biodatascience

This is the web resource for NTU's Bio-Data Science and Education Laboratory

View the Project on GitHub gohwils/biodatascience

Publications

Feature Selection and Network Modelling

  1. Goh WWB, Wong LS. NetProt: Complex-based feature selection. Journal of Proteome Research, 16(8):3102–3112, June 2017 #
  2. Goh WWB, Wong LS. Class-paired Fuzzy SubNETs: A paired variant of the rank-based network analysis family for feature selection based on protein complexes. Proteomics, 17(10):1700093, May 2017 #
  3. Goh WWB, Wong LS. Spectra-first feature analysis in clinical proteomics — A case study in renal cancer. Journal of Bioinformatics and Computational Biology, 14(5):1644004, Oct 2016
  4. Goh WWB. Fuzzy-FISHNET: A highly reproducible protein complex-based approach for feature selection in comparative proteomics. BMC Medical Genomics, 5;9(Suppl 3):67, Dec 2016 #
  5. Goh WWB, Wong LS. Evaluating feature-selection stability in next-generation proteomics. Journal of Bioinformatics and Computational Biology, 14(5):1650029, Oct 2016
  6. Goh WWB, Wong LS. Advancing clinical proteomics via networks: A tale of five paradigms. Journal of Proteome Research, 15(9):3167-3179, Jul 2016 #
  7. Iwata H, Goettsch C, Sharma A, Ricchiuto P, Goh WWB, Halu A, Yamada I, YoshidaH, Hara T, Wei M, Inoue N, Fukuda D, Mojcher A, Mattson PC, Barabási A, Boothby M, Aikawa E, Singh S, Aikawa M. PARP9 and PARP14 cross-regulate macrophage activation via STAT1 ADP-ribosylation. Nature Communications, 31(7):12849, Oct 2016 ##
  8. Singh SA, Andraski AB, Pieper B, Goh WWB, Mendivil CO, Sacks FM, Aikawa M. Multiple apolipoprotein kinetics measured in human HDL by high resolution/accurate mass parallel reaction monitoring. Journal of Lipid Research, 57(4):714-28, Feb 2016 #
  9. Hutcheson JD, Goettsch C, Bertazzo S, Maldonado N, Ruiz JL, Goh WWB, Yabusaki K, Faits T, Bouten C, Franck G, Quillard T, Libby P, Aikawa M, Weinbaum S, Aikawa E. Genesis and growth of extracellular-vesicle-derived microcalcification in atherosclerotic plaques. Nature Materials, 15(3):335-43, Jan 2016 ##
  10. Goh WWB, Guo T, Aebersold R, Wong LS. Quantitative proteomics signature profiling based on network contextualization. Biology Direct, 10:71, Dec 2015
  11. **Ricchiuto P, Sng J, Goh WWB. Analyzing extremely small sized ratio datasets. International Journal of Bioinformatics Research and Applications, 11(3):268-80 Jun 2015.
  12. Goh WWB, Fan MY, Low HS, Sergot M, Wong LS. Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies. BMC Genomics, 14(35), Feb 2013 #
  13. Goh WWB, Lee YH, Ramdzan Z, Chung MCM, Wong LS, Sergot MJ. A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression. International Journal of Bioinformatics Research and Applications, 8(3/4):155-170, Aug 2012
  14. Goh WWB, Lee YH, Ramdzan Z, Sergot M, Chung M, Wong LS. Proteomics Signature Profiling (PSP) – A novel contextualization approach applied towards proteomics analysis. Journal of Proteome Research, 11(3):1571-1581, Mar 2012 #
  15. Goh WWB, Oikawa H, Sng J, Sergot M, Wong LS. The role of miRNAs in regulating complex formation. Bioinformatics, 28(4):453-456, Feb 2012 ##
  16. Goh WWB, Lee YH, Ramdzan Z, Jin JJ, Dong DF, Lin QS, Chung M, Wong LS. A network-based pipeline for analyzing MS data – An application towards liver cancer. Journal of Proteome Research, 10(5):2261-2272, May 2011 #

