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  1. The increasing use of whole metagenome sequencing has spurred the need to improve de novo assemblers to facilitate the discovery of unknown species and the analysis of their genomic functions. MetaVelvet-SL is...

    Authors: Kuo-ching Liang and Yasubumi Sakakibara
    Citation: BMC Bioinformatics 2021 22(Suppl 6):427
    Content type: Research Published on:

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

  2. Coxiella burnetii is the Gram-negative bacterium responsible for Q fever in humans and coxiellosis in domesticated agricultural animals. Previous vaccination efforts with whole cell inactivated bacteria or surfac...

    Authors: Lindsay M. W. Piel, Codie J. Durfee and Stephen N. White
    Citation: BMC Bioinformatics 2021 22:296
    Content type: Research Published on:

  3. Biomedical named entity recognition is one of the most essential tasks in biomedical information extraction. Previous studies suffer from inadequate annotated datasets, especially the limited knowledge contain...

    Authors: Huiwei Zhou, Zhe Liu, Chengkun Lang, Yibin Xu, Yingyu Lin and Junjie Hou
    Citation: BMC Bioinformatics 2021 22:295
    Content type: Research Published on:

  4. While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a f...

    Authors: Gulden Olgun, Afshan Nabi and Oznur Tastan
    Citation: BMC Bioinformatics 2021 22:294
    Content type: Software Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:393

  5. Brain wave signal recognition has gained increased attention in neuro-rehabilitation applications. This has driven the development of brain–computer interface (BCI) systems. Brain wave signals are acquired usi...

    Authors: Shiu Kumar, Tatsuhiko Tsunoda and Alok Sharma
    Citation: BMC Bioinformatics 2021 22(Suppl 6):195
    Content type: Research Published on:

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

  6. Genomic reads from sequencing platforms contain random errors. Global correction algorithms have been developed, aiming to rectify all possible errors in the reads using generic genome-wide patterns. However, ...

    Authors: Xuan Zhang, Yuansheng Liu, Zuguo Yu, Michael Blumenstein, Gyorgy Hutvagner and Jinyan Li
    Citation: BMC Bioinformatics 2021 22(Suppl 6):142
    Content type: Research Published on:

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

  7. Recent advances in simultaneous measurement of RNA and protein abundances at single-cell level provide a unique opportunity to predict protein abundance from scRNA-seq data using machine learning models. Howev...

    Authors: Xinnan Dai, Fan Xu, Shike Wang, Piyushkumar A. Mundra and Jie Zheng
    Citation: BMC Bioinformatics 2021 22(Suppl 6):139
    Content type: Methodology Published on:

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

  8. The rapid development of single-cell RNA sequencing (scRNA-seq) enables the exploration of cell heterogeneity, which is usually done by scRNA-seq data clustering. The essence of scRNA-seq data clustering is to...

    Authors: Rui-Yi Li, Jihong Guan and Shuigeng Zhou
    Citation: BMC Bioinformatics 2021 22(Suppl 6):130
    Content type: Research Published on:

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

  9. Nucleosome plays an important role in the process of genome expression, DNA replication, DNA repair and transcription. Therefore, the research of nucleosome positioning has invariably received extensive attent...

    Authors: Guo-Sheng Han, Qi Li and Ying Li
    Citation: BMC Bioinformatics 2021 22(Suppl 6):129
    Content type: Research Published on:

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

  10. Drug repositioning, meanings finding new uses for existing drugs, which can accelerate the processing of new drugs research and development. Various computational methods have been presented to predict novel d...

    Authors: Hai-Cheng Yi, Zhu-Hong You, Lei Wang, Xiao-Rui Su, Xi Zhou and Tong-Hai Jiang
    Citation: BMC Bioinformatics 2021 22(Suppl 3):293
    Content type: Research Published on:

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

  12. DNA-Binding Proteins (DBP) plays a pivotal role in biological system. A mounting number of researchers are studying the mechanism and detection methods. To detect DBP, the tradition experimental method is time...

    Authors: Yuqing Qian, Limin Jiang, Yijie Ding, Jijun Tang and Fei Guo
    Citation: BMC Bioinformatics 2021 22(Suppl 3):291
    Content type: Research Published on:

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

  13. The quality of gene annotation determines the interpretation of results obtained in transcriptomic studies. The growing number of genome sequence information calls for experimental and computational pipelines for

    Authors: Maxim Ivanov, Albin Sandelin and Sebastian Marquardt
    Citation: BMC Bioinformatics 2021 22:290
    Content type: Research Published on:

    The Publisher Correction to this article has been published in BMC Bioinformatics 2021 22:370

  14. Germline cells are important carriers of genetic and epigenetic information transmitted across generations in mammals. During the mammalian germline cell development cycle (i.e., the germline cycle), cell pote...

