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  1. This paper is devoted to distance measures for leaf-labelled trees on free leafset. A leaf-labelled tree is a data structure which is a special type of a tree where only leaves (terminal) nodes are labelled. T...

    Authors: Jakub Koperwas and Krzysztof Walczak
    Citation: BMC Bioinformatics 2011 12:204
    Content type: Methodology article Published on:

  2. A B-cell epitope is a group of residues on the surface of an antigen which stimulates humoral responses. Locating these epitopes on antigens is important for the purpose of effective vaccine design. In recent ...

    Authors: Wen Han Chen, Ping Ping Sun, Yang Lu, William W Guo, Yan Xin Huang and Zhi Qiang Ma
    Citation: BMC Bioinformatics 2011 12:199
    Content type: Software Published on:

  4. Elucidating the exact relationship between gene copy number and expression would enable identification of regulatory mechanisms of abnormal gene expression and biological pathways of regulation. Most current a...

    Authors: Hiroko K Solvang, Ole Christian Lingjærde, Arnoldo Frigessi, Anne-Lise Børresen-Dale and Vessela N Kristensen
    Citation: BMC Bioinformatics 2011 12:197
    Content type: Research article Published on:

  5. Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have bee...

    Authors: Jacek Sroka, Łukasz Bieniasz-Krzywiec, Szymon Gwóźdź, Dariusz Leniowski, Jakub Łącki, Mateusz Markowski, Claudio Avignone-Rossa, Michael E Bushell, Johnjoe McFadden and Andrzej M Kierzek
    Citation: BMC Bioinformatics 2011 12:196
    Content type: Software Published on:

  6. Mapping protein primary sequences to their three dimensional folds referred to as the 'second genetic code' remains an unsolved scientific problem. A crucial part of the problem concerns the geometrical specif...

    Authors: Sankar Basu, Dhananjay Bhattacharyya and Rahul Banerjee
    Citation: BMC Bioinformatics 2011 12:195
    Content type: Research article Published on:

  8. The automatic identification of syntenies across multiple species is a key step in comparative genomics that helps biologists shed light both on evolutionary and functional problems.

    Authors: Yves-Pol Deniélou, Marie-France Sagot, Frédéric Boyer and Alain Viari
    Citation: BMC Bioinformatics 2011 12:193
    Content type: Research article Published on:

  9. Graphical models of network associations are useful for both visualizing and integrating multiple types of association data. Identifying modules, or groups of functionally related gene products, is an importan...

    Authors: Kahn Rhrissorrakrai and Kristin C Gunsalus
    Citation: BMC Bioinformatics 2011 12:4581
    Content type: Methodology article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2016 17:89

  10. The Structural Classification of Proteins (SCOP) database uses a large number of hidden Markov models (HMMs) to represent families and superfamilies composed of proteins that presumably share the same evolutio...

    Authors: Liqing Zhang, Layne T Watson and Lenwood S Heath
    Citation: BMC Bioinformatics 2011 12:191
    Content type: Research article Published on:

  11. Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an...

    Authors: Eduard Schreiner, Leonardo G Trabuco, Peter L Freddolino and Klaus Schulten
    Citation: BMC Bioinformatics 2011 12:190
    Content type: Methodology article Published on:

  13. Identification of discourse relations, such as causal and contrastive relations, between situations mentioned in text is an important task for biomedical text-mining. A biomedical text corpus annotated with di...

    Authors: Rashmi Prasad, Susan McRoy, Nadya Frid, Aravind Joshi and Hong Yu
    Citation: BMC Bioinformatics 2011 12:188
    Content type: Research article Published on:

  15. Two Bayesian methods, BayesCπ and BayesDπ, were developed for genomic prediction to address the drawback of BayesA and BayesB regarding the impact of prior hyperparameters and treat the prior probability π that a...

    Authors: David Habier, Rohan L Fernando, Kadir Kizilkaya and Dorian J Garrick
    Citation: BMC Bioinformatics 2011 12:186
    Content type: Research article Published on:

  16. G protein-coupled receptors (GPCRs) transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction i...

    Authors: Catherine L Worth, Annika Kreuchwig, Gunnar Kleinau and Gerd Krause
    Citation: BMC Bioinformatics 2011 12:185
    Content type: Database Published on:

  18. Hybridization of heterologous (non-specific) nucleic acids onto arrays designed for model-organisms has been proposed as a viable genomic resource for estimating sequence variation and gene expression in non-m...

