Publications

The following information is available:

Papers whose copyright have not been transferred to the publisher are available for public download. As for the slides, note that sometimes, I have used pictures from other sources (i.e., books, papers, etc.) -- if you choose to use them, make sure you credit the original source.

Additional information about me can be found on other sites (note that authors with the same name as me may also be included in these automatically generated lists):

Recent posters and slides are done in LaTeX using the sciposter and powerdot classes, respectively. The PhD thesis was done using the memoir class.


Journals

SummaryPaperSlides/BibTex
Poster
A. K.-Y. Leung, T.-P. Kwok, R. Wan, M. Xiao, P.-Y. Kwok, K. Y. Yip, and T.F. Chan. OMBlast: Alignment Tool for Optical Mapping Using a Seed-and-extend Approach. Bioinformatics, 33(3):311-319, 2017. [Software] [Abstract] [Publisher] [BibTex]
J.-W. Li, R. Wan, C.-S. Yu, N. N. Co, N. Wong, and T.-F. Chan. ViralFusionSeq: Accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. Bioinformatics, 29(5):649-651, 2013. [Software] [Abstract] [Publisher] [BibTex]
R. Wan, V. N. Anh, and K. Asai. Transformations for the Compression of FASTQ Quality Scores of Next Generation Sequencing Data. Bioinformatics, 28(5):623-635, 2012. [Software] [Abstract] [Publisher] [BibTex]
S. M. Kiełbasa, R. Wan, K. Sato, P. Horton, and M. C. Frith. Adaptive seeds tame genomic sequence comparison. Genome Research, 21(3):487-493, 2011. [Publisher]
M. C. Frith, R. Wan and P. Horton. Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Research, 38(7):e100, 2010. [Publisher]
R. Wan, L. Kiseleva, H. Harada, H. Mamitsuka and P. Horton. HAMSTER: visualizing microarray experiments as a set of minimum spanning trees. Source Code for Biology and Medicine, 4(8), 2009 (PMID 19925686 [Software] [Errata]). [Abstract] [Publisher] [BibTex]
[Kyoto University library repository]
R. Wan and A. Moffat. Block merging for off-line compression. Journal of the American Society for Information Science and Technology, 58(1):3-14, 2007. [Abstract] [Publisher] [BibTex]

Books and Book Chapters

SummaryPaperSlides/BibTex
Poster
R. Wan and H. Mamitsuka. Chapter 8: Discovering network motifs in protein interaction networks. In Biological Data Mining in Protein Interaction Networks, pgs. 117-143, IGI Global, 2009 ([Software] [Google books preview]). [Abstract] [Publisher] [BibTex]
R. Wan. Browsing and Searching Compressed Documents. PhD thesis, University of Melbourne, Australia, December 2003. (Supervised by Alistair Moffat). [Archived at the University of Melbourne repository] ([Software] [Errata]) [Abstract] [PDF] [Slides] [BibTex]

Conferences (peer-reviewed)

