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  1. The fidelity and reliability of disease model predictions depend on accurate and precise descriptions of processes and determination of parameters. Various models exist to describe within-host dynamics during ...

    Authors: Shade Horn, Jacky L. Snoep and David D. van Niekerk

    Citation: BMC Bioinformatics 2021 22:384

    Content type: Research

    Published on:

  2. Biomacromolecular structural data outgrew the legacy Protein Data Bank (PDB) format which the scientific community relied on for decades, yet the use of its successor PDBx/Macromolecular Crystallographic Infor...

    Authors: Glen van Ginkel, Lukáš Pravda, José M. Dana, Mihaly Varadi, Peter Keller, Stephen Anyango and Sameer Velankar

    Citation: BMC Bioinformatics 2021 22:383

    Content type: Software

    Published on:

  3. Neoantigen based personalized immune therapies achieve promising results in melanoma and lung cancer, but few neoantigen based models perform well in IDH wild-type GBM, and the association between neoantigen i...

    Authors: Ting Sun, Yufei He, Wendong Li, Guang Liu, Lin Li, Lu Wang, Zixuan Xiao, Xiaohan Han, Hao Wen, Yong Liu, Yifan Chen, Haoyu Wang, Jing Li, Yubo Fan, Wei Zhang and Jing Zhang

    Citation: BMC Bioinformatics 2021 22:382

    Content type: Research

    Published on:

  4. Authors: Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordoñez, Andrew E. Jaffe and Leonardo Collado-Torres

    Citation: BMC Bioinformatics 2021 22:381

    Content type: Correction

    Published on:

    The original article was published in BMC Bioinformatics 2021 22:224

  5. RNA degradation is important for the regulation of gene expression. Despite the identification of proteins and sequences related to deadenylation-dependent RNA degradation in plants, endonucleolytic cleavage-d...

    Authors: Daishin Ueno, Harunori Kawabe, Shotaro Yamasaki, Taku Demura and Ko Kato

    Citation: BMC Bioinformatics 2021 22:380

    Content type: Research

    Published on:

  6. Autism spectrum disorders (ASD) imply a spectrum of symptoms rather than a single phenotype. ASD could affect brain connectivity at different degree based on the severity of the symptom. Given their excellent ...

    Authors: Jinlong Hu, Lijie Cao, Tenghui Li, Shoubin Dong and Ping Li

    Citation: BMC Bioinformatics 2021 22:379

    Content type: Methodology article

    Published on:

  7. Due to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential st...

    Authors: Zhenmiao Zhang and Lu Zhang

    Citation: BMC Bioinformatics 2021 22(Suppl 10):378

    Content type: Methodology

    Published on:

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

  8. Data integration to build a biomedical knowledge graph is a challenging task. There are multiple disease ontologies used in data sources and publications, each having its hierarchy. A common task is to map bet...

    Authors: Natalja Kurbatova and Rowan Swiers

    Citation: BMC Bioinformatics 2021 22:377

    Content type: Software

    Published on:

  9. Illumina is the dominant sequencing technology at this time. Short length, short insert size, some systematic biases, and low-level carryover contamination in Illumina reads continue to make assembly of repeat...

    Authors: Alexandre Souvorov and Richa Agarwala

    Citation: BMC Bioinformatics 2021 22:375

    Content type: Software

    Published on:

  10. As exome sequencing (ES) integrates into clinical practice, we should make every effort to utilize all information generated. Copy-number variation can lead to Mendelian disorders, but small copy-number varian...

    Authors: Dayne L. Filer, Fengshen Kuo, Alicia T. Brandt, Christian R. Tilley, Piotr A. Mieczkowski, Jonathan S. Berg, Kimberly Robasky, Yun Li, Chris Bizon, Jeffery L. Tilson, Bradford C. Powell, Darius M. Bost, Clark D. Jeffries and Kirk C. Wilhelmsen

    Citation: BMC Bioinformatics 2021 22:374

    Content type: Research

    Published on:

  11. SARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged globally, of which the most notable and concerning currently are the UK va...

    Authors: Phuoc Thien Truong Nguyen, Ilya Plyusnin, Tarja Sironen, Olli Vapalahti, Ravi Kant and Teemu Smura

    Citation: BMC Bioinformatics 2021 22:373

    Content type: Software

    Published on:

  12. Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Effector proteins are the tools such pathogens use to infect the cell, predicting effectors de ...

