Reichman University School of Computer Science
and Technion Computer Science Faculty
Group Members
Dr. Zohar Yakhini
zohar.yakhini@gmail.com
Technion:
Room: Taub 524
Tel: +972 4 829 4937
IDC:
Room: Arazi C121
Tel: +972 9 952 7941
Dr. Shay Ben-Elazar
Research associate and project adviser
During my PhD (graduated 2020) I have focused on understanding how to utilize Chromosome Conformation Capture techniques (3C and derivatives, such as Hi-C) to enable the 3-dimensional exploration of genomes.
Currently supporting exciting machine learning and computational biology projects in the group.
Alona Levy-Jurgenson
PhD student, Technion
My PhD is focused on developing deep learning models to drive the analysis and interpretation of data derived from genomic measurements, pathology whole-slide images, clinical records and DNA sequences. Currently, my main goal is to combine data from several resources and molecular levels to provide better tumor profiling and identification of tumor sub-populations that may be resistant to drugs, especially in breast and ovarian cancer.
Hadas Biran
PhD student, Technion (joint with Prof. Yael Mandel-Gutfreund)
I aim to focus my PhD research on improving statistics and machine learning based methods for single cell RNA sequencing data analysis, and on developing techniques designed to use this data to provide new biological insights.I aim to focus my PhD research on improving statistics and machine learning based methods for single cell RNA sequencing data analysis, and on developing techniques designed to use this data to provide new biological insights.
Roy Shafir
PhD student, Technion
Information aspects of DNA sequence analysis. I am specifically working on reconstruction algorithms for DNA string traces, in the context of storage. Also working on measuring and using heterogeneity in spatial genomics.
Shuli Finley
MSc student, Reichman University (joint with Elette Boyle)
Exploring machine learning methods to contextualize research on permuted puzzles providing cryptographic hardness in private information retrieval (PIR). (factcenter.org)
Joint with Elette Boyle (https://cs.idc.ac.il/~elette/)
Efi Herbst
MSc student, Reichman University
Analyzing breast cancer pathology images and spatial transcriptomics. Developing statistical approaches to assess miRNA activity.
Ilan Geffen
MSc student, Reichman University
Applying deep learning to WSIs, to learn models that can produce spatial transcriptomics maps. Using those learned models I am analyzing breast cancer pathology images (from RESCUER https://www.rescuer.uio.no/) to infer clinically relevant properties.
Shahar Mor
MSc student, Technion
Discovering enriched sequence elements in ranked DNA lists
Michal Amit
Research Support Associate
Supporting research and grant management processes in the group. Also working with Prof Elette Boyle (FACT), at Reichman University.
Dr. Edward Vitkin
Research associate and project adviser
During my PhD studies I focused on modeling, simulating and optimizing metabolic behaviour of living organisms. Currently, together with Prof. Yakhini, I jointly supervise exciting MSc computational biology projects in the group.
Ben Galili
PhD student, Technion
I am a PhD student at the Computer Science Department at the Technion in the field of ML and Bioinformatics. I received my B.Sc. degrees in mathematics and computer science in 2005 , and my M.Sc. degree in computer science in 2016. My PhD is focused on analyzing the stability of different statistical tests and on feature selection techniques for gene expression signatures.
Alon Oring
PhD student, Reichman University. Research associate and project adviser
Working on developing digital pathology and spatial transcriptomic methods. Supervising machine learning and data science projects in the MLDS program.
https://www.datasci-ml-msc.education/
Inbal Preuss
PhD student, Reichman University
Working on synthetic biology projects including studying aspects of different coding schemes for data storage in DNA. Also working on applying CRISPR screening to understand regulation of cellular growth.
Chloé Benmussa
MSc student, Reichman University
Developed machine learning methods to generate and communicate alerts based on measured physiological parameters (joint with Jessica Cauchard, BGU). Working on measuring and using heterogeneity in spatial genomics and digital pathology.
Guy Assa
MSc student, Reichman University
Working on improved and novel machine learning and data science approaches to measuring off target activity in genome editing. We applied our methods to analyze human and plant edit experiments.
Noam Weinfeld
MSc student, Reichman University
Developing statistical approaches to assess higher dimensional correlation structures
Yoni Peleg
MSc student, Reichman University
Studying and developing methods for analyzing allele specific and differential gene expression
Amit Zrihan
MSc student, Technion
Working on cost-efficient DNA synthesis through innovative fusion of composite methods and photolithography.
