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  1. Ontological concepts are useful for many different biomedical tasks. Concepts are difficult to recognize in text due to a disconnect between what is captured in an ontology and how the concepts are expressed i...

    Authors: Christopher Funk, William Baumgartner Jr, Benjamin Garcia, Christophe Roeder, Michael Bada, K Bretonnel Cohen, Lawrence E Hunter and Karin Verspoor
    Citation: BMC Bioinformatics 2014 15:59
    Content type: Research article Published on:

  2. RNA molecules, especially non-coding RNAs, play vital roles in the cell and their biological functions are mostly determined by structural properties. Often, these properties are related to dynamic changes in ...

    Authors: Jiabin Huang and Björn Voß
    Citation: BMC Bioinformatics 2014 15:60
    Content type: Research article Published on:

  4. Evidence suggests that common complex diseases may be partially due to SNP-SNP interactions, but such detection is yet to be fully established in a high-dimensional small-sample (small-n-large-p) study. A numb...

    Authors: Jianwei Gou, Yang Zhao, Yongyue Wei, Chen Wu, Ruyang Zhang, Yongyong Qiu, Ping Zeng, Wen Tan, Dianke Yu, Tangchun Wu, Zhibin Hu, Dongxin Lin, Hongbing Shen and Feng Chen
    Citation: BMC Bioinformatics 2014 15:62
    Content type: Research article Published on:

  5. Whole-genome sequencing represents a powerful experimental tool for pathogen research. We present methods for the analysis of small eukaryotic genomes, including a streamlined system (called Platypus) for find...

    Authors: Micah J Manary, Suriya S Singhakul, Erika L Flannery, Selina ER Bopp, Victoria C Corey, Andrew Taylor Bright, Case W McNamara, John R Walker and Elizabeth A Winzeler
    Citation: BMC Bioinformatics 2014 15:63
    Content type: Software Published on:

  6. Many biomedical relation extraction systems are machine-learning based and have to be trained on large annotated corpora that are expensive and cumbersome to construct. We developed a knowledge-based relation ...

    Authors: Ning Kang, Bharat Singh, Chinh Bui, Zubair Afzal, Erik M van Mulligen and Jan A Kors
    Citation: BMC Bioinformatics 2014 15:64
    Content type: Research article Published on:

  8. Genomic information allows population relatedness to be inferred and selected genes to be identified. Single nucleotide polymorphism microarray (SNP-chip) data, a proxy for genome composition, contains pattern...

    Authors: Nicholas J Hudson, Laercio R Porto-Neto, James Kijas, Sean McWilliam, Ryan J Taft and Antonio Reverter
    Citation: BMC Bioinformatics 2014 15:66
    Content type: Research article Published on:

  9. The editors of BMC Bioinformatics would like to thank all our reviewers who have contributed their time to the journal in Volume 14 (2013).

    Authors: Irene Pala
    Citation: BMC Bioinformatics 2014 15:67
    Content type: Reviewer acknowledgement Published on:

  10. Information about drug-target relations is at the heart of drug discovery. There are now dozens of databases providing drug-target interaction data with varying scope, and focus. Therefore, and due to the larg...

    Authors: Helge G Roider, Nadia Pavlova, Ivaylo Kirov, Stoyan Slavov, Todor Slavov, Zlatyo Uzunov and Bertram Weiss
    Citation: BMC Bioinformatics 2014 15:68
    Content type: Database Published on:

  11. Mandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets. Anal...

    Authors: Zhuohui Gan, Jianwu Wang, Nathan Salomonis, Jennifer C Stowe, Gabriel G Haddad, Andrew D McCulloch, Ilkay Altintas and Alexander C Zambon
    Citation: BMC Bioinformatics 2014 15:69
    Content type: Software Published on:

  13. Transposition event detection of transposable element (TE) in the genome using short reads from the next-generation sequence (NGS) was difficult, because the nucleotide sequence of TE itself is repetitive, mak...

