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  1. This work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein follo...

    Authors: Teng-Ruei Chen, Yen-Cheng Lin, Yu-Wei Huang, Chih-Chieh Chen and Wei-Cheng Lo

    Citation: BMC Bioinformatics 2021 22(Suppl 10):494

    Content type: Methodology

    Published on:

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

  2. Taxonomic classification of genetic markers for microbiome analysis is affected by the numerous choices made from sample preparation to bioinformatics analysis. Paired-end read merging is routinely used to cap...

    Authors: Daniel P. Dacey and Frédéric J. J. Chain

    Citation: BMC Bioinformatics 2021 22:493

    Content type: Research article

    Published on:

  3. Data visualization, especially the genome track plots, is crucial for genomics researchers to discover patterns in large-scale sequencing dataset. Although existing tools works well for producing a normal view...

    Authors: Weize Xu, Quan Zhong, Da Lin, Ya Zuo, Jinxia Dai, Guoliang Li and Gang Cao

    Citation: BMC Bioinformatics 2021 22:489

    Content type: Software

    Published on:

  4. Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools an...

    Authors: Gwenna Breton, Anna C. V. Johansson, Per Sjödin, Carina M. Schlebusch and Mattias Jakobsson

    Citation: BMC Bioinformatics 2021 22:488

    Content type: Research article

    Published on:

  5. Alignment-free methods are a popular approach for comparing biological sequences, including complete genomes. The methods range from probability distributions of sequence composition to first and higher-order ...

    Authors: Joel Gustafsson, Peter Norberg, Jan R. Qvick-Wester and Alexander Schliep

    Citation: BMC Bioinformatics 2021 22:487

    Content type: Software

    Published on:

  6. Protein protein interactions (PPIs) are essential to most of the biological processes. The prediction of PPIs is beneficial to the understanding of protein functions and thus is helpful to pathological analysi...

    Authors: Weixia Xu, Yangyun Gao, Yang Wang and Jihong Guan

    Citation: BMC Bioinformatics 2021 22(Suppl 6):485

    Content type: Research

    Published on:

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

  7. Traditional methods for single-variant genome-wide association study (GWAS) incur a substantial multiple-testing burden because of the need to test for associations with a vast number of single-nucleotide poly...

    Authors: William R. P. Denault, Håkon K. Gjessing, Julius Juodakis, Bo Jacobsson and Astanand Jugessur

    Citation: BMC Bioinformatics 2021 22:484

    Content type: Methodology article

    Published on:

  8. Blood cancers (BCs) are responsible for over 720 K yearly deaths worldwide. Their prevalence and mortality-rate uphold the relevance of research related to BCs. Despite the availability of different resources ...

    Authors: Nícia Rosário-Ferreira, Victor Guimarães, Vítor S. Costa and Irina S. Moreira

    Citation: BMC Bioinformatics 2021 22:482

    Content type: Research

    Published on:

  9. Identifying interaction effects between genes is one of the main tasks of genome-wide association studies aiming to shed light on the biological mechanisms underlying complex diseases. Multifactor dimensionali...

    Authors: Mira Park, Hoe-Bin Jeong, Jong-Hyun Lee and Taesung Park

    Citation: BMC Bioinformatics 2021 22:480

    Content type: Research

    Published on:

  10. Long noncoding RNAs (lncRNAs) play important roles in various biological and pathological processes. Discovery of lncRNA–protein interactions (LPIs) contributes to understand the biological functions and mecha...

    Authors: Liqian Zhou, Zhao Wang, Xiongfei Tian and Lihong Peng

    Citation: BMC Bioinformatics 2021 22:479

    Content type: Research

    Published on:

  11. Nonlinear mixed effects models provide a way to mathematically describe experimental data involving a lot of inter-individual heterogeneity. In order to assess their practical identifiability and estimate conf...

    Authors: Ronan Duchesne, Anissa Guillemin, Olivier Gandrillon and Fabien Crauste

    Citation: BMC Bioinformatics 2021 22:478

    Content type: Research

    Published on:

  12. Deep learning methods are a proven commodity in many fields and endeavors. One of these endeavors is predicting the presence of adverse drug–drug interactions (DDIs). The models generated can predict, with rea...

    Authors: Rogia Kpanou, Mazid Abiodoun Osseni, Prudencio Tossou, Francois Laviolette and Jacques Corbeil

    Citation: BMC Bioinformatics 2021 22:477

    Content type: Research

    Published on:

  13. Quantitative, reverse transcription PCR (qRT-PCR) is currently the gold-standard for SARS-CoV-2 detection and it is also used for detection of other virus. Manual data analysis of a small number of qRT-PCR pla...

    Authors: S. Olaechea-Lázaro, I. García-Santisteban, J. R. Pineda, I. Badiola, S. Alonso, Jose Ramon Bilbao and Nora Fernandez-Jimenez

    Citation: BMC Bioinformatics 2021 22:476

    Content type: Software

    Published on:

  14. Correctly classifying the subtypes of cancer is of great significance for the in-depth study of cancer pathogenesis and the realization of personalized treatment for cancer patients. In recent years, classific...

