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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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

  15. 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

  16. 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. 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:

  19. 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:

  20. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  27. 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:

  28. 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:

  29. 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:

  31. 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:

  32. 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:

  33. Molecular data, e.g. arising from microarray technology, is often used for predicting survival probabilities of patients. For multivariate risk prediction models on such high-dimensional data, there are establ...

    Authors: Murat Sariyar, Isabell Hoffmann and Harald Binder
    Citation: BMC Bioinformatics 2014 15:58
    Content type: Research article Published on:

  34. Binding free energy and binding hot spots at protein-protein interfaces are two important research areas for understanding protein interactions. Computational methods have been developed previously for accurat...

    Authors: Qian Liu, Steven CH Hoi, Chee Keong Kwoh, Limsoon Wong and Jinyan Li
    Citation: BMC Bioinformatics 2014 15:57
    Content type: Research article Published on:

  35. Visualization of protein-ligand complex plays an important role in elaborating protein-ligand interactions and aiding novel drug design. Most existing web visualizers either rely on slow software rendering, or...

    Authors: Hongjian Li, Kwong-Sak Leung, Takanori Nakane and Man-Hon Wong
    Citation: BMC Bioinformatics 2014 15:56
    Content type: Software Published on:

  36. True date palms (Phoenix dactylifera L.) are impressive trees and have served as an indispensable source of food for mankind in tropical and subtropical countries for centuries. The aim of this study is to differ...

    Authors: Vladimir Arinkin, Ilya Digel, Dariusz Porst, Aysegül Temiz Artmann and Gerhard M Artmann
    Citation: BMC Bioinformatics 2014 15:55
    Content type: Research article Published on:

  37. Amyloids are proteins capable of forming fibrils whose intramolecular contact sites assume densely packed zipper pattern. Their oligomers can underlie serious diseases, e.g. Alzheimer’s and Parkinson’s disease...

    Authors: Pawel Gasior and Malgorzata Kotulska
    Citation: BMC Bioinformatics 2014 15:54
    Content type: Research article Published on:

  39. Along with the improvement of high throughput sequencing technologies, the genetics community is showing marked interest for the rare variants/common diseases hypothesis. While sequencing can still be prohibitive...

    Authors: Louis-Philippe Lemieux Perreault, Marc-André Legault, Amina Barhdadi, Sylvie Provost, Valérie Normand, Jean-Claude Tardif and Marie-Pierre Dubé
    Citation: BMC Bioinformatics 2014 15:52
    Content type: Methodology article Published on:

  40. Principal component analysis (PCA) has been widely used to visualize high-dimensional metabolomic data in a two- or three-dimensional subspace. In metabolomics, some metabolites (e.g., the top 10 metabolites) ...

    Authors: Hiroyuki Yamamoto, Tamaki Fujimori, Hajime Sato, Gen Ishikawa, Kenjiro Kami and Yoshiaki Ohashi
    Citation: BMC Bioinformatics 2014 15:51
    Content type: Methodology article Published on:

  41. Copy Number Variations (CNVs) are usually inferred from Single Nucleotide Polymorphism (SNP) arrays by use of some software packages based on given algorithms. However, there is no clear understanding of the p...

    Authors: Xin Zhang, Renqian Du, Shilin Li, Feng Zhang, Li Jin and Hongyan Wang
    Citation: BMC Bioinformatics 2014 15:50
    Content type: Software Published on:

  42. In the application of microarray data, how to select a small number of informative genes from thousands of genes that may contribute to the occurrence of cancers is an important issue. Many researchers use var...

    Authors: Kun-Huang Chen, Kung-Jeng Wang, Min-Lung Tsai, Kung-Min Wang, Angelia Melani Adrian, Wei-Chung Cheng, Tzu-Sen Yang, Nai-Chia Teng, Kuo-Pin Tan and Ku-Shang Chang
    Citation: BMC Bioinformatics 2014 15:49
    Content type: Methodology article Published on:

  43. As a fundamental genomic element, meiotic recombination hotspot plays important roles in life sciences. Thus uncovering its regulatory mechanisms has broad impact on biomedical research. Despite the recent ide...

    Authors: Peng Yang, Min Wu, Jing Guo, Chee Keong Kwoh, Teresa M Przytycka and Jie Zheng
    Citation: BMC Bioinformatics 2014 15:48
    Content type: Software Published on:

  44. PSEUDOMARKER is a software package that performs joint linkage and linkage disequilibrium analysis between a marker and a putative disease locus. A key feature of PSEUDOMARKER is that it can combine case-contr...

    Authors: Edward Michael Gertz, Tero Hiekkalinna, Sébastien Le Digabel, Charles Audet, Joseph D Terwilliger and Alejandro A Schäffer
    Citation: BMC Bioinformatics 2014 15:47
    Content type: Software Published on:

  50. This report summarizes the scientific content and activities of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB), held in conjunction with the...

    Authors: Tomás Di Domenico, Cynthia Prudence, Esmeralda Vicedo, Emre Guney, Anupama Jigisha and Avinash Shanmugam
    Citation: BMC Bioinformatics 2014 15(Suppl 3):A1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 15 Supplement 3

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