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  1. During the last decade, there has been a surge towards computational drug repositioning owing to constantly increasing -omics data in the biomedical research field. While numerous existing methods focus on the in...

    Authors: Mohammad Asif Emon, Daniel Domingo-Fernández, Charles Tapley Hoyt and Martin Hofmann-Apitius

    Citation: BMC Bioinformatics 2020 21:231

    Content type: Methodology article

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  2. Inferring diseases related to the patient’s electronic medical records (EMRs) is of great significance for assisting doctor diagnosis. Several recent prediction methods have shown that deep learning-based meth...

    Authors: Tong Wang, Ping Xuan, Zonglin Liu and Tiangang Zhang

    Citation: BMC Bioinformatics 2020 21:230

    Content type: Methodology article

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  3. Mutations arise in the human genome in two major settings: the germline and the soma. These settings involve different inheritance patterns, time scales, chromatin structures, and environmental exposures, all ...

    Authors: William Meyerson, John Leisman, Fabio C. P. Navarro and Mark Gerstein

    Citation: BMC Bioinformatics 2020 21:227

    Content type: Research article

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  4. Currently the combination of molecular tools, imaging techniques and analysis software offer the possibility of studying gene activity through the use of fluorescent reporters and infer its distribution within...

    Authors: David R. Espeso, Elena Algar, Esteban Martínez-García and Víctor de Lorenzo

    Citation: BMC Bioinformatics 2020 21:224

    Content type: Methodology article

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  5. The latest works on CRISPR genome editing tools mainly employs deep learning techniques. However, deep learning models lack explainability and they are harder to reproduce. We were motivated to build an accura...

    Authors: Ali Haisam Muhammad Rafid, Md. Toufikuzzaman, Mohammad Saifur Rahman and M. Sohel Rahman

    Citation: BMC Bioinformatics 2020 21:223

    Content type: Methodology Article

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  6. The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly incre...

    Authors: William S. Pearman, Nikki E. Freed and Olin K. Silander

    Citation: BMC Bioinformatics 2020 21:220

    Content type: Research article

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  7. Reverse engineering of transcriptional regulatory networks (TRN) from genomics data has always represented a computational challenge in System Biology. The major issue is modeling the complex crosstalk among t...

    Authors: Elisabetta Sauta, Andrea Demartini, Francesca Vitali, Alberto Riva and Riccardo Bellazzi

    Citation: BMC Bioinformatics 2020 21:219

    Content type: Methodology article

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  8. Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of th...

    Authors: Emily K. Mallory, Matthieu de Rochemonteix, Alex Ratner, Ambika Acharya, Chris Re, Roselie A. Bright and Russ B. Altman

    Citation: BMC Bioinformatics 2020 21:217

    Content type: Research article

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  9. The number of porcine Single Nucleotide Polymorphisms (SNPs) used in genetic association studies is very large, suitable for statistical testing. However, in breed classification problem, one needs to have a m...

    Authors: Kitsuchart Pasupa, Wanthanee Rathasamuth and Sissades Tongsima

    Citation: BMC Bioinformatics 2020 21:216

    Content type: Methodology Article

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  10. Recently, it has become possible to collect next-generation DNA sequencing data sets that are composed of multiple samples from multiple biological units where each of these samples may be from a single cell o...

    Authors: Collin Giguere, Harsh Vardhan Dubey, Vishal Kumar Sarsani, Hachem Saddiki, Shai He and Patrick Flaherty

    Citation: BMC Bioinformatics 2020 21:215

    Content type: Software

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  11. Mounting evidence suggests several diseases and biological processes target transcription termination to misregulate gene expression. Disruption of transcription termination leads to readthrough transcription ...

    Authors: Samuel J. Roth, Sven Heinz and Christopher Benner

    Citation: BMC Bioinformatics 2020 21:214

    Content type: Software

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  12. Semantic resources such as knowledge bases contains high-quality-structured knowledge and therefore require significant effort from domain experts. Using the resources to reinforce the information retrieval fr...

