Dr Agus

Dr Agus Salim

Associate Professor

College of Science, Health and Engineering

School of Engineering and Mathematical Sciences

Department of Mathematics and Statistics

PS2 226, Melbourne (Bundoora)

Qualifications

PhD (Cork), Bsc (Bogor Agricultural University, Indonesia)

Role

Academic

Membership of professional associations

Statistical Society Australia, International Society for Clinical Biostatistics

Area of study

Mathematics and Statistics

Brief profile

Dr Agus Salim is Associate Professor at the Department of Mathematic and Statistics, La Trobe University. He came to La Trobe in April 2013 having previously held positions at the Australian National University and National University of Singapore. Agus has over 12 years experience as biostatistician and has extensive records of collaboration with clinicians and epidemiologists and has received competitive funding from the National Health and Medical Research Council (NHMRC) for his applied and methodological works. His main methodological interest is in the area of survival analysis with a focus on analysis of nested case-control data and the analysis of high-throughput data from next-generation sequencing.

Research interests

Bioinformatics

- Analysis of next-gen sequencing data; normalization issues in 'omics data; pathway-based analysis

Biostatistics

- Risk Prediction Models;Stats Methods for Nested Case-Control Data;Epidemiology of CVD and Cancer

Teaching units

STA2ABS   Applied Biostatistics

STA2AMS  Applied Medical Statistics

STA3LM     Analysis of Linear Models

STA4AMD  Analysis of Medical Data

STA5MB     Models for Bionformatics (Msc Data Science)

Recent publications

1.  Dona MSI, Prendergast LA, Keerthikumar S, Mathivanan S, Salim A.  Powerful differential expression analysis incorporating network topology for next-generation sequencing data. Bioinformatics. Accepted. doi: 10.1093/bioinformatics/btw833.

1.      Stroud DA, Surgenor EE, Formosa LE, Reljic B, Frazier AE, Dibley MG, OSselame LD, Stait T, Beilharz TH, Thorburn DR, Salim A, Ryan MT. (2016). Accessory subunits are integral for assembly and 1 function of human mitochondrial complex I. Nature. Accepted.

2.      Chang X, Salim A, Dorajoo R et al. (2016). Utility of genetic and non-genetic risk factors in predicting Coronary Heart Disease in Singaporean Chinese. Eur J Prev Cardiol. Accepted.

3.      Salim A, Delcoigne B, Villaflores K, Koh WP, Yuan JM, van Dam RM, Reilly M. (2016). Comparisons of Risk Prediction Methods Using Nested Case-Control Data. Statistics in Medicine. Accepted.

4.      Delcoigne B, Hagenbuch N, Sandberg MEC, Salim A, Lindström LS, Bergh J, Czene K and Reilly M. (2016). Feasibility of reusing time-matched controls in an overlapping cohort. Statistical Methods in Medical Research. Accepted.

5.      Salim A, Tai ES, Tan VY, Welsh AH, Liew R, Naidoo N, Wu Y, Yuan JM, Koh WP, van Dam RM. C-reactive protein and serum creatinine, but not haemoglobin A1c, are independent predictors of coronary heart disease risk in non-diabetic Chinese. Eur J Prev Cardiol 2016,;23(12):1339-49. doi: 10.1177/2047487315626547

6.      Morgan AJ, Rapee RM, Tamir E, Goharpey N, Salim A, McLellan LF, Bayer JK. Preventing anxiety problems in children with Cool Little Kids Online: study protocol for a randomised controlled trial. Trials 2015, 16:507. doi: 10.1186/s13063-015-1022-5.

7.      YD Apalasamy, S Rampal, A Salim, FM Moy, TT Su, HA Majid, A Bulgiba, Z Mohamed. Polymorphisms of the Resistin Gene and Their Association with Obesity and Resistin Levels in Malaysian Malays. Biochemical genetics 2015, 53(4-6), 120-131.

