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  1. The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is incr...

    Authors: Fernando I. Gutiérrez, Felipe Rodriguez-Valenzuela, Ignacio L. Ibarra, Damien P. Devos and Francisco Melo
    Citation: BMC Bioinformatics 2016 17:20
    Content type: Methodology article Published on:

  2. In genome-wide association studies (GWAS) for complex diseases, the association between a SNP and each phenotype is usually weak. Combining multiple related phenotypic traits can increase the power of gene sea...

    Authors: James J. Yang, Jia Li, L. Keoki Williams and Anne Buu
    Citation: BMC Bioinformatics 2016 17:19
    Content type: Methodology Article Published on:

  3. Differential networks have recently been introduced as a powerful way to study the dynamic rewiring capabilities of an interactome in response to changing environmental conditions or stimuli. Currently, such d...

    Authors: Sofie Van Landeghem, Thomas Van Parys, Marieke Dubois, Dirk Inzé and Yves Van de Peer
    Citation: BMC Bioinformatics 2016 17:18
    Content type: Research Article Published on:

  4. Signaling pathways play important roles in the life processes of cell growth, cell apoptosis and organism development. At present the signal transduction networks are far from complete. As an effective complem...

    Authors: Suyu Mei and Hao Zhu
    Citation: BMC Bioinformatics 2015 16:417
    Content type: Research article Published on:

  5. The detection of pathogens in complex sample backgrounds has been revolutionized by wide access to next-generation sequencing (NGS) platforms. However, analytical methods to support NGS platforms are not as un...

    Authors: Andy Kilianski, Patrick Carcel, Shijie Yao, Pierce Roth, Josh Schulte, Greg B. Donarum, Ed T. Fochler, Jessica M. Hill, Alvin T. Liem, Michael R. Wiley, Jason T. Ladner, Bradley P. Pfeffer, Oliver Elliot, Alexandra Petrosov, Dereje D. Jima, Tyghe G. Vallard…
    Citation: BMC Bioinformatics 2015 16:416
    Content type: Software Published on:

  6. Precision medicine requires the tight integration of clinical and molecular data. To this end, it is mandatory to define proper technological solutions able to manage the overwhelming amount of high throughput...

    Authors: Matteo Gabetta, Ivan Limongelli, Ettore Rizzo, Alberto Riva, Daniele Segagni and Riccardo Bellazzi
    Citation: BMC Bioinformatics 2015 16:415
    Content type: Software Published on:

  9. Microarray analysis represents a powerful way to test scientific hypotheses on the functionality of cells. The measurements consider the whole genome, and the large number of generated data requires sophistica...

    Authors: Bogdan Belean, Monica Borda, Jörg Ackermann, Ina Koch and Ovidiu Balacescu
    Citation: BMC Bioinformatics 2015 16:412
    Content type: Research Article Published on:

  10. GIW/InCoB2015 the joint 26th International Conference on Genome Informatics (GIW) and 14th International Conference on Bioinformatics (InCoB) held in Tokyo, September 9-11, 2015 was attended by over 200 delega...

    Authors: Christian Schönbach, Paul Horton, Siu-Ming Yiu, Tin Wee Tan and Shoba Ranganathan
    Citation: BMC Bioinformatics 2015 16(Suppl 18):I1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  11. The human immunodeficiency virus (HIV-1) is a retrovirus causing acquired immunodeficiency syndrome (AIDS), which has become a serious problem across the world and has no cure reported to date. Human immunodef...

    Authors: Ankita Gupta, Salma Jamal, Sukriti Goyal, Ritu Jain, Divya Wahi and Abhinav Grover
    Citation: BMC Bioinformatics 2015 16(Suppl 19):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 19

  12. Complex diseases are characterized as being polygenic and multifactorial, so this poses a challenge regarding the search for genes related to them. With the advent of high-throughput technologies for genome se...