    Authors: Zhijing Li, Yuchen Lian, Xiaoyong Ma, Xiangrong Zhang and Chen Li

    Citation: BMC Bioinformatics 2020 21:213

    Content type: Methodology article

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  13. Apoptosis, also called programmed cell death, refers to the spontaneous and orderly death of cells controlled by genes in order to maintain a stable internal environment. Identifying the subcellular location o...

    Authors: Lei Du, Qingfang Meng, Yuehui Chen and Peng Wu

    Citation: BMC Bioinformatics 2020 21:212

    Content type: Methodology Article

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  14. GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used t...

    Authors: Alejandro A. Schäffer, Eneida L. Hatcher, Linda Yankie, Lara Shonkwiler, J. Rodney Brister, Ilene Karsch-Mizrachi and Eric P. Nawrocki

    Citation: BMC Bioinformatics 2020 21:211

    Content type: Software

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  15. Analysis of secondary structures is essential for understanding the functions of RNAs. Because RNA molecules thermally fluctuate, it is necessary to analyze the probability distributions of their secondary str...

    Authors: Hiroki Takizawa, Junichi Iwakiri and Kiyoshi Asai

    Citation: BMC Bioinformatics 2020 21:210

    Content type: Methodology Article

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  16. Landmark-based approaches of two- or three-dimensional coordinates are the most widely used in geometric morphometrics (GM). As human face hosts the organs that act as the central interface for identification,...

    Authors: Azree Nazri, Olalekan Agbolade, Razali Yaakob, Abdul Azim Ghani and Yoke Kqueen Cheah

    Citation: BMC Bioinformatics 2020 21:208

    Content type: Research article

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  17. Plastid genomes typically display a circular, quadripartite structure with two inverted repeat regions, which challenges automatic assembly procedures. The correct assembly of plastid genomes is a prerequisite...

    Authors: Michael Gruenstaeudl and Nils Jenke

    Citation: BMC Bioinformatics 2020 21:207

    Content type: Software

    Published on:

  18. With the explosion in the number of methods designed to analyze bulk and single-cell RNA-seq data, there is a growing need for approaches that assess and compare these methods. The usual technique is to compar...

    Authors: David Gerard

    Citation: BMC Bioinformatics 2020 21:206

    Content type: Methodology Article

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  19. Repetitive DNA elements such as direct and inverted repeat sequences are present in every genome, playing numerous biological roles. In amphibians, the functions and effects of the repeat sequences have not be...

    Authors: Noel Cabañas, Arturo Becerra, David Romero, Tzipe Govezensky, Jesús Javier Espinosa-Aguirre and Rafael Camacho-Carranza

    Citation: BMC Bioinformatics 2020 21:197

    Content type: Research article

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  20. Compared to the many uses of DNA-level testing in clinical oncology, development of RNA-based diagnostics has been more limited. An exception to this trend is the growing use of mRNA-based methods in early-sta...

    Authors: Hersh D. Ravkin, Ofer Givton, David B. Geffen and Eitan Rubin

    Citation: BMC Bioinformatics 2020 21:196

    Content type: Research article

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  21. The aim of gene expression-based clinical modelling in tumorigenesis is not only to accurately predict the clinical endpoints, but also to reveal the genome characteristics for downstream analysis for the purp...

    Authors: Yiru Zhao, Yifan Zhou, Yuan Liu, Yinyi Hao, Menglong Li, Xuemei Pu, Chuan Li and Zhining Wen

    Citation: BMC Bioinformatics 2020 21:195

    Content type: Methodology article

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  22. Single cell RNA sequencing (scRNAseq) has provided invaluable insights into cellular heterogeneity and functional states in health and disease. During the analysis of scRNAseq data, annotating the biological i...

    Authors: H. Atakan Ekiz, Christopher J. Conley, W. Zac Stephens and Ryan M. O’Connell

    Citation: BMC Bioinformatics 2020 21:191

    Content type: Software

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  23. In the era of information overload, natural language processing (NLP) techniques are increasingly needed to support advanced biomedical information management and discovery applications. In this paper, we pres...

