Publications – Cochella Lab

An ancient and essential miRNA family controls cellular interaction pathways in C. elegans. Santillan, E. M., Cormack, E. D., Wang, J., Rodriguez-Steube, M., Cochella, L. Science Advances. 2025 Sept 03. doi: 10.1126/sciadv.adz1934. PMID: 40901950 PMCID: PMC12407057. [PDF]
Neurogenesis in C. elegans. Poole, R.J.*, Flames, N.*, Cochella, L.* Genetics. 2024 Aug 21. doi:10.1093/genetics/iyae116. Part of the WormBook series. *Equally contributing authors. [PDF]
Mechanism for the initiation of spliceosome disassembly. Vorländer MK, Rothe P, Kleifeld J, Cormack E, Veleti L, Riabov-Bassat D, Fin L, Phillips AW, Cochella L, Plaschka C. Nature. 2024 Jun 26. doi: 10.1038/s41586-024-07741-1. Epub ahead of print. PMID: 38925148. [PDF]
Genomic surveillance of SARS-CoV-2 evolution by a centralised pipeline and weekly focused sequencing, Austria, January 2021 to March 2023. Frank O, Balboa DA, Novatchkova M, Özkan E, Strobl MM, Yelagandula R, Albanese TG, Endler L, Amman F, Felsenstein V, Gavrilovic M, Acosta M, Patocka T, Vogt A, Tamir I, Klikovits J, Zoufaly A, Seitz T, Födinger M, Bergthaler A, Indra A, Schmid D, Klimek P, Stark A, Allerberger F, Benka B, Reich K, Cochella L, Elling U. Euro Surveill. 2024 Jun;29(23):2300542. doi: 10.2807/1560-7917.ES.2024.29.23.2300542. PMID: 38847119; PMCID: PMC11158012. [PDF]
Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types. Mandlbauer A, Sun Q, Popitsch N, Schwickert T, Spanova M, Wang J, Ameres SL, Busslinger M, Cochella L. EMBO J. 2024 Jun;43(12):2506-2525. doi: 10.1038/s44318-024-00102-8. Epub 2024 Apr 30. PMID: 38689024; PMCID: PMC11183118. [PDF]
Paternal methotrexate exposure affects sperm small RNA content and causes craniofacial defects in the offspring.
Alata Jimenez N, Castellano M, Santillan EM, Boulias K, Boan A, Arias Padilla LF, Fernandino JI, Greer EL, Tosar JP, Cochella L, Strobl-Mazzulla PH. Nat Commun. 2023 Mar 23;14(1):1617. doi: 10.1038/s41467-023-37427-7. PMID: 36959185; PMCID: PMC10036556. [PDF]
miR-1 sustains muscle physiology by controlling V-ATPase complex assembly.
Gutiérrez-Pérez P, Santillán EM, Lendl T, Wang J, Schrempf A, Steinacker TL, Asparuhova M, Brandstetter M, Haselbach D, Cochella L. Sci Adv. 2021 Oct 15;7(42):eabh1434. PubMed PMID: 34652942; PubMed Central PMCID: PMC8519577 [PDF]
High-throughput Mutational Surveillance of the SARS-CoV-2 Spike Gene.
Özkan E, Strobl M, Novatchkova M, Yelagandula R, Albanese T, Triska P, Endler L, Penz T, Patocka T, Felsenstein V, Vogt A, Tamir I, Seitz T, Födinger M, Herwig R, Indra A, Schmid D, Bock C, Bergthaler A, Stark A, Allerberger F, Elling U, Cochella L. medRxiv 2021.07.22.21259587; doi: https://doi.org/10.1101/2021.07.22.21259587 [PDF]
Pax5 regulates B cell immunity by promoting PI3K signaling via PTEN down-regulation.
Calderón L, Schindler K, Malin SG, Schebesta A, Sun Q, Schwickert T, Alberti C, Fischer M, Jaritz M, Tagoh H, Ebert A, Minnich M, Liston A, Cochella L, Busslinger M. Sci Immunol. 2021 Jul 23;6(61) PubMed PMID: 34301800; PubMed Central PMCID: PMC7611449. [PDF]
Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq.
