Friedländer Lab

Selected Publications

Mármol-Sánchez, E., Fromm, B., Oskolkov, N., et al., Friedländer, M.R., Dalén, L. (2026).
Ancient RNA expression profiles from the extinct woolly mammoth.
Cell, 189(1), 52–69.e22. (Open access)

Tarbier, M., Mackowiak, S. D., Frade, J., Catuara-Solarz, S., Biryukova, I., Gelali, E., … & Friedländer, M. R. (2020). Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells. Nature communications, 11(1), 5445.

 

Publications

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).

Mazza T, Aslanzadeh M, Berentsen L, Bonath F, Friedländer MR, Barragan A. ‘Cytoskeletal alterations in neuronal cells implicate Toxoplasma gondii secretory machinery and host microRNA-containing extracellular vesicles‘. Scientific Reports (2025).

Brown T, Mishra K, Elewa A, Iarovenko S, Subramanian E, Araus AJ, Petzold A, Fromm B, Friedländer MR …
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).

Clarke AW, Høye E, Hembrom AA, Paynter VM … Friedländer 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).

Aslanzadeh M; Stanicek L; Tarbier M; Mármol-Sánchez E; Biryukova I; Friedländer MR, 2024. Malat1 affects transcription and splicing through distinct pathways in mouse embryonic stem cells.  NAR Genom Bioinform 6(2):lqae045

Edelbroek B; Kjellin J; Biryukova I; Liao Z; Lundberg T; Noegel AA; Eichinger L; Friedländer MR; Söderbom F, 2024. Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.  Nucleic Acids Res 52(6):3121-3136

Friedländer MR; Gilbert MTP, 2024. How ancient RNA survives and what we can learn from it.  Nat Rev Mol Cell Biol 25(6):417-418

Sekar V; Mármol-Sánchez E; Kalogeropoulos P; Stanicek L; Sagredo EA; Widmark A; Doukoumopoulos E; Bonath F; Biryukova I; Friedländer MR, 2023. Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.  Nat Biotechnol.

Mármol-Sánchez E; Fromm B; Oskolkov N; Pochon Z; Kalogeropoulos P; Eriksson E; Biryukova I; Sekar V; Ersmark E; Andersson B; Dalén L; Friedländer MR, 2023. Historical RNA expression profiles from the extinct Tasmanian tiger.  Genome Res 33(8):1299-1316

Mohammed M; Dziedziech A; Sekar V; Ernest M; Alves E Silva TL; Balan B; Emami SN; Biryukova I; Friedländer MR; Jex A; Jacobs-Lorena M; Henriksson J; Vega-Rodriguez J; Ankarklev J, 2023. Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut.  Microbiol Spectr 11(2):e0367122

Widmark A; Sagredo EA; Karlström V; Behm M; Biryukova I; Friedländer MR; Daniel C; Öhman M, 2022. ADAR1- and ADAR2-mediated regulation of maturation and targeting of miR-376b to modulate GABA neurotransmitter catabolism.  J Biol Chem 298(3):101682

Fromm B; Høye E; Domanska D; Zhong X; Aparicio-Puerta E; Ovchinnikov V; Umu SU; Chabot PJ; Kang W; Aslanzadeh M; Tarbier M; Mármol-Sánchez E; Urgese G; Johansen M; Hovig E; Hackenberg M; Friedländer MR; Peterson KJ, 2022. MirGeneDB 2.1: toward a complete sampling of all major animal phyla.  Nucleic Acids Res 50(D1):D204-D210

Gañez-Zapater A; Mackowiak SD; Guo Y; Tarbier M; Jordán-Pla A; Friedländer MR; Visa N; Östlund Farrants AK, 2022. The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA.  Mol Genet Genomics 297(2):463-484

Fromm B; Zhong X; Tarbier M; Friedländer MR; Hackenberg M, 2022. The limits of human microRNA annotation have been met.  RNA 28(6):781-785

Pålsson SA; Sekar V; Kutter C; Friedländer MR; Spetz AL, 2022. Inhibition of Respiratory Syncytial Virus Infection by Small Non-Coding RNA Fragments.  Int J Mol Sci 23.

