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  1. The development of single-cell RNA sequencing has enabled profound discoveries in biology, ranging from the dissection of the composition of complex tissues to the identification of novel cell types and dynami...

    Authors: Zhuo Wang, Shuilin Jin, Guiyou Liu, Xiurui Zhang, Nan Wang, Deliang Wu, Yang Hu, Chiping Zhang, Qinghua Jiang, Li Xu and Yadong Wang
    Citation: BMC Bioinformatics 2017 18:270
    Content type: Methodology Article Published on:

  2. The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-mo...

    Authors: Zhenqing Ye, Tao Ma, Michael T. Kalmbach, Surendra Dasari, Jean-Pierre A. Kocher and Liguo Wang
    Citation: BMC Bioinformatics 2017 18:269
    Content type: Software Published on:

  3. The stress fibers are prominent organization of actin filaments that perform important functions in cellular processes such as migration, polarization, and traction force generation, and whose collective organ...

    Authors: Zhen Zhang, Shumin Xia and Pakorn Kanchanawong
    Citation: BMC Bioinformatics 2017 18:268
    Content type: Methodology article Published on:

  5. Analysis of genome-wide association studies (GWAS) with “time to event” outcomes have become increasingly popular, predominantly in the context of pharmacogenetics, where the survival endpoint could be death, ...

    Authors: Hamzah Syed, Andrea L. Jorgensen and Andrew P. Morris
    Citation: BMC Bioinformatics 2017 18:265
    Content type: Software Published on:

  6. A visualization referred to as rainfall plot has recently gained popularity in genome data analysis. The plot is mostly used for illustrating the distribution of somatic cancer mutations along a reference geno...

    Authors: Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig and Geir Kjetil Sandve
    Citation: BMC Bioinformatics 2017 18:264
    Content type: Research Article Published on:

  7. It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represe...

    Authors: Knut D. Rand, Ivar Grytten, Alexander J. Nederbragt, Geir O. Storvik, Ingrid K. Glad and Geir K. Sandve
    Citation: BMC Bioinformatics 2017 18:263
    Content type: Research Article Published on:

  8. Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are u...

    Authors: Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hao Hong, Xiaochen Bo and Fei Li
    Citation: BMC Bioinformatics 2017 18:262
    Content type: Software Published on:

  10. Exponentially increasing numbers of NGS-based epigenomic datasets in public repositories like GEO constitute an enormous source of information that is invaluable for integrative and comparative studies of gene...

    Authors: Mohamed-Ashick M. Saleem, Marco-Antonio Mendoza-Parra, Pierre-Etienne Cholley, Matthias Blum and Hinrich Gronemeyer
    Citation: BMC Bioinformatics 2017 18:259
    Content type: Methodology Article Published on:

  11. Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, ...

    Authors: Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim and Jongsun Jung
    Citation: BMC Bioinformatics 2017 18:258
    Content type: Methodology Article Published on:

  13. There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment...

    Authors: Joanna Zyla, Michal Marczyk, January Weiner and Joanna Polanska
    Citation: BMC Bioinformatics 2017 18:256
    Content type: Research Article Published on:

  14. Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that a...

    Authors: Ian H. Holmes
    Citation: BMC Bioinformatics 2017 18:255
    Content type: Commentary Published on:

  15. Spectral imaging with polarity-sensitive fluorescent probes enables the quantification of cell and model membrane physical properties, including local hydration, fluidity, and lateral lipid packing, usually ch...

    Authors: Miles Aron, Richard Browning, Dario Carugo, Erdinc Sezgin, Jorge Bernardino de la Serna, Christian Eggeling and Eleanor Stride
    Citation: BMC Bioinformatics 2017 18:254
    Content type: Software Published on:

  16. Species-level classification for 16S rRNA gene sequences remains a serious challenge for microbiome researchers, because existing taxonomic classification tools for 16S rRNA gene sequences either do not provid...

    Authors: Xiang Gao, Huaiying Lin, Kashi Revanna and Qunfeng Dong
    Citation: BMC Bioinformatics 2017 18:247
    Content type: Software Published on:

  17. Mathematical modeling and in silico analysis are widely acknowledged as complementary tools to biological laboratory methods, to achieve a thorough understanding of emergent behaviors of cellular processes in ...