    Authors: Shiyang Zeng, Yuwei Hua, Yong Zhang, Guifen Liu and Chengchen Zhao
    Citation: BMC Bioinformatics 2021 22:289
    Content type: Database Published on:

  15. As a common and abundant RNA methylation modification, N6-methyladenosine (m6A) is widely spread in various species' transcriptomes, and it is closely related to the occurrence and development of various life pro...

    Authors: Lin Zhang, Gangshen Li, Xiuyu Li, Honglei Wang, Shutao Chen and Hui Liu
    Citation: BMC Bioinformatics 2021 22:288
    Content type: Methodology article Published on:

  16. 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 Published on:

  18. Many important applications in bioinformatics, including sequence alignment and protein family profiling, employ sequence weighting schemes to mitigate the effects of non-independence of homologous sequences a...

    Authors: Nicola De Maio, Alexander V. Alekseyenko, William J. Coleman-Smith, Fabio Pardi, Marc A. Suchard, Asif U. Tamuri, Jakub Truszkowski and Nick Goldman
    Citation: BMC Bioinformatics 2021 22:285
    Content type: Research Published on:

  21. With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from...

    Authors: Jindan Guo, Erli Pang, Hongtao Song and Kui Lin
    Citation: BMC Bioinformatics 2021 22:282
    Content type: Methodology article Published on:

  22. Single-cell RNA sequencing (scRNA-seq) has emerged has a main strategy to study transcriptional activity at the cellular level. Clustering analysis is routinely performed on scRNA-seq data to explore, recogniz...

    Authors: Madalina Ciortan and Matthieu Defrance
    Citation: BMC Bioinformatics 2021 22:280
    Content type: Research Published on:

  23. With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation ...

    Authors: Swapna Vidhur Daulatabad, Rajneesh Srivastava and Sarath Chandra Janga
    Citation: BMC Bioinformatics 2021 22:279
    Content type: Database Published on:

  25. Small Proteins have received increasing attention in recent years. They have in particular been implicated as signals contributing to the coordination of bacterial communities. In genome annotations they are o...

    Authors: John Anders, Hannes Petruschke, Nico Jehmlich, Sven-Bastiaan Haange, Martin von Bergen and Peter F Stadler
    Citation: BMC Bioinformatics 2021 22:277
    Content type: Research Published on:

  27. Histone post-translational modifications (PTMs) play an important role in our system by regulating the structure of chromatin and therefore contribute to the regulation of gene and protein expression. Irregula...

    Authors: Kevin Chappell, Stefan Graw, Charity L. Washam, Aaron J. Storey, Chris Bolden, Eric C. Peterson and Stephanie D. Byrum
    Citation: BMC Bioinformatics 2021 22:275
    Content type: Software Published on:

  28. Clinically effective and safe genotyping relies on correct reference sequences, often represented by haplotypes. The 1000 Genomes Project recorded individual genotypes across 26 different populations and, usin...

    Authors: Kshitij Srivastava, Anne-Sophie Fratzscher, Bo Lan and Willy Albert Flegel
    Citation: BMC Bioinformatics 2021 22:273
    Content type: Research Published on:

  29. Biomedical question answering (QA) is a sub-task of natural language processing in a specific domain, which aims to answer a question in the biomedical field based on one or more related passages and can provi...

    Authors: Gezheng Xu, Wenge Rong, Yanmeng Wang, Yuanxin Ouyang and Zhang Xiong
    Citation: BMC Bioinformatics 2021 22:272
    Content type: Research Published on:

  30. Translational regulation is one important aspect of gene expression regulation. Dysregulation of translation results in abnormal cell physiology and leads to diseases. Ribosome profiling (RP), also called ribo...

    Authors: Wei-Sheng Wu, Yi-Hong Tsao, Sheng-Cian Shiue, Ting-Yu Chen, Yan-Yuan Tseng and Joseph T. Tseng
    Citation: BMC Bioinformatics 2021 22(Suppl 10):271
    Content type: Research Published on:

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

  31. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal carcinoma and patients at advanced stage showed poor survival rate. Despite microRNAs (miRNAs) are used as potential biomarkers in ma...