8.      Scully OJ, Yu Y, Salim A, Thike AA, Yip GW, Baeg GH, Tan PH, Matsumoto K, Bay BH. Complement component 1, q subcomponent binding protein is a marker for proliferation in breast cancer. Exp Biol Med 2015, 240(7):846-53. doi: 10.1177/1535370214565075.

9.      Teh JL, Tan JR, Lau L, Saxena N, Salim A, et al. Longer Examination Time Improves Detection of Neoplastic Gastric Lesions During Upper Gastrointestinal Endoscopy. Clinical Gastroenterology and Hepatology 2015, 13 (3), 480-487.

10.   Rebora P, Salim A, Reilly M. bshazard: A Flexible Tool for Nonparametric Smoothing of the Hazard Function. The R Journal 2014. 6:114-122.

11.   Salim A et al. Analysis of incidence and prognosis from ‘extreme’ case-control designs. Statistics in Medicine. 2014. DOI: 10.1002/sim.6245

12.   Salim A, Ma X, Li J, Reilly M. A maximum likelihood method for secondary analysis of nested case-control data. Statistics in Medicine 2014; 33(11):1842-52. doi: 10.1002/sim.6084

13.   Chen S, Calza S, Salim A, Pawitan Y. Joint estimation of read intensity and isoform expression using multi-sample RNA-seq data. Bioinformatics 2014; 30(4):506-13. doi: 10.1093/bioinformatics/btt704.

14.   Zakharov S, Teoh GHK, Salim A, Thalamuthu A. A method to incorporate prior information into score test for genetic association studies. BMC Bioinformatics. 2014. 15:24. DOI: 10.1186/1471-2105-15-24.

15.   Nang EE, Salim A, Wu Y, Tai ES, Lee J, Van Dam RM. Television screen time, but not computer use and reading time, is associated with cardio-metabolic biomarkers in a multiethnic Asian population: a cross-sectional study. Int J Behav Nutr Phys Act. 2013 May 30;10:70.

16.    Hartman M, Liu J, Czene K, Miao H, Chia KS, Salim A, Verkooijen HM. Birth rates among female cancer survivors: a population-based cohort study in Sweden. Cancer. 2013; 119:1892-9. doi: 10.1002/cncr.27929. Epub 2013 Feb 21.

17.   Zain SM, Mohamed Z, Mahadeva S, Rampal S, Basu RC, Cheah PL, Salim A, Mohamed R. Susceptibility and gene interaction study of  the angiotensin II type 1 receptor (AGTR1) gene polymorphisms with non-alcoholic fatty liver disease in a multi-ethnic population. PLoS One. 2013;8(3):e58538. doi: 10.1371/journal.pone.0058538.

18.   Zakharov S, Salim A, Thalamuthu A. Comparison of similarity-based tests and pooling strategies for rare variants. BMC Genomics. 2013 Jan 24; 14:50. DOI: 10.1186/1471-2164-14-50.

19.   Koomanan N, Ko Y, Yong WP, Ng R, Wong YP, Lim SW, Salim A, Chan A. Clinical impact of drug-drug interaction between aspirin and prednisolone at a cancer center. Clin Ther. 2012 Dec; 34(12):2259-67. doi: 10.1016/j.clinthera.2012.11.002.

20.   Teo SM, Pawitan Y, Ku CS, Chia KS, Salim A*. Statistical challenges associated with detecting copy number variations with next-generation sequencing. Bioinformatics. 2012 Nov 1; 28(21):2711-8. doi: 10.1093/bioinformatics/bts535. Corresponding author

21.   Ko Y, Tan SL, Chan A, Wong YP, Yong WP, Ng RC, Lim SW, Salim A. Prevalence of the co-prescription of clinically important interacting drug combinations involving oral anticancer agents in Singapore: a retrospective database study. Clin Ther. 2012 Aug; 34(8):1696-704. doi: 10.1016/j.clinthera.2012.06.025.

