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  1. Modern Next Generation- and Third Generation- Sequencing methods such as Illumina and PacBio Circular Consensus Sequencing platforms provide accurate sequencing data. Parallel developments in Deep Learning hav...

    Authors: Anand Ramachandran, Steven S. Lumetta, Eric W. Klee and Deming Chen

    Citation: BMC Bioinformatics 2021 22:404

    Content type: Methodology article

    Published on:

  2. Reproducible benchmarking is important for assessing the effectiveness of novel feature selection approaches applied on gene expression data, especially for prior knowledge approaches that incorporate biologic...

    Authors: Cindy Perscheid

    Citation: BMC Bioinformatics 2021 22:401

    Content type: Software

    Published on:

  3. The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ri...

    Authors: Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch-Mizrachi and Eric P. Nawrocki

    Citation: BMC Bioinformatics 2021 22:400

    Content type: Software

    Published on:

  4. Numerous genomes are sequenced and made available to the community through the NCBI portal. However, and, unlike what happens for gene function annotation, annotation of promoter sequences and the underlying p...

    Authors: Jorge Oliveira, Miguel Antunes, Claudia P. Godinho, Miguel C. Teixeira, Isabel Sá-Correia and Pedro T. Monteiro

    Citation: BMC Bioinformatics 2021 22:399

    Content type: Methodology article

    Published on:

  5. Meiotic recombination is a vital biological process playing an essential role in genome's structural and functional dynamics. Genomes exhibit highly various recombination profiles along chromosomes associated ...

    Authors: Yasmine Mansour, Annie Chateau and Anna-Sophie Fiston-Lavier

    Citation: BMC Bioinformatics 2021 22(Suppl 6):396

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 6

  6. Cancer genomic studies often include data collected from several omics platforms. Each omics data source contributes to the understanding of the underlying biological process via source specific (“individual”)...

    Authors: Erica Ponzi, Magne Thoresen, Therese Haugdahl Nøst and Kajsa Møllersen

    Citation: BMC Bioinformatics 2021 22:395

    Content type: Research article

    Published on:

  7. Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and th...

    Authors: Jingyi Liu, Ross Mawhorter, Nuo Liu, Santi Santichaivekin, Eliot Bush and Ran Libeskind-Hadas

    Citation: BMC Bioinformatics 2021 22(Suppl 10):394

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  8. Integrating data from different sources is a recurring question in computational biology. Much effort has been devoted to the integration of data sets of the same type, typically multiple numerical data tables...

    Authors: Audrey Hulot, Denis Laloë and Florence Jaffrézic

    Citation: BMC Bioinformatics 2021 22:392

    Content type: Methodology article

    Published on:

  9. A range of spatially resolved transcriptomic methods has recently emerged as a way to spatially characterize the molecular and cellular diversity of a tissue. As a consequence, an increasing number of computat...

    Authors: Sergio Marco Salas, Daniel Gyllborg, Christoffer Mattsson Langseth and Mats Nilsson

    Citation: BMC Bioinformatics 2021 22:391

    Content type: Software

    Published on:

  10. Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is ne...

    Authors: Santiago Redondo-Salvo, Roger Bartomeus-Peñalver, Luis Vielva, Kaitlin A. Tagg, Hattie E. Webb, Raúl Fernández-López and Fernando de la Cruz

    Citation: BMC Bioinformatics 2021 22:390

    Content type: Software

    Published on:

  11. Antimicrobial peptides (AMPs) are oligopeptides that act as crucial components of innate immunity, naturally occur in all multicellular organisms, and are involved in the first line of defense function. Recent...

    Authors: Onkar Singh, Wen-Lian Hsu and Emily Chia-Yu Su

    Citation: BMC Bioinformatics 2021 22:389

    Content type: Methodology article

    Published on:

  12. Stroke has an acute onset and a high mortality rate, making it one of the most fatal diseases worldwide. Its underlying biology and treatments have been widely studied both in the “Western” biomedicine and the...

    Authors: Xi Yang, Chengkun Wu, Goran Nenadic, Wei Wang and Kai Lu

    Citation: BMC Bioinformatics 2021 22(Suppl 10):387

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  13. The fidelity and reliability of disease model predictions depend on accurate and precise descriptions of processes and determination of parameters. Various models exist to describe within-host dynamics during ...

    Authors: Shade Horn, Jacky L. Snoep and David D. van Niekerk

    Citation: BMC Bioinformatics 2021 22:384

    Content type: Research

    Published on:

  14. Biomacromolecular structural data outgrew the legacy Protein Data Bank (PDB) format which the scientific community relied on for decades, yet the use of its successor PDBx/Macromolecular Crystallographic Infor...

