Group members


Zohar

 

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

 
link to gallery

Michal Amit, Research Support Associate

 

michalamit100@gmail.com

Supporting research and grant management processes in the group. Also working with Prof Elette Boyle (FACT), at IDC.

Dr. Shay Ben-Elazar, Research associate and project adviser

 

shaybenelazar@hotmail.com

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.

Dr. Edward Vitkin, Research associate and project adviser

 

edward.vitkin@gmail.com

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.

Alona Levy-Jurgenson, PhD student, Technion

 

levy.alona@gmail.com

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.

Ben Galili, PhD student, Technion

 

benga9@gmail.com

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.

Hadas Biran, PhD student, Technion (joint with Prof. Yael Mandel-Gutfreund)

 

hadas.moriah@gmail.com

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.

Alon Oring, MSc, Research associate and project adviser

 

alon.oring@post.idc.ac.il

Supervising machine learning and data science projects.

Roy Shafir, MSc student, Technion.

 

royshafir8@gmail.com

Information aspects of DNA sequence analysis. Algorithms and statistical analysis of synthetic oligonucleotide libraries.

Inbal Preuss, MSc student, IDC.

 

inbalpreuss@gmail.com

Working on synthetic biology projects including studying aspects of different coding schemes for data storage in DNA.

Guy Gozlan, MSc student, IDC

 

Gozlang1@gmail.com

Developing algorithmic and statistical methods to support the measurement and characterization of CRISPR-Cas9 on and off target events. In collaboration with the Hendel Lab in Bar Ilan University.

Anat Samohi, MSc student, IDC

 

anatsamohi@gmail.com

Together with Dr. Adi Akavia from University of Haifa,  I am working on developing secure protocols for machine learning and statistical tasks. I am also investigating aspects related to labelling errors and how they can affect statistical tests.

Shay Adadi, MSc student, IDC

 

shay.adaddi@post.idc.ac.il

Developing algorithmic and statistical methods to support the measurement and characterization of CRISPR-Cas9 on and off target events. In collaboration with the Hendel Lab in Bar Ilan University.

Shuli Finley, MSc student, IDC (joint with Elette Boyle)

 

shulifinley@gmail.com

Exploring machine learning methods to contextualize research on permuted puzzles providing cryptographic hardness in private information retrieval (PIR).

Ori Schneebaum, MSc student, IDC

 

orisbaum@gmail.com

Working on developing a novel feature selection approach, in the context of using gene expression data, to predict survival.

Chloé Benmussa, MSc student, IDC (joint with Jessica Cauchard, BGU)

 

chloebenmussa@gmail.com

Using machine learning to generate and communicate alerts based on measured physiological parameters.

Efi Herbst, MSc student, IDC

 

efiherbst@gmail.com

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 to infer clinically relevant properties. Also working with hospital clinical data to predict treatment outcomes.

Ilai Genish, MSc project student, IDC

 

ilai.genish@post.idc.ac.il

Working on developing methods for analyzing proteomics and gene expression data. Collaborating with Alex Golberg’s Lab at TAU (link) on developing e-biopsy technology. Also working on developing software for analyzing CRISPR editing experiments, in collaboration with the Hendel Lab in Bar Ilan University.

Maya Kerem, MSc project student, IDC

 

mayakerem21@gmail.com

Working on predictions in health and disease. In particular on predicting Anastomotic Leakage (AL) following bowel resection surgeries. The project includes Exploratory Data Analysis, Statistical analysis, and Machine Learning.

Natalie Iram, Research Support Associate

 

natalie.iram@post.idc.ac.il

MSc in biochemistry from Tel aviv University (YEAR 2007). Supporting research and grant management processes in the group. Also working with Prof Elette Boyle (FACT) and Prof Gil Kalai, at IDC.

Guy Assa, MSc student, IDC

 

guyassa@gmail.com

Working on improved and novel machine learning and data science approaches to measuring off target activity in genome editing.

Ilan Geffen, BSc project student, IDC

 

ilagef@gmail.com

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 to infer clinically relevant properties.

Noam Weinfeld, MSc student, IDC

 

noam.weinfeld@gmail.com

Developing a tool to analyze the stability of logrank statistics, under labeling errors. Working with Ben Galili.

Alumni:

PhD Students
  1. 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 IDC Herzliya.
  2. 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.
  3. Edward Vitkin, PhD 2018 – Metabolic modeling and its applications for Synthetic Biology and Biotechnology. Thesis. Currently at IBM Haifa.
  4. Israel Steinfeld, PhD 2013 – Assay design and data analysis in studies combining multiple high throughput measurement technologies. Thesis. Currently at Agilent Laboratories.
  5. Limor Leibovich, PhD 2013 – Statistical enrichment in ranked lists. Thesis. Currently at Google.
  6. Doron Lipson, PhD 2007 – 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.
  7. Chaya Ben-Zaken Zilberstein, PhD 2006 – Spotting Regulatory Elements by Micro-Arrays. Thesis.
MSc Students
  1. Sharon Sultan, MSc 2021, IDC – Deep Learning and Sequence Determinants of Gene Co-Expression. Thesis.
  2. Alon Oring, MSc 2021, IDC – Autoencoder Image Interpolation by Shaping the Latent Space. Thesis
  3. Yoav Orlev, MSc 2021, IDC – 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.
  4. Ido Amit , MSc 2020, IDC – Accurate estimation of genome editing off-target activity.
  5. Gal Novich , MSc student, Technion. In Prof. Roy Kishony’s Lab, 2019 – Linkage inference methods for phylogenetic relationships.
  6. Dalia Alperovich, MSc 2017 – Efficient Search for Optimally Enriched Combination of Ranked Lists. Thesis. Currently at Microsoft.
  7. Yaara David, MSc 2011- Analysis of time of replication data; Joint with Prof Yonina Eldar, Technion. Thesis.
  8. Roy Navon, MSc 2010 – Rank based statistics in analyzing high-throughput genomic data; Joint with Prof Benny Chor, TAU. Thesis. Currently at MeMed Diagnostics.
  9. Eran Eden, MSc 2007. Discovering Motifs in Ranked Lists of DNA Sequences. Thesis. Currently at MeMed Diagnostics.
  10. Ari Frank, MSc 2002 – Feature selection in gene expression data; Joint with Prof Dan Geiger, Technion. 
BSc Students
  1. Shlomo Amor, BSc project student, IDC, 2021 – a study of rank based classifiers
  2. Idan David, BSc project student, IDC, 2020 – Statistical method to detect port scanning in corporate networks
  3. Abigail Beck (ChiHong Choi), BSc project student, IDC, 2020, studied the relationship between gene expression and protein expression.
  4. Gon Chalamish, BSc project student, IDC, 2018 – Deep generative adversarial networks on genetic sequence data.
  5. Yoni Peleg, BSc project student, TAU (Joint with Dr. Alexander Golberg), 2017-2018 – Optimization of sugar quantification by near infrared spectra.
  6. Nir Levin, BSc project student, IDC, 2016-2017 – Joint analysis of transcriptomic and proteomic data.
Others
  1. Oz Solomon, Postdoctoral fellow, Technion and IDC, 2015-2018 – Bacterial gene expression regulation using bacterial genomics analysis and RNA structural analysis. Currently at Ayala Pharma.
  2. Ayala Polikovsky, Research Assistant, IDC, 2017-2018 – miRNA normalization. Currently an MSc student at TAU.
  3. Omri Matalon, Postdoctoral fellow, IDC, 2020-2021 – Genome editing (CRISPR cas9) off-target activity measurement.