Yaron Orenstein

Publication Activity (10 Years)

Years Active: 2011-2023
Publications (10 Years): 26

Top Topics

Protein Families

Top Venues

J. Comput. Biol.

Briefings Bioinform.

Publications

Mira Barshai, Barak Engel, Idan Haim, Yaron Orenstein
G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data. PLoS Comput. Biol. 19 (3) (2023)
Karin Elimelech-Zohar, Yaron Orenstein
An overview on nucleic-acid G-quadruplex prediction: from rule-based methods to deep neural networks. Briefings Bioinform. 24 (4) (2023)
Ofir Yaish, Yaron Orenstein
Computational modeling of mRNA degradation dynamics using deep neural networks. Bioinform. 38 (4) (2022)
Ofir Yaish, Maor Asif, Yaron Orenstein
A systematic evaluation of data processing and problem formulation of CRISPR off-target site prediction. Briefings Bioinform. 23 (5) (2022)
Maor Turner, Mira Barshai, Yaron Orenstein
rG4detector: convolutional neural network to predict RNA G-quadruplex propensity based on rG4-seq data. BCB (2022)
Shaked Naor-Hoffmann, Dina Svetlitsky, Neta Sal-Man, Yaron Orenstein, Michal Ziv-Ukelson
Predicting the pathogenicity of bacterial genomes using widely spread protein families. BMC Bioinform. 23 (1) (2022)
Mira Barshai, Alice Aubert, Yaron Orenstein
G4detector: Convolutional Neural Network to Predict DNA G-Quadruplexes. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (4) (2022)
Eitamar Tripto, Yaron Orenstein
A comparative analysis of RNA-binding proteins binding models learned from RNAcompete, RNA Bind-n-Seq and eCLIP data. Briefings Bioinform. 22 (6) (2021)
Jonathan Karin, Hagai Michel, Yaron Orenstein
MultiRBP: multi-task neural network for protein-RNA binding prediction. BCB (2021)
Yael Ben-Ari, Dan Flomin, Lianrong Pu, Yaron Orenstein, Ron Shamir
Improving the efficiency of de Bruijn graph construction using compact universal hitting sets. BCB (2021)
Yaron Orenstein
Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers. J. Comput. Biol. 27 (3) (2020)
Tyler Shimko, Polly Fordyce, Yaron Orenstein
DeCoDe: degenerate codon design for complete protein-coding DNA libraries. Bioinform. 36 (11) (2020)
Tyler C. Shimko, Polly M. Fordyce, Yaron Orenstein
DeCoDe: degenerate codon design for complete protein-coding DNA libraries. BCB (2020)
Baris Ekim, Bonnie Berger, Yaron Orenstein
A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. RECOMB (2020)
Mira Barshai, Yaron Orenstein
Predicting G-quadruplexes from DNA Sequences Using Multi-Kernel Convolutional Neural Networks. BCB (2019)
Mira Barshai, Yaron Orenstein
Predicting G-Quadruplexes from DNA Sequences Using Multi-Kernel Convolutional Neural Networks. BCB (2019)
Yaron Orenstein, Yun William Yu, Bonnie Berger
-Mers Using Joker Characters. J. Comput. Biol. 25 (11) (2018)
Yaron Orenstein
Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers. RECOMB (2018)
Ilan Ben-Bassat, Benny Chor, Yaron Orenstein
A deep neural network approach for learning intrinsic protein-RNA binding preferences. Bioinform. 34 (17) (2018)
Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford
Improving the performance of minimizers and winnowing schemes. Bioinform. 33 (14) (2017)
Yaron Orenstein
Computational Modeling of Protein-RNA Interactions. BCB (2017)
Yaron Orenstein, Ryan Kim, Polly Fordyce, Bonnie Berger
Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters. RECOMB (2017)
Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford
Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing. PLoS Comput. Biol. 13 (10) (2017)
Yaron Orenstein, Bonnie Berger
-mers. J. Comput. Biol. 23 (2) (2016)
Yaron Orenstein, Yuhao Wang, Bonnie Berger
RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data. Bioinform. 32 (12) (2016)
Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford
Compact Universal k-mer Hitting Sets. WABI (2016)
Yaron Orenstein, Bonnie Berger
Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. WABI (2015)
Yaron Orenstein, Ron Shamir
-mers with applications to protein-binding microarrays and synthetic enhancers. Bioinform. 31 (8) (2015)
Yaron Orenstein, Eran Mick, Ron Shamir
RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data. J. Comput. Biol. 20 (5) (2013)
Yaron Orenstein, Ron Shamir
-mers with applications to protein-binding microarrays and synthetic enhancers. Bioinform. 29 (13) (2013)
Yaron Orenstein, Dana Ron
Testing Eulerianity and connectivity in directed sparse graphs. Theor. Comput. Sci. 412 (45) (2011)