    Authors: Andrea Tangherloni, Marco S. Nobile, Daniela Besozzi, Giancarlo Mauri and Paolo Cazzaniga
    Citation: BMC Bioinformatics 2017 18:246
    Content type: Research Article Published on:

  19. Immunoinformatics has become a crucial part in biomedical research. Yet many immunoinformatics tools have command line interfaces only and can be difficult to install. Web-based immunoinformatics tools, on the...

    Authors: Benjamin Schubert, Luis de la Garza, Christopher Mohr, Mathias Walzer and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2017 18:242
    Content type: Software Published on:

  20. Reconstructing gene regulatory networks (GRNs) from expression data plays an important role in understanding the fundamental cellular processes and revealing the underlying relations among genes. Although many...

    Authors: Jing Liu, Yaxiong Chi, Chen Zhu and Yaochu Jin
    Citation: BMC Bioinformatics 2017 18:241
    Content type: Research Article Published on:

  21. The Geminiviridae family encompasses a group of single-stranded DNA viruses with twinned and quasi-isometric virions, which infect a wide range of dicotyledonous and monocotyledonous plants and are responsible fo...

    Authors: Jose Cleydson F. Silva, Thales F. M. Carvalho, Marcos F. Basso, Michihito Deguchi, Welison A. Pereira, Roberto R. Sobrinho, Pedro M. P. Vidigal, Otávio J. B. Brustolini, Fabyano F. Silva, Maximiller Dal-Bianco, Renildes L. F. Fontes, Anésia A. Santos, Francisco Murilo Zerbini, Fabio R. Cerqueira and Elizabeth P. B. Fontes
    Citation: BMC Bioinformatics 2017 18:240
    Content type: Database Published on:

  22. A major challenge of high throughput transcriptome studies is presenting the data to researchers in an interpretable format. In many cases, the outputs of such studies are gene lists which are then examined fo...

    Authors: Liang Sun, Yongnan Zhu, A. S. M. Ashique Mahmood, Catalina O. Tudor, Jia Ren, K. Vijay-Shanker, Jian Chen and Carl J. Schmidt
    Citation: BMC Bioinformatics 2017 18:237
    Content type: Software Published on:

  23. Sample size calculation and power estimation are essential components of experimental designs in biomedical research. It is very challenging to estimate power for RNA-Seq differential expression under complex ...

    Authors: Lianbo Yu, Soledad Fernandez and Guy Brock
    Citation: BMC Bioinformatics 2017 18:234
    Content type: Methodology Article Published on:

  24. Recent advances in high-throughput sequencing allow for much deeper exploitation of natural and engineered microbial communities, and to unravel so-called “microbial dark matter” (microbes that until now have ...

    Authors: Bertjan Broeksema, Magdalena Calusinska, Fintan McGee, Klaas Winter, Francesco Bongiovanni, Xavier Goux, Paul Wilmes, Philippe Delfosse and Mohammad Ghoniem
    Citation: BMC Bioinformatics 2017 18:233
    Content type: Software Published on:

  26. Reconstructing transcript models from RNA-sequencing (RNA-seq) data and establishing these as independent transcriptional units can be a challenging task. Current state-of-the-art tools for long non-coding RNA...

    Authors: Francisco Avila Cobos, Jasper Anckaert, Pieter-Jan Volders, Celine Everaert, Dries Rombaut, Jo Vandesompele, Katleen De Preter and Pieter Mestdagh
    Citation: BMC Bioinformatics 2017 18:231
    Content type: Methodology Article Published on:

  28. Image registration is an important research topic in the field of image processing. Applying image registration to vascular image allows multiple images to be strengthened and fused, which has practical value ...

    Authors: Li Chen, Yuxi Lian, Yi Guo, Yuanyuan Wang, Thomas S. Hatsukami, Kristi Pimentel, Niranjan Balu and Chun Yuan
    Citation: BMC Bioinformatics 2017 18:229
    Content type: Research Article Published on:

  30. Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to f...

    Authors: Loris Bertoldi, Claudio Forcato, Nicola Vitulo, Giovanni Birolo, Fabio De Pascale, Erika Feltrin, Riccardo Schiavon, Franca Anglani, Susanna Negrisolo, Alessandra Zanetti, Francesca D’Avanzo, Rosella Tomanin, Georgine Faulkner, Alessandro Vezzi and Giorgio Valle
    Citation: BMC Bioinformatics 2017 18:225
    Content type: Software Published on:

  31. Myc is an essential gene having multiple functions such as in cell growth, differentiation, apoptosis, genomic stability, angiogenesis, and disease biology. A large number of researchers dedicated to Myc biolo...

