linguistically motivated perspective (2009)
Bmc Bioinformatics, Halil Kilicoglu, Sabine Bergler
This is an open access article distributed under the terms of the Creative Commons Attribution License
Version VI of the ESTree db: an improved tool for peach (2009)
Bmc Bioinformatics, Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli, Francesca Barale, ...
transcriptome analysis
Bmc Bioinformatics, Robert R Delongchamp, Cruz Velasco, Stacey Dial, Angela J Harris
Proceedings Genome-wide estimation of gender differences in the gene expression of human livers: Statistical design and analysis
Bmc Bioinformatics, Nameeta Shah, Michael V Teplitsky, Simon Minovitsky, Len A Pennacchio, Philip Hugenholtz, ...
Software SNP-VISTA: An interactive SNP visualization tool
Emerging strengths in Asia Pacific bioinformatics (2009)
Bmc Bioinformatics, Shoba Ranganathan, Wen-lian Hsu, Ueng-cheng Yang, Wee Tan
Bmc Bioinformatics, N Ancona, R Maglietta, A Piepoli, R Cotugno, M Savino, ...
Research article On the statistical assessment of classifiers using DNA microarray data
BioMed Central Research How to make the most of NE dictionaries in statistical NER (2009)
Bmc Bioinformatics, Yutaka Sasaki, Yoshimasa Tsuruoka, John Mcnaught, Sophia Ananiadou, John Mcnaught, ...
growth of a wide range of repositories of biomedical data and literature. The automatic construction and update of scientific knowledge bases is a major research topic in Biofrom
Bmc Bioinformatics, Tao Han, Jianyong Wang, Weida Tong, Martha M Moore, James C Fuscoe, ...
Proceedings Microarray analysis distinguishes differential gene expression patterns from large and small colony Thymidine kinase mutants of L5178Y mouse lymphoma cells
The BioScope corpus: biomedical texts annotated for uncertainty, (2009)
Bmc Bioinformatics, Veronika Vincze, György Szarvas, Richárd Farkas, György Móra, János Csirik
negation and their scopes
Bmc Bioinformatics, Yong Seok Lee, Tae-hyung Kim, Tae-wook Kang, Won-hyong Chung, Gwang-sik Shin
WSPMaker: a web tool for calculating selection pressure in proteins and domains using window-sliding
Bmc Bioinformatics, Yong Tang, Yingfeng Chen, Cheryl F Lichti, Roger A Hall, Kevin D Raney, ...
doi:10.1186/1471-2105-6-S2-S9 <supplement> <title> <p>Second Annual MidSouth Computational Biology and Bioinformatics Society Conference. Bioinformatics: a systems...
Bmc Bioinformatics, Taewon Lee, Varsha G Desai, Cruz Velasco, Robert J Reis, Robert R Delongchamp
Proceedings
Bmc Bioinformatics, Zhenqiang Su, Huixiao Hong, Hong Fang, Leming Shi, Roger Perkins, ...
Proceedings Very Important Pool (VIP) genes – an application for microarray-based molecular signatures
Bmc Bioinformatics, Hapmap Samples, Huixiao Hong, Zhenqiang Su, Weigong Ge, Leming Shi, ...
Proceedings Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270
Bmc Bioinformatics, Margherita Mutarelli, Luigi Cicatiello, Lorenzo Ferraro, Olì Mv Grober, Maria Ravo, ...
Time-course analysis of genome-wide gene expression data from
Bmc Bioinformatics, Federico E Turkheimer, Federico Roncaroli, Benoit Hennuy, Christian Herens, Minh Nguyen, ...
Research article Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas
Software High-throughput bioinformatics with the Cyrille2 pipeline system Mark WEJ Fiers, Ate van der Burgt, Erwin Datema, Joost CW de Groot and
Bmc Bioinformatics, Kang Ning, Hon Wai Leong, Kang Ning, Hon Wai Leong
Background: The problem of finding a Shortest Common Supersequence (SCS) of a set of sequences is an important problem with applications in many areas. It is a key problem in biological sequences...
The Seventh Asia Pacific Bioinformatics Conference (APBC 2009) (2009)
Bmc Bioinformatics, Qian Xu, Derek Hao Hu, Hong Xue, Weichuan Yu, Qiang Yang, ...
endoplasmic reticulum, cell nucleus and Golgi apparatus. These compartments play different roles, for instance, mitochondria supply chemical energy ATP for cell survive; chloroplasts transform light...
Bmc Bioinformatics, Yun Xu, Zhihao Wang, Yiming Lei, Yuzhong Zhao, Yu Xue
Research article MBA: a literature mining system for extracting biomedical abbreviations
Bmc Bioinformatics, Steffen Durinck, James Bullard, Paul T Spellman
Software GenomeGraphs: integrated genomic data visualization with R
Bmc Bioinformatics, J. B. Brown, Tatsuya Akutsu, J. B. Brown, Tatsuya Akutsu
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Identification of novel DNA repair...
Bmc Bioinformatics, Tatsunori B Hashimoto, Kaname Kojima, Satoru Miyano, Tatsunori B Hashimoto, Masao Nagasaki, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. BFL: a node and edge betweenness based...
Bmc Bioinformatics, Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Biomedical word sense disambiguation...
Bmc Bioinformatics, Guanrao Chen, Peter Larsen, Eyad Almasri, Yang Dai
Research article Rank-based edge reconstruction for scale-free genetic regulatory networks
Bmc Bioinformatics, Sohrab P Shah, David Ym He, Jessica N Sawkins, Jeffrey C Druce
Software Pegasys: software for executing and integrating analyses of biological sequences
Bmc Bioinformatics, William S S, Susan M Bridges, Fiona M Mccarthy, Bindu N, Shane C Burgess, ...
Proceedings Prediction of peptides observable by mass spectrometry applied at the experimental set level
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2008)
Bmc Bioinformatics, Manuela Helmer-citterich, Rita Casadio, Ro Guffanti, Giancarlo Mauri, Luciano Milanesi, ...
Bmc Bioinformatics, Mehdi Pirooznia, Youping Deng
SVM Classifier – a comprehensive java interface for support vector machine classification of microarray data
Bmc Bioinformatics, Christopher Jo Baker, Rajaraman Kanagasabai, Wee Tiong Ang, Anitha Veeramani, Hong-sang Low, ...