    Authors: Mariko Nakagome, Elena Solovieva, Akira Takahashi, Hiroshi Yasue, Hirohiko Hirochika and Akio Miyao
    Citation: BMC Bioinformatics 2014 15:71
    Content type: Research article Published on:

  14. The correlations of genotypic and phenotypic tests with treatment, clinical history and the significance of mutations in viruses of HIV-infected patients are used to establish resistance mutations to protease ...

    Authors: Carlos Mata-Munguía, Martha Escoto-Delgadillo, Blanca Torres-Mendoza, Mario Flores-Soto, Mildred Vázquez-Torres, Francisco Gálvez-Gastelum, Arturo Viniegra-Osorio, Marcelo Castillero-Manzano and Eduardo Vázquez-Valls
    Citation: BMC Bioinformatics 2014 15:72
    Content type: Research article Published on:

  15. MicroRNAs (miRNAs) are short (19-23 nucleotides) non-coding RNAs that bind to sites in the 3’untranslated regions (3’UTR) of a targeted messenger RNA (mRNA). Binding leads to degradation of the transcript or b...

    Authors: Mehmet Deveci, Ümit V Çatalyürek and Amanda Ewart Toland
    Citation: BMC Bioinformatics 2014 15:73
    Content type: Software Published on:

  17. Following last year's computational vaccinology workshop in Shanghai, China, the third ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2013) was held in Barcelona, Spain. ICoVax 2013 provided an ...

    Authors: Anne S De Groot, Phoebe De Groot and Yongqun He
    Citation: BMC Bioinformatics 2014 15(Suppl 4):I1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

  18. Immune recognition of foreign proteins by T cells hinges on the formation of a ternary complex sandwiching a constituent peptide of the protein between a major histocompatibility complex (MHC) molecule and a T...

    Authors: Lu He, Anne S De Groot, Andres H Gutierrez, William D Martin, Lenny Moise and Chris Bailey-Kellogg
    Citation: BMC Bioinformatics 2014 15(Suppl 4):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

  20. Western drugs have achieved great successes in CVDs treatment. However, they may lead to some side effects and drug resistance. On the other hand, more and more studies found that Traditional Chinese herbs hav...

    Authors: Peng Fu, Linlin Yang, Yi Sun, Li Ye, Zhiwei Cao and Kailin Tang
    Citation: BMC Bioinformatics 2014 15(Suppl 4):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 4

  21. CA_C2195 from Clostridium acetobutylicum is a protein of unknown function. Sequence analysis predicted that part of the protein contained a metallopeptidase-related domain. There are over 200 homologs of similar ...

    Authors: Debanu Das, Alexey G Murzin, Neil D Rawlings, Robert D Finn, Penelope Coggill, Alex Bateman, Adam Godzik and L Aravind
    Citation: BMC Bioinformatics 2014 15:75
    Content type: Research article Published on:

  22. Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances i...

    Authors: Simon Roux, Jeremy Tournayre, Antoine Mahul, Didier Debroas and François Enault
    Citation: BMC Bioinformatics 2014 15:76
    Content type: Software Published on:

  23. Recent efforts in HIV-1 vaccine design have focused on immunogens that evoke potent neutralizing antibody responses to a broad spectrum of viruses circulating worldwide. However, the development of effective v...

    Authors: Mark C Evans, Pham Phung, Agnes C Paquet, Anvi Parikh, Christos J Petropoulos, Terri Wrin and Mojgan Haddad
    Citation: BMC Bioinformatics 2014 15:77
    Content type: Research article Published on:

  24. Chromothripsis, a newly discovered type of complex genomic rearrangement, has been implicated in the evolution of several types of cancers. To date, it has been described in bone cancer, SHH-medulloblastoma an...

