(Pupacdi was previously spelled Phoophakdee.)

This site is no longer maintained. Please see my Current Website.

Email:
Chulabhorn Research Institute
Biomedical Science Building, FL 3
54 Moo 4, Vibhavadee-Rangsit Highway
Laksi, Bangkok, Thailand 10120

Research Interest: Bioinformatics and Data Mining

Education

Ph.D., Computer Science, August 2007.
Rensselaer Polytechnic Institute, Troy, NY, USA
Advisor: Prof. Mohammed J. Zaki Homepage

M.S., Computer Science, May 2002.
Rensselaer Polytechnic Institute, Troy, NY, USA

B.S., Computer Science, May 2000.
Johns Hopkins University, Baltimore, MD, USA

High school, May 1996.
The Peddie School, Hightstown, NJ, USA

Software

• NSIT
• TRELLIS

Publications

• J. Chaisaingmongkol, A. Budhu, H. Dang, S. Rabibhadana, B. Pupacdi, M. Forgues, V. Bhudhisawasdi, N. Lertprasertsuke, A. Chotirosniramit, C. Pairojkul, C. U. Auewarakul, T. Sricharunrat, K. Phornphutkul, S. Sangrajrang, M. Cam, P. He, S. M. Hewitt, X. Wu, S. S. Thorgeirsson, P. S. Meltzer, C. A. Loffredo, R. H. Wiltrout, C. C. Harris, C. Mahidol, M. Ruchirawat, X. W. Wang; on behalf of the TIGER-LC Consortium, Race/Ethnicity-related Common Molecular Subtypes among Asian Cholangiocarcinoma and Hepatocellular Carcinoma Identified by Integrated Genomics, Cancer Cell, 2017 (Impact Factor 23.2) Link to Paper
• Pupacdi B, Javed A, Zaki MJ, Ruchirawat M (2014) NSIT: Novel Sequence Identification Tool. PLoS ONE 9(9): e108011. doi:10.1371/journal.pone.0108011 (Corresponding Author) Link to Paper
• M. S. Yin, S. Tangsripairoj, and B. Pupacdi, Variable Length Motif-based Time Series Classification, The 10th International Conference on Computing and Information Technology, May, 2014
• K. Sirikanchana, U. Wongpijit, B. Pupacdi, and S. Mongkolsuk, Genomic Differences between Human-specific and Non-specific Strains of Bacteriophages of Bacteroides fragilis as Fecal Source Identifiers, 1st International Conference on Environmental Science, Engineering and Management, Environmental Engineering Association of Thailand, March 2012.
• M. Al Hasan, S. Salem, B. Pupacdi, and M. Zaki, Clustering with Lower Bound on Similarity, Proceedings of Pacic-Asia Conference on Knowledge Discovery and Data Mining, April 2009. (Best Paper Award)
• B. Phoophakdee and M. Zaki, TRELLIS+: An Effective Approach for Indexing Massive Sequence, Pacic Symposium on Biocomputing, January 2008.
• B. Phoophakdee and M. Zaki, Genome-scale Disk-based Suffix Tree Indexing, ACM SIGMOD International Conference on Management of Data, June 2007.
• M. Zaki, N. Parimi, N. De, F. Gao, B. Phoophakdee, J. Urban, V. Chaoji, M. Hasan, and S. Salem, Towards Generic Pattern Mining, International Conference on Formal Concept Analysis, February 2005. (Shorter version published as an invited paper in Pattern Recognition and Machine Intelligence)
• M. Zaki, N. De, F. Gao, P. Palmerini, N. Parimi, J. Pathuri, B. Phoophakdee, and J. Urban, Generic Pattern Mining Via Data Mining Template Library, Constraint-Based Mining and Inductive Databases, 2004

