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  1. Ubiquitylation is an important post-translational modification of proteins that not only plays a central role in cellular coding, but is also closely associated with the development of a variety of diseases. T...

    Authors: Mengqi Luo, Zhongyan Li, Shangfu Li and Tzong-Yi Lee
    Citation: BMC Bioinformatics 2021 22:507
    Content type: Research Published on:

  3. Glycan-related genes play a fundamental role in various processes for energy acquisition and homeostasis maintenance while adapting to the environment in which the organism exists; however, their role in the m...

    Authors: Hayato Takihara, Nobuaki Miura, Kiyoko F. Aoki-Kinoshita and Shujiro Okuda
    Citation: BMC Bioinformatics 2021 22:505
    Content type: Research Published on:

  4. The functions of RNA molecules are mainly determined by their secondary structures. These functions can also be predicted using bioinformatic tools that enable the alignment of multiple RNAs to determine funct...

    Authors: Tomasz Woźniak, Małgorzata Sajek, Jadwiga Jaruzelska and Marcin Piotr Sajek
    Citation: BMC Bioinformatics 2021 22:504
    Content type: Software Published on:

  5. Piwi-interacting RNAs (piRNAs) are the small non-coding RNAs (ncRNAs) that silence genomic transposable elements. And researchers found out that piRNA also regulates various endogenous transcripts. However, th...

    Authors: Tzu-Hsien Yang, Sheng-Cian Shiue, Kuan-Yu Chen, Yan-Yuan Tseng and Wei-Sheng Wu
    Citation: BMC Bioinformatics 2021 22:503
    Content type: Methodology article Published on:

  8. Identifying human protein-phenotype relationships has attracted researchers in bioinformatics and biomedical natural language processing due to its importance in uncovering rare and complex diseases. Since exp...

    Authors: Morteza Pourreza Shahri and Indika Kahanda
    Citation: BMC Bioinformatics 2021 22:500
    Content type: Methodology article Published on:

  10. Identifying gene interactions is a topic of great importance in genomics, and approaches based on network models provide a powerful tool for studying these. Assuming a Gaussian graphical model, a gene associat...

    Authors: Camilla Lingjærde, Tonje G. Lien, Ørnulf Borgan, Helga Bergholtz and Ingrid K. Glad
    Citation: BMC Bioinformatics 2021 22:498
    Content type: Methodology article Published on:

  11. The study of drug–target interactions (DTIs) affinity plays an important role in safety assessment and pharmacology. Currently, quantitative structure–activity relationship (QSAR) and molecular docking (MD) ar...

    Authors: Xian-rui Wang, Ting-ting Cao, Cong Min Jia, Xue-mei Tian and Yun Wang
    Citation: BMC Bioinformatics 2021 22:497
    Content type: Research article Published on:

  12. Circular RNA (circRNA) is an emerging class of RNA molecules attracting researchers due to its potential for serving as markers for diagnosis, prognosis, or therapeutic targets of cancer, cardiovascular, and a...

    Authors: Dat Thanh Nguyen, Quang Thinh Trac, Thi-Hau Nguyen, Ha-Nam Nguyen, Nir Ohad, Yudi Pawitan and Trung Nghia Vu
    Citation: BMC Bioinformatics 2021 22:495
    Content type: Research Published on:

  13. 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

  14. 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:

  17. 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:

  18. 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:

  19. 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:

  21. 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

  22. 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:

  23. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  32. 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:

  34. 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

  35. 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

  36. 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

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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

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