Mayrose Lab: Publications

Peer review articles

Loewenthal G, Rapoport D, Avram O, Moshe A, Itzkovitch A, Israeli O, Azouri D, Cartwright RA, Mayrose I, Pupko T. 2021. A probabilistic model for indel evolution: differentiating insertions from deletions. Molecular Biology and Evolution. 38(12): 5769-5781. [abs]

Glick L, Mayrose I. 2021. Panoramic: A package for constructing eukaryotic pan-genomes. Molecular Ecology Resources. 21(4):1393-1403. [abs]

Dorchin A, Shafir A; Neumann FH, Langgut D, Vereecken N, Mayrose I. 2021. Bee-flowers and bees, evidence for interaction-driven diversification. Proc Royal Soc B. 288:20210533. [abs]

Halabi K, Mayrose I. 2021. Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models. Journal of Molecular Evolution. 89(6):329-340. [abs]

Halabi K, Levy Karin E, Guéguen L, Mayrose I. 2021. A Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution. Systematic Biology. 70(3):608-622. [abs]

Azouri D, Abadi S, Mansour Y, Mayrose I, Pupko T. 2021. Harnessing machine learning to guide phylogenetic-tree search algorithms. Nature communication. 12:1983. [abs]

Rice A, Mayrose I. 2021. Model Adequacy Tests for Likelihood Models of Chromosome-Number Evolution. New Phytologist. 229(6):3602-3613. [abs] [pdf]

Halabi K, Mayrose I. 2021. Mechanisms Underlying Host Range Variation in Flavivirus: From Empirical Knowledge to Predictive Models. Journal of Molecular Evolution. 89(6):329-340. [abs]

Mayrose I, Lysak MA. 2021. The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches. Genome Biology and Evolution. 13(2):evaa220. [abs]

Glick L, Mayrose I. 2021. Panoramic: A package for constructing eukaryotic pan-genomes. Molecular Ecology Resources. 21(4):1393-1403. [abs] [pdf]

Loewenthal G, Abadi S, Avram O, Halabi K, Ecker N, Nagar N, Mayrose I, Pupko T. 2020. COVID-19 pandemic-related lockdown: response time is more important than its strictness. EMBO Molecular Medicine. 12(11):e13171 [abs] [Press Release (Hebrew)] [Media]

Abadi S, Avram O, Rosset S, Pupko T, Mayrose I. 2020. ModelTeller: model selection for optimal phylogenetic reconstruction using machine learning. Molecular Biology and Evolution. 37(11):3338–3352. [abs] [pdf]

Shafir A, Azouri D, Goldberg EE, Mayrose I. 2020. Heterogeneity in the rate of molecular sequence evolution substantially impacts the accuracy of detecting shifts in diversification rates. Evolution. 74(8):1620-1639. [abs]

Kattge J et al. 2020. TRY plant trait database – enhanced coverage and open access. Global Change Biology. 26(1):119-188. [abs]

Penner S, Dror B, Aviezer I, Bar-Lev Y, Salman-Minkov A, Mandakova T, Smarda P, Mayrose I, Sapir Y. 2020. Phenology and polyploidy in annual Brachypodium species (Poaceae) along the aridity gradient in Israel. Journal of Systematics and Evolution. 58(2):189-199. [abs]

Zenil-Ferguson R, Burleigh JG, Freyman WA, Igic B, Mayrose I, Goldberg EE. 2019. Interaction among ploidy, breeding system and lineage diversification. New Phytologist. 224(3):1252-1265. [abs] [pdf]

Abadi S, Azouri D, Pupko T, Mayrose I. 2019. Model selection may not be a mandatory step for phylogeny reconstruction. Nature Communication. 10:934. [abs]

Blackmon H, Justison J, Mayrose I, Goldberg EE. 2019. Meiotic drive shapes rates of karyotype evolution in mammals. Evolution. 73(3): 511-523. [abs]

Rice A, Smarda P, Novosolov M, Drori M, Glick L, Sabath N, Meiri S, Belmaker J, Mayrose I. 2019 The Global Biogeography of Polyploid Plants. Nature Ecology and Evolution. 3(2): 265-273 [abs]

