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  1. Microalgae are emerging as promising sustainable sources for biofuels, biostimulants in agriculture, soil bioremediation, feed and human nutrients. Nonetheless, the molecular mechanisms underpinning microalgae...

    Authors: Ana B. Romero-Losada, Christina Arvanitidou, Pedro de los Reyes, Mercedes García-González and Francisco J. Romero-Campero
    Citation: BMC Bioinformatics 2022 23:113
  2. Delivering tools for genome analysis to users is often difficult given the complex dependencies and conflicts of such tools. Container virtualization systems (such as Singularity) isolate environments, thereby...

    Authors: Xu Yang and Masahiro Kasahara
    Citation: BMC Bioinformatics 2022 23:112
  3. Identification of biomarkers, which are measurable characteristics of biological datasets, can be challenging. Although amplicon sequence variants (ASVs) can be considered potential biomarkers, identifying imp...

    Authors: Josip Rudar, Teresita M. Porter, Michael Wright, G. Brian Golding and Mehrdad Hajibabaei
    Citation: BMC Bioinformatics 2022 23:110
  4. Barcode-based multiplexing methods can be used to increase throughput and reduce batch effects in large single-cell genomics studies. Despite advantages in flexibility of sample collection and scale, there are...

    Authors: Elliott Swanson, Julian Reading, Lucas T. Graybuck and Peter J. Skene
    Citation: BMC Bioinformatics 2022 23:106
  5. Necrotizing enterocolitis (NEC) is a common, potentially catastrophic intestinal disease among very low birthweight premature infants. Affecting up to 15% of neonates born weighing less than 1500 g, NEC causes...

    Authors: Yun Chao Lin, Ansaf Salleb-Aouissi and Thomas A. Hooven
    Citation: BMC Bioinformatics 2022 23:104
  6. Named Entity Recognition (NER) and Normalisation (NEN) are core components of any text-mining system for biomedical texts. In a traditional concept-recognition pipeline, these tasks are combined in a serial wa...

    Authors: Lenz Furrer, Joseph Cornelius and Fabio Rinaldi
    Citation: BMC Bioinformatics 2022 22(Suppl 1):623

    This article is part of a Supplement: Volume 22 Supplement 1

  7. Just Another Gibbs Sampling (JAGS) is a convenient tool to draw posterior samples using Markov Chain Monte Carlo for Bayesian modeling. However, the built-in function dinterval() for censored data misspecifies th...

    Authors: Xinyue Qi, Shouhao Zhou and Martyn Plummer
    Citation: BMC Bioinformatics 2022 23:102

    The Correction to this article has been published in BMC Bioinformatics 2022 23:238

  8. lncRNAs play a critical role in numerous biological processes and life activities, especially diseases. Considering that traditional wet experiments for identifying uncovered lncRNA-disease associations is lim...

    Authors: Zhen-Hao Guo, Zhan-Heng Chen, Zhu-Hong You, Yan-Bin Wang, Hai-Cheng Yi and Mei-Neng Wang
    Citation: BMC Bioinformatics 2022 22(Suppl 5):622

    This article is part of a Supplement: Volume 22 Supplement 5

  9. Given the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome...

    Authors: Lindsay V. Clark, Wittney Mays, Alexander E. Lipka and Erik J. Sacks
    Citation: BMC Bioinformatics 2022 23:101
  10. The prediction of protein secondary structures is a crucial and significant step for ab initio tertiary structure prediction which delivers the information about proteins activity and functions. As the experim...

    Authors: Katarzyna Stapor, Krzysztof Kotowski, Tomasz Smolarczyk and Irena Roterman
    Citation: BMC Bioinformatics 2022 23:100
  11. Ontologies of precisely defined, controlled vocabularies are essential to curate the results of biological experiments such that the data are machine searchable, can be computationally analyzed, and are intero...

    Authors: Malcolm E. Fisher, Erik Segerdell, Nicolas Matentzoglu, Mardi J. Nenni, Joshua D. Fortriede, Stanley Chu, Troy J. Pells, David Osumi-Sutherland, Praneet Chaturvedi, Christina James-Zorn, Nivitha Sundararaj, Vaneet S. Lotay, Virgilio Ponferrada, Dong Zhuo Wang, Eugene Kim, Sergei Agalakov…
    Citation: BMC Bioinformatics 2022 23:99
  12. Although both copy number variations (CNVs) and single nucleotide variations (SNVs) detected by single-cell RNA sequencing (scRNA-seq) are used to study intratumor heterogeneity and detect clonal groups, a sof...

