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  1. A typical task in bioinformatics consists of identifying which features are associated with a target outcome of interest and building a predictive model. Automated machine learning (AutoML) systems such as the...

    Authors: Elisabetta Manduchi, Weixuan Fu, Joseph D. Romano, Stefano Ruberto and Jason H. Moore

    Citation: BMC Bioinformatics 2020 21:430

    Content type: Methodology article

    Published on:

  2. Second messengers, c-di-GMP and (p)ppGpp, are vital regulatory molecules in bacteria, influencing cellular processes such as biofilm formation, transcription, virulence, quorum sensing, and proliferation. Whil...

    Authors: Chunrui Xu, Bronson R. Weston, John J. Tyson and Yang Cao

    Citation: BMC Bioinformatics 2020 21(Suppl 14):408

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  3. Chromosome conformation capture-based methods, especially Hi-C, enable scientists to detect genome-wide chromatin interactions and study the spatial organization of chromatin, which plays important roles in ge...

    Authors: Chanaka Bulathsinghalage and Lu Liu

    Citation: BMC Bioinformatics 2020 21(Suppl 14):369

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  4. Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, int...

    Authors: Talip Zengin and Tuğba Önal-Süzek

    Citation: BMC Bioinformatics 2020 21(Suppl 14):368

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  5. Essential genes are those genes that are critical for the survival of an organism. The prediction of essential genes in bacteria can provide targets for the design of novel antibiotic compounds or antimicrobia...

    Authors: Md Abid Hasan and Stefano Lonardi

    Citation: BMC Bioinformatics 2020 21(Suppl 14):367

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  6. Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning mo...

    Authors: Evan A. Clayton, Toyya A. Pujol, John F. McDonald and Peng Qiu

    Citation: BMC Bioinformatics 2020 21(Suppl 14):364

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  7. The abundance of molecular profiling of breast cancer tissues entailed active research on molecular marker-based early diagnosis of metastasis. Recently there is a surging interest in combining gene expression...

    Authors: Nahim Adnan, Chengwei Lei and Jianhua Ruan

    Citation: BMC Bioinformatics 2020 21(Suppl 14):359

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  8. Multi-gene expression assays are an attractive tool in revealing complex regulatory mechanisms in living organisms. Normalization is an indispensable step of data analysis in all those studies, since it remove...

    Authors: Szymon Grabia, Urszula Smyczynska, Konrad Pagacz and Wojciech Fendler

    Citation: BMC Bioinformatics 2020 21:425

    Content type: Software

    Published on:

  9. Quantitative polymerase chain reaction (qPCR) is the technique of choice for quantifying gene expression. While the technique itself is well established, approaches for the analysis of qPCR data continue to im...

    Authors: Michael T. Ganger, Geoffrey D. Dietz, Patrick Headley and Sarah J. Ewing

    Citation: BMC Bioinformatics 2020 21:423

    Content type: Methodology article

    Published on:

  10. Antigen receptors are characterized by an extreme diversity of specificities, which poses major computational and analytical challenges, particularly in the era of high-throughput immunoprofiling by next gener...

    Authors: Maria Th. Kotouza, Katerina Gemenetzi, Chrysi Galigalidou, Elisavet Vlachonikola, Nikolaos Pechlivanis, Andreas Agathangelidis, Raphael Sandaltzopoulos, Pericles A. Mitkas, Kostas Stamatopoulos, Anastasia Chatzidimitriou and Fotis E. Psomopoulos

    Citation: BMC Bioinformatics 2020 21:422

    Content type: Software

    Published on:

  11. The treatment of complex diseases by taking multiple drugs becomes increasingly popular. However, drug-drug interactions (DDIs) may give rise to the risk of unanticipated adverse effects and even unknown toxic...

    Authors: Yue-Hua Feng, Shao-Wu Zhang and Jian-Yu Shi

    Citation: BMC Bioinformatics 2020 21:419

    Content type: Methodology article

    Published on:

  12. Strand cross-correlation profiles are used for both peak calling pre-analysis and quality control (QC) in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis. Despite its potential for rob...

    Authors: Hayato Anzawa, Hitoshi Yamagata and Kengo Kinoshita

    Citation: BMC Bioinformatics 2020 21:417

    Content type: Research article

    Published on:

  13. Protein microarray is a well-established approach for characterizing activity levels of thousands of proteins in a parallel manner. Analysis of protein microarray data is complex and time-consuming, while exis...

    Authors: Dmytro Fishman, Ivan Kuzmin, Priit Adler, Jaak Vilo and Hedi Peterson

    Citation: BMC Bioinformatics 2020 21:411

    Content type: Software

    Published on:

  14. Drug-target interaction prediction is of great significance for narrowing down the scope of candidate medications, and thus is a vital step in drug discovery. Because of the particularity of biochemical experi...