Masrati G, Dwivedi M, Rimon M, Gluck-Margolin Y, Kessel A, Ashkenazy H, Mayrose I, Padan E, Ben-Tal N. 2018. Broad phylogenetic analysis of cation/proton antiporters reveals transport determinants. Nature Communications. 9:4205. [abs]

Drori M, Rice A, Einhorn M, Chay O, Glick L, Mayrose I. 2018. OneTwoTree: An online tool for phylogeny reconstruction. Molecular Ecology Resources. 18(6): 1492-1499. [abs] [pdf]

Vamosi JC, Magallon S, Mayrose I, Otto SP, Sauquet H. 2018. Macroevolutionary patterns of flowering plant speciation and extinction. Annual Review of Plant Biology. 69:685-706 [abs]

Hyams G, Abadi S, Lahav S, Avni A, Halperin E, Shani E, Mayrose I. 2018. CRISPys: Optimal sgRNA design for editing multiple members of a gene family using the CRISPR system. Journal of Molecular Biology. 430(15):2184-2195. [abs] [pdf]

Terezie M, Pouch M, Harmanov K, Zhan SH, Mayrose I, Lysak M. 2017. Multi-speed genome diploidization and diversification after an ancient allopolyploidization. Molecular Ecology. 26(22): 6445-6462. [abs]

Abadi S, Yan WX, Amar D, Mayrose I. 2017. A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action. PLoS Computational Biology. 13(10): e1005807. [abs] [pdf]

Levy-Karin E, Ashkenazy H, Wicke S, Pupko T, Mayrose I. 2017. TraitRateProp: A web server for the detection of trait-dependent evolutionary rate shifts in sequence sites. Nucleic Acids Research. 45(W1): W260-W264. [abs] [pdf]

Levy-Karin E, Wicke S, Pupko T, Mayrose I. 2017. An integrated model of phenotypic trait changes and site-specific sequence evolution. Systematic Biology. 66(6): 917-933. [abs] [pdf]

Goldberg EE, Otto SP, Vamosi JC, Mayrose I, Sabath N, Ming R, Ashman TL. 2017. Macroevolutionary synthesis of flowering plant sexual systems. Evolution. 71(4):898–912. [abs] [pdf]

Glick L, Sabath N, Ashman TL, Goldberg E, Mayrose I. 2016. Polyploidy and sexual system in angiosperms - is there an association? American Journal of Botany. 103(7):1223-1235. [abs] [pdf]

Zhan SH, Drori M, Goldberg E, Otto SP, Mayrose I. 2016. Phylogenetic evidence for cladogenetic polyploidy in land plants. American Journal of Botany. 103(7):1252-1258. [abs] [pdf]

Salman-Minkov A, Sabath N, and Mayrose I. 2016. Whole genome duplication as a key factor in crop domestication. Nature Plants. 2:16115. [abs] [Press Release (Hebrew)] [NaturePlants: news & Views]

Sabath N, Itescu Y, Feldman A, Meiri S, Mayrose I, Valenzuela N. 2016. Sex determination, longevity and the birth and death of reptilian species. Ecology and Evolution. 6(15):5207–5220. [abs] [pdf]

Ashkenazy H, Abadi S, Martz E, Chay O, Mayrose I, Pupko T, Ben-Tal N. 2016. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Research. 44(W1): W344–W350. [pdf], [abs]

Sabath N, Goldberg EE, Glick L, Einhorn M, Ashman TL, Ming R, Otto SP, Vamosi JC, Mayrose I. 2016. Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms. New Phytologist. 209(3): 1290-1300. [pdf], [abs]

Faigenbloom L, Rubinstein ND, Kloog Y, Mayrose I, Pupko T, Stein R. 2016. Regulation of alternative splicing at the single-cell level. Molecular Systems Biology. 11(12): 845. [pdf], [abs]

Feldman A, Sabath N, Pyron RA, Mayrose I, Meiri S. 2015. Body sizes and diversification rates of lizards, snakes, amphisbaenians and the tuatara. Global Ecology and Biogeography. 25(2): 187-197. [pdf], [abs]

Mayrose I, Freilich S. 2015. The Interplay between Scientific Overlap and Cooperation and the Resulting Gain in Co-Authorship Interactions. Plos One. 10(9): e0137856. [pdf], [abs] Faculty of 1000

