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  1. Utilization of quantitative proteomics data on the network level is still a challenge in proteomics data analysis. Currently existing models use sophisticated, sometimes hard to implement analysis techniques. ...

    Authors: Éva Csősz, Ferenc Tóth, Mohamed Mahdi, George Tsaprailis, Miklós Emri and József Tőzsér

    Citation: BMC Bioinformatics 2019 20:398

    Content type: Research article

    Published on:

  2. Since the number of known lncRNA-disease associations verified by biological experiments is quite limited, it has been a challenging task to uncover human disease-related lncRNAs in recent years. Moreover, con...

    Authors: Jingwen Yu, Zhanwei Xuan, Xiang Feng, Quan Zou and Lei Wang

    Citation: BMC Bioinformatics 2019 20:396

    Content type: Research article

    Published on:

  3. Ordinary differential equation systems are frequently utilized to model biological systems and to infer knowledge about underlying properties. For instance, the development of drugs requires the knowledge to w...

    Authors: Pascal Dolejsch, Helge Hass and Jens Timmer

    Citation: BMC Bioinformatics 2019 20:395

    Content type: Methodology article

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  4. High-dimensional data of discrete and skewed nature is commonly encountered in high-throughput sequencing studies. Analyzing the network itself or the interplay between genes in this type of data continues to ...

    Authors: Anjali Silva, Steven J. Rothstein, Paul D. McNicholas and Sanjeena Subedi

    Citation: BMC Bioinformatics 2019 20:394

    Content type: Methodology article

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  5. MicroRNAs (miRNAs) are small RNAs that regulate gene expression at a post-transcriptional level and are emerging as potentially important biomarkers for various disease states, including pancreatic cancer. In ...

    Authors: Emmy Borgmästars, Hendrik Arnold de Weerd, Zelmina Lubovac-Pilav and Malin Sund

    Citation: BMC Bioinformatics 2019 20:393

    Content type: Research article

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  6. Clustering methods are essential to partitioning biological samples being useful to minimize the information complexity in large datasets. Tools in this context usually generates data with greed algorithms tha...

    Authors: Bruno Thiago de Lima Nichio, Aryel Marlus Repula de Oliveira, Camilla Reginatto de Pierri, Leticia Graziela Costa Santos, Alexandre Quadros Lejambre, Ricardo Assunção Vialle, Nilson Antônio da Rocha Coimbra, Dieval Guizelini, Jeroniza Nunes Marchaukoski, Fabio de Oliveira Pedrosa and Roberto Tadeu Raittz

    Citation: BMC Bioinformatics 2019 20:392

    Content type: Software

    Published on:

  7. Asymmetry during cellular division, both in the uneven partitioning of damaged cellular components and of cell volume, is a cell biological phenomenon experienced by many unicellular organisms. Previous work b...

    Authors: Ruijie Song and Murat Acar

    Citation: BMC Bioinformatics 2019 20:391

    Content type: Research article

    Published on:

  8. Human papillomavirus (HPV) is a common sexually transmitted infection associated with cervical cancer that frequently occurs as a coinfection of types and subtypes. Highly similar sublineages that show over 10...

    Authors: Eric T. Dawson, Sarah Wagner, David Roberson, Meredith Yeager, Joseph Boland, Erik Garrison, Stephen Chanock, Mark Schiffman, Tina Raine-Bennett, Thomas Lorey, Phillip E. Castle, Lisa Mirabello and Richard Durbin

    Citation: BMC Bioinformatics 2019 20:389

    Content type: Software

    Published on:

  9. Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits in replacing a ...

    Authors: Vincent Demolombe, Alexandre G. de Brevern, Liza Felicori, Christophe NGuyen, Ricardo Andrez Machado de Avila, Lionel Valera, Bénédicte Jardin-Watelet, Géraldine Lavigne, Aurélien Lebreton, Franck Molina and Violaine Moreau

    Citation: BMC Bioinformatics 2019 20:387

    Content type: Methodology article

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  10. Mathematical models of biological networks can provide important predictions and insights into complex disease. Constraint-based models of cellular metabolism and probabilistic models of gene regulatory networ...

    Authors: Han Yu and Rachael Hageman Blair

    Citation: BMC Bioinformatics 2019 20:386

    Content type: Research article

    Published on:

  11. In cancer research, robustness of a complex biochemical network is one of the most relevant properties to investigate for the development of novel targeted therapies. In cancer systems biology, biological netw...