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

    Citation: BMC Bioinformatics 2021 22:475

    Content type: Methodology article

    Published on:

  15. Quantification of tumor heterogeneity is essential to better understand cancer progression and to adapt therapeutic treatments to patient specificities. Bioinformatic tools to assess the different cell populat...

    Authors: Clémentine Decamps, Alexis Arnaud, Florent Petitprez, Mira Ayadi, Aurélia Baurès, Lucile Armenoult, Sergio Escalera, Isabelle Guyon, Rémy Nicolle, Richard Tomasini, Aurélien de Reyniès, Jérôme Cros, Yuna Blum and Magali Richard

    Citation: BMC Bioinformatics 2021 22:473

    Content type: Software

    Published on:

  16. With the advancements of Next Generation Techniques, a tremendous amount of genomic information has been made available to be analyzed by means of computational methods. Bioinformatics Tertiary Analysis is a c...

    Authors: Sara Pidò, Pietro Crovari and Franca Garzotto

    Citation: BMC Bioinformatics 2021 22(Suppl 13):452

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 13

  17. Pathway enrichment analysis (PEA) is a well-established methodology for interpreting a list of genes and proteins of interest related to a condition under investigation. This paper aims to extend our previous ...

    Authors: Giuseppe Agapito and Mario Cannataro

    Citation: BMC Bioinformatics 2021 22(Suppl 13):376

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 13

  18. Understanding the genome, with all of its components and intrinsic relationships, is a great challenge. Conceptual modeling techniques have been used as a means to face this challenge. The heterogeneity and id...

    Authors: Alberto García S. and Juan Carlos Casamayor

    Citation: BMC Bioinformatics 2021 22(Suppl 13):353

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 13

  19. Janus-activated kinase-1 (JAK1) plays a crucial role in many aspects of cell proliferation, differentiation, apoptosis and immune regulation. However, correlations of JAK1 with prognosis and immune infiltration i...

    Authors: Kaikai Shen, Yuqing Wei, Tangfeng Lv, Yong Song, Xiaogan Jiang, Zhiwei Lu, Ping Zhan, Xianghai Wang, Meng Fan and Weihua Lu

    Citation: BMC Bioinformatics 2021 22:471

    Content type: Research

    Published on:

  20. Identification of selection signatures between populations is often an important part of a population genetic study. Leveraging high-throughput DNA sequencing larger sample sizes of populations with similar an...

    Authors: Jonas Meisner, Anders Albrechtsen and Kristian Hanghøj

    Citation: BMC Bioinformatics 2021 22:470

    Content type: Research

    Published on:

  21. Metabolomic biomarkers offer potential for objective and reliable food intake assessment, and there is growing interest in using biomarkers in place of or with traditional self-reported approaches. Ongoing res...

    Authors: Silvia D’Angelo, Isobel Claire Gormley, Aoife E. McNamara and Lorraine Brennan

    Citation: BMC Bioinformatics 2021 22:469

    Content type: Software

    Published on:

  22. The advent of population-scale genome projects has revolutionized our biological understanding of parasitic protozoa. However, while hundreds to thousands of nuclear genomes of parasitic protozoa have been gen...

    Authors: Manon Geerts, Achim Schnaufer and Frederik Van den Broeck

    Citation: BMC Bioinformatics 2021 22:468

    Content type: Software

    Published on:

  23. The rising consensus that the cell can dynamically allocate its resources provides an interesting angle for discovering the governing principles of cell growth and metabolism. Extensive efforts have been made ...

    Authors: Hong Zeng, Reza Rohani, Wei E. Huang and Aidong Yang

    Citation: BMC Bioinformatics 2021 22:467

    Content type: Review

    Published on:

  24. Structural variants (SVs) represent an important source of genetic variation. One of the most critical problems in their detection is breakpoint uncertainty associated with the inability to determine their exa...

    Authors: Jan Geryk, Alzbeta Zinkova, Iveta Zedníková, Halina Simková, Vlastimil Stenzl and Marie Korabecna

    Citation: BMC Bioinformatics 2021 22:464

    Content type: Research

    Published on:

  25. Phylogeographic reconstructions serve as a basis to understand the spread and evolution of pathogens. Visualization of these reconstructions often lead to complex graphical representations which are difficult ...

    Authors: François Chevenet, Denis Fargette, Stéphane Guindon and Anne-Laure Bañuls

    Citation: BMC Bioinformatics 2021 22:463

    Content type: Software

    Published on:

  26. To avoid false-positive findings and detect cell-type specific associations in methylation and transcription investigations with bulk samples, it is critical to know the proportions of the major cell-types.

    Authors: Edwin J. C. G. van den Oord, Lin Y. Xie, Charles J. Tran, Min Zhao and Karolina A. Aberg

    Citation: BMC Bioinformatics 2021 22:462

    Content type: Methodology article

    Published on:

  27. Accurate identification of Transcriptional Regulator binding locations is essential for analysis of genomic regions, including Cis Regulatory Elements. The customary NGS approaches, predominantly ChIP-Seq, can...

