Publications
These are all publications related to the MIRevolution project.
A complete and continuously updated record of publications, citations, and scholarly output is available via my Google Scholar profile.
2026
| Peterson KJ, Clarke AW, Zolotarov G, Deline B, Lamb TD, McPeek MA, Martinez P, Fromm B. Exploring the Genotype-to-Phenotype Map Using Quantifiable Patterns in Metazoan Genomic and Morphological Data. American Naturalist. 2026. | March |
| Tarbier M, Mackowiak SD, Sekar V, Bonath F, Yapar E, Fromm B, Faridani O, Biryukova I, Friedländer MR. Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells. Genome Research. 2026. doi: 10.1101/gr.279914.124. PMID: 41526192. | January |
| The RNAcentral Consortium. RNAcentral in 2026: genes and literature integration. Nucleic Acids Research. 2026;54(D1):D303–D313. doi: 10.1093/nar/gkaf1329. PMID: 41404707. | January |
2025
| Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Dehasque M, Aslanzadeh M, Bozlak E, Brown K, van der Valk T, Kalogeropoulos P, Chacón-Duque JC, Biryukova I, Heintzman PD, Furugård C, Plotnikov V, Protopopov A, Andersson B, Ersmark E, Peterson KJ, Friedländer MR, Dalén L. Ancient RNA expression profiles from the extinct woolly mammoth. Cell. 2026. doi: 10.1016/j.cell.2025.10.025. PMID: 41240910. | November |
| Mardahl M, Hansen EP, Fromm B, Borup A, Whitehead B, Boysen AT, Stensballe A, Andersen KL, Williams AR, Jex AR, Gasser RB, Fredholm M, Thamsborg SM, Nejsum P. Analysis of Oesophagostomum dentatum excretory-secretory molecules and extracellular vesicles uncovers a repertoire of microRNAs shared with A. suum and T. suis and ES containing Paz and Piwi domain proteins implicated in RNAi signaling. International Journal for Parasitology. 2025. doi: 10.1016/j.ijpara.2025.10.006. PMID: 41173446. | October |
| Hackenberg M, Kalogeropoulos P, Peterson KJ, Friedländer MR, Fromm B. Knowing is not enough; we must apply: the case for rigorous microRNA annotation standards. Nucleic Acids Research. 2025. doi: 10.1093/nar/gkaf1049. | October |
| Javad-Zada MM, Zou X, Okamura K, Shang R, Garg A, Lee E, Joshua-Tor L, Fromm B, Lai EC. Repeated emergence of giant microRNA hairpins across invertebrates. Cell Reports. 2025. doi: 10.1016/j.celrep.2025.116243. PMID: 40934082. | September |
| Mutemi KN, Simakov O, Pan L, Santangeli L, Null RW, Handberg-Thorsager M, Vellutini BC, Peterson KJ, Fromm B, Larsson T, Savage EL, Lopez MO, Hercog R, Provaznik J, Ordonez-Rueda D, Azevedo N, Gazave E, Vervoort M, Tomancak P, Tan W, Winkler S, Benes V, Hui J, Helm C, Ozpolat BD, Arendt D. A genome resource for the marine annelid Platynereis spp. BMC Genomics. 2025. doi: 10.1186/s12864-025-11727-2. PMID: 40660120. | July |
| Papadopoulos N, Kulkarni S, Baranyi C, Fromm B, Setton E, Sharma PP, Wanninger A, Brenneis G. The genome of a sea spider corroborates a shared Hox cluster motif in arthropods with a reduced posterior tagma. BMC Biology. 2025. doi: 10.1186/s12915-025-02276-x. PMID: 40598291. | July |