    Authors: Eskezeia Y. Dessie, Jeffrey J. P. Tsai, Jan-Gowth Chang and Ka-Lok Ng
    Citation: BMC Bioinformatics 2021 22(Suppl 10):270
    Content type: Methodology Published on:

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

  34. Network-based analysis of gene expression through co-expression networks can be used to investigate modular relationships occurring between genes performing different biological functions. An extended descript...

    Authors: Gwenaëlle G. Lemoine, Marie-Pier Scott-Boyer, Bathilde Ambroise, Olivier Périn and Arnaud Droit
    Citation: BMC Bioinformatics 2021 22:267
    Content type: Research Published on:

  35. Full-length isoform quantification from RNA-Seq is a key goal in transcriptomics analyses and has been an area of active development since the beginning. The fundamental difficulty stems from the fact that RNA...

    Authors: Dimitra Sarantopoulou, Thomas G. Brooks, Soumyashant Nayak, Antonijo Mrčela, Nicholas F. Lahens and Gregory R. Grant
    Citation: BMC Bioinformatics 2021 22:266
    Content type: Review Published on:

  36. Testing for differential abundance of microbes in disease is a common practice in microbiome studies. Numerous differential abundance (DA) testing methods exist and range from traditional statistical tests to ...

    Authors: Zachary D. Wallen
    Citation: BMC Bioinformatics 2021 22:265
    Content type: Research article Published on:

  37. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally via base-pairing with complementary sequences on messenger RNAs (mRNAs). Due to the technical challenges involv...

    Authors: Gilad Ben Or and Isana Veksler-Lublinsky
    Citation: BMC Bioinformatics 2021 22:264
    Content type: Research article Published on:

  40. Moonlighting proteins (MPs) are a subclass of multifunctional proteins in which more than one independent or usually distinct function occurs in a single polypeptide chain. Identification of unknown cellular p...

    Authors: Farshid Shirafkan, Sajjad Gharaghani, Karim Rahimian, Reza Hasan Sajedi and Javad Zahiri
    Citation: BMC Bioinformatics 2021 22:261
    Content type: Research Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:366

  41. Recent advances in tissue clearing techniques, combined with high-speed image acquisition through light sheet microscopy, enable rapid three-dimensional (3D) imaging of biological specimens, such as whole mous...

    Authors: David Borland, Carolyn M. McCormick, Niyanta K. Patel, Oleh Krupa, Jessica T. Mory, Alvaro A. Beltran, Tala M. Farah, Carla F. Escobar-Tomlienovich, Sydney S. Olson, Minjeong Kim, Guorong Wu and Jason L. Stein
    Citation: BMC Bioinformatics 2021 22:260
    Content type: Software Published on:

  42. Whole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential false negatives due to incomplete breadth and depth of coverage for sev...

    Authors: In-Hee Lee, Yufei Lin, William Jefferson Alvarez, Carles Hernandez-Ferrer, Kenneth D. Mandl and Sek Won Kong
    Citation: BMC Bioinformatics 2021 22:259
    Content type: Software Published on:

  45. Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcodi...

    Authors: T. M. Porter and M. Hajibabaei
    Citation: BMC Bioinformatics 2021 22:256
    Content type: Methodology article Published on:

  46. With the development of the technology of single-cell sequence, revealing homogeneity and heterogeneity between cells has become a new area of computational systems biology research. However, the clustering of...

    Authors: Yuanyuan Li, Ping Luo, Yi Lu and Fang-Xiang Wu
    Citation: BMC Bioinformatics 2021 22(Suppl 3):255
    Content type: Methodology Published on:

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

  47. 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 Published on:

  48. DNA-binding hot spots are dominant and fundamental residues that contribute most of the binding free energy yet accounting for a small portion of protein–DNA interfaces. As experimental methods for identifying...

    Authors: Sijia Zhang, Lihua Wang, Le Zhao, Menglu Li, Mengya Liu, Ke Li, Yannan Bin and Junfeng Xia
    Citation: BMC Bioinformatics 2021 22(Suppl 3):253
    Content type: Research Published on:

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

  49. Motivated by the size and availability of cell line drug sensitivity data, researchers have been developing machine learning (ML) models for predicting drug response to advance cancer treatment. As drug sensit...

    Authors: Alexander Partin, Thomas Brettin, Yvonne A. Evrard, Yitan Zhu, Hyunseung Yoo, Fangfang Xia, Songhao Jiang, Austin Clyde, Maulik Shukla, Michael Fonstein, James H. Doroshow and Rick L. Stevens
    Citation: BMC Bioinformatics 2021 22:252
    Content type: Research article Published on:

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