    Authors: Quentin Ferré, Jeanne Chèneby, Denis Puthier, Cécile Capponi and Benoît Ballester

    Citation: BMC Bioinformatics 2021 22:460

    Content type: Methodology article

    Published on:

  28. We present ARCHes, a fast and accurate haplotype-based approach for inferring an individual’s ancestry composition. Our approach works by modeling haplotype diversity from a large, admixed cohort of hundreds o...

    Authors: Yong Wang, Shiya Song, Joshua G. Schraiber, Alisa Sedghifar, Jake K. Byrnes, David A. Turissini, Eurie L. Hong, Catherine A. Ball and Keith Noto

    Citation: BMC Bioinformatics 2021 22:459

    Content type: Methodology article

    Published on:

  29. Antibiotic resistance is a global health crisis. The adage that “prevention is better than cure” is especially true regarding antibiotic resistance because the resistance appears and spreads much faster than t...

    Authors: Matin Fathollahi, Anwar Fathollahi, Hamid Motamedi, Jale Moradi, Amirhooshang Alvandi and Ramin Abiri

    Citation: BMC Bioinformatics 2021 22:458

    Content type: Research

    Published on:

  30. As one of the deadliest diseases in the world, cancer is driven by a few somatic mutations that disrupt the normal growth of cells, and leads to abnormal proliferation and tumor development. The vast majority ...

    Authors: Yun-Yun Tang, Pi-Jing Wei, Jian-ping Zhao, Junfeng Xia, Rui-Fen Cao and Chun-Hou Zheng

    Citation: BMC Bioinformatics 2021 22(Suppl 3):457

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  31. The use of sound to represent sequence data—sonification—has great potential as an alternative and complement to visual representation, exploiting features of human psychoacoustic intuitions to convey nuance m...

    Authors: Edward J. Martin, Thomas R. Meagher and Daniel Barker

    Citation: BMC Bioinformatics 2021 22:456

    Content type: Research

    Published on:

  32. With the rapid advancement of genomic sequencing techniques, massive production of gene expression data is becoming possible, which prompts the development of precision medicine. Deep learning is a promising a...

    Authors: Victoria Bourgeais, Farida Zehraoui, Mohamed Ben Hamdoune and Blaise Hanczar

    Citation: BMC Bioinformatics 2021 22(Suppl 10):455

    Content type: Research

    Published on:

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

  33. Adenocarcinoma and squamous cell carcinoma are the two most prevalent lung cancer types, and their distinction requires different screenings, such as the visual inspection of histology slides by an expert path...

    Authors: Francisco Carrillo-Perez, Juan Carlos Morales, Daniel Castillo-Secilla, Yésica Molina-Castro, Alberto Guillén, Ignacio Rojas and Luis Javier Herrera

    Citation: BMC Bioinformatics 2021 22:454

    Content type: Research

    Published on:

  34. The liver plays a major role in the metabolic activation of xenobiotics (drugs, chemicals such as pollutants, pesticides, food additives...). Among environmental contaminants of concern, heterocyclic aromatic ...

    Authors: Mael Conan, Nathalie Théret, Sophie Langouet and Anne Siegel

    Citation: BMC Bioinformatics 2021 22:450

    Content type: Research

    Published on:

  35. This paper exploits recent developments in topological data analysis to present a pipeline for clustering based on Mapper, an algorithm that reduces complex data into a one-dimensional graph.

    Authors: Ewan Carr, Mathieu Carrière, Bertrand Michel, Frédéric Chazal and Raquel Iniesta

    Citation: BMC Bioinformatics 2021 22:449

    Content type: Software

    Published on:

  36. The growing researches of molecular biology reveal that complex life phenomena have the ability to demonstrating various types of interactions in the level of genomics. To establish the interactions between ge...

    Authors: Bin Yang, Wenzheng Bao, Wei Zhang, Haifeng Wang, Chuandong Song, Yuehui Chen and Xiuying Jiang

    Citation: BMC Bioinformatics 2021 22(Suppl 3):448

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  37. Studies have proven that the same family of non-coding RNAs (ncRNAs) have similar functions, so predicting the ncRNAs family is helpful to the research of ncRNAs functions. The existing calculation methods ma...

    Authors: Linyu Wang, Xiaodan Zhong, Shuo Wang and Yuanning Liu

    Citation: BMC Bioinformatics 2021 22:447

    Content type: Research

    Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:583

  38. Protein kinases are among the largest druggable family of signaling proteins, involved in various human diseases, including cancers and neurodegenerative disorders. Despite their clinical relevance, nearly 30%...

    Authors: Liang-Chin Huang, Rahil Taujale, Nathan Gravel, Aarya Venkat, Wayland Yeung, Dominic P. Byrne, Patrick A. Eyers and Natarajan Kannan

    Citation: BMC Bioinformatics 2021 22:446

    Content type: Methodology article

    Published on:

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