SummaryPaperSlides/BibTex
Poster
R. Wan and K. Asai. Sorting next generation sequencing data improves compression effectiveness. In Proc. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Workshops and Posters, pages 567-572, December 2010 ([Software] [Errata]). [Abstract] [Publisher] [Slides] [BibTex]
R. Wan, V. N. Anh, and H. Mamitsuka. Efficient Probabilistic Latent Semantic Analysis Through Parallelization. In Proc. 5th Asia Information Retrieval Symposium (AIRS 2009) [poster session], volume 5839 of Lecture Notes in Computer Science, pages 432-443, October 2009 ([Software]). [Abstract] [Publisher] [Poster] [BibTex]
V. N. Anh, R. Wan, and A. Moffat. Term impacts as normalized term frequencies for BM25 similarity scoring. In Proc. 15th International Symposium on String Processing and Information Retrieval, volume 5280 of LNCS, pages 51-62, November 2008. [Abstract] [Publisher] [BibTex]
R. Wan, Å. M. Wheelock, and H. Mamitsuka. A framework for determining outlying microarray experiments. In Proc. 8th International Workshop on Bioinformatics and Systems Biology (IBSB), volume 20 of Genome Informatics, pages 64-76, October 2008. (PMID 19425123 [Data] [Errata]) [Abstract] [Publisher] [Slides] [BibTex]
R. Wan, I. Takigawa, and H. Mamitsuka. Applying Gaussian distribution-dependent criteria to decision trees for high-dimensional microarray data. In Proc. Data Mining in Bioinformatics (VDMB) Workshop at the 32nd International Conference on Very Large Data Bases, volume 4316 of LNBI, pages 40-49. Springer-Verlag, September 2006. [Abstract] [Publisher] [Slides] [BibTex]
R. Wan, H. Mamitsuka, and K. F. Aoki. Cleaning microarray expression data using Markov Random Fields based on profile similarity. In Proc. 20th ACM Symposium on Applied Computing (poster session), pages 206-207, March 2005. [Abstract] [Publisher] [Poster] [BibTex]
R. Wan and A. Moffat. Evaluating statistically generated phrases. In Proc. 8th Australasian Document Computing Symposium (poster session), pages 67-70. CSIRO ICT Centre, December 2003. [Abstract] [PDF] [Poster] [BibTex]
R. Wan and A. Moffat. Block merging for off-line compression. In Proc. 13th Annual Symposium on Combinatorial Pattern Matching, pages 32-41. Springer-Verlag Berlin, July 2002. ([Software]) [Abstract] [Publisher] [BibTex]
A. Moffat and R. Wan. Re-Store: A system for compressing, browsing, and searching large documents. In Proc. 8th International Symposium on String Processing and Information Retrieval, pages 162-174. November 2001. (Invited talk.) [Abstract] [BibTex]
R. Wan and A. Moffat. Interactive phrase browsing within compressed text. In Proc. 24th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval (poster session), pages 410-411. September 2001. [Publisher] [Poster] [BibTex]
R. Wan and A. Moffat. Effective compression for the web: Exploiting document linkages. In Proc. 12th Australasian Database Conference, pages 68-75. IEEE Press, February 2001. [Abstract] [Publisher] [Slides] [BibTex]

Others (not peer-reviewed)

