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  1. Cryo-electron tomography is an important and powerful technique to explore the structure, abundance, and location of ultrastructure in a near-native state. It contains detailed information of all macromolecula...

    Authors: Sinuo Liu, Xiaojuan Ban, Xiangrui Zeng, Fengnian Zhao, Yuan Gao, Wenjie Wu, Hongpan Zhang, Feiyang Chen, Thomas Hall, Xin Gao and Min Xu

    Citation: BMC Bioinformatics 2020 21:399

    Content type: Methodology article

    Published on:

  2. Protein biomarkers play important roles in cancer diagnosis. Many efforts have been made on measuring abnormal expression intensity in biological samples to identity cancer types and stages. However, the chang...

    Authors: Zhen-Zhen Xue, Yanxia Wu, Qing-Zu Gao, Liang Zhao and Ying-Ying Xu

    Citation: BMC Bioinformatics 2020 21:398

    Content type: Research article

    Published on:

  3. MicroRNAs are a class of important small noncoding RNAs, which have been reported to be involved in the processes of tumorigenesis and development by targeting a few genes. Existing studies show that the imbal...

    Authors: Peng Xu, Qian Wu, Deyang Lu, Jian Yu, Yongsheng Rao, Zheng Kou, Gang Fang, Wenbin Liu and Henry Han

    Citation: BMC Bioinformatics 2020 21:396

    Content type: Research article

    Published on:

  4. Neurons are the basic structural unit of the brain, and their morphology is a key determinant of their classification. The morphology of a neuronal circuit is a fundamental component in neuron modeling. Recent...

    Authors: Siqi Jiang, Zhengyu Pan, Zhao Feng, Yue Guan, Miao Ren, Zhangheng Ding, Shangbin Chen, Hui Gong, Qingming Luo and Anan Li

    Citation: BMC Bioinformatics 2020 21:395

    Content type: Methodology article

    Published on:

  5. The improvements in genomics methods coupled with readily accessible high-throughput sequencing have contributed to our understanding of microbial species, metagenomes, infectious diseases and more. To maximiz...

    Authors: Mariam Quiñones, David T. Liou, Conrad Shyu, Wongyu Kim, Ivan Vujkovic-Cvijin, Yasmine Belkaid and Darrell E. Hurt

    Citation: BMC Bioinformatics 2020 21:378

    Content type: Software

    Published on:

  6. A large number of experimental studies show that the mutation and regulation of long non-coding RNAs (lncRNAs) are associated with various human diseases. Accurate prediction of lncRNA-disease associations can...

    Authors: Yuan Zhang, Fei Ye, Dapeng Xiong and Xieping Gao

    Citation: BMC Bioinformatics 2020 21:377

    Content type: Research article

    Published on:

  7. Two-dimensional gel electrophoresis (2-DGE) is a commonly used tool for proteomic analysis. This gel-based technique separates proteins in a sample according to their isoelectric point and molecular weight. 2-...

    Authors: Manuel Mauricio Goez, Maria C. Torres-Madronero, Sarah Rothlisberger and Edilson Delgado-Trejos

    Citation: BMC Bioinformatics 2020 21:376

    Content type: Methodology article

    Published on:

  8. As the barriers to incorporating RNA sequencing (RNA-Seq) into biomedical studies continue to decrease, the complexity and size of RNA-Seq experiments are rapidly growing. Paired, longitudinal, and other corre...

    Authors: Brian E. Vestal, Camille M. Moore, Elizabeth Wynn, Laura Saba, Tasha Fingerlin and Katerina Kechris

    Citation: BMC Bioinformatics 2020 21:375

    Content type: Methodology article

    Published on:

  9. In this era of data science-driven bioinformatics, machine learning research has focused on feature selection as users want more interpretation and post-hoc analyses for biomarker detection. However, when ther...

    Authors: Samir Rachid Zaim, Colleen Kenost, Joanne Berghout, Wesley Chiu, Liam Wilson, Hao Helen Zhang and Yves A. Lussier

    Citation: BMC Bioinformatics 2020 21:374

    Content type: Methodology article

    Published on:

  10. About 90% of patients who have diabetes suffer from Type 2 DM (T2DM). Many studies suggest using the significant role of lncRNAs to improve the diagnosis of T2DM. Machine learning and Data Mining techniques ar...