| Herlyn H, Hembrom AA, Tosar JP, Mauer KM, Schmidt H, Dezfuli BS, Hankeln T, Bachmann L, Sarkies P, Peterson KJ, Fromm B. Substantial hierarchical reductions of genetic and morphological traits in the evolution of rotiferan parasites. Genome Biology and Evolution. 2025. doi: 10.1093/gbe/evaf124. PMID: 40577491. | June |
| Toft K, Mardahl M, Hedberg-Alm Y, Anlén K, Tyden E, Nielsen MK, Honoré ML, Fromm B, Nielsen LN, Nejsum P, Thamsborg SM, Cirera SM, Pihl TH. Evaluation of circulating microRNAs in plasma from horses with non-strangulating intestinal infarction and idiopathic peritonitis. The Veterinary Journal. 2025. doi: 10.1016/j.tvjl.2025.106378. PMID: 40374098. | October |
| Brown A, Lucas M, Alsos IG, Fromm B, Hudson S. The sedaDNA revolution and archaeology: Progress, challenges, and a research agenda. Journal of Archaeological Science. 2025. doi: 10.1016/j.jas.2024.106132. | February |
| Toft K, Honoré ML, Ripley NE, Nielsen MK, Mardahl M, Fromm B, Hedberg-Alm Y, Tyden E, Nielsen LN, Nejsum P, Thamsborg SM, Cirera SM, Pihl TH. Profiling host-and parasite-derived miRNAs associated with Strongylus vulgaris infection in horses. Veterinary Parasitology. 2025. doi: 10.1016/j.vetpar.2024.110379. PMID: 39721258. | March |
| Clarke AW*, Hoye E*, Hembrom AA, Paynter VM, Vinther J, Wyrozzemski L, Biryukova I, Formaggioni A, Ovchinnikov V, Herlyn H, Pierce A, Wu C, Aslanzadeh M, Cheneby J, Martinez P, Friedlander MR, Hovig E, Hackenberg M, Umu SU, Johansen M, Peterson KJ, Fromm B. MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families, and updated covariance models. Nucleic Acids Research. 2025. doi: 10.1093/nar/gkae1094. PMID: 39673268. | March |
| Toft K, Honoré ML, Ripley NE, Nielsen MK, Fromm B, Mardahl M, Nielsen LN, Nejsum P, Thamsborg SM, Cirera SM, Pihl TH. The microRNAome of Strongylus vulgaris larvae and their excretory/secretory products with identification of parasite-derived microRNAs in horse arterial tissue. International Journal for Parasitology. 2025. doi: 10.1016/j.ijpara.2025.10.005. PMID: 39510492. | February |
| Brown T, Mishra K, Elewa A, Iarovenko S, Subramanian E, Araus AJ, Petzold A, Fromm B, Friedländer MR, Suzuki M, Suzuki KT, Hayashi T, Toyoda A, Oliveira C, Osipova E, Leigh ND, Yun MH, Simon A. Chromosome-Scale Genome Assembly Reveals How Repeat Elements Shape Non-Coding RNA Landscapes Active During Newt Limb Regeneration. Cell Genomics. 2025. doi: 10.1016/j.xgen.2025.100761. PMID: 39874962. | January |
2024
| Schiffer PH, Natsidis P, Leite DJ, Robertson HE, Lapraz F, Marlétaz F, Fromm B, Baudry L, Simpson F, Høye E, Zakrzewski AC, Kapli P, Hoff KJ, Müller S, Marbouty M, Marlow H, Copley RR, Koszul R, Sarkies P, Telford MJ. Insights into early animal evolution from the genome of the xenacoelomorph worm Xenoturbella bocki. eLife. 2024. | August |
| Fromm B. A renaissance of microRNAs as taxonomic and phylogenetic markers in animals. Zoologica Scripta. 2024. | June |
| Sorger T, Fromm B. Clockwork Orangutan: microRNAs, thermoregulatory tradeoffs, and models of brain size evolution. bioRxiv. 2024. | March |
| Fromm B, Sorger T. Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy. iScience. 2024. | February |
