“The joy of discovery is certainly the liveliest that the mind of man can ever feel”

- Claude Bernard -


  1. Khan A, Plana-Ripoll O, Antonsen S, Brandt J, Geels C, Landecker H, Sullivan PF, Pedersen CB, Rzhetsky A, “Environmental pollution is associated with increased risk of psychiatric disorders in the US and Denmark”, PLOS Biology, August 2019, 17(8): e3000353. (Read Paper)

  2. Zhang H, Dahlen T, Khan A, Edgren G, and Rzhetsky A, “Measurable health effects associated with the daylight saving time shift”. PLOS Computational Biology, June 2020, 16(6): e1007927. (Read Paper).

  3. Basit A, Khan SA, Maroof N, Saadi M, Khan A, “A novel dissimilarity of activity biomarker and functional connectivity analysis for the epilepsy diagnosis.” Symmetry 2019; 11(8);979:1-14; Special Issue: Symmetry and Asymmetry in Computational Biology and Bioinformatics. (Read Paper)

  4. Khan A, Thatcher T, Woeller C, Sime P, Phipps RP, Hopke PK, Utell MJ, Krahl P, Mallon TM, and Thakar J, “Machine learning approach for predicting past environmental exposures from molecular profiling of post-exposure human serum samples”, Journal of Occupational and Environmental MedicineDecember 2019; 61(Supplement 12):S55–S64. (Read Paper) 

  5. Thatcher T, Woeller C, Thakar J, Khan A, Hopke PK, Smith MR, Uppal K, Walker DI, Go Y, Jones DP, Krahl P, Mallon TM, Sime PJ, Phipps RP, and Utell MJ, “Analysis of post-deployment serum samples identifies potential biomarkers of exposure to burn pits and other environmental hazards”, Journal of Occupational and Environmental MedicineDecember 2019, 61(Supplement 12): S45–S54. (Read Paper)

  6. Khan A, Katanic D, and Thakar J, “Meta-analysis of cell-specific transcriptomic data using fuzzy c-means clustering discovers versatile viral responsive genes.” BMC Bioinformatics. June 2017; 18(295):1-13. (Read Paper)

  7. Katanic D, Khan A, Thakar J. PathCellNet: Cell-type specific pathogen-response network explorer. Journal of Immunological Methods. Dec 2016 31;439:15-22. (Read Paper)

  8. Piepenbrink MS, Samuel M, Zheng B, Carter B, Fucile C, Bunce C, Kiebala M, Khan AA, Thakar J, Maggirwar SB, Morse D, Rosenberg AF, Haughey NJ, Valenti W, Keefer MC, and Kobie JJ, “Humoral dysregulation associated with increased systemic inflammation among injection heroin users.” PLOS ONE. Jul 2016 5;11(7):e0158641. (Read Paper) 

  9. Rebhahn JA, Roumanes DR, Qi Y, Khan A, Thakar J, Rosenberg A, Lee F, Quataert SA, Sharma G, and Mosmann TR; “Competitive SWIFT cluster templates enhance detection of aging changes.” Cytometry Part A, Jan 2016; 89(1):59-70. (Read Paper) 

  10. Khan AA, Iliescu DD, Sneath RJ, Hutchinson CE, and Shah AA, “Principal component and factor analysis to study variations in the aging lumbar spine.” IEEE Journal of Biomedical and Health Informatics (J-BHI), Special Issue: Bioinformatics in Clinical Environments, Mar 2015;19(2):745-751. (Read Paper) 


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  1. “An objective assessment of lumbar spine degeneration/aging seen on MRI with machine learning approach”. (Working manuscript).

  2. “Clinical predictors and the environmental risk factors of intentional self-inflicted injury and attempted suicide in the U.S. ”. (Working manuscript). 

  3. “A principal component support vector machine model for classifying seasonal and pandemic H1N1 influenza response within the first 4-hours post-infection.” (Working manuscript).

  4. “Data-driven and knowledge-based gene set enrichment analysis by using positive sample only machine learning approach.” (working manuscript).