    Authors: Sérgio N Simões, David C Martins Jr, Carlos AB Pereira, Ronaldo F Hashimoto and Helena Brentani
    Citation: BMC Bioinformatics 2015 16(Suppl 19):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 19

  13. Cytotoxicity assays have been used by researchers to screen for cytotoxicity in compound libraries. Researchers can either look for cytotoxic compounds or screen "hits" from initial high-throughput drug screen...

    Authors: Alessandra C Faria-Campos, Luciene B Balottin, Gianlucca Zuin, Vinicius Garcia, Paulo HS Batista, José M Granjeiro and Sérgio VA Campos
    Citation: BMC Bioinformatics 2015 16(Suppl 19):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 19

  14. The humoral immune system response is based on the interaction between antibodies and antigens for the clearance of pathogens and foreign molecules. The interaction between these proteins occurs at specific po...

    Authors: Edgar Ernesto Gonzalez Kozlova, Benjamin Thomas Viart, Ricardo Andrez Machado de Avila, Liza Figueredo Felicori and Carlos Chavez-Olortegui
    Citation: BMC Bioinformatics 2015 16(Suppl 19):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 19

  15. The reconstruction of evolutionary scenarios for whole genomes in terms of genome rearrangements is a fundamental problem in evolutionary and comparative genomics. The DeCo algorithm, recently introduced by Bé...

    Authors: Cedric Chauve, Yann Ponty and João Paulo Pereira Zanetti
    Citation: BMC Bioinformatics 2015 16(Suppl 19):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 19

  16. The advent of rapid evolution on sequencing capacity of new genomes has evidenced the need for data analysis automation aiming at speeding up the genomic annotation process and reducing its cost. Given that on...

    Authors: Sávio G Carvalho, Renata Guerra-Sá and Luiz H de C Merschmann
    Citation: BMC Bioinformatics 2015 16(Suppl 19):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 19

  17. There exists a large number of rare and complex diseases that are neglected due to the difficulty in diagnosis and treatment. Being rare, they normally do not justify the costs of developing an especialized El...

    Authors: Alessandra C Faria-Campos, Lucas A Hanke, Paulo HS Batista, Vinicius Garcia and Sérgio VA Campos
    Citation: BMC Bioinformatics 2015 16(Suppl 19):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 19

  18. Large-scale mutational events that occur when stretches of DNA sequence move throughout genomes are called genome rearrangements. In bacteria, inversions are one of the most frequently observed rearrangements....

    Authors: Christian Baudet, Ulisses Dias and Zanoni Dias
    Citation: BMC Bioinformatics 2015 16(Suppl 19):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 19

  19. Dynamic programming algorithms provide exact solutions to many problems in computational biology, such as sequence alignment, RNA folding, hidden Markov models (HMMs), and scoring of phylogenetic trees. Struct...

    Authors: Christian Höner zu Siederdissen, Sonja J Prohaska and Peter F Stadler
    Citation: BMC Bioinformatics 2015 16(Suppl 19):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 19

  20. Finding the smallest sequence of operations to transform one genome into another is an important problem in comparative genomics. The breakpoint graph is a discrete structure that has proven to be effective in...

    Authors: Pedro Feijão, Fábio Viduani Martinez and Annelyse Thévenin
    Citation: BMC Bioinformatics 2015 16(Suppl 19):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 19

  23. Short and long range correlations in biological sequences are central in genomic studies of covariation. These correlations can be studied using mutual information because it measures the amount of information...

    Authors: Flavio Lichtenstein, Fernando Antoneli Jr and Marcelo R. S. Briones
    Citation: BMC Bioinformatics 2015 16:409
    Content type: Software Published on:

  24. Hepatocellular carcinoma (HCC) is an aggressive epithelial tumor which shows very poor prognosis and high rate of recurrence, representing an urgent problem for public healthcare. MicroRNAs (miRNAs/miRs) are a...