    Authors: Fortunato Bianconi, Chiara Antonini, Lorenzo Tomassoni and Paolo Valigi

    Citation: BMC Bioinformatics 2019 20:385

    Content type: Software

    Published on:

  12. Alkaloids, a class of organic compounds that contain nitrogen bases, are mainly synthesized as secondary metabolites in plants and fungi, and they have a wide range of bioactivities. Although there are thousan...

    Authors: Ryohei Eguchi, Naoaki Ono, Aki Hirai Morita, Tetsuo Katsuragi, Satoshi Nakamura, Ming Huang, Md. Altaf-Ul-Amin and Shigehiko Kanaya

    Citation: BMC Bioinformatics 2019 20:380

    Content type: Research article

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  13. Unsupervised machine learning methods (deep learning) have shown their usefulness with noisy single cell mRNA-sequencing data (scRNA-seq), where the models generalize well, despite the zero-inflation of the da...

    Authors: Savvas Kinalis, Finn Cilius Nielsen, Ole Winther and Frederik Otzen Bagger

    Citation: BMC Bioinformatics 2019 20:379

    Content type: Methodology article

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  14. The QuantiGene® Plex 2.0 platform (ThermoFisher Scientific) combines bDNA with the Luminex/xMAP magnetic bead capturing technology to assess differential gene expression in a compound exposure setting. This te...

    Authors: Bie Verbist, Eva Adriaensen, Vikki Keersmaekers, Dea Putri, Marjolein Crabbe, Maarten Derks, Rytis Bagdziunas, Griet Laenen and Hans De Wolf

    Citation: BMC Bioinformatics 2019 20:378

    Content type: Methodology article

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  15. Molecule identification is a crucial step in metabolomics and environmental sciences. Besides in silico fragmentation, as performed by MetFrag, also machine learning and statistical methods evolved, showing an...

    Authors: Christoph Ruttkies, Steffen Neumann and Stefan Posch

    Citation: BMC Bioinformatics 2019 20:376

    Content type: Research article

    Published on:

  16. One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytica...

    Authors: Teresia M. Buza, Triza Tonui, Francesca Stomeo, Christian Tiambo, Robab Katani, Megan Schilling, Beatus Lyimo, Paul Gwakisa, Isabella M. Cattadori, Joram Buza and Vivek Kapur

    Citation: BMC Bioinformatics 2019 20:374

    Content type: Software

    Published on:

  17. RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions. Therefore, understanding RNA folding conformations, in particu...

    Authors: Congzhe Su, Jeffery D. Weir, Fei Zhang, Hao Yan and Teresa Wu

    Citation: BMC Bioinformatics 2019 20:373

    Content type: Research article

    Published on:

  18. Predicting the effect of single point variations on protein stability constitutes a crucial step toward understanding the relationship between protein structure and function. To this end, several methods have ...

    Authors: Ludovica Montanucci, Emidio Capriotti, Yotam Frank, Nir Ben-Tal and Piero Fariselli

    Citation: BMC Bioinformatics 2019 20(Suppl 14):335

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 14

  19. The studies of functions of circular RNAs (circRNAs) are heavily focused on the regulation of gene expression through interactions with multiple miRNAs. However, the number of predicted target genes is typical...

    Authors: Ya-Chi Lin, Yueh-Chun Lee, Kai-Li Chang and Kuei-Yang Hsiao

    Citation: BMC Bioinformatics 2019 20:372

    Content type: Software

    Published on:

  20. In spite of the abundance of genomic data, predictive models that describe phenotypes as a function of gene expression or mutations are difficult to obtain because they are affected by the curse of dimensional...

    Authors: Marina Esteban-Medina, María Peña-Chilet, Carlos Loucera and Joaquín Dopazo

    Citation: BMC Bioinformatics 2019 20:370

    Content type: Research article

    Published on:

  21. Single cell RNA sequencing (scRNA-seq) brings unprecedented opportunities for mapping the heterogeneity of complex cellular environments such as bone marrow, and provides insight into many cellular processes. ...

    Authors: Sergii Domanskyi, Anthony Szedlak, Nathaniel T Hawkins, Jiayin Wang, Giovanni Paternostro and Carlo Piermarocchi

    Citation: BMC Bioinformatics 2019 20:369

    Content type: Methodology article

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  22. Mass Spectrometry (MS) is a widely used technique in biology research, and has become key in proteomics and metabolomics analyses. As a result, the amount of MS data has significantly increased in recent years...

