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  1. The Hedgehog Signaling Pathway is one of signaling pathways that are very important to embryonic development. The participation of inhibitors in the Hedgehog Signal Pathway can control cell growth and death, a...

    Authors: Jun Gao, Dongsheng Che, Vincent W Zheng, Ruixin Zhu and Qi Liu
    Citation: BMC Bioinformatics 2012 13:186
    Content type: Methodology article Published on:

  17. Short-read data from next-generation sequencing technologies are now being generated across a range of research projects. The fidelity of this data can be affected by several factors and it is important to hav...

    Authors: Xin Victoria Wang, Natalie Blades, Jie Ding, Razvan Sultana and Giovanni Parmigiani
    Citation: BMC Bioinformatics 2012 13:185
    Content type: Methodology article Published on:

  18. Human TWIST1 is a highly conserved member of the regulatory basic helix-loop-helix (bHLH) transcription factors. TWIST1 forms homo- or heterodimers with E-box proteins, such as E2A (isoforms E12 and E47), MYOD...

    Authors: Amanda M Maia, João HM da Silva, André L Mencalha, Ernesto R Caffarena and Eliana Abdelhay
    Citation: BMC Bioinformatics 2012 13:184
    Content type: Research article Published on:

  19. Gene prediction algorithms (or gene callers) are an essential tool for analyzing shotgun nucleic acid sequence data. Gene prediction is a ubiquitous step in sequence analysis pipelines; it reduces the volume o...

    Authors: William L Trimble, Kevin P Keegan, Mark D’Souza, Andreas Wilke, Jared Wilkening, Jack Gilbert and Folker Meyer
    Citation: BMC Bioinformatics 2012 13:183
    Content type: Research article Published on:

  22. Correction to A. Lourenço, M. Conover, A. Wong, A. Nematzadeh, F. Pan, H. Shatkay, and L.M. Rocha."A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the P...

    Authors: Anália Lourenço, Michael Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay and Luis M Rocha
    Citation: BMC Bioinformatics 2012 13:180
    Content type: Erratum Published on:

    The original article was published in BMC Bioinformatics 2011 12:S12

  23. Many problems in bioinformatics involve classification based on features such as sequence, structure or morphology. Given multiple classifiers, two crucial questions arise: how does their performance compare, ...

    Authors: Jonathan M Keith, Christian M Davey and Sarah E Boyd
    Citation: BMC Bioinformatics 2012 13:179
    Content type: Methodology article Published on:

  25. Based on available biological information, genomic data can often be partitioned into pre-defined sets (e.g. pathways) and subsets within sets. Biologists are often interested in determining whether some pre-d...

    Authors: Wenge Guo, Mingan Yang, Chuanhua Xing and Shyamal D Peddada
    Citation: BMC Bioinformatics 2012 13:177
    Content type: Methodology article Published on:

  26. Chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-Seq) is the most frequently used method to identify the binding sites of transcription factors. Active binding sites can be seen as ...

    Authors: Karl Kornacker, Morten Beck Rye, Tony Håndstad and Finn Drabløs
    Citation: BMC Bioinformatics 2012 13:176
    Content type: Methodology article Published on:

  27. Seqcrawler takes its roots in software like SRS or Lucegene. It provides an indexing platform to ease the search of data and meta-data in biological banks and it can scale to face the current flow of data. Whi...

    Authors: Olivier Sallou, Anthony Bretaudeau and Aurelien Roult
    Citation: BMC Bioinformatics 2012 13:175
    Content type: Software Published on:

  28. Clustering DNA sequences into functional groups is an important problem in bioinformatics. We propose a new alignment-free algorithm, mBKM, based on a new distance measure, DMk, for clustering gene sequences. ...

    Authors: Dan Wei, Qingshan Jiang, Yanjie Wei and Shengrui Wang
    Citation: BMC Bioinformatics 2012 13:174
    Content type: Methodology article Published on:

  31. The enteric pathogen Salmonella is the causative agent of the majority of food-borne bacterial poisonings. Resent research revealed that colonization of plants by Salmonella is an active infection process. Salmon...

