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Abstract
Since the large-scale experimental characterization of protein–protein interactions (PPIs) is not possible for all species, several computational PPI prediction methods have been developed that harness existing data from other species. While PPI network prediction has been extensively used in eukaryotes, microbial network inference has lagged behind. However, bacterial interactomes can be built using the same principles and techniques; in fact, several methods are better suited to bacterial genomes. These predicted networks allow systems-level analyses in species that lack experimental interaction data. This review describes the current network inference and analysis techniques and summarizes the use of computationally-predicted microbial interactomes to date.
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Ko G, Kim PG, Cho Y, Jeong S, Kim JY, Kim KH, Lee HY, Han J, Yu N, Ham S, Jang I, Kang B, Shin S, Kim L, Lee SW, Nam D, Kim JF, Kim N, Kim SY, Lee S, Roh TY, Lee B. Bioinformatics services for analyzing massive genomic datasets. Genomics Inform 2020; 18:e8. [PMID: 32224841 PMCID: PMC7120352 DOI: 10.5808/gi.2020.18.1.e8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/11/2020] [Indexed: 11/25/2022] Open
Abstract
The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and ensuing computational problems. In Korea, the amount of genomic data has been increasing rapidly in the recent years. Leveraging these big data requires researchers to use large-scale computational resources and analysis pipelines. A promising solution for addressing this computational challenge is cloud computing, where CPUs, memory, storage, and programs are accessible in the form of virtual machines. Here, we present a cloud computing-based system, Bio-Express, that provides user-friendly, cost-effective analysis of massive genomic datasets. Bio-Express is loaded with predefined multi-omics data analysis pipelines, which are divided into genome, transcriptome, epigenome, and metagenome pipelines. Users can employ predefined pipelines or create a new pipeline for analyzing their own omics data. We also developed several web-based services for facilitating downstream analysis of genome data. Bio-Express web service is freely available at https://www.bioexpress.re.kr/.
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Affiliation(s)
- Gunhwan Ko
- Korea Bioinformation Center (KOBIC), KRIBB, Daejeon 34141, Korea
| | - Pan-Gyu Kim
- Korea Bioinformation Center (KOBIC), KRIBB, Daejeon 34141, Korea
| | - Youngbum Cho
- Genome Editing Research Center, KRIBB, Daejeon 34141, Korea
| | - Seongmun Jeong
- Genome Editing Research Center, KRIBB, Daejeon 34141, Korea
| | - Jae-Yoon Kim
- Genome Editing Research Center, KRIBB, Daejeon 34141, Korea
| | | | - Ho-Yeon Lee
- Genome Editing Research Center, KRIBB, Daejeon 34141, Korea
| | - Jiyeon Han
- Department of BioInformation Science, Ewha Womans University, Seoul 03760, Korea
| | - Namhee Yu
- Department of BioInformation Science, Ewha Womans University, Seoul 03760, Korea
| | - Seokjin Ham
- Department of Life Sciences and Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Insoon Jang
- Department of Life Sciences and Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Byunghee Kang
- Department of Life Sciences and Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea
| | - Sunguk Shin
- Department of Systems, Biology Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Lian Kim
- Bioposh Inc., Daejeon 34016, Korea
| | | | - Dougu Nam
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Jihyun F Kim
- Department of Systems, Biology Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.,Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, Seoul 03722, Korea
| | - Namshin Kim
- Genome Editing Research Center, KRIBB, Daejeon 34141, Korea
| | - Seon-Young Kim
- Genome Structure Research Center, KRIBB, Daejeon 34141, Korea
| | - Sanghyuk Lee
- Department of BioInformation Science, Ewha Womans University, Seoul 03760, Korea
| | - Tae-Young Roh
- Department of Life Sciences and Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang 37673, Korea.,SysGenLab Inc., Pohang 37613, Korea
| | - Byungwook Lee
- Korea Bioinformation Center (KOBIC), KRIBB, Daejeon 34141, Korea
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