    Authors: Ruth Kristianingsih and Dan MacLean

    Citation: BMC Bioinformatics 2021 22:372

    Content type: Software

    Published on:

  13. More and more evidence shows that circRNA plays an important role in various biological processes and human health. Therefore, inferring the circRNA’s potential functions and obtaining circRNA functional simil...

    Authors: Liang Shu, Cheng Zhou, Xinxu Yuan, Jingpu Zhang and Lei Deng

    Citation: BMC Bioinformatics 2021 22(Suppl 10):371

    Content type: Methodology

    Published on:

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

  14. Mitochondria play essential roles in regulating cellular functions. Some drug treatments and molecular interventions have been reported to have off-target effects damaging mitochondria and causing severe side ...

    Authors: Yu-Te Lin, Ko-Hong Lin, Chi-Jung Huang and An-Chi Wei

    Citation: BMC Bioinformatics 2021 22(Suppl 10):369

    Content type: Research

    Published on:

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

  15. Introns are generally removed from primary transcripts to form mature RNA molecules in a post-transcriptional process called splicing. An efficient splicing of primary transcripts is an essential step in gene ...

    Authors: Verônica R. de Melo Costa, Julianus Pfeuffer, Annita Louloupi, Ulf A. V. Ørom and Rosario M. Piro

    Citation: BMC Bioinformatics 2021 22:368

    Content type: Software

    Published on:

  16. The topology of metabolic networks is both well-studied and remarkably well-conserved across many species. The regulation of these networks, however, is much more poorly characterized, though it is known to be...

    Authors: Justin Y. Lee, Britney Nguyen, Carlos Orosco and Mark P. Styczynski

    Citation: BMC Bioinformatics 2021 22:365

    Content type: Methodology article

    Published on:

  17. Analyzing single-cell RNA sequencing (scRNAseq) data plays an important role in understanding the intrinsic and extrinsic cellular processes in biological and biomedical research. One significant effort in thi...

    Authors: Tianyu Wang, Jun Bai and Sheida Nabavi

    Citation: BMC Bioinformatics 2021 22:364

    Content type: Methodology article

    Published on:

  18. Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Her...

    Authors: Ian Leifer, Mishael Sánchez-Pérez, Cecilia Ishida and Hernán A. Makse

    Citation: BMC Bioinformatics 2021 22:363

    Content type: Research

    Published on:

  19. Microbiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and opti...

    Authors: Emily Goren, Chong Wang, Zhulin He, Amy M. Sheflin, Dawn Chiniquy, Jessica E. Prenni, Susannah Tringe, Daniel P. Schachtman and Peng Liu

    Citation: BMC Bioinformatics 2021 22:362

    Content type: Methodology article

    Published on:

  20. Facing the diversity of omics data and the difficulty of selecting one result over all those produced by several methods, consensus strategies have the potential to reconcile multiple inputs and to produce rob...

    Authors: Galadriel Brière, Élodie Darbo, Patricia Thébault and Raluca Uricaru

    Citation: BMC Bioinformatics 2021 22:361

    Content type: Methodology article

    Published on:

  21. Despite decades on developing dedicated Web tools, it is still difficult to predict correctly the changes of the thermodynamic stability of proteins caused by mutations. Here, we assessed the reliability of fi...

    Authors: Anna Marabotti, Eugenio Del Prete, Bernardina Scafuri and Angelo Facchiano

    Citation: BMC Bioinformatics 2021 22(Suppl 7):345

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 7

  22. Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing not only the identification of known phyla and strains but a...

    Authors: Carlo Ferravante, Domenico Memoli, Domenico Palumbo, Paolo Ciaramella, Antonio Di Loria, Ylenia D’Agostino, Giovanni Nassa, Francesca Rizzo, Roberta Tarallo, Alessandro Weisz and Giorgio Giurato

    Citation: BMC Bioinformatics 2021 22(Suppl 7):106

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 7

  23. Tumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using C...

    Authors: Marilisa Montemurro, Elena Grassi, Carmelo Gabriele Pizzino, Andrea Bertotti, Elisa Ficarra and Gianvito Urgese

    Citation: BMC Bioinformatics 2021 22:360

    Content type: Software

    Published on:

  24. Systems biology increasingly relies on deep sequencing with combinatorial index tags to associate biological sequences with their sample, cell, or molecule of origin. Accurate data interpretation depends on th...

    Authors: Lior Galanti, Dennis Shasha and Kristin C. Gunsalus

    Citation: BMC Bioinformatics 2021 22:359

    Content type: Software

    Published on:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

  38. 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

  39. 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:

  40. 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:

  41. 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:

  42. 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:

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