Publications
2026
Overcoming the widespread flaws in the annotation of vertebrate and mammalian selenoproteomes
Ticó M, Sullivan E, Guigó R, Mariotti M
PLOS Computational Biology 22 (1) e1013885
2025
Conservation and mechanism of the methionine reductase C family
Márquez De Los Santos M B, Sastre S, Costa D, Ferrer-Sueta G, Binolfi A, Mariotti M, Zeida A, Berkmen M, Mondino S, Manta B
Dietary Selenium Deficiency Accelerates the Onset of Aging-Related Gut Microbial Changes in Aged Telomere-Humanized Mice, With Akkermansia muciniphila Being the Most Prominent and Alleviating Selenium Deficiency-Induced Type 2 Diabetes
Huang Y-C, Lu H-Y, Zhang L, Olivier A, Wu T-L, Hsu C-Y, LeGrand C, Zeng H, Curran S, Wang Q, others
Aging Cell e70130
Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR)
Loughran G, Andreev D E, Terenin I M, Namy O, Mikl M, Yordanova M M, Mcmanus C J, Firth A E, Atkins J F, Fraser C S, others
Nature Structural & Molecular Biology 1--13
Pyranges v1: a Python framework for ultrafast sequence interval operations
Stovner E B, Ticó M, del Campo EM, Pallarès-Albanell J, Chawla K, Sætrom P, Mariotti M
bioRxiv (preprint) 2025--12
The Metazoan Selenoproteome
Ticó M, Mariotti M
Annual Review of Animal Biosciences 14
Tracing the vertebrate selenoproteome reveals expansions in ray-finned fishes and convergent depletions in tetrapods
Ticó M, Mariotti M
bioRxiv (preprint) 2025--05
Translon: a single term for translated regions
Świrski M I, Tierney J A S, Albà M M, Andreev D E, Aspden J L, Atkins J F, Bassani-Sternberg M, Berry M J, Biffo S, Boris-Lawrie K, others
Nature methods 1--5
2024
Abstract We010: In Vivo Partial Reprogramming of Cardiomyocytes to a Molecularly Rejuvenated State Ameliorates Cardiac Failure
De Lazaro I, Zhang B, Makarova N, Mariotti M, Gladyshev V, Mooney D
Circulation Research 135 (Suppl_1) AWe010--AWe010
Age-associated clonal B cells drive B cell lymphoma in mice
Castro J P, Shindyapina A V, Barbieri A, Ying K, Strelkova O S, Paulo J A, Tyshkovskiy A, Meinl R, Kerepesi C, Petrashen A P, others
Nature Aging 1--15
2023
Annotation, Diversity and Evolution of Selenocysteine-containing Oxidoreductases in Eukaryotes
Miñarro M T, Moragues S S, Makarova N, Mariotti M
Free Radical Biology and Medicine 208 S130--S131
In vivo reprogramming and epigenetic rejuvenation of adult cardiomyocytes ameliorate heart failure in mice
de Lázaro I, Zhang B, Makarova N, Mariotti M, Orejón-Sánchez T L, Tringides C M, Gladyshev V N, Mooney D J
bioRxiv (preprint) 2021--12
2022
Characterization of naked mole-rat hematopoiesis reveals unique stem and progenitor cell patterns and neotenic traits
Emmrich S, Trapp A, Tolibzoda Zakusilo F, Straight M E, Ying A K, Tyshkovskiy A, Mariotti M, Gray S, Zhang Z, Drage M G, others
The EMBO Journal 41 (15) e109694
Deterioration of the human transcriptome with age due to increasing intron retention and spurious splicing
Mariotti M, Kerepesi C, Oliveros W, Mele M, Gladyshev V N
BioRxiv (preprint) 2022--03
Selenocysteine-containing proteins
Mariotti M, Gladyshev V N
Redox Chemistry and Biology of Thiols 405--421
Selenoprotein TXNRD3 supports male fertility via the redox regulation of spermatogenesis
Dou Q, Turanov A A, Mariotti M, Hwang J Y, Wang H, Lee S-G, Paulo J A, Yim S H, Gygi S P, Chung J-J, others
Journal of Biological Chemistry 298 (8)
The selenophosphate synthetase family: A review