    Authors: Jiajie Peng, Jingyi Li and Xuequn Shang

    Citation: BMC Bioinformatics 2020 21(Suppl 13):394

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  15. High-dimensional flow cytometry and mass cytometry allow systemic-level characterization of more than 10 protein profiles at single-cell resolution and provide a much broader landscape in many biological appli...

    Authors: Ko Abe, Kodai Minoura, Yuka Maeda, Hiroyoshi Nishikawa and Teppei Shimamura

    Citation: BMC Bioinformatics 2020 21(Suppl 13):393

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  16. In recent years, the rapid development of single-cell RNA-sequencing (scRNA-seq) techniques enables the quantitative characterization of cell types at a single-cell resolution. With the explosive growth of the...

    Authors: Xiaoyang Chen, Shengquan Chen and Rui Jiang

    Citation: BMC Bioinformatics 2020 21(Suppl 13):392

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  17. Resolution estimation is the main evaluation criteria for the reconstruction of macromolecular 3D structure in the field of cryoelectron microscopy (cryo-EM). At present, there are many methods to evaluate the...

    Authors: Yongchun Lü, Xiangrui Zeng, Xinhui Tian, Xiao Shi, Hui Wang, Xiaohui Zheng, Xiaodong Liu, Xiaofang Zhao, Xin Gao and Min Xu

    Citation: BMC Bioinformatics 2020 21(Suppl 13):391

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  18. Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually desig...

    Authors: Benjamin Albrecht, Caner Bağcı and Daniel H. Huson

    Citation: BMC Bioinformatics 2020 21(Suppl 13):390

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  19. MicroRNAs (miRNAs) play a key role in mediating the action of insulin on cell growth and the development of diabetes. However, few studies have been conducted to provide a comprehensive overview of the miRNA-m...

    Authors: Yang-Chi-Dung Lin, Hsi-Yuan Huang, Sirjana Shrestha, Chih-Hung Chou, Yen-Hua Chen, Chi-Ru Chen, Hsiao-Chin Hong, Jing Li, Yi-An Chang, Men-Yee Chiew, Ya-Rong Huang, Siang-Jyun Tu, Ting-Hsuan Sun, Shun-Long Weng, Ching-Ping Tseng and Hsien-Da Huang

    Citation: BMC Bioinformatics 2020 21(Suppl 13):389

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  20. In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo asse...

    Authors: Nauman Ahmed, Tong Dong Qiu, Koen Bertels and Zaid Al-Ars

    Citation: BMC Bioinformatics 2020 21(Suppl 13):388

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  21. Drug discovery is known for the large amount of money and time it consumes and the high risk it takes. Drug repositioning has, therefore, become a popular approach to save time and cost by finding novel indica...

    Authors: Renyi Zhou, Zhangli Lu, Huimin Luo, Ju Xiang, Min Zeng and Min Li

    Citation: BMC Bioinformatics 2020 21(Suppl 13):387

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  22. In the field of computational biology, analyzing complex data helps to extract relevant biological information. Sample classification of gene expression data is one such popular bio-data analysis technique. Ho...

    Authors: Sudipta Acharya, Laizhong Cui and Yi Pan

    Citation: BMC Bioinformatics 2020 21(Suppl 13):386

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  23. Network alignment is an efficient computational framework in the prediction of protein function and phylogenetic relationships in systems biology. However, most of existing alignment methods focus on aligning ...

    Authors: Yuanke Zhong, Jing Li, Junhao He, Yiqun Gao, Jie Liu, Jingru Wang, Xuequn Shang and Jialu Hu

    Citation: BMC Bioinformatics 2020 21(Suppl 13):385

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  24. Protein-DNA interaction governs a large number of cellular processes, and it can be altered by a small fraction of interface residues, i.e., the so-called hot spots, which account for most of the interface bindin...

    Authors: Yuliang Pan, Shuigeng Zhou and Jihong Guan

    Citation: BMC Bioinformatics 2020 21(Suppl 13):384

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  25. Glioblastoma multiforme (GBM) is one of the most common malignant brain tumors and its average survival time is less than 1 year after diagnosis.

    Authors: Yujie You, Xufang Ru, Wanjing Lei, Tingting Li, Ming Xiao, Huiru Zheng, Yujie Chen and Le Zhang

    Citation: BMC Bioinformatics 2020 21(Suppl 13):383

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  26. Introducing deep learning approach to medical images has rendered a large amount of un-decoded information into usage in clinical research. But mostly, it has been focusing on the performance of the prediction...

    Authors: Sangwoo Lee, Eun Kyung Choe, So Yeon Kim, Hua Sun Kim, Kyu Joo Park and Dokyoon Kim

    Citation: BMC Bioinformatics 2020 21(Suppl 13):382

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  27. Identification of hot spots in protein-DNA interfaces provides crucial information for the research on protein-DNA interaction and drug design. As experimental methods for determining hot spots are time-consum...