Proceedings
BioMed Central Proceedings Protein Ranking by Semi-Supervised Network Propagation (2008)
Bmc Bioinformatics, Jason Weston, Rui Kuang, Christina Leslie, William Stafford Noble
Background: Biologists regularly search DNA or protein databases for sequences that share an evolutionary or functional relationship with a given query sequence. Traditional search methods, such as...
The 2006 Automated Function Prediction Meeting (2008)
Bmc Bioinformatics, Barry J Grant, Adam Godzik, Iddo Friedberg
Bmc Bioinformatics, Andrey A Ptitsyn, Sanjin Zvonic, Jeffrey M Gimble
Proceedings
Bmc Bioinformatics, Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Wang, ...
Proceedings Motif-directed network component analysis for regulatory network inference
Bmc Bioinformatics, Michael Wagner, N Naik, Alex Pothen, Srinivas Kasukurti, Raghu Ram Devineni, ...
Computational protein biomarker prediction: a case study for
Bmc Bioinformatics, Zina Zhang, Maksim V. Plikus, Zina Zhang, Cheng-ming Chuong
This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon. PubFocus: Semantic...
BioMed Central Open Access (2008)
Bmc Bioinformatics, Hong-woo Chun, Yoshimasa Tsuruoka, Jin-dong Kim, Rie Shiba, Naoki Nagata, ...
Proceedings Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts
Distinguishing isoforms and paralogs on the protein level (2008)
Bmc Bioinformatics, Michael Spitzer, Stefan Lorkowski, Paul Cullen, Er Sczyrba, Georg Fuellen, ...
Research article
Research Constrained hidden Markov models for population-based haplotyping (2008)
Bmc Bioinformatics, Niels L, Taneli Mielikäinen, Lauri Eronen, Hannu Toivonen, Heikki Mannila
This is an open access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Vijayaraj Nagarajan, Navodit Kaushik, Beddhu Murali, Chaoyang Zhang, Sanyogita Lakhera, ...
Background: Naturally occurring antimicrobial peptides are currently being explored as potential candidate peptide drugs. Since antimicrobial peptides are part of the innate immune system of every...
Article type Methodology article (2008)
Bmc Bioinformatics, Herbert Pang, Hongyu Zhao, Herbert Pang, Hongyu Zhao
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Building pathway clusters from Random...
Bmc Bioinformatics, Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, ...
Validating module network learning algorithms using simulated data
Selective prediction of interaction sites in protein structures with THEMATICS (2008)
Bmc Bioinformatics, Ying Wei, Jaeju Ko, Leonel F Murga, Mary Jo Ondrechen, Jo Ondrechen
© 2007 Wei et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Clustering of gene expression data: performance and similarity (2008)
Background: DNA Microarray technology is an innovative methodology in experimental molecular biology, which has produced huge amounts of valuable data in the profile of gene expression. Many...
Bmc Bioinformatics, S June Oh, Je-gun Joung, Jeong-ho Chang, Byoung-tak Zhang
Research article Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks
Bmc Bioinformatics, Filip Pattyn, Jasmien Hoebeeck, Piet Robbrecht, Evi Michels, Anne De, ...
Research article methBLAST and methPrimerDB: web-tools for PCR based methylation analysis
Research Constrained hidden Markov models for population-based haplotyping (2008)
Bmc Bioinformatics, Niels L, Taneli Mielikäinen, Lauri Eronen, Hannu Toivonen, Heikki Mannila
This is an open access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Stephen A Racunas, Nigam H Shah, Nina V Fedoroff
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Soumya Ray, Mark Craven
2005 BMC Bioinformatics 2005, 6(Suppl 1):S18 doi:10.1186/1471-2105-6-S1-S18 <supplement> <title> <p>A critical assessment of text mining methods in molecular biology</p>...
Bmc Bioinformatics, S June Oh, Je-gun Joung, Jeong-ho Chang, Byoung-tak Zhang
Research article Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks
Bmc Bioinformatics, Björn H Junker, Dirk Koschützki, Falk Schreiber
of biological network centralities with CentiBiN
Bmc Bioinformatics, Tapio Pahikkala, Filip Ginter, Jorma Boberg, Jouni Järvinen, Tapio Salakoski
mining: an application to gene versus protein name disambiguation
Bmc Bioinformatics, Tao Han, Cathy D Melvin, Leming Shi, William S Branham, Carrie L Mol, ...
© 2006 Han et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Xiaoyi Gao, Joshua D Starmer, Open Access, Xiaoyi Gao, Joshua D Starmer
Software AWclust: point-and-click software for non-parametric population structure analysis
Signature Evaluation Tool (SET): a Java-based tool to evaluate and (2008)
Bmc Bioinformatics, Hung Lin, Ming-ta Hsu, Hsei-wei Wang
Software
Bmc Bioinformatics, Romesh Stanislaus, Balaji Rajagopalan, Rick Moerschell, Brian Mcglothlen, ...
Research article An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis
Bmc Bioinformatics, Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qingming Luo, ...
Proceedings GORouter: an RDF model for providing semantic query and
algorithm for clustering biological interactions (2008)
Bmc Bioinformatics, Woochang Hwang, Young-rae Cho, Aidong Zhang, Murali Ramanathan, Murali Ramanathan
CASCADE: a novel quasi all paths-based network analysis
Bmc Bioinformatics, Wouter Meuleman, Judith Ymn Engwegen, Jos H Beijnen, Marcel Jt Reinders, ...
Research article Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data
Article type Methodology article (2008)
Bmc Bioinformatics, Holger Schwender, Katja Ickstadt
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Empirical Bayes analysis of single...
Bmc Bioinformatics, Bolan Linghu, Evan S Snitkin, Dustin T Holloway, Adam M Gustafson, Yu Xia, ...
Research article High-precision high-coverage functional inference from integrated data sources
Bmc Bioinformatics, Jonathan D Moore, Shelagh P Kell, Jose M Iriondo, Nigel Maxted, ...
Software
Bmc Bioinformatics, Madhavi Ganapathiraju, N Balakrishnan, Raj Reddy, Biomed Central
Proceedings Transmembrane helix prediction using amino acid property features and latent semantic analysis
Generating samples for association studies based on HapMap data (2008)
Bmc Bioinformatics, Jing Li, Yixuan Chen
Software
Bmc Bioinformatics, Paul D Yoo, Abdur R Sikder, Bing Bing Zhou, Albert Y Zomaya
Proceedings Improved general regression network for protein domain boundary prediction
Bmc Bioinformatics, Changhui Yan, Jing Hu, Yingfeng Wang
Discrimination of outer membrane proteins with improved
Bmc Bioinformatics, Frédéric Chalmel, Michael Primig
Software The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology
Bmc Bioinformatics, Yeong Tae Kim, Hee Jung Cho
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Predicting the Interactome of...
