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  1. Protein–protein interaction (PPI) prediction is an important task towards the understanding of many bioinformatics functions and applications, such as predicting protein functions, gene-disease associations an...

    Authors: Xiaoshi Zhong and Jagath C. Rajapakse

    Citation: BMC Bioinformatics 2020 21(Suppl 16):560

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 16

  2. Millions of people are suffering from cancers, but accurate early diagnosis and effective treatment are still tough for all doctors. Common ways against cancer include surgical operation, radiotherapy and chem...

    Authors: Tianyi Zhao, Yang Hu and Tianyi Zang

    Citation: BMC Bioinformatics 2020 21(Suppl 16):559

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 16

  3. Although biomedical publications and literature are growing rapidly, there still lacks structured knowledge that can be easily processed by computer programs. In order to extract such knowledge from plain text...

    Authors: Rui Xing, Jie Luo and Tengwei Song

    Citation: BMC Bioinformatics 2020 21(Suppl 16):543

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 16

  4. Single-cell RNA sequencing can be used to fairly determine cell types, which is beneficial to the medical field, especially the many recent studies on COVID-19. Generally, single-cell RNA data analysis pipelin...

    Authors: Ruiyu Xiao, Guoshan Lu, Wanqian Guo and Shuilin Jin

    Citation: BMC Bioinformatics 2020 21(Suppl 16):540

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 16

  5. Protein–protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to th...

    Authors: Leilei Liu, Xianglei Zhu, Yi Ma, Haiyin Piao, Yaodong Yang, Xiaotian Hao, Yue Fu, Li Wang and Jiajie Peng

    Citation: BMC Bioinformatics 2020 21(Suppl 16):537

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 16

  6. With the rapid development of medical treatment, many patients not only consider the survival time, but also care about the quality of life. Changes in physical, psychological and social functions after and du...

    Authors: Huijuan Xu, Hairong Wang, Chenshan Yuan, Qinghua Zhai, Xufeng Tian, Lei Wu and Yuanyuan Mi

    Citation: BMC Bioinformatics 2020 21(Suppl 16):504

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 16

  7. Maize (Zea mays ssp. mays L.) is the most widely grown and yield crop in the world, as well as an important model organism for fundamental research of the function of genes. The functions of Maize proteins are an...

    Authors: Guangjie Zhou, Jun Wang, Xiangliang Zhang, Maozu Guo and Guoxian Yu

    Citation: BMC Bioinformatics 2020 21(Suppl 16):420

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 16

  8. Gene fusion events are significant sources of somatic variation across adult and pediatric cancers and are some of the most clinically-effective therapeutic targets, yet low consensus of RNA-Seq fusion predict...

    Authors: Krutika S. Gaonkar, Federico Marini, Komal S. Rathi, Payal Jain, Yuankun Zhu, Nicholas A. Chimicles, Miguel A. Brown, Ammar S. Naqvi, Bo Zhang, Phillip B. Storm, John M. Maris, Pichai Raman, Adam C. Resnick, Konstantin Strauch, Jaclyn N. Taroni and Jo Lynne Rokita

    Citation: BMC Bioinformatics 2020 21:577

    Content type: Software

    Published on:

  9. Digital plant images are becoming increasingly important. First, given a large number of images deep learning algorithms can be trained to automatically identify plants. Second, structured image-based observat...

    Authors: David Boho, Michael Rzanny, Jana Wäldchen, Fabian Nitsche, Alice Deggelmann, Hans Christian Wittich, Marco Seeland and Patrick Mäder

    Citation: BMC Bioinformatics 2020 21:576

    Content type: Software

    Published on:

  10. The immune checkpoint receptor programmed cell death protein I (PD-1) has been identified as a key target in immunotherapy. PD-1 reduces the risk of autoimmunity by inducing apoptosis in antigen-specific T cel...

    Authors: Bernhard Roither, Chris Oostenbrink and Wolfgang Schreiner

    Citation: BMC Bioinformatics 2020 21(Suppl 17):557

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  11. An effective yellow fever (YF) vaccine has been available since 1937. Nevertheless, questions regarding its use remain poorly understood, such as the ideal dose to confer immunity against the disease, the need...