    Authors: Ruochen Yang, Xi Chen and Idoia Ochoa

    Citation: BMC Bioinformatics 2019 20:368

    Content type: Methodology article

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  23. Missense mutations in the first five exons of F9, which encodes factor FIX, represent 40% of all mutations that cause hemophilia B. To address the ongoing debate regarding in silico identification of disease-caus...

    Authors: Lennon Meléndez-Aranda, Ana Rebeca Jaloma-Cruz, Nina Pastor and Marina María de Jesús Romero-Prado

    Citation: BMC Bioinformatics 2019 20:363

    Content type: Research article

    Published on:

  24. Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.

    Authors: Akio Miyao, Jianyu Song Kiyomiya, Keiko Iida, Koji Doi and Hiroshi Yasue

    Citation: BMC Bioinformatics 2019 20:362

    Content type: Research article

    Published on:

  25. Exploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies...

    Authors: Leandro Gabriel Roser, Fernán Agüero and Daniel Oscar Sánchez

    Citation: BMC Bioinformatics 2019 20:361

    Content type: Software

    Published on:

  26. Because of its non-destructive nature, label-free imaging is an important strategy for studying biological processes. However, routine microscopic techniques like phase contrast or DIC suffer from shadow-cast ...

    Authors: Tomas Vicar, Jan Balvan, Josef Jaros, Florian Jug, Radim Kolar, Michal Masarik and Jaromir Gumulec

    Citation: BMC Bioinformatics 2019 20:360

    Content type: Methodology article

    Published on:

  27. Essential proteins are distinctly important for an organism’s survival and development and crucial to disease analysis and drug design as well. Large-scale protein-protein interaction (PPI) data sets exist in Sac...

    Authors: Bihai Zhao, Yulin Zhao, Xiaoxia Zhang, Zhihong Zhang, Fan Zhang and Lei Wang

    Citation: BMC Bioinformatics 2019 20:355

    Content type: Research article

    Published on:

  28. Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated.

    Authors: Kaining Hu, Kai Xu, Jing Wen, Bin Yi, Jinxiong Shen, Chaozhi Ma, Tingdong Fu, Yidan Ouyang and Jinxing Tu

    Citation: BMC Bioinformatics 2019 20:354

    Content type: Research article

    Published on:

  29. Predicting meaningful miRNA-disease associations (MDAs) is costly. Therefore, an increasing number of researchers are beginning to focus on methods to predict potential MDAs. Thus, prediction methods with impr...

    Authors: Ying-Lian Gao, Zhen Cui, Jin-Xing Liu, Juan Wang and Chun-Hou Zheng

    Citation: BMC Bioinformatics 2019 20:353

    Content type: Methodology article

    Published on:

  30. Third-generation sequencing platforms, such as PacBio sequencing, have been developed rapidly in recent years. PacBio sequencing generates much longer reads than the second-generation sequencing (or the next g...

    Authors: Wenmin Zhang, Ben Jia and Chaochun Wei

    Citation: BMC Bioinformatics 2019 20:352

    Content type: Software

    Published on:

  31. Protein feature extraction plays an important role in the areas of similarity analysis of protein sequences and prediction of protein structures, functions and interactions. The feature extraction based on gra...

    Authors: Zengchao Mu, Ting Yu, Enfeng Qi, Juntao Liu and Guojun Li

    Citation: BMC Bioinformatics 2019 20:351

    Content type: Methodology article

    Published on:

  32. Testing model adequacy is important before a DNA substitution model is chosen for phylogenetic inference. Using a mis-specified model can negatively impact phylogenetic inference, for example, the maximum like...

    Authors: Wei Chen, Toby Kenney, Joseph Bielawski and Hong Gu

    Citation: BMC Bioinformatics 2019 20:349

    Content type: Methodology article

    Published on:

  33. Missing values frequently arise in modern biomedical studies due to various reasons, including missing tests or complex profiling technologies for different omics measurements. Missing values can complicate th...

    Authors: Shahin Boluki, Siamak Zamani Dadaneh, Xiaoning Qian and Edward R. Dougherty

    Citation: BMC Bioinformatics 2019 20(Suppl 12):321

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  34. Real biological and social data is increasingly being represented as graphs. Pattern-mining-based graph learning and analysis techniques report meaningful biological subnetworks that elucidate important intera...

    Authors: Mohammed Alokshiya, Saeed Salem and Fidaa Abed

    Citation: BMC Bioinformatics 2019 20(Suppl 12):319

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

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