    Authors: Jeerthi Kannan, Liza Mathews, Zhijie Wu, Neal S. Young and Shouguo Gao
    Citation: BMC Bioinformatics 2022 23(Suppl 3):98

    This article is part of a Supplement: Volume 23 Supplement 3

  13. Genetic risk scores (GRS) summarize genetic features such as single nucleotide polymorphisms (SNPs) in a single statistic with respect to a given trait. So far, GRS are typically built using generalized linear...

    Authors: Michael Lau, Claudia Wigmann, Sara Kress, Tamara Schikowski and Holger Schwender
    Citation: BMC Bioinformatics 2022 23:97
  14. Protein–protein interactions have pivotal roles in life processes, and aberrant interactions are associated with various disorders. Interaction site identification is key for understanding disease mechanisms a...

    Authors: Michela Quadrini, Sebastian Daberdaku and Carlo Ferrari
    Citation: BMC Bioinformatics 2022 23:96
  15. Third-generation sequencing offers some advantages over next-generation sequencing predecessors, but with the caveat of harboring a much higher error rate. Clustering-related sequences is an essential task in ...

    Authors: Robert Logan, Zoe Fleischmann, Sofia Annis, Amy Wangsness Wehe, Jonathan L. Tilly, Dori C. Woods and Konstantin Khrapko
    Citation: BMC Bioinformatics 2022 23:95
  16. Cell and circadian cycles control a large fraction of cell and organismal physiology by regulating large periodic transcriptional programs that encompass anywhere from 15 to 80% of the genome despite performin...

    Authors: Francis C. Motta, Robert C. Moseley, Bree Cummins, Anastasia Deckard and Steven B. Haase
    Citation: BMC Bioinformatics 2022 23:94
  17. The accuracy of protein 3D structure prediction has been dramatically improved with the help of advances in deep learning. In the recent CASP14, Deepmind demonstrated that their new version of AlphaFold (AF) p...

    Authors: Yiyu Hong, Juyong Lee and Junsu Ko
    Citation: BMC Bioinformatics 2022 23:93
  18. Upland cotton provides the most natural fiber in the world. During fiber development, the quality and yield of fiber were influenced by gene transcription. Revealing sequence features related to transcription ...

    Authors: Shang Liu, Hailiang Cheng, Javaria Ashraf, Youping Zhang, Qiaolian Wang, Limin Lv, Man He, Guoli Song and Dongyun Zuo
    Citation: BMC Bioinformatics 2022 23:91
  19. Measuring similarity between complex diseases has significant implications for revealing the pathogenesis of diseases and development in the domain of biomedicine. It has been consentaneous that functional ass...

    Authors: Ningyi Zhang and Tianyi Zang
    Citation: BMC Bioinformatics 2022 23(Suppl 1):89

    This article is part of a Supplement: Volume 23 Supplement 1

  20. Drug–drug interactions (DDIs) are the reactions between drugs. They are compartmentalized into three types: synergistic, antagonistic and no reaction. As a rapidly developing technology, predicting DDIs-associ...

    Authors: Chengcheng Zhang, Yao Lu and Tianyi Zang
    Citation: BMC Bioinformatics 2022 23(Suppl 1):88

    This article is part of a Supplement: Volume 23 Supplement 1

  21. To date, cancer still is one of the leading causes of death worldwide, in which the cumulative of genes carrying mutations was said to be held accountable for the establishment and development of this disease ...

    Authors: Quang-Huy Nguyen, Tin Nguyen and Duc-Hau Le
    Citation: BMC Bioinformatics 2022 23:86
  22. A typical Copy Number Variations (CNVs) detection process based on the depth of coverage in the Whole Exome Sequencing (WES) data consists of several steps: (I) calculating the depth of coverage in sequencing ...

    Authors: Wiktor Kuśmirek and Robert Nowak
    Citation: BMC Bioinformatics 2022 23:85
  23. Transcription factor (TF) binding motifs are identified by high throughput sequencing technologies as means to capture Protein-DNA interactions. These motifs are often represented by consensus sequences in for...

    Authors: Omer Ali, Amna Farooq, Mingyi Yang, Victor X. Jin, Magnar Bjørås and Junbai Wang
    Citation: BMC Bioinformatics 2022 23:83
  24. Long non-coding RNAs (lncRNAs) play a crucial role in diverse biological processes and have been confirmed to be concerned with various diseases. Largely uncharacterized of the physiological role and functions...

    Authors: Long Yang, Li-Ping Li and Hai-Cheng Yi
    Citation: BMC Bioinformatics 2022 22(Suppl 12):621

    This article is part of a Supplement: Volume 22 Supplement 12

  25. To construct gene co-expression networks, it is necessary to evaluate the correlation between different gene expression profiles. However, commonly used correlation metrics, including both linear (such as Pear...

