Yaron Orenstein

According to our database, Yaron Orenstein authored at least 31 papers between 2011 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

FiSSC: Finding smallest sequence covers to sets of degenerate reads with applications to RNA editing.

Ido Tziony, Jonathan Mandl, Kobi Shapira, Eli Eisenberg, Ely Porat, Yaron Orenstein

Proceedings of the 15th ACM International Conference on Bioinformatics, 2024

2023

An overview on nucleic-acid G-quadruplex prediction: from rule-based methods to deep neural networks.

Karin Elimelech-Zohar, Yaron Orenstein

Briefings Bioinform., July, 2023

G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data.

Mira Barshai, Barak Engel, Idan Haim, Yaron Orenstein

PLoS Comput. Biol., March, 2023

2022

G4detector: Convolutional Neural Network to Predict DNA G-Quadruplexes.

Mira Barshai, Alice Aubert, Yaron Orenstein

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Predicting the pathogenicity of bacterial genomes using widely spread protein families.

Shaked Naor-Hoffmann, Dina Svetlitsky, Neta Sal-Man, Yaron Orenstein, Michal Ziv-Ukelson

BMC Bioinform., 2022

Computational modeling of mRNA degradation dynamics using deep neural networks.

Ofir Yaish, Yaron Orenstein

Bioinform., 2022

DeepZF: improved DNA-binding prediction of C2H2-zinc-finger proteins by deep transfer learning.

Sofia Aizenshtein-Gazit, Yaron Orenstein

Bioinform., 2022

A systematic evaluation of data processing and problem formulation of CRISPR off-target site prediction.

Ofir Yaish, Maor Asif, Yaron Orenstein

Briefings Bioinform., 2022

rG4detector: convolutional neural network to predict RNA G-quadruplex propensity based on rG4-seq data.

Maor Turner, Mira Barshai, Yaron Orenstein

Proceedings of the BCB '22: 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Northbrook, Illinois, USA, August 7, 2022

2021

A comparative analysis of RNA-binding proteins binding models learned from RNAcompete, RNA Bind-n-Seq and eCLIP data.

Eitamar Tripto, Yaron Orenstein

Briefings Bioinform., 2021

MultiRBP: multi-task neural network for protein-RNA binding prediction.

Jonathan Karin, Hagai Michel, Yaron Orenstein

Proceedings of the BCB '21: 12th ACM International Conference on Bioinformatics, 2021

Improving the efficiency of de Bruijn graph construction using compact universal hitting sets.

Yael Ben-Ari, Dan Flomin, Lianrong Pu, Yaron Orenstein, Ron Shamir

Proceedings of the BCB '21: 12th ACM International Conference on Bioinformatics, 2021

2020

Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers.

Yaron Orenstein

J. Comput. Biol., 2020

DeCoDe: degenerate codon design for complete protein-coding DNA libraries.

Tyler Shimko, Polly Fordyce, Yaron Orenstein

Bioinform., 2020

DeepSELEX: inferring DNA-binding preferences from HT-SELEX data using multi-class CNNs.

Maor Asif, Yaron Orenstein

Bioinform., 2020

A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets.

Baris Ekim, Bonnie Berger, Yaron Orenstein

Proceedings of the Research in Computational Molecular Biology, 2020

2019

Predicting G-quadruplexes from DNA Sequences Using Multi-Kernel Convolutional Neural Networks.

Mira Barshai, Yaron Orenstein

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018

Joker de Bruijn: Covering <i>k</i>-Mers Using Joker Characters.

Yaron Orenstein, Yun William Yu, Bonnie Berger

J. Comput. Biol., 2018

A deep neural network approach for learning intrinsic protein-RNA binding preferences.

Ilan Ben-Bassat, Benny Chor, Yaron Orenstein

Bioinform., 2018

2017

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing.

Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford

PLoS Comput. Biol., 2017

Improving the performance of minimizers and winnowing schemes.

Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford

Bioinform., 2017

Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters.

Yaron Orenstein, Ryan Kim, Polly Fordyce, Bonnie Berger

Proceedings of the Research in Computational Molecular Biology, 2017

Computational Modeling of Protein-RNA Interactions.

Yaron Orenstein

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016

Efficient Design of Compact Unstructured RNA Libraries Covering All <i>k</i>-mers.

Yaron Orenstein, Bonnie Berger

J. Comput. Biol., 2016

RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.

Yaron Orenstein, Yuhao Wang, Bonnie Berger

Bioinform., 2016

Compact Universal k-mer Hitting Sets.

Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford

Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

2015

Design of shortest double-stranded DNA sequences covering all <i>k</i>-mers with applications to protein-binding microarrays and synthetic enhancers.

Yaron Orenstein, Ron Shamir

Bioinform., 2015

Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers.

Yaron Orenstein, Bonnie Berger

Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

2014

Discovering motifs using high-throughput in vitro data

Yaron Orenstein

PhD thesis, 2014

2013

RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data.

Yaron Orenstein, Eran Mick, Ron Shamir

J. Comput. Biol., 2013

2011

Testing Eulerianity and connectivity in directed sparse graphs.

Yaron Orenstein, Dana Ron

Theor. Comput. Sci., 2011