Yelagandula R, Bykov A, Vogt A, Heinen R, Özkan E, Strobl MM, Baar JC, Uzunova K, Hajdusits B, Kordic D, Suljic E, Kurtovic-Kozaric A, Izetbegovic S, Schaeffer J, Hufnagl P, Zoufaly A, Seitz T, Födinger M, Allerberger F, Stark A, Cochella L, Elling U. Nat Commun. 2021 May 25;12(1):3132. PubMed PMID: 34035246; PubMed Central PMCID: PMC8149640. [PDF]
Two distinct types of neuronal asymmetries are controlled by the Caenorhabditis elegans zinc finger transcription factor die-1.
Cochella L, Tursun B, Hsieh YW, Galindo S, Johnston RJ, Chuang CF, Hobert O. Genes Dev. 2014 Jan 1;28(1):34-43. Epub 2013 Dec 20. PubMed PMID: 24361693; PubMed Central PMCID: PMC3894411. [PDF]
Concepts and functions of small RNA pathways in C. elegans.
Ketting RF, Cochella L.Curr Top Dev Biol. 2021;144:45-89. Epub 2020 Oct 3. Review. PubMed PMID: 33992161. [PDF]
Two MicroRNAs Are Sufficient for Embryonic Patterning in C. elegans.
Dexheimer PJ, Wang J, Cochella L. Curr Biol. 2020 Dec 21;30(24):5058-5065.e5. Epub 2020 Oct 29. PubMed PMID: 33125867; PubMed Central PMCID: PMC7758728. [PDF]
Combinatorial Action of Temporally Segregated Transcription Factors.
Charest J, Daniele T, Wang J, Bykov A, Mandlbauer A, Asparuhova M, Röhsner J, Gutiérrez-Pérez P, Cochella L Dev Cell. 2020 Nov 23;55(4):483-499.e7. Epub 2020 Sep 30. PubMed PMID: 33002421; PubMed Central PMCID: PMC7704111. [PDF]
MicroRNAs: From Mechanism to Organism.
Dexheimer PJ, Cochella L. Front Cell Dev Biol. 2020;8:409. eCollection 2020. Review. PubMed PMID: 32582699; PubMed Central PMCID: PMC7283388. [PDF]
Evolution of neuronal anatomy and circuitry in two highly divergent nematode species.
Hong RL, Riebesell M, Bumbarger DJ, Cook SJ, Carstensen HR, Sarpolaki T, Cochella L, Castrejon J, Moreno E, Sieriebriennikov B, Hobert O, Sommer RJ. Elife. 2019 Sep 17;8. PubMed PMID: 31526477; PubMed Central PMCID: PMC6748829. [PDF]
Olfaction regulates organismal proteostasis and longevity via microRNA-dependent signaling.
Finger F, Ottens F, Springhorn A, Drexel T, Proksch L, Metz S, Cochella L, Hoppe T. Nat Metab. 2019 Mar;1(3):350-359. Epub 2019 Feb 18. PubMed PMID: 31535080; PubMed Central PMCID: PMC6751085. [PDF]
Cell-type specific sequencing of microRNAs from complex animal tissues.
Alberti C, Manzenreither RA, Sowemimo I, Burkard TR, Wang J, Mahofsky K, Ameres SL, Cochella L.Nat Methods. 2018 Apr;15(4):283-289. Epub 2018 Feb 26. PubMed PMID: 29481550; PubMed Central PMCID: PMC5886366. [PDF]
A framework for understanding the roles of miRNAs in animal development.
Alberti C, Cochella L. Development. 2017 Jul 15;144(14):2548-2559. Review. PubMed PMID: 28720652. [PDF]
Neuron type-specific miRNA represses two broadly expressed genes to modulate an avoidance behavior in C. elegans.
