PUBLISHED WORK

The Fruits of Our Labor

While we try to update this page frequently, we are humans. The most current list can be found at Google Scholar

Undergraduate Era - Andreas Teske Lab, University of North Carolina - Chapel Hill

Yang T, Lyons S,Aguilar C, Cuhel R, Teske A. (2011). Microbial communities and chemosynthesis in Yellowstone Lake sublacustrine hydrothermal vent waters. Frontiers in Microbiology. 2:130.

The Lyons Lab Era - Boston University School of Medicine

Aldrich A, Thomas R, Blower MD, Lyons SM. Metal stress uncouples early pre-rRNA processing from ISR activation and reveals flexible checkpoints in human ribosome biogenesis. bioRxiv. https://doi.org/10.1101/2025.07.14.664728

Kharel P, Bhatter N, Zubair S, Lyons SM, Anderson PJ, Ivanov P. G-Quadruplex topologies determine the functional outcome of guanine-rich bioactive oligonucleotides. Nucleic Acids Research. 2025 June 20; 53(12), gkaf590 PMID: 40580035

Keiser PT, Zhang W, Ricca M, Wacquiez A, Grimins A, Cencic R, Patten JJ, Shah P, Padilha E, Connor JH, Pelletier J, Lyons SM, Saeed M, Brown LE, Porco JA Jr, Davey RA. Amidino-rocoglates (ADRs), a class of synthetic rocoglates, are potent inhibitors of SARS-CoV-2 replication through inhibition of viral protein synthesis. Antiviral Research. 2024. Oct;230:105976. doi: 10.1016/j.antiviral.2024.105976. Epub 2024 Aug 6. PMID: 39117283

Johnston R, Aldrich A, Lyons SM. (2024) Roles of ribosomal RNA in health and disease. Frontiers in RNA Research (1), 1331185

Gao Y, Kwan J, Orofino J, Burrone G, Mitra S, Fan TY, English J, Hekman R, Emili A, Lyons SM, Cardamone MD, Perissi V. Inhibition of K63 ubiquitination by G-Protein pathway suppressor 2 (GPS2) regulates mitochondria-associated translation. Pharmacology Research. 2024 Sep; 207:107336. doi: 10.1016/j.phrs.2024.107336. Epub 2024 Jul 31. PMID: 39094987

Leśniczak-Staszak M, Pietras P, Ruciński M, Johnston R, Sowiński M, Andrzejewska M, Nowicki M, Gowin E, Lyons SM, Ivanov P, Szaflarski W. Stress Granule-mediated sequestration of EGR1 mRNAs correlates with lomustine-induced cell death prevention. Journal of Cell Science. 2024 June 15; 137 (12): jcs261825. doi: 10.1242/jcs.261825. Epub 2024 Jun 28. PMID: 38940347

Dalal J, Lyons SM. (2023) Ribosomal RNA Processing. The Encyclopedia of Cell Biology. (pp. 71–86). Elsevier. https://doi.org/10.1016/b978-0-12-821618-7.00184-x

Nelson EV, Ross SJ, Olejnik J, Hume AJ, Deeney DJ, King E, Grimins AO, Lyons SM, Cifuentes D, Mühlberger E. (2023) The 3’ Untranslated Regions of Ebola Virus mRNAs contain AU-Rich elements involved in post-transcriptional stabilization and decay. Journal of Infectious Diseases 2023 Nov 13; 228(Suppl 7):S488-S497. doi: 10.1093/infdis/jiad312. PubMed PMID: 37551415; PubMed Central PMCID: PMC10651315

Werder RB, Berthiaume KA, Merritt C, Gallagher M, Villacorta-Martin C, Wang F, Bawa P, Malik V, Lyons SM, Basil MC, Morrisey EE, Kotton DN, Zhou X, Cho MH, Wilson AA. (2023) The COPD GWAS gene ADGRG6 instructs function and injury response in human iPSC-derived type II alveolar epithelial cells. American Journal of Human Genetics. 2023 Oct 5;110(10):1735-1749. doi: 10.1016/j.ajhg.2023.08.017. Epub 2023 Sep 20. PubMed PMID: 37734371; PubMed Central PMCID: PMC10577075

