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  1. Text mining services are rapidly becoming a crucial component of various knowledge management pipelines, for example in the process of database curation, or for exploration and enrichment of biomedical data wi...

    Authors: Fabio Rinaldi, Simon Clematide, Hernani Marques, Tilia Ellendorff, Martin Romacker and Raul Rodriguez-Esteban
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 14

  2. The reliability and reproducibility of experimental procedures is a cornerstone of scientific practice. There is a pressing technological need for the better representation of biomedical protocols to enable ot...

    Authors: Larisa N Soldatova, Daniel Nadis, Ross D King, Piyali S Basu, Emma Haddi, Véronique Baumlé, Nigel J Saunders, Wolfgang Marwan and Brian B Rudkin
    Citation: BMC Bioinformatics 2014 15(Suppl 14):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 14

  3. Label-free quantitation of mass spectrometric data is one of the simplest and least expensive methods for differential expression profiling of proteins and metabolites. The need for high accuracy and performan...

    Authors: Ken Aoshima, Kentaro Takahashi, Masayuki Ikawa, Takayuki Kimura, Mitsuru Fukuda, Satoshi Tanaka, Howell E Parry, Yuichiro Fujita, Akiyasu C Yoshizawa, Shin-ichi Utsunomiya, Shigeki Kajihara, Koichi Tanaka and Yoshiya Oda
    Citation: BMC Bioinformatics 2014 15:376
    Content type: Methodology article Published on:

  4. Several types of genetic interactions in humans can be directly or indirectly associated with the causal effects of mutations. These interactions are usually based on their co-associations to biological proces...

    Authors: Rocío Rodríguez-López, Armando Reyes-Palomares, Francisca Sánchez-Jiménez and Miguel Ángel Medina
    Citation: BMC Bioinformatics 2014 15:375
    Content type: Software Published on:

  5. Most of the approaches for splice site prediction are based on machine learning techniques. Though, these approaches provide high prediction accuracy, the window lengths used are longer in size. Hence, these a...

    Authors: Prabina Kumar Meher, Tanmaya Kumar Sahu, Atmakuri Ramakrishna Rao and Sant Dass Wahi
    Citation: BMC Bioinformatics 2014 15:362
    Content type: Methodology article Published on:

  6. High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultane...

    Authors: Thorfinn Sand Korneliussen, Anders Albrechtsen and Rasmus Nielsen
    Citation: BMC Bioinformatics 2014 15:356
    Content type: Software Published on:

  7. Ribosome profiling (ribo-seq) provides experimental data on the density of elongating or initiating ribosomes at the whole transcriptome level that can be potentially used for estimating absolute levels of tra...

    Authors: Audrey M Michel, Dmitry E Andreev and Pavel V Baranov
    Citation: BMC Bioinformatics 2014 15:380
    Content type: Methodology article Published on:

  9. The rank product method is a powerful statistical technique for identifying differentially expressed molecules in replicated experiments. A critical issue in molecule selection is accurate calculation of the p-va...

    Authors: Tom Heskes, Rob Eisinga and Rainer Breitling
    Citation: BMC Bioinformatics 2014 15:367
    Content type: Methodology article Published on:

  11. Identification of the recombination hot/cold spots is critical for understanding the mechanism of recombination as well as the genome evolution process. However, experimental identification of recombination sp...

    Authors: Liqi Li, Sanjiu Yu, Weidong Xiao, Yongsheng Li, Lan Huang, Xiaoqi Zheng, Shiwen Zhou and Hua Yang
    Citation: BMC Bioinformatics 2014 15:340
    Content type: Research article Published on:

  12. Gene co-expression analysis has previously been based on measures that include correlation coefficients and mutual information, as well as newcomers such as MIC. These measures depend primarily on the degree o...

    Authors: Anna CT Abelin, Georgi K Marinov, Brian A Williams, Kenneth McCue and Barbara J Wold
    Citation: BMC Bioinformatics 2014 15:331
    Content type: Methodology article Published on:

  13. Transposable elements (TEs) are DNA sequences that are able to move from their location in the genome by cutting or copying themselves to another locus. As such, they are increasingly recognized as impacting a...

    Authors: Arthur Gilly, Mathilde Etcheverry, Mohammed-Amin Madoui, Julie Guy, Leandro Quadrana, Adriana Alberti, Antoine Martin, Tony Heitkam, Stefan Engelen, Karine Labadie, Jeremie Le Pen, Patrick Wincker, Vincent Colot and Jean-Marc Aury
    Citation: BMC Bioinformatics 2014 15:377
    Content type: Methodology article Published on:

  15. With the advance of next generation sequencing (NGS) technologies, a large number of insertion and deletion (indel) variants have been identified in human populations. Despite much research into variant callin...