    Authors: Debangana Chakravorty, Tanmoy Jana, Sukhen Das Mandal, Anuradha Seth, Anubrata Bhattacharya and Sudipto Saha
    Citation: BMC Bioinformatics 2017 18:224
    Content type: Database Published on:

  32. The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together...

    Authors: You-Yu Lin, Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen and Hurng-Yi Wang
    Citation: BMC Bioinformatics 2017 18:223
    Content type: Methodology Article Published on:

  34. DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorith...

    Authors: Mark D. Temple
    Citation: BMC Bioinformatics 2017 18:221
    Content type: Software Published on:

  35. Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the...

    Authors: Tanchanok Wisitponchai, Watshara Shoombuatong, Vannajan Sanghiran Lee, Kuntida Kitidee and Chatchai Tayapiwatana
    Citation: BMC Bioinformatics 2017 18:220
    Content type: Research Article Published on:

  37. Knowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases. While ther...

    Authors: Sarvesh Nikumbh and Nico Pfeifer
    Citation: BMC Bioinformatics 2017 18:218
    Content type: Research Article Published on:

  38. Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical m...

    Authors: Meiling Liu, Sanghoon Moon, Longfei Wang, Sulgi Kim, Yeon-Jung Kim, Mi Yeong Hwang, Young Jin Kim, Robert C. Elston, Bong-Jo Kim and Sungho Won
    Citation: BMC Bioinformatics 2017 18:217
    Content type: Research Article Published on:

  39. Whole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. These associations can be confounded by cellular h...

    Authors: Akhilesh Kaushal, Hongmei Zhang, Wilfried J. J. Karmaus, Meredith Ray, Mylin A. Torres, Alicia K. Smith and Shu-Li Wang
    Citation: BMC Bioinformatics 2017 18:216
    Content type: Research article Published on:

  40. Somatic alterations, including loss of heterozygosity, can affect the expression of oncogenes and tumor suppressor genes. Whole genome sequencing enables detailed characterization of such aberrations. However,...

    Authors: Ebrahim Afyounian, Matti Annala and Matti Nykter
    Citation: BMC Bioinformatics 2017 18:215
    Content type: Software Published on:

  41. Carbohydrate-active enzymes are found in all organisms and participate in key biological processes. These enzymes are classified in 274 families in the CAZy database but the sequence diversity within each fami...

    Authors: P. K. Busk, B. Pilgaard, M. J. Lezyk, A. S. Meyer and L. Lange
    Citation: BMC Bioinformatics 2017 18:214
    Content type: Software Published on:

  45. Aggregating gene expression data across experiments via meta-analysis is expected to increase the precision of the effect estimates and to increase the statistical power to detect a certain fold change. This s...

    Authors: Putri W. Novianti, Victor L. Jong, Kit C. B. Roes and Marinus J. C. Eijkemans
    Citation: BMC Bioinformatics 2017 18:210
    Content type: Research Article Published on:

  46. Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological chal...

    Authors: Rasha E. Boulos, Nicolas Tremblay, Alain Arneodo, Pierre Borgnat and Benjamin Audit
    Citation: BMC Bioinformatics 2017 18:209
    Content type: Research Article Published on:

  47. Advances in cloning and sequencing technology are yielding a massive number of viral genomes. The classification and annotation of these genomes constitute important assets in the discovery of genomic variabil...

    Authors: Mohamed Amine Remita, Ahmed Halioui, Abou Abdallah Malick Diouara, Bruno Daigle, Golrokh Kiani and Abdoulaye Baniré Diallo
    Citation: BMC Bioinformatics 2017 18:208
    Content type: Research Article Published on:

  48. Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, a...

    Authors: William W. Greenwald, He Li, Erin N. Smith, Paola Benaglio, Naoki Nariai and Kelly A. Frazer
    Citation: BMC Bioinformatics 2017 18:207
    Content type: Software Published on:

  49. Intrinsically unstructured or disordered proteins function via interacting with other molecules. Annotation of these binding sites is the first step for mapping functional impact of genetic variants in coding ...

    Authors: Jia-Feng Yu, Xiang-Hua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou and Ji-Hua Wang
    Citation: BMC Bioinformatics 2017 18:206
    Content type: Database Published on:

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