    Authors: Brian J Darby, Kenneth L Jones, David Wheeler and Michael A Herman
    Citation: BMC Bioinformatics 2011 12:183
    Content type: Research article Published on:

  19. The implementation of high throughput sequencing for exploring biodiversity poses high demands on bioinformatics applications for automated data processing. Here we introduce CLOTU, an online and open access pipe...

    Authors: Surendra Kumar, Tor Carlsen, Bjørn-Helge Mevik, Pål Enger, Rakel Blaalid, Kamran Shalchian-Tabrizi and Håvard Kauserud
    Citation: BMC Bioinformatics 2011 12:182
    Content type: Software Published on:

  20. Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest futur...

    Authors: Jacek Blazewicz, Wojciech Frohmberg, Michal Kierzynka, Erwin Pesch and Pawel Wojciechowski
    Citation: BMC Bioinformatics 2011 12:181
    Content type: Software Published on:

  21. The analysis of gene expression from time series underpins many biological studies. Two basic forms of analysis recur for data of this type: removing inactive (quiet) genes from the study and determining which...

    Authors: Alfredo A Kalaitzis and Neil D Lawrence
    Citation: BMC Bioinformatics 2011 12:180
    Content type: Research article Published on:

  22. Compound profiling and drug screening generates large amounts of data and is generally based on microplate assays. Current information systems used for handling this are mainly commercial, closed source, expen...

    Authors: Jonathan Alvarsson, Claes Andersson, Ola Spjuth, Rolf Larsson and Jarl ES Wikberg
    Citation: BMC Bioinformatics 2011 12:179
    Content type: Software Published on:

  26. Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects...

    Authors: Arun Rangarajan, Tim Schedl, Karen Yook, Juancarlos Chan, Stephen Haenel, Lolly Otis, Sharon Faelten, Tracey DePellegrin-Connelly, Ruth Isaacson, Marek S Skrzypek, Steven J Marygold, Raymund Stefancsik, J Michael Cherry, Paul W Sternberg and Hans-Michael Müller
    Citation: BMC Bioinformatics 2011 12:175
    Content type: Correspondence Published on:

  27. Mitochondrial DNA is an ideal source of information to conduct evolutionary and phylogenetic studies due to its extraordinary properties and abundance. Many insights can be gained from these, including but not...

    Authors: Roberto Blanco, Elvira Mayordomo, Julio Montoya and Eduardo Ruiz-Pesini
    Citation: BMC Bioinformatics 2011 12:174
    Content type: Research article Published on:

  30. A major challenge in genomic research is identifying significant biological processes and generating new hypotheses from large gene sets. Gene sets often consist of multiple separate biological pathways, contr...

    Authors: Mitja I Kurki, Jussi Paananen, Markus Storvik, Seppo Ylä-Herttuala, Juha E Jääskeläinen, Mikael von und zu Fraunberg, Garry Wong and Petri Pehkonen
    Citation: BMC Bioinformatics 2011 12:171
    Content type: Methodology article Published on:

  34. The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating bi...

    Authors: Augustin Luna, Evrim I Karac, Margot Sunshine, Lucas Chang, Ruth Nussinov, Mirit I Aladjem and Kurt W Kohn
    Citation: BMC Bioinformatics 2011 12:167
    Content type: Research article Published on:

  35. Mosaicism for copy number and copy neutral chromosomal rearrangements has been recently identified as a relatively common source of genetic variation in the normal population. However its prevalence is poorly ...

    Authors: Juan R González, Benjamín Rodríguez-Santiago, Alejandro Cáceres, Roger Pique-Regi, Nathaniel Rothman, Stephen J Chanock, Lluís Armengol and Luis A Pérez-Jurado
    Citation: BMC Bioinformatics 2011 12:166
    Content type: Methodology article Published on:

  36. MicroRNAs (miRNAs) play a key role in regulating various biological processes such as participating in the post-transcriptional pathway and affecting the stability and/or the translation of mRNA. Current metho...