Reiss M, Keegan J, Aldrich A, Lyons SM, Flynn RL. (2023) The exoribonuclease XRN2 mediates degradation of the long non-coding telomeric RNA TERRA. FEBS Letters. 2023 Jul; 597(14): 1818-1836. doi: 10.1002/1873-3468.14639. Epub 2023 May 26. PubMed PMID: 37191774; PubMed Central PMCID: PMC10524182

Paget M, Cadena C, Ahmad S, Wang HT, Jordan TX, Kim E, Koo B, Lyons SM, Ivanov P, tenOever B, Mu X, Hur S. (2023) Stress granules are shock absorbers that prevent excess innate immune responses to dsRNA. Molecular Cell. 2023 Apr 6; 83(7):1180-1196.e8. doi: 10.1016/j.molcel.2023.03.010. PubMed PMID: 37028415; PubMed Central PMCID: PMC10170497

Akiyama Y, Lyons SM, Fay MM, Tomiaka Y, Abe T, Anderson PJ, Ivanov P. (2022) Selective Cleavage at CCA Ends and Anticodon Loops of tRNAs by Stress Induced RNases. Frontiers in Molecular Biosciences 9:791094 PubMed PMID: 35300117; PubMed Central PMCID: PMC8920990

Szaflarski W, Leśniczak-Staszak M, Sowiński M, Ojha S, Aulas A, Dave D, Malla S, Anderson P, Ivanov P, Lyons SM (2022). Early rRNA processing is a stress-dependent regulatory event whose inhibition maintains nucleolar integrity. Nucleic Acids Research. 50(2):1033-1051 PubMed PMID: 34928368; PubMed Central PMCID: PMC8789083

Pietras P, Aulas A, Fay MM, Leśniczak-Staszak M, Sowiński M, Lyons SM, Szaflasrki W, Ivanov P. (2022). Translation inhibition and suppression of stress granules formation by cisplatin. Biomedicine and Pharmacotheraphy. 145: 112382 PubMed PMID: 34864307; PubMed Central PMCID: PMC8782064

Pietras P, Leśniczak-Staszak M, Kasprazak A, Andrezejewska M, Jopek K, Sowiński M, Rucinski M, Lyons SM, Ivanov P, Szaflarski W (2021). MVP Expression Facilitates Tumor Cell Proliferation and Migration Supporting the Metastasis of Colorectal Cancer Cells. International Journal of Molecular Science. 22(22):12121 PubMed PMID: 34829999; PubMed Central PMCID: PMC8623820

Floro J, Dai A, Metzger A, Mora-Martin A, Ganem NJ, Cifuentes D, Wu CS, Dalal J, Lyons SM, Labradorf A, Flynn RL. (2021). SDE2 is an essential gene required for ribosome biogenesis and the regulation of alternative splicing. Nucleic Acids Research. 49 (16):9424-9443 PubMed PMID: 34365507; PubMed Central PMCID: PMC8450105.

Aulas A, Finetti P, Lyons SM, Bertucci F, Birnbaum D, Acquaviva C, Mamessier E. (2020) Revisiting the Concept of Stress in the Prognosis of Solid Tumors: A role for Stress Granule Proteins. Cancers. 12 (9): 2470 PubMed PMID: 32882814; PubMed Central PMCID: PMC7564653

Ojha S, Malla S, Lyons SM. (2020) snoRNPs: Functions in Ribosome Biogenesis. Biomolecules. 10(5): 783 PubMed PMID: 32443616; PubMed Central PMCID: PMC7277114

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, Varma 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, Conner JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Emili A, Mühlberger E. (2020). Systems Level Survey of Actionable Cytopathogenic Host Responses of Human Lung Alveolar Type 2 Cells to SARS-CoV-2 Infection. Molecular Cell. 80: 1 – 19 PubMed PMID: 33259812; PubMed Central PMCID: PMC7674017

Fernandes N, Nero L, Lyons SM, Ivanov P, Mittelmeier, Bolger TA, Buchan JR. (2020) Stress Granule Assembly Can Facilitate but is Not Required for TDP-43 Cytoplasmic Aggregation. Biomolecules. 10(10): 1367 PubMed PMID: 32992901; PubMed Central PMCID: PMC7650667.