    Authors: Faranak Kazerouni, Azadeh Bayani, Farkhondeh Asadi, Leyla Saeidi, Nasrin Parvizi and Zahra Mansoori

    Citation: BMC Bioinformatics 2020 21:372

    Content type: Research article

    Published on:

  11. Deciphering the relationship between clinical responses and gene expression profiles may shed light on the mechanisms underlying diseases. Most existing literature has focused on exploring such relationship fr...

    Authors: Fangli Dong, Yong He, Tao Wang, Dong Han, Hui Lu and Hongyu Zhao

    Citation: BMC Bioinformatics 2020 21:370

    Content type: Research article

    Published on:

  12. Type A influenza viruses circulate and spread among wild birds and mostly consist of low pathogenic strains. However, fast genome variation timely results in the insurgence of high pathogenic strains, which wh...

    Authors: Irene Righetto and Francesco Filippini

    Citation: BMC Bioinformatics 2020 21(Suppl 10):354

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  13. RNA editing is a widespread co-/post-transcriptional mechanism that alters primary RNA sequences through the modification of specific nucleotides and it can increase both the transcriptome and proteome diversi...

    Authors: Tiziano Flati, Silvia Gioiosa, Nicola Spallanzani, Ilario Tagliaferri, Maria Angela Diroma, Graziano Pesole, Giovanni Chillemi, Ernesto Picardi and Tiziana Castrignanò

    Citation: BMC Bioinformatics 2020 21(Suppl 10):353

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  14. The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Mo...

    Authors: Tiziana Castrignanò, Silvia Gioiosa, Tiziano Flati, Mirko Cestari, Ernesto Picardi, Matteo Chiara, Maddalena Fratelli, Stefano Amente, Marco Cirilli, Marco Antonio Tangaro, Giovanni Chillemi, Graziano Pesole and Federico Zambelli

    Citation: BMC Bioinformatics 2020 21(Suppl 10):352

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  15. Oscillatory genes, with periodic expression at the mRNA and/or protein level, have been shown to play a pivotal role in many biological contexts. However, with the exception of the circadian clock and cell cyc...

    Authors: Luisa Cutillo, Alexis Boukouvalas, Elli Marinopoulou, Nancy Papalopulu and Magnus Rattray

    Citation: BMC Bioinformatics 2020 21(Suppl 10):351

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  16. High throughput methods, in biological and biomedical fields, acquire a large number of molecular parameters or omics data by a single experiment. Combining these omics data can significantly increase the capa...

    Authors: Angelo Ciaramella, Davide Nardone and Antonino Staiano

    Citation: BMC Bioinformatics 2020 21(Suppl 10):350

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  17. Biological networks are representative of the diverse molecular interactions that occur within cells. Some of the commonly studied biological networks are modeled through protein-protein interactions, gene reg...

    Authors: Ichcha Manipur, Ilaria Granata, Lucia Maddalena and Mario R. Guarracino

    Citation: BMC Bioinformatics 2020 21(Suppl 10):349

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  18. Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science c...

    Authors: Ludovica Liguori, Maria Monticelli, Mariateresa Allocca, Maria Vittoria Cubellis and Bruno Hay Mele

    Citation: BMC Bioinformatics 2020 21(Suppl 10):348

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  19. The scope of this work is to build a Machine Learning model able to predict patients risk to contract a multidrug resistant urinary tract infection (MDR UTI) after hospitalization. To achieve this goal, we use...

    Authors: Alessio Mancini, Leonardo Vito, Elisa Marcelli, Marco Piangerelli, Renato De Leone, Sandra Pucciarelli and Emanuela Merelli

    Citation: BMC Bioinformatics 2020 21(Suppl 10):347

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 10

  20. The amount of published full-text articles has increased dramatically. Text mining tools configure an essential approach to building biological networks, updating databases and providing annotation for new pat...

    Authors: Bruna Piereck, Marx Oliveira-Lima, Ana Maria Benko-Iseppon, Sarah Diehl, Reinhard Schneider, Ana Christina Brasileiro-Vidal and Adriano Barbosa-Silva

    Citation: BMC Bioinformatics 2020 21:365

    Content type: Software

    Published on:

  21. Gene co-expression networks (GCNs) are powerful tools that enable biologists to examine associations between genes during different biological processes. With the advancement of new technologies, such as singl...

    Authors: Michael Sekula, Jeremy Gaskins and Susmita Datta

    Citation: BMC Bioinformatics 2020 21:361

    Content type: Methodology article

    Published on:

  22. Discovering single nucleotide polymorphisms (SNPs) from agriculture crop genome sequences has been a widely used strategy for developing genetic markers for several applications including marker-assisted breed...

