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  1. 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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  2. 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:

  3. 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

    Published on:

  4. 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

    Published on:

  5. 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

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  6. 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:

  7. 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:

  8. The Sackin indexS of a rooted phylogenetic tree, defined as the sum of its leaves’ depths, is one of the most popular balance indices in phylogenetics, and Sackin’s paper (Syst Zool 21:225–6, 1972) is usually cit...

    Authors: Tomás M. Coronado, Arnau Mir, Francesc Rosselló and Lucía Rotger

    Citation: BMC Bioinformatics 2020 21:154

    Content type: Research Article

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  9. Nanopore sequencing is a rapidly developing third-generation sequencing technology, which can generate long nucleotide reads of molecules within a portable device in real-time. Through detecting the change of ...

    Authors: Yao-zhong Zhang, Arda Akdemir, Georg Tremmel, Seiya Imoto, Satoru Miyano, Tetsuo Shibuya and Rui Yamaguchi

    Citation: BMC Bioinformatics 2020 21(Suppl 3):136

    Content type: Methodology

    Published on:

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

  10. 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

  11. Protein succinylation has recently emerged as an important and common post-translation modification (PTM) that occurs on lysine residues. Succinylation is notable both in its size (e.g., at 100 Da, it is one o...

    Authors: Niraj Thapa, Meenal Chaudhari, Sean McManus, Kaushik Roy, Robert H. Newman, Hiroto Saigo and Dukka B. KC

    Citation: BMC Bioinformatics 2020 21(Suppl 3):63

    Content type: Research

    Published on:

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

  12. Membrane transport proteins (transporters) play an essential role in every living cell by transporting hydrophilic molecules across the hydrophobic membranes. While the sequences of many membrane proteins are ...

    Authors: Munira Alballa and Gregory Butler

    Citation: BMC Bioinformatics 2020 21(Suppl 3):25

    Content type: Research

    Published on:

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

  13. Molecular characters have been added in integrative taxonomic approaches in recent years. Nevertheless, taxon diagnoses are still widely restricted to morphological characters. The inclusion of molecular chara...

    Authors: Thomas Hütter, Maximilian H Ganser, Manuel Kocher, Merima Halkic, Sabine Agatha and Nikolaus Augsten

    Citation: BMC Bioinformatics 2020 21:151

    Content type: Software

    Published on:

  14. After publication of this supplement article [1], it is requested the grant ID in the Funding section should be corrected from NSF grant IIS-7811367 to NSF grant IIS-1902617. Therefore, the correct ‘Funding’ s...

    Authors: Zhongming Zhao, Yulin Dai, Chi Zhang, Ewy Mathé, Lai Wei and Kai Wang

    Citation: BMC Bioinformatics 2020 21:148

    Content type: Correction

    Published on:

    The original article was published in BMC Bioinformatics 2019 20:676

  15. Detection of DNA copy number alterations (CNAs) is critical to understand genetic diversity, genome evolution and pathological conditions such as cancer. Cancer genomes are plagued with widespread multi-level ...

    Authors: Ahmed Ibrahim Samir Khalil, Costerwell Khyriem, Anupam Chattopadhyay and Amartya Sanyal

    Citation: BMC Bioinformatics 2020 21:147

    Content type: Methodology article

    Published on:

  16. Recent years have witnessed an increasing interest in multi-omics data, because these data allow for better understanding complex diseases such as cancer on a molecular system level. In addition, multi-omics d...

    Authors: Amina Lemsara, Salima Ouadfel and Holger Fröhlich

    Citation: BMC Bioinformatics 2020 21:146

    Content type: Methodology article

    Published on:

  17. The advent of mass cytometry has dramatically increased the parameter limit for immunological analysis. New approaches to analysing high parameter cytometry data have been developed to ease analysis of these c...

    Authors: Samuel E. Norton, Julia K. H. Leman, Tiffany Khong, Andrew Spencer, Barbara Fazekas de St Groth, Helen M. McGuire and Roslyn A. Kemp

    Citation: BMC Bioinformatics 2020 21:145

    Content type: Methodology article

    Published on:

  18. The study of cancer genomics continually matures as the number of patient samples sequenced increases. As more data is generated, oncogenic drivers for specific cancer types are discovered along with their ass...

    Authors: Cody Ashby, Michael Rutherford, Michael A. Bauer, Erich A. Peterson, Yan Wang, Eileen M. Boyle, Christopher P. Wardell and Brian A. Walker

    Citation: BMC Bioinformatics 2020 21:144

    Content type: Software

    Published on:

  19. Protein-protein interactions (PPIs) are fundamental in many biological processes and understanding these interactions is key for a myriad of applications including drug development, peptide design and identifi...

    Authors: Felippe C. Queiroz, Adriana M. P. Vargas, Maria G. A. Oliveira, Giovanni V. Comarela and Sabrina A. Silveira

    Citation: BMC Bioinformatics 2020 21:143

    Content type: Research Article

    Published on:

  20. An important process for plant survival is the immune system. The induced systemic resistance (ISR) triggered by beneficial microbes is an important cost-effective defense mechanism by which plants are primed ...

    Authors: Tania Timmermann, Bernardo González and Gonzalo A. Ruz

    Citation: BMC Bioinformatics 2020 21:142

    Content type: Research Article

    Published on:

  21. Epistasis is defined as the interaction between different genes when expressing a specific phenotype. The most common way to characterize an epistatic relationship is using a penetrance table, which contains t...

