วรรณวิภา วงศ์แสงนาค

t28

Name: Dr. Wanwipa Vongsangnak

Tel. + 66 2 5625555 ext. 647818

E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it., This email address is being protected from spambots. You need JavaScript enabled to view it.

Nationality: Thai

Current Position: Associate Professor

Education

-   Ph.D. in Bioscience (Teknologie Doctor/Bioengineering), Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden, 2009.

-    M.Sc. in Bioinformatics (First honor), School of Bioresources and Technology and School of Information Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand, 2006.

-     B.Sc. in Biotechnology (First honor), Faculty of Science, Mahidol University, Bangkok, Thailand, 2004.

Employment

-          Associate Professor, Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand

-          Associate Professor, Center for Systems Biology, Soochow University, Suzhou, China

-          Visiting Professor, Department of Computer Science, School of Computing, National University of Singapore (NUS), Singapore

-          Visiting Professor, Systems Biology Group, King Mongkut'sUniversity of Technology Thonburi (KMUTT), Thailand

-          Post-Doc, Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden

-          Research Assistant, Department of Systems Biology, Technical University of Denmark, Denmark.

Scholarships and Grants

2014            Visiting professor from King Mongkut'sUniversity of            

                  Technology Thonburi (KMUTT), Thailand.

2013          Visiting Professor, National University of Singapore (NUS), Singapore.

2013          National Science Foundation of China (NSFC)

(No. 31200989 and No. K124810312)

2012          Visiting professor from King Mongkut'sUniversity of            

                  Technology Thonburi (KMUTT), Thailand.

2011           Initial grant from Soochow University (No. Q410700111)

2008          Full Scholarship in Bioscience Program, Chalmers University of Technology,

                  Sweden.

2006           Full Scholarship in Biotechnology Program, Technical University of Denmark

                   and Novozymes Bioprocess Academy, Denmark.

2003          Full Scholarship in Bioinformatics Program, King Mongkut’s University of

                  Technology Thonburi, Thailand.

2002          Student scholarship in Biological Engineering Program, East China University of

                   Science and Technology, China.

2000          Student Scholarship in Universal Cultural Exchange Program, New Zealand.                                       

International Journals

Editor

-          Translational Biomedical Informatics and Computational Systems Medicine

Academic Editor

-          International Journal of Genomics

Reviewer

-          Microbiology

-          BMC Research Notes

-          Translational Biomedical Informatics and Computational Systems Medicine

-          The journal BBA - General Subjects

Research Interests

-          Bioinformatics techniques and analysis

-          Multilevel –omics data analysis and integrations (Systems Biology approach)

-          Biological networks analysis, graph theory and topology

-          Comparative genomics and transcriptomics analysis

-          Biological sequence analysis

-          Molecular biology

-          DNA Microarray

 

1. List of Publications

Books publication:

Vongsangnak W, Nielsen J. Systems biology methods and developments for filamentous fungi in relation to the production of food ingredients. Microbial production of food ingredients, enzymes and nutraceuticals. Woodhead Publishing Ltd. 2013.

Vongsangnak. W, Nielsen. J. Systems Biology of Aspergilli: Molecular Biology and Genomics, Horizon Scientific Press 2010. 61-83.

Vongsangnak. W. SYSBIOMICS of Aspergilli: SYStems Biology, BIoinformatics and OMICS analysis of Aspergilli cell factories, Ph.D. thesis 2009, Chalmers University of Technology, Sweden.

Articles publication:

 

Vongsangnak W, Raethong N, Mujchariyakul W, Nguyen NN, Leong HW, Laoteng K. Genome-scale metabolic network of Cordyceps militaris useful for comparative analysis of entomopathogenic fungi. Gene. 2017 Aug 30;626:132-139.

Vongsangnak W, Chumnanpuen P, Sriboonlert A(2016) Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae).PeerJ 4:e2534.