    Authors: Marek Schikora, Balram Neupane, Satish Madhogaria, Wolfgang Koch, Daniel Cremers, Heribert Hirt, Karl-Heinz Kogel and Adam Schikora
    Citation: BMC Bioinformatics 2012 13:171
    Content type: Research article Published on:

  32. The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the...

    Authors: Berat Z Haznedaroglu, Darryl Reeves, Hamid Rismani-Yazdi and Jordan Peccia
    Citation: BMC Bioinformatics 2012 13:170
    Content type: Research article Published on:

  35. Although genome-scale expression experiments are performed routinely in biomedical research, methods of analysis remain simplistic and their interpretation challenging. The conventional approach is to compare ...

    Authors: David Edwards, Lei Wang and Peter Sørensen
    Citation: BMC Bioinformatics 2012 13:167
    Content type: Methodology article Published on:

  36. The emergence of Next Generation Sequencing technologies has made it possible for individual investigators to generate gigabases of sequencing data per week. Effective analysis and manipulation of these data i...

    Authors: Georgiy Golovko, Kamil Khanipov, Mark Rojas, Antonio Martinez-Alcántara, Jesse J Howard, Efren Ballesteros, Sharu Gupta, William Widger and Yuriy Fofanov
    Citation: BMC Bioinformatics 2012 13:166
    Content type: Software Published on:

  38. Identifying variants associated with complex human traits in high-dimensional data is a central goal of genome-wide association studies. However, complicated etiologies such as gene-gene interactions are ignor...

    Authors: Stacey J Winham, Colin L Colby, Robert R Freimuth, Xin Wang, Mariza de Andrade, Marianne Huebner and Joanna M Biernacka
    Citation: BMC Bioinformatics 2012 13:164
    Content type: Research article Published on:

  39. In bioinformatics, it is important to build extensible and low-maintenance systems that are able to deal with the new tools and data formats that are constantly being developed. The traditional and simplest im...

    Authors: Maíra R Rodrigues, Wagner CS Magalhães, Moara Machado and Eduardo Tarazona-Santos
    Citation: BMC Bioinformatics 2012 13:163
    Content type: Methodology article Published on:

  40. There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Prog...

    Authors: Jose C A Santos, Houssam Nassif, David Page, Stephen H Muggleton and Michael J E Sternberg
    Citation: BMC Bioinformatics 2012 13:162
    Content type: Research article Published on:

  41. More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS). Although OLS provides ample possibility for querying and browsing ter...

    Authors: Steven Vercruysse, Aravind Venkatesan and Martin Kuiper
    Citation: BMC Bioinformatics 2012 13:116
    Content type: Software Published on:

  42. Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text.

    Authors: Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner Jr, K Bretonnel Cohen, Karin Verspoor, Judith A Blake and Lawrence E Hunter
    Citation: BMC Bioinformatics 2012 13:161
    Content type: Research article Published on:

  48. Due to hybridization events in evolution, studying two different genes of a set of species may yield two related but different phylogenetic trees for the set of species. In this case, we want to combine the tw...

    Authors: Zhi-Zhong Chen, Lusheng Wang and Satoshi Yamanaka
    Citation: BMC Bioinformatics 2012 13:155
    Content type: Research article Published on:

  49. Next generation sequencing approaches applied to the analyses of transposon insertion junction fragments generated in high throughput forward genetic screens has created the need for clear informatics and stat...

    Authors: Aaron L Sarver, Jesse Erdman, Tim Starr, David A Largaespada and Kevin A T Silverstein
    Citation: BMC Bioinformatics 2012 13:154
    Content type: Software Published on:

  50. Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical ro...

    Authors: Joanna M Kasprzak, Anna Czerwoniec and Janusz M Bujnicki
    Citation: BMC Bioinformatics 2012 13:153
    Content type: Research article Published on:

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