Ofir received a fellowship from the Council for Higher Education
This fellowship is awarded to excellent PhD students from the periphery
Shaked's paper titled "Predicting the pathogenicity of bacterial genomes using widely spread protein families" is now published in BMC Bioinformatics
The Orenstein Lab is moving to Bar-Ilan University!
Yaron will hold a joint appointment in Computer Science and Life Sciences. Interested students are welcome to contact Yaron directly by email.
Ori participated in the RBP Footprint challenge
Ori participated in the RBP Footprint challenge and achieved the highest number of correct predictions that were experimentally validated
Ofir's paper titled "systematic evaluation of data processing and problem formulation of CRISPR off-target site prediction" is now published in Briefings in Bioinformatics
Shai's paper titled "DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 functional and endogenous on-target editing efficiency" is now published in Bioinformatics
Ofir's paper titled "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.
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.
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.
Eitamar compared RNA-binding models inferrred from RNA Bind-n-Seq and RNAcompete.
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'.
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.
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).
Maor developed a new algorithm to infer intrinsic DNA-binding preferences using deep neural networks.
Ofir will take part in the poster session at this year's MLCB, presenting his work on mRNA degradation dynamics.
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.
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.
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.
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.
Ilia Goland will present our poster on deep learning for microarray data preprocessing at IBS 2018.
Yaron taught a tutorial on deep learning for predicting protein-DNA and -RNA binding.
Ilan Ben-Bassat presented a joint work on deep learning for protein-RNA binding.