Raethong N, Wong-Ekkabut J, Laoteng K, Vongsangnak W (2016) Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study. Biomed Res Int: 8124636. doi: 10.1155/2016/8124636.

Patumcharoenpol P, Doungpan N, Meechai A, Shen B, Chan JH, Vongsangnak W (2016) An integrated text mining framework for metabolic interaction network reconstruction. PeerJ 4:e1811. doi: 10.7717/peerj.1811.

Vongsangnak W, Klanchui A, Tawornsamretkit I, Tatiyaborwornchai W, Laoteng K, Meechai A. (2016) Genome-scale metabolic modeling of Mucor circinelloides and comparative analysis with other oleaginous species. Gene 583(2):121-9. doi: 10.1016/j.gene.2016.02.028.

Xiao F, Yang M, Xu Y, Vongsangnak W (2015) Comparisons of Prostate Cancer Inhibitors Abiraterone and TOK-001 Binding with CYP17A1 through Molecular Dynamics. Comput Struct Biotechnol J 13:520-7. doi: 10.1016/j.csbj.2015.10.001.

Nguyen NN#, Vongsangnak W#, Shen B, Nguyen P, Leong HW. Megafiller: A Retrofitted Protein Function Predictor for Filling Gaps in Metabolic Networks, Journal of Proteomics and Bioinformatics S9: 003.

Li Y*, Vongsangnak. W*, Chen. L, Shen B. (2014) Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression, BMC Medical Genomics 7. (Suppl 1):S3.

Huang M, Wattanachaisaereekul S, Han Y, Vongsangnak W# (2014) In silico analysis of plant and animal transposable elements, International Journal of Bioinformatics Research and Applications 10:297-306. (Scopus (Elsevier), SJR: Q3)

Jiang J, Cui W, Vongsangnak W, Hu G, Shen B. (2013) Post genome-wide association studies functional characterization of prostate cancer risk loci, BMC Genomics 14: Suppl 8:S9.

Zhao Z, Shen B, Lu X, Vongsangnak W. (2013) Translational biomedical informatics and computational systems medicine, Biomed Research International, 237465.

Vongsangnak W#, Ruenwai R, Xin T, Xinjie H, Hao Z, Shen B, Song Y, Laoteng K#. (2013) Genome-scale analysis of the metabolic networks of oleaginous Zygomycete fungi, Gene, 25: 180-190.

Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J (2013) The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum, PLoS Computational Biology 9: e1002980.

Zhu F, Patumcharoenpol P, Zhang C, Yang Y, Chan J, Meechai A, Vongsangnak W, Shen B (2013) Biomedical text mining and its applications in cancer research, Journal of Biomedical Informatics46: 200-211.

Klanchui A, Vorapreeda T, Vongsangnak W, Kannapho C, Cheevadhanarak S, Meechai A (2012) Systems biology and metabolic engineering of Arthrospira cell factories, Computational and Structural Biotechnology Journal 3: e201210015.

Patumcharoenpol P, Chan J, Meechai A, Shen B, Vongsangnak W# (2012) Bibliome Mining Platform and Application for Building Metabolic Interaction Network, Procedia Computer Science 11: 55-62.

Geijer C, Pirkov I, Vongsangnak W, Ericsson A, Nielsen J, Krantz M, Hohmann S (2012) Time course gene expression profiling of yeast spore germination reveals a network of transcription factors orchestrating the global response, BMC Genomics 13: 554.

Nijkamp JF, van den Broek M, Datema E, de Kok S, Bosman L, Luttik MA, Daran-Lapujade P, Vongsangnak W, Nielsen J, Heijne WH, Klaassen P, Paddon CJ, Platt D, Kötter P, van Ham RC, Reinders MJ, Pronk JT, de Ridder D, Daran JM (2012) De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology, Microbial Cell Factories 11:36.

Li Y, Zhang Z, Liu F, Vongsangnak W, Jing Q, Shen B (2012) Performance comparison and evaluation of software tools for microRNA deep sequencing data analysis, Nucleic Acid Research 40:4298-305.

