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  1. There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape (http://​cytoscape.​org/​) is one of ...

    Authors: Zakhar Sergeevich Mustafin, Sergey Alexandrovich Lashin, Yury Georgievich Matushkin, Konstantin Vladimirovich Gunbin and Dmitry Arkadievich Afonnikov
    Citation: BMC Bioinformatics 2017 18(Suppl 1):1427
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  2. Gene prediction is one of the most important steps in the genome annotation process. A large number of software tools and pipelines developed by various computing techniques are available for gene prediction. ...

    Authors: Kuang-Lim Chan, Rozana Rosli, Tatiana V. Tatarinova, Michael Hogan, Mohd Firdaus-Raih and Eng-Ti Leslie Low
    Citation: BMC Bioinformatics 2017 18(Suppl 1):1426
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  3. RNA editing is a co-transcriptional modification that increases the molecular diversity, alters secondary structure and protein coding sequences by changing the sequence of transcripts. The most common RNA edi...

    Authors: Michael Piechotta, Emanuel Wyler, Uwe Ohler, Markus Landthaler and Christoph Dieterich
    Citation: BMC Bioinformatics 2017 18:7
    Content type: Software Published on:

  5. Inferring the topology of gene regulatory networks (GRNs) from microarray gene expression data has many potential applications, such as identifying candidate drug targets and providing valuable insights into t...

    Authors: Shun Guo, Qingshan Jiang, Lifei Chen and Donghui Guo
    Citation: BMC Bioinformatics 2016 17:545
    Content type: Research article Published on:

  6. Gene expression data produced on high-throughput platforms such as microarrays is susceptible to much variation that obscures useful biological information. Therefore, preprocessing data with a suitable normal...

    Authors: Abha Belorkar and Limsoon Wong
    Citation: BMC Bioinformatics 2016 17(Suppl 17):540
    Content type: Research Published on:

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

  7. Since traditional drug research and development is often time-consuming and high-risk, there is an increasing interest in establishing new medical indications for approved drugs, referred to as drug reposition...

    Authors: Hui Liu, Yinglong Song, Jihong Guan, Libo Luo and Ziheng Zhuang
    Citation: BMC Bioinformatics 2016 17(Suppl 17):539
    Content type: Research Published on:

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

  8. De novo peptide sequencing via tandem mass spectrometry (MS/MS) has been developed rapidly in recent years. With the use of spectra pairs from the same peptide under different fragmentation modes, performance ...

    Authors: Yan Yan and Kaizhong Zhang
    Citation: BMC Bioinformatics 2016 17(Suppl 17):538
    Content type: Research Published on:

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

  9. Differentiation of human embryonic stem cells requires precise control of gene expression that depends on specific spatial and temporal epigenetic regulation. Recently available temporal epigenomic data derive...

    Authors: YangLan Gan, Han Tao, Guobing Zou, Cairong Yan and Jihong Guan
    Citation: BMC Bioinformatics 2016 17(Suppl 17):537
    Content type: Research Published on:

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

  10. Pathway analysis combining multiple types of high-throughput data, such as genomics and proteomics, has become the first choice to gain insights into the pathogenesis of complex diseases. Currently, several pa...

    Authors: Qiaosheng Zhang, Jie Li, Haozhe Xie, Hanqing Xue and Yadong Wang
    Citation: BMC Bioinformatics 2016 17(Suppl 17):536
    Content type: Research Published on:

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

  11. A gene regulatory network (GRN) represents interactions of genes inside a cell or tissue, in which vertexes and edges stand for genes and their regulatory interactions respectively. Reconstruction of gene regu...

    Authors: Guangyong Zheng, Yaochen Xu, Xiujun Zhang, Zhi-Ping Liu, Zhuo Wang, Luonan Chen and Xin-Guang Zhu
    Citation: BMC Bioinformatics 2016 17(Suppl 17):535
    Content type: Research Published on:

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

  12. Identification and analysis of recurrent combinatorial patterns of multiple chromatin modifications provide invaluable information for understanding epigenetic regulations. Furthermore, as more data becomes av...

    Authors: Nan Meng, Raghu Machiraju and Kun Huang
    Citation: BMC Bioinformatics 2016 17(Suppl 17):534
    Content type: Research Published on:

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

  13. The human immunodeficiency virus type 1 (HIV-1) aspartic protease is an important enzyme owing to its imperative part in viral development and a causative agent of deadliest disease known as acquired immune de...

    Authors: Onkar Singh and Emily Chia-Yu Su
    Citation: BMC Bioinformatics 2016 17(Suppl 17):478
    Content type: Research Published on:

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

  14. The primary goal of pathway analysis using transcriptome data is to find significantly perturbed pathways. However, pathway analysis is not always successful in identifying pathways that are truly relevant to ...

