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  1. Content type: Research article

    Diagnosis and treatment decisions in cancer increasingly depend on a detailed analysis of the mutational status of a patient’s genome. This analysis relies on previously published information regarding the ass...

    Authors: Jurica Ševa, David Luis Wiegandt, Julian Götze, Mario Lamping, Damian Rieke, Reinhold Schäfer, Patrick Jähnichen, Madeleine Kittner, Steffen Pallarz, Johannes Starlinger, Ulrich Keilholz and Ulf Leser

    Citation: BMC Bioinformatics 2019 20:429

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  2. Content type: Software

    Advances in medical technology have allowed for customized prognosis, diagnosis, and treatment regimens that utilize multiple heterogeneous data sources. Multiple kernel learning (MKL) is well suited for the i...

    Authors: Christopher M. Wilson, Kaiqiao Li, Xiaoqing Yu, Pei-Fen Kuan and Xuefeng Wang

    Citation: BMC Bioinformatics 2019 20:426

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  6. Content type: Software

    One of the main issues in the automated protein function prediction (AFP) problem is the integration of multiple networked data sources. The UNIPred algorithm was thereby proposed to efficiently integrate —in ...

    Authors: Paolo Perlasca, Marco Frasca, Cheick Tidiane Ba, Marco Notaro, Alessandro Petrini, Elena Casiraghi, Giuliano Grossi, Jessica Gliozzo, Giorgio Valentini and Marco Mesiti

    Citation: BMC Bioinformatics 2019 20:422

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  7. Content type: Methodology article

    Ultra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantificat...

    Authors: Mohamed K Gunady, Stephen M Mount and Héctor Corrada Bravo

    Citation: BMC Bioinformatics 2019 20:421

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  8. Content type: Software

    Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast...

    Authors: Carlos J. Rivera-Rivera and Juan I. Montoya-Burgos

    Citation: BMC Bioinformatics 2019 20:420

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  10. Content type: Software

    Standard RNAseq methods using bulk RNA and recent single-cell RNAseq methods use DNA barcodes to identify samples and cells, and the barcoded cDNAs are pooled into a library pool before high throughput sequenc...

    Authors: Shintaro Katayama, Tiina Skoog, Cilla Söderhäll, Elisabet Einarsdottir, Kaarel Krjutškov and Juha Kere

    Citation: BMC Bioinformatics 2019 20:418

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  11. Content type: Software

    The development of high throughput sequencing techniques provides us with the possibilities to obtain large data sets, which capture the effect of dynamic perturbations on cellular processes. However, because ...

    Authors: T. J. M. Kuijpers, J. E. J. Wolters, J. C. S. Kleinjans and D. G. J. Jennen

    Citation: BMC Bioinformatics 2019 20:417

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  13. Content type: Software

    R-loops are three-stranded nucleic acid structures that usually form during transcription and that may lead to gene regulation or genome instability. DRIP (DNA:RNA Immunoprecipitation)-seq techniques are widel...

    Authors: Marco Russo, Bruno De Lucca, Tiziano Flati, Silvia Gioiosa, Giovanni Chillemi and Giovanni Capranico

    Citation: BMC Bioinformatics 2019 20:414

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  14. Content type: Research article

    Cartilage damage is a crucial feature involved in several pathological conditions characterized by joint disorders, such as osteoarthritis and rheumatoid arthritis. Accumulated evidences showed that Wnt/β-cate...

    Authors: Wei Zhou, Xiaojuan He, Ziyi Chen, Danping Fan, Yonghua Wang, Hui Feng, Ge Zhang, Aiping Lu and Lianbo Xiao

    Citation: BMC Bioinformatics 2019 20:412

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  18. Content type: Methodology article

    Understanding the phenotypic drug response on cancer cell lines plays a vital role in anti-cancer drug discovery and re-purposing. The Genomics of Drug Sensitivity in Cancer (GDSC) database provides open data ...

