Geoffrey Siwo Research Assistant Professor

Genomic Medicine, Open Science, Artificial Intelligence
Geoffrey Siwo

Research Interests:

My research interests range from computational biology, network science, artificial intelligence and nanotechnology. My current research work includes developing computational methods for predicting drug resistance, open platforms for crowdsourcing computational challenges, personalizing targeted therapeutics using genomic information and designing programmable nucleic acid therapeutics or genome editing technologies. Previously, I was a lead researcher at IBM Research Africa and a co-founder of Helix Nanotechnologies, a DNA nanotechnology company. My work has been featured in several media including CNN, USA Today, Fast Company, Ozy, among other media.



  • Research Assistant Professor, Department of Biological Sciences, Center for Research Computing, Eck Institute for Global Health, University of Notre Dame
  • Research Scientist and Team Lead, Data Driven Healthcare, IBM Research Africa, Johannesburg, South Africa. 2016-2017
  • Genomics Specialist, IBM TJ Watson Research Center, Yorktown Heights, NY. 2015-2016
  • Postdoctoral Fellow, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA. 2015
  • Research Associate, Geisel School of Medicine, Dartmouth College. 2014-2015
  • PhD. Department of Biological Sciences, University of Notre Dame, IN, USA. 2008-2014
  • Bsc Biomedical Science and Technology. Egerton University, Njoro, Kenya. 2000-2005


Selected Publications:

  • Ghouila A, Siwo GH, Entfellner JD, Panji S, Button-Simons KA, Davis SZ, Fadlelmola FM; DREAM of Malaria Hackathon Participants, Ferdig MT, Mulder N.(2018).
    Hackathons as a means of accelerating scientific discoveries and knowledge transfer. Genome Res. 28(5):759-765. doi: 10.1101/gr.228460.117. Epub 2018 Apr 12.
  • Turnbull LB, Siwo GH, Button-Simons KA, Tan A, Checkley LA, Painter HJ, Llinás M, Ferdig MT. (2017). Simultaneous genome-wide gene expression and transcript isoform profiling in the human malaria parasite. PLoS ONE. 12(11):e0187595. doi: 10.1371/journal.pone.0187595. eCollection 2017.
  • Siwo GH, Stolovitzky GA, Assefa S. (2016) Prediction of Molecular Mechanisms of Breast Cancer Metastasis. bioRxiv 106179; doi:
  • Siwo G, Rider A, Tan A, Pinapati R, Emrich S, Chawla N, Ferdig M. (2016). Prediction of fine-tuned promoter activity from DNA sequence. F1000Res. 5:158. doi: 10.12688/f1000research.7485.1. eCollection 2016.
  • MetaSUB International Consortium (2016). The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome. 4(1):24. doi: 10.1186/s40168-016-0168-z.
  • Pradhan A, Siwo GH, Singh N, Martens B, Balu B, Button-Simons KA, Tan A, Zhang M, Udenze KO, Jiang RH, Ferdig MT, Adams JH, Kyle DE. (2015). Chemogenomic profiling of Plasmodium falciparum as a tool to aid antimalarial drug discovery. Sci Rep. 5:15930. doi: 10.1038/srep15930.
  • Siwo GH, Scott Williams, Jason H. Moore (2015). The Future of Genomic Medicine Education in Africa. Genome Medicine. 7:47.
  • Siwo GH, Tan A, Katrina BS, Samarakoon UP, Checkley L, Pinapati RS, Ferdig MT (2015). Predicting functional and regulatory divergence of a drug resistance transporter gene in the human malaria parasite. BMC Genomics. 16:115.
  • Siwo GH, Smith RS, Tan A, Checkley L, Ferdig MT (2014). An Integrative Analysis of Small Molecule Transcriptional Responses in the Human Malaria Parasite Plasmodium falciparum. BMC Genomics.16:1030. doi: 10.1186/s12864-015-2165-1.
  • International Glossina Genome Initiative (2014). Genome Sequence of the Tsetse Fly (Glossina morsitans): Vector of African Trypanosomiasis. Science. 344(6182):380-6.