Bmc Bioinformatics, Bmc Bioinformatics, Scott Christley, Neil F Lobo, Greg Madey, Scott Christley, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon.
Bmc Bioinformatics, Stefan Kurtz, David Ellinghaus, Stefan Kurtz, Ute Willhoeft
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. LTRharvest, an efficient and flexible...
Article type Methodology article (2008)
Bmc Bioinformatics, Kalman Somogyi, Botond Sipos, Kálmán Somogyi, István Andó, Zsolt Pénzes
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. t2prhd: a tool to study the patterns of...
Article type Methodology article (2008)
Bmc Bioinformatics, Wei-sheng Wu, Wen-hsiung Li
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Systematic identification of yeast cell...
Bmc Bioinformatics, Svetlin A Manavski, Giorgio Valle
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
BioMed Central Open Access (2008)
Research article Probe signal correction for differential methylation hybridization experiments
Structural assembly of two-domain proteins by rigid-body docking (2008)
Bmc Bioinformatics, Tammy Mk Cheng, Tom L Blundell, Juan Fern
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
XplorSeq: A software environment for integrated management and (2008)
Bmc Bioinformatics, Daniel N Frank
Software
© 2008 Saha et al; licensee BioMed Central Ltd Background (2008)
Bmc Bioinformatics, Surya Saha
Discovering relationships among dispersed repeats using spatial association rule mining Surya Saha * 1,2,3, Susan Bridges1,2, Zenaida Magbanua1,3,4 and
Bmc Bioinformatics, Biomed Central, Shengqi Wang
A novel representation of RNA secondary structure based on element-contact graphs
and gene expression information (2008)
Bmc Bioinformatics, Caroline Truntzer, Delphine Maucort-boulch, Pascal Roy, Biomed Central, Pascal Roy
Comparative optimism in models involving both classical clinical
Bmc Bioinformatics, Er Garcia, Anita Schwegmann, Rafael C Jimenez, Dan Jacobson, Henning Hermjakob, ...
Software
Bmc Bioinformatics, Guang Lan Zhang, Asif M Khan, Kellathur N Srinivasan, At Heiny, Kx Lee, ...
Proceedings Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes
Bmc Bioinformatics, Jesper Nielsen, Jesper Nielsen, Thomas Mailund
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. SNPFile- A software library and file...
Article type Methodology article (2008)
Bmc Bioinformatics, Hao Li, Katerina Kechris, Hao Li
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. c-REDUCE: Incorporating sequence...
Bmc Bioinformatics, Minghui Jiang, James Anderson, Joel Gillespie, Martin Mayne, Martin Mayne
Software uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts
Bmc Bioinformatics, Jerzy S Zielinski, Nidhal Bouaynaya, Dan Schonfeld
Proceedings
CellProfiler Analyst: data exploration and analysis software for (2008)
Bmc Bioinformatics, Thouis R Jones, In Han Kang, Douglas B Wheeler, Robert A Lindquist, Adam Papallo, ...
Software
Bmc Bioinformatics, Arnaud Krebs, Mattia Frontini, Làszlò Tora
Software GPAT: Retrieval of genomic annotation from large genomic position datasets
Bmc Bioinformatics, Xiaojing Wang, Di Wu, Siyuan Zheng, Jing Sun, Lin Tao, ...
Ab-origin: an enhanced tool to identify the sourcing gene segments
Bmc Bioinformatics, Christine Fong, Laurence Rohmer, Matthew Radey, Michael Wasnick
Software PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes
Bmc Bioinformatics, Eyal Gruntman, Yijun Qi, R Keith Slotkin, Ted Roeder, Robert A Martienssen, ...
Software Kismeth: Analyzer of plant methylation states through bisulfite sequencing
Bmc Bioinformatics, Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, ...
All-paths graph kernel for protein-protein interaction extraction
Bmc Bioinformatics, Alberto I Roca, Albert E Almada, Aaron C Abajian, Alberto I Roca, Albert E Almada, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. ProfileGrids as a new visual...
Bmc Bioinformatics, Marcin Pawlowski, Michal J Gajda, Ryszard Matlak, Janusz M Bujnicki
Software MetaMQAP: A meta-server for the quality assessment of protein models
Bmc Bioinformatics, Klaas J. Hofstede, Remko Silvis
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. DISCLOSE: DISsection of CLusters...
Bmc Bioinformatics, Hisakazu Iwama, Yukio Hori, Kensuke Matsumoto, Koji Murao, Toshihiko Ishida
Software ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences
Bmc Bioinformatics, Uta Bohnebeck, Thierry Lombardot, Renzo Kottmann
Software MetaMine – A tool to detect and analyse gene patterns in their environmental context
Bmc Bioinformatics, Chung-chin Lu, Wei-hao Yuan, Te-ming Chen
Extracting transcription factor binding sites from unaligned gene sequences with statistical models
Virtual screening of GPCRs: An in silico chemogenomics approach (2008)
Bmc Bioinformatics, Laurent Jacob, Brice Hoffmann, Véronique Stoven
© 2008 Jacob et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Yan Xin Huang, Yong Li Bao, Shu Yan Guo, Yan Wang, Chun Guang Zhou, ...
Software Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis
Bmc Bioinformatics, Lucia Peixoto, Nils Gehlenborg, Sarath Ch, Ra Janga
BMC Bioinformatics 2008, 9(Suppl 10):I1 doi:10.1186/1471-2105-9-S10-I1 <supplement> <title> <p>Highlights from the Fourth International Society for Computational Biology (ISCB)...
Research article Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks Iaroslav Ispolatov * 1,2 and Sergei Maslov3 Open Access
Proceedings Multivariate hierarchical Bayesian model for differential gene expression analysis in microarray experiments
Bmc Bioinformatics, Amber J Hackstadt, Ann M Hess, Amber J Hackstadt, Ann M Hess
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon.
Bmc Bioinformatics, Lesheng Kong, Shoba Ranganathan
Proceedings Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors
Bmc Bioinformatics, Richard Js Baerends, Aldert L Zomer, Oscar P Kuipers
Research article Supervised Lowess normalization of comparative genome hybridization data – application to lactococcal strain comparisons
Bmc Bioinformatics, Woo-yeon Kim, Sungsoo Kang, Byoung-chul Kim, Jeehyun Oh, Seongwoong Cho, ...