    Authors: Glen van Ginkel, Lukáš Pravda, José M. Dana, Mihaly Varadi, Peter Keller, Stephen Anyango and Sameer Velankar

    Citation: BMC Bioinformatics 2021 22:383

    Content type: Software

    Published on:

  15. Neoantigen based personalized immune therapies achieve promising results in melanoma and lung cancer, but few neoantigen based models perform well in IDH wild-type GBM, and the association between neoantigen i...

    Authors: Ting Sun, Yufei He, Wendong Li, Guang Liu, Lin Li, Lu Wang, Zixuan Xiao, Xiaohan Han, Hao Wen, Yong Liu, Yifan Chen, Haoyu Wang, Jing Li, Yubo Fan, Wei Zhang and Jing Zhang

    Citation: BMC Bioinformatics 2021 22:382

    Content type: Research

    Published on:

  16. Authors: Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe and Leonardo Collado-Torres

    Citation: BMC Bioinformatics 2021 22:381

    Content type: Correction

    Published on:

    The original article was published in BMC Bioinformatics 2021 22:224

  17. RNA degradation is important for the regulation of gene expression. Despite the identification of proteins and sequences related to deadenylation-dependent RNA degradation in plants, endonucleolytic cleavage-d...

    Authors: Daishin Ueno, Harunori Kawabe, Shotaro Yamasaki, Taku Demura and Ko Kato

    Citation: BMC Bioinformatics 2021 22:380

    Content type: Research

    Published on:

  18. Autism spectrum disorders (ASD) imply a spectrum of symptoms rather than a single phenotype. ASD could affect brain connectivity at different degree based on the severity of the symptom. Given their excellent ...

    Authors: Jinlong Hu, Lijie Cao, Tenghui Li, Shoubin Dong and Ping Li

    Citation: BMC Bioinformatics 2021 22:379

    Content type: Methodology article

    Published on:

  19. Due to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential st...

    Authors: Zhenmiao Zhang and Lu Zhang

    Citation: BMC Bioinformatics 2021 22(Suppl 10):378

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  20. Data integration to build a biomedical knowledge graph is a challenging task. There are multiple disease ontologies used in data sources and publications, each having its hierarchy. A common task is to map bet...

    Authors: Natalja Kurbatova and Rowan Swiers

    Citation: BMC Bioinformatics 2021 22:377

    Content type: Software

    Published on:

  21. Illumina is the dominant sequencing technology at this time. Short length, short insert size, some systematic biases, and low-level carryover contamination in Illumina reads continue to make assembly of repeat...

    Authors: Alexandre Souvorov and Richa Agarwala

    Citation: BMC Bioinformatics 2021 22:375

    Content type: Software

    Published on:

  22. As exome sequencing (ES) integrates into clinical practice, we should make every effort to utilize all information generated. Copy-number variation can lead to Mendelian disorders, but small copy-number varian...

    Authors: Dayne L. Filer, Fengshen Kuo, Alicia T. Brandt, Christian R. Tilley, Piotr A. Mieczkowski, Jonathan S. Berg, Kimberly Robasky, Yun Li, Chris Bizon, Jeffery L. Tilson, Bradford C. Powell, Darius M. Bost, Clark D. Jeffries and Kirk C. Wilhelmsen

    Citation: BMC Bioinformatics 2021 22:374

    Content type: Research

    Published on:

  23. SARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the most notable and concerning currently are the UK va...

    Authors: Phuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant and Teemu Smura

    Citation: BMC Bioinformatics 2021 22:373

    Content type: Software

    Published on:

  24. Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Effector proteins are the tools such pathogens use to infect the cell, predicting effectors de ...

    Authors: Ruth Kristianingsih and Dan MacLean

    Citation: BMC Bioinformatics 2021 22:372

    Content type: Software

    Published on:

  25. More and more evidence shows that circRNA plays an important role in various biological processes and human health. Therefore, inferring the circRNA’s potential functions and obtaining circRNA functional simil...

    Authors: Liang Shu, Cheng Zhou, Xinxu Yuan, Jingpu Zhang and Lei Deng

    Citation: BMC Bioinformatics 2021 22(Suppl 10):371

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  26. Mitochondria play essential roles in regulating cellular functions. Some drug treatments and molecular interventions have been reported to have off-target effects damaging mitochondria and causing severe side ...