    Authors: Shaylan K Govind, Amin Zia, Pablo H Hennings-Yeomans, John D Watson, Michael Fraser, Catalina Anghel, Alexander W Wyatt, Theodorus van der Kwast, Colin C Collins, John D McPherson, Robert G Bristow and Paul C Boutros
    Citation: BMC Bioinformatics 2014 15:78
    Content type: Software Published on:

  25. Identifying differentially expressed genes (DEG) is a fundamental step in studies that perform genome wide expression profiling. Typically, DEG are identified by univariate approaches such as Significance Anal...

    Authors: Neil R Clark, Kevin S Hu, Axel S Feldmann, Yan Kou, Edward Y Chen, Qiaonan Duan and Avi Ma’ayan
    Citation: BMC Bioinformatics 2014 15:79
    Content type: Research article Published on:

  26. A number of evolutionary models have been widely used for sequence alignment, phylogenetic tree reconstruction, and database searches. These models focus on how sets of independent substitutions between amino ...

    Authors: Dawit Nigatu, Attiya Mahmood and Werner Henkel
    Citation: BMC Bioinformatics 2014 15:80
    Content type: Research article Published on:

  27. RNA-seq data is currently underutilized, in part because it is difficult to predict the functional impact of alternate transcription events. Recent software improvements in full-length transcript deconvolution...

    Authors: Kristoffer Vitting-Seerup, Bo Torben Porse, Albin Sandelin and Johannes Waage
    Citation: BMC Bioinformatics 2014 15:81
    Content type: Software Published on:

  28. Transient protein-protein interactions (PPIs), which underly most biological processes, are a prime target for therapeutic development. Immense progress has been made towards computational prediction of PPIs u...

    Authors: Calem J Bendell, Shalon Liu, Tristan Aumentado-Armstrong, Bogdan Istrate, Paul T Cernek, Samuel Khan, Sergiu Picioreanu, Michael Zhao and Robert A Murgita
    Citation: BMC Bioinformatics 2014 15:82
    Content type: Research article Published on:

  29. The circadian clock is a critical regulator of biological functions controlling behavioral, physiological and biochemical processes. Because the liver is the primary regulator of metabolites within the mammali...

    Authors: Tung T Nguyen, John SA Mattick, Qian Yang, Mehmet A Orman, Marianthi G Ierapetritou, Francois Berthiaume and Ioannis P Androulakis
    Citation: BMC Bioinformatics 2014 15:83
    Content type: Research article Published on:

  30. New experimental methods must be developed to study interaction networks in systems biology. To reduce biological noise, individual subjects, such as single cells, should be analyzed using high throughput appr...

    Authors: Chandrasekhar Ramakrishnan, Andrej Bieri, Nora Sauter, Sophie Roizard, Philippe Ringler, Shirley A Müller, Kenneth N Goldie, Kaloyan Enimanev, Henning Stahlberg, Bernd Rinn and Thomas Braun
    Citation: BMC Bioinformatics 2014 15:84
    Content type: Software Published on:

  31. 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein...

    Authors: László Kaján, Thomas A Hopf, Matúš Kalaš, Debora S Marks and Burkhard Rost
    Citation: BMC Bioinformatics 2014 15:85
    Content type: Software Published on:

  32. It is well known that the development of cancer is caused by the accumulation of somatic mutations within the genome. For oncogenes specifically, current research suggests that there is a small set of "driver"...

    Authors: Gregory A Ryslik, Yuwei Cheng, Kei-Hoi Cheung, Yorgo Modis and Hongyu Zhao
    Citation: BMC Bioinformatics 2014 15:86
    Content type: Methodology article Published on:

  33. The accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. T...

    Authors: Brett Hanson, Charles Westin, Mario Rosa, Alexander Grier, Mikhail Osipovitch, Madolyn L MacDonald, Greg Dodge, Paule M Boli, Cyprian W Corwin, Haeja Kessler, Talia McKay, Herbert J Bernstein and Paul A Craig
    Citation: BMC Bioinformatics 2014 15:87
    Content type: Software Published on:

  35. Differential RNA sequencing (dRNA-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (TSS) ...

    Authors: Fabian Amman, Michael T Wolfinger, Ronny Lorenz, Ivo L Hofacker, Peter F Stadler and Sven Findeiß
    Citation: BMC Bioinformatics 2014 15:89
    Content type: Software Published on:

  37. High-throughput sequencing is now regularly used for studies of the transcriptome (RNA-seq), particularly for comparisons among experimental conditions. For the time being, a limited number of biological repli...

