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  1. Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus

    Authors: Francesco Di Palma, Sandro Bottaro and Giovanni Bussi
    Citation: BMC Bioinformatics 2015 16(Suppl 9):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  2. The high throughput of modern NGS sequencers coupled with the huge sizes of genomes currently analysed, poses always higher algorithmic challenges to align short reads quickly and accurately against a referenc...

    Authors: Alberto Policriti and Nicola Prezza
    Citation: BMC Bioinformatics 2015 16(Suppl 9):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  3. RNA-Seq provides remarkable power in the area of biomarkers discovery and disease characterization. Two crucial steps that affect RNA-Seq experiment results are Library Sample Preparation (LSP) and Bioinformat...

    Authors: Matteo Carrara, Josephine Lum, Francesca Cordero, Marco Beccuti, Michael Poidinger, Susanna Donatelli, Raffaele Adolfo Calogero and Francesca Zolezzi
    Citation: BMC Bioinformatics 2015 16(Suppl 9):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 9

  4. Both differential expression (DE) and differential co-expression (DC) analyses are appreciated as useful tools in understanding gene regulation related to complex diseases. The performance of integrating DE an...

    Authors: Thomas WH Lui, Nancy BY Tsui, Lawrence WC Chan, Cesar SC Wong, Parco MF Siu and Benjamin YM Yung
    Citation: BMC Bioinformatics 2015 16:182
    Content type: Methodology article Published on:

  5. The Electron Microscopy DataBank (EMDB) is growing rapidly, accumulating biological structural data obtained mainly by electron microscopy and tomography, which are emerging techniques for determining large bi...

    Authors: Juan Esquivel-Rodríguez, Yi Xiong, Xusi Han, Shuomeng Guang, Charles Christoffer and Daisuke Kihara
    Citation: BMC Bioinformatics 2015 16:181
    Content type: Software Published on:

  6. Protein function in eukaryotic cells is often controlled in a cell cycle-dependent manner. Therefore, the correct assignment of cellular phenotypes to cell cycle phases is a crucial task in cell biology resear...

    Authors: Felix Schönenberger, Anja Deutzmann, Elisa Ferrando-May and Dorit Merhof
    Citation: BMC Bioinformatics 2015 16:180
    Content type: Research article Published on:

  7. Several methods exist for the prediction of precursor miRNAs (pre-miRNAs) in genomic or sRNA-seq (small RNA sequences) data produced by NGS (Next Generation Sequencing). One key information used for this task ...

    Authors: Susan Higashi, Cyril Fournier, Christian Gautier, Christine Gaspin and Marie-France Sagot
    Citation: BMC Bioinformatics 2015 16:179
    Content type: Methodology Article Published on:

  8. Evolutionary variations let us define a set of similar nucleic acid sequences as a family if these different molecules execute a common function. Capturing their sequence variation by using e. g. position spec...

    Authors: Stefan Janssen and Robert Giegerich
    Citation: BMC Bioinformatics 2015 16:178
    Content type: Research Article Published on:

  9. The subcellular distribution of synapses is fundamentally important for the assembly, function, and plasticity of the nervous system. Automated and effective quantification tools are a prerequisite to large-sc...

    Authors: Jonathan Sanders, Anil Singh, Gabriella Sterne, Bing Ye and Jie Zhou
    Citation: BMC Bioinformatics 2015 16:177
    Content type: Research article Published on:

  11. The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an o...

    Authors: Vadim I. Nazarov, Mikhail V. Pogorelyy, Ekaterina A. Komech, Ivan V. Zvyagin, Dmitry A. Bolotin, Mikhail Shugay, Dmitry M. Chudakov, Yury B. Lebedev and Ilgar Z. Mamedov
    Citation: BMC Bioinformatics 2015 16:175
    Content type: Software Published on:

  14. High-throughput technologies such as flow and mass cytometry have the potential to illuminate cellular networks. However, analyzing the data produced by these technologies is challenging. Visualization is need...

    Authors: Jonathan R Karr, Harendra Guturu, Edward Y Chen, Stuart L Blair, Jonathan M Irish, Nikesh Kotecha and Markus W Covert
    Citation: BMC Bioinformatics 2015 16:172
    Content type: Software Published on:

  15. A variety of DNA binding proteins are involved in regulating and shaping the packing of chromatin. They aid the formation of loops in the DNA that function to isolate different structural domains. A recent exp...