  1. Khan AA, Katanic D, and Thakar J, “FIGS: Fuzzy Inference of Gene-Sets, a data-driven clustering approach”, Presented in International Conference on Intelligent Biology and Medicine (ICIBM ’16), Houston, TX, USA, 8-10 December 2016. (NSF travel award recipient).

  2. Khan AA, Iliescu DD, Hines E, Hutchinson CE, and Sneath RJ, “Neural network based spinal age estimation using lumbar spine magnetic resonance images (MRI).” Proceedings of the 4th IEEE International Conference on Intelligent Systems Modelling & Simulation (ISMS’13), Bangkok, Thailand, 29-31 January 2013.

  3. Khan AA, Hines EL, and Iliescu DD, “Using self-organizing maps to visualize age-related changes in lumbar vertebrae and intervertebral discs”, In the Proceedings of 24th Midwest Artificial Intelligence and Cognitive Science Conference (MAICS’13), Indiana University Southeast, New Albany, IN, USA, April 13-14, 2013.

  4. Khan AA, Naseer O, Iliescu DD, and Hines EL, "Fuzzy controller design for assisted omni-directional treadmill therapy." In the Proceeding of International Conference on Soft Computing and Software Engineering (SCSE’13), San Francisco State University, CA, USA, March 2013. 

  5. Naseer O, Shah A, and Khan AA, "Feedback control scheduling for crane control system." In 20th IEEE International Conference and Workshops on the Engineering of Computer Based Systems (ECBS’13), Phoenix, AZ, USA, 22-24 April 2013.

  6. Khan AA, Yakzan AIE, and Ali M, "Radio frequency identification based toll collection system." In 3rd International Conference on Computational Intelligence, Communication Systems and Networks (CICSyN’2011), Bali, Indonesia, 26-28 July 2011.

  7. Naseer O, Jhumka A, and Khan AA, “Dependability driven feedback control scheduling for real time embedded systems.” In International Conference on Embedded Systems and Applications (ESA’12), Las Vegas, USA, July 16-19, 2012.

  8. Khan AA, Khan MU, and Iqbal M., "Multilevel graph partitioning scheme to solve traveling salesman problem." In 9th International Conference on Information Technology: New Generations (ITNG’12), Las Vegas, USA, April 16-18, 2012. (Recipient of best conference paper award).

  9. Khan AA, and Iqbal M, "A motion detection based surveillance system (MDSS)." In IEEE International Conference on Informatics and Computational Intelligence (ICI’11), Bandung, Indonesia, 12-14 December 2011.

  10. Naseer O, and Khan AA, "Hybrid fuzzy logic and PID controller based PH neutralization pilot plant." In International Journal of Fuzzy Logic Systems, 3(2), 1-14, 2013.

  11. Yakzan AIE, and Khan AA, “A cohesive FPGA design for an optimized global positioning system.” Presented in IEEE Conference on Communication, Science & Information Engineering (CCSIE’11), 25-27 July 2011, London UK.

  12. Naseer O, and Khan AA, "Online adaptive fault tolerant based feedback control scheduling algorithm for multiprocessor embedded systems." In International Journal of Embedded Systems and Applications, 2(3):1-9, 2012. 

  13. Yakzan AIE, Khan AA, Hines EH, and Iliescu DD, "Adaptive control of an intelligent tank using fuzzy logic." 14th International Conference on Modelling and Simulation (UKSim’12), University of Cambridge, Cambridge, UK, 28 - 30 March 2012.

  14. Naseer O, and Khan AA, “Fuzzy logic controller based task scheduler for android operating systems.” In Euro American Multidisciplinary Conference, 8-11 April 2013, Paris France.

  15. Khan AA, Iliescu DD, Hines EL, Hutchinson CE, and Sneath RJ, "Classification of age-related changes in lumbar spine with the help of MRI scores," Proceedings of the 29th IEEE-EMB Southern Biomedical Engineering Conference (SBEC’13), Miami, Florida, USA, 3-5 May 2013.




  1. Poster Presentation: “Environmental pollution is strongly associated with increased risk of psychiatric disorders in the United States”, Presented at the 6th Annual Research Symposium of Center for Chronic Disease Research and Policy; Advancing Population Health through Medical Education, Health Policy, and System Change, University of Chicago, IL, USA, October 23, 2018. 

