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Kridsadakorn Chaichoompu - Publications ORBI
Chaichoompu, K., Abegaz Yazew, F., Tongsima, S., Shaw, P. J., Sakuntabhai, A., Pereira, L., & Van Steen, K. (in press). IPCAPS: an R package for iterative pruning to capture population structure. Bioinformatics : Application Notes.
Resolving population genetic structure is challenging, especially when dealing with closely related populations. Although Principal Component Analysis (PCA)-based methods and genomic var- iation with single ...
Chaichoompu, K. (2017). Capturing fine-scale population structure towards molecular reclassification of patients. Unpublished doctoral thesis, Université de Liège, ​Liège, ​​Belgique.
During the past decades, population structure analysis has been playing an important role for stratifying populations and tracking back population ancestries. Population structure is mainly due to non-random ...
Chaichoompu, K., Yazew, F. A., Tongsima, S., Shaw, P. J., Sakuntabhai, A., Pereira, L., & Van Steen, K. (2017, July 10). Determining fine population structure using iterative pruning. Poster session presented at Drug Discovery & Therapy World Congress 2017, Boston, USA.
SNP-based information is used in several existing clustering methods to detect shared genetic ancestry or to identify population substructure (Price et al. 2006, Raj et al. 2016). Here, we present an ...
Chaichoompu, K., Tongsima, S., Shaw, P. J., Sakuntabhai, A., & Van Steen, K. (2016, May 21). A novel unsupervised clustering approach with multiple data types to reveal fine-level structure. Poster session presented at the European Human Genetics Conference 2016 (ESHG 2016), Barcelona, Barcelona, Spain.
Introduction: Several methods exist to identify population substructure that is due to shared genetic ancestry or regional proximity. These may be SNP-based or haplotype-based (Price et al. 2006, Lawson et al ...
Chaichoompu, K., Tongsima, S., Shaw, P. J., Sakuntabhai, A., & Van Steen, K. (2016, April 03). Iterative pruning method of unsupervised clustering for categorical data. Poster session presented at the 13th International Congress of Human Genetics (ICHG 2016), Kyoto, Japan.
Single Nucleotide Polymorphisms (SNPs) are commonly used to identify population structures. Iterative pruning Principal Component Analysis (ipPCA) utilizes SNP profiles to assign individuals to subpopulations ...
Wangkumhang, P., Shaw, P. J., Chaichoompu, K., Ngamphiw, C., Assawamakin, A., Nuinoon, M., Sripichai, O., Svasti, S., Fucharoen, S., Praphanphoj, V., & Tongsima, S. (2013). Insight into the peopling of mainland southeast Asia from thai population genetic structure. PloS one, 8(11), 79522.
Peer reviewed (verified by ORBi)
There is considerable ethno-linguistic and genetic variation among human populations in Asia, although tracing the origins of this diversity is complicated by migration events. Thailand is at the center of ...
Chaichoompu, K., Pongsakorn, W., Anunchai, A., & Sissades, T. (2012, October). Encoded haplotype data as input to ipPCA can better resolve population clustering. Poster session presented at the 11th International Conference on Bioinformatics (InCoB2012), Bangkok, Thailand.
Background Studies in population genetics are mainly based on the analysis of genetic variations among different populations. With the advent of advanced genotyping technology, large number of Single ...
Intarapanich, A., Shaw, P. J., Assawamakin, A., Wangkumhang, P., Ngamphiw, C., Chaichoompu, K., Piriyapongsa, J., & Tongsima, S. (2009). Iterative pruning PCA improves resolution of highly structured populations. BMC bioinformatics, 10, 382.
Peer reviewed (verified by ORBi)
BACKGROUND: Non-random patterns of genetic variation exist among individuals in a population owing to a variety of evolutionary factors. Therefore, populations are structured into genetically distinct ...
Chaichoompu, K., Kittitornkun, S., & Tongsima, S. (2007). Speedup bioinformatics applications on multicore-based processor using vectorizing and multithreading strategies. Bioinformation, 2(5), 182-4.
Peer reviewed (verified by ORBi)
Many computational intensive bioinformatics software, such as multiple sequence alignment, population structure analysis, etc., written in C/C++ are not multicore-aware. A multicore processor is an emerging ...
Wangkumhang, P., Chaichoompu, K., Ngamphiw, C., Ruangrit, U., Chanprasert, J., Assawamakin, A., & Tongsima, S. (2007). WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations. BMC genomics, 8, 275.
Peer reviewed (verified by ORBi)
BACKGROUND: Allele-specific (AS) Polymerase Chain Reaction is a convenient and inexpensive method for genotyping Single Nucleotide Polymorphisms (SNPs) and mutations. It is applied in many recent studies ...
Chaichoompu, K., & Kittitornkun, S. (2006). Multithreaded ClustalW with improved optimization for intel multi-core processor. the International Symposium on Communications and Information Technologies, 2006 (ISCIT2006) (pp. 590-594).
Peer reviewed
This paper presents the methodology that assists the compiler to optimize ClustalW; the most widely used tool for aligning multiple text-based protein or nucleotide sequences in Bioinformatics. Our goal is to ...
Chaichoompu, K., Kittitornkun, S., & Tongsima, S. (2006). MT-ClustalW: Multithreading multiple sequence alignment. the 20th International Parallel and Distributed Processing Symposium, 2006 (IPDPS 2006).
Peer reviewed
ClustalW is the most widely used tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three stages: pairwise alignment, guide tree generation and progressive alignment ...
Chaichoompu, K., Kittitornkun, S., & Tongsima, S. (2006). Performance comparison of Multifactor Dimensionality Reduction: JVM vs. Native code. ITC-CSCC: International Technical Conference on Circuits Systems, Computers and Communications. 2006 (pp. 185-188).
Peer reviewed
Multifactor Dimensionality Reduction (MDR) was originally developed to detect gene-gene interactions in the domain of human genetics. MDR algorithm collapses high-dimensional genetic data, into a single ...