22.   Chin WLC, Chia EHS, Ma S, Heng D, Tan M, Lee J, Tai ES, Salim A*. The ARIC predictive model reliably predicted risk of type II diabetes in Asian populations. BMC Medical Research Methodology 2012 12:48 DOI:10.1186/1471-2288-12-48.*Corresponding author.

23.   Salim A, Yang Q, Reilly M. The value of re-using prior nested case-control data in new studies with different outcomes. Statistics in Medicine. 2012 31(11-12):1291-1302.

24.   Chan MY, Tan K, Tan HC, Huan PT, Li B, Phua QH, Lee HK, Lee CH, Low A, Becker RC, Ong WC, Richards MA, Salim A, Koay E and Tai ES. CYP2C19 and PON1 polymorphisms regulating clopidogrel bioactivation in Chinese, Malay and Indian subjects. Pharmacogenomics 2012 13(5): 533-542.

25.   Venkataraman, K., Kao SL, Thai AC, Salim A, Lee JJM, Heng D, Tai ES and Khoo EYH. Ethnicity modifies the relation between fasting plasma glucose and HbA1c in Indians, Malays and Chinese. Diabetic Medicine 2012 29: 911–917. doi: 10.1111/j.1464-5491.2012.03599.x

26.   Lim WY, Chen Y, Chuah KL, Eng P, Leong SS, Lim E, Lim TK, Ng A, Poh WT, Tee A, Teh M, Salim A, Seow A. Female Reproductive Factors, Gene Polymorphisms in the Estrogen Metabolism Pathway, and Risk of Lung Cancer in Chinese Women Am J Epidemiology. 2012 Feb 13. [Epub ahead of print]

27.   Ng DP, Salim A, Liu Y, Zou L, Xu FG, Huang S, Leong H, Ong CN. A metabolomic study of Low estimated glomerular filtration rate in Non-proteinuric type 2 diabetes Mellitus. Diabelotogia.  2012 Feb;55(2):499-508.

28.    Ng DP, Salim A, Lim XL, Nurbaya S. Estimated glomerular filtration rate and its association with the retinol-binding protein 4 (RBP4) locus on human chromosome 10q23. Nephrol Dial Transplant. 2011 Aug 5. [Epub ahead of print]

29.   Lee W, Gusnanto A, Salim A, Magnusson P, Sim X, Tai ES, Pawitan Y. Estimating the number of true discoveries in genome-wide association studies. Statistics in Medicine 2011 DOI: 10.1002/sim.4391