| Yu D, Ren Y, Uesaka M, Ferrandez-Roldan A, Teraoka Y, Sun J, Yonezawa T, Kiryu I, Kohara Y, Tatsumi K, Kuratani S, Murakumo K, Hyodo S, Kikuchi K, Kondo M, Zhao M, Hara Y, Kuraku S. Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences. Nature Ecology & Evolution. 2024. | January |
2023
| Marmol-Sanchez E, Fromm B, Oskolkov N, Pochon Z, Kalogeropoulos P, Eriksson E, Biryukova I, Sekar V, Ersmark E, Andersson B, Dalen L. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Research. 2023. | July |
| Umu SU, Paynter VM, Trondsen H, Buschmann T, Rounge TB, Peterson KJ, Fromm B. Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine. Cell Genomics. 2023. | June |
| Jenike AE, Jenike KM, Peterson KJ, Fromm B*, Halushka MK*. Direct observation of the evolution of cell-type specific microRNA expression signatures supports the hematopoietic origin model of endothelial cells. Evolution & Development. 2023. | May |
| Høye E, Dagenborg VJ, Torgunrud A, Lund-Andersen C, Fretland Å, Lorenz S, Edwin B, Hovig E, Fromm B, Inderberg EM, Greiff V. T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases. GigaScience. 2023. | May |
2022
| Zolotarov G, Fromm B, Legnini I, Ayoub S, Polese G, Maselli V, Chabot PJ, Vinther J, Styfhals R, Seuntjens E, Cosmo AD, Peterson KJ, Rajewsky N. MicroRNAs are deeply linked to the emergence of the complex octopus brain. Science Advances. 2022. | November |
| Fromm B, Patil AH, Halushka MK. Comment on A Novel Circulating MicroRNA for the Detection of Acute Myocarditis. The New England Journal of Medicine. 2022;387(13):1240–1240. | September |
| Aparicio-Puerta E, Gómez-Martín C, Giannoukakos S, Medina JM, Scheepbouwer C, García-Moreno A, Carmona-Saez P, Fromm B, Pegtel M, Keller A, Marchal JA, Hackenberg M. sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. Nucleic Acids Research. 2022. | July |
| Fromm B, Zhong X, Tarbier M, Friedländer MR, Hackenberg M. The Limits of Human MicroRNA Annotation Have Been Met. RNA. 2022;28(6):781–785. | May |
| Høye E*, Fromm B*, Böttger PHM, Domanska D, Torgunrud A, Lund-Andersen C, Abrahamsen TW, Fretland ÅA, Dagenborg VJ, Lorenz S, Edwin B, Hovig E, Flatmark K. A Comprehensive Framework for Analysis of MicroRNA Sequencing Data in Metastatic Colorectal Cancer. NAR Cancer. 2022;4(1):zcab051. | March |
| Fromm B, Høye E, Domanska D, Zhong X, Aparicio-Puerta E, Ovchinnikov V, Umu SU, Chabot PJ, Kang W, Aslanzadeh M, Tarbier M. MirGeneDB 2.1: toward a complete sampling of all major animal phyla. Nucleic Acids Research. 2022;50(D1):D204–D210. | January |
| Peterson KJ, Beavan A, Chabot PJ, McPeek MA, Pisani D, Fromm B, Simakov O. MicroRNAs as Indicators into the Causes and Consequences of Whole-Genome Duplication Events. Molecular Biology and Evolution. 2022;39(1). | January |
2021
| Patil AH, Halushka MK, Fromm B. No evidence of paralogous loci or new bona fide microRNAs in telomere to telomere (T2T) genomic data. bioRxiv. 2021. | December |
| Kang W, Fromm B, Houben AJ, Høye E, Bezdan D, Arnan C, Thrane K, Asp M, Johnson R, Biryukova I, Friedländer MR. MapToCleave: High-Throughput Profiling of MicroRNA Biogenesis in Living Cells. Cell Reports. 2021. | November |