    Authors: Jiamin Xiao, Xiaojing Tang, Yizhou Li, Zheng Fang, Daichuan Ma, Yangzhige He and Menglong Li
    Citation: BMC Bioinformatics 2011 12:165
    Content type: Research article Published on:

  37. Signal transduction is an essential biological process involved in cell response to environment changes, by which extracellular signaling initiates intracellular signaling. Many computational methods have been...

    Authors: Kai Wang, Fuyan Hu, Kejia Xu, Hua Cheng, Meng Jiang, Ruili Feng, Jing Li and Tieqiao Wen
    Citation: BMC Bioinformatics 2011 12:164
    Content type: Research article Published on:

  38. Over the past few years, new massively parallel DNA sequencing technologies have emerged. These platforms generate massive amounts of data per run, greatly reducing the cost of DNA sequencing. However, these t...

    Authors: Francisco Fernandes, Paulo GS da Fonseca, Luis MS Russo, Arlindo L Oliveira and Ana T Freitas
    Citation: BMC Bioinformatics 2011 12:163
    Content type: Methodology article Published on:

  40. Protein-protein interactions play a fundamental role in elucidating the molecular mechanisms of biomolecular function, signal transductions and metabolic pathways of living organisms. Although high-throughput ...

    Authors: Haibin Gu, Pengcheng Zhu, Yinming Jiao, Yijun Meng and Ming Chen
    Citation: BMC Bioinformatics 2011 12:161
    Content type: Database Published on:

  41. The accurate prediction of ligand binding residues from amino acid sequences is important for the automated functional annotation of novel proteins. In the previous two CASP experiments, the most successful me...

    Authors: Daniel B Roche, Stuart J Tetchner and Liam J McGuffin
    Citation: BMC Bioinformatics 2011 12:160
    Content type: Software Published on:

  43. Molecular dynamics (MD) simulations are powerful tools to investigate the conformational dynamics of proteins that is often a critical element of their function. Identification of functionally relevant conform...

    Authors: Domenico Fraccalvieri, Alessandro Pandini, Fabio Stella and Laura Bonati
    Citation: BMC Bioinformatics 2011 12:158
    Content type: Research article Published on:

  45. Recent association analyses in genome-wide association studies (GWAS) mainly focus on single-locus association tests (marginal tests) and two-locus interaction detections. These analysis methods have provided ...

    Authors: Can Yang, Xiang Wan, Qiang Yang, Hong Xue, Nelson LS Tang and Weichuan Yu
    Citation: BMC Bioinformatics 2011 12:156
    Content type: Methodology article Published on:

  46. Gene expression is regulated at both the DNA sequence level and through modification of chromatin. However, the effect of chromatin on tissue/cell-type specific gene regulation (TCSR) is largely unknown. In th...

    Authors: Zhihua Zhang and Michael Q Zhang
    Citation: BMC Bioinformatics 2011 12:155
    Content type: Research article Published on:

  48. High-throughput functional genomics technologies generate large amount of data with hundreds or thousands of measurements per sample. The number of sample is usually much smaller in the order of ten or hundred...

    Authors: Cheng-Jian Xu, Huub CJ Hoefsloot and Age K Smilde
    Citation: BMC Bioinformatics 2011 12:153
    Content type: Research article Published on:

  49. Zinc Finger Nucleases (ZFNs) are man-made restriction enzymes useful for manipulating genomes by cleaving target DNA sequences. ZFNs allow therapeutic gene correction or creation of genetically modified model ...

    Authors: Thomas J Cradick, Giovanna Ambrosini, Christian Iseli, Philipp Bucher and Anton P McCaffrey
    Citation: BMC Bioinformatics 2011 12:152
    Content type: Software Published on:

  50. The rational design of modified proteins with controlled stability is of extreme importance in a whole range of applications, notably in the biotechnological and environmental areas, where proteins are used fo...

    Authors: Yves Dehouck, Jean Marc Kwasigroch, Dimitri Gilis and Marianne Rooman
    Citation: BMC Bioinformatics 2011 12:151
    Content type: Software Published on:

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