Mineo M, Lyons SM, Zdioruk M, von Spreckelsen N, Ferrer-Luna R, Ito H, Alayo QA, Kharel P, Giantini Larsen A, Fan WY, Auduong S, Grauwet K, Passaro C, Khalsa JK, Shah K, Reardon DA, Ligon KL, Beroukhim R, Nakashima H, Ivanov P, Anderson JP, Lawler SE, Chiocca EA. (2020) Tumor Interferon Signaling is Regulated by a lncRNA INCR1 Transcribed from the PD-L1 Locus. Molecular Cell. 78(6): 1207-1223 PubMed PMID: 32504554; PubMed Central PMCID: PMC7377926.

Lyons SM, Kharel P, Akiyama Y, Ojha S, Dave D, Gsvetkov V, Merrick W, Ivanov P, Anderson P (2020) eIF4G has intrinsic G-quadruplex binding activity that is required for tiRNA function. Nucleic Acids Research. 48 (11): 6223 – 6233 PubMed PMID: 32374873; PubMed Central PMCID: PMC7293036

Post-Doc Era

Paul J. Anderson & Pavel Ivanov labs, Harvard Medical School and Brigham & Women's Hosptial

Smith JA, Curry EG, Blue RE, Roden C, Dundon SER, Rodríguez-Vargas A, Jordan DC, Chen X, Lyons SM, Crutchley J, Anderson P, Horb ME, Gladfelter AS, Giudice J (2020). FXR splicing is important for muscle development and biomolecular condensates in muscle cells. Journal of Cell Biology. 219 (4): e20191129 PubMed PMID: 32328638; PubMed Central PMCID: PMC714710

Sanders DW, Kedersha N, Lee DSW, Strom AR, Drake V, Riback JA, Bracha D, Eeftens JM, Iwanicki A, Wang A, Wei MT, Whitney G, Lyons SM, Anderson P, Jacobs WM, Ivanov P, Brangwynne CP. (2020). Competing Protein-RNA Interaction Networks Control Mulitphase Intercellular Organization. Cell 181(2): 306 - 324

Gámbaro F, Li Calzi M, Gagúndez P, Costa B, Greif G, Mallick E, Lyons S, Ivanov P, Witwer K, Cayota A, Tosar JP (2019) Stable tRNA halves can be sorted into extracellular vesicles and delivered to recipient cells in a concentration-dependent manner. RNA Biology Dec 29:1-15 EPub ahead of print

Aulas A, Lyons SM, Fay MM, Ivanov P, Anderson P. (2018) Nitric oxide triggers the assembly of “type II” stress granules linked to decreased cell viability. Cell Death and Disease. 9(11):1129

Lyons SM, Fay MM, Ivanov P. (2018) The role of RNA modifications in tRNA cleavage. FEBS Letters. 592: 2828 – 2844

Lyons SM, Gudanis D, Gdaniec Z, Ivanov P. (2017) Identification of functional tetramolecular RNA G-quadruplexes derived from transfer RNAs. Nature Communications. 8(1):2020

Fay MM, Lyons SM, Ivanov P. (2017) RNA G-quadruplexes in biology: Principles and molecular mechanisms. Journal of Molecular Biology. 429(14): 2127 - 2147

Aulas A, Fay MM, Lyons SM, Achorn, CA, Kedersha, N, Anderson P, Ivanov P. (2017) Stress specific differences in assembly and composition of stress granules and related foci. Journal of Cell Science. 130(5) 927- 937