    Authors: Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman and Dongwook Shin

    Citation: BMC Bioinformatics 2020 21:188

    Content type: Software

    Published on:

  24. Cardiotoxicity, characterized by severe cardiac dysfunction, is a major problem in patients treated with different classes of anticancer drugs. Development of predictable human-based models and assays for drug...

    Authors: Lu Cao, Andries D. van der Meer, Fons J. Verbeek and Robert Passier

    Citation: BMC Bioinformatics 2020 21:187

    Content type: Methodology Article

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  25. Even though R is one of the most commonly used statistical computing environments, it lacks a graphical user interface (GUI) that appeals to students, researchers, lecturers, and practitioners in medicine and ...

    Authors: Yi Zhou, Siu-wai Leung, Shosuke Mizutani, Tatsuya Takagi and Yu-Shi Tian

    Citation: BMC Bioinformatics 2020 21:183

    Content type: Software

    Published on:

  26. In addition to causing the pandemic influenza outbreaks of 1918 and 2009, subtype H1N1 influenza A viruses (IAVs) have caused seasonal epidemics since 1977. Antigenic property of influenza viruses are determin...

    Authors: Lei Li, Deborah Chang, Lei Han, Xiaojian Zhang, Joseph Zaia and Xiu-Feng Wan

    Citation: BMC Bioinformatics 2020 21:182

    Content type: Methodology article

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  27. Recently, DNA methylation has drawn great attention due to its strong correlation with abnormal gene activities and informative representation of the cancer status. As a number of studies focus on DNA methylat...

    Authors: Joungmin Choi and Heejoon Chae

    Citation: BMC Bioinformatics 2020 21:181

    Content type: Research Article

    Published on:

  28. Protein repeats can confound sequence analyses because the repetitiveness of their amino acid sequences lead to difficulties in identifying whether similar repeats are due to convergent or divergent evolution....

    Authors: Matthew Merski, Krzysztof Młynarczyk, Jan Ludwiczak, Jakub Skrzeczkowski, Stanisław Dunin-Horkawicz and Maria W. Górna

    Citation: BMC Bioinformatics 2020 21:179

    Content type: Research article

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  29. Heterogeneity in the definition and measurement of complex diseases in Genome-Wide Association Studies (GWAS) may lead to misdiagnoses and misclassification errors that can significantly impact discovery of di...

    Authors: Afrah Shafquat, Ronald G. Crystal and Jason G. Mezey

    Citation: BMC Bioinformatics 2020 21:178

    Content type: Research article

    Published on:

  30. In the current supplement, we are proud to present seventeen relevant contributions from the 6th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2018), which was held during ...

    Authors: Olga Valenzuela, Fernando Rojas, Ignacio Rojas and Peter Glosekotter

    Citation: BMC Bioinformatics 2020 21(Suppl 7):153

    Content type: Introduction

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    This article is part of a Supplement: Volume 21 Supplement 7

  31. Cervical cancer is the fourth most common tumor in women worldwide, mostly resulting from high-risk human papillomavirus (HR-HPV) with persistent infection.

    Authors: Wenting Wu, Lei Song, Yongtao Yang, Jianxin Wang, Hongtu Liu and Le Zhang

    Citation: BMC Bioinformatics 2020 21(Suppl 7):152

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 7

  32. As regulators of gene expression, microRNAs (miRNAs) are increasingly recognized as critical biomarkers of human diseases. Till now, a series of computational methods have been proposed to predict new miRNA-di...

    Authors: Hailin Chen, Ruiyu Guo, Guanghui Li, Wei Zhang and Zuping Zhang

    Citation: BMC Bioinformatics 2020 21:176

    Content type: Research article

    Published on:

  33. In the last decade, a large number of common variants underlying complex diseases have been identified through genome-wide association studies (GWASs). Summary data of the GWASs are freely and publicly availab...

    Authors: Jianjun Zhang, Xuan Guo, Samantha Gonzales, Jingjing Yang and Xuexia Wang

    Citation: BMC Bioinformatics 2020 21:172

    Content type: Research Article

    Published on:

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