Drexel T, Mahofsky K, Latham R, Zimmer M, Cochella L. Genes Dev. 2016 Sep 15;30(18):2042-2047. Epub 2016 Sep 29. PubMed PMID: 27688400; PubMed Central PMCID: PMC5066611. [PDF]
Embryonic priming of a miRNA locus predetermines postmitotic neuronal left/right asymmetry in C. elegans.
Cochella L, Hobert O. Cell. 2012 Dec 7;151(6):1229-42. Epub 2012 Nov 29. PubMed PMID: 23201143; PubMed Central PMCID: PMC3529140. [PDF]
Diverse functions of microRNAs in nervous system development.
Cochella L, Hobert O. Curr Top Dev Biol. 2012;99:115-43. Review. PubMed PMID: 22365737. [PDF]
Temporal and spatial regulation of microRNA activity with photoactivatable cantimirs.
Zheng G, Cochella L, Liu J, Hobert O, Li WH. ACS Chem Biol. 2011 Dec 16;6(12):1332-8. Epub 2011 Oct 11. PubMed PMID: 21977972; PubMed Central PMCID: PMC3643504. [PDF]
A Genome-Wide RNAi Screen for Factors Involved in Neuronal Specification in Caenorhabditis elegans.
Poole RJ, Bashllari E, Cochella L, Flowers EB, Hobert O. PLoS Genet. 2011 Jun;7(6):e1002109. Epub 2011 Jun 16. PubMed PMID: 21698137; PubMed Central PMCID: PMC3116913. [PDF]
Neuron-type specific regulation of a 3’UTR through redundant and combinatorially acting cis-regulatory elements.
Didiano D, Cochella L, Tursun B, Hobert O.RNA. 2010 Feb;16(2):349-63. Epub 2009 Dec 29. PubMed PMID: 20040592; PubMed Central PMCID: PMC2811664. [PDF]
A toolkit and robust pipeline for the generation of fosmid-based reporter genes in C. elegans.
Tursun B, Cochella L, Carrera I, Hobert O. PLoS One. 2009;4(3):e4625. Epub 2009 Mar 4. PubMed PMID: 19259264; PubMed Central PMCID: PMC2649505. [PDF]
Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome.
Cochella L, Brunelle JL, Green R. Nat Struct Mol Biol. 2007 Jan;14(1):30-6. Epub 2006 Dec 10. PubMed PMID: 17159993. [PDF]
Two distinct conformations of the conserved RNA-rich decoding center of the small ribosomal subunit are recognized by tRNAs and release factors.
Youngman EM, Cochella L, Brunelle JL, He S, Green R. Cold Spring Harb Symp Quant Biol. 2006;71:545-9. Review. PubMed PMID: 17381338. [PDF]
Fidelity in protein synthesis.
Cochella L, Green R.Curr Biol. 2005 Jul 26;15(14):R536-40. Review. PubMed PMID: 16051156. [PDF]
An active role for tRNA in decoding beyond codon:anticodon pairing.
Cochella L, Green R. Science. 2005 May 20;308(5725):1178-80. PubMed PMID: 15905403; PubMed Central PMCID: PMC1687177. [PDF]
Wobble during decoding: more than third-position promiscuity.
Cochella L, Green R. Nat Struct Mol Biol. 2004 Dec;11(12):1160-2. PubMed PMID: 15578054. [PDF]
Isolation of antibiotic resistance mutations in the rRNA by using an in vitro selection system.
Cochella L, Green R.Proc Natl Acad Sci U S A. 2004 Mar 16;101(11):3786-91. Epub 2004 Mar 4. PubMed PMID: 15001709; PubMed Central PMCID: PMC374322. [PDF]
Arginine kinase of the flagellate protozoa Trypanosoma cruzi. Regulation of its expression and catalytic activity.
Alonso GD, Pereira CA, Remedi MS, Paveto MC, Cochella L, Ivaldi MS, Gerez de Burgos NM, Torres HN, Flawiá MM. FEBS Lett. 2001 Jun 1;498(1):22-5.PubMed PMID: 11389891. [PDF]