Kang W; Fromm B; Houben AJ; Høye E; Bezdan D; Arnan C; Thrane K; Asp M; Johnson R; Biryukova I; Friedländer MR, 2021. MapToCleave: High-throughput profiling of microRNA biogenesis in living cells.  Cell Rep 37(7):110015

Reimegård J; Tarbier M; Danielsson M; Schuster J; Baskaran S; Panagiotou S; Dahl N; Friedländer MR; Gallant CJ, 2021. A combined approach for single-cell mRNA and intracellular protein expression analysis.  Commun Biol 4(1):624

Espeso-Gil S; Holik AZ; Bonnin S; Jhanwar S; Chandrasekaran S; Pique-Regi R; Albaigès-Ràfols J; Maher M; Permanyer J; Irimia M; Friedländer MR; Pons-Espinal M; Akbarian S; Dierssen M; Maass PG; Hor CN; Ossowski S, 2021. Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition.  Front Mol Neurosci 14:664912

Baronti L; Guzzetti I; Ebrahimi P; Friebe Sandoz S; Steiner E; Schlagnitweit J; Fromm B; Silva L; Fontana C; Chen AA; Petzold K, 2020. Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA.  Nature 583(7814):139-144

Desvignes T; Loher P; Eilbeck K; Ma J; Urgese G; Fromm B; Sydes J; Aparicio-Puerta E; Barrera V; Espín R; Thibord F; Bofill-De Ros X; Londin E; Telonis AG; Ficarra E; Friedländer MR; Postlethwait JH; Rigoutsos I; Hackenberg M; Vlachos IS; Halushka MK; Pantano L, 2020. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API.  Bioinformatics 36(3):698-703

Fromm B; Domanska D; Høye E; Ovchinnikov V; Kang W; Aparicio-Puerta E; Johansen M; Flatmark K; Mathelier A; Hovig E; Hackenberg M; Friedländer MR; Peterson KJ, 2020. MirGeneDB 2.0: the metazoan microRNA complement.  Nucleic Acids Res 48(D1):D132-D141

Malkani S; Chin CR; Cekanaviciute E; Mortreux M; Okinula H; Tarbier M; Schreurs AS; Shirazi-Fard Y; Tahimic CGT; Rodriguez DN; Sexton BS; Butler D; Verma A; Bezdan D; Durmaz C; MacKay M; Melnick A; Meydan C; Li S; Garrett-Bakelman F; Fromm B; Afshinnekoo E; Langhorst BW; Dimalanta ET; Cheng-Campbell M; Blaber E; Schisler JC; Vanderburg C; Friedländer MR; McDonald JT; Costes SV; Rutkove S; Grabham P; Mason CE; Beheshti A, 2020. Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development.  Cell Rep 33(10):108448

Fromm B; Keller A; Yang X; Friedlander MR; Peterson KJ; Griffiths-Jones S, 2020. Quo vadis microRNAs?  Trends Genet 36(7):461-463

Mozūraitis R; Hajkazemian M; Zawada JW; Szymczak J; Pålsson K; Sekar V; Biryukova I; Friedländer MR; Koekemoer LL; Baird JK; Borg-Karlson AK; Emami SN, 2020. Male swarming aggregation pheromones increase female attraction and mating success among multiple African malaria vector mosquito species.  Nat Ecol Evol 4(10):1395-1401

Tarbier M; Mackowiak SD; Frade J; Catuara-Solarz S; Biryukova I; Gelali E; Menéndez DB; Zapata L; Ossowski S; Bienko M; Gallant CJ; Friedländer MR, 2020. Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.  Nat Commun 11(1):5445

Masser AE; Kang W; Roy J; Mohanakrishnan Kaimal J; Quintana-Cordero J; Friedländer MR; Andréasson C, 2019. Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.  Elife 8.

