Group members

The new website: Yakhini Research Group (yakhini-research-group.org)

Dr. Zohar Yakhini zohar.yakhini@gmail.com Technion: Room: Taub 524 Tel: +972 4 829 4937 Reichman University: Room: Arazi C121 Tel: +972 9 952 7941
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 Reichman University.	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, PhD student, Technion.   royshafir8@gmail.com 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.
Inbal Preuss, PhD student, Reichman University.   inbalpreuss@gmail.com 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.	Ilan Geffen, MSc student, Reichman University   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.
Guy Assa, MSc student, Reichman University   guyassa@gmail.com Working on improved and novel machine learning and data science approaches to measuring off target activity in genome editing.	Noam Weinfeld, MSc student, Reichman University   noam.weinfeld@gmail.com Developing statistical approaches to assess higher dimensional correlation structures
Shuli Finley, MSc student, Reichman University (joint with Elette Boyle, FACT)   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, Reichman University   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, Reichman University (joint with Jessica Cauchard, BGU)   chloebenmussa@gmail.com Using machine learning to generate and communicate alerts based on measured physiological parameters. Also working on measuring and using heterogeneity in spatial genomics.	Efi Herbst, MSc student, Reichman University   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.
Ilai Genish, MSc project student, Reichman University   ilai.genish@post.idc.ac.il 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.	Shahar Mor, MSc student, Technion   shaharmor98@gmail.com Discovering enriched sequence elements in ranked DNA lists

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 Reichman University 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. Shay Adaddi, MSc 2022,  Reichman University- Algorithms and statistical methods for efficient inference of structural variations in enriched genome sequencing experiments. Thesis.
2. Guy Gozlan, MSc 2022, Reichman University- Improved detection and characterization of CRISPR-Cas9 off-target events. Thesis.
3. Anat Samohi, MSc 2022, Reichman University- Privacy preserving protocol for LogRank. Thesis.
4. Maya Kerem, MSc 2022, Reichman University- Prediction of gastric surgery complications from pre and post surgery data.
5. Sharon Sultan, MSc 2021, Reichman University- Deep Learning and Sequence Determinants of Gene Co-Expression. Thesis.
6. Alon Oring, MSc 2021, Reichman University- Autoencoder Image Interpolation by Shaping the Latent Space. Thesis. 
7. 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.
8. Ido Amit , MSc 2020, Reichman University- Accurate estimation of genome editing off-target activity.
9. Gal Novich , MSc student, Technion. In Prof. Roy Kishony’s Lab, 2019 – Linkage inference methods for phylogenetic relationships.
10. Dalia Alperovich, MSc 2017 – Efficient Search for Optimally Enriched Combination of Ranked Lists. Thesis. Currently at Microsoft.
11. Yaara David, MSc 2011- Analysis of time of replication data; Joint with Prof Yonina Eldar, Technion. Thesis.
12. Roy Navon, MSc 2010 – Rank based statistics in analyzing high-throughput genomic data; Joint with Prof Benny Chor, TAU. Thesis. Currently at MeMed Diagnostics.
13. Eran Eden, MSc 2007. Discovering Motifs in Ranked Lists of DNA Sequences. Thesis. Currently at MeMed Diagnostics.
14. Ari Frank, MSc 2002 – Feature selection in gene expression data; Joint with Prof Dan Geiger, Technion. 

BSc Students

1. Amit Shani, BSc project student, Reichman University, 2021-2022 – finetuning BWA to analyze structural variations.
2. Shlomo Amor, BSc project student, Reichman University, 2021 – a study of rank based classifiers
3. Idan David, BSc project student, Reichman University, 2020 – Statistical method to detect port scanning in corporate networks
4. Abigail Beck (ChiHong Choi), BSc project student, Reichman University, 2020, studied the relationship between gene expression and protein expression.
5. Gon Chalamish, BSc project student, Reichman University, 2018 – Deep generative adversarial networks on genetic sequence data.
6. Yoni Peleg, BSc project student, TAU (Joint with Dr. Alexander Golberg), 2017-2018 – Optimization of sugar quantification by near infrared spectra.
7. Nir Levin, BSc project student, Reichman University, 2016-2017 – Joint analysis of transcriptomic and proteomic data.

Others

1. 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.
2. Ayala Polikovsky, Research Assistant, Reichman University, 2017-2018 – miRNA normalization. Currently an MSc student at TAU.
3. Omri Matalon, Postdoctoral fellow, Reichman University, 2020-2021 – Genome editing (CRISPR cas9) off-target activity measurement.
4. Natalie Iram, Research support until 2021 (joint with FACT).