Proceedings SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803
: an Italian SOLAnaceae genomics resource (2008)
Bmc Bioinformatics, Maria Luisa Chiusano, Ra Traini, Concetta Licciardello, Enrico Raimondo, Mario Aversano, ...
This article is available from:
Shape-IT: new rapid and accurate algorithm for haplotype inference (2008)
Bmc Bioinformatics, Olivier Delaneau, Cédric Coulonges, Jean-françois Zagury
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Examining the significance of fingerprint-based classifiers (2008)
Bmc Bioinformatics, Brian T Luke, Jack R Collins, Brian T Luke, Jack R Collins
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: Experimental examinations of biofluids to measure...
Bmc Bioinformatics, Yuchen Yang, Yu-ping Wang, Kuo-bin Li
MiRTif: a support vector machine-based microRNA target interaction filter
Bmc Bioinformatics, Andreas Keller, Christina Backes, Maher Al-awadhi, Andreas Gerasch, Jan Küntzer, ...
Software GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments
Bmc Bioinformatics, Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay, Ujjwal Maulik, Anirban Mukhopadhyay, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Combining Pareto-optimal clusters using...
Fast splice site detection using information content and feature reduction
Bmc Bioinformatics, Thomas Naiser, Jona Kayser, Timo Mai, Wolfgang Michel, Albrecht Ott, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Position dependent mismatch...
Bmc Bioinformatics, Vladimir Paar, Nenad Pavin, Ivan Basar, Marija Rosandic, Matko Gluncic, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Hierarchical structure of cascade of...
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI (2008)
Bmc Bioinformatics, Anna-lena Lamprecht, Tiziana Margaria, Bernhard Steffen, Er Sczyrba, Sven Hartmeier, ...
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Bmc Bioinformatics, M Slawski, M Daumer, A-l Boulesteix
Software CMA – a comprehensive Bioconductor package for supervised classification with high dimensional data
BioMed Central Software SPRINT: A new parallel framework for R (2008)
Bmc Bioinformatics, Jon Hill, Matthew Hambley, Thorsten Forster, Muriel Mewissen, Terence M Sloan, ...
© 2008 Hill et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Accelerating the annotation of sparse named entities by dynamic sentence selection
Research article Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure
Snagger: A user-friendly program for incorporating additional (2008)
Bmc Bioinformatics, Christopher K Edlund, Won H Lee, Dalin Li, David V Conti
Software
BioMed Central Software CBESW: Sequence Alignment on the Playstation 3 (2008)
Bmc Bioinformatics, Adrianto Wirawan, Chee Keong Kwoh, Nim Tri Hieu, Bertil Schmidt, Bertil Schmidt
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Lawrence Hunter, Zhiyong Lu, James Firby, William A Baumgartner, Helen L Johnson, ...
Software OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene...
Bmc Bioinformatics, Robin P Smith, William J Buchser, Jose R Pardinas, John L Bixby, Vance P Lemmon
Software EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries
Bmc Bioinformatics, Jung Soh, Paul Mk Gordon, Morgan L Taschuk, Anguo Dong, ...
Software Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking
Bmc Bioinformatics, Tsong Yueh Chen, Joshua Wk Ho, Huai Liu, Xiaoyuan Xie, Tsong Yueh Chen, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. An innovative approach for testing...
Bmc Bioinformatics, Ro Orro, Guia Guffanti, Erika Salvi, Fabio Macciardi, Fabio Macciardi, ...
SNPLims: a data management system for genome wide association studies
Bmc Bioinformatics, Hong Huang Lin, Guang Lan Zhang, Songsak Tongchusak, Ellis L Reinherz, Vladimir Brusic, ...
Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research
BioMed Central Software IDEA: Interactive Display for Evolutionary Analyses (2008)
Bmc Bioinformatics, Amy Egan, Anup Mahurkar, Jonathan Crabtree, Jonathan H Badger, Jane M Carlton, ...
© 2008 Egan et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Bioconductor-compliant R package 'annotationTools' (2008)
Bmc Bioinformatics, Re Kuhn, Ruth Luthi-carter, Mauro Delorenzi, Open Access, Mauro Delorenzi
Software
Bmc Bioinformatics, Jin Ok Yang, Sohyun Hwang, Jeongsu Oh, Jong Bhak, Kwon Sohn, ...
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases
SWS: accessing SRS sites contents through Web Services (2008)
Bmc Bioinformatics, Paolo Romano, Domenico Marra
This is an open access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Wei Yu, Melinda Clyne, Siobhan M Dolan, Ajay Yesupriya, Anja Wulf, ...
Software GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique
Bmc Bioinformatics, Luigi Buonaguro, Ro Monaco, Eleonora Aricò, Ena Wang, Lina Tornesello, ...
Gene expression profile of peripheral blood mononuclear cells in response to HIV-VLPs stimulation
Bmc Bioinformatics, Ernesto Picardi, Carla Quagliariello
Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets
Bmc Bioinformatics, Sudhakar Jonnalagadda, Rajagopalan Srinivasan, Sudhakar Jonnalagadda, Rajagopalan Srinivasan
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. NIFTI: An evolutionary approach for...
Mining protein networks for synthetic genetic interactions (2008)
Bmc Bioinformatics, Sri R Paladugu, Shan Zhao, Animesh Ray, Alpan Raval
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, M Michael Gromiha, Yukimitsu Yabuki
Research article Functional discrimination of membrane proteins using machine learning techniques
Bmc Bioinformatics, Patrick E Meyer, Frédéric Lafitte, Gianluca Bontempi
© 2008 Meyer et al; licensee BioMed Central Ltd.
Bmc Bioinformatics, Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio, Rita Casadio
A three-state prediction of single point mutations on protein stability changes
Bmc Bioinformatics, Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne
Research article Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation
CellExcite: an efficient simulation environment for excitable cells (2008)
Bmc Bioinformatics, Ezio Bartocci, Flavio Corradini, Emilia Entcheva, Radu Grosu, Scott A Smolka, ...
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Bmc Bioinformatics, Johannes Tuikkala, Laura L Elo, Olli S Nevalainen, Tero Aittokallio
Research article Missing value imputation improves clustering and interpretation of gene expression microarray data
Bmc Bioinformatics, Peter Langfelder, Steve Horvath
Software WGCNA: an R package for weighted correlation network analysis
In silico docking of urokinase plasminogen activator and integrins (2008)
Bmc Bioinformatics, Bernard Degryse, Juan Fern, Valentina Citro, Francescol Blasi, Maria Vittoria Cubellis, ...