    Authors: Pengfei Liu, Hongjian Li, Shuai Li and Kwong-Sak Leung

    Citation: BMC Bioinformatics 2019 20:408

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  19. Content type: Software

    Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, ext...

    Authors: Rebecca C. Jackson, James P. Balhoff, Eric Douglass, Nomi L. Harris, Christopher J. Mungall and James A. Overton

    Citation: BMC Bioinformatics 2019 20:407

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  20. Content type: Software

    Next-generation sequencing technologies can produce tens of millions of reads, often paired-end, from transcripts or genomes. But few programs can align RNA on the genome and accurately discover introns, espec...

    Authors: Grzegorz M. Boratyn, Jean Thierry-Mieg, Danielle Thierry-Mieg, Ben Busby and Thomas L. Madden

    Citation: BMC Bioinformatics 2019 20:405

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  21. Content type: Research article

    It has been shown that the deregulation of miRNAs is associated with the development and progression of many human diseases. To reduce time and cost of biological experiments, a number of algorithms have been ...

    Authors: Hailin Chen, Zuping Zhang and Dayi Feng

    Citation: BMC Bioinformatics 2019 20:404

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  22. Content type: Research

    The development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certificati...

    Authors: Jungmin Ha, Ho Hwi Jeon, Dong U. Woo, Yejin Lee, Halim Park, Joohyeong Lee and Yang Jae Kang

    Citation: BMC Bioinformatics 2019 20(Suppl 13):384

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    This article is part of a Supplement: Volume 20 Supplement 13

  23. Content type: Research

    Drug repurposing has been motivated to ameliorate low probability of success in drug discovery. For the recent decade, many in silico attempts have received primary attention as a first step to alleviate the h...

    Authors: Yonghyun Nam, Myungjun Kim, Hang-Seok Chang and Hyunjung Shin

    Citation: BMC Bioinformatics 2019 20(Suppl 13):383

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    This article is part of a Supplement: Volume 20 Supplement 13

  24. Content type: Research

    Pathogenic protist membrane transporter proteins play important roles not only in exchanging molecules into and out of cells but also in acquiring nutrients and biosynthetic compounds from their hosts. Current...

    Authors: Chi-Ching Lee, Po-Jung Huang, Yuan-Ming Yeh, Sin-You Chen, Cheng-Hsun Chiu, Wei-Hung Cheng and Petrus Tang

    Citation: BMC Bioinformatics 2019 20(Suppl 13):382

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    This article is part of a Supplement: Volume 20 Supplement 13

  25. Content type: Research

    How can we obtain fast and high-quality clusters in genome scale bio-networks? Graph clustering is a powerful tool applied on bio-networks to solve various biological problems such as protein complexes detecti...

    Authors: Yongsub Lim, Injae Yu, Dongmin Seo, U Kang and Lee Sael

    Citation: BMC Bioinformatics 2019 20(Suppl 13):381

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    This article is part of a Supplement: Volume 20 Supplement 13

  27. Content type: Software

    Today a variety of phylogenetic file formats exists, some of which are well-established but limited in their data model, while other more recently introduced ones offer advanced features for metadata represent...

    Authors: Ben C. Stöver, Sarah Wiechers and Kai F. Müller

    Citation: BMC Bioinformatics 2019 20:402

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  31. Content type: Research article

    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

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  33. Content type: Research article

    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

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  34. Content type: Methodology article

    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

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  35. Content type: Methodology article

    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

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  36. Content type: Research article

    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

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  37. Content type: Software

    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

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  38. Content type: Research article

    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

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  39. Content type: Software

    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

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  41. Content type: Methodology article

    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

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  42. Content type: Research article

    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

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  43. Content type: Software

    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

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  44. Content type: Research article

    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

    Published on:

  45. Content type: Methodology article

    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

    Published on:

  46. Content type: Methodology article

    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

    Published on:

  48. Content type: Research article

    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

    Published on:

  50. Content type: Software

    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

    Published on:

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