Education
- 2014: PhD in Biotechnology, Technical University of Denmark (DTU).
- 2010: Master of Science in Computer Science (Bioinformatics), University of Trento, Italy.
- 2006: Bachelor of Science in Computer Science (Bioinformatics), University of Catania, Italy.
Professional Experiences
- 2025~: Program-Specific Assistant Professor, Informatics Platform, Center for Cancer Immunotherapy and Immunobiology (CCII), Graduate School of Medicine, Kyoto University.
- 2020-2025: Research Associate, Graduate School of Science, The University of Tokyo.
- 2016-2020: Postodoctoral Fellow, Graduate School of Science, The University of Tokyo.
- 2014-2016: JSPS International Research Fellow (Postdoc), Research Institute for Microbial Diseases (RIMD), Osaka University.
Research Focus
Since the last decade, Artificial Intelligence is having an increasingly profound impact on scientific research, driven by a deluge of data that is only expected to continue. The CCII itself generates a great amount of data, ranging from omics-data (sequencing, mass spectrometry, imaging, etc.) to results from wet-lab experiments and clinical records.
We aim to use the wealth of both original and publicly available data to develop algorithms that can accelerate research in cancer biology and immunology. This can be achieved by integrating such diverse type of datasets in order to extract novel biological insights. In addition, CCII provides advanced HPC Servers, on which data analyses and software development is carried out. Finally, we collaborate with other groups at CCII by assisting them in obtaining, analyzing, and interpret the omics-data they produce or require to pursue their research goals.
Selected Publications
Cosentino S., Sriswasdi S. & Iwasaki W. (2024). SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models. Genome Biology, 25(1), 195.
Cosentino S., & Iwasaki W. (2019). SonicParanoid: fast, accurate and easy orthology inference. Bioinformatics, 35(1), 149–151.
Cosentino S., Voldby Larsen, M., Møller Aarestrup, F., & Lund, O. (2013). PathogenFinder-distinguishing friend from foe using bacterial whole genome sequence data. PloS One, 8(10), e77302.
Larsen M.V., Cosentino S., Rasmussen S., Friis C., Hasman H., Lykke Marvig R., Jelsbak L., Sicheritz-Pontén T., Ussery D., Aarestrup M. F., Lund O. (2012). Multilocus sequence typing of total-genome-sequenced bacteria. Journal of Clinical Microbiology, 50(4), 1355–1361.