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Automatic inference of indexing rules for MEDLINE (2008)
Bmc Bioinformatics, Aurélie Névéol, Sonya E Shooshan, Vincent Claveau
This is an open access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Wing-sze Leung, Marie Cm Lin, David W Cheung, Sm Yiu
Filtering of false positive microRNA candidates by a clustering-based approach
Bmc Bioinformatics, Laurent Bréhélin, Jean-françois Dufayard, Olivier Gascuel
Research article PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data
Bmc Bioinformatics, Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures
Bmc Bioinformatics, Dang Hung Tran, Kenji Satou, Tu Bao, Ho Open Access
Finding microRNA regulatory modules in human genome using rule induction
Bmc Bioinformatics, Lucia Peixoto, Nils Gehlenborg, Sarath Ch, Ra Janga
Abstract: In this meeting report we give an overview of the talks and presentations from the Fourth International Society for Computational Biology (ISCB) Student Council Symposium held as part of...
Bmc Bioinformatics, Kyoung-jae Won, Iouri Chepelev, Bing Ren, Wei Wang, Kyoung-jae Won, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Prediction of regulatory elements in...
Bmc Bioinformatics, Hsuan-yu Huang, Yu-tang Syu, Peng Wu, Open Access, ...
Real value prediction of protein solvent accessibility using enhanced PSSM features
Bmc Bioinformatics, Adriano Barbosa-silva, Venkata P Satagopam, Reinhard Schneider, Miguel Ortega
Software Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence
BioMed Central Research VarDetect: a nucleotide sequence variation exploratory tool (2008)
Bmc Bioinformatics, Chumpol Ngamphiw, Supasak Kulawonganunchai, Anunchai Assawamakin, Ekachai Jenwitheesuk, Sissades Tongsima
phisms (SNPs) is at the forefront of genomic research. The discovery of SNPs may help to identify causative gene mutations in monogenic diseases as well as SNPs associfrom Asia Pacific Bioinformatics...
Bmc Bioinformatics, Kyle C Chipman, Ambuj K Singh, Open Access, Kyle C Chipman, Ambuj K Singh
Research article Predicting genetic interactions with random walks on biological networks
Discovering multi–level structures in bio-molecular data through the Bernstein inequality (2008)
Bmc Bioinformatics, Alberto Bertoni, Giorgio Valentini
with malignancies differentiated at bio-molecular level can be discovered through clustering algorithms, and several other tasks related to the analysis of bio-molecular data require the development...
The MoVIN server for the analysis of protein interaction networks (2008)
Bmc Bioinformatics, Paolo Marcatili, Giovanni Bussotti, Anna Tramontano, Anna Tramontano
This article is available from:
Bmc Bioinformatics, Khar Heng Choo, Shoba Ranganathan
Flanking signal and mature peptide residues influence signal peptide cleavage
SIGMA2: A system for the integrative genomic multi-dimensional (2008)
Bmc Bioinformatics, Raj Chari, Bradley P Coe, Craig Wedseltoft, Marie Benetti, Emily A Vucic, ...
Software
Pathological rate matrices: from primates to pathogens (2008)
Bmc Bioinformatics, Harold W Schranz, Von Bing Yap, Simon Easteal, Rob Knight, Gavin A Huttley
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Methods for evaluating gene expression from Affymetrix (2008)
Bmc Bioinformatics, Ning Jiang, Lindsey J Leach, Xiaohua Hu, Elena Potokina, Tianye Jia, ...
Research article
Mining clinical relationships from patient narratives (2008)
Bmc Bioinformatics, Angus Roberts, Robert Gaizauskas, Yikun Guo
© 2008 Roberts et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License
BATS: a Bayesian user-friendly software for Analyzing Time Series (2008)
Bmc Bioinformatics, Claudia Angelini, Luisa Cutillo, Daniela De C, Margherita Mutarelli, Marianna Pensky, ...
Software
Bmc Bioinformatics, Pornpat Nikamanon, Elroy Pun, Wayne Chou, Marek D Koter, Paul D Gershon, ...
Research article "TOF2H": A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from...
Bmc Bioinformatics, Michael T Sykes, James R Williamson, Open Access, Michael T Sykes, James R Williamson
Software Envelope: interactive software for modeling and fitting complex isotope distributions
Dynamic sensitivity analysis of biological systems (2008)
Bmc Bioinformatics, Wu Hsiung Wu, Feng Sheng Wang, Maw Shang Chang
This is an open access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Shen Jean Lim, Joo Chuan Tong, Fook Tim Chew, Martti T Tammi, Martti T Tammi
The value of position-specific scoring matrices for assessment of protein allegenicity
Bmc Bioinformatics, Peter Frommolt, Roman K Thomas
Software Standardized high-throughput evaluation of cell-based compound screens
Bmc Bioinformatics, Chih-ching Wang, Jian-wei Chen, Wei Chen
Using a kernel density estimation based classifier to predict species-specific microRNA precursors
BioMed Central Research Semi-automatic conversion of BioProp semantic annotation to (2008)
Bmc Bioinformatics, Pasbio Annotation, Hong-jie Dai, Chi-hsin Huang, Lian Hsu, ...
This article is available from:
Bmc Bioinformatics, Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purkayastha, Raja Mazumder, Charles Buck, ...
Software GeneOrder3.0: Software for comparing the order of genes in pairs of small bacterial genomes
Article type Methodology article (2007)
Bmc Bioinformatics, Helene H Thygesen, Helene H Thygesen, Aeilko H Zwinderman
This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available shortly after the date of publication, from the URL listed below....
x Methodology article FunSpec: a web-based cluster interpreter for yeast (2007)
Bmc Bioinformatics, Mark D Robinson, Jörg Grigull, Naveed Mohammad, Naveed Mohammad, Timothy R Hughes, ...
Background: For effective exposition of biological information, especially with regard to analysis of large-scale data types, researchers need immediate access to multiple categorical knowledge bases...
Bmc Bioinformatics, Michel Dumontier, Katerina Michalickova, Christopher Wv Hogue
Background: An organism's ability to adapt to its particular environmental niche is of fundamental importance to its survival and proliferation. In the largest study of its kind, we sought to...
Research article The functional importance of disease-associated mutation (2007)
Bmc Bioinformatics, Sean D Mooney, Sean D Mooney, Teri E Klein, Teri E Klein
Background: For many years, scientists believed that point mutations in genes are the genetic switches for somatic and inherited diseases such as cystic fibrosis, phenylketonuria and cancer. Some of...