    Authors: Carla Rezende Barbosa Bonin, Guilherme Côrtes Fernandes, Reinaldo de Menezes Martins, Luiz Antonio Bastos Camacho, Andréa Teixeira-Carvalho, Licia Maria Henrique da Mota, Sheila Maria Barbosa de Lima, Ana Carolina Campi-Azevedo, Olindo Assis Martins-Filho, Rodrigo Weber dos Santos and Marcelo Lobosco

    Citation: BMC Bioinformatics 2020 21(Suppl 17):551

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  12. Multiple Sclerosis (MS) represents nowadays in Europe the leading cause of non-traumatic disabilities in young adults, with more than 700,000 EU cases. Although huge strides have been made over the years, MS e...

    Authors: Simone Pernice, Laura Follia, Alessandro Maglione, Marzio Pennisi, Francesco Pappalardo, Francesco Novelli, Marinella Clerico, Marco Beccuti, Francesca Cordero and Simona Rolla

    Citation: BMC Bioinformatics 2020 21(Suppl 17):550

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  13. The 3rd edition of the computational methods for the immune system function workshop has been held in San Diego, CA, in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIB...

    Authors: Francesco Pappalardo, Giulia Russo and Pedro A. Reche

    Citation: BMC Bioinformatics 2020 21(Suppl 17):546

    Content type: Introduction

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  14. SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgentl...

    Authors: Giulia Russo, Marzio Pennisi, Epifanio Fichera, Santo Motta, Giuseppina Raciti, Marco Viceconti and Francesco Pappalardo

    Citation: BMC Bioinformatics 2020 21(Suppl 17):527

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  15. The aim of a recent research project was the investigation of the mechanisms involved in the onset of type 2 diabetes in the absence of familiarity. This has led to the development of a computational model tha...

    Authors: Paola Stolfi, Ilaria Valentini, Maria Concetta Palumbo, Paolo Tieri, Andrea Grignolio and Filippo Castiglione

    Citation: BMC Bioinformatics 2020 21(Suppl 17):508

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  16. We previously introduced PCPS (Proteasome Cleavage Prediction Server), a web-based tool to predict proteasome cleavage sites using n-grams. Here, we evaluated the ability of PCPS immunoproteasome cleavage model t...

    Authors: Marta Gomez-Perosanz, Alvaro Ras-Carmona, Esther M. Lafuente and Pedro A. Reche

    Citation: BMC Bioinformatics 2020 21(Suppl 17):484

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  17. Prediction of patient outcome in medical intensive care units (ICU) may help for development and investigation of early interventional strategies. Several ICU scoring systems have been developed and are used t...

    Authors: Ping Zhang, Tegan Roberts, Brent Richards and Luke J. Haseler

    Citation: BMC Bioinformatics 2020 21(Suppl 17):481

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  18. In 2018, about 10 million people were found infected by tuberculosis, with approximately 1.2 million deaths worldwide. Despite these numbers have been relatively stable in recent years, tuberculosis is still c...

    Authors: Giulia Russo, Giuseppe Sgroi, Giuseppe Alessandro Parasiliti Palumbo, Marzio Pennisi, Miguel A. Juarez, Pere-Joan Cardona, Santo Motta, Kenneth B. Walker, Epifanio Fichera, Marco Viceconti and Francesco Pappalardo

    Citation: BMC Bioinformatics 2020 21(Suppl 17):458

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  19. The STriTuVaD project, funded by Horizon 2020, aims to test through a Phase IIb clinical trial one of the most advanced therapeutic vaccines against tuberculosis. As part of this initiative, we have developed ...

    Authors: Miguel A. Juárez, Marzio Pennisi, Giulia Russo, Dimitrios Kiagias, Cristina Curreli, Marco Viceconti and Francesco Pappalardo

    Citation: BMC Bioinformatics 2020 21(Suppl 17):449

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 17

  20. Pedigree files are ubiquitously used within bioinformatics and genetics studies to convey critical information about relatedness, sex and affected status of study samples. While the text based format of ped fi...

    Authors: Matt Velinder, Dillon Lee and Gabor Marth

    Citation: BMC Bioinformatics 2020 21:569

    Content type: Software

    Published on:

  21. Protein phosphoglycerylation, the addition of a 1,3-bisphosphoglyceric acid (1,3-BPG) to a lysine residue of a protein and thus to form a 3-phosphoglyceryl-lysine, is a reversible and non-enzymatic post-transl...

    Authors: Kai-Yao Huang, Fang-Yu Hung, Hui-Ju Kao, Hui-Hsuan Lau and Shun-Long Weng

    Citation: BMC Bioinformatics 2020 21:568

    Content type: Research article

    Published on:

  22. A low replication rate has been reported in some scientific areas motivating the creation of resource intensive collaborations to estimate the replication rate by repeating individual studies. The substantial ...

