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Novel computational methods for analysis of biological systems

  1. Interactions of single nucleotide polymorphisms (SNPs) and environmental factors play an important role in understanding complex diseases' pathogenesis. A growing number of SNP-environment studies have been co...

    Authors: Hui-Yi Lin, Po-Yu Huang, Tung-Sung Tseng and Jong Y. Park

    Citation: BMC Bioinformatics 2021 22:425

    Content type: Software

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  2. 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

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  3. Phylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed fo...

    Authors: Luna L. Sánchez-Reyes, Martha Kandziora and Emily Jane McTavish

    Citation: BMC Bioinformatics 2021 22:355

    Content type: Software

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  4. Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capt...

    Authors: Song Feng, Emily Heath, Brett Jefferson, Cliff Joslyn, Henry Kvinge, Hugh D. Mitchell, Brenda Praggastis, Amie J. Eisfeld, Amy C. Sims, Larissa B. Thackray, Shufang Fan, Kevin B. Walters, Peter J. Halfmann, Danielle Westhoff-Smith, Qing Tan, Vineet D. Menachery…

    Citation: BMC Bioinformatics 2021 22:287

    Content type: Methodology article

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  5. Colocalization is a statistical method used in genetics to determine whether the same variant is causal for multiple phenotypes, for example, complex traits and gene expression. It provides stronger mechanisti...

    Authors: Emily A. King, Fengjiao Dunbar, Justin Wade Davis and Jacob F. Degner

    Citation: BMC Bioinformatics 2021 22:254

    Content type: Methodology article

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  6. Rapid analysis of SARS-CoV-2 genomic data plays a crucial role in surveillance and adoption of measures in controlling spread of Covid-19. Fast, inclusive and adaptive methods are required for the heterogenous SA...

    Authors: Sanket Desai, Aishwarya Rane, Asim Joshi and Amit Dutt

    Citation: BMC Bioinformatics 2021 22:247

    Content type: Software

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  7. Brain image genetics provides enormous opportunities for examining the effects of genetic variations on the brain. Many studies have shown that the structure, function, and abnormality (e.g., those related to ...

    Authors: Jin Li, Wenjie Liu, Huang Li, Feng Chen, Haoran Luo, Peihua Bao, Yanzhao Li, Hailong Jiang, Yue Gao, Hong Liang and Shiaofen Fang

    Citation: BMC Bioinformatics 2021 22:223

    Content type: Research article

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  8. A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. Accurate simulation of ChIP-seq data can mitigate this ch...

    Authors: An Zheng, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren and Melissa Gymrek

    Citation: BMC Bioinformatics 2021 22:201

    Content type: Software

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  9. ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and a...

    Authors: Xi Chen, Xu Shi, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke and Jianhua Xuan

    Citation: BMC Bioinformatics 2021 22:193

    Content type: Methodology article

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  10. The nucleus of eukaryotic cells spatially packages chromosomes into a hierarchical and distinct segregation that plays critical roles in maintaining transcription regulation. High-throughput methods of chromos...

    Authors: Haipeng Xing, Yingru Wu, Michael Q. Zhang and Yong Chen

    Citation: BMC Bioinformatics 2021 22:183

    Content type: Methodology article

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  11. Permutation testing is often considered the “gold standard” for multi-test significance analysis, as it is an exact test requiring few assumptions about the distribution being computed. However, it can be comp...

    Authors: James M. Kunert-Graf, Nikita A. Sakhanenko and David J. Galas

    Citation: BMC Bioinformatics 2021 22:180

    Content type: Methodology article

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  12. For multivariate data analysis involving only two input matrices (e.g., X and Y), the previously published methods for variable influence on projection (e.g., VIPOPLS or VIPO2PLS) are widely used for variable sel...

    Authors: Beatriz Galindo-Prieto, Paul Geladi and Johan Trygg

    Citation: BMC Bioinformatics 2021 22:176

    Content type: Methodology article

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  13. Nowadays, multiple omics data are measured on the same samples in the belief that these different omics datasets represent various aspects of the underlying biological systems. Integrating these omics datasets...