Lyons SM, Fay MM, Akiyama Y, Anderson PJ, Ivanov P. (2017) RNA biology of angiogenin: Current state and perspectives. RNA Biology. 14(2): 171 – 178

Lyons SM, Anderson P (2016) RNA-seeded functional amyloids balance growth and survival. Developmental Cell. 39(2): 131-132

Lyons SM, Achorn C, Kedersha NL, Anderson PJ, Ivanov P. (2016) YB-1 regulates tiRNA-induced stress granule formation but not translational repression. Nucleic Acids Research. 44(14): 6949 – 6960

Mineo M, Rickles F, Rooj AK,Lyons SM, Ivanov P, Ansari KI, Nakano I, Chiocca EA, Godlewski, Bronisz A. (2016) The long non-coding RNA HIF1A-AS2 facilitates the maintenance of mesenchymal glioblastoma stem-like cells in hypoxic niches. Cell Reports: 15(11), 2500 – 2509

Kedersha N, Panas MD, Achorn CA, Lyons SM, Tisdale S, Hickman T, Thomas M, Lieberman J, McInerney GM, Ivanov P, Anderson P(2016) G3BP-Caprin1-USP10 complexes mediate stress granule condensation and associate with 40S subunits. Journal of Cell Biology. 212(7): 845 – 860

Lyons SM,Fay MM, Ivanov PI. (2016) Regulated tRNA cleavage in biology and medicine: Roles of tRNA modifications. Modified nucleic acids in biology and medicine. S. Jurga, V. Erdmann and J. Barciszweski. New York, NY, Springer Berlin Heidelberg: 27 – 54

Johnson ME, Grassetti, AV, Taroni JN, Lyons SM, Schweppe D, Gordon JK, Spiera RF, Lafyatis R, Anderson PJ, Gerber SA, Whitfield ML (2016). Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis. Arthritis Research and Therapy. 18(1): 27

Graduate Era - William F. Marzluff Lab, University of North Carolina - Chapel Hill

Lyons SM, Cunningham CH, Welch JD, Groh B, Guo AY, Wei B, Whitfield ML, Xiong Y, Marzluff WF. (2016) A subset of replication dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues. Nucleic Acids Research. 44(19), 9190-9205

Brooks L, Lyons SM, Mahoney JM, Liu Z, Marzluff WF, Whitfield ML. (2015) A multiprotein occupancy map of the mRNP on the 3’ end of histone mRNAs. RNA. 21(11) 1943 – 1965

Terzo EA, Lyons SM, Poulton JS, Temple BRS Marzluff WF, Duronio RJ. Distinct self-interaction domains promote Multiple Sex Combs accumulation in and formation of the Drosophila Histone Locus Body. (2015). Molecular Biology of the Cell. 26(8): 1559 – 1574

Lyons SM, Guo AY, Ricciardi AS, Kambach KS, Marzluff WF. (2014) The C-terminal extension of Lsm4 interacts directly with the 3’ end of the histone mRNP and is required for efficient histone mRNA. RNA. 20(1) 88 – 102

Su W, Slepenkov SV, Slevin MK, Lyons SM, Ziemniak M, Kowalska J, Darzynkiewicz E, Jemielity J, Marzluff WF, Rhoads RE. (2013) mRNAs containing the histone 3' stem-loop are degraded primarily by recapping mediated by oliouridylation of the 3' end. RNA.19(1): 1-16

Martin L, Meier M, Lyons SM, Sit RV, Marzluff WF, Quake SR, Chang HY. (2012) Systematic reconstruction of RNA functional motifs with high-throughput microfluidics. Nature Methods. 9(12): 1192 -1194

Undergraduate Era - Andreas Teske Lab, University of North Carolina - Chapel Hill

Yang T, Lyons SM, Aguilar C, Cuhel R, Teske A. (2011). Microbial communities and chemosynthesis in Yellowstone Lake sublacustrine hydrothermal vent waters. Frontiers in Microbiology. 2:130. PubMed PMID: 21716640; PubMed Central PMCID: PMC3116135