    Authors: Jusang Lee, Kyuri Jo, Sunwon Lee, Jaewoo Kang and Sun Kim
    Citation: BMC Bioinformatics 2016 17(Suppl 17):477
    Content type: Research Published on:

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

  15. With the developments of DNA sequencing technology, large amounts of sequencing data have become available in recent years and provide unprecedented opportunities for advanced association studies between somat...

    Authors: Yuchen Yuan, Yi Shi, Changyang Li, Jinman Kim, Weidong Cai, Zeguang Han and David Dagan Feng
    Citation: BMC Bioinformatics 2016 17(Suppl 17):476
    Content type: Research Published on:

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

  16. Pooled library screen analysis using shRNAs or CRISPR-Cas9 hold great promise to genome-wide functional studies. While pooled library screens are effective tools, erroneous barcodes can potentially be generate...

    Authors: Jihyeob Mun, Dong-Uk Kim, Kwang-Lae Hoe and Seon-Young Kim
    Citation: BMC Bioinformatics 2016 17(Suppl 17):475
    Content type: Research Published on:

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

  17. A draft genome assembled by current next-generation sequencing techniques from short reads is just a collection of contigs, whose relative positions and orientations along the genome being sequenced are unknow...

    Authors: Kun-Tze Chen, Cheih-Jung Chen, Hsin-Ting Shen, Chia-Liang Liu, Shang-Hao Huang and Chin Lung Lu
    Citation: BMC Bioinformatics 2016 17(Suppl 17):469
    Content type: Research Published on:

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

  18. Whole exome sequencing (WES) has recently emerged as an effective approach for identifying genetic variants underlying human diseases. However, considerable time and labour is needed for careful investigation ...

    Authors: Mengmeng Wu, Ting Chen and Rui Jiang
    Citation: BMC Bioinformatics 2016 17(Suppl 17):468
    Content type: Research Published on:

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

  19. Cancer is a complex disease which is characterized by the accumulation of genetic alterations during the patient’s lifetime. With the development of the next-generation sequencing technology, multiple omics da...

    Authors: Pi-Jing Wei, Di Zhang, Junfeng Xia and Chun-Hou Zheng
    Citation: BMC Bioinformatics 2016 17(Suppl 17):467
    Content type: Research Published on:

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

  20. The next-generation of sequencing technologies, along with the development of bioinformatics, are generating a growing number of reads every day. For the convenience of further research, these reads should be ...

    Authors: Song Liu, Yi Wang and Fei Wang
    Citation: BMC Bioinformatics 2016 17(Suppl 17):466
    Content type: Research Published on:

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

  21. Advances in experimental biology have enabled the collection of enormous troves of data on genomic variation in living organisms. The interpretation of this data to extract actionable information is one of the...

    Authors: Zeina Z. Shreif, Daniel M. Gatti and Vipul Periwal
    Citation: BMC Bioinformatics 2016 17:544
    Content type: Methodology Article Published on:

  22. The International Conference on Bioinformatics (InCoB) has been publishing peer-reviewed conference papers in BMC Bioinformatics since 2006. Of the 44 articles accepted for publication in supplement issues of ...

    Authors: Christian Schönbach, Chandra Verma, Peter J. Bond and Shoba Ranganathan
    Citation: BMC Bioinformatics 2016 17(Suppl 19):524
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  23. Microscopic analysis requires that foreground objects of interest, e.g. cells, are in focus. In a typical microscopic specimen, the foreground objects may lie on different depths of field necessitating capture...

    Authors: Apichart Intarapanich, Saowaluck Kaewkamnerd, Montri Pannarut, Philip J. Shaw and Sissades Tongsima
    Citation: BMC Bioinformatics 2016 17(Suppl 19):516
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  24. Tar DNA binding protein 43 (TDP-43) hyperphosphorylation, caused by Casein kinase 1 (CK-1) protein isoforms, is associated with the onset and progression of Amyotrophic Lateral Sclerosis (ALS). Among the repor...

    Authors: Kopal Joshi, Sukriti Goyal, Sonam Grover, Salma Jamal, Aditi Singh, Pawan Dhar and Abhinav Grover
    Citation: BMC Bioinformatics 2016 17(Suppl 19):515
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  25. Bacterial tyrosine-kinases (BY-kinases), which play an important role in numerous cellular processes, are characterized as a separate class of enzymes and share no structural similarity with their eukaryotic c...

    Authors: Tamara Vasylenko, Yi-Fan Liou, Po-Chin Chiou, Hsiao-Wei Chu, Yung-Sung Lai, Yu-Ling Chou, Hui-Ling Huang and Shinn-Ying Ho
    Citation: BMC Bioinformatics 2016 17(Suppl 19):514
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  26. Next-generation sequencing promises the de novo genomic and transcriptomic analysis of samples of interests. However, there are only a few organisms having reference genomic sequences and even fewer having well-d...