Domingo-Prim J; Endara-Coll M; Bonath F; Jimeno S; Prados-Carvajal R; Friedländer MR; Huertas P; Visa N, 2019. EXOSC10 is required for RPA assembly and controlled DNA end resection at DNA double-strand breaks.  Nat Commun 10(1):2135

Hansen EP; Fromm B; Andersen SD; Marcilla A; Andersen KL; Borup A; Williams AR; Jex AR; Gasser RB; Young ND; Hall RS; Stensballe A; Ovchinnikov V; Yan Y; Fredholm M; Thamsborg SM; Nejsum P, 2019. Exploration of extracellular vesicles from Ascaris suum provides evidence of parasite-host cross talk.  J Extracell Vesicles 8(1):1578116

Fromm B; Tosar JP; Aguilera F; Friedländer MR; Bachmann L; Hejnol A, 2019. Evolutionary Implications of the microRNA- and piRNA Complement of Lepidodermella squamata (Gastrotricha).  Noncoding RNA 5.

Solé C; Tramonti D; Schramm M; Goicoechea I; Armesto M; Hernandez LI; Manterola L; Fernandez-Mercado M; Mujika K; Tuneu A; Jaka A; Tellaetxe M; Friedländer MR; Estivill X; Piazza P; Ortiz-Romero PL; Middleton MR; Lawrie CH, 2019. The Circulating Transcriptome as a Source of Biomarkers for Melanoma.  Cancers (Basel) 11.

Fromm B; Kang W; Rovira C; Cayota A; Witwer K; Friedländer MR; Tosar JP, 2019. Plant microRNAs in human sera are likely contaminants.  J Nutr Biochem 65:139-140

Langlet F; Tarbier M; Haeusler RA; Camastra S; Ferrannini E; Friedländer MR; Accili D, 2018. microRNA-205-5p is a modulator of insulin sensitivity that inhibits FOXO function.  Mol Metab 17:49-60

Bhambri A; Dhaunta N; Patel SS; Hardikar M; Bhatt A; Srikakulam N; Shridhar S; Vellarikkal S; Pandey R; Jayarajan R; Verma A; Kumar V; Gautam P; Khanna Y; Khan JA; Fromm B; Peterson KJ; Scaria V; Sivasubbu S; Pillai B, 2018. Large scale changes in the transcriptome of Eisenia fetida during regeneration.  PLoS One 13(9):e0204234

Bråte J; Neumann RS; Fromm B; Haraldsen AAB; Tarver JE; Suga H; Donoghue PCJ; Peterson KJ; Ruiz-Trillo I; Grini PE; Shalchian-Tabrizi K, 2018. Unicellular Origin of the Animal MicroRNA Machinery.  Curr Biol 28(20):3288-3295.e5

Yan X; Wang Z; Bishop CA; Weitkunat K; Feng X; Tarbier M; Luo J; Friedländer MR; Burkhardt R; Klaus S; Willnow TE; Poy MN, 2018. Control of hepatic gluconeogenesis by Argonaute2.  Mol Metab 18:15-24

Kang W; Eldfjell Y; Fromm B; Estivill X; Biryukova I; Friedländer MR, 2018. miRTrace reveals the organismal origins of microRNA sequencing data.  Genome Biol 19(1):213

Bonath F; Domingo-Prim J; Tarbier M; Friedländer MR; Visa N, 2018. Next-generation sequencing reveals two populations of damage-induced small RNAs at endogenous DNA double-strand breaks.  Nucleic Acids Res 46(22):11869-11882

Zapata L; Susak H; Drechsel O; Friedländer MR; Estivill X; Ossowski S, 2017. Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes.  Sci Rep 7(1):13124

Yan X; Wang Z; Westberg-Rasmussen S; Tarbier M; Rathjen T; Tattikota SG; Peck BCE; Kanke M; Oxvig C; Frystyk J; Starup-Linde J; Sethupathy P; Friedländer MR; Gregersen S; Poy MN, 2017. Differential Impact of Glucose Administered Intravenously and Orally on Circulating miR-375 Levels in Human Subjects.  J Clin Endocrinol Metab 102(10):3749-3755