    Authors: Filippo Del Vecchio, Francesco Gallo, Antinisca Di Marco, Valentina Mastroiaco, Pasquale Caianiello, Francesca Zazzeroni, Edoardo Alesse and Alessandra Tessitore
    Citation: BMC Bioinformatics 2015 16:408
    Content type: Research article Published on:

  27. Transgenerational epigenetics (TGE) are currently considered important in disease, but the mechanisms involved are not yet fully understood. TGE abnormalities expected to cause disease are likely to be initiat...

    Authors: Y-h Taguchi
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  28. In recent years, high throughput and non-invasive Raman spectrometry technique has matured as an effective approach to identification of individual cells by species, even in complex, mixed populations. Raman p...

    Authors: Shiwei Sun, Xuetao Wang, Xin Gao, Lihui Ren, Xiaoquan Su, Dongbo Bu and Kang Ning
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  29. Protein-protein interactions (PPIs) are involved in various biological processes, and underlying mechanism of the interactions plays a crucial role in therapeutics and protein engineering. Most machine learnin...

    Authors: Yerukala Sathipati Srinivasulu, Jyun-Rong Wang, Kai-Ti Hsu, Ming-Ju Tsai, Phasit Charoenkwan, Wen-Lin Huang, Hui-Ling Huang and Shinn-Ying Ho
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  30. Next-generation sequencing (NGS) technology has transformed metagenomics because the high-throughput data allow an in-depth exploration of a complex microbial community. However, accurate species identificatio...

    Authors: Yi-Lin Chen, Chuan-Chun Lee, Ya-Lan Lin, Kai-Min Yin, Chung-Liang Ho and Tsunglin Liu
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  31. The incomplete ground truth of training data of B-cell epitopes is a demanding issue in computational epitope prediction. The challenge is that only a small fraction of the surface residues of an antigen are c...

    Authors: Jing Ren, Qian Liu, John Ellis and Jinyan Li
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  32. Next-generation sequencing (NGS) technologies has brought an unprecedented amount of genomic data for analysis. Unlike array-based profiling technologies, NGS can reveal the expression profile across a transcr...

    Authors: Che-Wei Chang, Wen-Bin Lee, An Chen-Deng, Tsunglin Liu, Joseph T Tseng and Darby Tien-Hao Chang
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  33. Protein O-GlcNAcylation, involving the β-attachment of single N-acetylglucosamine (GlcNAc) to the hydroxyl group of serine or threonine residues, is an O-linked glycosylation catalyzed by O-GlcNAc transferase (OG...

    Authors: Hui-Ju Kao, Chien-Hsun Huang, Neil Arvin Bretaña, Cheng-Tsung Lu, Kai-Yao Huang, Shun-Long Weng and Tzong-Yi Lee
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  34. Neddylation is a reversible post-translational modification that plays a vital role in maintaining cellular machinery. It is shown to affect localization, binding partners and structure of target proteins. Dis...

    Authors: Ahmet Sinan Yavuz, Namık Berk Sözer and Osman Uğur Sezerman
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  35. Protein-protein interaction (PPI) is essential for molecular functions in biological cells. Investigation on protein interfaces of known complexes is an important step towards deciphering the driving forces of...

    Authors: Gopichandran Sowmya and Shoba Ranganathan
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  37. Searching for similar compounds in a database is the most important process for in-silico drug screening. Since a query compound is an important starting point for the new drug, a query holder, who is afraid o...

    Authors: Kana Shimizu, Koji Nuida, Hiromi Arai, Shigeo Mitsunari, Nuttapong Attrapadung, Michiaki Hamada, Koji Tsuda, Takatsugu Hirokawa, Jun Sakuma, Goichiro Hanaoka and Kiyoshi Asai
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  38. The potential utility of the Burrows-Wheeler transform (BWT) of a large amount of short-read data ("reads") has not been fully studied. The BWT basically serves as a lossless dictionary of reads, unlike the he...

    Authors: Kouichi Kimura and Asako Koike
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  39. Copepods are planktonic organisms that play a major role in the marine food chain. Studying the community structure and abundance of copepods in relation to the environment is essential to evaluate their contr...

