KEY PUBLICATIONS
Ross SJ, Ye C, Moxon S, Mühlberger E, Martinez-Sobrido L, Cifuentes D. RNA Folding Energy of Long-Range Genomic Interactions Regulates Discontinuous Transcription in SARS-CoV-2.
Viruses. 2026 May 29;18(6):620
Kretov DA, Cifuentes D. RBPscan measures protein-RNA interactions in living cells.
Nature Review Genetics 2026 Jun 8.
Sanborn O, Cifuentes D. It takes two to cleave: the logic of cluster assistance.
Genes & Development. 2026 Apr 1;40(7-8):409-410.
Kretov DA, Sanborn O, McIsaac T, Park E, Imrat I, Wu S, Régis M, Harvey LM, Cifuentes D. RBPscan: A quantitative in vivo tool for profiling RNA-binding protein interactions.
Molecular Cell. 2026 Feb 19;86(4):774-789.e7.
Galeano D, Imrat, Haltom J, Andolino C, Yousey A, Zaksas V, Das S, Baylin SB, Wallace DC, Slack FJ, Enguita FJ, Wurtele ES, Teegarden D, Meller R, Cifuentes D, Beheshti A. sChemNET: a deep learning framework for predicting small molecules targeting microRNA function.
Nature Communications. 2024 Oct 23;15(1):9149
Ross SJ, Hume AJ, Olejnik J, Turcinovic J, Honko AN, McKay LGA, Connor JH, Griffiths A, Mühlberger E, Cifuentes D.Low-Input, High-Resolution 5' Terminal Filovirus RNA Sequencing with ViBE-Seq.
Viruses. 2024 Jul 1;16(7):1064
Kretov DA, Folkes L, Mora-Martin A, Walawalkar IA, Imrat, Syedah N, Vanuytsel K, Moxon S, Murphy GJ, Cifuentes D. The miR-144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. Nature Communications 2024 May 7;15(1):3821.
Nelson EV, Ross SJ, Olejnik J, Hume AJ, Deeney DJ, King E, Grimins AO, Lyons SM, Cifuentes D, Mühlberger E. The 3' Untranslated Regions of Ebola Virus mRNAs Contain AU-Rich Elements Involved in Posttranscriptional Stabilization and Decay.
Journal of Infectious Diseases. 2023 Nov 13;228(Suppl 7):S488-S497.
Hume AJ, Heiden B, Olejnik J, Suder EL, Ross S, Scoon WA, Bullitt E, Ericsson M, White MR, Turcinovic J, Thao TTN, Hekman RM, Kaserman JE, Huang J, Alysandratos KD, Toth GE, Jakab F, Kotton DN, Wilson AA, Emili A, Thiel V, Connor JH, Kemenesi G, Cifuentes D, Mühlberger E. Recombinant Lloviu virus as a tool to study viral replication and host responses.
PLoS Pathog. 2022 Feb;18(2):e1010268. PMID: 35120176
Floro J, Dai A, Metzger A, Mora-Martin A, Ganem NJ, Cifuentes D, Wu CS, Dalal J, Lyons SM, Labadorf A, Flynn RL. SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing.
Nucleic Acids Res. 2021 Sep 20;49(16):9424-9443. PMID: 34365507
Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2.
Molecular Cell. 2020 Dec 17;80(6):1104-1122.e9. PMID: 33259812
Kretov DA, Walawalkar IA, Mora-Martin A, Shafik AM, Moxon S, Cifuentes D. Ago2-Dependent Processing Allows miR-451 to Evade the Global MicroRNA Turnover Elicited during Erythropoiesis.
Molecular Cell. 2020 Apr 16;78(2):317-328.e6. PMID: 32191872
Vejnar CE, Abdel Messih M, Takacs CM, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D†, Giraldez AJ†. Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish.
Genome Research 2019 Jul;29(7):1100-1114. PMID: 31227602 † Co-corresponding authors
Kretov DA, Shafik AM, Cifuentes D. Assessing miR-451 Activity and Its Role in Erythropoiesis.
Methods Mol Biol. 2018;1680:179-190.
Vejnar CE, Moreno-Mateos MA, Cifuentes D, Bazzini AA, Giraldez AJ. Optimized CRISPR-Cas9 System for Genome Editing in Zebrafish.
Cold Spring Harbor Protocols 2016 Oct 3;2016(10).
Hoffman EJ, Turner KJ, Fernandez JM, Cifuentes D, Ghosh M, Ijaz S, Jain RA, Kubo F, Bill BR, Baier H, Granato M, Barresi MJ, Wilson SW, Rihel J, State MW, Giraldez AJ. Estrogens Suppress a Behavioral Phenotype in Zebrafish Mutants of the Autism Risk Gene, CNTNAP2.
Neuron 2016 Feb 17;89(4):725-33.
Yoda M*, Cifuentes D*, Izumi N, Sakaguchi Y, Suzuki T, Giraldez AJ, Tomari Y. Poly(A)-specific ribonuclease mediates 3'-end trimming of Argonaute2-cleaved precursor microRNAs.
Cell Reports. 2013 Nov 14;5(3):715-26.
*Co-first authors
Cifuentes D, Xue H, Taylor DW, Patnode H, Mishima Y, Cheloufi S, Ma E, Mane S, Hannon GJ, Lawson ND, Wolfe SA, Giraldez AJ. A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity. Science 2010 Jun 25.
