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  1. 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
    Content type: Research Published on:

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

  2. 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
    Content type: Research Published on:

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

  3. 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
    Content type: Research Published on:

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

  4. 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
    Content type: Research Published on:

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

  5. 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
    Content type: Research Published on:

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

  6. 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
    Content type: Research Published on:

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

  7. 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
    Content type: Research Published on:

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

  8. 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
    Content type: Research Published on:

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

  9. 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
    Content type: Methodology article Published on:

  10. 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
    Content type: Software Published on:

  11. 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
    Content type: Software Published on:

  13. 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
    Content type: Software Published on:

  15. 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
    Content type: Methodology article Published on:

  17. 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
    Content type: Research article Published on:

  18. 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
    Content type: Methodology article Published on:

  20. 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
    Content type: Introduction Published on:

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

  21. 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
    Content type: Research Published on:

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

  22. 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
    Content type: Research Published on:

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

  23. 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
    Content type: Research Published on:

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

  24. 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
    Content type: Research Published on:

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

  26. 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
    Content type: Methodology article Published on:

  27. 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
    Content type: Research article Published on:

  28. 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
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2019 20:727

  29. Quorum sensing drives biofilm formation in bacteria in order to ensure that biofilm formation only occurs when colonies are of a sufficient size and density. This spatial behaviour is achieved by the broadcast...

    Authors: David Gilbert, Monika Heiner, Leila Ghanbar and Jacek Chodak
    Citation: BMC Bioinformatics 2019 20(Suppl 4):173
    Content type: Methodology Published on:

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

  30. In order to fully characterize the genome of an individual, the reconstruction of the two distinct copies of each chromosome, called haplotypes, is essential. The computational problem of inferring the full ha...

    Authors: Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Pietro Liò, Ivan Merelli and Daniela Besozzi
    Citation: BMC Bioinformatics 2019 20(Suppl 4):172
    Content type: Research Published on:

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

  31. Next Generation Sequencing (NGS) experiments produce millions of short sequences that, mapped to a reference genome, provide biological insights at genomic, transcriptomic and epigenomic level. Typically the a...

    Authors: Mara Sangiovanni, Ilaria Granata, Amarinder Singh Thind and Mario Rosario Guarracino
    Citation: BMC Bioinformatics 2019 20(Suppl 4):168
    Content type: Research Published on:

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

  32. Obesity is a complex disorder associated with an increased risk of developing several comorbid chronic diseases, including postmenopausal breast cancer. Although many studies have investigated this issue, the ...

    Authors: Ilaria Granata, Enrico Troiano, Mara Sangiovanni and Mario Rosario Guarracino
    Citation: BMC Bioinformatics 2019 20(Suppl 4):162
    Content type: Research Published on:

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

  33. RNA secondary structure comparison is a fundamental task for several studies, among which are RNA structure prediction and evolution. The comparison can currently be done efficiently only for pseudoknot-free s...

    Authors: Michela Quadrini, Luca Tesei and Emanuela Merelli
    Citation: BMC Bioinformatics 2019 20(Suppl 4):161
    Content type: Methodology Published on:

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

  34. The somatic mutations found in a tumor have in most cases been caused by multiple mutational processes such as those related to extrinsic carcinogens like cigarette smoke, and those related to intrinsic proces...

    Authors: Sandra Krüger and Rosario M. Piro
    Citation: BMC Bioinformatics 2019 20(Suppl 4):152
    Content type: Research Published on:

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

  35. 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
    Content type: Software Published on:

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

  36. Bacterial surfaces are complex systems, constructed from membranes, peptidoglycan and, importantly, proteins. The proteins play crucial roles as critical regulators of how the bacterium interacts with and surv...

    Authors: Hamed Khakzad, Johan Malmström and Lars Malmström
    Citation: BMC Bioinformatics 2019 20(Suppl 4):141
    Content type: Research Published on:

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

  37. The interplay between metabolic processes and signalling pathways remains poorly understood. Global, detailed and comprehensive reconstructions of human metabolism and signalling pathways exist in the form of ...

