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  1. High-throughput gene expression technologies provide complex datasets reflecting mechanisms perturbed in an experiment, typically in a treatment versus control design. Analysis of these information-rich data c...

    Authors: Florian Martin, Sylvain Gubian, Marja Talikka, Julia Hoeng and Manuel C. Peitsch

    Citation: BMC Bioinformatics 2019 20:451

    Content type: Software

    Published on:

  2. Mutational signatures are specific patterns of somatic mutations introduced into the genome by oncogenic processes. Several mutational signatures have been identified and quantified from multiple cancer studie...

    Authors: Franziska Schumann, Eric Blanc, Clemens Messerschmidt, Thomas Blankenstein, Antonia Busse and Dieter Beule

    Citation: BMC Bioinformatics 2019 20:450

    Content type: Software

    Published on:

  6. Protein interaction databases often provide confidence scores for each recorded interaction based on the available experimental evidence. Protein interaction networks (PINs) are then built by thresholding on t...

    Authors: Lyuba V. Bozhilova, Alan V. Whitmore, Jonny Wray, Gesine Reinert and Charlotte M. Deane

    Citation: BMC Bioinformatics 2019 20:446

    Content type: Research article

    Published on:

  8. Mining epistatic loci which affects specific phenotypic traits is an important research issue in the field of biology. Bayesian network (BN) is a graphical model which can express the relationship between gene...

    Authors: Yang Guo, Zhiman Zhong, Chen Yang, Jiangfeng Hu, Yaling Jiang, Zizhen Liang, Hui Gao and Jianxiao Liu

    Citation: BMC Bioinformatics 2019 20:444

    Content type: Methodology article

    Published on:

  9. Cryo-electron tomography (Cryo-ET) is an imaging technique used to generate three-dimensional structures of cellular macromolecule complexes in their native environment. Due to developing cryo-electron microsc...

    Authors: Yongchun Lü, Xiangrui Zeng, Xiaofang Zhao, Shirui Li, Hua Li, Xin Gao and Min Xu

    Citation: BMC Bioinformatics 2019 20:443

    Content type: Methodology article

    Published on:

  10. Contemporary biological observations have revealed a large variety of mechanisms acting during the expansion of a tumor. However, there are still many qualitative and quantitative aspects of the phenomenon tha...

    Authors: Markos Antonopoulos, Dimitra Dionysiou, Georgios Stamatakos and Nikolaos Uzunoglu

    Citation: BMC Bioinformatics 2019 20:442

    Content type: Research article

    Published on:

    The Publisher Correction to this article has been published in BMC Bioinformatics 2019 20:500

  11. Although a few comparison methods based on the biological meaning of gene lists have been developed, the goProfiles approach is one of the few that are being used for that purpose. It consists of projecting li...

    Authors: Alex Sánchez-Pla, Miquel Salicrú and Jordi Ocaña

    Citation: BMC Bioinformatics 2019 20:441

    Content type: Methodology article

    Published on:

  12. With every new genome that is sequenced, thousands of species-specific genes (orphans) are found, some originating from ultra-rapid mutations of existing genes, many others originating de novo from non-genic r...

    Authors: Zebulun Arendsee, Jing Li, Urminder Singh, Priyanka Bhandary, Arun Seetharam and Eve Syrkin Wurtele

    Citation: BMC Bioinformatics 2019 20:440

    Content type: Software

    Published on:

  13. Following publication of the original article [1], the author noticed that the following lines were missing from the published article. The original article has been corrected.

    Authors: Mai Anh BUI T, Nick Papoulias, Serge Stinckwich, Mikal Ziane and Benjamin Roche

    Citation: BMC Bioinformatics 2019 20:439

    Content type: Correction

    Published on:

    The original article was published in BMC Bioinformatics 2019 20:312

  15. Batch effects were not accounted for in most of the studies of computational drug repositioning based on gene expression signatures. It is unknown how batch effect removal methods impact the results of signatu...