    Authors: Lee Kien Leow, Li-Lee Chew, Ving Ching Chong and Sarinder Kaur Dhillon
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  40. Estimating the number of different species (richness) in a mixed microbial population has been a main focus in metagenomic research. Existing methods of species richness estimation ride on the assumption that the...

    Authors: Duleepa Jayasundara, I Saeed, BC Chang, Sen-Lin Tang and Saman K Halgamuge
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  41. Computational identification of cooperative transcription factor (TF) pairs helps understand the combinatorial regulation of gene expression in eukaryotic cells. Many advanced algorithms have been proposed to ...

    Authors: Fu-Jou Lai, Hong-Tsun Chang and Wei-Sheng Wu
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  42. Alzheimer's disease is a multifactorial disorder that may be diagnosed earlier using a combination of tests rather than any single test. Search algorithms and optimization techniques in combination with model ...

    Authors: Luke Vandewater, Vladimir Brusic, William Wilson, Lance Macaulay and Ping Zhang
    Citation: BMC Bioinformatics 2015 16(Suppl 18):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 18

  43. Next-generation RNA sequencing technologies have been widely applied in transcriptome profiling. This facilitates further studies of gene structure and expression on the genome wide scale. It is an important s...

    Authors: Chong Chu, Xin Li and Yufeng Wu
    Citation: BMC Bioinformatics 2015 16(Suppl 17):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 17

  44. The loss of duplicate genes - fractionation - after whole genome doubling (WGD) is the subject to a debate as to whether it proceeds gene by gene or through deletion of multi-gene chromosomal segments.

    Authors: David Sankoff, Chunfang Zheng, Baoyong Wang and Carlos Fernando Buen Abad Najar
    Citation: BMC Bioinformatics 2015 16(Suppl 17):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 17

  45. Probabilistic models have gained widespread acceptance in the systems biology community as a useful way to represent complex biological systems. Such models are developed using existing knowledge of the struct...

    Authors: Faraz Hussain, Christopher J Langmead, Qi Mi, Joyeeta Dutta-Moscato, Yoram Vodovotz and Sumit K Jha
    Citation: BMC Bioinformatics 2015 16(Suppl 17):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 17

  46. Continued advances in next generation short-read sequencing technologies are increasing throughput and read lengths, while driving down error rates. Taking advantage of the high coverage sampling used in many ...

    Authors: Soumitra Pal and Srinivas Aluru
    Citation: BMC Bioinformatics 2015 16(Suppl 17):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 17

  47. Studying biological networks is of extreme importance in understanding cellular functions. These networks model interactions between molecules in each cell. A large volume of research has been done to uncover ...

    Authors: Haitham Gabr and Tamer Kahveci
    Citation: BMC Bioinformatics 2015 16(Suppl 17):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 17

  48. The identification of new therapeutic uses of existing drugs, or drug repositioning, offers the possibility of faster drug development, reduced risk, lesser cost and shorter paths to approval. The advent of hi...

    Authors: KM Shabana, KA Abdul Nazeer, Meeta Pradhan and Mathew Palakal
    Citation: BMC Bioinformatics 2015 16(Suppl 17):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 17

  49. The digitization of health-related information through electronic health records (EHR) and electronic healthcare reimbursement claims and the continued growth of self-reported health information through social...

    Authors: Arvind Ramanathan, Laura L Pullum, Tanner C Hobson, Chad A Steed, Shannon P Quinn, Chakra S Chennubhotla and Silvia Valkova
    Citation: BMC Bioinformatics 2015 16(Suppl 17):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 17

  50. In highly parallel next-generation sequencing (NGS) techniques millions to billions of short reads are produced from a genomic sequence in a single run. Due to the limitation of the NGS technologies, there cou...

    Authors: Subrata Saha and Sanguthevar Rajasekaran
    Citation: BMC Bioinformatics 2015 16(Suppl 17):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 16 Supplement 17

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