    Authors: Ke Li, Sijia Zhang, Di Yan, Yannan Bin and Junfeng Xia

    Citation: BMC Bioinformatics 2020 21(Suppl 13):381

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  28. Biomedical document triage is the foundation of biomedical information extraction, which is important to precision medicine. Recently, some neural networks-based methods have been proposed to classify biomedic...

    Authors: Jian Wang, Mengying Li, Qishuai Diao, Hongfei Lin, Zhihao Yang and YiJia Zhang

    Citation: BMC Bioinformatics 2020 21(Suppl 13):380

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  29. Protein phosphorylation networks play an important role in cell signaling. In these networks, phosphorylation of a protein kinase usually leads to its activation, which in turn will phosphorylate its downstrea...

    Authors: Jinling Liu, Xiaojun Ma, Gregory F. Cooper and Xinghua Lu

    Citation: BMC Bioinformatics 2020 21(Suppl 13):379

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  30. The 16th Annual Meeting of the Bioinformatics Italian Society was held in Palermo, Italy, on June 26-28, 2019. More than 80 scientific contributions were presented, including 4 keynote lectures, 31 oral commun...

    Authors: Alfonso Urso, Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Giosue’ Lo Bosco and Riccardo Rizzo

    Citation: BMC Bioinformatics 2020 21(Suppl 8):363

    Content type: Introduction

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  31. Emerging and re-emerging infectious diseases such as Zika, SARS, ncovid19 and Pertussis, pose a compelling challenge for epidemiologists due to their significant impact on global public health. In this context...

    Authors: Paolo Castagno, Simone Pernice, Gianni Ghetti, Massimiliano Povero, Lorenzo Pradelli, Daniela Paolotti, Gianfranco Balbo, Matteo Sereno and Marco Beccuti

    Citation: BMC Bioinformatics 2020 21(Suppl 8):344

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  32. Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, includ...

    Authors: Domenico Amato, Giosue’ Lo Bosco and Riccardo Rizzo

    Citation: BMC Bioinformatics 2020 21(Suppl 8):326

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  33. Positron Emission Tomography (PET) is increasingly utilized in radiomics studies for treatment evaluation purposes. Nevertheless, lesion volume identification in PET images is a critical and still challenging ...

    Authors: Alessandro Stefano, Albert Comelli, Valentina Bravatà, Stefano Barone, Igor Daskalovski, Gaetano Savoca, Maria Gabriella Sabini, Massimo Ippolito and Giorgio Russo

    Citation: BMC Bioinformatics 2020 21(Suppl 8):325

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  34. A Virtual Screening algorithm has to adapt to the different stages of this process. Early screening needs to ensure that all bioactive compounds are ranked in the first positions despite of the number of false...

    Authors: Isabella Mendolia, Salvatore Contino, Ugo Perricone, Edoardo Ardizzone and Roberto Pirrone

    Citation: BMC Bioinformatics 2020 21(Suppl 8):310

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  35. The development of Next Generation Sequencing (NGS) has had a major impact on the study of genetic sequences. Among problems that researchers in the field have to face, one of the most challenging is the taxon...

    Authors: Veronica Guerrini, Felipe A. Louza and Giovanna Rosone

    Citation: BMC Bioinformatics 2020 21(Suppl 8):299

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  36. The prediction of protein subcellular localization is a key step of the big effort towards protein functional annotation. Many computational methods exist to identify high-level protein subcellular compartment...

    Authors: Castrense Savojardo, Pier Luigi Martelli, Giacomo Tartari and Rita Casadio

    Citation: BMC Bioinformatics 2020 21(Suppl 8):266

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  37. Properly scoring protein-protein docking models to single out the correct ones is an open challenge, also object of assessment in CAPRI (Critical Assessment of PRedicted Interactions), a community-wide blind d...

    Authors: Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo and Romina Oliva

    Citation: BMC Bioinformatics 2020 21(Suppl 8):262

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  38. In [Prezza et al., AMB 2019], a new reference-free and alignment-free framework for the detection of SNPs was suggested and tested. The framework, based on the Burrows-Wheeler Transform (BWT), significantly im...

    Authors: Nicola Prezza, Nadia Pisanti, Marinella Sciortino and Giovanna Rosone

    Citation: BMC Bioinformatics 2020 21(Suppl 8):260

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  39. MicroRNA are small non-coding RNAs that post-transcriptionally regulate the expression levels of messenger RNAs. MicroRNA regulation activity depends on the recognition of binding sites located on mRNA molecul...

    Authors: Giorgio Bertolazzi, Panayiotis V. Benos, Michele Tumminello and Claudia Coronnello

    Citation: BMC Bioinformatics 2020 21(Suppl 8):201

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

  40. Non-coding RNAs include different classes of molecules with regulatory functions. The most studied are microRNAs (miRNAs) that act directly inhibiting mRNA expression or protein translation through the interac...

    Authors: Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo and Alfonso Urso

    Citation: BMC Bioinformatics 2020 21(Suppl 8):199

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 8

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