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  1. The Raffinose synthetase (RAFS) genes superfamily is critical for the synthesis of raffinose, which accumulates in plant leaves under abiotic stress. However, it remains unclear whether RAFS contributes to resist...

    Authors: Ruifeng Cui, Xiaoge Wang, Waqar Afzal Malik, Xuke Lu, Xiugui Chen, Delong Wang, Junjuan Wang, Shuai Wang, Chao Chen, Lixue Guo, Quanjia Chen and Wuwei Ye
    Citation: BMC Bioinformatics 2021 22:356
    Content type: Research article Published on:

  2. 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:

  4. StrongestPath is a Cytoscape 3 application that enables the analysis of interactions between two proteins or groups of proteins in a collection of protein–protein interaction (PPI) network or signaling network...

    Authors: Zaynab Mousavian, Mehran Khodabandeh, Ali Sharifi-Zarchi, Alireza Nadafian and Alireza Mahmoudi
    Citation: BMC Bioinformatics 2021 22:352
    Content type: Software Published on:

  5. 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:

  6. 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:

  7. 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:

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  22. 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:

  25. 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

  27. 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:

  33. 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:

  35. 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

  36. 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:

  37. 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:

  38. 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:

  39. 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: J 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:

  40. 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:

  42. 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:

  43. 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:

  45. 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:

  47. 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:

  49. 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

  50. 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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