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  2. 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

    Published on:

  3. 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

  4. 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

  5. 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

  6. 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:

  9. 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

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  19. 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:

  20. 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:

  21. 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:

  26. New technologies have given rise to an abundance of -omics data, particularly metabolomic data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring t...

    Authors: Lea F. Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur E. Sigurjónsson, Óttar Rolfsson, Julian Heinrich and Andreas Dräger

    Citation: BMC Bioinformatics 2020 21:130

    Content type: Methodology Article

    Published on:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  39. After publication of the original article [1], we were notified that legends of Fig. 1 and Fig. 2 have been swapped.

    Authors: Monica J. Quinzo, Esther M. Lafuente, Pilar Zuluaga, Darren R. Flower and Pedro A. Reche

    Citation: BMC Bioinformatics 2020 21:116

    Content type: Correction

    Published on:

    The original article was published in BMC Bioinformatics 2019 20:476

  41. Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix by mechanical loa...

    Authors: Gianluca Ascolani, Timothy M. Skerry, Damien Lacroix, Enrico Dall’Ara and Aban Shuaib

    Citation: BMC Bioinformatics 2020 21:114

    Content type: Methodology article

    Published on:

  43. Lung cancer is the leading cause of cancer-related deaths in both men and women in the United States, and it has a much lower five-year survival rate than many other cancers. Accurate survival analysis is urge...

    Authors: Lei Cui, Hansheng Li, Wenli Hui, Sitong Chen, Lin Yang, Yuxin Kang, Qirong Bo and Jun Feng

    Citation: BMC Bioinformatics 2020 21:112

    Content type: Methodology Article

    Published on:

  45. With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq da...

    Authors: Xiaokang Zhang and Inge Jonassen

    Citation: BMC Bioinformatics 2020 21:110

    Content type: Software

    Published on:

  47. DNA methylation (DNAm) is an epigenetic regulator of gene expression programs that can be altered by environmental exposures, aging, and in pathogenesis. Traditional analyses that associate DNAm alterations wi...

    Authors: Joshua J. Levy, Alexander J. Titus, Curtis L. Petersen, Youdinghuan Chen, Lucas A. Salas and Brock C. Christensen

    Citation: BMC Bioinformatics 2020 21:108

    Content type: Methodology article

    Published on:

  49. Function genomic studies will generally result in lists of genes that may provide clues for exploring biological questions and discovering unanticipated functions, based on differential gene expression analysi...

    Authors: Du Zhang, Qi Hu, Xinxing Liu, Kai Zou, Emmanuel Konadu Sarkodie, Xueduan Liu and Fei Gao

    Citation: BMC Bioinformatics 2020 21:106

    Content type: Software

    Published on:

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