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  1. 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 Published on:

  2. RNA sequencing allows the study of both gene expression changes and transcribed mutations, providing a highly effective way to gain insight into cancer biology. When planning the sequencing of a large cohort o...

    Authors: Anna Quaglieri, Christoffer Flensburg, Terence P. Speed and Ian J. Majewski
    Citation: BMC Bioinformatics 2020 21:553
    Content type: Methodology article Published on:

  4. 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:

  5. Human skeletal muscle responds to weight-bearing exercise with significant inter-individual differences. Investigation of transcriptome responses could improve our understanding of this variation. However, thi...

    Authors: Yusuf Khan, Daniel Hammarström, Bent R. Rønnestad, Stian Ellefsen and Rafi Ahmad
    Citation: BMC Bioinformatics 2020 21:548
    Content type: Research article Published on:

  6. Quantitative real-time PCR (qPCR) is one of the most widely used methods to measure gene expression. An important aspect of qPCR data that has been largely ignored is the presence of non-detects: reactions fai...

    Authors: Valeriia Sherina, Helene R. McMurray, Winslow Powers, Harmut Land, Tanzy M. T. Love and Matthew N. McCall
    Citation: BMC Bioinformatics 2020 21:545
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2024 25:63

  7. Elucidation of interactive relation between chemicals and genes is of key relevance not only for discovering new drug leads in drug development but also for repositioning existing drugs to novel therapeutic ta...

    Authors: Wei Wang, Xi Yang, Chengkun Wu and Canqun Yang
    Citation: BMC Bioinformatics 2020 21:544
    Content type: Methodology article Published on:

  9. Mixed linear models (MLM) have been widely used to account for population structure in case-control genome-wide association studies, the status being analyzed as a quantitative phenotype. Chen et al. proved in...

    Authors: Jacqueline Milet, David Courtin, André Garcia and Hervé Perdry
    Citation: BMC Bioinformatics 2020 21:536
    Content type: Methodology article Published on:

  10. Accurate protocols and methods to robustly detect the mosaic loss of chromosome Y (mLOY) are needed given its reported role in cancer, several age-related disorders and overall male mortality. Intensity SNP-ar...

    Authors: Juan R. González, Marcos López-Sánchez, Alejandro Cáceres, Pere Puig, Tonu Esko and Luis A. Pérez-Jurado
    Citation: BMC Bioinformatics 2020 21:533
    Content type: Software Published on:

  11. Neoantigen-based personal vaccines and adoptive T cell immunotherapy have shown high efficacy as a cancer treatment in clinical trials. Algorithms for the accurate prediction of neoantigens have played a pivot...

    Authors: Yunxia Tang, Yu Wang, Jiaqian Wang, Miao Li, Linmin Peng, Guochao Wei, Yixing Zhang, Jin Li and Zhibo Gao
    Citation: BMC Bioinformatics 2020 21:532
    Content type: Research article Published on:

  12. The alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software t...

    Authors: Mercè Llabrés, Gabriel Riera, Francesc Rosselló and Gabriel Valiente
    Citation: BMC Bioinformatics 2020 21(Suppl 6):434
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  13. Alignment-free methods for sequence comparisons have become popular in many bioinformatics applications, specifically in the estimation of sequence similarity measures to construct phylogenetic trees. Recently...

    Authors: Sriram P. Chockalingam, Jodh Pannu, Sahar Hooshmand, Sharma V. Thankachan and Srinivas Aluru
    Citation: BMC Bioinformatics 2020 21(Suppl 6):404
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  14. DNA methylation in the human genome is acknowledged to be widely associated with biological processes and complex diseases. The Illumina Infinium methylation arrays have been approved as one of the most effici...

    Authors: Xinyu Hu, Li Tang, Linconghua Wang, Fang-Xiang Wu and Min Li
    Citation: BMC Bioinformatics 2020 21(Suppl 6):403
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  15. Biological data has grown explosively with the advance of next-generation sequencing. However, annotating protein function with wet lab experiments is time-consuming. Fortunately, computational function predic...

