Bastian Fromm
group leader
Job description
Dr. Fromm is the leader of the 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. The group employs cutting edge molecular biology methods (single cell sequencing) and computational tools (Machine Learning on covariance models)
See project MIRevolution
Daqi Yu,
Yandong Ren,
Masahiro Uesaka,
Alan Beavan,
Matthieu Muffato,
Jieyu Shen
et al.:
Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences
Nature Ecology and Evolution 2024 DOI
Bastian Fromm,
Thomas Sorger
:
Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy
iScience 2024 DOI
Emilio Mármol-Sánchez,
Bastian Fromm,
Nikolay Oskolkov,
Zoé Pochon,
Panagiotis Kalogeropoulos,
Eli Eriksson
et al.:
Historical RNA expression profiles from the extinct Tasmanian tiger
Ana E. Jenike,
Katharine M. Jenike,
Kevin J. Peterson,
Bastian Fromm,
Marc K. Halushka
:
Direct observation of the evolution of cell-type-specific microRNA expression signatures supports the hematopoietic origin model of endothelial cells
Sinan Ugur Umu,
Vanessa Molin Paynter,
Håvard Trondsen,
Tilo Buschmann,
Trine Ballestad Rounge,
Kevin J. Peterson
et al.:
Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine
Eirik Høye,
Vegar Johansen Dagenborg,
Annette Torgunrud Kristensen,
Christin Lund-Andersen,
Åsmund Avdem Fretland,
Susanne Lorenz
et al.:
T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases
Eirik Høye,
Bastian Fromm,
Paul H.M. Böttger,
Diana Domanska,
Annette Torgunrud Kristensen,
Christin Lund-Andersen
et al.:
A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer
Grygoriy Zolotarov,
Bastian Fromm,
Ivano Legnini,
Salah Ayoub,
Gianluca Polese,
Valeria Maselli
et al.:
MicroRNAs are deeply linked to the emergence of the complex octopus brain
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
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
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
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
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
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 for Parasitology 2021 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
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
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
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
Bastian Fromm,
Diana Ewa Domanska,
Eirik Høye,
Vladimir Ovchinnikov,
Wenjing Kang,
Ernesto Aparicio-Puerta
et al.:
MirGeneDB 2.0: the metazoan microRNA complement
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
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
Vladimir Y. Ovchinnikov,
Viatcheslav A Mordvinov,
Bastian Fromm
:
Extreme conservation of miRNA complements in opisthorchiids
Parasitology international 2017 DOI
Bernhard Egger,
Lutz Bachmann,
Bastian Fromm
:
Atp8 is in the ground pattern of flatworm mitochondrial genomes
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
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
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
Guillem Ylla,
Bastian Fromm,
Maria-Dolors Piulachs,
Xavier Belles
:
The microRNA toolkit of insects
Scientific Reports 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
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
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 for Parasitology 2015 DOI
Bastian Fromm,
Jutta Bachmann,
Lutz Bachmann
:
In search for the genetic basis of ectoparasitism and endoparasitism of flatworms
Biologie in unserer Zeit 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 for 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,
Arun H. Patil,
Marc K. Halushka
:
A Novel Circulating MicroRNA for the Detection of Acute Myocarditis
New England Journal of Medicine 2022 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
2016
Bastian Fromm,
Jutta Bachmann,
Lutz Bachmann
:
Tilpassninger i arvematerialet hos parasittiske flatormer
Naturen 2015
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,
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
2013
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
2012
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
2012
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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.
