The Arctic University Museum of Norway bastian.fromm@uit.no Tromsø

Bastian Fromm

group leader

Job description

Dr. Fromm is the leader of the recently established research group for biosystematics and paleotranscriptomics funded by the Tromsø Research foundation. The groups main interest is animal evolution using non-coding RNA genes such as microRNAs in modern, historic and ancient samples.

See project MIRevolution

  • Ernesto Aparicio-Puerta, Cristina Gómez-Martín, Stavros Giannoukakos, José María Medina, Chantal Scheepbouwer, Adrián García-Moreno et al.:
    sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms
    Nucleic Acids Research (NAR) 2022 DOI
  • Kevin Peterson, Alan Beavan, Peter J Chabot, Mark A McPeek, Davide Pisani, Bastian Fromm et al.:
    MicroRNAs as Indicators into the Causes and Consequences of Whole-Genome Duplication Events
    Molecular Biology and Evolution (MBE) 2022 ARKIV / DOI
  • Bastian Fromm, Eirik Høye, Diana Domanska, Xiangfu Zhong, Ernesto Aparicio-Puerta, Vladimir Ovchinnikov et al.:
    MirGeneDB 2.1: toward a complete sampling of all major animal phyla
    Nucleic Acids Research (NAR) 2022 ARKIV / DOI
  • Bastian Fromm, Xiangfu Zhong, Marcel Tarbier, Marc R. Friedländer, Michael Hackenberg :
    The limits of human microRNA annotation have been met
    RNA: A publication of the RNA Society 2022 DOI
  • Wenjing Kang, Bastian Fromm, Anna J. Houben, Eirik Høye, Daniela Bezdan, Carme Arnan et al.:
    MapToCleave: High-throughput profiling of microRNA biogenesis in living cells
    Cell reports 2021 ARKIV / DOI
  • Umberto Rosani, Enrico Bortoletto, Chang-Ming Bai, Beatriz Novoa, Antonio Figueras, Paola Venier et al.:
    Digging into bivalve miRNAomes: between conservation and innovation
    Philosophical Transactions of the Royal Society of London. Biological Sciences 2021 DOI
  • Rui-Si Hu, Xiao-Xuan Zhang, Qiao-Ni Ma, Hany M Elsheika, Muhammad Ehsan, Quan Zhao et al.:
    Differential expression of microRNAs and tRNA fragments mediate the adaptation of the liver fluke Fasciola gigantica to its intermediate snail and definitive mammalian hosts
    International Journal of Parasitology 2021 DOI
  • Baoqing Chen, Mihnea Paul Dragomir, Linda Fabris, Recep Bayraktar, Erik Knutsen, Xu Liu et al.:
    The long noncoding RNA CCAT2 induces chromosomal instability through BOP1-AURKB signaling
    Gastroenterology 2020 DOI
  • Eline P. Hansen, Bastian Fromm, Sidsel D. Andersen, Antonio Marcilla, Kasper L. Andersen, Anne Borup et al.:
    Exploration of extracellular vesicles from Ascaris suum provides evidence of parasite-host cross talk
    Journal of Extracellular Vesicles 2019 DOI
  • Christin Lund-Andersen, Sigve Nakken, Ståle Nygård, Bastian Fromm, Lars Birger Aasheim, Ben Davidson et al.:
    Integrative genomic analysis of peritoneal malignant mesothelioma: Understanding a case with extraordinary chemotherapy response
    Cold Spring Harbor Molecular Case Studies 2019 FULLTEKST / ARKIV / DOI
  • Bastian Fromm, Diana Ewa Domanska, Eirik Høye, Vladimir Ovchinnikov, Wenjing Kang, Ernesto Aparicio-Puerta et al.:
    MirGeneDB 2.0: the metazoan microRNA complement
    Nucleic Acids Research (NAR) 2019 ARKIV / DOI
  • Sinan Ugur Umu, Hilde Langseth, Cecilie Bucher-Johannessen, Bastian Fromm, Andreas Keller, Eckart Meese et al.:
    A comprehensive profile of circulating RNAs in human serum
    RNA Biology 2018 DOI
  • James E. Tarver, Richard S. Taylor, Mark N. Puttick, Graeme T. Lloyd, Walker Pett, Bastian Fromm et al.:
    Well-annotated microRNAomes do not evidence pervasive miRNA loss
    Genome Biology and Evolution (GBE) 2018 DOI
  • Jon Bråte, Ralf Stefan Neumann, Bastian Fromm, Arthur Alexander Blørstad Haraldsen, James E. Tarver, Hiroshi Suga et al.:
    Unicellular origin of the animal microRNA machinery