Bmc Bioinformatics, Junbai Wang, Jan Delabie, Hans Christian Aasheim, Erlend Smel, Biomed Central, ...
Research article Clustering of the SOM easily reveals distinct gene expression patterns: results of a reanalysis of lymphoma study
resampled inference of orthologs (2007)
Bmc Bioinformatics, Christian M Zmasek, Christian M Zmasek, Sean R Eddy, Sean R Eddy
RIO: Analyzing proteomes by automated phylogenomics using
Bmc Bioinformatics, Korbinian Strimmer, Korbinian Strimmer
Modeling gene expression measurement error: a quasi-likelihood
Methodology article NBLAST: a cluster variant of BLAST for NxN comparisons (2007)
Bmc Bioinformatics, Michel Dumontier, Christopher Wv Hogue
© 2002 Dumontier and Hogue; licensee BioMed Central Ltd. Verbatim copying and redistribution of this article are permitted in any medium for any purpose, provided this notice is preserved along with...
Bmc Bioinformatics, Ian Donaldson, Joel Martin, Berry De Bruijn, Cheryl Wolting, Vicki Lay, ...
Research article PreBIND and Textomy – mining the biomedical literature for protein-protein interactions using a support vector machine
Research article RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited – bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein...
Article type Methodology article (2007)
Bmc Bioinformatics, J. W. Bizzaro, J. W. Bizzaro, Kenneth A. Marx, Kenneth A. Marx
This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available in approximately two weeks after the date of publication, from...
Bmc Bioinformatics, Hj Purohit, Dv Raje, A Kapley
Identification of signature and primers specific to genus
A Data Review and Re-assessment of Ovarian Cancer Serum Proteomic Profiling (2007)
Bmc Bioinformatics, Bmc Bioinformatics, James M. Sorace, Min Zhan, Min Zhan
This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available in approximately two weeks after the date of publication, from...
sequence similarity searches (2007)
Bmc Bioinformatics, Andreas Karwath, Ross D King
Homology Induction: the use of machine learning to improve
Identification and characterization of subfamily-specific signatures (2007)
Bmc Bioinformatics, Kevin Truong, Mitsuhiko Ikura
Methodology article
Bmc Bioinformatics, Jamie J Cannone, Sankar Subramanian, Murray N Schnare, James R Collett, Lisa M D'souza, ...
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal,
differentially expressed genes from microarray data (2007)
Bmc Bioinformatics, David M Mutch, Alvin Berger, Robert Mansourian, Andreas Rytz, Matthew-alan Roberts
The limit fold change model: A practical approach for selecting
Bmc Bioinformatics, Claudine Médigue
Research article Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes
Bmc Bioinformatics, O Di Cunto, Paolo Provero
Methodology article Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
oligo-nucleotide probes for species identification (2007)
Bmc Bioinformatics, Er E Pozhitkov, Diethard Tautz
An algorithm and program for finding sequence specific
Bmc Bioinformatics, Nikhat Zafar, Raja Mazumder, Donald Seto
Methodology article CoreGenes: A computational tool for identifying and cataloging "core " genes in a set of small genomes
Bmc Bioinformatics, Jamie J Cannone, Sankar Subramanian, Murray N Schnare, James R Collett, Lisa M D'souza, ...
Research article
Bmc Bioinformatics, Yong-chuan Tao
Research article Identifying functional relationships among human genes by systematic analysis of biological literature
Methodology article x BioMed Central (2007)
Bmc Bioinformatics, Doron Betel, Christopher Wv Hogue
Background: Biologists are often interested in performing a simple database search to identify proteins or genes that contain a well-defined sequence pattern. Many databases do not provide...
Bmc Bioinformatics, Yingyao Zhou, Yingyao Zhou, Ruben Abagyan, Ruben Abagyan
This 'Manuscript PDF ' corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available within a few days, from the URL listed below....
Bmc Bioinformatics, Alex Bateman
Background: Post transcriptional gene silencing (PTGS) is a recently discovered phenomenon that is an area of intense research interest. Components of the PTGS machinery are being discovered by...
Efficient Boolean implementation of universal sequence maps (bUSM) (2007)
Bmc Bioinformatics, Jonas S Almeida, John Schwacke, John Schwacke, Jonas S. Almeida
corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available within a few days, from the URL listed below.
Bmc Bioinformatics, Eric D Siggia, Nikolaus Rajewsky, Massimo Vergassola, Massimo Vergassola, Ulrike Gaul, ...
This 'Manuscript PDF ' corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available within a few days, from the URL listed below....
UK Please address correspondence to: (2007)
Bmc Bioinformatics, Bmc Bioinformatics, John Parkinson, John Parkinson, David Guiliano, David Guiliano, ...
This 'Manuscript PDF ' corresponds to the article as it appeared upon acceptance. The fully-formatted
Article type Methodology article (2007)
Bmc Bioinformatics, Gary D Bader, Michel Dumontier, Hao C Lieu, Ruth Isserlin, Christopher Wv Hogue, ...
This 'Manuscript PDF ' corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available within a few days, from the URL listed below....
Methodology article x BioMed Central Open Access (2007)
Bmc Bioinformatics, Hao Chen, Burt M Sharp
Oliz, a suite of Perl scripts that assist in the design of microarrays
Bmc Bioinformatics, Eric H Baehrecke, Eric H. Baehrecke, Eric H. Baehrecke, Niem Dang, Niem Dang, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. The fully-formatted PDF version will become available shortly after the date of publication, from the URL listed below....
BioMed Central Open Access (2007)
Bmc Bioinformatics, Dankyu Yoon, Sung-gon Yi, Ju-han Kim, Taesung Park
Two-stage normalization using background intensities in cDNA microarray data
Reduced modeling of signal transduction – a modular approach (2007)
Bmc Bioinformatics, Markus Koschorreck, Holger Conzelmann, Sybille Ebert, Michael Ederer, Ernst Dieter Gilles
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
MScanner: a classifier for retrieving Medline citations (2007)
Bmc Bioinformatics, Graham L Poulter, Daniel L Rubin, Russ B Altman, Cathal Seoighe, Cathal Seoighe
© 2008 Poulter et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
* Corresponding authors (2007)
Bmc Bioinformatics, Trevor I Dix, David R Powell, Lloyd Allison, Julie Bernal, Samira Jaeger, ...