    Authors: L. M. Hall and A. E. Hendricks

    Citation: BMC Bioinformatics 2020 21:564

    Content type: Research article

    Published on:

  23. Cancer progression reconstruction is an important development stemming from the phylogenetics field. In this context, the reconstruction of the phylogeny representing the evolutionary history presents some pec...

    Authors: Simone Ciccolella, Mauricio Soto Gomez, Murray D. Patterson, Gianluca Della Vedova, Iman Hajirasouliha and Paola Bonizzoni

    Citation: BMC Bioinformatics 2020 21(Suppl 1):413

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  24. Automatic segmentation and localization of lesions in mammogram (MG) images are challenging even with employing advanced methods such as deep learning (DL) methods. We developed a new model based on the archit...

    Authors: Dina Abdelhafiz, Jinbo Bi, Reda Ammar, Clifford Yang and Sheida Nabavi

    Citation: BMC Bioinformatics 2020 21(Suppl 1):192

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  25. Identifying one or more biologically-active/native decoys from millions of non-native decoys is one of the major challenges in computational structural biology. The extreme lack of balance in positive and nega...

    Authors: Nasrin Akhter, Gopinath Chennupati, Hristo Djidjev and Amarda Shehu

    Citation: BMC Bioinformatics 2020 21(Suppl 1):189

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  26. The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another...

    Authors: Chunchun Zhao and Sartaj Sahni

    Citation: BMC Bioinformatics 2020 21(Suppl 1):4

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  27. Partial Least-Squares Discriminant Analysis (PLS-DA) is a popular machine learning tool that is gaining increasing attention as a useful feature selector and classifier. In an effort to understand its strength...

    Authors: Daniel Ruiz-Perez, Haibin Guan, Purnima Madhivanan, Kalai Mathee and Giri Narasimhan

    Citation: BMC Bioinformatics 2020 21(Suppl 1):2

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 1

  28. High resolution 2D whole slide imaging provides rich information about the tissue structure. This information can be a lot richer if these 2D images can be stacked into a 3D tissue volume. A 3D analysis, howev...

    Authors: Mahsa Paknezhad, Sheng Yang Michael Loh, Yukti Choudhury, Valerie Koh Cui Koh, Timothy Tay Kwang Yong, Hui Shan Tan, Ravindran Kanesvaran, Puay Hoon Tan, John Yuen Shyi Peng, Weimiao Yu, Yongcheng Benjamin Tan, Yong Zhen Loy, Min-Han Tan and Hwee Kuan Lee

    Citation: BMC Bioinformatics 2020 21:558

    Content type: Methodology article

    Published on:

  29. Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers. Over 95% of human genes are estimated to be alternatively spliced as a powerful means of producing functiona...

    Authors: Fan Zhang, Chris K. Deng, Mu Wang, Bin Deng, Robert Barber and Gang Huang

    Citation: BMC Bioinformatics 2020 21(Suppl 9):541

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 9

  30. This is an editorial report of the supplements to BMC Bioinformatics that includes 6 papers selected from the BIOCOMP’19—The 2019 International Conference on Bioinformatics and Computational Biology. These art...

    Authors: Yuanyuan Fu, Zhougui Ling, Hamid Arabnia and Youping Deng

    Citation: BMC Bioinformatics 2020 21(Suppl 9):538

    Content type: Introduction

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 9

  31. Cancer is one of the leading causes of morbidity and mortality in the globe. Microbiological infections account for up to 20% of the total global cancer burden. The human microbiota within each organ system is...

    Authors: Rebecca M. Rodriguez, Vedbar S. Khadka, Mark Menor, Brenda Y. Hernandez and Youping Deng

    Citation: BMC Bioinformatics 2020 21(Suppl 9):523

    Content type: Review

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 9

  32. Evaluating the toxicity of chemical mixture and their possible mechanism of action is still a challenge for humans and other organisms. Microarray classifier analysis has shown promise in the toxicogenomic are...

    Authors: Zongtao Yu, Yuanyuan Fu, Junmei Ai, Jicai Zhang, Gang Huang and Youping Deng

    Citation: BMC Bioinformatics 2020 21(Suppl 9):239

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 9

  33. Lung cancer is the number one cancer killer in the world with more than 142,670 deaths estimated in the United States alone in the year 2019. Consequently, there is an overreaching need to identify the key bio...