Bustamante M; Hernandez-Ferrer C; Sarria Y; Harrison GI; Nonell L; Kang W; Friedländer MR; Estivill X; González JR; Nieuwenhuijsen M; Young AR, 2017. The acute effects of ultraviolet radiation on the blood transcriptome are independent of plasma 25OHD(3).  Environ Res 159:239-248

Nejedla M; Li Z; Masser AE; Biancospino M; Spiess M; Mackowiak SD; Friedländer MR; Karlsson R, 2017. A Fluorophore Fusion Construct of Human Profilin I with Non-Compromised Poly(L-Proline) Binding Capacity Suitable for Imaging.  J Mol Biol 429(7):964-976

Kang W; Bang-Berthelsen CH; Holm A; Houben AJ; Müller AH; Thymann T; Pociot F; Estivill X; Friedländer MR, 2017. Survey of 800+ data sets from human tissue and body fluid reveals xenomiRs are likely artifacts.  RNA 23(4):433-445

Ferreira PG; Oti M; Barann M; Wieland T; Ezquina S; Friedländer MR; Rivas MA; Esteve-Codina A; Rosenstiel P; Strom TM; Lappalainen T; Guigó R; Sammeth M, 2016. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.  Sci Rep 6:32406

Gowda NK; Kaimal JM; Masser AE; Kang W; Friedländer MR; Andréasson C, 2016. Cytosolic splice isoform of Hsp70 nucleotide exchange factor Fes1 is required for the degradation of misfolded proteins in yeast.  Mol Biol Cell 27(8):1210-9

Pantano L; Friedländer MR; Escaramís G; Lizano E; Pallarès-Albanell J; Ferrer I; Estivill X; Martí E, 2016. Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis.  Bioinformatics 32(5):673-81

Tattikota SG; Rathjen T; Hausser J; Khedkar A; Kabra UD; Pandey V; Sury M; Wessels HH; Mollet IG; Eliasson L; Selbach M; Zinzen RP; Zavolan M; Kadener S; Tschöp MH; Jastroch M; Friedländer MR; Poy MN, 2015. miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism.  J Biol Chem 290(33):20284-94

Rivas MA; Pirinen M; Conrad DF; Lek M; Tsang EK; Karczewski KJ; Maller JB; Kukurba KR; DeLuca DS; Fromer M; Ferreira PG; Smith KS; Zhang R; Zhao F; Banks E; Poplin R; Ruderfer DM; Purcell SM; Tukiainen T; Minikel EV; Stenson PD; Cooper DN; Huang KH; Sullivan TJ; Nedzel J; Bustamante CD; Li JB; Daly MJ; Guigo R; Donnelly P; Ardlie K; Sammeth M; Dermitzakis ET; McCarthy MI; Montgomery SB; Lappalainen T; MacArthur DG, 2015. Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.  Science 348(6235):666-9

Kang W; Friedländer MR, 2015. Computational Prediction of miRNA Genes from Small RNA Sequencing Data.  Front Bioeng Biotechnol 3:7

Friedländer MR; Lizano E; Houben AJ; Bezdan D; Báñez-Coronel M; Kudla G; Mateu-Huertas E; Kagerbauer B; González J; Chen KC; LeProust EM; Martí E; Estivill X, 2014. Evidence for the biogenesis of more than 1,000 novel human microRNAs.  Genome Biol 15(4):R57

Greger L; Su J; Rung J; Ferreira PG; Lappalainen T; Dermitzakis ET; Brazma A, 2014. Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.  PLoS One 9(8):e104567

Cowled C; Stewart CR; Likic VA; Friedländer MR; Tachedjian M; Jenkins KA; Tizard ML; Cottee P; Marsh GA; Zhou P; Baker ML; Bean AG; Wang LF, 2014. Characterisation of novel microRNAs in the Black flying fox (Pteropus alecto) by deep sequencing.  BMC Genomics 15(1):682

