YAP Von Bing's Homepage

YAP Von Bing's Homepage

Department of Statistics and Applied Probability, National University of Singapore
S16 06-105, 6 Science Drive 2, Singapore 117546
Tel: (65) 6516 7143 Fax: (65) 6872 3919 email: stayapvb{at}nus.edu.sg

My surname (family or last name), is Yap. My given (first) name is Von Bing. I have no middle name.


Teaching

Stripped to its bare essentials, teaching is show-and-tell, which looks easier than it is. The general technique is brilliantly developed in Statistics 4e by Freedman, Pisani and Purves (Norton), ideal for an introductory undergraduate course. The Analysis of Variance by Scheffé (Wiley) is great for a course on linear models. I plan to build a graduate applied statistics course on Statistical Models by Freedman (Cambridge University Press).

Courses

FMS1201S, FMS1202S Freshman Seminars
MDG5108 Biostatistics for Basic Research
ST1232 Statistics for Life Sciences
ST2132 Mathematical Statistics
ST2137 Computer Aided Data Analysis
ST4233 Linear Models
ST5213 Categorical Data Analysis II
UQF2101C DNA Evidence in a Court of Law

Articles

1. The standard deviation as a descriptive statistics. Singapore Mathematical Medley, 34 (2007).
2. An elementary proof that row rank equals column rank. Singapore Mathematical Medley, 35 (2008).

Supervision (past and current)

2 PhD, 1 MSc, 7 Honours students (2 shared), 2 Computational Biology Honours students, 2 Undergraduate Research Opportunity Programme students, and one project group of the Special Programme in Science.

Teaching tools

Companion notes on Mathematical Statistics and Data Analysis 3e by John A Rice.
Visualisation of the Strong Law of Large Numbers for the uniform distribution on {0,1,2}.
Note on principal component analysis and singular value decomposition.


Research

Markov chains, molecular evolution, computational genomics. In general applied statistics in biology.

Journal papers

ADP ribosyl-cyclases (CD38/CD157), social skills and friendship. A Chong, F Malavasi, S Israel, CC Khor, VB Yap, M Monakov, SH Chew, PS Lai and R Ebstein. Psychoneuroendocrinology (2017).

Reconstructing the invasion history of a spreading, non-native, tropical tree through a snapshot of current distribution, sizes, and growth rates. KY Chong, M Raphael, R Carrasco, A Yee, X Giam, VB Yap and HTW Tan. Plant Ecology (2017).

Standard codon substitution models overestimate purifying selection for non-stationary data. BD Kaehler, VB Yap and GA Huttley. Genome Biology and Evolution (2017).

Statistical methods for identifying sequence motifs affecting point mutations. Y Zhu, T Neeman, VB Yap and GA Huttley. Genetics (2016).

Comparing germination success and seedling traits between exotic and native pioneers: Cecropia pachystachya versus Macaranga gigantea. MB Raphael, KY Chong, VB Yap and HTW Tan. Plant Ecology, 216:1019 (2015).

Genetic distance for a general non-stationary Markov substitution process. BD Kaehler, VB Yap, R Zhang and GA Huttley. Systematic Biology, 64:281--293 (2015).

Status and distribution in Singapore of Ficus vasculosa Wall. ex Miq. (Moraceae). HTW Tan, ABC Ng, YS Yeoh, WF Ang, ZY Ooi, VB Yap, XY Ng, RCJ Lim and L Neo. Nature in Singapore, 7:155--165 (2014).

The urban pteridophyte flora of Singapore. BC Tan, ALS Ng-Chua, A Chong, C Lao, M Tan-Takako, S-T Ngiam, A Tay and VB Yap. Journal of Tropical Biology and Conservation, 11:13--26 (2014).

Syndecan-1 is a potential biomarker for triple-positive breat carcinomas in Asian women with correlation to survival. G-H Lim, P-H Tan, AR Jara-Lazaro, AA Thike, W-C Sim, VB Yap and GW-C Yip. Singapore Medical Journal, 55:468--472 (2014).

Does minimally invasive surgery have a lower risk of surgical site infections compared to open spinal surgery? WWG Ee, WLJ Lau, W Yeo, VB Yap and WM Yue. Clinical Orthopaedics and Related Research, 472:1718--1724 (2014).

Application of statistics and machine learning for risk stratification of heritable cardiac arrhythmias. PS Wasan, M Uttamchandani, S Moochhala, VB Yap and PH Yap. Expert Systems with Applications, 40:2476--2486 (2013).

The embedding problem for Markov models of nucleotide substitution. KL Verbyla, VB Yap, A Pahwa, Y Shao and GA Huttley. PLoS ONE 8:e69187 (2013).

Context-dependent substitution models for circular DNA. R Zhang and VB Yap. Infection, Genetics and Evolution, 18:362--366 (2013).

A unified approach to the transition matrices of DNA substitution models. VB Yap. Mathematical Biosciences, 242:111--116 (2013).