    Authors: Zhujie Gu, Said el Bouhaddani, Jiayi Pei, Jeanine Houwing-Duistermaat and Hae-Won Uh

    Citation: BMC Bioinformatics 2021 22:131

    Content type: Methodology article

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  14. VCF formatted files are the lingua franca of next-generation sequencing, whereas HL7 FHIR is emerging as a standard language for electronic health record interoperability. A growing number of FHIR-based clinic...

    Authors: Robert H. Dolin, Shaileshbhai R. Gothi, Aziz Boxwala, Bret S. E. Heale, Ammar Husami, James Jones, Himanshu Khangar, Shubham Londhe, Frank Naeymi-Rad, Soujanya Rao, Barbara Rapchak, James Shalaby, Varun Suraj, Ning Xie, Srikar Chamala and Gil Alterovitz

    Citation: BMC Bioinformatics 2021 22:104

    Content type: Software

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  15. Linkage and linkage disequilibrium (LD) between genome regions cause dependencies among genomic markers. Due to family stratification in populations with non-random mating in livestock or crop, the standard me...

    Authors: Dörte Wittenburg, Michael Doschoris and Jan Klosa

    Citation: BMC Bioinformatics 2021 22:79

    Content type: Research article

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  16. Conformational transitions are implicated in the biological function of many proteins. Structural changes in proteins can be described approximately as the relative movement of rigid domains against each other...

    Authors: Truong Khanh Linh Dang, Thach Nguyen, Michael Habeck, Mehmet Gültas and Stephan Waack

    Citation: BMC Bioinformatics 2021 22:66

    Content type: Methodology article

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  17. We present here a computational shortcut to improve a powerful wavelet-based method by Shim and Stephens (Ann Appl Stat 9(2):665–686, 2015.

    Authors: William R. P. Denault and Astanand Jugessur

    Citation: BMC Bioinformatics 2021 22:61

    Content type: Methodology article

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    The Correction to this article has been published in BMC Bioinformatics 2021 22:276

  18. Microbiomes consist of bacteria, viruses, and other microorganisms, and are responsible for many different functions in both organisms and the environment. Past analyses of microbiomes focused on using correla...

    Authors: Daniella Vo, Shayal Charisma Singh, Sara Safa and Debashis Sahoo

    Citation: BMC Bioinformatics 2021 22:49

    Content type: Research article

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  19. Several bioinformatics pipelines have been developed to detect sequences from viruses that integrate into the human genome because of the health relevance of these integrations, such as in the persistence of v...

    Authors: Elisa Pischedda, Cristina Crava, Martina Carlassara, Susanna Zucca, Leila Gasmi and Mariangela Bonizzoni

    Citation: BMC Bioinformatics 2021 22:45

    Content type: Methodology article

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  20. Brain Computer Interfaces (BCIs) translate the activity of the nervous system to a control signal which is interpretable for an external device. Using continuous motor BCIs, the user will be able to control a ...

    Authors: Mehrdad Kashefi and Mohammad Reza Daliri

    Citation: BMC Bioinformatics 2021 22:26

    Content type: Research article

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  21. Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessmen...

    Authors: Bing Song, August E. Woerner and John Planz

    Citation: BMC Bioinformatics 2021 22:12

    Content type: Methodology article

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  22. Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships betw...

    Authors: Yubin Xiao, Zheng Xiao, Xiang Feng, Zhiping Chen, Linai Kuang and Lei Wang

    Citation: BMC Bioinformatics 2020 21:555

    Content type: Methodology article

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  23. The widespread adoption of high throughput technologies has democratized data generation. However, data processing in accordance with best practices remains challenging and the data capital often becomes siloe...

    Authors: Juan S. Medina-Martínez, Juan E. Arango-Ossa, Max F. Levine, Yangyu Zhou, Gunes Gundem, Andrew L. Kung and Elli Papaemmanuil

    Citation: BMC Bioinformatics 2020 21:549

    Content type: Software

    Published on: