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  1. Phylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed fo...

    Authors: Luna L. Sánchez-Reyes, Martha Kandziora and Emily Jane McTavish

    Citation: BMC Bioinformatics 2021 22:355

    Content type: Software

    Published on:

  2. Fragment libraries play a key role in fragment-assembly based protein structure prediction, where protein fragments are assembled to form a complete three-dimensional structure. Rich and accurate structural in...

    Authors: Siyuan Liu, Tong Wang, Qijiang Xu, Bin Shao, Jian Yin and Tie-Yan Liu

    Citation: BMC Bioinformatics 2021 22:351

    Content type: Research

    Published on:

  3. An individual’s genetics play a role in how RNA transcripts are generated from DNA and consequently in their translation into protein. Transcriptional and translational profiling of patients furnishes the info...

    Authors: Ching-Yu Shih, Amrita Chattopadhyay, Chien-Hui Wu, Yu-Wen Tien and Tzu-Pin Lu

    Citation: BMC Bioinformatics 2021 22:350

    Content type: Software

    Published on:

  4. Plasmids are mobile genetic elements that often carry accessory genes, and are vectors for horizontal transfer between bacterial genomes. Plasmid detection in large genomic datasets is crucial to analyze their...

    Authors: Léa Pradier, Tazzio Tissot, Anna-Sophie Fiston-Lavier and Stéphanie Bedhomme

    Citation: BMC Bioinformatics 2021 22:349

    Content type: Methodology article

    Published on:

  5. Low-depth sequencing allows researchers to increase sample size at the expense of lower accuracy. To incorporate uncertainties while maintaining statistical power, we introduce MCPCA_PopGen to analyze population ...

    Authors: Miao Zhang, Yiwen Liu, Hua Zhou, Joseph Watkins and Jin Zhou

    Citation: BMC Bioinformatics 2021 22:348

    Content type: Methodology article

    Published on:

  6. Computational tools analyzing RNA-sequencing data have boosted alternative splicing research by identifying and assessing differentially spliced genes. However, common alternative splicing analysis tools diffe...

    Authors: Ittai B. Muller, Stijn Meijers, Peter Kampstra, Steven van Dijk, Michel van Elswijk, Marry Lin, Anna M. Wojtuszkiewicz, Gerrit Jansen, Robert de Jonge and Jacqueline Cloos

    Citation: BMC Bioinformatics 2021 22:347

    Content type: Research article

    Published on:

  7. Recent advances in 3D imaging technologies provide novel insights to researchers and reveal finer and more detail of examined specimen, especially in the biomedical domain, but also impose huge challenges rega...

    Authors: Dominik Drees, Aaron Scherzinger, René Hägerling, Friedemann Kiefer and Xiaoyi Jiang

    Citation: BMC Bioinformatics 2021 22:346

    Content type: Methodology article

    Published on:

  8. VISPR is an interactive visualization and analysis framework for CRISPR screening experiments. However, it only supports the output of MAGeCK, and requires installation and manual configuration. Furthermore, V...

    Authors: Yingbo Cui, Zihang Wang, Johannes Köster, Xiangke Liao, Shaoliang Peng, Tao Tang, Chun Huang and Canqun Yang

    Citation: BMC Bioinformatics 2021 22:344

    Content type: Software

    Published on:

  9. Autoimmune diseases are heterogeneous pathologies with difficult diagnosis and few therapeutic options. In the last decade, several omics studies have provided significant insights into the molecular mechanism...

    Authors: Jordi Martorell-Marugán, Raúl López-Domínguez, Adrián García-Moreno, Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Guillermo Barturen, Adoración Martín-Gómez, Kevin Troule, Gonzalo Gómez-López, Fátima Al-Shahrour, Víctor González-Rumayor, María Peña-Chilet, Joaquín Dopazo, Julio Sáez-Rodríguez, Marta E. Alarcón-Riquelme and Pedro Carmona-Sáez

    Citation: BMC Bioinformatics 2021 22:343

    Content type: Database

    Published on:

  10. Localization of messenger RNAs (mRNAs) plays a crucial role in the growth and development of cells. Particularly, it plays a major role in regulating spatio-temporal gene expression. The in situ hybridization ...

    Authors: Prabina Kumar Meher, Anil Rai and Atmakuri Ramakrishna Rao

    Citation: BMC Bioinformatics 2021 22:342

    Content type: Methodology article

    Published on:

  11. Epigenetic modifications, including CG methylation (a major form of DNA methylation) and histone modifications, interact with each other to shape their genomic distribution patterns. However, the entire pictur...

    Authors: Wan Kin Au Yeung, Osamu Maruyama and Hiroyuki Sasaki

    Citation: BMC Bioinformatics 2021 22:341

    Content type: Research article

    Published on:

  12. Antifreeze proteins (AFPs) are a group of proteins that inhibit body fluids from growing to ice crystals and thus improve biological antifreeze ability. It is vital to the survival of living organisms in extre...

    Authors: Shunfang Wang, Lin Deng, Xinnan Xia, Zicheng Cao and Yu Fei

    Citation: BMC Bioinformatics 2021 22(Suppl 3):340

    Content type: Research

    Published on:

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

  13. Approximate Bayesian Computation (ABC) has become a key tool for calibrating the parameters of discrete stochastic biochemical models. For higher dimensional models and data, its performance is strongly depend...

    Authors: Richard M. Jiang, Fredrik Wrede, Prashant Singh, Andreas Hellander and Linda R. Petzold

    Citation: BMC Bioinformatics 2021 22:339

    Content type: Methodology article

    Published on:

  14. Drug discovery is a multi-stage process that comprises two costly major steps: pre-clinical research and clinical trials. Among its stages, lead optimization easily consumes more than half of the pre-clinical ...

    Authors: Leili Zhang, Giacomo Domeniconi, Chih-Chieh Yang, Seung-gu Kang, Ruhong Zhou and Guojing Cong

    Citation: BMC Bioinformatics 2021 22:338

    Content type: Research

    Published on:

  15. With the rapid growth in the use of high-throughput methods for characterizing translation and the continued expansion of multi-omics, there is a need for back-end functions and streamlined tools for processin...

    Authors: Håkon Tjeldnes, Kornel Labun, Yamila Torres Cleuren, Katarzyna Chyżyńska, Michał Świrski and Eivind Valen

    Citation: BMC Bioinformatics 2021 22:336

    Content type: Software

    Published on:

  16. Once aligned, long-reads can be a useful source of information to identify the type and position of structural variations. However, due to the high sequencing error of long reads, long-read structural variatio...

    Authors: Shaya Akbarinejad, Mostafa Hadadian Nejad Yousefi and Maziar Goudarzi

    Citation: BMC Bioinformatics 2021 22:335

    Content type: Software

    Published on:

  17. In eukaryotes, proteins targeted for secretion contain a signal peptide, which allows them to proceed through the conventional ER/Golgi-dependent pathway. However, an important number of proteins lacking a sig...

    Authors: Alvaro Ras-Carmona, Marta Gomez-Perosanz and Pedro A. Reche

    Citation: BMC Bioinformatics 2021 22:333

    Content type: Research

    Published on:

  18. Accurately forecasting the prognosis could improve cervical cancer management, however, the currently used clinical features are difficult to provide enough information. The aim of this study is to improve for...

    Authors: Dongyan Ding, Tingyuan Lang, Dongling Zou, Jiawei Tan, Jia Chen, Lei Zhou, Dong Wang, Rong Li, Yunzhe Li, Jingshu Liu, Cui Ma and Qi Zhou

    Citation: BMC Bioinformatics 2021 22:331

    Content type: Research

    Published on:

  19. Proteins are of extremely vital importance in the human body, and no movement or activity can be performed without proteins. Currently, microscopy imaging technologies developed rapidly are employed to observe...

    Authors: Enze Zhang, Boheng Zhang, Shaohan Hu, Fa Zhang, Zhiyong Liu and Xiaohua Wan

    Citation: BMC Bioinformatics 2021 22(Suppl 3):327

    Content type: Research

    Published on:

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

  20. Automated segmentation of nuclei in microscopic images has been conducted to enhance throughput in pathological diagnostics and biological research. Segmentation accuracy and speed has been significantly enhan...

    Authors: Christopher A. Mela and Yang Liu

    Citation: BMC Bioinformatics 2021 22:325

    Content type: Research

    Published on:

  21. 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:

  22. 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

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

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