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  1. Content type: Research article

    c-Myc plays an important role in cell proliferation, cell growth and in differentiation, making it a key regulator for carcinogenesis and pluripotency. Tight control of c-myc turnover is required by ubiquitin-...

    Authors: Debangana Chakravorty, Krishnendu Banerjee, Tarunendu Mapder and Sudipto Saha

    Citation: BMC Bioinformatics 2019 20:230

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  2. Content type: Methodology article

    An orthologous group (OG) comprises a set of orthologous and paralogous genes that share a last common ancestor (LCA). OGs are defined with respect to a chosen taxonomic level, which delimits the position of t...

    Authors: Davide Heller, Damian Szklarczyk and Christian von Mering

    Citation: BMC Bioinformatics 2019 20:228

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  3. Content type: Research article

    Serratia marcescens is a chitinolytic bacterium that can potentially be used for consolidated bioprocessing to convert chitin to value-added chemicals. Currently, S. marcescens is poorly characterized and studies...

    Authors: Qiang Yan, Seth Robert, J. Paul Brooks and Stephen S. Fong

    Citation: BMC Bioinformatics 2019 20:227

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  4. Content type: Software

    RNA sequencing (RNA-seq) has become the standard means of analyzing gene and transcript expression in high-throughput. While previously sequence alignment was a time demanding step, fast alignment methods and ...

    Authors: Paula Pérez-Rubio, Claudio Lottaz and Julia C. Engelmann

    Citation: BMC Bioinformatics 2019 20:226

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  5. Content type: Methodology article

    Characterizing the modular structure of cellular network is an important way to identify novel genes for targeted therapeutics. This is made possible by the rising of high-throughput technology. Unfortunately,...

    Authors: Lifan Liang, Vicky Chen, Kunju Zhu, Xiaonan Fan, Xinghua Lu and Songjian Lu

    Citation: BMC Bioinformatics 2019 20:225

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  6. Content type: Methodology article

    Gene networks in living cells can change depending on various conditions such as caused by different environments, tissue types, disease states, and development stages. Identifying the differential changes in ...

    Authors: Chen Wang, Feng Gao, Georgios B. Giannakis, Gennaro D’Urso and Xiaodong Cai

    Citation: BMC Bioinformatics 2019 20:224

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  7. Content type: Research article

    Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methyl...

    Authors: Xiangyu Wu, Zhen Wei, Kunqi Chen, Qing Zhang, Jionglong Su, Hui Liu, Lin Zhang and Jia Meng

    Citation: BMC Bioinformatics 2019 20:223

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  8. Content type: Research article

    Inference of gene regulatory networks from gene expression data has been a long-standing and notoriously difficult task in systems biology. Recently, single-cell transcriptomic data have been massively used fo...

    Authors: Arnaud Bonnaffoux, Ulysse Herbach, Angélique Richard, Anissa Guillemin, Sandrine Gonin-Giraud, Pierre-Alexis Gros and Olivier Gandrillon

    Citation: BMC Bioinformatics 2019 20:220

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  9. Content type: Research

    Experimental studies have demonstrated that both the extracellular vasculature or microenvironment and intracellular molecular network (e.g., epidermal growth factor receptor (EGFR) signaling pathway) are impo...

    Authors: Weishan Liang, Yongjiang Zheng, Ji Zhang and Xiaoqiang Sun

    Citation: BMC Bioinformatics 2019 20(Suppl 7):203

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    This article is part of a Supplement: Volume 20 Supplement 7

  10. Content type: Research

    Most researches of chronic myeloid leukemia (CML) are currently focused on the treatment methods, while there are relatively few researches on the progress of patients’ condition after drug treatment. Traditio...

    Authors: Junhua Xu, Min Wu, Shanshan Zhu, Jinzhi Lei and Jie Gao

    Citation: BMC Bioinformatics 2019 20(Suppl 7):202

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    This article is part of a Supplement: Volume 20 Supplement 7

  11. Content type: Research

    A key problem in systems biology is the determination of the regulatory mechanism corresponding to a phenotype. An empirical approach in this regard is to compare the expression profiles of cells under two con...