    Authors: Saeed Saberi, Pau Farré, Olivier Cuvier and Eldon Emberly
    Citation: BMC Bioinformatics 2015 16:171
    Content type: Research Article Published on:

  16. Partitioning the human immunoglobulin variable region into variable (V), diversity (D), and joining (J) segments is a common sequence analysis step. We introduce a novel approximate dynamic programming method ...

    Authors: Daniel E Russ, Kwan-Yuet Ho and Nancy S Longo
    Citation: BMC Bioinformatics 2015 16:170
    Content type: Methodology article Published on:

  17. Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited.

    Authors: Henry Heberle, Gabriela Vaz Meirelles, Felipe R da Silva, Guilherme P Telles and Rosane Minghim
    Citation: BMC Bioinformatics 2015 16:169
    Content type: Software Published on:

  19. The well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveries using SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other structu...

    Authors: Carles Hernandez-Ferrer, Ines Quintela Garcia, Katharina Danielski, Ángel Carracedo, Luis A. Pérez-Jurado and Juan R. González
    Citation: BMC Bioinformatics 2015 16:167
    Content type: Software Published on:

  20. Traditional cancer treatments have centered on cytotoxic drugs and general purpose chemotherapy that may not be tailored to treat specific cancers. Identification of molecular markers that are related to diffe...

    Authors: Vasily Sachnev, Saras Saraswathi, Rashid Niaz, Andrzej Kloczkowski and Sundaram Suresh
    Citation: BMC Bioinformatics 2015 16:166
    Content type: Research Article Published on:

  21. High-throughput methods are generating biological data on a vast scale. In many instances, genomic, transcriptomic, and proteomic data must be interpreted in the context of signaling and metabolic pathways to ...

    Authors: Yongnan Zhu, Liang Sun, Alexander Garbarino, Carl Schmidt, Jinglong Fang and Jian Chen
    Citation: BMC Bioinformatics 2015 16:165
    Content type: Software Published on:

  22. Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their h...

    Authors: Roie Levy, Rogan Carr, Anat Kreimer, Shiri Freilich and Elhanan Borenstein
    Citation: BMC Bioinformatics 2015 16:164
    Content type: Software Published on:

  23. Adjusting the capacity of metabolic pathways in response to rapidly changing environmental conditions is an important component of microbial adaptation strategies to stochastic environments. In this work, we u...

    Authors: Gundián M de Hijas-Liste, Eva Balsa-Canto, Jan Ewald, Martin Bartl, Pu Li, Julio R Banga and Christoph Kaleta
    Citation: BMC Bioinformatics 2015 16:163
    Content type: Research Article Published on:

  24. The exponential growth of protein structural and sequence databases is enabling multifaceted approaches to understanding the long sought sequence-structure-function relationship. Advances in computation now ma...

    Authors: Yasser B Ruiz-Blanco, Waldo Paz, James Green and Yovani Marrero-Ponce
    Citation: BMC Bioinformatics 2015 16:162
    Content type: Software Published on:

  26. Founder populations have an important role in the study of genetic diseases. Access to detailed genealogical records is often one of their advantages. These genealogical data provide unique information for res...

    Authors: Héloïse Gauvin, Jean-François Lefebvre, Claudia Moreau, Eve-Marie Lavoie, Damian Labuda, Hélène Vézina and Marie-Hélène Roy-Gagnon
    Citation: BMC Bioinformatics 2015 16:160
    Content type: Software Published on:

  27. Rapid evolutions in sequencing technology force read mappers into flexible adaptation to longer reads, changing error models, memory barriers and novel applications.

    Authors: Michaël Vyverman, Bernard De Baets, Veerle Fack and Peter Dawyndt
    Citation: BMC Bioinformatics 2015 16:159
    Content type: Software Published on:

  28. Effective management of patients with diabetic foot infection is a crucial concern. A delay in prescribing appropriate antimicrobial agent can lead to amputation or life threatening complications. Thus, this e...

