Selected Publications
Kang, W., Fromm, B., Houben, A. J., Høye, E., Bezdan, D., Arnan, C., … & Friedländer, M. R. (2021). MapToCleave: high-throughput profiling of microRNA biogenesis in living cells. Cell Rep. 37, 110015.
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.
Friedländer, M. R., Mackowiak, S. D., Li, N., Chen, W., & Rajewsky, N. (2012). miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic acids research, 40(1), 37-52.
Publications
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
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