Kopelman NM, Mayzel J, Jakobsson M, Rosenberg NA, Mayrose I. 2015. Clumpak: a program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources. 15(5): 1179-1191. [pdf], [abs]

Rice A, Glick L, Abadi S, Einhorn M, Kopelman NM, Salman-Minkov A, Mayzel J, Chay O, Mayrose, I. 2015. The Chromosome Counts Database (CCDB)–a community resource of plant chromosome numbers. New Phytologist. 206(1): 19-26. [pdf], [abs]

Mayrose I, Zhan SH, Rothfels CJ, Arrigo N, Barker MS, Rieseberg LH, Otto SP. 2015. Methods for studying polyploid diversification and the dead end hypothesis: a reply to Soltis et al. (2014). New Phytologist. 206(1): 27-35. [pdf], [abs]

The Tree of Sex Consortium - Bachtrog D, Mank JE, Peichel CL, Kirkpatrick M, Otto SP, Ashman T-L, Hahn MW, Kitano J, Mayrose I, Ming R, Perrin N, Ross L, Valenzuela N, Vamosi JC. 2014. Sex Determination: Why so many ways of doing it? PLoS Biology. 12(7): e1001899. [pdf], [abs] Science Made Easy coverage

Glick L, Mayrose I. 2014. ChromEvol: Assessing the Pattern of Chromosome Number Evolution and the Inference of Polyploidy along a Phylogeny. Molecular Biology and Evolution. 31(7): 1914-1922 [pdf], [abs]

The Tree of Sex Consortium - Ashman T-L, Bachtrog D, Blackmon H, Goldberg EE, Hahn MW, Kirkpatrick M, Kitano J, Mank JE, Mayrose I, Ming R, Otto SP, Peichel CL, Pennell MW, Perrin N, Valenzuela N, Vamosi JC. 2014. Tree of Sex: A database of sexual systems. Scientific Data. 1:140015 [pdf], [abs]

Zhan SH, Glick L, Tsigenopoulos CS, Otto SP, Mayrose I. 2014. Comparative analysis reveals that polyploidy does not decelerate diversification in fish. Journal of Evolutionary Biology. 27(2):391-403. [pdf], [abs]

Escudero M, Martin-Bravo S, Mayrose I, Fernandez-Mazuecos M, Fiz-Palacios O, Hipp A, Pimentel M, Jimenez-Mejias P, Valcarcel V, Vargas P, luceño M. 2014. Karyotypic changes through dysploidy persist longer over evolutionary time than polyploid changes. Plos One. 9(1):e58266. [pdf], [abs]

Mayrose I, Stern A, Burdelova EO, Sabo Y, Laham-Karam N, Zamostiano R, Bacharach E, Pupko T. 2013. Synonymous site conservation in the HIV-1 genome. BMC Evolutionary Biology. 13:164. [pdf], [abs]

Celniker G, Nimrod G, Ashkenazy H, Glaser F, Martz E, Mayrose I, Pupko T, Ben-Tal N. 2013. ConSurf: Using Evolutionary Data to Raise Testable Hypotheses about Protein Function. Israel Journal of Chemistry. 53(3-4):199–206. [pdf], [abs]

Mayrose I, Zhan SH, Rothfels CJ, Magnuson-Ford K, Barker MS, Rieseberg LH, Otto SP. 2011. Recently-formed polyploid plants diversify at lower rates. Science. 333(6047):1257. [pdf], [abs], Faculty of 1000, media release

Mayrose M, Kane N, Mayrose I, Rieseberg L. 2011 Increased growth in sunflower correlates with reduced defences and altered gene expression in response to biotic and abiotic stress. Molecular Ecology. 20(22):4683-4694 [pdf] [abs]

Rubinstein ND, Doron-Faigenboim A, Mayrose I, Pupko T. 2011. Evolutionary models accounting for layers of selection in protein coding genes and their impact on the inference of positive selection. Molecular Biology and Evolution. 28(12):3297-3308 [pdf] [abs]

Mayrose I, Otto SP. 2011. A Likelihood Method for Detecting Trait-Dependent Shifts in the Rate of Molecular Evolution. Molecular Biology and Evolution. 28:781-791. [pdf] [abs] Selected for Faculty of 1000, Treethinkers

Mayrose I, Barker MS, Otto SP. 2010.Probabilistic Models of Chromosome Number Evolution and the Inference of Polyploidy. Systematic Biology. 59(2):132-144 [pdf] [abs]