    Authors: Christian Ponte-Fernández, Jorge González-Domínguez, Antonio Carvajal-Rodríguez and María J. Martín

    Citation: BMC Bioinformatics 2020 21:138

    Content type: Software

    Published on:

  22. Hinge-bending movements in proteins comprising two or more domains form a large class of functional movements. Hinge-bending regions demarcate protein domains and collectively control the domain movement. Cons...

    Authors: Ruth Veevers, Gavin Cawley and Steven Hayward

    Citation: BMC Bioinformatics 2020 21:137

    Content type: Research article

    Published on:

  23. Microarray technology provides the expression level of many genes. Nowadays, an important issue is to select a small number of informative differentially expressed genes that provide biological knowledge and m...

    Authors: José María Martínez-Otzeta, Itziar Irigoien, Basilio Sierra and Concepción Arenas

    Citation: BMC Bioinformatics 2020 21:135

    Content type: Software

    Published on:

  24. Processing and analysis of DNA sequences obtained from next-generation sequencing (NGS) face some difficulties in terms of the correct prediction of DNA sequencing outcomes without the implementation of bioinf...

    Authors: Sergey Shityakov, Elena Bencurova, Carola Förster and Thomas Dandekar

    Citation: BMC Bioinformatics 2020 21:132

    Content type: Software

    Published on:

  25. Imaging mass spectrometry (imaging MS) is an enabling technology for spatial metabolomics of tissue sections with rapidly growing areas of applications in biology and medicine. However, imaging MS data is poll...

    Authors: Katja Ovchinnikova, Vitaly Kovalev, Lachlan Stuart and Theodore Alexandrov

    Citation: BMC Bioinformatics 2020 21:129

    Content type: Methodology article

    Published on:

  26. DNA damage accumulates over the course of cancer development. The often-substantial amount of somatic mutations in cancer poses a challenge to traditional methods to characterize tumors based on driver mutatio...

    Authors: Jessada Thutkawkorapin, Jesper Eisfeldt, Emma Tham and Daniel Nilsson

    Citation: BMC Bioinformatics 2020 21:128

    Content type: Software

    Published on:

  27. Hybrid capture-based next-generation sequencing of DNA has been widely applied in the detection of circulating tumor DNA (ctDNA). Various methods have been proposed for ctDNA detection, but low-allelic-fractio...

    Authors: Leilei Wu, Qinfang Deng, Ze Xu, Songwen Zhou, Chao Li and Yi-Xue Li

    Citation: BMC Bioinformatics 2020 21:127

    Content type: Research article

    Published on:

  28. Accumulated evidence shows that the abnormal regulation of long non-coding RNA (lncRNA) is associated with various human diseases. Accurately identifying disease-associated lncRNAs is helpful to study the mech...

    Authors: Dengju Yao, Xiaojuan Zhan, Xiaorong Zhan, Chee Keong Kwoh, Peng Li and Jinke Wang

    Citation: BMC Bioinformatics 2020 21:126

    Content type: Methodology article

    Published on:

  29. Both intra- and inter-sentential semantic relations in biomedical texts provide valuable information for biomedical research. However, most existing methods either focus on extracting intra-sentential relation...

    Authors: Zhiheng Li, Zhihao Yang, Yang Xiang, Ling Luo, Yuanyuan Sun and Hongfei Lin

    Citation: BMC Bioinformatics 2020 21:125

    Content type: Methodology article

    Published on:

  30. The notion of heme as a regulator of many physiological processes via transient binding to proteins is one that is recently being acknowledged. The broad spectrum of the effects of heme makes it important to i...

    Authors: Ajay Abisheck Paul George, Mauricio Lacerda, Benjamin Franz Syllwasschy, Marie-Thérèse Hopp, Amelie Wißbrock and Diana Imhof

    Citation: BMC Bioinformatics 2020 21:124

    Content type: Research article

    Published on:

  31. Feature selection in class-imbalance learning has gained increasing attention in recent years due to the massive growth of high-dimensional class-imbalanced data across many scientific fields. In addition to r...

    Authors: Guang-Hui Fu, Yuan-Jiao Wu, Min-Jie Zong and Jianxin Pan

    Citation: BMC Bioinformatics 2020 21:121

    Content type: Research Article

    Published on:

  32. In unsupervised learning and clustering, data integration from different sources and types is a difficult question discussed in several research areas. For instance in omics analysis, dozen of clustering metho...

    Authors: Audrey Hulot, Julien Chiquet, Florence Jaffrézic and Guillem Rigaill

    Citation: BMC Bioinformatics 2020 21:120

    Content type: Methodology Article

    Published on:

  33. The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatu...

    Authors: Aaron M. Smith, Jonathan R. Walsh, John Long, Craig B. Davis, Peter Henstock, Martin R. Hodge, Mateusz Maciejewski, Xinmeng Jasmine Mu, Stephen Ra, Shanrong Zhao, Daniel Ziemek and Charles K. Fisher

    Citation: BMC Bioinformatics 2020 21:119

    Content type: Research Article

    Published on:

  34. mRNA interaction with other mRNAs and other signaling molecules determine different biological pathways and functions. Gene co-expression network analysis methods have been widely used to identify correlation ...

    Authors: Anna M. Nia, Tianlong Chen, Brooke L. Barnette, Kamil Khanipov, Robert L. Ullrich, Suresh K. Bhavnani and Mark R. Emmett

    Citation: BMC Bioinformatics 2020 21:118

    Content type: Methodology article

    Published on:

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