    Authors: Yi-Wei Liu, Tz-Wei Hsu, Che-Yu Chang, Wen-Hung Liao and Jia-Ming Chang
    Citation: BMC Bioinformatics 2020 21(Suppl 6):276
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  16. All molecular functions and biological processes are carried out by groups of proteins that interact with each other. Metaproteomic data continuously generates new proteins whose molecular functions and relati...

    Authors: Adrià Alcalá, Ricardo Alberich, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente
    Citation: BMC Bioinformatics 2020 21(Suppl 6):265
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  17. Integrative network methods are commonly used for interpretation of high-throughput experimental biological data: transcriptomics, proteomics, metabolomics and others. One of the common approaches is finding a...

    Authors: Nikita Alexeev, Javlon Isomurodov, Vladimir Sukhov, Gennady Korotkevich and Alexey Sergushichev
    Citation: BMC Bioinformatics 2020 21(Suppl 6):261
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  18. With the rapid development of high-throughput technique, multiple heterogeneous omics data have been accumulated vastly (e.g., genomics, proteomics and metabolomics data). Integrating information from multiple...

    Authors: Yuanyuan Ma, Junmin Zhao and Yingjun Ma
    Citation: BMC Bioinformatics 2020 21(Suppl 6):234
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  19. One of the most essential problems in structural bioinformatics is protein fold recognition. In this paper, we design a novel deep learning architecture, so-called DeepFrag-k, which identifies fold discriminat...

    Authors: Wessam Elhefnawy, Min Li, Jianxin Wang and Yaohang Li
    Citation: BMC Bioinformatics 2020 21(Suppl 6):203
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  20. Electron tomography (ET) is an important technique for the study of complex biological structures and their functions. Electron tomography reconstructs the interior of a three-dimensional object from its proje...

    Authors: Lun Li, Renmin Han, Zhaotian Zhang, Tiande Guo, Zhiyong Liu and Fa Zhang
    Citation: BMC Bioinformatics 2020 21(Suppl 6):202
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  21. Screening of the brain computerised tomography (CT) images is a primary method currently used for initial detection of patients with brain trauma or other conditions. In recent years, deep learning technique h...

    Authors: Jianqiang Li, Guanghui Fu, Yueda Chen, Pengzhi Li, Bo Liu, Yan Pei and Hui Feng
    Citation: BMC Bioinformatics 2020 21(Suppl 6):200
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  22. The identification of early mild cognitive impairment (EMCI), which is an early stage of Alzheimer’s disease (AD) and is associated with brain structural and functional changes, is still a challenging task. Re...

    Authors: Jin Liu, Guanxin Tan, Wei Lan and Jianxin Wang
    Citation: BMC Bioinformatics 2020 21(Suppl 6):123
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 6

  23. The large-scale availability of whole-genome sequencing profiles from bulk DNA sequencing of cancer tissues is fueling the application of evolutionary theory to cancer. From a bulk biopsy, subclonal deconvolut...

    Authors: Giulio Caravagna, Guido Sanguinetti, Trevor A. Graham and Andrea Sottoriva
    Citation: BMC Bioinformatics 2020 21:531
    Content type: Software Published on:

  24. Nutrigenomics aims at understanding the interaction between nutrition and gene information. Due to the complex interactions of nutrients and genes, their relationship exhibits non-linearity. One of the most ef...

    Authors: Xiangnan Xu, Samantha M. Solon-Biet, Alistair Senior, David Raubenheimer, Stephen J. Simpson, Luigi Fontana, Samuel Mueller and Jean Y. H. Yang
    Citation: BMC Bioinformatics 2020 21:530
    Content type: Methodology article Published on:

  25. Antibodies revolutionized cancer treatment over the past decades. Despite their successfully application, there are still challenges to overcome to improve efficacy, such as the heterogeneous distribution of a...