    Authors: Zhiyi Li, Xiaowei Wu, Bin He and Liqing Zhang
    Citation: BMC Bioinformatics 2014 15:359
    Content type: Research article Published on:

  16. Deep shotgun sequencing on next generation sequencing (NGS) platforms has contributed significant amounts of data to enrich our understanding of genomes, transcriptomes, amplified single-cell genomes, and meta...

    Authors: Jamison M McCorrison, Pratap Venepally, Indresh Singh, Derrick E Fouts, Roger S Lasken and Barbara A Methé
    Citation: BMC Bioinformatics 2014 15:357
    Content type: Software Published on:

  17. Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is th...

    Authors: Daniel I Speiser, M Sabrina Pankey, Alexander K Zaharoff, Barbara A Battelle, Heather D Bracken-Grissom, Jesse W Breinholt, Seth M Bybee, Thomas W Cronin, Anders Garm, Annie R Lindgren, Nipam H Patel, Megan L Porter, Meredith E Protas, Ajna S Rivera, Jeanne M Serb, Kirk S Zigler…
    Citation: BMC Bioinformatics 2014 15:350
    Content type: Software Published on:

  18. Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is know...

    Authors: Lukáš Pravda, Karel Berka, Radka Svobodová Vařeková, David Sehnal, Pavel Banáš, Roman A Laskowski, Jaroslav Koča and Michal Otyepka
    Citation: BMC Bioinformatics 2014 15:379
    Content type: Research article Published on:

  19. One of the major challenges in the field of vaccine design is identifying B-cell epitopes in continuously evolving viruses. Various tools have been developed to predict linear or conformational epitopes, each ...

    Authors: Yuh-Jyh Hu, Shun-Chien Lin, Yu-Lung Lin, Kuan-Hui Lin and Shun-Ning You
    Citation: BMC Bioinformatics 2014 15:378
    Content type: Methodology article Published on:

  21. The excessive production of lactic acid by L. bulgaricus during yogurt storage is a phenomenon we are always tried to prevent. The methods used in industry either control the post-acidification inefficiently or k...

    Authors: Ke Liu, Xiangmiao Zeng, Lei Qiao, Xisheng Li, Yubo Yang, Cuihong Dai, Aiju Hou and Dechang Xu
    Citation: BMC Bioinformatics 2014 15(Suppl 13):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 13

  22. There is an ever-expanding range of technologies that generate very large numbers of biomarkers for research and clinical applications. Choosing the most informative biomarkers from a high-dimensional data set...

    Authors: Edward Hemphill, James Lindsay, Chih Lee, Ion I Măndoiu and Craig E Nelson
    Citation: BMC Bioinformatics 2014 15(Suppl 13):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 13

  23. Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees,...

    Authors: Pawel Górecki and Oliver Eulenstein
    Citation: BMC Bioinformatics 2014 15(Suppl 13):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 13

  24. Frequent subgraph mining is a useful method for extracting meaningful patterns from a set of graphs or a single large graph. Here, the graph represents all possible RNA structures and interactions. Patterns th...

    Authors: Alex R Gawronski and Marcel Turcotte
    Citation: BMC Bioinformatics 2014 15(Suppl 13):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 15 Supplement 13

  26. Terminal restriction fragment length polymorphism (T-RFLP) analysis is a DNA-fingerprinting method that can be used for comparisons of the microbial community composition in a large number of samples. There is...

    Authors: Nils Johan Fredriksson, Malte Hermansson and Britt-Marie Wilén
    Citation: BMC Bioinformatics 2014 15:361
    Content type: Software Published on:

  27. Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common DNA-fingerprinting technique used for comparisons of complex microbial communities. Although the technique is well established th...

    Authors: Nils Johan Fredriksson, Malte Hermansson and Britt-Marie Wilén
    Citation: BMC Bioinformatics 2014 15:360
    Content type: Methodology article Published on:

  29. In recent years, the biomedical literature has been growing rapidly. These articles provide a large amount of information about proteins, genes and their interactions. Reading such a huge amount of literature ...

    Authors: Yue Shang, Huihui Hao, Jiajin Wu and Hongfei Lin
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  30. The amount of biomedical literature available is growing at an explosive speed, but a large amount of useful information remains undiscovered in it. Researchers can make informed biomedical hypotheses through ...

    Authors: Liangxi Cheng, Hongfei Lin, Feng Zhou, Zhihao Yang and Jian Wang
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  31. The 3D chromatogram generated by High Performance Liquid Chromatography-Diode Array Detector (HPLC-DAD) has been researched widely in the field of herbal medicine, grape wine, agriculture, petroleum and so on....

    Authors: Lizhi Cui, Josiah Poon, Simon K Poon, Hao Chen, Junbin Gao, Paul Kwan, Kei Fan and Zhihao Ling
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  32. In recent years, many protein complex mining algorithms, such as classical clique percolation (CPM) method and markov clustering (MCL) algorithm, have developed for protein-protein interaction network. However...