    Authors: Yu-Te Lin, Ko-Hong Lin, Chi-Jung Huang and An-Chi Wei

    Citation: BMC Bioinformatics 2021 22(Suppl 10):369

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  27. Introns are generally removed from primary transcripts to form mature RNA molecules in a post-transcriptional process called splicing. An efficient splicing of primary transcripts is an essential step in gene ...

    Authors: Verônica R. de Melo Costa, Julianus Pfeuffer, Annita Louloupi, Ulf A. V. Ørom and Rosario M. Piro

    Citation: BMC Bioinformatics 2021 22:368

    Content type: Software

    Published on:

  28. The topology of metabolic networks is both well-studied and remarkably well-conserved across many species. The regulation of these networks, however, is much more poorly characterized, though it is known to be...

    Authors: Justin Y. Lee, Britney Nguyen, Carlos Orosco and Mark P. Styczynski

    Citation: BMC Bioinformatics 2021 22:365

    Content type: Methodology article

    Published on:

  29. Analyzing single-cell RNA sequencing (scRNAseq) data plays an important role in understanding the intrinsic and extrinsic cellular processes in biological and biomedical research. One significant effort in thi...

    Authors: Tianyu Wang, Jun Bai and Sheida Nabavi

    Citation: BMC Bioinformatics 2021 22:364

    Content type: Methodology article

    Published on:

  30. Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Her...

    Authors: Ian Leifer, Mishael Sánchez-Pérez, Cecilia Ishida and Hernán A. Makse

    Citation: BMC Bioinformatics 2021 22:363

    Content type: Research

    Published on:

  31. Microbiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and opti...

    Authors: Emily Goren, Chong Wang, Zhulin He, Amy M. Sheflin, Dawn Chiniquy, Jessica E. Prenni, Susannah Tringe, Daniel P. Schachtman and Peng Liu

    Citation: BMC Bioinformatics 2021 22:362

    Content type: Methodology article

    Published on:

  32. Facing the diversity of omics data and the difficulty of selecting one result over all those produced by several methods, consensus strategies have the potential to reconcile multiple inputs and to produce rob...

    Authors: Galadriel Brière, Élodie Darbo, Patricia Thébault and Raluca Uricaru

    Citation: BMC Bioinformatics 2021 22:361

    Content type: Methodology article

    Published on:

  33. Despite decades on developing dedicated Web tools, it is still difficult to predict correctly the changes of the thermodynamic stability of proteins caused by mutations. Here, we assessed the reliability of fi...

    Authors: Anna Marabotti, Eugenio Del Prete, Bernardina Scafuri and Angelo Facchiano

    Citation: BMC Bioinformatics 2021 22(Suppl 7):345

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 7

  34. Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing not only the identification of known phyla and strains but a...

    Authors: Carlo Ferravante, Domenico Memoli, Domenico Palumbo, Paolo Ciaramella, Antonio Di Loria, Ylenia D’Agostino, Giovanni Nassa, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz and Giorgio Giurato

    Citation: BMC Bioinformatics 2021 22(Suppl 7):106

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 7

  35. Tumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using C...

    Authors: Marilisa Montemurro, Elena Grassi, Carmelo Gabriele Pizzino, Andrea Bertotti, Elisa Ficarra and Gianvito Urgese

    Citation: BMC Bioinformatics 2021 22:360

    Content type: Software

    Published on:

  36. Systems biology increasingly relies on deep sequencing with combinatorial index tags to associate biological sequences with their sample, cell, or molecule of origin. Accurate data interpretation depends on th...

    Authors: Lior Galanti, Dennis Shasha and Kristin C. Gunsalus

    Citation: BMC Bioinformatics 2021 22:359

    Content type: Software

    Published on:

  37. The Raffinose synthetase (RAFS) genes superfamily is critical for the synthesis of raffinose, which accumulates in plant leaves under abiotic stress. However, it remains unclear whether RAFS contributes to resist...

    Authors: Ruifeng Cui, Xiaoge Wang, Waqar Afzal Malik, Xuke Lu, Xiugui Chen, Delong Wang, Junjuan Wang, Shuai Wang, Chao Chen, Lixue Guo, Quanjia Chen and Wuwei Ye

    Citation: BMC Bioinformatics 2021 22:356

    Content type: Research article

    Published on:

  38. StrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins or groups of proteins in a collection of protein–protein interaction (PPI) network or signaling network...

    Authors: Zaynab Mousavian, Mehran Khodabandeh, Ali Sharifi-Zarchi, Alireza Nadafian and Alireza Mahmoudi

    Citation: BMC Bioinformatics 2021 22:352

    Content type: Software

    Published on:

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