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Group Members

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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

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

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)

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

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)

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

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

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

MSc student, Technion

Discovering enriched sequence elements in ranked DNA lists

Michal Amit

Research Support Associate

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

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

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

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

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

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

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

MSc student, Reichman University

Developing statistical approaches to assess higher dimensional correlation structures

Yoni Peleg

MSc student, Reichman University

MSc student, Reichman University

Studying and developing methods for analyzing allele specific and differential gene expression

Amit Zrihan

MSc student, Technion

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. Shay Ben-Elazar

PhD 2020, TAU (joint with Prof. Benny Chor)

Statistical and Computational Methods for Studying Genomic Spatial Structure and Properties. Thesis. Currently at Microsoft.

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.

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