Normalization Techniques, Batch Effects and Pure Statistics

  1. **Zhao Y, Wong LS, Goh WWB. **Zhao Y, Wong LS, Goh WWB. Doing quantile normalization right (Under review at Scientific Reports). Scientific Reports, Accepted
  2. *Zhou LJ, Sue ACH, Goh WWB. Examining the practical limits of batch effect correction algorithms: When should you care about batch effects? Journal of Genetics and Genomics, 46(9):433-443, Sep 2019
  3. Goh WWB, Wong LS. Turning straw into gold: how to build robustness into gene signature inference. Drug Discovery Today, 24(1):31-36, Jan 2019 ##
  4. Goh WWB, Wong LS. Breast Cancer Signatures Are No Better Than Random Signatures Explained. Drug Discovery Today, 23(11):1818-1823, Nov 2018 ##
  5. **Wang W, Sue ACH, Goh WWB. Null-hypothesis statistical testing in clinical proteomics: With great power comes great reproducibility. Drug Discovery Today, 22(6):912-918, June 2017 ##
  6. **Wang W, Goh WWB. Sample-to-sample p-value variability and its implications in multivariate analysis. International Journal of Bioinformatics Research and Applications, 14(3):235-254, Jan 2018
  7. **Goh WWB, Wang W, Wong LS. Why batch effects matter in omics data, and how to avoid them. Trends in Biotechnology, S0167-7799(17)30036-7, Mar 2017 ##
  8. Goh WWB, Wong LS. Protein complex-based analysis is resistant to the obfuscating consequences of batch effects — A case study in clinical proteomics. BMC Genomics, 18(Suppl 2):142, Mar 2017 #

Missing Protein Prediction (Proteomics)

  1. **Zhao Y, Sue ACH, Goh WWB. Deeper investigation into the utility of functional class scoring in missing protein prediction from proteomics data. Journal of Bioinformatics and Computational Biology, 17(2):1950013, Apr 2019
  2. *Zhou L, Wong LS, Goh WWB. Understanding missing proteins: a functional perspective. Drug Discovery Today, 23(3):644-651, Mar 2018 ##
  3. Goh WWB, Sergot M, Sng J, Wong LS. Comparative network-based recovery analysis and proteomic profiling of neurological changes in valproic acid-treated mice. Journal of Proteome Research, 12(5):2116-27, May 2013 #

Experimental Design and Principles

  1. Goh WWB, Wong LS. Advanced bioinformatics methods for practical applications of proteomics. Briefings in Bioinformatics, 20(1):347-355, Jan 2019 ##
  2. Goh WWB, Wong LS. Dealing with confounders in -omics analysis. Trends in Biotechnology, 36(5):488-498, May 2018 ##
  3. Goh WWB, Wong LS. Integrating networks and proteomics: moving forward. Trends in Biotechnology, 34(12):951-959, Dec 2016 ##
  4. Goh WWB, Wong LS. Design principles for clinical network-based proteomics. Drug Discovery Today, 21(7):1130-1138, Jul 2016 ##
  5. Goh WWB, Wong LS. Computational proteomics: Developing a robust analytical strategy. Drug Discovery Today, 19(3):266-274, Mar 2014 ##
  6. Goh WWB, Sng J, Wong L. Contemporary network proteomics and its requirements. Biology, 3:22-38, Feb 2014
  7. Goh WWB, Wong LS. Networks in proteomics analysis of cancer. Current Opinion in Biotechnology, 24(6):1122–1128, Dec 2013 ##
  8. Goh WWB, Lee YH, Chung MCM, Wong LS. How advancement in biological network analyses methods empowers proteomics analyses. Proteomics, 12(4-5):550-563, Feb 2012 #