    Authors: Yance Feng, Sheng Zhang, Liang Li and Lei M. Li

    Citation: BMC Bioinformatics 2019 20(Suppl 7):201

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  12. Content type: Research

    Transcription factors (TFs) play important roles in the regulation of gene expression. They can activate or block transcription of downstream genes in a manner of binding to specific genomic sequences. Therefo...

    Authors: Jialu Hu, Jingru Wang, Jianan Lin, Tianwei Liu, Yuanke Zhong, Jie Liu, Yan Zheng, Yiqun Gao, Junhao He and Xuequn Shang

    Citation: BMC Bioinformatics 2019 20(Suppl 7):200

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    This article is part of a Supplement: Volume 20 Supplement 7

  13. Content type: Research

    Drug adverse events (AEs), or called adverse drug events (ADEs), are ranked one of the leading causes of mortality. The Ontology of Adverse Events (OAE) has been widely used for adverse event AE representation...

    Authors: Hong Yu, Solomiya Nysak, Noemi Garg, Edison Ong, Xianwei Ye, Xiangyan Zhang and Yongqun He

    Citation: BMC Bioinformatics 2019 20(Suppl 7):199

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    This article is part of a Supplement: Volume 20 Supplement 7

  14. Content type: Research

    For treating a complex disease such as cancer, some effective means are needed to control biological networks that underlies the disease. The one-target one-drug paradigm has been the dominating drug discovery...

    Authors: Min Luo, Jianfeng Jiao and Ruiqi Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 7):198

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    This article is part of a Supplement: Volume 20 Supplement 7

  15. Content type: Research

    Lung adenocarcinoma is the most common type of lung cancer, with high mortality worldwide. Its occurrence and development were thoroughly studied by high-throughput expression microarray, which produced abunda...

    Authors: Xuemeng Fan, Yaolai Wang and Xu-Qing Tang

    Citation: BMC Bioinformatics 2019 20(Suppl 7):197

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  16. Content type: Research

    Gene Co-expression Network Analysis (GCNA) helps identify gene modules with potential biological functions and has become a popular method in bioinformatics and biomedical research. However, most current GCNA ...

    Authors: Tongxin Wang, Jie Zhang and Kun Huang

    Citation: BMC Bioinformatics 2019 20(Suppl 7):196

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  17. Content type: Research

    Lipid metabolism reprogramming is a hallmark for tumor which contributes to tumorigenesis and progression, but the commonality and difference of lipid metabolism among pan-cancer is not fully investigated. Inc...

    Authors: Yang Hao, Daixi Li, Yong Xu, Jian Ouyang, Yongkun Wang, Yuqi Zhang, Baoguo Li, Lu Xie and Guangrong Qin

    Citation: BMC Bioinformatics 2019 20(Suppl 7):195

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  18. Content type: Research

    The mechanism of many complex diseases has not been detected accurately in terms of their stage evolution. Previous studies mainly focus on the identification of associations between genes and individual disea...

    Authors: Chaima Aouiche, Bolin Chen and Xuequn Shang

    Citation: BMC Bioinformatics 2019 20(Suppl 7):194

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  19. Content type: Research

    Haemorrhagic stroke accounts for approximately 31.52% of all stroke cases, and the most common origin is hypertension. However, little is known about the method to identify high-risk populations of hypertensiv...

    Authors: Le Zhang, Jin Li, Kaikai Yin, Zhouyang Jiang, Tingting Li, Rong Hu, Zheng Yu, Hua Feng and Yujie Chen

    Citation: BMC Bioinformatics 2019 20(Suppl 7):193

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  20. Content type: Research

    The Iridoviridae family is categorized into five genera and clustered into two subfamilies: Alphairidovirinae includes Lymphocystivirus, Ranavirus (GIV), and Megalocystivirus (TGIV), which infect vertebrate hosts...

    Authors: Tao-Chuan Shih, Li-Ping Ho, Jen-Leih Wu, Hsin-Yiu Chou and Tun-Wen Pai

    Citation: BMC Bioinformatics 2019 20(Suppl 7):192

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  21. Content type: Research

    Single-cell RNA-sequencing (scRNA-seq) technologies have advanced rapidly in recent years and enabled the quantitative characterization at a microscopic resolution. With the exponential growth of the number of...