    Authors: Andrea Rau, Guillemette Marot and Florence Jaffrézic
    Citation: BMC Bioinformatics 2014 15:91
    Content type: Methodology article Published on:

  39. Amino acid sequences and features extracted from such sequences have been used to predict many protein properties, such as subcellular localization or solubility, using classifier algorithms. Although software...

    Authors: Bastiaan A van den Berg, Marcel JT Reinders, Johannes A Roubos and Dick de Ridder
    Citation: BMC Bioinformatics 2014 15:93
    Content type: Software Published on:

  40. In this study we consider DNA sequences as mathematical strings. Total and reduced alignments between two DNA sequences have been considered in the literature to measure their similarity. Results for explicit ...

    Authors: Helena Andrade, Iván Area, Juan J Nieto and Ángela Torres
    Citation: BMC Bioinformatics 2014 15:94
    Content type: Research article Published on:

  42. The identification of functionally or structurally important non-conserved residue sites in protein MSAs is an important challenge for understanding the structural basis and molecular mechanism of protein func...

    Authors: Mehmet Gültas, Güncel Düzgün, Sebastian Herzog, Sven Joachim Jäger, Cornelia Meckbach, Edgar Wingender and Stephan Waack
    Citation: BMC Bioinformatics 2014 15:96
    Content type: Methodology article Published on:

  43. Over the last decade, metabolomics has evolved into a mainstream enterprise utilized by many laboratories globally. Like other “omics” data, metabolomics data has the characteristics of a smaller sample size c...

    Authors: Suyan Tian, Howard H Chang, Chi Wang, Jing Jiang, Xiaomei Wang and Junqi Niu
    Citation: BMC Bioinformatics 2014 15:97
    Content type: Research article Published on:

  44. Measuring the impact of combinations of genetic or chemical perturbations on cellular fitness, sometimes referred to as synthetic lethal screening, is a powerful method for obtaining novel insights into gene f...

    Authors: Markus K Muellner, Gerhard Duernberger, Florian Ganglberger, Claudia Kerzendorfer, Iris Z Uras, Andreas Schoenegger, Klaudia Bagienski, Jacques Colinge and Sebastian MB Nijman
    Citation: BMC Bioinformatics 2014 15:98
    Content type: Software Published on:

  45. Recent advances in rapid, low-cost sequencing have opened up the opportunity to study complete genome sequences. The computational approach of multiple genome alignment allows investigation of evolutionarily r...

    Authors: Birte Kehr, Kathrin Trappe, Manuel Holtgrewe and Knut Reinert
    Citation: BMC Bioinformatics 2014 15:99
    Content type: Research article Published on:

  47. It is a common practice in bioinformatics to validate each group returned by a clustering algorithm through manual analysis, according to a-priori biological knowledge. This procedure helps finding functionally r...

    Authors: Diego H Milone, Georgina Stegmayer, Mariana López, Laura Kamenetzky and Fernando Carrari
    Citation: BMC Bioinformatics 2014 15:101
    Content type: Research article Published on:

  49. Protein–protein interactions can be seen as a hierarchical process occurring at three related levels: proteins bind by means of specific domains, which in turn form interfaces through patches of residues. Detaile...

    Authors: Claudio Saccà, Stefano Teso, Michelangelo Diligenti and Andrea Passerini
    Citation: BMC Bioinformatics 2014 15:103
    Content type: Methodology article Published on:

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