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  1. 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

  2. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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:

  17. 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:

  18. 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:

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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

  25. 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

  26. 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:

  28. 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:

  29. 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:

  30. Ion Torrent is one of the major next generation sequencing (NGS) technologies and it is frequently used in medical research and diagnosis. The built-in software for the Ion Torrent sequencing machines delivers...

    Authors: Moustafa Shokrof and Mohamed Abouelhoda
    Citation: BMC Bioinformatics 2020 21:397
    Content type: Software Published on:

    The Correction to this article has been published in BMC Bioinformatics 2020 21:435

  31. 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:

  32. 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:

  33. 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:

  34. 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:

  35. 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:

  36. 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:

  37. 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:

    The Correction to this article has been published in BMC Bioinformatics 2020 21:495

  39. 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:

  41. 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:

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

    The Correction to this article has been published in BMC Bioinformatics 2020 21:494

  48. 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

  49. 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

  50. 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:

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