Comparative analysis of long DNA sequences by per element information content using different contexts
protein-protein interaction networks (2007)
Bmc Bioinformatics, Gurkan Bebek, Jiong Yang
PathFinder: mining signal transduction pathway segments from
Bmc Bioinformatics, Ivan Porro, Livia Torterolo, Luca Corradi, Marco Fato, Adam Papadimitropoulos, ...
A Grid-based solution for management and analysis of microarrays in distributed experiments
Bmc Bioinformatics, Carl Gustafson, William J Bug, Jonathan Nissanov, Jonathan Nissanov
Software NeuroTerrain – a client-server system for browsing 3D biomedical image data sets
Bmc Bioinformatics, Jahangheer S Shaik, Mohammed Yeasin
Research article A unified framework for finding differentially expressed genes from microarray experiments
Bmc Bioinformatics, Vijayaraj Nagarajan, Mohamed O Elasri, Vijayaraj Nagarajan, Mohamed O Elasri
Proceedings
Merja Oja, Jaakko Peltonen, Jonas Blomberg, Samuel Kaski Methods, Bmc Bioinformatics, Merja Oja, ...
for estimating human endogenous retrovirus activities from EST
Bmc Bioinformatics, Doheon Lee, Sangwoo Kim, Younghoon Kim
Proceedings BioCAD: an information fusion platform for bio-network inference and analysis
Research article Assessment of composite motif discovery methods (2007)
Bmc Bioinformatics, Geir K S, Osman Abul, Jostein Johansen, Finn Drablos, Jostein Johansen, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Research article Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment
Bmc Bioinformatics, Chen-ming Hsu, Chien-yu Chen, Baw-jhiune Liu, Chih-chang Huang
Identification of hot regions in protein-protein interactions by sequential pattern mining
Research On consensus biomarker selection (2007)
Bmc Bioinformatics, Janusz Dutkowski, Anna Gambin
Background: Recent development of mass spectrometry technology enabled the analysis of complex peptide mixtures. A lot of effort is currently devoted to the identification of biomarkers in human body...
Analyzing M-CSF dependent monocyte/macrophage (2007)
Bmc Bioinformatics, Dominik Lutter, Peter Ugocsai, Margot Gr, Evelyn Orso, Fabian Theis, ...
Research article
Bmc Bioinformatics, Shuxing Zhang, Kamal Kumar, Xiaohui Jiang, Anders Wallqvist, Jaques Reifman, ...
Software DOVIS: an implementation for high-throughput virtual screening using AutoDock
Bmc Bioinformatics, Manabu Torii, Zhang-zhi Hu, Min Song, Cathy H Wu, Hongfang Liu
Proceedings A comparison study on algorithms of detecting long forms for short forms in biomedical text
Bmc Bioinformatics, Meng Wang, Xiaobo Zhou, Y W King, Stephen Tc Wong, Randy W King, ...
Research article Context based mixture model for cell phase identification in automated fluorescence microscopy
Bmc Bioinformatics, Mutlu Mete, Xiaowei Xu, Chun-yang Fan, Gal Shafirstein, Open Access, ...
Proceedings Automatic delineation of malignancy in histopathological head and neck slides
Bmc Bioinformatics, Dimos Gaidatzis, Erik Van Nimwegen, Jean Hausser, Mihaela Zavolan
Inference of miRNA targets using evolutionary conservation and
Bmc Bioinformatics, Benjamin Schuster-böckler, Alex Bateman
Reuse of structural domain–domain interactions in protein
application in cancer subtyping (2007)
Bmc Bioinformatics, Zhipeng Cai, Y Goebel, Mohammad R Salavatipour, Guohui Lin, Guohui Lin
Selecting dissimilar genes for multi-class classification, an
Bmc Bioinformatics, Hybrid Algorithms, Jung-hsien Chiang, Shih-yi Chao
Modeling human cancer-related regulatory modules by GA-RNN
sequences be used in RNA secondary structure prediction? (2007)
Bmc Bioinformatics, Marcel Turcotte, Marcel Turcotte
Can Clustal-style progressive pairwise alignment of multiple
Research article Using a logical model to predict the growth of yeast (2007)
Bmc Bioinformatics, Ke Whelan, Rd King
Background: A logical model of the known metabolic processes in S. cerevisiae was constructed from iFF708, an existing Flux Balance Analysis (FBA) model, and augmented with information from the KEGG...
Bmc Bioinformatics, Eider B Moore, Andrew V Poliakov, Peter Lincoln, James F Brinkley, James F Brinkley
Software MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data
Nearest Neighbor Networks: clustering expression data based on (2007)
Bmc Bioinformatics, Curtis Huttenhower, Avi I Flamholz, Jessica N L, Sauhard Sahi, Chad L Myers, ...
Software
Bmc Bioinformatics, Angelica Tulipano, Giacinto Donvito, Flavio Licciulli, Giorgio Maggi, Andreas Gisel
Research article Gene analogue finder: a GRID solution for finding functionally analogous gene products
Bmc Bioinformatics, Lei Xie, Philip E Bourne
Proceedings A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites
Bmc Bioinformatics, Roberta Bosotti, Ra Healy, Emanuela Scacheri, Luca Sartori, Ciro Mercurio, ...
Cross platform microarray analysis for robust identification of differentially expressed genes
Article type Methodology article (2007)
Bmc Bioinformatics, Markus Brameier, Carsten Wiuf
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Ab initio identification of human...
protein conformational states as applied to (2007)
Bmc Bioinformatics, Jenny Gu, Philip E Bourne, Biomed Central, Jenny Gu, Philip E Bourne
Identifying allosteric fluctuation transitions between different
Bmc Bioinformatics, Wasinee Rungsarityotin, Roland Krause, Arno Schodl, Wasinee Rungsarityotin, Arno Schödl, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Identifying protein complexes directly...
Research article Multiple non-collinear TF-map alignments of promoter regions (2007)
Bmc Bioinformatics, Enrique Blanco, Roderic Guigó, Xavier Messeguer, Biomed Central
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Egon L Willighagen, Harini Gopalakrishnan, Dazhi Jiao, Rajarshi Guha, David J Wild, ...
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon.
