Skip to main content

Articles

Page 5 of 220

  1. Drug-drug interaction (DDI) is a serious public health issue. The L1000 database of the LINCS project has collected millions of genome-wide expressions induced by 20,000 small molecular compounds on 72 cell li...

    Authors: Qichao Luo, Shenglong Mo, Yunfei Xue, Xiangzhou Zhang, Yuliang Gu, Lijuan Wu, Jia Zhang, Linyan Sun, Mei Liu and Yong Hu

    Citation: BMC Bioinformatics 2021 22:318

    Content type: Research

    Published on:

  2. The novel coronavirus (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2, and within a few months, it has become a global pandemic. This forced many affected countries to take stringent me...

    Authors: Shiu Kumar, Ronesh Sharma, Tatsuhiko Tsunoda, Thirumananseri Kumarevel and Alok Sharma

    Citation: BMC Bioinformatics 2021 22(Suppl 6):316

    Content type: Research

    Published on:

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

  3. Except for bacteria, the taxonomic diversity of the human fecal metagenome has not been widely studied, despite the potential importance of viruses and eukaryotes. Widely used bioinformatic tools contain limit...

    Authors: Theo R. Allnutt, Alexandra J. Roth-Schulze and Leonard C. Harrison

    Citation: BMC Bioinformatics 2021 22:312

    Content type: Research article

    Published on:

  4. Single-cell RNA sequencing (scRNA-Seq) experiments are gaining ground to study the molecular processes that drive normal development as well as the onset of different pathologies. Finding an effective and effi...

    Authors: Andrea Tangherloni, Federico Ricciuti, Daniela Besozzi, Pietro Liò and Ana Cvejic

    Citation: BMC Bioinformatics 2021 22:309

    Content type: Research

    Published on:

  5. Circular RNAs (circRNAs) are a class of single-stranded RNA molecules with a closed-loop structure. A growing body of research has shown that circRNAs are closely related to the development of diseases. Becaus...

    Authors: Zong-Lan Zuo, Rui-Fen Cao, Pi-Jing Wei, Jun-Feng Xia and Chun-Hou Zheng

    Citation: BMC Bioinformatics 2021 22:307

    Content type: Research

    Published on:

  6. Even when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insi...

    Authors: Jake L. Weissman, Sonia Dogra, Keyan Javadi, Samantha Bolten, Rachel Flint, Cyrus Davati, Jess Beattie, Keshav Dixit, Tejasvi Peesay, Shehar Awan, Peter Thielen, Florian Breitwieser, Philip L. F. Johnson, David Karig, William F. Fagan and Sharon Bewick

    Citation: BMC Bioinformatics 2021 22:306

    Content type: Research article

    Published on:

  7. Early detection of bladder cancer remains challenging because patients with early-stage bladder cancer usually have no incentive to take cytology or cystoscopy tests if they are asymptomatic. Our goal is to fi...

    Authors: Jia-You Lin, Bao-Rong Juo, Yu-Hsuan Yeh, Shu-Hsuan Fu, Yi-Ting Chen, Chien-Lun Chen and Kun-Pin Wu

    Citation: BMC Bioinformatics 2021 22:305

    Content type: Research

    Published on:

  8. Long-read sequencing is revolutionizing genome assembly: as PacBio and Nanopore technologies become more accessible in technicity and in cost, long-read assemblers flourish and are starting to deliver chromoso...

    Authors: Nadège Guiglielmoni, Antoine Houtain, Alessandro Derzelle, Karine Van Doninck and Jean-François Flot

    Citation: BMC Bioinformatics 2021 22:303

    Content type: Research article

    Published on:

  9. Quantitative proteomics studies are often used to detect proteins that are differentially expressed across different experimental conditions. Functional enrichment analyses are then typically used to detect an...

    Authors: Rachel Nadeau, Anastasiia Byvsheva and Mathieu Lavallée-Adam

    Citation: BMC Bioinformatics 2021 22:302

    Content type: Methodology article

    Published on:

  10. Accurate prognosis and identification of cancer subtypes at molecular level are important steps towards effective and personalised treatments of breast cancer. To this end, many computational methods have been...

    Authors: Xiaomei Li, Buu Truong, Taosheng Xu, Lin Liu, Jiuyong Li and Thuc D. Le

    Citation: BMC Bioinformatics 2021 22:300

    Content type: Research

    Published on:

  11. RNA-Seq is a well-established technology extensively used for transcriptome profiling, allowing the analysis of coding and non-coding RNA molecules. However, this technology produces a vast amount of data requ...

    Authors: Alessandro La Ferlita, Salvatore Alaimo, Sebastiano Di Bella, Emanuele Martorana, Georgios I. Laliotis, Francesco Bertoni, Luciano Cascione, Philip N. Tsichlis, Alfredo Ferro, Roberta Bosotti and Alfredo Pulvirenti

    Citation: BMC Bioinformatics 2021 22:298

    Content type: Software

    Published on:

  12. 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

  13. 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:

  14. 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:

  15. 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

  16. 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

  17. Taxonomic assignment is a key step in the identification of human viral pathogens. Current tools for taxonomic assignment from sequencing reads based on alignment or alignment-free k-mer approaches may not perfor...

    Authors: Haoran Ma, Tin Wee Tan and Kenneth Hon Kim Ban

    Citation: BMC Bioinformatics 2021 22(Suppl 6):194

    Content type: Software

    Published on:

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

  18. 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

  19. 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

  20. 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

  21. 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

  22. Understanding the functional effects of non-coding variants is important as they are often associated with gene-expression alteration and disease development. Over the past few years, many computational tools ...

    Authors: Hao Jia, Sung-Joon Park and Kenta Nakai

    Citation: BMC Bioinformatics 2021 22(Suppl 6):128

    Content type: Research

    Published on:

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

  23. 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

  24. 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

  25. 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

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

Featured videos

View featured videos from across the BMC-series journals

Annual Journal Metrics

  • Speed
    70 days to first decision for reviewed manuscripts only
    44 days to first decision for all manuscripts
    163 days from submission to acceptance
    36 days from acceptance to publication

    Citation Impact
    3.169 - 2-year Impact Factor
    3.629 - 5-year Impact Factor
    1.276 - Source Normalized Impact per Paper (SNIP)
    1.567 - SCImago Journal Rank (SJR)

    Usage 
    5,167,186 Downloads
    5089 Altmetric Mentions