't Hoen PA; Friedländer MR; Almlöf J; Sammeth M; Pulyakhina I; Anvar SY; Laros JF; Buermans HP; Karlberg O; Brännvall M; den Dunnen JT; van Ommen GJ; Gut IG; Guigó R; Estivill X; Syvänen AC; Dermitzakis ET; Lappalainen T, 2013. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.  Nat Biotechnol 31(11):1015-22

Lappalainen T; Sammeth M; Friedländer MR; 't Hoen PA; Monlong J; Rivas MA; Gonzàlez-Porta M; Kurbatova N; Griebel T; Ferreira PG; Barann M; Wieland T; Greger L; van Iterson M; Almlöf J; Ribeca P; Pulyakhina I; Esser D; Giger T; Tikhonov A; Sultan M; Bertier G; MacArthur DG; Lek M; Lizano E; Buermans HP; Padioleau I; Schwarzmayr T; Karlberg O; Ongen H; Kilpinen H; Beltran S; Gut M; Kahlem K; Amstislavskiy V; Stegle O; Pirinen M; Montgomery SB; Donnelly P; McCarthy MI; Flicek P; Strom TM; Lehrach H; Schreiber S; Sudbrak R; Carracedo A; Antonarakis SE; Häsler R; Syvänen AC; van Ommen GJ; Brazma A; Meitinger T; Rosenstiel P; Guigó R; Gut IG; Estivill X; Dermitzakis ET, 2013. Transcriptome and genome sequencing uncovers functional variation in humans.  Nature 501(7468):506-11

Miñones-Moyano E; Friedländer MR; Pallares J; Kagerbauer B; Porta S; Escaramís G; Ferrer I; Estivill X; Martí E, 2013. Upregulation of a small vault RNA (svtRNA2-1a) is an early event in Parkinson disease and induces neuronal dysfunction.  RNA Biol 10(7):1093-106

Li N; You X; Chen T; Mackowiak SD; Friedländer MR; Weigt M; Du H; Gogol-Döring A; Chang Z; Dieterich C; Hu Y; Chen W, 2013. Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.  Nucleic Acids Res 41(6):3619-34

Song JL; Stoeckius M; Maaskola J; Friedländer M; Stepicheva N; Juliano C; Lebedeva S; Thompson W; Rajewsky N; Wessel GM, 2012. Select microRNAs are essential for early development in the sea urchin.  Dev Biol 362(1):104-13

Friedländer MR; Mackowiak SD; Li N; Chen W; Rajewsky N, 2012. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades.  Nucleic Acids Res 40(1):37-52

Sharbati S; Friedländer MR; Sharbati J; Hoeke L; Chen W; Keller A; Stähler PF; Rajewsky N; Einspanier R, 2010. Deciphering the porcine intestinal microRNA transcriptome.  BMC Genomics 11:275

Stoeckius M; Maaskola J; Colombo T; Rahn HP; Friedländer MR; Li N; Chen W; Piano F; Rajewsky N, 2009. Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression.  Nat Methods 6(10):745-51

Friedländer MR; Adamidi C; Han T; Lebedeva S; Isenbarger TA; Hirst M; Marra M; Nusbaum C; Lee WL; Jenkin JC; Sánchez Alvarado A; Kim JK; Rajewsky N, 2009. High-resolution profiling and discovery of planarian small RNAs.  Proc Natl Acad Sci U S A 106(28):11546-51

Ender C; Krek A; Friedländer MR; Beitzinger M; Weinmann L; Chen W; Pfeffer S; Rajewsky N; Meister G, 2008. A human snoRNA with microRNA-like functions.  Mol Cell 32(4):519-28

Friedländer MR; Chen W; Adamidi C; Maaskola J; Einspanier R; Knespel S; Rajewsky N, 2008. Discovering microRNAs from deep sequencing data using miRDeep.  Nat Biotechnol 26(4):407-15

Publication list retrieved from NCBI using ImpactPubs

.