  2. Poster Presentation: “Machine learning approaches to predict effects of exposure on health outcome in service members”, Presented at the Military Health System Research Symposium (MHSRS), Kissimmee FL, USA, August 20-23, 2018.

  3. Poster Presentation: “Quantifying the influence of environmental quality on mental disorders”, In 26th International Conference on Intelligent Systems for Molecular Biology (ISMB-2018), Special Session: Translational Medicine Informatics and Applications, Chicago IL, USA, July 6-10, 2018. (Recipient of Best Poster Award).

  4. Poster Presentation: “Quantifying the association between environmental quality and mental disorders.” Presented at the Institute for Genomics and Systems Biology annual retreat, University of Chicago, Chicago IL, USA May 29th, 2018. 

  5. Poster Presentation: “Quantifying the association between environmental quality and mental disorders.” Presented at Mind Bytes: 4th Annual Research Computing Expo and Symposium, 2018, Chicago IL, USA May 8th, 2018. (Recipient of Best Poster Award in the Data Science Category)

  6. Research Talk: “Machine learning based computational pipelines for biomarker discovery and gene-set analysis.” Presented at Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia (CHOP), Philadelphia PA, February 23rd, 2017.

  7. Research Talk: “Machine learning based computational pipelines for biomarker discovery and gene-set analysis.” Presented at The Jackson Laboratory for Genomic Medicine, Farmington CT, January 30, 2017.

  8. Research Talk: “Gene-set analysis of cell-type specific transcriptomic data using fuzzy c-means clustering.” In Transcriptomics and Integrated Genomics Research (TIGR) seminar series at the University of Rochester, NY, January 19th, 2017.

  9. Poster Presentation: “Computational opportunities for identification of cell-type-specific immune relevant gene-sets in HIV disease.” Presented at Center for Aids Research ‘World AIDS Day’ Scientific Symposium and Poster Session, University of Rochester Medical Center, Rochester, NY, December 1st, 2016.  

  10. Poster Presentation: “FIGS: Fuzzy Inference of Gene-Sets, a data-driven clustering approach.” In Biophysics, Structural and Computational Biology Annual Retreat, University of Rochester Medical Center, Rochester, NY, October 25th, 2016. 

  11. Poster Presentation: “F-GRN: A fuzzy gene regulatory network package for data-driven pathway analysis.” In 2016 National Postdoc Appreciation Week Poster Competition, University of Rochester, NY, September 22nd, 2016. 

  12. Research Talk: “Early prediction of seasonal and pandemic H1N1 influenza viruses by using machine learning techniques.” In Transcriptomics and Integrated Genomics Research (TIGR) seminar at the University of Rochester, NY, May 14th, 2015.

  13. Poster Presentation: “Computational analysis and modeling of the human lumbar spine by using intelligent systems techniques.” In Health Research at Warwick (Demonstrating Impact and Vitality) Event, January 29th, 2013.

  14. Research Talk: “Intelligent data analysis for analyzing changes in the human lumbar spine.” In Annual Postgraduate Symposium, School of Engineering, University of Warwick, March 18th, 2013.

  15. Poster Paper: “Visualization of multivariate lumbar spine MRI data using principal component analysis (PCA).” In 35th Annual International IEEE-EMBS Conference of the IEEE Engineering in Medicine and Biology, Osaka, Japan, July 3-7, 2013. 

  16. Research Talk: “Artificial intelligence in medicine with special focus on lumbar spine aging.” In Integrated Clinical Academic Training Program at Clinical Science Research Labs, University Hospital Coventry and Warwickshire, Coventry, UK, February 13th, 2013.

  17. Poster Presentation: “Artificial intelligence in medicine: Transforming big data into knowledge.” At Warwick Engineering in Biomedicine Open Day Poster Competition, October 31st, 2012.

Peer-Reviewed Journal Publications

Conference and other Publications

Poster Presentations and Talks

Work in Progress

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© 2020 by Atif Khan