Wilson confidence intervals for the two-sample log-odds-ratio in stratified 2x2 contingency tables. T Suesse, VB Yap and BM Brown. Communications in Statistics - Theory and Methods, 41:3355--3370 (2013).

Current distribution and density of horseshoe crabs, Tachypleus gigas and Carcinoscorpius rotundicauda, around the main island of Singapore. L Cartwright-Taylor, VB Yap, CC Hsu and ST Lou. Aquatic Biology, 13:127--136 (2011).

Statistical analysis of binary data generated from multilocus dominant DNA markers. TF Khang and VB Yap. Molecular Ecology Resources, 10:995--1008 (2010).

The extent of undiscovered species in Southeast Asia. X Giam, TH Ng, VB Yap and HTW Tan. Biodiversity and Conservation, 19:943--954 (2010).

The apportionment of total genetic variation by categorical analysis of variance. TF Khang and VB Yap. Statistical Applications in Genetics and Molecular Biology, 9:7 (2010).

Estimates of the effect of natural selection on protein coding content. VB Yap, H Lindsay, S Easteal and GA Huttley. Molecular Biology and Evolution, 27:726--734 (2010).

Effects of normalisation on quantitative traits in association test. LK Goh and VB Yap. BMC Bioinformatics, 10:415 (2009).

Similar states in continuous-time Markov chains. VB Yap. Journal of Applied Probability, 46:497--506 (2009).

Data-driven optimization of metabolomics methods using rat liver samples. GS Parab, P Rao, S Lakshminarayanan, VB Yap, SM Moochhala and S Swarup. Analytical Chemistry, 81:1315--1323 (2009).

Pitfalls of the most commonly used models of context dependent substitution. H Lindsay, VB Yap and GA Huttley. Biology Direct, 3:52 (2008).

Pathological rate matrices: from primates to pathogens. HW Schranz, VB Yap, S Easteal, R Knight and GA Huttley. BMC Bioinformatics, 9:550 (2008).

Comparison of methods for estimating the nucleotide substitution matrix. M Oscamou, D McDonald, VB Yap, GA Huttley, ME Lladser and R Knight. BMC Bioinformatics, 9:511 (2008).

The defensive role of scutes in juvenile fluted giant clams (Tridacna squamosa). L Han, PT Todd, LM Chou, VB Yap and B Sivaloganathan. Journal of Experimental Marine Biology and Ecology, 359:77--83 (2008).

Rooting a phylogenetic tree with nonreversible substitution models. VB Yap and TP Speed. BMC Evolutionary Biology, 5:2 (2005).

Comparative immunopeptidomics of humans and their pathogens. S Istrail, L Florea, BV Halldorsson, O Kohlbacher, RS Schwartz, VB Yap, JW Yewdell and SL Hoffman. Proceedings of the National Academy of Sciences of the USA, 101:13268--13272 (2004).

Genome sequence of the brown Norway rat yields insights into mammalian evolution. The Rat Genome Sequencing Consortium. Nature, 428:493--521 (2004).

Identification of evolutionary hotspots in the rodent genomes. VB Yap and L Pachter. Genome Research, 14:574--579 (2004).

Modeling DNA base substitution in large genomic regions from two organisms. VB Yap and TP Speed. Journal of Molecular Evolution, 58:12--18 (2004).

Association between divergence and interspersed repeats in mammalian noncoding genomic DNA. F Chiaromonte, S Yang, L Elnitski, VB Yap, W Miller and RC Hardison. Proceedings of the National Academy of Sciences of the USA, 98:14503--14508 (2001).

Matrix extension and biorthogonal multiwavelet construction. SS Goh and VB Yap. Linear Algebra and its Applications, 269:139--157 (1998).

Book chapters

Robust estimation of natural selection using parametric codon models (with GA Huttley). In Codon Evolution: Mechanisms and Models, edited by A Schneider and G Cannarozzi (2012).

Estimating substitution matrices (with TP Speed). In Statistical Methods in Molecular Evolution, edited by R Nielsen (2005).

Conference proceedings

Modeling genomic DNA base substitution (with TP Speed). Proceedings of the American Statistical Association, 3855--3864 (2002).

Scoring pairwise genomic sequence alignments (with F Chiaromonte and W Miller). Proceedings of the Pacific Symposium on Biocomputing, 115--126 (2002).


Service

Local places/meetings I have gone to talk statistics to teachers and students:

1. National University of Singapore: Department of Anatomy, Open House, Science Research Programme, Centre for Development of Teaching and Learning, Science Faculty Teaching Workshop, Science Focus, Statistics Camp.

2. Schools: Hwa Chong Institution, Raffles Junior College, Victoria Junior College.

3. Ministry of Education: Gifted Education Programme Annual Conference 2004, 'A' Level Mathematics Teachers Sharing Session 2009.

4. Singapore Mathematics Society: Mathematics Enrichment Programme, Primary Mathematics Olympiad Programme.

I supervised three projects under the Science Mentorship Programme for secondary schools.