Resume

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Older publications

  1.  Ku CS, Loy EY, Salim A, Pawitan Y, Chia KS. The discovery of human genetic variations and their use as disease markers: past, present and future. J Hum Genet. 2010 Jul;55(7):403-15
  2. Huang J, Salim A, Lei K et al. (2009). Classification of array CGH data using smoothed logistic regression model. Statistics in Medicine, 28:3798-810.
  3. Salim A, Welsh AH. (2009) Designing two-stage prevalence studies in the absence of gold standard test. American Journal of Epidemiology 170(3):369-378; doi:10.1093/aje/kwp122.
  4. Tan CS, Salim A, Ploner A, et al. (2009).Correlating gene and protein expression data using correlated factor analysis. BMC Bioinformatics, 10:272.
  5. Salim, A., Hultman, C., Sparen, P. and Reilly, M. (2009). Combining data from two nested case control studies of overlapping cohort to improve study efficiency. Biostatistics, 10: 70-79.
  6. Salim, A., Mackinnon, A.J., Christensen, H. and Griffiths, K Comparison of data analysis strategies for intent-to-treat analysis in pre-test-post-test designs with substantial dropout rates. Psychiatry Research 160(3):335-45 DOI: 10.1016/j.psychres.2007.08.005.
  7. Salim, A., Mackinnon, A.J. and Griffiths, K. Sensitivity analysis of intention-to-treat estimates when withdrawals are related to unobserved compliance status. Statistics in Medicine 28, 1164-1179; DOI: 10.1002/sim.3025.
  8. Anstey, K.J., von Sanden, C., Salim, A., O’Kearney, R. Smoking as a risk factor for dementia and cognitive decline: a meta analysis. American Journal of Epidemiology, 166: 367-378; DOI:10.1093/aje/kwm116.
  9. Salim, A, Becker, N.G., Moller, J and Hessen-Soerman, A-C. (2007). An analysis for a crossover cohort study with application to the study of triggers of Meniere’s disease. Statistics in Medicine, 26, 1136-1149.
  10. Kivi, M., Johansson, A.L.V, Salim, A, Tindberg, Y and Reilly, M. (2005). Accommodation of additional non-randomly sampled cases in a study of Helicobacter pylori infection in families. Statistics in Medicine, 24: 4045-4054.
  11. Perry, IJ., Villegas, R., Salim, A., Flynn, A. (2005). Clustering of protective factors for glucose intolerance and insulin resistance: a cross-sectional study. Diabetic Medicine, 22: 1091-1097.
  12. Salim, A., Pawitan, Y and Bond, K. (2005). Modelling association between two irregularly observed spatio-temporal processes by using smoothed maximum covariance analysis. Applied Statistics, 54: 555-573.
  13. Villegas R, Salim A, Collins MM, Flynn A, Perry IJ. (2004). Prudent diet and the risk of insulin resistance. Nutrition Metabolism and Cardiovascular Diseases, 14: 334-343.
  14. Reilly, M., Salim, A., Lawlor, E., Smith, O., Temperley, I. and Pawitan, Y. (2004). Modelling infectious disease transmission with complex exposure pattern and sparse outcome data. Statistics in Medicine, 23: 3013-3032.
  15. Villegas R, Salim A, Collins MM, Flynn A, Perry IJ. (2004). Dietary patterns in middle-aged Irish men and women defined by cluster analysis. Public Health Nutrition, 7:1017-24.

Research projects

COLLABORATIONS

  1. Statistical Methods for RNA-seq expression data (with Yudi Pawitan's group at Karolinska Institutet, http://fafner.meb.ki.se/personal/yudpaw/)
  2. Statistical Methods for Absolute Risk Estimation Using sub-cohort Data (with Marie Reilly at Karolinska Institutet, http://ki.se/en/people/mareil)
  3. Identification of colorectal cancer biomarkers: Integrated experimental and bioinformatics analysis of transcriptomic, proteomic and metabolomic data of colorectal cancer cell derived exosome (with Mathivanan Research Group, http://www.mathivananlab.org/)
  4. Annotating functions of human MT proteomes (with Ryan Research Group, http://www.latrobe.edu.au/biochemistry/specialisations/ryan)
  5. Using hsCRP and serum creatinine to improve risk prediction of myocardial infarction in Singaporean Chinese (with Rob van Dam's group at National University of Singapore, http://www.sph.nus.edu.sg/index.php/component/virtuemart/academic/rob-m-van-dam-detail?Itemid=0)
  6. Using genetic scores to improve risk prediction of CHD in Singaporean Chinese population (with Heng Chew Kiat's group at National University of Singapore)
  7. Mediterranean Diet and the prevention of secondary myocardial infarction (with Catherine Itsiopoulos's Group, http://www.latrobe.edu.au/health/about/staff/profile?uname=citsiopoulos)
  8. Mediterranean Diet and the prevention of non-alcoholic fatty liver disease (NAFLD) (with Audrey Tierney's Group, http://www.latrobe.edu.au/health/about/staff/profile?uname=A2Tierney)
  9. The Genetics of Obesity and NAFLD in Malaysian Population (with Zahurin Mohammed's group at University of Malaya, http://malaya.academia.edu/ZahurinMohamed). 

RECENT WORKSHOPS

Big Data Workshop at Jember University (Indonesia), 23-24 December 2015 (Pictures from Workshop and Travel to the Beautiful Papuma Beach)

Big Data Workshop at Bogor Agricultural University, 14-14 December 2015

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