Simple and efficient network decomposition and synchronization. - Shlomo Moran; Sagi Snir (Theor. Comput. Sci., 2000)

Maximum likelihood on four taxa phylogenetic trees: analytic solutions. - Benny Chor; Amit Khetan; Sagi Snir (RECOMB, 2003)

Computational issues in phylogenetic reconstruction : analytic maximum likelihood solutions and convex recoloring. - Sagi Snir (2004)

The Homology Kernel: A Biologically Motivated Sequence Embedding into Euclidean Space. - Eleazar Eskin; Sagi Snir (CIBCB, 2005)

Using Semi-definite Programming to Enhance Supertree Resolvability. - Shlomo Moran; Satish Rao; Sagi Snir (WABI, 2005)

Phylogenetic Profiling of Insertions and Deletions in Vertebrate Genomes. - Sagi Snir; Lior Pachter (RECOMB, 2006)

Maximum likelihood of phylogenetic networks. - Guohua Jin; Luay Nakhleh; Sagi Snir; Tamir Tuller (Bioinform., 2006)

Maximum Likelihood Molecular Clock Comb: Analytic Solutions. - Benny Chor; Amit Khetan; Sagi Snir (J. Comput. Biol., 2006)

Using Max Cut to Enhance Rooted Trees Consistency. - Sagi Snir; Satish Rao (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Connected Coloring Completion for General Graphs: Algorithms and Complexity. - Benny Chor; Michael R. Fellows; Mark A. Ragan; Igor Razgon; Frances A. Rosamond; Sagi Snir (COCOON, 2007)

A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. - Guohua Jin; Luay Nakhleh; Sagi Snir; Tamir Tuller (ISBRA, 2007)

Efficient parsimony-based methods for phylogenetic network reconstruction. - Guohua Jin; Luay Nakhleh; Sagi Snir; Tamir Tuller (Bioinform., 2007)

Restricting SBH ambiguity via restriction enzymes. - Steven Skiena; Sagi Snir (Discret. Appl. Math., 2007)

Incorporating homologues into Sequence Embeddings for protein Analysis. - Eleazar Eskin; Sagi Snir (J. Bioinform. Comput. Biol., 2007)

Efficient approximation of convex recolorings. - Shlomo Moran; Sagi Snir (J. Comput. Syst. Sci., 2007)

Fast and reliable reconstruction of phylogenetic trees with very short edges. - Ilan Gronau; Shlomo Moran; Sagi Snir (SODA, 2008)

Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. - Sagi Snir; Tamir Tuller (WABI, 2008)

Short Quartet Puzzling: A New Quartet-Based Phylogeny Reconstruction Algorithm. - Sagi Snir; Tandy J. Warnow; Satish Rao (J. Comput. Biol., 2008)

Convex recolorings of strings and trees: Definitions, hardness results and algorithms. - Shlomo Moran; Sagi Snir (J. Comput. Syst. Sci., 2008)

Hadamard Conjugation for the Kimura 3ST Model: Combinatorial Proof Using Path Sets. - Michael D. Hendy; Sagi Snir (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

The Net-HMM Approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. - Sagi Snir; Tamir Tuller (J. Bioinform. Comput. Biol., 2009)

Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. - Guohua Jin; Luay Nakhleh; Sagi Snir; Tamir Tuller (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space. - Sagi Snir; Edward N. Trifonov (J. Comput. Biol., 2010)

Quartets MaxCut: A Divide and Conquer Quartets Algorithm. - Sagi Snir; Satish Rao (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

Tracing the Most Parsimonious Indel History. - Sagi Snir; Lior Pachter (J. Comput. Biol., 2011)

A Linear Time Approximation Scheme for Maximum Quartet Consistency on Sparse Sampled Inputs. - Sagi Snir; Raphael Yuster (SIAM J. Discret. Math., 2011)

Partial convex recolorings of trees and galled networks: Tight upper and lower bounds. - Shlomo Moran; Sagi Snir; Wing-Kin Sung (ACM Trans. Algorithms, 2011)

Recovering the Tree-Like Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis. - Sebastien Roch; Sagi Snir (RECOMB, 2012)

Universal Pacemaker of Genome Evolution. - Sagi Snir; Yuri I. Wolf; Eugene V. Koonin (PLoS Comput. Biol., 2012)

Fast and reliable reconstruction of phylogenetic trees with indistinguishable edges. - Ilan Gronau; Shlomo Moran; Sagi Snir (Random Struct. Algorithms, 2012)

Reconstructing Approximate Phylogenetic Trees from Quartet Samples. - Sagi Snir; Raphael Yuster (SIAM J. Comput., 2012)

Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: A Probabilistic Analysis. - Sebastien Roch; Sagi Snir (J. Comput. Biol., 2013)

Pacemaker Partition Identification. - Sagi Snir (WABI, 2014)

On the number of genomic pacemakers: a geometric approach. - Sagi Snir (Algorithms Mol. Biol., 2014)

On the Compatibility of Quartet Trees. - Noga Alon; Sagi Snir; Raphael Yuster (SIAM J. Discret. Math., 2014)

Gene-Gene Interactions Detection Using a Two-stage Model. - Zhanyong Wang; Jae Hoon Sul; Sagi Snir; José Antonio Lozano 001; Eleazar Eskin (J. Comput. Biol., 2015)

Detecting Horizontal Gene Transfer between Closely Related Taxa. - Orit Adato; Noga Ninyo; Uri Gophna; Sagi Snir (PLoS Comput. Biol., 2015)

A Statistical Framework to Identify Deviation from Time Linearity in Epigenetic Aging. - Sagi Snir; Bridgett M. Vonholdt; Matteo Pellegrini (PLoS Comput. Biol., 2016)

Applying meta-analysis to genotype-tissue expression data from multiple tissues to identify eQTLs and increase the number of eGenes. - Dat Duong; Lisa Gai; Sagi Snir; Eun Yong Kang; Buhm Han; Jae Hoon Sul; Eleazar Eskin (Bioinform., 2017)

Multi-SpaM: A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees. - Thomas Dencker; Chris-André Leimeister; Michael Gerth; Christoph Bleidorn; Sagi Snir; Burkhard Morgenstern (RECOMB-CG, 2018)

Greedy Partition Distance Under Stochastic Models - Analytic Results. - Sagi Snir (ISBRA, 2019)

Prokaryotic evolutionary mechanisms accelerate learning. - Sagi Snir; Ben Yohay (Discret. Appl. Math., 2019)

A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized Hoeffding Inequality. - Eliran Avni; Sagi Snir (J. Comput. Biol., 2019)

Bounds on Identification of Genome Evolution Pacemakers. - Sagi Snir (J. Comput. Biol., 2019)

Extending the Evolvability Model to the Prokaryotic World: Simulations and Results on Real Data. - Ben Yohay; Sagi Snir (J. Comput. Biol., 2019)

The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework. - Colin Farrell; Sagi Snir; Matteo Pellegrini (Bioinform., 2020)

Inference of mutability landscapes of tumors from single cell sequencing data. - Viachaslau Tsyvina; Alex Zelikovsky; Sagi Snir; Pavel Skums (PLoS Comput. Biol., 2020)

Private Epigenetic PaceMaker Detector Using Homomorphic Encryption - Extended Abstract. - Meir Goldenberg; Sagi Snir; Adi Akavia (ISBRA, 2022)

On the quartet distance given partial information. - Sagi Snir; Osnat Weissberg; Raphael Yuster (J. Graph Theory, 2022)

Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics - Extended Abstract. - Guy Katriel; Udi Mahanaymi; Christoph Koutschan; Doron Zeilberger; Mike A. Steel; Sagi Snir (ISBRA, 2023)

Inferring Temporally Consistent Migration Histories. - Mrinmoy Saha Roddur; Sagi Snir; Mohammed El-Kebir (WABI, 2023)

Identifying epigenetic aging moderators using the epigenetic pacemaker. - Colin Farrell; Chanyue Hu; Kalsuda Lapborisuth; Kyle Pu; Sagi Snir; Matteo Pellegrini (Frontiers Bioinform., 2023)

Privacy Preserving Epigenetic PaceMaker: Stronger Privacy and Improved Efficiency. - Meir Goldenberg; Loay Mualem; Amit Shahar; Sagi Snir; Adi Akavia (RECOMB, 2024)

Gene-Adjacency-Based Phylogenetics Under a Stochastic Gain-Loss Model. - Yoav Dvir; Shelly Brezner; Sagi Snir (RECOMB-CG, 2024)

On the Distribution of Synteny Blocks Under a Neutral Model of Genome Dynamics. - Sagi Snir; Yuri I. Wolf; Shelly Brezner; Eugene V. Koonin; Mike A. Steel (RECOMB-CG, 2024)

Enforcing Temporal Consistency in Migration History Inference. - Mrinmoy Saha Roddur; Sagi Snir; Mohammed El-Kebir (J. Comput. Biol., 2024)

Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach. - Yoav Dvir; Sagi Snir (RECOMB, 2025)