Research

Our lab develops algorithms to infer predictive models of molecular interactions based on high-throughput biological data.

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People

Meet our esteemed team of computational biologists including senior scientisis, programmers, grad students and undergrads.

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Publications

Our publication record includes papers at top bioinformatics journals and collaborations published in biological journals.

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Software

All the software developed in the lab is freely available. We encourage their wide-spread use and welcome your comments.

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Videos

Our team members present their work and share their knowledge in a variety of events and conferences.

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News

New paper in Bioinformatics

Ofir's paper on computational modeling of mRNA degredation dynamics using deep neural networks is now published in Bioinformatics

The Orenstein Lab has received continued support from Israel Innovation Authority

This support was recieved to develop on-target and off-target prediction algorithms

The Orenstein Lab was awarded a Kamin grant from Israel Innovation Authority

The grant was recieved together with Prof. Roee Amit from the Technion to develop a universal promoter library in mammalian cells

The Orenstein Lab was awarded an R01 grant from the National Institute of Health

The grant was recieved together with Prof. Niv Papo from BGU and his collaborators to develop methods to predict mutation effect on trypsin inhibitors

Sofia received a fellowship from Apple

This fellowship is awarded to excellent M.Sc. students

Ofir Yaish was awarded computational power by the Inter-University Computational Center

The computational power will be used to support Ofir's research in modeling mRNA degredation

Ofir Yaish received the High-tech, Bio-tech and Chem-tech doctoral fellowship

This fellowship is awarded to excellent new doctoral students

The first-ever Orenstein Lab social event

The event took place at 13th October with a BBQ at Park Hayarkon. It was a pleasure!

The Orenstein lab received funding for 4 years from the Israel Science Foundation

The grant was awarded for the grant titled "Bridging the gap between in vitro and in vivo protein-RNA binding prediction"

The Orenstein lab received funding for 2 years from the Binational United States - Israel Science Foundation

The grant was awarded for the grant titled "Improving high-throughput DNA sequence analysis using universal hitting sets" with Prof. Bonnier Berger from MIT

Reut Moshe received a fellowship for interdisciplinary research

This fellowship is awarded to excellent M.Sc. students conducting research involving multiple scientific disciplines.

We are excited to host Dr. Stephan Sinn

Stephan made the unbelievable effort to travel to Israel during a pandemic. His visit transforms his remote data science internship on small molecule interactions into a physical one.

Group meeting

An unbelievable full house and the first physical group meeting since March 20 at the Orenstein Lab! Today we heard from Reut about AlphaFold and enjoyed fresh sandwiches from Aroma.

New papers accepted to ACM-BCB 2021

Hagai Michel and Jonathan Karin, undergraduate electrical and computer engineering students, will be presenting MultiRBP, a multi-task neural-network for protein-RNA binding prediction. In addition, Yaron's collaboration with the Algorithms in Computational Genomics group at Tel-Aviv University, on improving the efficiency of de-Bruijn graph construction using compact universal hitting sets, will also be presented.

We welcome Dr. Stephan Sinn from Karlsruher Institut of Technologie for a summer internship

Stephan will be working on predicting small molecule interactions based on the SupraBank data base.

We welcome MIT undergraduate student Evelyn Peters for a summer internship

Evelyn will be working on computational models for CRISPR off-target prediction.

New paper in Briefings in Bioinformatics

Eitamar compared RNA-binding models inferrred from RNA Bind-n-Seq and RNAcompete.

New paper in IEEE

Mira and Alice's work on G-quadruplex prediction was accepted to IEEE/ACM Transactions on Computational Biology and Bioinformatics, continuing Mira's work presented at ACM-BCB 19'.

New paper in Nature Communications

Eitamar's colaboration with the team from the synthetic biology laboratory for the decipherment of genomic codes the Technion is out. In their work they characterized the sequence and structural determinants of binding of the phage coat proteins of different bacteriopages to RNA.

New paper in Methods in Molecular Biology

Yaron's paper on improved analysis of high-throughput sequencing data using small universal k-mer hitting sets is published as part of the Methods in Molecular Biology book series (MIMB, volume 2243).

New paper in Bioinformatics: DeepSELEX

Maor developed a new algorithm to infer intrinsic DNA-binding preferences using deep neural networks.

Deep learning poster at MLCB 2020

Ofir will take part in the poster session at this year's MLCB, presenting his work on mRNA degradation dynamics.

Group meeting

In the spirit of social distancing we have moved our meetings to Zoom.

We welcome new M.Sc. student Ori Feldman

Ori will work on predicting icSHAPE reactivity.

We welcome new M.Sc. student Maor Turner

Maor will work an developing predictive algorithms for RNA G-quadruplex detection.

Sofia received a the fellowship for interdisciplinary research

This fellowship is awarded to excellent MSc students conductig research involving multiple scientific disciplines.

We welcome new M.Sc. student Shai Elkayam

Shai will work on CRISPR-related algorithms, mainly on- and off-target prediction as part of CRISPRIL consortium.

We welcome new M.Sc. student Reut Moshe

Reut will work on analysis of high-throughput data of protein interactions jointly with Prof. Niv Papo.

We welcome summer intern Alice Aubert from Ecole Polytechnique

Alice will work on analysis of high-throughput RNA probing data.

New paper in Bioinformatics: DeCoDe

Tyler solved the problem of generating an efficient degenerate codon library to cover as many protein sequences under an experimenta limit.

We welcome M.Sc. student Moshe Shalom

Moshe will be working on predicting CRISPR sgRNA on-target efficiency.

Sofia received a fellowship to support students in high-tech subjects

This fellowship is awarded by the Ministry of Science and Technology to excellent MSc female students in high-tech subjects.

Paper and poster presentation at ACM-BCB 2019

Yaron will present Mira's study on predicting G-quadruplexes using deep neural neutworks.

We welcome M.Sc. student Sofia Aizenshtein

Sofia will be working on predicting DNA-binding prefrences of zinc finger proteins.

We welcome M.Sc. student Maor Asif

Maor will be working on inferring protein-DNA binding specificities from HT-SELEX data.

We are extremely happy to host MIT undergraduate student Baris Ekim

Baris will work on algorithms for generating compact universal k-mer hitting sets.

Deep learning poster at RECOMB 19

Mira will present her work on predicting G-quadruplexes using deep neural neutworks.

Yahel received the Yaacov Ben-Yitzhak Hacohen MSc fellowship

This fellowship is awarded to excellent MSc Engineering students.

We are extremely happy to host Stanford PhD student Tyler Shimko

Tyler will spend the next two months working with us on algorithms for sequence design problems.

We welcome M.Sc. student Yifat Shemesh

Yifat will be working on a joing project with Dr. Kobi Cohen on predicting RNA probing data.

We welcome M.Sc. student Yahel Salomon

Yahel will be working on a joing project with Dr. Ramon Birnbaum deciphering the transcriptional program of neuronal cell differentiation.

Deep learning poster at IBS 2018

Ilia Goland will present our poster on deep learning for microarray data preprocessing at IBS 2018.

Deep learning tutorial at ECCB 18

Yaron taught a tutorial on deep learning for predicting protein-DNA and -RNA binding.

Paper presentation at ECCB 18

Ilan Ben-Bassat presented a joint work on deep learning for protein-RNA binding.