Simone Ciccolella
PostDoc at Bias Lab May 2025
I am currently a PostDoc in the
BIAS Lab
at the Computer Science Department -
University of Study Milano-Bicocca, Italy.
Research Interest
My personal research activity has focused on the development of combinatorial
and heuristic algorithms in Bioinformatics, with a strong focus
on praticality and efficiency.
I have paid special attention to implementation, validation and experimentation.
In my reasearch I focused on Combinatorial and Heuristic Algorithms
for cancer and viral phylogenetics;
Machine Learning and Deep Learning for classification
of images and tabular genomic data;
Graph-based algorithms, data structure and indexing in the field
of pangenomics.
Lastly, I am interested in general algorithms and data structure,
not necessarly related to bioinformatics,
and their implementations,
especially regarding low-level coding optimizations in C.
Education
International collaborations
-
Georgia State University -- Atlanta, GA, USA
I have been collaborating with Dr. Murray Patterson
on various projects regarding cancer phylogenomics,
evolutionary studies of viruses, clustering and machine learning techniques for biological data, mostly regarding Single Cell sequencing data.
-
Weill Cornell Medicine -- New York City, NY, USA
I have been collaborating with Prof. Iman Hajirasouilha on the design and implementation of novel and
efficient algorithms for cancer phylogeny reconstructions as well as novel evolutionary models
to overcome the current limitations of the available approaches.
-
University of Tokyo -- Tokyo, Japan
I have been collaborating with Prof. Kunihiko Sadakane with goal of developing
succinct data structures and efficient algorithms for strings and graphs.
We worked on a graph indexing for pangenome graphs and are currently collaborating
on block decomposition using string-based indices.