Bmc Bioinformatics, Ji He, Xinbin Dai, Xuechun Zhao
Software PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results
Bmc Bioinformatics, Vladimir Vacic, Vladimir N Uversky, A Keith Dunker, Stefano Lonardi, Stefano Lonardi
Software Composition Profiler: a tool for discovery and visualization of amino acid composition differences
This is an Open Access article distribut... (2007)
Bmc Bioinformatics, Michael C Wendl, Michael C Wendl
Algebraic correction methods for computational assessment of
Research article Dependence of paracentric inversion rate on tract length (2007)
Bmc Bioinformatics, Thomas L York, Rick Durrett, Rasmus Nielsen
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Research article Protein subcellular localization prediction based on compartment-specific features and structure conservation
BioMed Central Open Access (2007)
Bmc Bioinformatics, Paolo Romano, Ezio Bartocci, Guglielmo Bertolini, Flavio De Paoli, Domenico Marra, ...
Biowep: a workflow enactment portal for bioinformatics applications
Bmc Bioinformatics, Ricardo Zn Vêncio, Ilya Shmulevich
Software ProbCD: enrichment analysis accounting for categorization uncertainty
Bmc Bioinformatics, Drena Dobbs, Vasant Honavar
Glycosylation site prediction using ensembles of Support Vector
Bmc Bioinformatics, Jürgen Hartler, Gerhard G Thallinger, Gernot Stocker, Er Sturn, Thomas R Burkard, ...
Software MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data
Software Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'
Bmc Bioinformatics, Yair Horesh, Tirza Doniger, Shulamit Michaeli, Ron Unger
RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules
Bmc Bioinformatics, Daniel Barthel, Jonathan D Hirst, Jacek Błażewicz, Edmund K Burke, Natalio Krasnogor, ...
© 2007 Barthel et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Bmc Bioinformatics, Tobias Wittkop, Jan Baumbach, Francisco P Lobo, Francisco P Lobo, Sven Rahmann
Research article Large scale clustering of protein sequences with FORCE-A layout based heuristic for weighted cluster editing
Bmc Bioinformatics, Kellie J Archer, Catherine I Dumur, G Scott Taylor, Michael D Chaplin, Geraldine Grant, ...
Research article Application of a correlation correction factor in a microarray cross-platform reproducibility study
Bmc Bioinformatics, Amit U Sinha, Jaroslaw Meller, Amit U Sinha, Jaroslaw Meller
Software Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms
Bmc Bioinformatics, Daniel D Sommer, Arthur L Delcher, Steven L Salzberg, Biomed Central, Daniel D Sommer, ...
Software Minimus: a fast, lightweight genome assembler
Bmc Bioinformatics, Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, ...
Research article False occurrences of functional motifs in protein sequences highlight evolutionary constraints
simple way to reveal common prognostic markers (2007)
Bmc Bioinformatics, Xinan Yang, Xiao Sun
Meta-analysis of several gene lists for distinct types of cancer: A
Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, (2007)
Bmc Bioinformatics, Namshin Kim, Christopher Lee
Software
Bmc Bioinformatics, Chris Thachuk, Alena Shmygelska, Holger H Hoos
Research article A replica exchange Monte Carlo algorithm for protein folding in the HP model
Bmc Bioinformatics, Timur Shtatl, Daniel Guettler, Misha Kossodo, Misha Pivovarov, Ralph Weissleder, ...
PepBank- a database of peptides based on sequence text mining and public peptide data sources
Article type Methodology article (2007)
Bmc Bioinformatics, Harald Binder, Martin Schumacher, Harald Binder, Martin Schumacher
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Allowing for mandatory covariates in...
Bmc Bioinformatics, Jian Qiu, William S Noble, Open Access
Proceedings A new pairwise kernel for biological network inference with support vector machines
Bmc Bioinformatics, Jing Chen, Huan Xu, Bruce J Aronow, Anil G Jegga
Research article Improved human disease candidate gene prioritization using mouse phenotype
obtained by accurate mass spectrometry (2007)
Bmc Bioinformatics, Tobias Kind, Oliver Fiehn
Seven Golden Rules for heuristic filtering of molecular formulas
Bmc Bioinformatics, Yang Zhang
This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. I-TASSER server for protein 3D structure...
e-Science and biological pathway semantics (2007)
Bmc Bioinformatics, Joanne S Luciano, Joanne S Luciano, Robert D Stevens, Robert D Stevens
Background: The development of e-Science presents a major set of opportunities and challenges for the future progress of biological and life scientific research. Major new tools are required and...
Bmc Bioinformatics, Antonio Marco, Ignacio Marín
A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification
Bmc Bioinformatics, Content Similarity
PubMed related articles: a probabilistic topic-based model for
Bmc Bioinformatics, Evolutionary Conservation
Identification of putative regulatory upstream ORFs in the yeast
BioMed Central Open Access (2007)
Bmc Bioinformatics, Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini, Matteo Pellegrini
Proceedings An improved method for identifying functionally linked proteins using phylogenetic profiles
Bmc Bioinformatics, Rui-sheng Wang, Yong Wang, Ling-yun Wu, Xiang-sun Zhang, Luonan Chen
Research article Analysis on multi-domain cooperation for predicting protein-protein interactions
Bmc Bioinformatics, Gong Zhang, Zoya Ignatova, Zoya Ignatova, Karl-heinz Zimmermann
Research article Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype
Bmc Bioinformatics, Andreas Henschel, Christof Winter, Wan Kyu Kim, Michael Schroeder
Proceedings Using structural motif descriptors for sequence-based binding site prediction
Bmc Bioinformatics, Bingjun Jiang, Hong Qu, Yuanlei Hu, Ting Ni, Zhongping Lin
Research article Computational analysis of the relationship between allergenicity and digestibility of allergenic proteins in simulated gastric fluid
Bmc Bioinformatics, Yao Qing Shen, Gertraud Burger
'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools
Research article DNA-based watermarks using the DNA-Crypt algorithm (2007)
Bmc Bioinformatics, Dominik Heider, Angelika Barnekow
Background: The aim of this paper is to demonstrate the application of watermarks based on DNA sequences to identify the unauthorized use of genetically modified organisms (GMOs) protected by...
BioMed Central Open Access (2007)
Bmc Bioinformatics, Tianwei Yu, Hui Ye, Wei Sun, Ker-chau Li, Zugen Chen, ...
A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array
Refining intra-protein contact prediction by graph analysis (2007)
Bmc Bioinformatics, Milana Frenkel-morgenstern, Rachel Magid, Eran Eyal
This is an open access article distributed under the terms of the Creative Commons Attribution License
Research article Stratification bias in low signal microarray studies (2007)
Bmc Bioinformatics, Brian J Parker, Simon Günter, Justin Bedo
This is an Open Access article distributed under the terms of the Creative Commons Attribution License