Manta B, Makarova N, Mariotti M
Free Radical Biology and Medicine 192 63--76
2021
A user's guide to the encyclopedia of DNA elements (ENCODE)
ENCODE Project Consortium
PLoS biology 9 (4) e1001046
Aging predisposes B cells to malignancy by activating c-Myc and perturbing the genome and epigenome
Shindyapina A V, Castro J P, Barbieri A, Strelkova O S, Paulo J A, Kerepesi C, Petrashen A P, Mariotti M, Meer M, Hu Y, others
preprint, Cancer Biology (preprint)
Genetic and phenotypic analysis of the causal relationship between aging and COVID-19
Ying K, Zhai R, Pyrkov T V, Shindyapina A V, Mariotti M, Fedichev P O, Shen X, Gladyshev V N
Communications Medicine 1 (1) 35
Genetic and Phenotypic Evidence for the Causal Relationship Between Aging and COVID-19
Zhai R, Pyrkov T, Shindyapina A, Mariotti M, Fedichev P, Shen X, Gladyshev V, Ying K
Innovation in Aging 5 (Suppl 1) 332--332
Integrative analysis reveals aged clonal B cells, microenvironment and c-Myc activation in the origin of age-related lymphoma
Shindyapina A V, Castro J P, Barbieri A, Strelkova O S, Paulo J A, Kerepesi C, Petrashen A P, Mariotti M, Meer M, Hu Y, others
Immune Aging Cancer 10 (2021.02) 23--432500
Naked mole rat TRF1 safeguards glycolytic capacity and telomere replication under low oxygen
Augereau A, Mariotti M, Pousse M, Filipponi D, Libert F, Beck B, Gorbunova V, Gilson E, Gladyshev V N
Science Advances 7 (8) eabe0174
Naked mole-rat hematopoietic stem and progenitors are highly quiescent with an inherent myeloid bias
Emmrich S, Trapp A, Zakusilo F T, Mariotti M, Straight M E, Zhang Z, Gray S, Drage M G, Ke Z, Takasugi M, others
bioRxiv (preprint) 2021--08
Roadmap for the use of base editors to decipher drug mechanism of action
Aparicio-Prat E, Yan D, Mariotti M, Bassik M, Hess G, Fortin J-P, Weston A, Xi H S, Stanton R
PloS one 16 (9) e0257537
2020
Bioinformatics of selenoproteins
Santesmasses D, Mariotti M, Gladyshev V N
Antioxidants & redox signaling 33 (7) 525--536
Facultative protein selenation regulates redox sensitivity, adipose tissue thermogenesis, and obesity
Jedrychowski M P, Lu G Z, Szpyt J, Mariotti M, Garrity R, Paulo J A, Schweppe D K, Laznik-Bogoslavski D, Kazak L, Murphy M P, others
Proceedings of the National Academy of Sciences 117 (20) 10789--10796
Genetic and phenotypic evidence for the causal relationship between aging and covid-19
Ying K, Zhai R, Pyrkov T V, Mariotti M, Fedichev P O, Shen X, Gladyshev V N
medRxiv (preprint) 2020--08
Molecular signatures of aneuploidy-driven adaptive evolution
Kaya A, Mariotti M, Tyshkovskiy A, Zhou X, Hulke M L, Ma S, Gerashchenko M V, Koren A, Gladyshev V N
Nature Communications 11 (1) 588
Systematic age-, organ-, and diet-associated ionome remodeling and the development of ionomic aging clocks
Zhang B, Podolskiy D I, Mariotti M, Seravalli J, Gladyshev V N
Aging cell 19 (5) e13119
Tolerance to selenoprotein loss differs between human and mouse
Santesmasses D, Mariotti M, Gladyshev V N
Molecular Biology and Evolution 37 (2) 341--354
Low steady-state oxidative stress inhibits adipogenesis by altering mitochondrial dynamics and decreasing cellular respiration
Fernando R, Wardelmann K, Deubel S, Kehm R, Jung T, Mariotti M, Vasilaki A, Gladyshev V N, Kleinridders A, Grune T, others
Redox biology 32 101507
2019
Baclaocos, Processive recoding and metazoan evolution of selenoprotein P: up to 132 UGAs in molluscs
