Publications
2024
| Peterson, K.J., Clarke, A., Zolotarov, G., Deline, B., McPeek, M., Martinez, P. and Fromm, B., 2024. "Capturing changes to animal complexity from quantifiable patterns in genomic data". bioRxiv, pp.2024-08. | August |
| Schiffer, P.H., Natsidis, P., Leite, D.J., Robertson, H.E., Lapraz, F., Marlétaz, F., Fromm, B., Baudry, L., Simpson, F., Høye, E. and Zakrzewski, A.C., 2024. "Insights into early animal evolution form the genome of the xenacoelomorph worm Xenoturbella bocki". Elife, 13, p.e94948. | August |
| Herlyn, H., Hembrom, A.A., Tosar, J.P., Mauer, K.M., Schmidt, H., Dezfuli, B.S., Hankeln, T., Bachmann, L., Sarkies, P., Peterson, K.J. and Fromm, B., 2024. "Substantial hierarchical reductions of genetic and morphological traits in the evolution of rotiferan parasites". bioRxiv, pp.2024-08. | August |
| Fromm, B., 2024. "A renaissance of microRNAs as taxonomic and phylogenetic markers in animals". Zoologica Scripta. | June |
| Fromm, B. and Sorger, T., 2024. "Clockwork Orangutan: microRNAs, thermoregulatory tradeoffs, and the evolution of brain size." bioRxiv, pp.2024-05. | March |
| Tarbier, M., Mackowiak, S.D., Sekar, V., Bonath, F., Yapar, E., Fromm, B., Faridani, O.R., Biryukova, I. and Friedländer, M.R., 2024. "Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells". bioRxiv, pp.2024-03. | March |
| Fromm, B., & Sorger, T. (2023). "Rapid adaptation of cellular metabolic rate to the MicroRNA complements of mammals and its relevance to the evolution of endothermy". iScience, 27(2), 108740. | February |
| Yu, D., Ren, Y., Uesaka, M. et al. "Hagfish genome elucidates vertebrate whole-genome duplication events and their evolutionary consequences". Nat Ecol Evol 8, 519–535 (2024). | January |
2023
| Marmol-Sanchez, E., Fromm, B., Oskolkov, N., Pochon, Z., Kalogeropoulos, P., Eriksson, E., Biryukova, I., Sekar, V., Ersmark, E., Andersson, B. and Dalen, L., 2023. "Historical RNA expression profiles from the extinct Tasmanian tiger". Genome Research, pp.gr-277663. | July |
| June | |
| , , , , & (2023). "Direct observation of the evolution of cell-type specific microRNA expression signatures supports the hematopoietic origin model of endothelial cells." Evolution & Development, 1– 14. | May |
| Høye, E., Dagenborg, V.J., Torgunrud, A., Lund-Andersen, C., Fretland, Å.A., Lorenz, S., Edwin, B., Hovig, E., Fromm, B., Inderberg, E.M. and Greiff, V., 2023. "T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases". GigaScience, 12, p.giad032. |
May |
2022
| Zolotarov, G., Fromm, B., Legnini, I., Ayoub, S., Polese, G., Maselli, V., Chabot, P. J., Vinther, J., Styfhals, R., Seuntjens, E., Cosmo, A. D., Peterson, K. J., & Rajewsky, N. (2022). "MicroRNAs are deeply linked to the emergence of the complex octopus brain". Science Advances, 8 (47), eadd9938. | November |
| Fromm, B., Patil, AH & Halushka, MK, 2022. Comment on " A Novel Circulating MicroRNA for the Detection of Acute Myocarditis ". The New England Journal of Medicine , 387 (13), pp.1240-1240. | September |
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Aparicio-Puerta, E., Gómez-Martín, C., Giannoukakos, S., Medina, J. M., Scheepbouwer, C., García-Moreno, A., Carmona-Saez, P., Fromm, B., Pegtel, M., Keller, A., Marchal, J. A., & Hackenberg, M. (2022)." sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms ". Nucleic Acids Research. |
July |
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Schiffer, P. H., Natsidis, P., Leite, D. J., Robertson, H., Lapraz, F., Marlétaz, F., Fromm, B., Baudry, L., Simpson, F., Høye, E., Zakrzewski, A.-C., Kapli, P., Hoff, K. J., Mueller, S., Marbouty, M., Marlow, H., Copley, R. R., Koszul, R., Sarkies, P., & Telford, M. J. (2022)." The slowly evolving genome of the xenacoelomorph worm Xenoturbella bocki ". In bioRxiv (p. 2022.06.24.497508). |
June |
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Fromm, B., Zhong, X., Tarbier, M., Friedländer, M. R., & Hackenberg, M. (2022)."The Limits of Human MicroRNA Annotation Have Been Met". RNA , 28(6), 781–785. |
May |
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Høye, E., Fromm, B., Böttger, P. H. M., Domanska, D., Torgunrud, A., Lund-Andersen, C., Abrahamsen, T. W., Fretland, Å. A., Dagenborg, V. J., Lorenz, S., Edwin, B., Hovig, E., & Flatmark, K. (2022). "A Comprehensive Framework for Analysis of MicroRNA Sequencing Data in Metastatic Colorectal Cancer" NAR Cancer, 4(1), zcab051. |
March |
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Fromm, B., Høye, E., Domanska, D., Zhong, X., Aparicio-Puerta, E., Ovchinnikov, V., Umu, S.U., Chabot, P.J., Kang, W., Aslanzadeh, M. and Tarbier, M., 2022. "MirGeneDB 2.1: toward a complete sampling of all major animal phyla". Nucleic Acids Research, 50(D1), pp.D204-D210. |
January |
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Peterson, K. J., Beavan, A., Chabot, P. J., McPeek, M. A., Pisani, D., Fromm, B., & Simakov, O. (2022).“MicroRNAs as Indicators into the Causes and Consequences of Whole-Genome Duplication Events”. Molecular Biology and Evolution, 39(1). |
January |
2021
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Patil, A. H., Halushka, M. K., & Fromm, B. (2021)." No evidence of paralogous loci or new bona fide microRNAs in telomere to telomere (T2T) genomic data ". In bioRxiv (p. 2021.12.09.471935). |
December |
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Kang, W., Fromm, B., Houben, A. J., Høye, E., Bezdan, D., Arnan, C., Thrane, K., Asp, M., Johnson, R., Biryukova, I., & Friedländer, M. R. (2021). “ MapToCleave: High-Throughput Profiling of MicroRNA Biogenesis in Living Cells ” . Cell Reports, 37(7), 110015. |
November |