    Authors: Xianjun Shen, Yanli Zhao, Yanan Li, Tingting He, Jincai Yang and Xiaohua Hu
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  33. DNA methylation is a common epigenetic marker that regulates gene expression. A robust and cost-effective way for measuring whole genome methylation is Methyl-CpG binding domain-based capture followed by seque...

    Authors: Zijing Mao, Chifeng Ma, Tim H-M Huang, Yidong Chen and Yufei Huang
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  34. The accurate packing of protein side chains is important for many computational biology problems, such as ab initio protein structure prediction, homology modelling, and protein design and ligand docking appli...

    Authors: Lijun Quan, Qiang Lü, Haiou Li, Xiaoyan Xia and Hongjie Wu
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  35. Protein-DNA interactions are essential for many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. DNA binding proteins can be classified into doub...

    Authors: Wei Wang, Juan Liu and Xionghui Zhou
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  36. Mathematical modeling is an important tool in systems biology to study the dynamic property of complex biological systems. However, one of the major challenges in systems biology is how to infer unknown parame...

    Authors: Qianqian Wu, Kate Smith-Miles and Tianhai Tian
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  37. The large influx of biological sequences poses the importance of identifying and correlating conserved regions in homologous sequences to acquire valuable biological knowledge. These conserved regions contain ...

    Authors: En-Shiun Annie Lee, Sanderz Fung, Ho-Yin Sze-To and Andrew K C Wong
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  38. Currently, most people use NCBI's PubMed to search the MEDLINE database, an important bibliographical information source for life science and biomedical information. However, PubMed has some drawbacks that mak...

    Authors: James Z Wang, Yuanyuan Zhang, Liang Dong, Lin Li, Pradip K Srimani and Philip S Yu
    Citation: BMC Bioinformatics 2014 15(Suppl 12):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 15 Supplement 12

  39. High-throughput molecular profiling data has been used to improve clinical decision making by stratifying subjects based on their molecular profiles. Unsupervised clustering algorithms can be used for stratifi...

    Authors: Shicai Wang, Ioannis Pandis, David Johnson, Ibrahim Emam, Florian Guitton, Axel Oehmichen and Yike Guo
    Citation: BMC Bioinformatics 2014 15:351
    Content type: Research article Published on:

  40. In modern biomedical research of complex diseases, a large number of demographic and clinical variables, herein called phenomic data, are often collected and missing values (MVs) are inevitable in the data col...

    Authors: Serena G Liao, Yan Lin, Dongwan D Kang, Divay Chandra, Jessica Bon, Naftali Kaminski, Frank C Sciurba and George C Tseng
    Citation: BMC Bioinformatics 2014 15:346
    Content type: Research article Published on:

  41. Handling the vast amount of gene expression data generated by genome-wide transcriptional profiling techniques is a challenging task, demanding an informed combination of pre-processing, filtering and analysis...

    Authors: Maysson Ibrahim, Sabah Jassim, Michael Anthony Cawthorne and Kenneth Langlands
    Citation: BMC Bioinformatics 2014 15:358
    Content type: Software Published on:

  43. A typical affinity purification coupled to mass spectrometry (AP-MS) experiment includes the purification of a target protein (bait) using an antibody and subsequent mass spectrometry analysis of all proteins ...

    Authors: Christopher K Hobbs, Michelle Leung, Herbert H Tsang and H Alexander Ebhardt
    Citation: BMC Bioinformatics 2014 15:344
    Content type: Software Published on:

  45. The complexity of biological data related to the genetic origins of tumour cells, originates significant challenges to glean valuable knowledge that can be used to predict therapeutic responses. In order to di...

    Authors: Elisabetta Fersini, Enza Messina and Francesco Archetti
    Citation: BMC Bioinformatics 2014 15:353
    Content type: Methodology Article Published on:

  46. As time series experiments in higher eukaryotes usually obtain data from different individuals collected at the different time points, a time series sample itself is not equivalent to a true biological replica...

    Authors: Wencke Walter, Bernd Striberny, Emmanuel Gaquerel, Ian T Baldwin, Sang-Gyu Kim and Ines Heiland
    Citation: BMC Bioinformatics 2014 15:352
    Content type: Methodology article Published on:

  47. Amino acid replacement rate matrices are a crucial component of many protein analysis systems such as sequence similarity search, sequence alignment, and phylogenetic inference. Ideally, the rate matrix reflec...

    Authors: Cuong Cao Dang, Vinh Sy Le, Olivier Gascuel, Bart Hazes and Quang Si Le
    Citation: BMC Bioinformatics 2014 15:341
    Content type: Research article Published on:

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