I am a PhD student at the Artificial Intelligence (AI) Group, supervised by Dr Pietro Lio', and a Cambridge Trust Scholar (Cambridge International Scholarship). My current research focuses on developing algorithms and tools for integration and calibration of nucleomic data with the aim of reconstructing spatial (3D) genome networks at different resolutions and over time (4D).
Y. Shavit. Algorithms for reconstructing the 3D genome architecture. PhD thesis, University of Cambridge, 2015.
Y. Shavit, B.J. Walker and P. Lio’. Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration, Bioinformatics, 2015.
Y. Shavit, I. Merelli, L. Milanesi and P. Lio’. How computer science can help in understanding the 3D genome architecture, Brief. Bioinformatics, 2015.
Y. Shavit, B. Yordanov, S.J. Dunn, C.M. Wintersteiger, Y. Hamadi, and H. Kugler. Switching Gene Regulatory Networks, in 10th International Conference on Information Processing in Cells and Tissues (IPCAT 2015), Springer, September 2015, accepted.
F.K. Hamey, Y. Shavit, V. Maciulyte, C. Town, P. Lio' and S. Tosi . Automated Detection of Fluorescent Probes in Molecular Imaging, In Proceedings of the Eleventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) 2014, Lecture Notes in Computer Science (LNCS), Springer.
Y. Shavit, F.K. Hamey and P. Lio'. FisHiCal: an R package for iterative FISH-based calibration of Hi-C data, Bioinformatics, 2014.
Y. Shavit and P. Lio'. Combining a wavelet change point and the Bayes factor for analysing chromosomal interaction data, Molecular BioSystems, 2014.
Y. Shavit and P. Lio'. CytoHiC: A Cytoscape Plugin For Visual Comparison Of Hi-C Networks, Bioinformatics, 2013.
E. Mashiach, D. Schneidman-Duhovny, A. Peri, Y. Shavit, R. Nussinov and H.J. Wolfson. An integrated suite of fast docking algorithms. Proteins, 2010.
Code also available on github: https://github.com/yolish/
Selected Talks & Posters
Y. Shavit, Nuclear Cartography, a talk at the Bioinformatics Approaches to Adaptations, Genome Evolution and Biological Associations workshop, University of Cambridge, 2015.
Y. Shavit, A spatial problem in genomics, a talk at the Eleventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) 2014.
Y. Shavit and P. Lio'. Integrating multiple omics using change point statistics, a poster at the Inference for Change-Point and Related Processes workshop, Isaac Newton Institute for Mathematical Sciences (Cambridge, UK), January 13 - 17, 2014.
Y. Shavit and P. Lio'. Applications of Hi-C data to Cytogenetics, a poster at the Single Cell Genomics conference, Weizmann institute of science (Israel), October 1–3, 2013.
Y. Shavit and P. Lio'. Computational Modelling Of Nuclear Architecture, a poster at the PhD Summer School of Microsoft Research (Cambridge, UK), July 1-5, 2013.
Co-organizer of the 2nd Oxbridge Women in Computer Science Conference.
Bioinformatics, part II, Michaelmas term 2013, Computer Laboratory.
Bioinformatics, part II, Michaelmas term 2012, Computer Laboratory.