi-Ying F. Huang:
POINeT: protein interactome with sub-network analysis and hub prioritization.
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  - journals/bmcbi/CaiSWGWXSL09
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Zhipeng Cai, Hadi Sabaa, Yining Wang, Randy Goebel, Zhiquan Wang, Jiaofen Xu, Paul Stothard, Guohui Lin:
Most parsimonious haplotype allele sharing determination.
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  - journals/bmcbi/PrevitiHZV09
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Christopher Previti, Oscar Harari, Igor Zwir, Coral del Val:
Profile analysis and prediction of tissue-specific CpG island methylation classes.
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  - journals/bmcbi/DurekSWSW09
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Pawel Durek, Christian Schudoma, Wolfram Weckwerth, Joachim Selbig, Dirk Walther:
Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins.
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  - journals/bmcbi/JossKLPGSDB09
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Michael J. Joss, Jeremy E. Koenig, Maurizio Labbate, Martin F. Polz, Michael R. Gillings, Harold W. Stokes, W. Ford Doolittle, Yan Boucher:
ACID: annotation of cassette and integron data.
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  - journals/bmcbi/JiLZKY09
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Shuiwang Ji, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye:
A bag-of-words approach for Drosophila gene expression pattern annotation.
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  - journals/bmcbi/TannierZS09
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Eric Tannier, Chunfang Zheng, David Sankoff:
Multichromosomal median and halving problems under different genomic distances.
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  - journals/bmcbi/FukudaNDTGMKANT09
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Yoko Fukuda, Yasuo Nakahara, Hidetoshi Date, Yuji Takahashi, Jun Goto, Akinori Miyashita, Ryozo Kuwano, Hiroki Adachi, Eiji Nakamura, Shoji Tsuji:
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data.
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  - journals/bmcbi/ZouF09
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Cunlu Zou, Jianfeng Feng:
Granger causality vs. dynamic Bayesian network inference: a comparative study.
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  - journals/bmcbi/WuXXXYGLBZL09
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Jinyu Wu, Xiang Xu, Jian Xiao, Long Xu, Huiguang Yi, Shengjie Gao, Jing Liu, Qiyu Bao, Fangqing Zhao, Xiaokun Li:
FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families.
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  - journals/bmcbi/SorzanoMEBHNMC09
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Carlos Oscar Sánchez Sorzano, Cédric Messaoudi, Matthias Eibauer, Jose-Roman Bilbao-Castro, Reiner Hegerl, S. Nickell, Sergio Marco, José María Carazo:
Marker-free image registration of electron tomography tilt-series.
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  - journals/bmcbi/SchoberSLKLMTRS09
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Daniel Schober, Barry Smith, Suzanna E. Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F. Taylor, Philippe Rocca-Serra, Susanna-Assunta Sansone:
Survey-based naming conventions for use in OBO Foundry ontology development.
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