    Authors: Wei Zhou, Karel K. M. Koudijs and Stefan Böhringer

    Citation: BMC Bioinformatics 2019 20:437

    Content type: Methodology article

    Published on:

  16. Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant da...

    Authors: Hamid Bagheri, Usha Muppirala, Rick E. Masonbrink, Andrew J. Severin and Hridesh Rajan

    Citation: BMC Bioinformatics 2019 20:436

    Content type: Research article

    Published on:

  17. Gene and protein interaction data are often represented as interaction networks, where nodes stand for genes or gene products and each edge stands for a relationship between a pair of gene nodes. Commonly, tha...

    Authors: Joëlle Barido-Sottani, Samuel D. Chapman, Evsey Kosman and Arcady R. Mushegian

    Citation: BMC Bioinformatics 2019 20:435

    Content type: Research article

    Published on:

  18. The epidermal growth factor receptor (EGFR) is a major regulator of proliferation in tumor cells. Elevated expression levels of EGFR are associated with prognosis and clinical outcomes of patients in a variety...

    Authors: Claus Weinholdt, Henri Wichmann, Johanna Kotrba, David H. Ardell, Matthias Kappler, Alexander W. Eckert, Dirk Vordermark and Ivo Grosse

    Citation: BMC Bioinformatics 2019 20:434

    Content type: Research article

    Published on:

  19. Host immune response is coordinated by a variety of different specialized cell types that vary in time and location. While host immune response can be studied using conventional low-dimensional approaches, adv...

    Authors: Arezo Torang, Paraag Gupta and David J. Klinke II

    Citation: BMC Bioinformatics 2019 20:433

    Content type: Research article

    Published on:

  20. Relationships between specific microbes and proper immune system development, composition, and function have been reported in a number of studies. However, researchers have discovered only a fraction of the li...

    Authors: Janet C. Siebert, Charles Preston Neff, Jennifer M. Schneider, Emilie H. Regner, Neha Ohri, Kristine A. Kuhn, Brent E. Palmer, Catherine A. Lozupone and Carsten Görg

    Citation: BMC Bioinformatics 2019 20:432

    Content type: Research article

    Published on:

  22. Background Consisting of dictated free-text documents such as discharge summaries, medical narratives are widely used in medical natural language processing. Relationships between anatomical entities and human...

    Authors: Yipei Wang, Xingyu Fan, Luoxin Chen, Eric I-Chao Chang, Sophia Ananiadou, Junichi Tsujii and Yan Xu

    Citation: BMC Bioinformatics 2019 20:430

    Content type: Methodology article

    Published on:

  23. 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

    Content type: Research article

    Published on:

  24. With the advent of array-based techniques to measure methylation levels in primary tumor samples, systematic investigations of methylomes have widely been performed on a large number of tumor entities. Most of...

    Authors: Pascal David Johann, Natalie Jäger, Stefan M. Pfister and Martin Sill

    Citation: BMC Bioinformatics 2019 20:428

    Content type: Methodology article

    Published on:

  26. 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

    Content type: Software

    Published on:

  30. 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

    Content type: Software

    Published on:

  31. 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

    Content type: Methodology article

    Published on:

  32. 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

    Content type: Software

    Published on:

  34. 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

    Content type: Software

    Published on:

  35. 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

    Content type: Software

    Published on:

  37. 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

    Content type: Software

    Published on:

  38. 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

    Content type: Research article

    Published on:

  42. 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

    Content type: Methodology article

    Published on:

  43. 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

    Content type: Software

    Published on:

  44. 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

    Content type: Software

    Published on:

  45. 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

    Content type: Research article

    Published on:

  46. 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

    Content type: Research

    Published on:

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

  47. 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

    Content type: Research

    Published on:

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

  48. 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

    Content type: Research

    Published on:

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

  49. 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

    Content type: Research

    Published on:

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

  50. 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

    Content type: Software

    Published on:

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