    Authors: Mona Maharjan, Raihanul Bari Tanvir, Kamal Chowdhury, Wenrui Duan and Ananda Mohan Mondal

    Citation: BMC Bioinformatics 2020 21(Suppl 9):218

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 9

  34. Compositional data refer to the data that lie on a simplex, which are common in many scientific domains such as genomics, geology and economics. As the components in a composition must sum to one, traditional ...

    Authors: Qingyang Zhang and Thy Dao

    Citation: BMC Bioinformatics 2020 21(Suppl 9):205

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 9

  35. Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs). The use of NOEs as the ...

    Authors: Casey Cole, Caleb Parks, Julian Rachele and Homayoun Valafar

    Citation: BMC Bioinformatics 2020 21(Suppl 9):204

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 21 Supplement 9

  36. Data handling in clinical bioinformatics is often inadequate. No freely available tools provide straightforward approaches for consistent, flexible metadata collection and linkage of related experimental data ...

    Authors: Bo Zhao, Luke Bryant, Rebecca Cordell, Michael Wilde, Dahlia Salman, Dorota Ruszkiewicz, Wadah Ibrahim, Amisha Singapuri, Tim Coats, Erol Gaillard, Caroline Beardsmore, Toru Suzuki, Leong Ng, Neil Greening, Paul Thomas, Paul Monks…

    Citation: BMC Bioinformatics 2020 21:556

    Content type: Software

    Published on:

  37. Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships betw...

    Authors: Yubin Xiao, Zheng Xiao, Xiang Feng, Zhiping Chen, Linai Kuang and Lei Wang

    Citation: BMC Bioinformatics 2020 21:555

    Content type: Methodology article

    Published on:

  38. RNA sequencing allows the study of both gene expression changes and transcribed mutations, providing a highly effective way to gain insight into cancer biology. When planning the sequencing of a large cohort o...

    Authors: Anna Quaglieri, Christoffer Flensburg, Terence P. Speed and Ian J. Majewski

    Citation: BMC Bioinformatics 2020 21:553

    Content type: Methodology article

    Published on:

  39. The widespread adoption of high throughput technologies has democratized data generation. However, data processing in accordance with best practices remains challenging and the data capital often becomes siloe...

    Authors: Juan S. Medina-Martínez, Juan E. Arango-Ossa, Max F. Levine, Yangyu Zhou, Gunes Gundem, Andrew L. Kung and Elli Papaemmanuil

    Citation: BMC Bioinformatics 2020 21:549

    Content type: Software

    Published on:

  40. Human skeletal muscle responds to weight-bearing exercise with significant inter-individual differences. Investigation of transcriptome responses could improve our understanding of this variation. However, thi...

    Authors: Yusuf Khan, Daniel Hammarström, Bent R. Rønnestad, Stian Ellefsen and Rafi Ahmad

    Citation: BMC Bioinformatics 2020 21:548

    Content type: Research article

    Published on:

  41. Quantitative real-time PCR (qPCR) is one of the most widely used methods to measure gene expression. An important aspect of qPCR data that has been largely ignored is the presence of non-detects: reactions fai...

    Authors: Valeriia Sherina, Helene R. McMurray, Winslow Powers, Harmut Land, Tanzy M. T. Love and Matthew N. McCall

    Citation: BMC Bioinformatics 2020 21:545

    Content type: Methodology article

    Published on:

  42. Elucidation of interactive relation between chemicals and genes is of key relevance not only for discovering new drug leads in drug development but also for repositioning existing drugs to novel therapeutic ta...

    Authors: Wei Wang, Xi Yang, Chengkun Wu and Canqun Yang

    Citation: BMC Bioinformatics 2020 21:544

    Content type: Methodology article

    Published on:

  43. Mixed linear models (MLM) have been widely used to account for population structure in case-control genome-wide association studies, the status being analyzed as a quantitative phenotype. Chen et al. proved in...

    Authors: Jacqueline Milet, David Courtin, André Garcia and Hervé Perdry

    Citation: BMC Bioinformatics 2020 21:536

    Content type: Methodology article

    Published on:

  44. Accurate protocols and methods to robustly detect the mosaic loss of chromosome Y (mLOY) are needed given its reported role in cancer, several age-related disorders and overall male mortality. Intensity SNP-ar...

    Authors: Juan R. González, Marcos López-Sánchez, Alejandro Cáceres, Pere Puig, Tonu Esko and Luis A. Pérez-Jurado

    Citation: BMC Bioinformatics 2020 21:533

    Content type: Software

    Published on:

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