    Authors: Shengquan Chen, Kui Hua, Hongfei Cui and Rui Jiang

    Citation: BMC Bioinformatics 2019 20(Suppl 7):0

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  22. Content type: Methodology article

    Data from genome-wide association studies (GWASs) have been used to estimate the heritability of human complex traits in recent years. Existing methods are based on the linear mixed model, with the assumption ...

    Authors: Xin Li, Dongya Wu, Yue Cui, Bing Liu, Henrik Walter, Gunter Schumann, Chong Li and Tianzi Jiang

    Citation: BMC Bioinformatics 2019 20:219

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  23. Content type: Software

    When designing an epigenome-wide association study (EWAS) to investigate the relationship between DNA methylation (DNAm) and some exposure(s) or phenotype(s), it is critically important to assess the sample si...

    Authors: Stefan Graw, Rosalyn Henn, Jeffrey A. Thompson and Devin C. Koestler

    Citation: BMC Bioinformatics 2019 20:218

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  24. Content type: Software

    Lipidomics, the comprehensive measurement of lipids within a biological system or substrate, is an emerging field with significant potential for improving clinical diagnosis and our understanding of health and...

    Authors: Jeremy P. Koelmel, Jason A. Cochran, Candice Z. Ulmer, Allison J. Levy, Rainey E. Patterson, Berkley C. Olsen, Richard A. Yost, John A. Bowden and Timothy J. Garrett

    Citation: BMC Bioinformatics 2019 20:217

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  25. Content type: Software

    Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Immunological serotyping is the most commonly used typing method to characterize S. enterica isolates, but is time-consuming and req...

    Authors: Lang Yang, Xia Zhang, Yuqi Liu, Hao Li, Shaofu Qiu, Peng Li and Hongbin Song

    Citation: BMC Bioinformatics 2019 20:215

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  26. Content type: Methodology article

    Next Generation Sequencing (NGS) is a commonly used technology for studying the genetic basis of biological processes and it underpins the aspirations of precision medicine. However, there are significant chal...

    Authors: A. Iacoangeli, A. Al Khleifat, W. Sproviero, A. Shatunov, A. R. Jones, S. L. Morgan, A. Pittman, R. J. Dobson, S. J. Newhouse and A. Al-Chalabi

    Citation: BMC Bioinformatics 2019 20:213

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  27. Content type: Research article

    Computational approaches for the determination of biologically-active/native three-dimensional structures of proteins with novel sequences have to handle several challenges. The (conformation) space of possibl...

    Authors: Ahmed Bin Zaman and Amarda Shehu

    Citation: BMC Bioinformatics 2019 20:211

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  28. Content type: Methodology article

    A large number of algorithms is being developed to reconstruct evolutionary models of individual tumours from genome sequencing data. Most methods can analyze multiple samples collected either through bulk mul...

    Authors: Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti and Giulio Caravagna

    Citation: BMC Bioinformatics 2019 20:210

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  29. Content type: Introduction

    Cell cultures and cell lines are widely used in life science experiments. In conjunction with the 2018 International Conference on Biomedical Ontology (ICBO-2018), the 2nd International Workshop on Cells in Ex...

    Authors: Sirarat Sarntivijai, Yongqun He and Alexander D. Diehl

    Citation: BMC Bioinformatics 2019 20(Suppl 5):183

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 5

  30. Content type: Research

    Human immunology studies often rely on the isolation and quantification of cell populations from an input sample based on flow cytometry and related techniques. Such techniques classify cells into populations ...

    Authors: James A. Overton, Randi Vita, Patrick Dunn, Julie G. Burel, Syed Ahmad Chan Bukhari, Kei-Hoi Cheung, Steven H. Kleinstein, Alexander D. Diehl and Bjoern Peters

    Citation: BMC Bioinformatics 2019 20(Suppl 5):182

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 5

  31. Content type: Research

    Within the cancer domain, ontologies play an important role in the integration and annotation of data in order to support numerous biomedical tools and applications. This work seeks to leverage existing standa...