    Current Biology 11. October 2018 DATA / ARKIV / DOI
  • Bernhard Egger, Lutz Bachmann, Bastian Fromm :
    Atp8 is in the ground pattern of flatworm mitochondrial genomes
    BMC Genomics 2017 ARKIV / FULLTEKST / DOI
  • Boris Simovski, Daniel Vodak, Sveinung Gundersen, Diana Ewa Domanska, Abdulrahman Azab, Lars Holden et al.:
    GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome
    GigaScience 27. April 2017 ARKIV / FULLTEKST / DOI
  • Vladimir Y. Ovchinnikov, Viatcheslav A Mordvinov, Bastian Fromm :
    Extreme conservation of miRNA complements in opisthorchiids
    Parasitology international 2017 DOI
  • Alex Graudenzi, Claudia Cava, Gloria Bertoli, Bastian Fromm, Kjersti Flatmark, Giancarlo Mauri et al.:
    Pathway-based classification of breast cancer subtypes
    Frontiers in Bioscience 2017
  • Bastian Fromm, Vladimir Y. Ovchinnikov, Eirik Høye, Dolores Bernal, Michael Hackenberg, Antonio Marcilla :
    On the presence and immunoregulatory functions of extracellular microRNAs in the trematode Fasciola hepatica
    Parasite immunology (Print) 2017 DOI
  • Lutz Bachmann, Bastian Fromm, Luciana Patella de Azambuja, Walter Boeger :
    The mitochondrial genome of the egg-laying flatworm Aglaiogyrodactylus forficulatus (Platyhelminthes: Monogenoidea)
    Parasites & Vectors 2016 DOI
  • João Ramalho-Carvalho, Bastian Fromm, Rui Henrique, Carmen Jerónimo :
    Deciphering the function of non-coding RNAs in prostate cancer
    Cancer Metastasis Review 2016 DOI
  • Kjersti Flatmark, Erik Ulvolden Høye, Bastian Fromm :
    microRNAs as cancer biomarkers
    Scandinavian Journal of Clinical and Laboratory Investigation 2016 DOI
  • Vilde Drageset Haakensen, Vegard Nygaard, Liliana Greger, Miriam Ragle Aure, Bastian Fromm, Ida Rashida Khan Bukholm et al.:
    Subtype-specific micro-RNA expression signatures in breast cancer progression
    International Journal of Cancer 2016 DOI
  • Guillem Ylla, Bastian Fromm, Maria-Dolors Piulachs, Xavier Belles :
    The microRNA toolkit of insects
    Scientific Reports 2016 DOI
  • Bastian Fromm, Tyler Billipp, Liam E. Peck, Morten Johansen, James E. Tarver, Benjamin L. King et al.:
    A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome
    Annual Review of Genetics 2015 DOI
  • Bastian Fromm, María Trelis, Michael Hackenberg, Fernando Cantalapiedra, Dolores Bernal, Antonio Marcilla :
    The revised microRNA complement of Fasciola hepatica reveals a plethora of overlooked microRNAs and evidence for enrichment of immuno-regulatory microRNAs in extracellular vesicles
    International Journal of Parasitology 2015 DOI
  • Christoph Hahn, Bastian Fromm, Lutz Bachmann :
    Comparative genomics of flatworms (Platyhelminthes) reveals shared genomic features of ecto- and endoparastic neodermata
    Genome Biology and Evolution (GBE) 2014 DOI
  • Bastian Fromm, Susann Burow, Christoph Hahn, Lutz Bachmann :
    MicroRNA loci support conspecificity of Gyrodactylus salaris and G. thymalli (Platyhelminthes: Monogenea)
    International Journal of Parasitology 2014 DOI
  • Bastian Fromm, Merete Molton Worren, Christoph Hahn, Johannes Eivind Hovig, Lutz Bachmann :
    Substantial loss of conserved and gain of novel microRNA families in flatworms
    Molecular Biology and Evolution (MBE) 2013 DOI
  • Bastian Fromm, Philip David Harris, Lutz Bachmann :
    MicroRNA preparations from individual monogenean Gyrodactylus salaris – a comparison of six commercially available totalRNA extraction kits
    BMC Research Notes 2011 DOI
  • Bastian Fromm, Diana Domanska, Eirik Høye, Vladimir Ovchinnikov, Wenjing Kang, Ernesto Aparicio-Puerta et al.:
    Erratum: MirGeneDB 2.0: The metazoan microRNA complement (Nucleic Acids Research (2019) DOI: 10.1093/nar/gkz885)
    Nucleic Acids Research (NAR) 2020 DOI