    Authors: Ruei-Chi Gan, Ting-Wen Chen, Timothy H. Wu, Po-Jung Huang, Chi-Ching Lee, Yuan-Ming Yeh, Cheng-Hsun Chiu, Hsien-Da Huang and Petrus Tang
    Citation: BMC Bioinformatics 2016 17(Suppl 19):513
    Content type: Software Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  27. Influenza virus spreads infection by two main surface glycoproteins, namely hemagglutinin (HA) and neuraminidase (NA). NA cleaves the sialic acid receptors eventually releasing newly formed virus particles whi...

    Authors: Dhwani Dholakia, Sukriti Goyal, Salma Jamal, Aditi Singh, Asmita Das and Abhinav Grover
    Citation: BMC Bioinformatics 2016 17(Suppl 19):512
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  28. Monogeneans are flatworms (Platyhelminthes) that are primarily found on gills and skin of fishes. Monogenean parasites have attachment appendages at their haptoral regions that help them to move about the body...

    Authors: Elham Yousef Kalafi, Wooi Boon Tan, Christopher Town and Sarinder Kaur Dhillon
    Citation: BMC Bioinformatics 2016 17(Suppl 19):511
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  29. Restriction site analysis involves determining the locations of restriction sites after the process of digestion by reconstructing their positions based on the lengths of the cut DNA. Using different reaction ...

    Authors: Mostafa M. Abbas and Hazem M. Bahig
    Citation: BMC Bioinformatics 2016 17(Suppl 19):510
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  30. Multiple computational methods for predicting drug-target interactions have been developed to facilitate the drug discovery process. These methods use available data on known drug-target interactions to train ...

    Authors: Ali Ezzat, Min Wu, Xiao-Li Li and Chee-Keong Kwoh
    Citation: BMC Bioinformatics 2016 17(Suppl 19):509
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  31. Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional a...

    Authors: Chao Xie, Chin Lui Wesley Goi, Daniel H. Huson, Peter F. R. Little and Rohan B. H. Williams
    Citation: BMC Bioinformatics 2016 17(Suppl 19):508
    Content type: Software Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  32. Regulation mechanisms between miRNAs and genes are complicated. To accomplish a biological function, a miRNA may regulate multiple target genes, and similarly a target gene may be regulated by multiple miRNAs....

    Authors: Chaowang Lan, Qingfeng Chen and Jinyan Li
    Citation: BMC Bioinformatics 2016 17(Suppl 19):507
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  34. Taxonomists frequently identify specimen from various populations based on the morphological characteristics and molecular data. This study looks into another invasive process in identification of house shrew (Su...

    Authors: Arpah Abu, Lee Kien Leow, Rosli Ramli and Hasmahzaiti Omar
    Citation: BMC Bioinformatics 2016 17(Suppl 19):505
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  35. Intrinsically Disordered Proteins (IDPs) lack an ordered three-dimensional structure and are enriched in various biological processes. The Molecular Recognition Features (MoRFs) are functional regions within I...

    Authors: Ronesh Sharma, Shiu Kumar, Tatsuhiko Tsunoda, Ashwini Patil and Alok Sharma
    Citation: BMC Bioinformatics 2016 17(Suppl 19):504
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  36. Most of hydrophilic and hydrophobic residues are thought to be exposed and buried in proteins, respectively. In contrast to the majority of the existing studies on protein folding characteristics using protein...

    Authors: Yi-Fan Liou, Hui-Ling Huang and Shinn-Ying Ho
    Citation: BMC Bioinformatics 2016 17(Suppl 19):503
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  37. Topic models are statistical algorithms which try to discover the structure of a set of documents according to the abstract topics contained in them. Here we try to apply this approach to the discovery of the ...

    Authors: Josep Basha Gutierrez and Kenta Nakai
    Citation: BMC Bioinformatics 2016 17(Suppl 19):502
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  38. Guanonine-protein (G-protein) is known as molecular switches inside cells, and is very important in signals transmission from outside to inside cell. Especially in transport protein, most of G-proteins play an...

    Authors: Nguyen-Quoc-Khanh Le and Yu-Yen Ou
    Citation: BMC Bioinformatics 2016 17(Suppl 19):501
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  39. Strategies to control HIV for improving the quality of patient lives have been aided by the Highly Active Anti-Retroviral Therapy (HAART), which consists of a cocktail of inhibitors targeting key viral enzymes...

    Authors: Chinh Tran-To Su, Wei-Li Ling, Wai-Heng Lua, Yu-Xuan Haw and Samuel Ken-En Gan
    Citation: BMC Bioinformatics 2016 17(Suppl 19):500
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  40. Cephalometric analysis and measurements of skull parameters using X-Ray images plays an important role in predicating and monitoring orthodontic treatment. Manual analysis and measurements of cephalometric is ...

