Curriculum Vitae
Fernando Rodriguez, Ph.D.
ResearchID || ORCID || ResearchGate
Research Scientist
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Marine Biological Laboratory
Woods Hole, MA 02543
Tel. (508) 289-7510
Fax: (508) 457-4727
frodriguez@mbl.edu
http://www.mbl.edu/jbpc/staff/fernando-rodriguez/
Professional Positions
2018 – present
Research Scientist. Josephine Bay Paul Center, MBL
2015 – 2018
Research Associate. Josephine Bay Paul Center, MBL
Education and Postdoctoral Training
2010 – 2015
Postdoctoral position
Projects:
-Mobile genetic elements in sexual and ancient asexual taxa
-Reverse transcriptase-related genes and their biological significance
-Horizontal gene transfer as a source of evolutionary innovation in metazoans
Advisor: Irina Arkhipova – Marine Biological Laboratory
2004 – 2009
PhD, Biology, Molecular Biology and Biochemistry Program
Project: Phylogeography and evolutionary history in genus Rupicapra based on mitochondrial DNA
Advisor: Ana Dominguez Sanjurjo and Trinidad Perez Mendez – Universidad de Oviedo (Spain)
1998-2002
BS, Biology. Universidad de Oviedo (Spain)
Publications
Original Research in Peer-Reviewed Journals
Rodriguez, F., Arkhipova, I.R. (2023). An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes. In: Branco, M.R., de Mendoza Soler, A. (eds) Transposable Elements. Methods in Molecular Biology, vol 2607. Humana, New York, NY. Pubmed. PDF.
Darras, Hugo; De Souza Araujo, Natalia; Baudry, Lyam; Guiglielmoni, Nadège; Lorite, Pedro; Marbouty, Martial; Rodriguez, Fernando; Arkhipova, Irina; Koszul, Romain; Flot, Jean-François; Aron, Serge. (2022). Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: stepping stones towards genomic studies of hybridogenesis and thermal adaptation in desert ants. Peer Community Journal, Volume 2, article no. e40. DOI. PDF.
Fernando Rodriguez, Irina A. Yushenova, Daniel DiCorpo, Irina R. Arkhipova. (2022). Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA. Nature Communications 13, 1072. Pubmed. PDF.
Ruslan Kalendar, Francois Sabot, Fernando Rodriguez, Karine Alix, Lucia Natali and Gennady I. Karlov. (2021). Editorial: Mobile Elements and Plant Genome Evolution, Comparative Analyses, and Computational Tools. Frontiers in plant science vol. 12 735134. Pubmed. PDF.
Rory J. Craig, Irina A. Yushenova, Fernando Rodriguez, Irina R. Arkhipova. (2021). An Ancient Clade of Penelope-Like Retroelements with Permuted Domains Is Present in the Green Lineage and Protists, and Dominates Many Invertebrate Genomes. Molecular Biology and Evolution. Oct 27;38(11):5005-5020. Pubmed. PDF.
Isa Schön, Fernando Rodriguez, Matthew Dunn, Koen Martens, Michael Shribak, Irina R. Arkhipova. (2021). A Survey of Transposon Landscapes in the Putative Ancient Asexual Ostracod Darwinula stevensoni. Genes, 12(3), 401. Pubmed. PDF.
Reuben W Nowell , Christopher G Wilson, Pedro Almeida, Philipp H Schiffer, Diego Fontaneto, Lutz Becks, Fernando Rodriguez, Irina R Arkhipova, Timothy G Barraclough. (2021). Evolutionary dynamics of transposable elements in bdelloid rotifers. Elife Feb 5;10:e63194. Pubmed. PDF.
Olga A. Vakhrusheva, Elena A. Mnatsakanova, Yan R. Galimov, Tatiana V. Neretina, Evgeny S. Gerasimov, Sergey A. Naumenko, Svetlana G. Ozerova, Arthur O. Zalevsky, Irina A. Yushenova, Fernando Rodriguez, Irina R. Arkhipova, Aleksey A. Penin, Maria D. Logacheva, Georgii A. Bazykin & Alexey S. Kondrashov. (2020). Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga. Nature Communications volume 11, Article number: 6421. Pubmed. PDF.
Artem V. Nedoluzhko, Fedor S. Sharko, Brandon M. Lê, Svetlana V. Tsygankova, Eugenia S. Boulygina, Sergey M. Rastorguev, Alexey S. Sokolov, Fernando Rodriguez, Alexander M. Mazur, Alexey A. Polilov, Richard Benton, Michael B. Evgen’ev, Irina R. Arkhipova, Egor B. Prokhortchouk, Konstantin G. Skryabin1. (2019). A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum. PLOS ONE Dec 23;14(12):e0226485. Pubmed. PDF.
Fernando Rodriguez and Irina R. Arkhipova. Transposable elements and polyploid evolution in animals (2018). Current Opinion in Genetics & Development. 49:115-123. Pubmed. PDF.
Pérez T, Rodriguez F, Fernández M, Albornoz J, Domínguez A. Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus. (2017). Gene. 1119(17):30546-2. Pubmed. PDF.
Arkhipova IR, Yushenova IA, Rodriguez F. (2017) Giant reverse transcriptase-encoding transposable elements at telomeres. Mol Biol Evol. 34(9):2245-2257. Pubmed. PDF.