  • Bastian Fromm, Wenjing Kang, Carlos Rovira, Alfonso Cayota, Kenneth W Witwer, Marc R. Friedländer et al.:
    Plant microRNAs in human sera are likely contaminants
    Journal of Nutritional Biochemistry 2019 DOI
  • Bastian Fromm, Juan Pablo Tosar, Yin Lu, Marc K. Halushka, Kenneth W. Witwer :
    Human and Cow Have Identical miR-21-5p and miR-30a-5p Sequences, Which Are Likely Unsuited to Study Dietary Uptake from Cow Milk
    Journal of Nutrition 2018 DOI
  • Marta Rodriguez, Cristina Bajo-Santos, Nina Pettersen Hessvik, Susanne Lorenz, Bastian Fromm, Viktor Berge et al.:
    Identification of non-invasive miRNAs biomarkers for prostate cancer by deep sequencing analysis of urinary exosomes
    Molecular Cancer 2017 DOI
  • Arthur Alexander Blørstad Haraldsen, Jon Bråte, Ralf Stefan Neumann, Bastian Fromm, Paul Eivind Grini, Kamran Shalchian-Tabrizi :
    Pre-metazoan origin of animal microRNAs
  • Bastian Fromm, Jutta Bachmann, Lutz Bachmann :
    Auf der Suche nach der genetischen Basis von Ekto- und Endoparasitismus der Plattwürmer
    Biologie in unserer Zeit 2015
  • Bastian Fromm, Jutta Bachmann, Lutz Bachmann :
    Tilpassninger i arvematerialet hos parasittiske flatormer
    Naturen 2015
  • Bastian Fromm, Merete Molton Worren, Christoph Hahn, Johannes Eivind Hovig, Lutz Bachmann :
    Evolution of Parasitism in Flatworms Is Accompanied by Substantial Loss of Conserved microRNA Families and Increase of Novel microRNAs
  • Bastian Fromm, Thomas D. Otto, Christoph Hahn, Philip David Harris, Lutz Bachmann :
    MiRCandRef a local assembly algorithm for description of microRNAs in non-genome organisms
  • Christoph Hahn, Philip David Harris, Bastian Fromm, Tor A. Bakke, Lutz Bachmann :
    Genomic insights into the evolution of the economically important monogenean flatworm Gyrodactylus salaris
  • Bastian Fromm, Lutz Bachmann, Philip David Harris :
    MicroRNA preparations from individual monogenean Gyrodactylus salaris – comparison of six commercially available “totalRNA” extraction kits
  • Bastian Fromm, Merete Molton Worren, Philip David Harris, Lutz Bachmann :
    The miRNA complement of Gyrodactylus salaris (Platyhelminthes, Monogenea)

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    Research interests

    Is there one driving force of animal evolution that explains the immense diversity of life and can it also help us to understand the exceptional success of parasitic species that affect us?

    The underlying and very strong feature of both processes seems in fact to be very small: microRNAs. Since the discovery that they are found in all animals and regulate important biological processes about 20 years ago, these tiny fine-tuners of cellular programs are among the most studied molecules ever. However, with more than 16,000 annual publications, the rapidly growing microRNA field became riddled with contradicting reports that hindered novel discoveries and applications. In the recent research of Dr. Bastian Fromm, this was addressed with the microRNA gene database MirGeneDB and the foundations to transform the microRNA field from a qualitative research area to the quantitative level, and ask fundamental questions, were laid.

    In his TFS-project MIRevolution, Dr. Fromm and his group will use novel sequencing approaches, state of the art single cell experiments and take advantage of the unique biodiversity in Tromso, to deepen the understanding of animal evolution, and parasites in particular. Using microRNAs, open questions in systematics and gene-regulation will be addressed. Facilitated by the ancient DNA laboratory at the Museum, and the Museums collection, the Fromm lab will further set out to use microRNAs in the novel research line paleotranscriptomics that, for the first time, enables gene expression studies in long-dead biological material.