Baclaocos J, Santesmasses D, Mariotti M, Bierla K, Vetick M B, Lynch S, McAllen R, Mackrill J J, Loughran G, Guigó R, others
Journal of molecular biology 431 (22) 4381--4407
The hematopoietic landscape at single-cell resolution reveals unexpected stem cell features in naked mole-rats
Emmrich S, Mariotti M, Takasugi M, Straight M E, Trapp A, Gladyshev V N, Seluanov A, Gorbunova V
bioRxiv (preprint) 859454
The tuatara genome: insights into vertebrate evolution from the sole survivor of an ancient reptilian order
Gemmell N J, Rutherford K, Prost S, Tollis M, Winter D, Macey J R, Adelson D L, Suh A, Bertozzi T, Grau J H, others
bioRxiv (preprint) 867069
Utilization of selenocysteine in early-branching fungal phyla
Mariotti M, Salinas G, Gabaldón T, Gladyshev V N
Nature microbiology 4 (5) 759--765
2018
A study of selenoproteins in atlantic salmon (Salmo salar) using hyphenated mass spectrometry and bioinformatics
Sele V, Perez M, Raab A, Mariotti M, Krupp E, Feldmann J, Sloth J J, Ørnsrud R, Berntssen M H G, Rasinger J D
9th Nordic Conference on Plasma Spectrochemistry 45--45
AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation
Yordanova M M, Loughran G, Zhdanov A V, Mariotti M, Kiniry S J, O’Connor P B F, Andreev D E, Tzani I, Saffert P, Michel A M, others
Nature 553 (7688) 356--360
Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity
Ma S, Avanesov A S, Porter E, Lee B C, Mariotti M, Zemskaya N, Guigo R, Moskalev A A, Gladyshev V N
Aging cell 17 (4) e12740
Molecular footprints of aquatic adaptation including bone mass changes in cetaceans
Zhou X, Sun D, Guang X, Ma S, Fang X, Mariotti M, Nielsen R, Gladyshev V N, Yang G
Genome biology and evolution 10 (3) 967--975
Secisearch3 and seblastian: In-silico tools to predict secis elements and selenoproteins
Mariotti M
Selenoproteins: Methods and Protocols 3--16
Selenoprofiles: A computational pipeline for annotation of selenoproteins
Santesmasses D, Mariotti M, Guigó R
Selenoproteins: Methods and Protocols 17--28
2017
Computational identification of the selenocysteine tRNA (tRNASec) in genomes
Santesmasses D, Mariotti M, Guigó R
PLOS Computational Biology 13 (2) e1005383
Cytochrome c peroxidase facilitates the beneficial use of H2O2 in prokaryotes
Kaya A, Mariotti M, Gladyshev V N
Proceedings of the National Academy of Sciences 114 (33) 8678--8680
Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein P
Mariotti M, Shetty S, Baird L, Wu S, Loughran G, Copeland P R, Atkins J F, Howard M T
Nucleic acids research 45 (22) 13004--13015
Selenoprotein T is required for pathogenic bacteria avoidance in Caenorhabditis elegans
Romanelli-Cedrez L, Carrera I, Otero L, Miranda-Vizuete A, Mariotti M, Alkema M J, Salinas G
Free Radical Biology and Medicine 108 174--182
2016
Evolution of selenophosphate synthetase
Mariotti M, Santesmasses D, Guigó R
Selenium: Its Molecular Biology and Role in Human Health 85--99
Evolution of selenophosphate synthetase family: emergence and relocation of function through independent duplications and recurrent subfunctionalization
Mariotti M, Santesmasses D, Capella-Gutierrez S, Mateo A, Arnan C, Johnson R, D'Aniello S, Yim S H, Gladyshev V N, Serras F, others
Genome Research 25 (9) 1256--1267
Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of the roles of multiple SECIS elements