Rodriguez F, Kenefick AW, Arkhipova IR. LTR-Retrotransposons from Bdelloid Rotifers Capture Additional ORFs Shared between Highly Diverse Retroelement Types.(2017). Viruses. 11;9(4). Pubmed. PDF.
Rodriguez F, Arkhipova I. (2016). Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga. Genetics. 203(1):255-268. Pubmed. Selected article in Genetics Spotlight 2016. PDF.
Arkhipova IR, Yushenova IA, Rodriguez F. (2013). Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families. Mobile DNA. 4:19. Pubmed. PDF.
Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wajnberg E, Wirth B, Yushenova I, Kellis M, Kondrashov AS, Mark Welch DB, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K.(2013). Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature. 500:453-457. Pubmed. PDF.
Arkhipova IR, Rodriguez F. (2013). Genetic and epigenetic changes involving (retro)transposons in animal hybrids and polyploids. Cytogenet Genome Res. 140: 295-311. Pubmed. PDF.
Rodriguez F, Pérez T, Hammer S, Albornoz J, Domínguez A. (2010). Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus Rupicapra). BMC Evolutionary Biology. 10:222. Pubmed. PDF.
Rodriguez F, Hammer S, Pérez T, Suchentrunk F, Lorenzini R, Michallet J, Martinkova N, Albornoz J, Domínguez A. (2009). Cytochrome b phylogeography of chamois (Rupicapra spp.). Population contractions, expansions and hybridizations governed the diversification of the genus. Journal of heredity. 100: 47-55. Pubmed. PDF.
Rodriguez F, Albornoz J, Domínguez A. (2007). Cytochrome b pseudogene originated from a highly divergent mitochondrial lineage in genus Rupicapra. Journal of Heredity. 98: 243-249. Pubmed. PDF.
Reviews, Articles, Books, Book Chapters
Rodriguez F, Arkhipova I. Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga. Genetics Spotlight 2016. PDF.
Ana Domínguez Sanjurjo , Fernando Rodriguez Vazquez, Jesús Albornoz Pons, Trinidad Pérez Méndez. Book Chapter: El rebeco cantábrico, filogeografía e historia evolutiva. In: El Rebeco Cantábrico (Rupicapra pyrenaica parva), “Conservación y gestión de sus poblaciones”. Edited by Pérez-Barbería, F.J. & Palacios, B. Colección Naturaleza y Parques Nacionales. Serie Técnica. 2009. PDF.
Rodriguez F, Hammer S, Pérez T, Suchentrunk F, Lorenzini R, Michallet J, Martinkova N, Albornoz J, Domínguez A. (2008). Cytochrome b phylogeography of chamois (Rupicapra spp.): Population contractions, expansions and hybridizations characterize the diversification of the genus. 82nd Annual Meeting of the German Society of Mammalogy. Vienna, 14-18 September 2008. Mammalian Biology. 73 [Suppl. 1]: 16.
Domínguez, A. and Rodriguez, F. (2004). Beef traceability based on DNA fingerprinting. Feedinfo News Service.
Professional Service and Memberships
Invited Reviewer for:
BMC Biology, BMC Plant Biology journal, PeerJ, Molecular Biology and Evolution, Scientific Reports, Frontiers in Microbiology, Nucleid Acid Research, Mobile DNA. (https://publons.com/a/1320478).
Invited Guest Associate Editor for:
-Frontiers in Plant Systems and Synthetic Biology (Research topic: Mobile Elements and Plant Genome Evolution, Comparative Analyzes and Computational Tools).
-Genes (Basel).
Memberships:
• The Genetics Society of America. 2010 – present.
• AAAS/Science membership. Full membership in AAAS (the American Association for the Advancement of Science) sponsored by AAAS/Science Program for Excellence in Science (2 years full membership). 2015 – present.
• The Marine Biological Laboratory (MBL) Society. 2018 – present.
• The Global Invertebrate Genomics Alliance (GIGA). 2018 – present.
• The National Shellfisheries Association. 2020 – present.
Teaching
2008-Lecturer (invited speaker) in MSc Courses, Universidad de Oviedo
2005-Summer Course “Conservation and genetic characterization of plant resources”, Universidad de Oviedo
Research Mentoring
2010-2012-Graduate student supervision. Anupriya Dutta, Brown University.
2013-Undergraduate student supervision. Daniel DiCorpo, Brown University.
2014-Undergraduate student supervision. Aubrey W. Kenefick, Williams College.
2015-Undergraduate student supervision. Tatsiana Mello, Wellesley College.
2016-Undergraduate student supervision. Samantha Spear, Brown University; Brandon M. Le, Brown University; Vishok Srikanth, University of Chicago.
2017-Undergraduate student supervision. Jonathan N. Dow, Brown University; Brandon M. Le, Brown University; Katherine Dunham, Brown University; Laura Swain, University of Chicago.
2018-Undergraduate student supervision. Bria Metzger, Brown University.
2019-Undergraduate student supervision. Samuel Maffa, Brown University
2020-Undergraduate student supervision. Bridget Beaudoin, University of Massachusetts; Matthew Dunn, University of Massachusetts.
2021-Undergraduate student supervision. Ahmad Alkhatin, Brown University; Anton Tarazi, Brown University.
2022-Undergraduate student supervision. Daniel Pugatch, University of Massachusetts.High School student supervision. Feodor Morozov, Lexington High School; Adilya Sunyaev, High School.
Fernando Rodriguez 