Curriculum Vitae

CAREER OBJECTIVE

To utilize my bioinformatics and computer engineering skills to tackle new challenges in a research or academic institute and contribute to the development and better understanding of science

EMPLOYMENT HISTORY
  • IMMUNOSCAPE PTE LTD, SINGAPORE (JULY 2017-PRESENT) 
    • Head, Bioinformatics
    • Key Responsibilities
      • Build and lead the Bioinformatics Team within immunoSCAPE. 
      • Lead the migration of existing in-house pipelines to the cloud. 
      • Develop web application platform for immunoprofiling experimental setup, data analysis and data sharing. 
      • Streamline and improve the analytical pipeline and software in terms of features, accuracy and runtime. 
      • Develop machine learning algorithms for meaningful high-dimensional data mining, including integration of different experimental and phenotypic datasets. 
      • Guide organization through the selection of innovative computing and cloud technologies.
 
    • HUMAN LONGEVITY SINGAPORE PTE LTD, SINGAPORE (MAY 2015-MAY 2017) 
      • Senior Bioinformatics Scientist Engineer 
      • Key Responsibilities
        • Key leadership role in development of Human Longevity Inc. (HLI) Knowledgebase, winner of Bio-IT Best Practices Award 2016. 
        • Communication bridge translating bioinformatics analyses into production ready software.
        • Development of novel algorithms for the integration and analysis of various omics data. 
        • Carried out association analyses with genomic (30K+ whole genome sequences, 600M+ variants), microbiomic, metabolomic, and phenotypic information. 
        • Guided the organization through the selection of innovative computing technologies. 
        • Utilized Amazon Web Services (AWS) infrastructures. 
        • Followed Agile development methodologies. (Scrum, Kanban) 
      • Key Achievements 
        • 2016 BioIT World Best Practice Award for HLI Knowledgebase. 
        • Launch of HLI Knowledgebase beta version to Pharma clients and Physicians. 
        • Development of genome browser for HLI’s internal use. 
        • Development of analysis service and novel visualizations for genomic and metabolomic pathways. 
        • Development of novel visualizations for microbiomic phylogenetic tree triggered by AWS Lambda. 
        • Development of the Genome Wallmap, a software to produce personalized posters with the graphical representation of an individual’s whole genome. 
        • Company-wide adoption of the Genome Wallmap for all HLI and Health Nucleus clients. 
        • Continuous development and deployment of a pipeline that manages genome annotation sources.
     
    • INSTITUTE OF COMPUTER SCIENCE, JOHANNES GUTENBERG UNIVERSITÄT MAINZ, GERMANY (APR 2012-MAY 2015)  
      • Postdoctoral Research Fellow 
      • Key Responsibilities 
        • Led development of cutting-edge bioinformatics algorithms and tools using High Performance Computing for Next Generation Sequencing (NGS) data. 
        • Key role in several important external collaborations (Institute of Molecular Biology Mainz, ). 
        • Teaching Assistant and Tutor for Parallel Algorithms and Architecture, Theoretische Grundlagen der Informatik I / Berechenbarkeit und Komplexität (Theoretical Computer Science) and Technische Informatik (Technical Computer Science). Class size is up to 210 students.
        • Instructor for Parallel Programming with CUDA Practicals. Class size of 10 students. 
      • Key Achievements 
        • Developed a ChIP-Seq analysis pipeline for peak detection with respect to repetitive DNA regions.
        • Developed HECTOR, a parallel error corrector for 454 NGS data. 
        • Developed CUDASW++, one of the most popular parallel Smith Waterman protein database search algorithm for GPGPUs using CUDA. 

    • YONG LOO LIN SCHOOL OF MEDICINE, NATIONAL UNIVERSITY OF SINGAPORE, SINGAPORE (NOV 2009-MAR 2012) 
      • Postdoctoral Research Fellow 
      • Key Responsibilities 
        • Led identification of genetic mutations and phenotypic changes associated with the development of in vitro and in vivo polymyxin resistance in paired clinical Acinetobacter baumannii isolates. 
        • Key role in several important external collaborations (Genome Institute of Singapore, Singapore General Hospital, Singapore Eye Research Institute). 
      • Key Achievements 
        • Developed a pipeline used by Genome Institute of Singapore (GIS) for sequence assembly, single-nucleotide polymorphism (SNP) calling and gene annotation. 
        • Developed a variable tandem repeat finder and visualization tool in collaboration with biologists for National University of Singapore and Singapore General Hospital. 
        • Genomic analysis and development of a new multilocus variable-number tandem-repeat analysis scheme for molecular epidemiological typing of Acinetobacter baumannii. 
        • Developed a machine learning algorithm to select features for computer-aided Angle Closure Glaucoma mechanism detection from images of patients’ eyes. 

    • SCHOOL OF COMPUTER ENGINEERING, NANYANG TECHNOLOGICAL UNIVERSITY (JUL 2005-OCT 2010)
      • Doctorate Degree (PhD) student
        • See Qualifications/Education below for details. 
      • Key Achievements
        • Developed fast parallel Smith Waterman and BLAST protein database search algorithms on the PlayStation 3. 
        • Developed a multi-threaded vectorized distance matrix computation on the Cell Broadband Engine and x86/SSE2 architectures. 

    • SCHOOL OF COMPUTER ENGINEERING, NANYANG TECHNOLOGICAL UNIVERSITY (JUL 2005-NOV 2009) 
      • Research Assistant 
      • Responsibilities 
        • Co-Supervisor of Final Year Undergraduate Students’ and Masters’ Projects. 
        • Laboratory Supervisor and Instructor for Introduction to Programming. Class size of 40 students.

