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  1. 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:

  2. 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:

  3. 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:

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. Statistical analyses of biological problems in life sciences often lead to high-dimensional linear models. To solve the corresponding system of equations, penalization approaches are often the methods of choic...

    Authors: Jan Klosa, Noah Simon, Pål Olof Westermark, Volkmar Liebscher and Dörte Wittenburg

    Citation: BMC Bioinformatics 2020 21:407

    Content type: Software

    Published on:

  32. Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optima...

    Authors: Muaaz G. Awan, Jack Deslippe, Aydin Buluc, Oguz Selvitopi, Steven Hofmeyr, Leonid Oliker and Katherine Yelick

    Citation: BMC Bioinformatics 2020 21:406

    Content type: Software

    Published on:

  33. De Bruijn graphs are key data structures for the analysis of next-generation sequencing data. They efficiently represent the overlap between reads and hence, also the underlying genome sequence. However, seque...

    Authors: Aranka Steyaert, Pieter Audenaert and Jan Fostier

    Citation: BMC Bioinformatics 2020 21:402

    Content type: Methodology article

    Published on:

  34. The alignment of character sequences is important in bioinformatics. The quality of this procedure is determined by the substitution matrix and parameters of the insertion-deletion penalty function. These matr...

    Authors: Valery Polyanovsky, Alexander Lifanov, Natalia Esipova and Vladimir Tumanyan

    Citation: BMC Bioinformatics 2020 21(Suppl 11):294

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  35. S-glutathionylation is the formation of disulfide bonds between the tripeptide glutathione and cysteine residues of the protein, protecting them from irreversible oxidation and in some cases causing change in ...

    Authors: Anastasia A. Anashkina, Yuri M. Poluektov, Vladimir A. Dmitriev, Eugene N. Kuznetsov, Vladimir A. Mitkevich, Alexander A. Makarov and Irina Yu. Petrushanko

    Citation: BMC Bioinformatics 2020 21(Suppl 11):282

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  36. Melanoma is one of the most aggressive types of cancer that has become a world-class problem. According to the World Health Organization estimates, 132,000 cases of the disease and 66,000 deaths from malignant...

    Authors: Mila Efimenko, Alexander Ignatev and Konstantin Koshechkin

    Citation: BMC Bioinformatics 2020 21(Suppl 11):270

    Content type: Review

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  37. The key role in the dynamic regulation of synaptic protein turnover belongs to the Fragile X Mental Retardation Protein, which regulates the efficiency of dendritic mRNA translation in response to stimulation ...

    Authors: Tamara M. Khlebodarova, Vladislav V. Kogai and Vitaly A. Likhoshvai

    Citation: BMC Bioinformatics 2020 21(Suppl 11):258

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  38. The regulatory feedback loops that present in structural and functional organization of molecular-genetic systems and the phenomenon of the regulatory signal delay, a time period between the moment of signal r...

    Authors: Vitaly A. Likhoshvai, Vladimir P. Golubyatnikov and Tamara M. Khlebodarova

    Citation: BMC Bioinformatics 2020 21(Suppl 11):255

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  39. The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMe...

    Authors: Timofey V. Ivanisenko, Olga V. Saik, Pavel S. Demenkov, Nikita V. Ivanisenko, Alexander N. Savostianov and Vladimir A. Ivanisenko

    Citation: BMC Bioinformatics 2020 21(Suppl 11):228

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  40. As an important non-coding RNA, microRNA (miRNA) plays a significant role in a series of life processes and is closely associated with a variety of Human diseases. Hence, identification of potential miRNA-disease...

    Authors: Bo-Ya Ji, Zhu-Hong You, Zhan-Heng Chen, Leon Wong and Hai-Cheng Yi

    Citation: BMC Bioinformatics 2020 21:401

    Content type: Research article

    Published on:

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