    Authors: Zhen Yao, Frank M. You, Amidou N’Diaye, Ron E. Knox, Curt McCartney, Colin W. Hiebert, Curtis Pozniak and Wayne Xu

    Citation: BMC Bioinformatics 2020 21:360

    Content type: Research article

    Published on:

  23. The dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. No...

    Authors: Fernando Puente-Sánchez, Natalia García-García and Javier Tamames

    Citation: BMC Bioinformatics 2020 21:358

    Content type: Methodology article

    Published on:

  24. Previous studies have reported that labeling errors are not uncommon in omics data. Potential outliers may severely undermine the correct classification of patients and the identification of reliable biomarker...

    Authors: Hongwei Sun, Yuehua Cui, Hui Wang, Haixia Liu and Tong Wang

    Citation: BMC Bioinformatics 2020 21:357

    Content type: Research article

    Published on:

  25. Complex human health conditions with etiological heterogeneity like Autism Spectrum Disorder (ASD) often pose a challenge for traditional genome-wide association study approaches in defining a clear genotype t...

    Authors: Min Woo Sun, Stefano Moretti, Kelley M. Paskov, Nate T. Stockham, Maya Varma, Brianna S. Chrisman, Peter Y. Washington, Jae-Yoon Jung and Dennis P. Wall

    Citation: BMC Bioinformatics 2020 21:356

    Content type: Methodology article

    Published on:

  26. The accurate annotation of protein functions is of great significance in elucidating the phenomena of life, treating disease and developing new medicines. Various methods have been developed to facilitate the ...

    Authors: Bihai Zhao, Zhihong Zhang, Meiping Jiang, Sai Hu, Yingchun Luo and Lei Wang

    Citation: BMC Bioinformatics 2020 21:355

    Content type: Research article

    Published on:

  27. While technological advances have made it possible to profile the immune system at high resolution, translating high-throughput data into knowledge of immune mechanisms has been challenged by the complexity of...

    Authors: Michelle B. Atallah, Varun Tandon, Kamir J. Hiam, Hunter Boyce, Michelle Hori, Waleed Atallah, Matthew H. Spitzer, Edgar Engleman and Parag Mallick

    Citation: BMC Bioinformatics 2020 21:346

    Content type: Research article

    Published on:

  28. Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing...

    Authors: Stevenn Volant, Pierre Lechat, Perrine Woringer, Laurence Motreff, Pascal Campagne, Christophe Malabat, Sean Kennedy and Amine Ghozlane

    Citation: BMC Bioinformatics 2020 21:345

    Content type: Software

    Published on:

  29. The similarity or distance measure used for clustering can generate intuitive and interpretable clusters when it is tailored to the unique characteristics of the data. In time series datasets generated with hi...

    Authors: Thevaa Chandereng and Anthony Gitter

    Citation: BMC Bioinformatics 2020 21:21

    Content type: Methodology Article

    Published on:

  30. Nanopore sequencing enables portable, real-time sequencing applications, including point-of-care diagnostics and in-the-field genotyping. Achieving these outcomes requires efficient bioinformatic algorithms fo...

    Authors: Hasindu Gamaarachchi, Chun Wai Lam, Gihan Jayatilaka, Hiruna Samarakoon, Jared T. Simpson, Martin A. Smith and Sri Parameswaran

    Citation: BMC Bioinformatics 2020 21:343

    Content type: Research article

    Published on:

  31. Ribosome profiling has been widely used for studies of translation under a large variety of cellular and physiological contexts. Many of these studies have greatly benefitted from a series of data-mining tools...

    Authors: Fajin Li, Xudong Xing, Zhengtao Xiao, Gang Xu and Xuerui Yang

    Citation: BMC Bioinformatics 2020 21:340

    Content type: Software

    Published on:

  32. It has been widely accepted that long non-coding RNAs (lncRNAs) play important roles in the development and progression of human diseases. Many association prediction models have been proposed for predicting l...

    Authors: Wenwen Fan, Junliang Shang, Feng Li, Yan Sun, Shasha Yuan and Jin-Xing Liu

    Citation: BMC Bioinformatics 2020 21:339

    Content type: Methodology article

    Published on:

  33. Analysis of somatic mutations from tumor whole exomes has fueled discovery of novel cancer driver genes. However, ~ 98% of the genome is non-coding and includes regulatory elements whose normal cellular functi...