    Authors: Nurlisa Yusuf, Ammar Zakaria, Mohammad Iqbal Omar, Ali Yeon Md Shakaff, Maz Jamilah Masnan, Latifah Munirah Kamarudin, Norasmadi Abdul Rahim, Nur Zawatil Isqi Zakaria, Azian Azamimi Abdullah, Amizah Othman and Mohd Sadek Yasin
    Citation: BMC Bioinformatics 2015 16:158
    Content type: Research article Published on:

  30. Tumour samples containing distinct sub-populations of cancer and normal cells present challenges in the development of reproducible biomarkers, as these biomarkers are based on bulk signals from mixed tumour p...

    Authors: Catalina V Anghel, Gerald Quon, Syed Haider, Francis Nguyen, Amit G Deshwar, Quaid D Morris and Paul C Boutros
    Citation: BMC Bioinformatics 2015 16:156
    Content type: Software Published on:

  31. Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is prov...

    Authors: Ernest D Benavente, Francesc Coll, Nick Furnham, Ruth McNerney, Judith R Glynn, Susana Campino, Arnab Pain, Fady R Mohareb and Taane G Clark
    Citation: BMC Bioinformatics 2015 16:155
    Content type: Software Published on:

  32. Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison i...

    Authors: Tristan Bitard-Feildel, Carsten Kemena, Jenny M Greenwood and Erich Bornberg-Bauer
    Citation: BMC Bioinformatics 2015 16:154
    Content type: Methodology Article Published on:

  33. Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However,...

    Authors: Mihaly Varadi, Mainak Guharoy, Fruzsina Zsolyomi and Peter Tompa
    Citation: BMC Bioinformatics 2015 16:153
    Content type: Software Published on:

  34. The interactions between pathogen proteins and their hosts allow pathogens to manipulate host cellular mechanisms to their advantage. The identification of host proteins that are targeted by virulent pathogen ...

    Authors: Ailan F Arenas, Gladys E Salcedo, Andrey M Montoya and Jorge E Gomez-Marin
    Citation: BMC Bioinformatics 2015 16:152
    Content type: Research Article Published on:

  35. OMICs technologies allow to assay the state of a large number of different features (e.g., mRNA expression, miRNA expression, copy number variation, DNA methylation, etc.) from the same samples. The objective ...

    Authors: Michele Fratello, Angela Serra, Vittorio Fortino, Giancarlo Raiconi, Roberto Tagliaferri and Dario Greco
    Citation: BMC Bioinformatics 2015 16:151
    Content type: Research Article Published on:

  37. Electronic medical record (EMR) systems have become widely used throughout the world to improve the quality of healthcare and the efficiency of hospital services. A bilingual medical lexicon of Chinese and Eng...

    Authors: Yan Xu, Luoxin Chen, Junsheng Wei, Sophia Ananiadou, Yubo Fan, Yi Qian, Eric I-Chao Chang and Junichi Tsujii
    Citation: BMC Bioinformatics 2015 16:149
    Content type: Research article Published on:

  39. Profiling gene expression in brain structures at various spatial and temporal scales is essential to understanding how genes regulate the development of brain structures. The Allen Developing Mouse Brain Atlas...

    Authors: Tao Zeng, Rongjian Li, Ravi Mukkamala, Jieping Ye and Shuiwang Ji
    Citation: BMC Bioinformatics 2015 16:147
    Content type: Methodology Article Published on:

  44. Recent advances in synthetic biology have provided tools to efficiently construct complex DNA molecules which are an important part of many molecular biology and biotechnology projects. The planning of such co...

    Authors: Filipa Pereira, Flávio Azevedo, Ângela Carvalho, Gabriela F Ribeiro, Mark W Budde and Björn Johansson
    Citation: BMC Bioinformatics 2015 16:142
    Content type: Software Published on:

  45. Existing de novo software platforms have largely overlooked a valuable resource, the expertise of the intended biologist users. Typical data representations such as long gene lists, or highly dense and overlappin...

    Authors: Hieu T Nim, Milena B Furtado, Mauro W Costa, Nadia A Rosenthal, Hiroaki Kitano and Sarah E Boyd
    Citation: BMC Bioinformatics 2015 16:141
    Content type: Software Published on:

  46. For many years now, binding preferences of Transcription Factors have been described by so called motifs, usually mathematically defined by position weight matrices or similar models, for the purpose of predic...

    Authors: Michal Dabrowski, Norbert Dojer, Izabella Krystkowiak, Bozena Kaminska and Bartek Wilczynski
    Citation: BMC Bioinformatics 2015 16:140
    Content type: Research Article Published on:

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