    Authors: Ana Luísa Cartaxo, Jaime Almeida, Emilio J. Gualda, Maria Marsal, Pablo Loza-Alvarez, Catarina Brito and Inês A. Isidro
    Citation: BMC Bioinformatics 2020 21:529
    Content type: Research article Published on:

  27. Sequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processe...

    Authors: Marius Welzel, Anja Lange, Dominik Heider, Michael Schwarz, Bernd Freisleben, Manfred Jensen, Jens Boenigk and Daniela Beisser
    Citation: BMC Bioinformatics 2020 21:526
    Content type: Software Published on:

  28. The spread of infectious diseases is so important that changes the demography of the population. Therefore, prevention and intervention measures are essential to control and eliminate the disease. Among the dr...

    Authors: Mahmood Parsamanesh, Majid Erfanian and Saeed Mehrshad
    Citation: BMC Bioinformatics 2020 21:525
    Content type: Research article Published on:

  29. Medical decision making based on quantitative test results depends on reliable reference intervals, which represent the range of physiological test results in a healthy population. Current methods for the esti...

    Authors: Tobias Hepp, Jakob Zierk, Manfred Rauh, Markus Metzler and Andreas Mayr
    Citation: BMC Bioinformatics 2020 21:524
    Content type: Methodology article Published on:

  31. The study of mosaic mutation is important since it has been linked to cancer and various disorders. Single cell sequencing has become a powerful tool to study the genome of individual cells for the detection o...

    Authors: Vivekananda Sarangi, Alexandre Jourdon, Taejeong Bae, Arijit Panda, Flora Vaccarino and Alexej Abyzov
    Citation: BMC Bioinformatics 2020 21:521
    Content type: Methodology article Published on:

  32. Protein kinases are a large family of druggable proteins that are genomically and proteomically altered in many human cancers. Kinase-targeted drugs are emerging as promising avenues for personalized medicine ...

    Authors: Liang-Chin Huang, Wayland Yeung, Ye Wang, Huimin Cheng, Aarya Venkat, Sheng Li, Ping Ma, Khaled Rasheed and Natarajan Kannan
    Citation: BMC Bioinformatics 2020 21:520
    Content type: Research article Published on:

  33. Circular RNAs (circRNAs) are special noncoding RNA molecules with closed loop structures. Compared with the traditional linear RNA, circRNA is more stable and not easily degraded. Many studies have shown that ...

    Authors: Lei Deng, Wei Lin, Jiacheng Wang and Jingpu Zhang
    Citation: BMC Bioinformatics 2020 21:519
    Content type: Research article Published on:

  34. Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of differ...

    Authors: Ralf C. Mueller, Nicolai Mallig, Jacqueline Smith, Lél Eöry, Richard I. Kuo and Robert H. S. Kraus
    Citation: BMC Bioinformatics 2020 21:502
    Content type: Database Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:472

  35. DNBSEQ™ platforms are new massively parallel sequencing (MPS) platforms that use DNA nanoball technology. Use of data generated from DNBSEQ™ platforms to detect single nucleotide variants (SNVs) and small inse...

    Authors: Junhua Rao, Lihua Peng, Xinming Liang, Hui Jiang, Chunyu Geng, Xia Zhao, Xin Liu, Guangyi Fan, Fang Chen and Feng Mu
    Citation: BMC Bioinformatics 2020 21:518
    Content type: Research article Published on:

  36. Implementation of Third-Generation Sequencing approaches for Whole Genome Sequencing (WGS) all-in-one diagnostics in human and veterinary medicine, requires the rapid and accurate generation of consensus genom...

    Authors: Nick Vereecke, Jade Bokma, Freddy Haesebrouck, Hans Nauwynck, Filip Boyen, Bart Pardon and Sebastiaan Theuns
    Citation: BMC Bioinformatics 2020 21:517
    Content type: Methodology article Published on:

  37. Reconstructing ancestral genomes is one of the central problems presented in genome rearrangement analysis since finding the most likely true ancestor is of significant importance in phylogenetic reconstructio...

    Authors: Zhaojuan Zhang, Wanliang Wang, Ruofan Xia, Gaofeng Pan, Jiandong Wang and Jijun Tang
    Citation: BMC Bioinformatics 2020 21:516
    Content type: Research article Published on:

  38. Numerical solutions of the chemical master equation (CME) are important for understanding the stochasticity of biochemical systems. However, solving CMEs is a formidable task. This task is complicated due to t...

