Group member
*Equal contributions
Corresponding author

Adams R, Lozano JR, Duncan M, Green J, Assis R*, DeGiorgio M*. A tale of too many trees: a conundrum for phylogenetic regression. bioRxiv doi.org10.1101/2024.02.16.580530 (2024)

Campelo dos Santos AL, DeGiorgio M*, Assis R*. Predicting evolutionary targest and parameters of gene deletion from expression data. Bioinformatics Advances, doi:vbae002 (2024)

Adams R, Cain Z, Assis R*, DeGiorgio M*. Robust phylogenetic regression. Systematic Biology, doi:syad070 (2023)

Assis R, Conant G, Holland B, Liberles DA, O'Reilly MM, Wilson AE. Models for the retention of duplicate genes and their biological underpinnings. F1000Research 12:1400 (2023)

Piya AA, DeGiorgio M, Assis R. Predicting expression divergence and its evolutionary parameters between single-copy genes in two species. Genome Biology and Evolution 15:evad078 (2023)

Alemrajabi M*, Macias Calix K*, Assis R. Epistasis-driven evolution of the SARS-CoV-2 secondary structure. Journal of Molecular Evolution doi:10.1007/s00239-022-10073-1 (2022)

Assis R. No expression divergence despite transcriptional interference between nested protein-coding genes in mammals. Genes 12:1381 (2021)

Chain FJJ, Assis R. BLAST from the past: impacts of evolving approaches on studies of evolution by gene duplication. Genome Biology and Evolution 13:evab149 (2021)

DeGiorgio M, Assis R. Learning retention mechanisms and evolutionary parameters of duplicate genes from their expression data. Molecular Biology and Evolution 38:1209-1224 (2021)

Jiang X, Assis R. Population-specific sequence and expression differentiation in Europeans. Genome Biology and Evolution 12:358–369 (2020)

Assis R. Out of the testis, into the ovary: biased outcomes of gene duplication and deletion in Drosophila. Evolution 73:1850-1862 (2019)

Jiang X, Assis R. Rapid functional divergence after small-scale duplication in grasses. BMC Evolutionary Biology 19:97 (2019)

Assis R. Lineage-specific expression divergence in grasses is associated with male reproduction, host-pathogen defense, and domestication. Genome Biology and Evolution 11:207-219 (2019)

Jiang X, Assis R. Natural selection drives rapid functional evolution of young Drosophila duplicate genes. Molecular Biology and Evolution 34:3089-3098 (2017)

Assis R. Transcriptional interference promotes rapid expression divergence of Drosophila nested genes. Genome Biology and Evolution 8:3149-3158 (2016)

Perry BR, Assis R. CDROM: Classification of Duplicate gene RetentiOn Mechanisms. BMC Evolutionary Biology 16:82 (2016)

Assis R, Bachtrog D. Rapid divergence and diversification of mammalian duplicate gene functions. BMC Evolutionary Biology 15:138 (2015)

Assis R. Strong epistatic selection on the RNA secondary structure of HIV. PLoS Pathogens 10:e1004363 (2014)

Assis R. Drosophila duplicate genes evolve new functions on the fly. Fly 8 (2014)

Assis R, Kondrashov AS. Conserved proteins are fragile. Molecular Biology and Evolution 31:419-424 (2014)

Assis R, Bachtrog D. Neofunctionalization of young duplicate genes in Drosophila. Proceedings of the National Academy of Sciences of the United States of America 110:17409-17414 (2013)

Assis R, Zhou Q, Bachtrog D. Sex-biased transcriptome evolution in Drosophila. Genome Biology and Evolution 29:1189-1200 (2012)

Assis R, Kondrashov AS. Nonallelic gene conversion is not GC-biased in Drosophila or primates. Molecular Biology and Evolution 29:1291-1295 (2012)

Assis R, Kondrashov AS. A strong deletion bias in nonallelic gene conversion.PLoS Genetics 8:e1002508 (2012)

Kondrashov AS, Assis R. Bridges: A tool for identifying local similarities in long sequences. Bioinformatics 26:2055-2056 (2010)

Assis R, Kondrashov AS. Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution. Proceedings of the National Academy of Sciences of the United States of America 106:7079-7082 (2009)

Assis R, Kondrashov AS, Koonin EV, Kondrashov FA. Nested genes and increasing organizational complexity of metazoan genomes. Trends in Genetics 23:475-478 (2008)