{"id":23,"date":"2025-09-30T17:11:37","date_gmt":"2025-09-30T17:11:37","guid":{"rendered":"https:\/\/faculty.eng.fau.edu\/assis\/?page_id=23"},"modified":"2026-11-10T19:06:01","modified_gmt":"2026-11-10T19:06:01","slug":"publications","status":"publish","type":"page","link":"https:\/\/faculty.eng.fau.edu\/assis\/publications\/","title":{"rendered":"PUBLICATIONS"},"content":{"rendered":"\n

<\/p>\n\n\n

Group member<\/strong>
*Equal contributions
\u2709Corresponding author<\/p>\n

Preprints<\/strong><\/h5>\n

Cohen ZP<\/b>\u2709<\/sup>, Perkin L, Frandsen PB, DeGiorgio M\u2709<\/sup>, Assis R<\/b>\u2709<\/sup>. Bacterial DNA invasion triggers transposable element proliferation and genome expansion. <\/a>bioRxiv<\/i> doi:10.64898\/2026.07.14.738529 (2026)<\/p>\n

Tran E<\/b>, Xu PN<\/b>, Assis R<\/b>\u2709<\/sup>. Ecological context structures duplication and mobilization of antibiotic and metal resistance genes in bacteria. <\/a>bioRxiv<\/i> doi:10.64898\/2026.02.03.703612 (2026)<\/p>\n

Macias Calix K<\/b>, Borges C, Oliveira ALN, Albuquerque de Luna SC, Cunha CMS, Siqueira AM, Campelo dos Santos AL<\/b>, DeGiorgio M, Lindo J, Assis R<\/b>\u2709<\/sup>. Genomic insights into ancestry and infectious disease in 17th century colonial Brazil. <\/a>bioRxiv<\/i> doi:10.64898\/2025.12.10.693243 (2025)<\/p>\n

Journal Publications<\/h5>\n

Piya AA<\/b>, Macias Calix K<\/b>, Assis R<\/b>\u2709<\/sup>. Gene function predicts divergence across molecular levels. <\/a>Scientific Reports<\/i>, in press (2026)<\/p>\n

Campelo dos Santos AL<\/b>, Assis R<\/b>\u2709<\/sup>. Adaptive deletion of functional duplicate genes in Drosophila<\/i>. <\/a>Journal of Evolutionary Biology<\/i> doi:voag074 (2026)<\/p>\n

LaBoone PA<\/b>, Piya AA<\/b>, Assis R<\/b>\u2709<\/sup>. Taxonomic context and genomic architecture jointly shape expression divergence across animals. <\/a>Evolution<\/i> 80:1561\u20131570 (2026)<\/p>\n

Lozano JR, Jangra S, DeGiorgio M, Assis R<\/b>, Adams RH\u2709<\/sup>. Discriminating models of trait evolution. <\/a>Evolution<\/i> 80:697\u2013710 (2026)<\/p>\n

Macias Calix K<\/b>, Piya AA<\/b>, Assis R<\/b>\u2709<\/sup>. Correlated evolution drives structural convergence of interacting proteins. <\/a>Journal of Molecular Evolution<\/i> 94:136\u2013148 (2026)<\/p>\n

Duncan M, DeGiorgio M, Assis R<\/b>\u2709<\/sup>, Adams RH\u2709<\/sup>. Robust regression rescues poor phylogenetic decisions. <\/a>BMC Ecology and Evolution<\/i> 25:108 (2025)<\/p>\n

Kanjilal R<\/b>, Campelo dos Santos AL<\/b>, Arnab SP, DeGiorgio M\u2709<\/sup>, Assis R<\/b>\u2709<\/sup>. Genomic anomaly detection with functional data analysis. <\/a>Genes<\/i> 16:710 (2025)<\/p>\n

Adams RH\u2709<\/sup>, Lozano JR, Duncan M, Green J, Assis R<\/b>*<\/sup>, DeGiorgio M*<\/sup>. A tale of too many trees: a conundrum for phylogenetic regression. <\/a>Molecular Biology and Evolution<\/i> 42:msaf032 (2025)<\/p>\n