Presentations

• The TIGER-LC Consortium, Jittiporn Chaisaingmongkol, Anuradha Budhu, Hien Dang, Siritida Rabibhadana, Benjarath Pupacdi, Marshonna Forgues, Vajarabhongsa Bhudhisawasdi, Nirush Lertprasertsuke, Anon Chotirosniramit, Chawalit Pairojkul, Chirayu U. Auewarakul, Thaniya Sricharunrat, Kannika Phornphutkul, Suleeporn Sangrajrang, Maggie Cam, Ping He, Stephen M. Hewitt, Xiaolin Wu, Snorri S. Thorgeirsson, Paul S. Meltzer, Christopher A. Loffredo, Robert H. Wiltrout, Curtis C. Harris, Chulabhorn Mahidol, Mathuros Ruchirawat, Xin W. Wang, The Thailand initiative in genomics and expression research for liver cancer (TIGER-LC): Defining novel subtypes of hepatocellular carcinoma and cholangiocarcinoma, Oral presentation at the American Association for Cancer Research Annual Meeting, April, 2015, Philadelphia.
• Pupacdi B, Javed A, Zaki M J, Ruchirawat M, Improving the accuracy of novel sequence search in de novo human genomes with NSIT, Poster presented at the 63th Annual Meeting of The American Society of Human Genetics, October, 2013, Boston.
• Pupacdi B, Javed A, Zaki M J, Ruchirawat M, Fast and Accurate Identification of Novel Sequences in de novo Human Genome Assemblies using NSIT, Poster presented at the 62th Annual Meeting of The American Society of Human Genetics, November, 2012, San Francisco.
• Jinawath N, Pupacdi B, Wohler E, Charoensawan V, Wattanasirichaigoon D, Identification of a causative variant underlying nonsyndromic autosomal-dominant intellectual disability in an extended family, Poster presented at the 62th Annual Meeting of The American Society of Human Genetics, November, 2012, San Francisco.
• Jinawat N, Pupacdi B, Wohler E, Chuansumrit A, Wattanasirichaigoon D, Identification of a Causative Variant Underlying an Unknown Genetic Syndrome Presenting with Blue Irides, Platelet Disorder, Hearing Loss, and Developmental Delaying Nonsyndromic Autosomal-Dominant Intellectual Disability in a Large Thai Family, Days of Molecular Medicine 2012, October 2012, Vienna.
• Pupacdi B, Javed A, Zaki M J, NSIT: Novel Sequence Identification Tool (abstract/program #1743/W) Poster presented at the 60th Annual Meeting of The American Society of Human Genetics, November 3, 2010, Washington DC.

Invited Talks

• A fast and accurate approach to detect novel sequences in a de novo human genome assembly, Structure Discovery in Biology: Motifs, Networks & Phylogenies Seminar, SchlossDagstuhl, Saarbrucken, Germany, June 2010
• A software for scalable and efficient comparison of multiple human genome assemblies, Harvard School of Public Health, Harvard University, Boston, USA, October 2009

Grants

• Thailand Research Fund - Young Investigator Grant PI Pupacdi, 360,000 THB (12K USD Approx.), 2009-2011
• National Science and Technology Development Agency, Thailand - Young Investigator Grant PI Pupacdi, 250,000 Bahts (8,300 USD approx.), 2010-2011

Professional Activities

• Program Committee of the 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM’ 2015), Washington DC, USA, November, 9-12, 2015
• Program Committee of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM’ 2014), Belfast, UK, November, 2-5, 2014
• Career Committee for the 2014 Grace Hopper Celebration of Women in Computing Conference, Phoenix, AZ, USA, October 8-11, 2014
• Program Committee of the 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM’ 2013), Shanghai, China, December 18-21, 2013
• Poster Committee for the 2013 Grace Hopper Celebration of Women in Computing Conference, Minneapolis, MN, USA, October 2-5, 2013
• Program Committee of the 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM’ 2012), Philadelphia, USA, October 4-7, 2012
• Program Committee of the 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM’ 2011), Altanta, GA, USA, Nov. 12-15, 2011
• Member of the American Society of Human Genetics, 2009 – 2014
• A committee member for M.S. and Ph.D. students, Faculty of Information and Communication Technology, Mahidol University

Served as a reviewer for the followings:

• Bioinformatics Journal 2009
• Pacific-Asia Conference on Knowledge Discovery and Data Mining 2007
• Data Warehousing and Knowledge Discovery 2007
• Principles and Practice of Knowledge Discovery in Databases 2007
• SIAM Data Mining Conference 2006
• Pacific-Asia Conference on Knowledge Discovery and Data Mining 2006
• IEEE International Symposium on Computer-Based Medical Systems 2006
• International Conference on Management of Data 2006
• Workshop on Ontology Mining and Knowledge Discovery from Semistructured documents 2006

Personal: Married to Asif Javed, Ph.D.