    EDUCATION


    HONORS AND AWARDS
    • AWS Certified Developer, October 2015 - present
    • RSS Scholarship Award for Ph.D, Singapore, July 2005 – 2010
    • ASEAN Scholarship Award for B. Eng, Singapore, July 2001 – June 2005
    • NTU Cultural Activities Club (CAC) Merit Cultural Award, Singapore, 2003


    PUBLICATIONS

    Book Chapters
    1. A. Wirawan, C.K. Kwoh, L.Y. Hsu, T.H. Koh: INVERTER: INtegrated Variable numbER Tandem rEpeat findeR, Communications in Computer and Information Science, Volume 115, Part 4, pp. 151-164, Springer, 2010. DOI: 10.1007/978-3-642-16750-8_14. 
    2. A. Wirawan, B. Schmidt, C.K. Kwoh: Pairwise Distance Matrix Computation for Multiple Sequence Alignment on the Cell Broadband Engine,  Lecture Notes in Computer Science (LNCS), Vol. 5544, pp. 954-963, Springer, 2009. DOI: 10.1007/978-3-540-68111-3_132 
    3. A. Wirawan, B. Schmidt, C.K. Kwoh: Parallel DNA Sequence Alignment on the Cell Broadband Engine, Lecture Notes in Computer Science (LNCS),  Vol. 4967, pp. 1249-1256, Springer, 2008. DOI: 10.1007/978-3-642-01970-8_96

    Journals
    1. A. Wirawan, R.S. Harris, Y.Liu, B. Schmidt, J. Schröder: HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data. BMC Bioinformatics, 15:131, 2014.
    2. Y. Liu, A. Wirawan and B. Schmidt: CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions, BMC Bioinformatics, 14(117), 2013. Highly accessed 
    3. K.G. Lim, C.K. Kwoh, L.Y. Hsu, A. Wirawan: Review of Tandem Repeat Search Tools: A Systematic Approach to Evaluating Algorithmic Performance, Briefings in Bioinformatics, 14 (1): 67-81, 2013. (Impact factor: 5.202)
    4. A. Wirawan, C. K. Kwoh, P. T. K. Chew, M. C. D. Aquino, S. C. Loon, J. See, C. Zheng, W. Lin: Feature Selection for Computer-Aided Angle Closure Glaucoma Mechanism Detection, J. Med. Imaging Health Inf. Vol 2, No. 4, pp. 438-444, 2012
    5. A. Wirawan, C.K. Kwoh, B. Schmidt: Multi Threaded Vectorized Distance Matrix Computation on the Cell/BE and x86/SSE2 Architectures, Bioinformatics, Vol. 26, No. 10, pp. 1368-1369, 2010 (Impact factor: 5.468) 
    6. A. Wirawan, B. Schmidt, H. Zhang, C.K. Kwoh: High Performance Protein Sequence Database Scanning on the Cell B.E. Processor, Scientific Programming, Vol. 17, No. 1-2, pp. 97-111, 2009. 
    7. A. Wirawan, C.K. Kwoh, T.H. Nim, B. Schmidt: CBESW: Sequence Alignment on the Playstation 3, BMC Bioinformatics, Vol. 9:377, 2008 (Impact factor: 3.781). Highly accessed 

    International Conferences
    1. Z. Zhang, C.K. Kwoh, J. Liu, F. Yin, A. Wirawan, C. Cheung, M. Baskaran, T. Aung, T. Y. Wong: MRMR Optimized Classification for Automatic Glaucoma Diagnosis. 33rd Annual International IEEE EMBS Conference (EMBC 2011), Boston, MA, USA, 2011. Accepted for publication.
    2. N.T. Hieu, C.K. Kwoh. A. Wirawan, B. Schmidt: Applications of Heterogeneous Structure of Cell Broadband Engine Architecture for Biological Database Similarity Search, 2nd International Conference on Bioinformatics and Biomedical Engineering (iCBBE2008), IEEE Press, pp. 5-8, 2008.
    3. A. Wirawan, B. Schmidt: Parallel Discovery of Transcription Factor Binding Sites, IEEE Asia Pacific Conference on Circuits and Systems (APCCAS 2006), Singapore, IEEE Press, 2006.

    PROFESSIONAL ACTIVITIES

    COMPUTER SKILLS
    • Programming languages: C, C++, C#, Python, JavaScript, Scala, R, Matlab, SQL
    • Frameworks: .NET, ASP.NET MVC, Web API, Entity Framework, Node.js, AngularJS, ReactJS, Redux 
    • Data Visualization: D3.js, Cytoscape 
    • Applications: Docker, Spark, ElasticSearch, Samtools, Bcftools, GATK, WEKA, JetBrain Suite, MS Visual Studio, Eclipse, LaTeX
    • Platforms: Amazon Web Services (AWS), Windows/Windows Server, Linux, MacOS 
    • Agile methodology: Scrum, Kanban

    PERSONAL DATA
    • Indonesian Citizen, Singapore Permanent Resident (PR).
    • Open to relocation
    • Male, married, 34 years old.
    • Fluent in English, Malay and Bahasa Indonesia; Advance German (B1 Zertifikat Deutsch) and Introductory Chinese.
    • Hobbies: Football, Basketball, Travelling, Music.

    RESEARCH INTERESTS
    • Bioinformatics 
    • Sequence Analysis 
    • Genome Assembly
    • Tandem Repeats
    • High Performance Computing 
    • Parallel Algorithms and Architectures

    REFERENCES
    • Available upon request
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