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A bioinformatics potpourri

Abstract

The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics. New Delhi will be the location of InCoB2018, scheduled for September 26–28, 2018.

Introduction

InCoB2017 was co-organized by The University of Technology Sydney, Tsinghua University, Graduate School at Shenzhen and APBioNet [1]. Six keynote and two invited talks covered the latest bioinformatics applications and big data developments in basic and applied biomedical research. The theme of big data-driven bioinformatics and precision medicine was highlighted in a panel discussion on its current status and future. Jianzhu Chen (Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology) presented bioinformatics-driven immunological research towards the identification of transcription factors in memory CD8+ T cell development, and the screening of bioactive and natural compounds that are able to induce human macrophages into either inflammatory or anti-inflammatory states. Yuelong Shu of the School of Public Health (Shenzhen) at Sun Yat-sen University and WHO Collaborating Center for Reference and Research on Influenza demonstrated how large-scale sequencing of human influenza virus in combination with antigenic surveillance of hemagglutinin using the computational platform PREDAC improved vaccine strain recommendations for China.

Single cell RNA sequencing can reveal small differences among cells which are important to know in understanding of cellular responses to signals and variations among one cell type. Yong Hou (BGI-Shenzhen) gave in his invited talk a comprehensive overview of single cell sequencing, its application in cancer research and potential to improve cancer diagnosis. Limsoon Wong (National University of Singapore) provided insight into reproducibility and coverage issues of mass spectrometry-based proteomics data, and introduced algorithms that produce more robust and biologically meaningful proteomic profiling results.

Two keynotes covered epigenetic modifications in embryonic stem cells from the perspectives of miRNA regulation and networks of chromatin-related proteins. Xiujie Wang (Institute of Genetics and Developmental Biology, Chinese Academy of Sciences) reported on clusters of miRNAs that were positively correlated with the pluripotency level of embryonic stem cells. One of the miRNAs was involved in a new form of mRNA regulation through N6-methyladenosine modification. Alfonso Valencia (Barcelona Supercomputing Center) concentrated in his talk on network-based approaches in epigenomics, evolution and biomedicine on the role of 5-hydroxymethylcytosine as a communication hub in the chromatin network of embryonic stem cells, and concluded with a network property analysis that revealed inverse as well as direct co-morbidities between Alzheimer’s disease, glioblastoma and lung cancer.

Saman Halgamuge (The Australian National University) and Mindy Shi (University of North Carolina at Charlotte) offered in their presentations an impressive demonstration of deep learning applications. Saman Halgamuge showed in his keynote successful applications of unsupervised deep learning in the areas of direct drug-brain interactions, drug repositioning and multi-electrode array workflow applications for screening pharmacological compounds. Mindy Shi utilized deep learning to construct predictive models for quantitative trait locus network analysis using genomic and interactome data.

The Annual General Meeting of APBioNet on September 20th was opened with the President’s Report. Among the reporting items was a new simplified membership fee structure with details available at APBioNet website [2], and plans to utilize BioRxiv preprint server [3] and its feature to transfer manuscripts to partnering journals for article submissions related to InCoB or InSyB (International Symposium of Bioinformatics). The winner of the bid for InCoB2018, Shandar Ahmad, introduced next year’s conference venue at Jawaharlal Nehru University, New Delhi [4]. Jim Hogan (Queensland University of Technology) presented an Expression of Interest (EOI) to host InCoB2019 or InCoB2020 at Gold Coast, Australia. Parties interested in hosting InCoB or InSyB as stand-alone, joint or back-to-back events are encouraged to submit an EOI through APBioNet’s website [5].

Manuscript submission and review

In total 152 manuscripts were submitted through EasyChair conference management system [6] for consideration for publication as InCoB2017 supplement articles in Bioinformatics, BMC Genomics, BMC Bioinformatics, BMC Systems Biology, BMC Medical Genomics, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Journal of Bioinformatics and Computational Biology (JBCB) or PeerJ. After peer review by at least two reviewers of the Program Committee comprising 121 members, supported by 27 external sub-reviewers (Additional file 1), 65 (42.7%) manuscripts were provisionally accepted in revised form before the conference, pending final editorial approval. Fifty-seven articles are published in InCoB2017 supplement issues of BMC Bioinformatics (22) BMC Medical Genomics (7), BMC Systems Biology (14) and BMC Genomics (14). Eight articles will appear in PeerJ (1), JBCB (3), TCBB (3) and Bioinformatics (1). Best Paper Awards in the categories Gold, Silver and Bronze were given to authors of 28 manuscripts (Additional file 2). The articles included in the four BMC supplement issues are briefly summarized in Table 1 according to 12 topic groups arranged in alphabetical order.

Table 1 Summary of articles arranged by topic groups

Conclusion

The potpourri of bioinformatics research output showcased at InCoB2017 reflects APBioNet’s goal to cater to a diverse range of practitioners and developers in the field. One of the highly cited articles of the InCoB conference series is an evaluation of human protein-protein interaction data in the public domain by Mathivanan et al. [7] with an average of ten citations per year. The paper was presented at InCoB2006 in New Delhi where next year’s conference will be held.

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Acknowledgements

We thank all reviewers and volunteering students and staff of Graduate School at Shenzen, Tsinghua University for their time and effort. We also thank Precision Medicine Research Center of Taihe Hospital (Hubei), School of Public Health (Shenzhen) at Sun Yat-sen University, School of Electrical and Information Engineering at Anhui University of Technology and International Society for Computational Biology for supporting InCoB2017.

Funding

The publication charge for this article was funded by APBioNet Ltd., Singapore. The funder had no role in the decision to publish or preparation of the manuscript.

Availability of data and materials

Not applicable.

About this supplement

This article has been published as part of BMC Genomics Volume 19 Supplement 1, 2018: 16th International Conference on Bioinformatics (InCoB 2017): Genomics. The full contents of the supplement are available online at https://bmcgenomics.biomedcentral.com/articles/supplements/volume-19-supplement-1.

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CS and SR wrote manuscript. JL and LM organized the conference. CS, PH, MFS and SR managed reviewer assignments and communication with authors. All authors read and approved the final manuscript.

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Correspondence to Christian Schönbach or Shoba Ranganathan.

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CS, PH and MFS are elected office bearers of APBioNet. SR is a member of the Board of Directors of APBioNet Ltd., Singapore. All other authors have declared that no competing interests exist.

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Additional files

Additional file 1:

List of InCoB2017 Reviewers. (PDF 52 kb)

Additional file 2:

InCoB2017 Best Paper Awards. (PDF 73 kb)

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Schönbach, C., Li, J., Ma, L. et al. A bioinformatics potpourri. BMC Genomics 19, 920 (2018). https://doi.org/10.1186/s12864-017-4326-x

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Keywords

  • InCoB
  • International conference on bioinformatics
  • APBioNet
  • Asia-Pacific bioinformatics network