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
- HUMAN LONGEVITY SINGAPORE PTE, SINGAPORE (MAY 2015-PRESENT)
- 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- 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.
- 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
- 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- 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.
- 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.
 - 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)
- 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
- 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)
- 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.
- 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).
International Conferences- 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.
- 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.
- 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
- Invited Reviewer:
- Service on Editorial Board and Program Committees:
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, 33 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
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