    Authors: Rahul Kosarwal, Don Kulasiri and Sandhya Samarasinghe
    Citation: BMC Bioinformatics 2020 21:515
    Content type: Methodology article Published on:

  39. Recent advances in sequencing technologies have led to an explosion in the number of genomes available, but accurate genome annotation remains a major challenge. The prediction of protein-coding genes in eukar...

    Authors: Corentin Meyer, Nicolas Scalzitti, Anne Jeannin-Girardon, Pierre Collet, Olivier Poch and Julie D. Thompson
    Citation: BMC Bioinformatics 2020 21:513
    Content type: Research article Published on:

  40. An enzyme activity is influenced by the external environment. It is important to have an enzyme remain high activity in a specific condition. A usual way is to first determine the optimal condition of an enzym...

    Authors: Xiangjun Li, Zhixin Dou, Yuqing Sun, Lushan Wang, Bin Gong and Lin Wan
    Citation: BMC Bioinformatics 2020 21:512
    Content type: Methodology article Published on:

  41. The nonrandom radial organization of eukaryotic chromosome territories (CTs) inside the nucleus plays an important role in nuclear functional compartmentalization. Increasingly, chromosome conformation capture...

    Authors: Priyojit Das, Tongye Shen and Rachel Patton McCord
    Citation: BMC Bioinformatics 2020 21:511
    Content type: Methodology article Published on:

  42. The concept of minimal cut sets (MCS) has become an important mathematical framework for analyzing and (re)designing metabolic networks. However, the calculation of MCS in genome-scale metabolic models is a co...

    Authors: Steffen Klamt, Radhakrishnan Mahadevan and Axel von Kamp
    Citation: BMC Bioinformatics 2020 21:510
    Content type: Methodology article Published on:

  43. Cryo-electron microscopy (Cryo-EM) is widely used in the determination of the three-dimensional (3D) structures of macromolecules. Particle picking from 2D micrographs remains a challenging early step in the C...

    Authors: Adil Al-Azzawi, Anes Ouadou, Highsmith Max, Ye Duan, John J. Tanner and Jianlin Cheng
    Citation: BMC Bioinformatics 2020 21:509
    Content type: Methodology article Published on:

  44. Enhancer–promoter interactions (EPIs) play key roles in transcriptional regulation and disease progression. Although several computational methods have been developed to predict such interactions, their perfor...

    Authors: Fang Jing, Shao-Wu Zhang and Shihua Zhang
    Citation: BMC Bioinformatics 2020 21:507
    Content type: Methodology article Published on:

  45. Hi-C and its variant techniques have been developed to capture the spatial organization of chromatin. Normalization of Hi-C contact map is essential for accurate modeling and interpretation of high-throughput ...

    Authors: Ahmed Ibrahim Samir Khalil, Siti Rawaidah Binte Mohammad Muzaki, Anupam Chattopadhyay and Amartya Sanyal
    Citation: BMC Bioinformatics 2020 21:506
    Content type: Methodology article Published on:

  47. The formation of contacts among protein secondary structure elements (SSEs) is an important step in protein folding as it determines topology of protein tertiary structure; hence, inferring inter-SSE contacts ...

    Authors: Qi Zhang, Jianwei Zhu, Fusong Ju, Lupeng Kong, Shiwei Sun, Wei-Mou Zheng and Dongbo Bu
    Citation: BMC Bioinformatics 2020 21:503
    Content type: Methodology Published on:

  48. The use of predictive gene signatures to assist clinical decision is becoming more and more important. Deep learning has a huge potential in the prediction of phenotype from gene expression profiles. However, ...

    Authors: Blaise Hanczar, Farida Zehraoui, Tina Issa and Mathieu Arles
    Citation: BMC Bioinformatics 2020 21:501
    Content type: Research article Published on:

  49. High throughput experiments have generated a significantly large amount of protein interaction data, which is being used to study protein networks. Studying complete protein networks can reveal more insight ab...

    Authors: Umair Ayub, Imran Haider and Hammad Naveed
    Citation: BMC Bioinformatics 2020 21:500
    Content type: Methodology article Published on:

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