Wu S, Mariotti M, Santesmasses D, Hill K E, Baclaocos J, Aparicio-Prat E, Li S, Mackrill J, Wu Y, Howard M T, others
Open Biology 6 (11) 160241
Identification of a selenium-dependent glutathione peroxidase in the blood-sucking insect Rhodnius prolixus
Dias F A, Gandara A C P, Perdomo H D, Gonçalves R S, Oliveira C R, Oliveira R L L, Citelli M, Polycarpo C R, Santesmasses D, Mariotti M, others
Insect biochemistry and molecular biology 69 105--114
Lokiarchaeota marks the transition between the archaeal and eukaryotic selenocysteine encoding systems
Mariotti M, Lobanov A V, Manta B, Santesmasses D, Bofill A, Guigó R, Gabaldón T, Gladyshev V N
Molecular biology and evolution 33 (9) 2441--2453
Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum
Heaphy S M, Mariotti M, Gladyshev V N, Atkins J F, Baranov P V
Molecular Biology and Evolution 33 (11) 2885--2889
Selenocysteine extinctions in insects
Mariotti M
Short Views on Insect Genomics and Proteomics: Insect Proteomics, Vol. 2 113--140
Selenoprotein Gene Nomenclature
Gladyshev V N, Arnér E S, Berry M J, Brigelius-Flohé R, Bruford E A, Burk R F, Carlson B A, Castellano S, Chavatte L, Conrad M, others
Journal of Biological Chemistry 291 (46) 24036--24040
2015
Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection
Mesquita R D, Vionette-Amaral R J, Lowenberger C, Rivera-Pomar R, Monteiro F A, Minx P, Spieth J, Carvalho A B, Panzera F, Lawson D, others
Proceedings of the National Academy of Sciences 201506226
The genomes of two key bumblebee species with primitive eusocial organization
Sadd B M, Barribeau S M, Bloch G, De Graaf D C, Dearden P, Elsik C G, Gadau J, Grimmelikhuijzen C J P, Hasselmann M, Lozier J D, others
Genome biology 16 (1) 1--32
Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
Mariotti M, Santesmasses D, Capella-Gutierrez S, Mateo A, Arnan C, Johnson R, D'Aniello S, Yim S H, Gladyshev V N, Serras F, others
Genome Research 25 (9) 1256--1267
2014
Pseudogenization of testis-specific Lfg5 predates human/Neanderthal divergence
Mariotti M, Smith T F, Sudmant P H, Goldberger G
Journal of human genetics 59 (5) 288--291
SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
Romagné F, Santesmasses D, White L, Sarangi G K, Mariotti M, Hübler R, Weihmann A, Parra G, Gladyshev V N, Guigó R, others
Nucleic acids research 42 (D1) D437--D443
The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima
Chipman A D, Ferrier D E K, Brena C, Qu J, Hughes D S T, Schröder R, Torres-Oliva M, Znassi N, Jiang H, Almeida F C, others
PLoS biology 12 (11) e1002005
2013
Computational genomics of selenoproteins
Mariotti M
Universitat Pompeu Fabra
SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins
Mariotti M, Lobanov A V, Guigo R, Gladyshev V N
Nucleic acids research 41 (15) e149--e149
2012
An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium, others
Nature 489 (7414) 57--74
Composition and evolution of the vertebrate and mammalian selenoproteomes
Mariotti M, Ridge P G, Zhang Y, Lobanov A V, Pringle T H, Guigo R, Hatfield D L, Gladyshev V N
PLoS One 7 (3) e33066
2011
A user's guide to the encyclopedia of DNA elements (ENCODE)
ENCODE Project Consortium
PLoS biology 9 (4) e1001046
2010
Genome sequence of the pea aphid Acyrthosiphon pisum
International Aphid Genomics Consortium
PLoS biology 8 (2) e1000313
Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes
Mariotti M, Guigó R
Bioinformatics 26 (21) 2656--2663