    Authors: Mogeeb Ahmed Ahmed Mosleh, Mohd Sapiyan Baba, Sorayya Malek and Rasheed A. Almaktari
    Citation: BMC Bioinformatics 2016 17(Suppl 19):499
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  41. Mathematical and computational models showed to be a very important support tool for the comprehension of the immune system response against pathogens. Models and simulations allowed to study the immune system...

    Authors: Marzio Pennisi, Salvatore Cavalieri, Santo Motta and Francesco Pappalardo
    Citation: BMC Bioinformatics 2016 17(Suppl 19):498
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 19

  42. A major obstacle in single-cell sequencing is sample contamination with foreign DNA. To guarantee clean genome assemblies and to prevent the introduction of contamination into public databases, considerable qu...

    Authors: Markus Lux, Jan Krüger, Christian Rinke, Irena Maus, Andreas Schlüter, Tanja Woyke, Alexander Sczyrba and Barbara Hammer
    Citation: BMC Bioinformatics 2016 17:543
    Content type: Software Published on:

  43. Networks are popular and powerful tools to describe and model biological processes. Many computational methods have been developed to infer biological networks from literature, high-throughput experiments, and...

    Authors: Francesco Iorio, Marti Bernardo-Faura, Andrea Gobbi, Thomas Cokelaer, Giuseppe Jurman and Julio Saez-Rodriguez
    Citation: BMC Bioinformatics 2016 17:542
    Content type: Methodology Article Published on:

  44. Performing statistical tests is an important step in analyzing genome-wide datasets for detecting genomic features differentially expressed between conditions. Each type of statistical test has its own advanta...

    Authors: Yuanzhe Bei and Pengyu Hong
    Citation: BMC Bioinformatics 2016 17:541
    Content type: Methodology article Published on:

  45. Biological systems and processes are highly dynamic. To gain insights into their functioning time-resolved measurements are necessary. Time-resolved gene expression data captures temporal behaviour of the gene...

    Authors: Svetlana Bulashevska, Colin Priest, Daniel Speicher, Jörg Zimmermann, Frank Westermann and Armin B. Cremers
    Citation: BMC Bioinformatics 2016 17:532
    Content type: Research Article Published on:

  46. Tospovirus is a plant-infecting genus within the family Bunyaviridae, which also includes four animal-infecting genera: Hantavirus, Nairovirus, Phlebovirus and Orthobunyavirus. Compared to these members, the s...

    Authors: Rayane Nunes Lima, Muhammad Faheem, João Alexandre Ribeiro Gonçalves Barbosa, Marcelo Depólo Polêto, Hugo Verli, Fernando Lucas Melo and Renato Oliveira Resende
    Citation: BMC Bioinformatics 2016 17(Suppl 18):489
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 18

  47. MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics ...

    Authors: Yuri Bento Marques, Alcione de Paiva Oliveira, Ana Tereza Ribeiro Vasconcelos and Fabio Ribeiro Cerqueira
    Citation: BMC Bioinformatics 2016 17(Suppl 18):474
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 18

    The Erratum to this article has been published in BMC Bioinformatics 2017 18:113

  48. The median of k≥3 genomes was originally defined to find a compromise genome indicative of a common ancestor. However, in gene order comparisons, the usual definitions based on minimizing the sum of distances to ...

    Authors: Caroline Anne Larlee, Alex Brandts and David Sankoff
    Citation: BMC Bioinformatics 2016 17(Suppl 18):473
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 18

  49. The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of availabl...

    Authors: Diego C. B. Mariano, Felipe L. Pereira, Edgar L. Aguiar, Letícia C. Oliveira, Leandro Benevides, Luís C. Guimarães, Edson L. Folador, Thiago J. Sousa, Preetam Ghosh, Debmalya Barh, Henrique C. P. Figueiredo, Artur Silva, Rommel T. J. Ramos and Vasco A. C. Azevedo
    Citation: BMC Bioinformatics 2016 17(Suppl 18):456
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 18

  50. Azopirillum brasilense is a plant-growth promoting nitrogen-fixing bacteria that is used as bio-fertilizer in agriculture. Since nitrogen fixation has a high-energy demand, the reducti...

    Authors: Elisa Terumi Rubel, Roberto Tadeu Raittz, Nilson Antonio da Rocha Coimbra, Michelly Alves Coutinho Gehlen and Fábio de Oliveira Pedrosa
    Citation: BMC Bioinformatics 2016 17(Suppl 18):455
    Content type: Research Published on:

    This article is part of a Supplement: Volume 17 Supplement 18

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