TJU Professor Oversees Online Publication of Special Journal Issues

Prof. Feng GAO, the Executive Director of Tianjin University’s Center of Bioinformatics, recently supervised publication ofspecial issues for the scientific journals Briefings in Bioinformatics and Frontiers in Microbiology.

As the microbial genomic and functional genomic data increases exponentially, the scientific community is facing a major challenge to expound and understand the biological information expressed by the data. In the themed issue of Briefings in Bioinformatics, Prof. Gao invited the scientists who have made significant contributions in this field to review their influential work and discuss the upcoming challenges to further development.

This issue aims to provide a comprehensive overview of recent software and database developments in microbial genomics and functional genomics, including those for replication origin, prophage, operon, secondary metabolite biosynthetic gene clusters, antimicrobial resistance (AMR), orthologous genes/proteins, pathway/genome, genome visualization, metagenomic classification, assembly and analysis, and multiple sequence alignment. The articles in this themed issue have been consolidated into one collection available online at https://academic.oup.com/bib/pages/software_and_database_virtual_issue, and is promoted on the homepage ofBriefings in Bioinformatics.

As faculty members of F1000 Prime (a group that provides article recommendation service and up-to-date notifications and information about science),Prof Feng Gao and Prof. Burkhard Morgenstern from University of Göttingen, Germany, recommended three articles in this issue, which were contributed by Prof. Eugene V. Koonin (National Institutes of Health, Member of the National Academy of Sciences), Kazutaka Katoh (Osaka University) and Steven Salzberg (Johns Hopkins University, Fellow of the American Academy of Arts and Sciences) respectively. These articles were well-received by a wide international audience. Particularly, the article contributed by Prof. Katoh has been cited more than 550 times.

In thisthemedissue, as the corresponding author, Prof. Gao reviewed the recent development of Ori-Finder system and DoriC database for microbial replication origins. Based on the Z-curve method, Ori-Finder system was designed for the prediction of replication origins in bacterial and archaeal genomes with high accuracy and reliability.

The DoriC database was initially created to present the bacterial replication origins predicted by Ori-Finder or determined by experiments in 2007. Now, the DoriC database has become the most complete and scalable database of replication origins in prokaryotic genomes. The prediction results have been supported by a series of experimental research including those published in Nature and Science.

In addition, as Guest Editor, Prof. Gao organized the Research Topic "DNA Replication Origins in Microbial Genomes" for Frontiers in Microbiology in 2013. Given its previous success, Prof. Feng Gao together with Prof. Alan C. Leonard (Florida Institute of Technology) decided to revisit this Research Topic with a second edition, which is available athttps://www.frontiersin.org/research-topics/5862. Gratifyingly, the papers published in this topicseries were highly accessed, and the total views are around 100,000 now. In this issue, Prof. Gao presented a comprehensive study of budding yeast replication origins from both genome-wide and population genomics perspectives. At present, the first author of the article, Dan Wang, a PhD student from Tianjin University’s School of Science, has obtained a scholarship for six-month doctoral mobility at Université Nice Sophia Antipolis in France, and she is currently under the guidance of Prof. Gianni LITI, a well-known expert in population genomics of yeast.

By the School of Science

Editors: Eva Yin & Doris Harrington