Vongsangnak W, Zhang Y, Chen W, Ratledge C, Song Y (2012) Annotation and analysis of malic enzyme genes encoding for multiple isoforms in the fungus Mucor circinelloides CBS 277.49, Biotechnology Letter 34: 941-947.

Vongsangnak W, Figueiredo L F, Forster J, Weber T, Thykaer J, Stegmann E, Wohlleben, W, Nielsen J (2012) Genome-Scale Metabolic Representation of Amycolatopsis balhimycina. Biotechnology and Bioengineering 109:1798-807.

Hong K, Vongsangnak W, Vemuri G, Nielsen J (2011) Unraveling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis. Proceedings of the National Academy of Sciences108: 12179-12184.

Vongsangnak W, Hansen K, Nielsen J (2011) Integrated analysis of the global transcriptional response to α-amylase over-production by Aspergillus oryzae. Biotechnology and Bioengineering 108: 1130-1139.

Rokem S, Vongsangnak W, Nielsen J (2011) Comparative metabolic capabilities for Micrococcus luteus NCTC 2665, the “Fleming” Strain, and Actinobacteria. Biotechnology and Bioengineering 108: 2270-2275.

Piddocke M, Fazio A, Vongsangnak W, Wong M, Heldt-Hansen H, Workman C, Nielsen J, Olsson L (2011) Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using “–omics” techniques, Microbial Cell Factories 10: 27.

Ruenwai R, Neiss A, Laoteng K, Vongsangnak W, Dalfard A, Cheevadhanarak S, Petranovic D, Nielsen J (2011) Heterologous production of polyunsaturated fatty acids in Saccharomyces cerevisiae causes a global transcriptional response resulting in reduced proteasomal activity and increased oxidative stress. Biotechnology Journal  6: 343-356.

Otero J*, Vongsangnak W*, Asadollahi M, Olivares R, Maury J, Farinelli L, Barlocher L, Schalk M, Clark A, Nielsen J (2010) Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications, BMC Genomics 11: 723.

Cvijovic M, Olivares R, Agren R, Dahr N, Vongsangnak W, Nookaew I, Patil K, Nielsen J (2010) BioMet Toolbox: genome-wide analysis of metabolism, Nucleic Acid Research 38: W144–W149.

Vongsangnak W, Nookaew I, Salazar M, Nielsen J (2010) Analysis of genome-wide co- expression and co-evolution of Aspergillusoryzae and Aspergillusniger. OMICS A journal of Integrative Biology 14: 165-175.

Vongsangnak W*, Salazar M*, Hansen H, Nielsen J (2009) Genome-wide analysis of maltose utilization and regulation in aspergilli, Microbiology 155: 3893-3902.

Salazar M*, Vongsangnak W*, Andersen M, Panagiotou G, Nielsen J (2009) Uncovering transcriptional regulation of glycerol metabolism in aspergilli through genome-wide gene expression data analysis. Molecular Genetics and Genomics 282: 571-586.

Andersen M, Vongsangnak W, Panagiotou G, Margarita S, Lehmann L, Nielsen J (2008) A tri-species Aspergillusmicroarray - advancing comparative transcriptomics. Proceedings of the National Academy of Sciences105: 4387-4392.

Vongsangnak W, Olsen P, Hansen K, Krogsgaard S, Nielsen J (2008) Improved annotation through genome-scale metabolic modeling of Aspergillusoryzae. BMC Genomics 9: 245.

Vongsangnak W, Gua J, Chauvatcharin S, Zhong J J (2004) Towards efficient extraction of notoginsengsaponins from cultured cells of Panaxnotoginseng. Biochemical Engineering Journal 18:115–120.

 

2. Conference publications/presentations

Vongsangnak. W, Olsen. P, Krogsgaard. S, Nielsen. J. Genome annotation and metabolic network construction of Aspergillus oryzae. The International Conference on Systems Biology (ICSB), Yokohama, Japan, 2006. Poster presentation.