    Authors: Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M. T. Fleming, Andrei Zinovyev and Inna Kuperstein
    Citation: BMC Bioinformatics 2019 20(Suppl 4):140
    Content type: Research Published on:

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

  38. Pharmacogenomics (PGx) studies how genomic variations impact variations in drug response phenotypes. Knowledge in pharmacogenomics is typically composed of units that have the form of ternary relationships gene v...

    Authors: Pierre Monnin, Joël Legrand, Graziella Husson, Patrice Ringot, Andon Tchechmedjiev, Clément Jonquet, Amedeo Napoli and Adrien Coulet
    Citation: BMC Bioinformatics 2019 20(Suppl 4):139
    Content type: Methodology Published on:

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

    The Data Descriptor to this article has been published in Scientific Data 2020 7:3

  39. 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
    Content type: Research Published on:

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

  40. The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was “Methods, tools and platforms for Personalised Medicine in the Big Data Era”, bu...

    Authors: Paolo Romano, Arnaud Céol, Andreas Dräger, Antonino Fiannaca, Rosalba Giugno, Massimo La Rosa, Luciano Milanesi, Ulrich Pfeffer, Riccardo Rizzo, Soo-Yong Shin, Junfeng Xia and Alfonso Urso
    Citation: BMC Bioinformatics 2019 20(Suppl 4):125
    Content type: Introduction Published on:

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

  41. 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
    Content type: Software Published on:

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

  42. MicroRNAs (miRNAs) are small non-coding RNA molecules mediating the translational repression and degradation of target mRNAs in the cell. Mature miRNAs are used as a template by the RNA-induced silencing compl...

    Authors: Giovanni Perconti, Patrizia Rubino, Flavia Contino, Serena Bivona, Giorgio Bertolazzi, Michele Tumminello, Salvatore Feo, Agata Giallongo and Claudia Coronnello
    Citation: BMC Bioinformatics 2019 20(Suppl 4):120
    Content type: Research Published on:

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

  43. 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
    Content type: Research Published on:

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

  44. Amyotrophic lateral sclerosis (ALS) is an adult-onset neurodegenerative disease progressively affecting upper and lower motor neurons in the brain and spinal cord. Mean life expectancy is three to five years, ...

    Authors: Alessandro Zandonà, Rosario Vasta, Adriano Chiò and Barbara Di Camillo
    Citation: BMC Bioinformatics 2019 20(Suppl 4):118
    Content type: Methodology Published on:

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

  46. The rapid increase in High-throughput sequencing of RNA (RNA-seq) has led to tremendous improvements in the detection and reconstruction of both expressed coding and non-coding RNA transcripts. Yet, the comple...

    Authors: Thomas Gatter and Peter F Stadler
    Citation: BMC Bioinformatics 2019 20:190
    Content type: Methodology article Published on:

  48. The rapid growth of high-throughput sequencing-based microbiome profiling has yielded tremendous insights into human health and physiology. Data generated from high-throughput sequencing of 16S rRNA gene ampli...

    Authors: Nhan Thi Ho, Fan Li, Shuang Wang and Louise Kuhn
    Citation: BMC Bioinformatics 2019 20:188
    Content type: Software Published on:

  49. Malaria is a major global health problem, with the Plasmodium falciparum protozoan parasite causing the most severe form of the disease. Prevalence of drug-resistant P. falciparum highlights the need to understan...

    Authors: Ana M. Untaroiu, Maureen A. Carey, Jennifer L. Guler and Jason A. Papin
    Citation: BMC Bioinformatics 2019 20:186
    Content type: Research article Published on:

  50. Inexpensive high-throughput DNA sequencing has democratized access to genetic information for most organisms so that research utilizing a genome or transcriptome of an organism is not limited to model systems....

    Authors: Ousmane H. Cissé and Jason E. Stajich
    Citation: BMC Bioinformatics 2019 20:184
    Content type: Software Published on:

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