    Authors: Lucas M. Serra, William D. Duncan and Alexander D. Diehl

    Citation: BMC Bioinformatics 2019 20(Suppl 5):181

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 5

  32. Content type: Research

    Stem cells and stem cell lines are widely used in biomedical research. The Cell Ontology (CL) and Cell Line Ontology (CLO) are two community-based OBO Foundry ontologies in the domains of in vivo cells and in ...

    Authors: Yongqun He, William D. Duncan, Daniel J. Cooper, Jens Hansen, Ravi Iyengar, Edison Ong, Kendal Walker, Omar Tibi, Sam Smith, Lucas M. Serra, Jie Zheng, Sirarat Sarntivijai, Stephan Schürer, K. Sue O’Shea and Alexander D. Diehl

    Citation: BMC Bioinformatics 2019 20(Suppl 5):180

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 5

  33. Content type: Research

    The Chinese National Infrastructure of Cell Line stores and distributes cell lines for biomedical research in China. This study aims to represent and integrate the information of NICR cell lines into the commu...

    Authors: Hongjie Pan, Xiaocui Bian, Sheng Yang, Yongqun He, Xiaolin Yang and Yuqin Liu

    Citation: BMC Bioinformatics 2019 20(Suppl 5):179

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 5

  34. Content type: Methodology article

    Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation...

    Authors: Bastian Pfeifer and Durrell D. Kapan

    Citation: BMC Bioinformatics 2019 20:207

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  35. Content type: Research article

    Oral immunotherapy (OIT) is a promising therapeutic approach to treat food allergic patients. However, concerns with regards to safety and long-term efficacy of OIT remain. There is a need to identify biomarke...

    Authors: Jolanda H. M. van Bilsen, Lars Verschuren, Laura Wagenaar, Marlotte M. Vonk, Betty C. A. M. van Esch, Léon M. J. Knippels, Johan Garssen, Joost J. Smit, Raymond H. H. Pieters and Tim J. van den Broek

    Citation: BMC Bioinformatics 2019 20:206

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  36. Content type: Methodology article

    Sub-nuclear structures or locations are associated with various nuclear processes. Proteins localized in these substructures are important to understand the interior nuclear mechanisms. Despite advances in hig...

    Authors: Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén and Burkhard Rost

    Citation: BMC Bioinformatics 2019 20:205

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  37. Content type: Software

    The analysis of gene expression levels is used in many clinical studies to know how patients evolve or to find new genetic biomarkers that could help in clinical decision making. However, the techniques and so...

    Authors: Ismael Navas-Delgado, José García-Nieto, Esteban López-Camacho, Maciej Rybinski, Rocio Lavado, Miguel Ángel Berciano Guerrero and José F. Aldana-Montes

    Citation: BMC Bioinformatics 2019 20(Suppl 4):150

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  38. Content type: Research

    Distributed approaches based on the MapReduce programming paradigm have started to be proposed in the Bioinformatics domain, due to the large amount of data produced by the next-generation sequencing technique...

    Authors: Umberto Ferraro Petrillo, Mara Sorella, Giuseppe Cattaneo, Raffaele Giancarlo and Simona E. Rombo

    Citation: BMC Bioinformatics 2019 20(Suppl 4):138

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  39. Content type: Software

    RNA editing is an important mechanism for gene expression in plants organelles. It alters the direct transfer of genetic information from DNA to proteins, due to the introduction of differences between RNAs an...

    Authors: Fabio Fassetti, Claudia Giallombardo, Ofelia Leone, Luigi Palopoli, Simona E. Rombo and Adolfo Saiardi

    Citation: BMC Bioinformatics 2019 20(Suppl 4):124

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

  40. Content type: Research

    The search for molecular biomarkers of early-onset colorectal cancer (CRC) is an important but still quite challenging and unsolved task. Detection of CpG methylation in human DNA obtained from blood or stool ...

    Authors: Alexander Kel, Ulyana Boyarskikh, Philip Stegmaier, Leonid S. Leskov, Andrey V. Sokolov, Ivan Yevshin, Nikita Mandrik, Daria Stelmashenko, Jeannette Koschmann, Olga Kel-Margoulis, Mathias Krull, Anna Martínez-Cardús, Sebastian Moran, Manel Esteller, Fedor Kolpakov, Maxim Filipenko…

    Citation: BMC Bioinformatics 2019 20(Suppl 4):119

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

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