Islam UI<\/b>, Campelo dos Santos AL<\/b>, Kanjilal R<\/b>, Assis R<\/b>\u2709<\/sup>. Learning genotype-phenotype associations from gaps in multi-species sequence alignments. <\/a>Briefings in Bioinformatics<\/i> 26:bbaf022 (2025)<\/p>\n

LaBoone PA<\/b>, Assis R<\/b>\u2709<\/sup>. Stress-induced constraint on expression noise of essential genes in E. coli<\/i>. <\/a>Journal of Molecular Evolution<\/i> 92:834-841 (2024)<\/p>\n

Campelo dos Santos AL<\/b>\u2709<\/sup>, DeGiorgio M*<\/sup>, Assis R<\/b>*<\/sup>. Predicting evolutionary targets and parameters of gene deletion from expression data. <\/a>Bioinformatics Advances<\/i> 4:vbae002 (2024)<\/p>\n

Adams RH\u2709<\/sup>, Cain Z, Assis R<\/b>*<\/sup>, DeGiorgio M*<\/sup>. Robust phylogenetic regression. <\/a>Systematic Biology<\/i> 73:140-157 (2024)<\/p>\n

Assis R<\/b>, Conant G, Holland B, Liberles DA\u2709<\/sup>, O’Reilly MM, Wilson AE. Models for the retention of duplicate genes and their biological underpinnings. <\/a>F1000Research<\/i> 12:1400 (2023)<\/p>\n

Piya AA<\/b>, DeGiorgio M, Assis R<\/b>\u2709<\/sup>. Predicting expression divergence and its evolutionary parameters between single-copy genes in two species. <\/a>Genome Biology and Evolution<\/i> 15:evad078 (2023)<\/p>\n

Alemrajabi M<\/b>*<\/sup>, Macias Calix K<\/b>*<\/sup>, Assis R<\/b>\u2709<\/sup>. Epistasis-driven evolution of the SARS-CoV-2 secondary structure. <\/a>Journal of Molecular Evolution<\/i> 90:429-437 (2022)<\/p>\n

Assis R<\/b>\u2709<\/sup>. No expression divergence despite transcriptional interference between nested protein-coding genes in mammals. <\/a>Genes<\/i> 12:1381 (2021)<\/p>\n

Chain FJJ, Assis R<\/b>\u2709<\/sup>. BLAST from the past: impacts of evolving approaches on studies of evolution by gene duplication. <\/a>Genome Biology and Evolution<\/i> 13:evab149 (2021)<\/p>\n

DeGiorgio M\u2709<\/sup>, Assis R<\/b>\u2709<\/sup>. Learning retention mechanisms and evolutionary parameters of duplicate genes from their expression data. <\/a>Molecular Biology and Evolution<\/i> 38:1209-1224 (2021)<\/p>\n

Jiang X<\/b>, Assis R<\/b>\u2709<\/sup>. Population-specific sequence and expression differentiation in Europeans. <\/a>Genome Biology and Evolution<\/i> 12:358\u2013369 (2020)<\/p>\n

Assis R<\/b>\u2709<\/sup>. Out of the testis, into the ovary: biased outcomes of gene duplication and deletion in Drosophila<\/i>. <\/a>Evolution<\/i> 73:1850-1862 (2019)<\/p>\n

Jiang X<\/b>, Assis R<\/b>\u2709<\/sup>. Rapid functional divergence after small-scale duplication in grasses. <\/a>BMC Evolutionary Biology<\/i> 19:97 (2019)<\/p>\n

Assis R<\/b>\u2709<\/sup>. Lineage-specific expression divergence in grasses is associated with male reproduction, host-pathogen defense, and domestication. <\/a>Genome Biology and Evolution<\/i> 11:207-219 (2019)<\/p>\n

Jiang X<\/b>, Assis R<\/b>\u2709<\/sup>. Natural selection drives rapid functional evolution of young Drosophila<\/i> duplicate genes. <\/a>Molecular Biology and Evolution<\/i> 34:3089-3098 (2017)<\/p>\n

Assis R<\/b>\u2709<\/sup>. Transcriptional interference promotes rapid expression divergence of Drosophila<\/i> nested genes. <\/a>Genome Biology and Evolution<\/i> 8:3149-3158 (2016)<\/p>\n