Stern A, Mayrose I, Shaul S, Gophna U, Pupko T. 2010. An Evolutionary Analysis of Lateral Gene Transfer in Thymidylate Synthase Enzymes. Systematic Biology. 59(2):212-225. [pdf] [abs]

Rubinstein ND, Mayrose I, Martz E, Pupko T. 2009. Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics. 10:287. [pdf] [abs]

Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PE, Rieseberg LH. 2009. The frequency of polyploid speciation in vascular plants. Proceedings of the National Academy of Sciences USA. 106(33):13875-13879. [pdf] [abs]. Selected for Faculty of 1000, Nature's Research Highlight, IU Press Release

Rubinstein ND, Mayrose I, Pupko T. 2009. A machine learning approach for predicting B-cell epitopes. Molecular Immunology. 46(5):840-847. [pdf] [abs]

Rubinstein ND, Mayrose I, Halperin D, Yekutieli D, Gershoni JM, Pupko T. 2008. Computational characterization of B-cell epitopes. Molecular Immunology. 45(12):3477-89. [pdf] [abs]

Mayrose I, Penn O, Erez E, Rubinstein ND, Shlomi T, Tarnovitski-Freund N, Bublil EM, Ruppin E, Sharan R, Gershoni JM, Martz E, Pupko T. 2007. Pepitope: Inferring epitopes based on affinity-selected peptides. Bioinformatics. 23(23):3244-3246. [pdf] [abs]

Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T. 2007. Towards realistic codon models: among site variability and dependency of synonymous and nonsynonymous rates. ECCB/ISMB 2007. Bioinformatics. 23:i319-i327. [pdf] [abs]. Selected for Faculty of 1000.

Bublil EM, Tarnovitski N, Mayrose I, Penn O, Roitburd A, Pupko T, Gershoni JM. 2007. Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins. 10;68(1):294-304 [pdf] [abs]

Mayrose I, Shlomi T, Rubinstein ND, Gershoni JM, Ruppin E, Sharan R, Pupko T. 2007. Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Research. 35(1):69-78. [pdf] [abs]

Mayrose I, Friedman N, Pupko T. 2005. A Gamma mixture model better accounts for among site rate heterogeneity. ECCB 2005. Bioinformatics. 21:ii151-ii158. [pdf] [abs]

Landau M, Mayrose I, Pupko T. Ben-Tal N. 2005. ConSurf 2005: Presenting the evolutionary rate of amino acid sites on protein structures. Nucleic Acids Research. 33: W299-W302. [pdf] [abs]

Faigenboim DA, Stern A, Mayrose I, Bacharach E, Pupko T. 2005. Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics. 21(9): 2101-2103. [pdf] [abs]

Mayrose I, Mitchell A, Pupko T. 2005. Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. Journal of Molecular Evolution. 60(3):345-353. [pdf] [abs]

Mayrose I, Graur D, Ben-Tal N, Pupko T. 2004. Comparison of site-specific rate-inference methods for protein sequences: Bayesian methods are superior. Molecular Biology and Evolution. 21:1781-1791. [pdf] [abs]

Weiss S, Gottfried I, Mayrose I, Khare SL, Xiang M, Dawson SJ, Avraham KB. 2003. The DFNA15 deafness mutation affects POU4F3 protein stability, localization, and transcriptional activity. Molecular and Cellular Biology. 23(22):7957-64. [pdf] [abs]

Pupko T, Bell RE, Mayrose I, Glaser F, Ben-Tal N. 2002. Rate4Site: an algorithmic tool for the identification of functional regions on proteins by surface mapping of Evolutionary Determinants within their Homologues. Bioinformatics. 18 Suppl: S71-S77. [pdf] [abs]

Chapters in Books

Pupko T and Mayrose I. 2020. A gentle introduction to probabilistic evolutionary models. In Scornavacca C, Delsuc F and Galtier N. (editors) Phylogenetics in the Genomic Era. [abs] [pdf]

Pupko T and Mayrose I. 2009. Probabilistic methods and rate heterogeneity. In Lodhi H and Muggleton S. (editors). Element of Computational Systems Biology, Wiley book series on Bioinformatics: Computational Techniques and Engineering. John Wiley and Sons Inc.