Applied Bioinformatics and Data Science

  1. Ho, N, Wu H, Xu J, Koh JH, Yap WS, Goh WWB, Chong SC, Taubert S, Thibault G. The Unfolded Protein Response Activation and Transcriptome Are Orchestrated to Lipid Bilayer Stress. Journal of Cell Biology, Accepted ##
  2. **Ho SY, Wong L, Goh WWB. Avoid oversimplifications in machine learning: Going beyond the class-prediction accuracy. Patterns (Cellpress), 1(2):100025, May 2020
  3. Goh WWB, Wong LS. The Birth of Bio-Data Science: Trends, Expectations and Applications. Genomics, Proteomics and Bioinformatics, S1672-0229(20)30055-3, May 2020
  4. **Goh WWB, Thalappilly S, Thibault G. Moving beyond the current limits of data analysis in longevity and healthy lifespan studies (Keynote review). Drug Discovery Today, 24(12):2273-2285, Sep 2019 ##
  5. **Goh WWB, Zhao Y, Sue ACH, Guo T, Wong LS. Proteomic investigation of intra-tumor heterogeneity using network-based contextualizations, Journal of Proteomics, 30(206):103446, Jul 2019 #
  6. Lim MMK, Wee JWK, Soong JC, Chua D, Tan WR, Lizwan M, Li Y, Teo Z, Goh WWB, Zhu P, Tan NS. Targeting metabolic flexibility via angiopoietin-like 4 protein sensitizes metastatic cancer cells to chemotherapy drugs. Mol Cancer. 17(1):152, Oct 2018 ##
  7. Goh WWB, Sng J, Yee JY, See YM, Lee TS, Wong LS, Lee J. Can peripheral blood-derived gene expressions genetically characterize high risk subjects for psychosis? Computational Psychiatry, 0(1):1-16, Oct 2017
  8. Yang X, Hutter M, Goh WWB, Bureik, M. CYP4Z1 – A human Cytochrome P450 enzyme that might provide the key to treat breast cancer. Current Pharmaceutical Design, 23(14):2060-2064, Feb 2017 #
  9. *Tan P, Goh WWB, Sng J. Network-based characterization of the synaptic proteome reveals that removal of epigenetic regulator Prmt8 restricts proteins associated with synaptic maturation. Journal of Neurochemistry, 140(4):613-628, Feb 2017 #
  10. Oikawa H, Goh WWB, Lim V, Wong LS, Sng J. Valporic acid mediates BDNF through miR-124 by down-regulating a novel protein target, GNAI1. Neurochemistry International, 91:62–71, Dec 2015
  11. Wang Y, Goh WWB, Wong LS, Montana G, Alzheimers Disease Neuroimaging Initiative, PaRFR: Parallel random forest regression on hadoop for multivariate genome-wide association studies. BMC Bioinformatics, 14(Suppl 16):S6, Oct 2013 #
  12. Lee YH, Goh WWB, Lin T.K., Lin QS, Ng CK, Raida M, Boelsterli UA, Chung M. Integrative toxicoproteomics implicates impaired mitochondrial glutathione import as off-target effect of troglitazone. Journal of Proteome Research, 12(6):2933-45, Jun 2013 #
  13. Leow KY, Goh WWB, Tan SZ, Lim J, Ng KC, Low AF, Heng CK. Variant screening of the serum amyloid A1 gene and functional study of the p. Gly90Asp variant for its role in atherosclerosis. Atherosclerosis, 227(1):112-7, Mar 2013 #
  14. Leow KY, Goh WWB, Heng CK. Effect of SAA1 on global gene expression THP-1 derived macrophages. Inflammation Research, 61(4):391-398, Jan 2012
  15. Ruan Y, Ooi HS, Siew WC, Chiu, KP, Zhao XD, Srinivasa KG, Yao F, Choo CY, Nuwantha P, Kalpana R, Goh WWB, Shahab A, Sung WK, Bourque G, Pallanisamy N, Wei CL. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End Ditagging (PET). Genome Research, 17:828-838, Jun 2007 ##

Education

  1. **Ho SY, Sze CC, Wong L, Goh WWB. What can Venn diagrams teach us about doing data science better? International Journal of Data Science and Analytics, Accepted
  2. Goh WWB, Sze CC. AI paradigms for teaching biotechnology. Trends in Biotechnology, 37(1): 1-5, Jan 2019 ##
  3. **Ngan FD, Sze CC, Goh WWB. Give Swirl a Whirl: A Mixed-Method analysis on Swirl approach to teach applied statistics in a biology student cohort. The Asian Conference on Education 2019: Official Conference Proceedings, Oct 2019 [WWBG served as session chair]
  4. *Chon HM, Sze CC, Goh WWB. An Investigation into the Efficacy of Students-as-partner Pedagogy in a Singapore University Education Learning Context. The Asian Conference on Education 2019: Official Conference Proceedings Oct 2019 [WWBG served as session chair]

What the strange signs mean

Bold Denotes corresponding author

** Denotes directly supervised research staff, i.e. POs, RAs, RFs, postdocs, etc.

* Denotes PhD students (supervised or co-supervised)

## Denotes Tier 1A papers

# Denotes Tier 1B papers