Vongsangnak. W, Olsen. P, Krogsgaard. S, Nielsen. J. Bioinformatics based annotation and

metabolic model of Aspergillus oryzae. Eurofung, Wageningen, Netherlands, 2007. Poster

presentation.

Vongsangnak. W, Olsen. P, Krogsgaard. S, Nielsen. J. Annotation and validation through

genome-scale metabolic model of Aspergillus oryzae. 3rd European Federation of Biotechnology, Conference Physiology of Yeasts and Filamentous Fungi PYFF3, Helsinki, Finland, 2007. Poster presentation

Vongsangnak. W, Nielsen, J. Annotation and metabolic modelling, Bio-functions, Bremen, Germany, 2007, Oral presentation

Vongsangnak. W, Olsen. P, Krogsgaard. S, Nielsen. J. Beyond genome annotation: Building efficient cell factory for Aspergillus oryzae. Eurofung, Edinburg, Scotland, 2008. Oral presentation.

Vongsangnak. W, Olsen. P, Krogsgaard. S, Nielsen. J. Beyond genome annotation: Building efficient cell factory for Aspergillus oryzae. Arperfest and ECFG9, Edinburg, Scotland, 2008. Poster presentation.

Vongsangnak. W. Beyond genome annotation: Building efficient cell factory for Aspergillus oryzae. Systems Biology: From model organisms to applications (Nordforsk), Copenhagen, Denmark, 2008. Oral presentation.

Vongsangnak. W, Olsen. P, Hansen, K, Krogsgaard. S, Nielsen. J. Constructing Aspergillus oryzae as an efficient cell factory for protein production. The International Conference on Systems Biology (ICSB), Sweden, 2008. Poster presentation.

Vongsangnak. W, Olsen. P, Hansen, K, Krogsgaard. S, Nielsen. J. Building Aspergillus oryzae as an efficient cell factory for protein production. Biotechnology for Sustainability of Human Society (IBS), China, 2008. Poster presentation.

Salazar M, Vongsangnak. W, Nielsen J. Uncovering transcriptional regulation of glycerol metabolism in aspergilli through genome-wide gene expression data analysis. Fungal Biology and Biotechnology in the Genomic Era, Barcelona, Spain, 2008. Oral presentation.

Vongsangnak. W. Bioinformatics and systems biology of Aspergillus oryzae. The 9th annual Swedish bioinformatics workshop, Umeå, Sweden, 2009. Poster presentation.

Vongsangnak. W. Bioinformatics. Pan Fungal Data Resources Strategy Meeting, Washington DC metropolis, United States, 2010.

Vongsangnak. W. Systems Biology and Bioinformatics of Aspergillus oryzae. The 10th annual Swedish bioinformatics workshop, Göteborg, Sweden, 2010. Oral presentation.

Vongsangnak. W. Systems Biology, Bioinformatics and Omics analysis of Aspergillus oryzae and Saccharomyces cerevisiae. Systems Biology of Microorganisms Conference, Paris, France, 2010. Oral presentation.

Vongsangnak. W. Systems Biology of Fungal Cell Factories: From Sequence to Metabolism and Physiology, BIT's 2nd World DNA and Genome Day 2011, Dalian, China. Oral presentation.

Vongsangnak. W. 11th International Conference on Bioinformatics (InCoB) 2012, Bangkok, Thailand. Chairman (Systems biology section).

Nguyen. NN, Vongsangnak. W, Leong. HW. Retrofitting functional prediction methods to fill gaps in metabolic networks. Recomb 2013, Beijing, China. Poster presentatiom.

Li. Y*, Vongsangnak. W*, Chen. L, Shen. B. Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression. 3thTBC/ISCB-Asia 2013, Seoul, Korea. Oral presentation.

*Co-first authors

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