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  1. 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

    Published on:

  2. 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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  3. 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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  4. 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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  5. 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

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  6. 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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  7. 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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  8. 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

    Published on:

  9. 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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  10. 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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  11. 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

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  12. 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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  13. 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

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  14. 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

    Published on:

  15. 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:

  16. 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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  17. 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

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  18. 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

    Published on:

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

  19. 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

  20. Feature screening plays a critical role in handling ultrahigh dimensional data analyses when the number of features exponentially exceeds the number of observations. It is increasingly common in biomedical res...

    Authors: Xiaotian Dai, Guifang Fu and Randall Reese

    Citation: BMC Bioinformatics 2020 21:177

    Content type: Methodology Article

    Published on:

  21. 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

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  22. 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:

  23. Whenever suitable template structures are not available, usage of fragment-based protein structure prediction becomes the only practical alternative as pure ab initio techniques require massive computational r...

    Authors: Jad Abbass and Jean-Christophe Nebel

    Citation: BMC Bioinformatics 2020 21:170

    Content type: Methodology article

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  24. Analysing whole genome bisulfite sequencing datasets is a data-intensive task that requires comprehensive and reproducible workflows to generate valid results. While many algorithms have been developed for tas...

    Authors: Marius Wöste, Elsa Leitão, Sandra Laurentino, Bernhard Horsthemke, Sven Rahmann and Christopher Schröder

    Citation: BMC Bioinformatics 2020 21:169

    Content type: Software

    Published on:

  25. Motility in bacteria forms the basis for taxis and is in some pathogenic bacteria important for virulence. Video tracking of motile bacteria allows the monitoring of bacterial swimming behaviour and taxis on t...

    Authors: Julian Schwanbeck, Ines Oehmig, Jerôme Dretzke, Andreas E. Zautner, Uwe Groß and Wolfgang Bohne

    Citation: BMC Bioinformatics 2020 21:166

    Content type: Software

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  26. Circular RNAs (circRNAs) are a newly appreciated class of non-coding RNA molecules. Numerous tools have been developed for the detection of circRNAs, however computational tools to perform downstream functiona...

    Authors: Simona Aufiero, Yolan J. Reckman, Anke J. Tijsen, Yigal M. Pinto and Esther E. Creemers

    Citation: BMC Bioinformatics 2020 21:164

    Content type: Software

    Published on:

  27. While clinical trials are considered the gold standard for detecting adverse events, often these trials are not sufficiently powered to detect difficult to observe adverse events. We developed a preliminary ap...

    Authors: Chathuri Daluwatte, Peter Schotland, David G. Strauss, Keith K. Burkhart and Rebecca Racz

    Citation: BMC Bioinformatics 2020 21:163

    Content type: Research article

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  28. The reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studied Escherichia coli K-12 MG1655 strain. The combination of the tw...

    Authors: Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang and Bernhard O. Palsson

    Citation: BMC Bioinformatics 2020 21:162

    Content type: Research article

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  29. Cytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiot...

    Authors: Ohgew Kweon, Seong-Jae Kim, Jae Hyun Kim, Seong Won Nho, Dongryeoul Bae, Jungwhan Chon, Mark Hart, Dong-Heon Baek, Young-Chang Kim, Wenjun Wang, Sung-Kwan Kim, John B. Sutherland and Carl E. Cerniglia

    Citation: BMC Bioinformatics 2020 21:160

    Content type: Software

    Published on:

  30. Genomic islands are associated with microbial adaptations, carrying genomic signatures different from the host. Some methods perform an overall test to identify genomic islands based on their local features. H...

    Authors: Rui Kong, Xinnan Xu, Xiaoqing Liu, Pingan He, Michael Q. Zhang and Qi Dai

    Citation: BMC Bioinformatics 2020 21:159

    Content type: Methodology article

    Published on:

  31. Binary classification rules based on a small-sample of high-dimensional data (for instance, gene expression data) are ubiquitous in modern bioinformatics. Constructing such classifiers is challenging due to (a...

    Authors: Ali Foroughi pour, Maciej Pietrzak, Lori A Dalton and Grzegorz A. Rempała

    Citation: BMC Bioinformatics 2020 21:156

    Content type: Methodology Article

    Published on:

  32. Predicting of chemical compounds is one of the fundamental tasks in bioinformatics and chemoinformatics, because it contributes to various applications in metabolic engineering and drug discovery. The recent r...

    Authors: Shonosuke Harada, Hirotaka Akita, Masashi Tsubaki, Yukino Baba, Ichigaku Takigawa, Yoshihiro Yamanishi and Hisashi Kashima

    Citation: BMC Bioinformatics 2020 21(Suppl 3):94

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 3

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