    Authors: Anthony R. Soltis, Clifton L. Dalgard, Harvey B. Pollard and Matthew D. Wilkerson

    Citation: BMC Bioinformatics 2020 21:338

    Content type: Software

    Published on:

  34. Research on the molecular ecology of non-model organisms, while previously constrained, has now been greatly facilitated by the advent of reduced-representation sequencing protocols. However, tools that allow ...

    Authors: Steven M. Mussmann, Marlis R. Douglas, Tyler K. Chafin and Michael E. Douglas

    Citation: BMC Bioinformatics 2020 21:337

    Content type: Software

    Published on:

  35. Machine learning models for repeated measurements are limited. Using topological data analysis (TDA), we present a classifier for repeated measurements which samples from the data space and builds a network gr...

    Authors: Henri Riihimäki, Wojciech Chachólski, Jakob Theorell, Jan Hillert and Ryan Ramanujam

    Citation: BMC Bioinformatics 2020 21:336

    Content type: Research article

    Published on:

  36. The efficient and robust statistical analysis of the shape of plant organs of different cultivars is an important investigation issue in plant breeding and enables a robust cultivar description within the bree...

    Authors: Behrend Heeren, Stefan Paulus, Heiner Goldbach, Heiner Kuhlmann, Anne-Katrin Mahlein, Martin Rumpf and Benedikt Wirth

    Citation: BMC Bioinformatics 2020 21:335

    Content type: Research article

    Published on:

  37. Shotgun metagenomics based on untargeted sequencing can explore the taxonomic profile and the function of unknown microorganisms in samples, and complement the shortage of amplicon sequencing. Binning assemble...

    Authors: Yi Yue, Hao Huang, Zhao Qi, Hui-Min Dou, Xin-Yi Liu, Tian-Fei Han, Yue Chen, Xiang-Jun Song, You-Hua Zhang and Jian Tu

    Citation: BMC Bioinformatics 2020 21:334

    Content type: Research article

    Published on:

  38. Gene expression signatures for the prediction of differential survival of patients undergoing anti-cancer therapies are of great interest because they can be used to prospectively stratify patients entering ne...

    Authors: Joachim Theilhaber, Marielle Chiron, Jennifer Dreymann, Donald Bergstrom and Jack Pollard

    Citation: BMC Bioinformatics 2020 21:333

    Content type: Methodology article

    Published on:

  39. Graph-based representation of genome assemblies has been recently used in different contexts — from improved reconstruction of plasmid sequences and refined analysis of metagenomic data to read error correctio...

    Authors: Tatiana Dvorkina, Dmitry Antipov, Anton Korobeynikov and Sergey Nurk

    Citation: BMC Bioinformatics 2020 21(Suppl 12):306

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

  40. Horizontal gene transfer, i.e. the acquisition of genetic material from nonparent organism, is considered an important force driving species evolution. Many cases of horizontal gene transfer from prokaryotes t...

    Authors: Maria A. Daugavet, Sergey V. Shabelnikov and Olga I. Podgornaya

    Citation: BMC Bioinformatics 2020 21(Suppl 12):305

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

  41. The imputation of genotypes increases the power of genome-wide association studies. However, the imputation quality should be assessed in each particular case. Nevertheless, not all imputation softwares contro...

    Authors: Gennady V. Khvorykh and Andrey V. Khrunin

    Citation: BMC Bioinformatics 2020 21(Suppl 12):304

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

  42. Illumina paired-end reads are often used for 16S analysis in metagenomic studies. Since DNA fragment size is usually smaller than the sum of lengths of paired reads, reads can be merged for downstream analysis...

    Authors: Yulia Kondratenko, Anton Korobeynikov and Alla Lapidus

    Citation: BMC Bioinformatics 2020 21(Suppl 12):303

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

    The Correction to this article has been published in BMC Bioinformatics 2020 21:362

  43. De novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impos...

    Authors: Andrey D. Prjibelski, Giuseppe D. Puglia, Dmitry Antipov, Elena Bushmanova, Daniela Giordano, Alla Mikheenko, Domenico Vitale and Alla Lapidus

    Citation: BMC Bioinformatics 2020 21(Suppl 12):302

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

  44. Seeding is usually the initial step of high-throughput sequence aligners. Two popular seeding strategies are fixed-size seeding (k-mers, minimizers) and variable-size seeding (MEMs, SMEMs, maximal spanning seeds)...

    Authors: Arne Kutzner, Pok-Son Kim and Markus Schmidt

    Citation: BMC Bioinformatics 2020 21:328

    Content type: Methodology article

    Published on:

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