Alumni
PhD Students
Dr. Leon Anavy
PhD 2020, Technion
Synthetic DNA Libraries and their Applications in Data Storage and Biological Assays. Thesis. Currently an independent research fellow and program director at the CS Dept at Reichman University.
Dr. Edward Vitkin
PhD 2018, Technion
Metabolic modeling and its applications for Synthetic Biology and Biotechnology. Thesis. Currently at IBM Haifa.
Dr. Israel Steinfeld
PhD 2013, Technion
Assay design and data analysis in studies combining multiple high throughput measurement technologies. Thesis. Currently at Agilent Laboratories.
Dr. Limor Leibovich
PhD 2013, Technion
Statistical enrichment in ranked lists. Thesis. Currently at Google.
Dr. Doron Lipson
PhD 2007, Technion
Computational Aspects of DNA Copy Number Measurement. Thesis. Also completed his MSc studies at 2002 – Optimization Problems in Design of Oligonucleotides for Hybridization-based Methods; Joint with Prof Uri Sivan. Thesis.
Dr. Chaya Ben-Zaken Zilberstein
PhD 2006, Technion
Spotting Regulatory Elements by Micro-Arrays. Thesis.
MSc Students
Shay Adadi
MSc 2023, Reichman University
Optimization of capture seq alignment
Guy Gozlan
MSc 2023, Reichman University
ICEBERG- software tool for analyzing guide seq assay
Ori Schneebaum
MSc student, Reichman University
Feature selection
Maya Kerem
MSc 2022, Reichman University
Prediction of gastric surgery complications from pre and post surgery data.
Anat Samohi
MSc 2022, Reichman University
Privacy preserving protocol for LogRank
Sharon Sultan
MSc 2021, Reichman University
Deep Learning and Sequence Determinants of Gene Co-Expression
Alon Oring
MSc 2021, Reichman University
Autoencoder Image Interpolation by Shaping the Latent Space. Thesis.
Yoav Orlev
MSc 2021, Reichman University
SOLQC – a software tool to support quality analysis of oligonucleotide libraries (synthetic DNA). GANs in the context of synthetic DNA design. Currently at Zebra medical.
Ido Amit
MSc 2020, Reichman University
Accurate estimation of genome editing off-target activity.
Gal Novich
MSc 2020, Technion
Linkage inference methods for phylogenetic relationships.
Dalia Alperovich
MSc 2017, Technion
Efficient Search for Optimally Enriched Combination of Ranked Lists. Thesis. Currently at Microsoft.
Yaara David
MSc 2011, Technion
Analysis of time of replication data; Joint with Prof Yonina Eldar, Technion. Thesis.
BSc Students
Ilana Sivan
BSc project student, Reichman University, 2023 (Together with Inbal Preuss)
Analysis of UMI duplications
Amit Shani
BSc project student, Reichman University, 2021-2022
Fine tuning BWA to analyze structural variations
Shlomo Amor
BSc project student, Reichman University, 2021
a study of rank based classifiers
Idan David
BSc project student, Reichman University, 2020
Statistical method to detect port scanning in corporate networks
Abigail Beck (ChiHong Choi)
BSc project student, Reichman University, 2020
studied the relationship between gene expression and protein expression.
Gon Chalamish
BSc project student, Reichman University, 2018
Deep generative adversarial networks on genetic sequence data.
Yoni Peleg
BSc project student, TAU (Joint with Dr. Alexander Golberg), 2017-2018
Optimization of sugar quantification by near infrared spectra.
Nir Levin
BSc project student, Reichman University, 2016-2017
Joint analysis of transcriptomic and proteomic data.
Others
Ilai Genish
Research Assistant, Reichman University, 2020-2023
Developing software for analyzing CRISPR editing experiments, in collaboration with the Hendel Lab in Bar Ilan University. Also working on developing methods for analyzing proteomics and gene expression data.
Natalie Iram
Research Support Associate, until 2021
Research support until 2021 (joint with Prof Elette Boyle (FACT, factcenter.org) and Prof Gil Kalai, at Reichman University.
Dr. Omri Matalon
Postdoctoral Research Associate, 2020-2021
Worked on developing methods to measure CRISPR activity
Dr. Oz Solomon
Postdoctoral fellow, Technion and Reichman University, 2015-2018
Bacterial gene expression regulation using bacterial genomics analysis and RNA structural analysis. Currently at Ayala Pharma.
Ayala Polikovsky
Research Assistant, Reichman University, 2017-2018
miRNA normalization. Currently an MSc student at TAU.