Perry BR<\/b>, Assis R<\/b>\u2709<\/sup>. CDROM: Classification of Duplicate gene RetentiOn Mechanisms. <\/a>BMC Evolutionary Biology<\/i> 16:82 (2016)<\/p>\n

Assis R<\/b>\u2709<\/sup>, Bachtrog D. Rapid divergence and diversification of mammalian duplicate gene functions. <\/a>BMC Evolutionary Biology<\/i> 15:138 (2015)<\/p>\n

Assis R<\/b>\u2709<\/sup>. Strong epistatic selection on the RNA secondary structure of HIV. <\/a>PLoS Pathogens<\/i> 10:e1004363 (2014)<\/p>\n

Assis R<\/b>\u2709<\/sup>. Drosophila<\/i> duplicate genes evolve new functions on the fly. <\/a>Fly<\/i> 8 (2014)<\/p>\n

Assis R<\/b>\u2709<\/sup>, Kondrashov AS. Conserved proteins are fragile. <\/a>Molecular Biology and Evolution<\/i> 31:419-424 (2014)<\/p>\n

Assis R<\/b>\u2709<\/sup>, Bachtrog D. Neofunctionalization of young duplicate genes in Drosophila<\/i>. <\/a>Proceedings of the National Academy of Sciences of the United States of America<\/i> 110:17409-17414 (2013)<\/p>\n

Assis R<\/b>\u2709<\/sup>, Zhou Q, Bachtrog D. Sex-biased transcriptome evolution in Drosophila<\/i>. <\/a>Genome Biology and Evolution<\/i> 29:1189-1200 (2012)<\/p>\n

Assis R<\/b>\u2709<\/sup>, Kondrashov AS. Nonallelic gene conversion is not GC-biased in Drosophila<\/i> or primates. <\/a>Molecular Biology and Evolution<\/i> 29:1291-1295 (2012)<\/p>\n

Assis R<\/b>\u2709<\/sup>, Kondrashov AS. A strong deletion bias in nonallelic gene conversion.<\/a>PLoS Genetics<\/i> 8:e1002508 (2012)<\/p>\n

Kondrashov AS, Assis R<\/b>\u2709<\/sup>. Bridges: A tool for identifying local similarities in long sequences. <\/a>Bioinformatics<\/i> 26:2055-2056 (2010)<\/p>\n

Assis R<\/b>\u2709<\/sup>, Kondrashov AS. Rapid repetitive element-mediated expansion of piRNA clusters in mammalian evolution. <\/a>Proceedings of the National Academy of Sciences of the United States of America<\/i> 106:7079-7082 (2009)<\/p>\n

Assis R<\/b>, Kondrashov AS, Koonin EV, Kondrashov FA\u2709<\/sup>. Nested genes and increasing organizational complexity of metazoan genomes. <\/a>Trends in Genetics<\/i> 23:475-478 (2008)<\/p>","protected":false},"excerpt":{"rendered":"

Group member*Equal contributions\u2709Corresponding author Preprints Cohen ZP\u2709, Perkin L, Frandsen PB, DeGiorgio M\u2709, Assis R\u2709. Bacterial DNA invasion triggers transposable […]<\/p>\n","protected":false},"author":101,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"disabled","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","theme-transparent-header-meta":"default","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"class_list":["post-23","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/faculty.eng.fau.edu\/assis\/wp-json\/wp\/v2\/pages\/23","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/faculty.eng.fau.edu\/assis\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/faculty.eng.fau.edu\/assis\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/faculty.eng.fau.edu\/assis\/wp-json\/wp\/v2\/users\/101"}],"replies":[{"embeddable":true,"href":"https:\/\/faculty.eng.fau.edu\/assis\/wp-json\/wp\/v2\/comments?post=23"}],"version-history":[{"count":37,"href":"https:\/\/faculty.eng.fau.edu\/assis\/wp-json\/wp\/v2\/pages\/23\/revisions"}],"predecessor-version":[{"id":175,"href":"https:\/\/faculty.eng.fau.edu\/assis\/wp-json\/wp\/v2\/pages\/23\/revisions\/175"}],"wp:attachment":[{"href":"https:\/\/faculty.eng.fau.edu\/assis\/wp-json\/wp\/v2\/media?parent=23"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}