SummaryPaperSlides/BibTex
Poster
R. Wan, J. H.-K. Man, and T.-F. Chan. Query Modification through External Sources to Support Clinical Decisions. In Proc. 23rd Text Retrieval Conference (TREC 2014), National Institute of Standards and Technology (NIST), December 2014. [Abstract] [PDF] [BibTex]
Y. Fukasawa, R. Wan, S.-C. Fu, J. Tsuji, N. Sakiyama, K. Imai, and P. Horton. Mitochondrial protein cleavage site predictor. In Proc. 2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) - Workshops and Posters, pages 870-871, December 2010. [Publisher]
R. Wan. Book review of `Data Mining in Agriculture' by A. Mucherino, P. J. Papajorgji, and P. M. Pardalos. Journal of the Operational Research Society, 61(11):1682-1683, Edited by U. Aickelin, November 2010. [Publisher]
R. Wan, S. M. Kiełbasa, P. Horton, and M. C. Frith. The effect read length has on the performance of adaptive seeds for sequence alignment. In Proc. 20th International Conference on Genome Informatics, Posters and Software Demonstrations, pages P019-1 to P019-2, December 2009. [PDF] [Poster]
L. Kiseleva, R. Wan, and P. Horton. Introduction and application of CellExpress, a new database for studying human tissue-specific gene expression. In Proc. 2009 Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) [poster session], pages P? to P?, June 2009.
R. Wan, Å. M. Wheelock, and H. Mamitsuka. A framework for determining outlying microarray experiments. In Proc. 2008 Annual Conference of the Japanese Society for Bioinformatics, pages P48-1 to P48-2, December 2008. [PDF] [Poster]
R. Wan, V. N. Anh, and H. Mamitsuka. Passage retrieval with vector space and query-level aspect models. In Proc. 16th Text Retrieval Conference (TREC 2007), National Institute of Standards and Technology (NIST), December 2008. [Abstract] [PDF] [Poster] [BibTex]
R. Wan, H. Mamitsuka, L. Kiseleva, and P. Horton. Graphical representation of cell/tissue type relationships for the web. In Proc. 6th Asia Pacific Bioinformatics Conference (poster sessions), page P46, January 2008. [PDF] [Poster]
R. Wan, V. N. Anh, and H. Mamitsuka. Passage retrieval from genomic texts: An experience at TREC 2007. In Proc. 2007 Annual Conference of the Japanese Society for Bioinformatics, pages P107-1 to P107-2, December 2007. [PDF] [Poster]
R. Wan, V. N. Anh, I. Takigawa, and H. Mamitsuka. Combining vector-space and word-based aspect models for passage retrieval. In Proc. 15th Text Retrieval Conference (TREC 2006), National Institute of Standards and Technology (NIST), October 2007. [Abstract] [PDF] [Poster] [BibTex]
R. Wan, N. Hayes, S. Goto, and H. Mamitsuka. A guided sampling algorithm for identifying network motifs in a transcription regulatory network. In Proc. 5th Asia Pacific Bioinformatics Conference (poster sessions), page 64, January 2007. [MS Word] [Poster]
R. Wan, I. Takigawa, and H. Mamitsuka. Applying Gaussian distribution-dependent criteria to decision trees for high-dimensional microarray data. In Proc. 17th International Conference on Genome Informatics, Posters and Software Demonstrations, pages P023-1 to P023-2, December 2006. [PDF] [Poster]
R. Wan, Å. M. Wheelock, M. J. Bartosiewicz, and H. Mamitsuka. Classifying microarray data using pairwise similarity between gene profiles. In Proc. 16th International Conference on Genome Informatics, Posters and Software Demonstrations, pages P047-1 to P047-2, December 2005.[Errata] [PDF] [Poster]
R. Wan. Book review of 'Genomic Perl: From bioinformatics basics to working code by Rex A. Dwyer'. SIGACT News, 36(4):9-12, 2005. (This review was written in late 2003.) [PDF]
[Publisher]
R. Wan and H. Mamitsuka. Cleaning microarray expression data with Markov Random Fields based on profile similarity. In Proc. 15th International Conference on Genome Informatics, Posters and Software Demonstrations, pages P038-1 to P038-2, December 2004. [PDF] [Poster]
A. Moffat and R. Wan. Re-Store: A system for compression, browsing, and searching large documents (extended abstract of invited presentation). In Proc. 6th Australasian Document Computing Symposium, page ???, December 2001. [PDF]

Talks

The following are slides for external talks that are not conference presentations:

TitleDateLocationSlidesVideo
Transformations for Compressing Quality Scores of Next Generation Sequencing Data August 2, 2011 Ochanomizu University [Slides]
Bioinformatics as Viewed by a Computer Scientist May 14, 2011 Tokyo Linux User Group [Slides]
HAMSTER: Visualizing microarray experiments as a set of minimum spanning trees April 26, 2010 Chinese University of Hong Kong [Slides]
School of Biomedical Sciences
Microarray Data Analysis using Graph Theory: From Visualization to Outlier Detection December 17, 2008 Okinawa Institute of Science and Technology (OIST) [Slides]
The Kyoto Encyclopedia of Genes and Genomes August 22, 2007 University of Melbourne [Slides]
Was: Department of Computer Science and Software Engineering
(Guest lecture for 433-650 Computational Sequence Analysis;
lecturer: Dr. Linda Stern)
Classification and Outlier Detection of Microarray Data August 21, 2007 University of Melbourne [Slides]
Was: Department of Computer Science and Software Engineering