    Authors: Jie Hou, Xiufen Ye, Weixing Feng, Qiaosheng Zhang, Yatong Han, Yusong Liu, Yu Li and Yufen Wei
    Citation: BMC Bioinformatics 2022 23:81
  26. Dengue is a common vector-borne disease in tropical countries caused by the Dengue virus. This virus may trigger a disease with several symptoms like fever, headache, nausea, vomiting, and muscle pain. Indeed,...

    Authors: Leonardo R. Souza, Juan G. Colonna, Joseana M. Comodaro and Felipe G. Naveca
    Citation: BMC Bioinformatics 2022 23:80
  27. Differential co-expression network analysis has become an important tool to gain understanding of biological phenotypes and diseases. The CSD algorithm is a method to generate differential co-expression networ...

    Authors: Jakob P. Pettersen and Eivind Almaas
    Citation: BMC Bioinformatics 2022 23:79
  28. The investigation of possible interactions between two proteins in intracellular signaling is an expensive and laborious procedure in the wet-lab, therefore, several in silico approaches have been implemented ...

    Authors: Olivér M. Balogh, Bettina Benczik, András Horváth, Mátyás Pétervári, Péter Csermely, Péter Ferdinandy and Bence Ágg
    Citation: BMC Bioinformatics 2022 23:78
  29. PubMed contains millions of abstracts that co-mention terms that describe drugs with other biomedical terms such as genes or diseases. Unique opportunities exist for leveraging these co-mentions by integrating...

    Authors: Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik and Avi Ma’ayan
    Citation: BMC Bioinformatics 2022 23:76
  30. Naturally existing and human-produced heavy metals are released into the environment and cannot be completely decomposed by microorganisms, but they continue to accumulate in water and sediments, causing organ...

    Authors: Hao-Hsiang Ku, Pinpin Lin and Min-Pei Ling
    Citation: BMC Bioinformatics 2022 22(Suppl 5):620

    This article is part of a Supplement: Volume 22 Supplement 5

  31. Prediction of drug–drug interactions (DDIs) can reveal potential adverse pharmacological reactions between drugs in co-medication. Various methods have been proposed to address this issue. Most of them focus o...

    Authors: Zun Liu, Xing-Nan Wang, Hui Yu, Jian-Yu Shi and Wen-Min Dong
    Citation: BMC Bioinformatics 2022 23:75
  32. CRISPR/Cas9 technology has become an important tool to generate targeted, highly specific genome mutations. The technology has great potential for crop improvement, as crop genomes are tailored to optimize spe...

    Authors: Hans Müller Paul, Dave D. Istanto, Jacob Heldenbrand and Matthew E. Hudson
    Citation: BMC Bioinformatics 2022 23:74
  33. Nerve discharge is the carrier of information transmission, which can reveal the basic rules of various nerve activities. Recognition of the nerve discharge rhythm is the key to correctly understand the dynami...

    Authors: Zhongting Jiang, Dong Wang and Yuehui Chen
    Citation: BMC Bioinformatics 2022 22(Suppl 3):619

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

  34. The liquid–liquid phase separation (LLPS) of biomolecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles in cel...

    Authors: Xiaoquan Chu, Tanlin Sun, Qian Li, Youjun Xu, Zhuqing Zhang, Luhua Lai and Jianfeng Pei
    Citation: BMC Bioinformatics 2022 23:72
  35. Knowledge of protein motions is significant to understand its functions. While currently available databases for protein motions are mostly focused on overall domain motions, little attention is paid on local ...

    Authors: Cheng Peng, Xinben Zhang, Zhijian Xu, Zhaoqiang Chen, Yanqing Yang, Tingting Cai and Weiliang Zhu
    Citation: BMC Bioinformatics 2022 23:70
  36. Gene ontology (GO) enrichment analysis is frequently undertaken during exploration of various -omics data sets. Despite the wide array of tools available to biologists to perform this analysis, meaningful visu...

    Authors: Ziyin Xin, Yujun Cai, Louis T. Dang, Hannah M. S. Burke, Jerico Revote, Natalie Charitakis, Denis Bienroth, Hieu T. Nim, Yuan-Fang Li and Mirana Ramialison
    Citation: BMC Bioinformatics 2022 23:69
  37. Generating chromosome-scale haplotype resolved assembly is important for functional studies. However, current de novo assemblers are either haploid assemblers that discard allelic information, or diploid assemble...

    Authors: Min Xie, Linfeng Yang, Chenglin Jiang, Shenshen Wu, Cheng Luo, Xin Yang, Lijuan He, Shixuan Chen, Tianquan Deng, Mingzhi Ye, Jianbing Yan and Ning Yang
    Citation: BMC Bioinformatics 2022 23:68

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