Yaron Orenstein

39 papers B 3C 2Journal 23Unranked 10

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	EpiCRISPR: Improving CRISPR/Cas9 on- and off-target prediction by flanking sequences, epigenetic marks, and high-throughput datasets. BCB Alon Luboshitz, Michal Rahimi, Ayal Hendel, Yaron Orenstein
2025	—	`conf`	F-MoDA: Efficient Fourier-based motif discovery in attribution maps. MLCB Ofir Yaish, Yaron Orenstein
2025	J	`jnl`	GreedyMini: generating low-density DNA minimizers. Bioinform. Shay Golan, Ido Tziony, Matan Kraus, Yaron Orenstein, Arseny M. Shur
2024	J	`jnl`	DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 on-target editing efficiency in specific cellular contexts. Bioinform. Shai Elkayam, Ido Tziony, Yaron Orenstein
2024	—	`conf`	FiSSC: Finding smallest sequence covers to sets of degenerate reads with applications to RNA editing. BCB Ido Tziony, Jonathan Mandl, Kobi Shapira, Eli Eisenberg, Ely Porat, Yaron Orenstein
2023	J	`jnl`	An overview on nucleic-acid G-quadruplex prediction: from rule-based methods to deep neural networks. Briefings Bioinform. Karin Elimelech-Zohar, Yaron Orenstein
2023	J	`jnl`	G4mismatch: Deep neural networks to predict G-quadruplex propensity based on G4-seq data. PLoS Comput. Biol. Mira Barshai, Barak Engel, Idan Haim, Yaron Orenstein
2022	J	`jnl`	A systematic evaluation of data processing and problem formulation of CRISPR off-target site prediction. Briefings Bioinform. Ofir Yaish, Maor Asif, Yaron Orenstein
2022	J	`jnl`	Computational modeling of mRNA degradation dynamics using deep neural networks. Bioinform. Ofir Yaish, Yaron Orenstein
2022	J	`jnl`	DeepZF: improved DNA-binding prediction of C2H2-zinc-finger proteins by deep transfer learning. Bioinform. Sofia Aizenshtein-Gazit, Yaron Orenstein
2022	J	`jnl`	G4detector: Convolutional Neural Network to Predict DNA G-Quadruplexes. IEEE ACM Trans. Comput. Biol. Bioinform. Mira Barshai, Alice Aubert, Yaron Orenstein
2022	J	`jnl`	Predicting the pathogenicity of bacterial genomes using widely spread protein families. BMC Bioinform. Shaked Naor-Hoffmann, Dina Svetlitsky, Neta Sal-Man, Yaron Orenstein, Michal Ziv-Ukelson
2022	—	`conf`	rG4detector: convolutional neural network to predict RNA G-quadruplex propensity based on rG4-seq data. BCB Maor Turner, Mira Barshai, Yaron Orenstein
2021	J	`jnl`	A comparative analysis of RNA-binding proteins binding models learned from RNAcompete, RNA Bind-n-Seq and eCLIP data. Briefings Bioinform. Eitamar Tripto, Yaron Orenstein
2021	—	`conf`	Improving the efficiency of de Bruijn graph construction using compact universal hitting sets. BCB Yael Ben-Ari, Dan Flomin, Lianrong Pu, Yaron Orenstein, Ron Shamir
2021	—	`conf`	MultiRBP: multi-task neural network for protein-RNA binding prediction. BCB Jonathan Karin, Hagai Michel, Yaron Orenstein
2020	B	`conf`	A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting Sets. RECOMB Baris Ekim, Bonnie Berger, Yaron Orenstein
2020	—	`conf`	DeCoDe: degenerate codon design for complete protein-coding DNA libraries. BCB Tyler C. Shimko, Polly M. Fordyce, Yaron Orenstein
2020	J	`jnl`	DeCoDe: degenerate codon design for complete protein-coding DNA libraries. Bioinform. Tyler Shimko, Polly Fordyce, Yaron Orenstein
2020	J	`jnl`	DeepSELEX: inferring DNA-binding preferences from HT-SELEX data using multi-class CNNs. Bioinform. Maor Asif, Yaron Orenstein
2020	J	`jnl`	Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers. J. Comput. Biol. Yaron Orenstein
2019	—	`conf`	Predicting G-Quadruplexes from DNA Sequences Using Multi-Kernel Convolutional Neural Networks. BCB Mira Barshai, Yaron Orenstein
2019	—	`conf`	Predicting G-quadruplexes from DNA Sequences Using Multi-Kernel Convolutional Neural Networks. BCB Mira Barshai, Yaron Orenstein
2018	J	`jnl`	A deep neural network approach for learning intrinsic protein-RNA binding preferences. Bioinform. Ilan Ben-Bassat, Benny Chor, Yaron Orenstein
2018	J	`jnl`	Joker de Bruijn: Covering J. Comput. Biol. Yaron Orenstein, Yun William Yu, Bonnie Berger
2018	B	`conf`	Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers. RECOMB Yaron Orenstein
2017	—	`conf`	Computational Modeling of Protein-RNA Interactions. BCB Yaron Orenstein
2017	J	`jnl`	Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing. PLoS Comput. Biol. Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford
2017	J	`jnl`	Improving the performance of minimizers and winnowing schemes. Bioinform. Guillaume Marçais, David Pellow, Daniel Bork, Yaron Orenstein, Ron Shamir, Carl Kingsford
2017	B	`conf`	Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters. RECOMB Yaron Orenstein, Ryan Kim, Polly Fordyce, Bonnie Berger
2016	C	`conf`	Compact Universal k-mer Hitting Sets. WABI Yaron Orenstein, David Pellow, Guillaume Marçais, Ron Shamir, Carl Kingsford
2016	J	`jnl`	Efficient Design of Compact Unstructured RNA Libraries Covering All J. Comput. Biol. Yaron Orenstein, Bonnie Berger
2016	J	`jnl`	RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data. Bioinform. Yaron Orenstein, Yuhao Wang, Bonnie Berger
2015	J	`jnl`	Design of shortest double-stranded DNA sequences covering all Bioinform. Yaron Orenstein, Ron Shamir
2015	C	`conf`	Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers. WABI Yaron Orenstein, Bonnie Berger
2014	—	`—`	Discovering motifs using high-throughput in vitro data Yaron Orenstein
2013	J	`jnl`	Design of shortest double-stranded DNA sequences covering all Bioinform. Yaron Orenstein, Ron Shamir
2013	J	`jnl`	RAP: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data. J. Comput. Biol. Yaron Orenstein, Eran Mick, Ron Shamir
2011	J	`jnl`	Testing Eulerianity and connectivity in directed sparse graphs. Theor. Comput. Sci. Yaron Orenstein, Dana Ron