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Publications

January 2025

Design of a yeast SUMO tag to eliminate internal translation initiation.
Law JD, Gao Y, Wysocki VH, Gopalan V.
Protein Sci. 2025 Jan;34(1):e5256.  
PMID: 39692120   

Riluzole Enhancing Anti-PD-1 Efficacy by Activating cGAS/STING Signaling in Colorectal Cancer.
Liang B, Khan M, Storts H, Zhang EH, Zheng X, Xing X, Claybon H, Wilson J, Li C, Jin N, Fishel R, Miles WO, Wang J
J.Mol Cancer Ther. 2025 Jan 2;24(1):131-140. 
PMID: 39382075

Regulation of sod1 mRNA and protein abundance by zinc in fission yeast is dependent on the CCR4-NOT complex.
Weeks AT, Bird AJ.
J Biol Chem. 2025 Jan 4:108156. 
PMID: 39761853 

The Psu protein of phage satellite P4 inhibits transcription termination factor ρ by forced hyper-oligomerization.
Gjorgjevikj D, Kumar N, Wang B, Hilal T, Said N, Loll B, Artsimovitch I, Sen R, Wahl MC
Nat Commun
PMID: 39788982

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM
Li W, Yang H, Stachowski K, Norris AS, Lichtenthal K, Kelly S, Gollnick P, Wysocki VH, Foster MP
Proc Natl Acad Sci USA.
PMID: 39793047

Role of the sarcin-ricin loop of 23S rRNA in biogenesis of the 50S ribosomal subunit.
Fakhretaha Aval S, Seffouh A, Moon KM, Foster L, Ortega J, Fredrick K
RNA
PMID: 39875174.

Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels.
Giese APJ, Weng WH, Kindt KS, Chang HHV, Montgomery JS, Ratzan EM, Beirl AJ, Aponte Rivera R, Lotthammer JM, Walujkar S, Foster MP, Zobeiri OA, Holt JR, Riazuddin S, Cullen KE, Sotomayor M, Ahmed ZM. 
Elife.
PMID: 39773557.

Use of a small molecule microarray screen to identify inhibitors of the catalytic RNA subunit of Methanobrevibacter smithii RNase P.
Sidharthan V, Sibley CD, Dunne-Dombrink K, Yang M, Zahurancik WJ, Balaratnam S, Wilburn DB, Schneekloth JS Jr, Gopalan V
Nucleic Acids Res.
PMID: 39676671.

Histamine N-methyltransferase (HNMT) as a potential auxiliary biomarker for predicting adaptability to anti-HER2 drug treatment in breast cancer patients.
Cheng TC, Hung MC, Wang LH, Tu SH, Wu CH, Yen Y, Chen CL, Whang-Peng J, Lee WJ, Liao YC, Lee YC, Pan MH, Lin HK, Tzeng HE, Guo P, Chu CY, Chen LC, Ho YS
Biomark Res.
PMID: 39789599

Inhibition of Endothelial Cell Tube Formation by Anti-Vascular Endothelial Growth Factor/Anti-Angiopoietin-2 RNA Nanoparticles.
Zhong C, Shi Z, Liu CY, Binzel DW, Jin K, Li X, Guo P, Li SK.  
Pharmaceutics
PMID: 39861703


February 2025  

ncRNA Editing: Functional Characterization and Computational Resources.
Marceca GP, Romano G, Acunzo M, Nigita G.
Methods Mol Biol
PMID: 39702721

Free introns of tRNAs as complementarity-dependent regulators of gene expression. 
Nostramo RT, Sinopoli PL, Bao A, Metcalf S, Peltier LM, Hopper AK
Mol Cell. 
PMID: 39938518

Nucleotide-induced hyper-oligomerization inactivates transcription termination factor ρ
Wang B, Said N, Hilal T, Finazzo M, Wahl MC, Artsimovitch I.
Nat Commun
PMID: 39952913

Identification of inhibitors of the Salmonella FraB deglycase, a drug target.
Law JD, Gao Y, Kovvali S, Thirugnanasambantham P, Wysocki VH, Ahmer BMM, Gopalan V
FEBS Open Bio.
PMID: 39945759.

Protein bL38 facilitates incorporation of uL6 during assembly of the 50S subunit in Flavobacterium johnsoniae
Alom MS, Arpin D, Zhu H, Hay BN, Foster LJ, Ortega J, Fredrick K
Nucleic Acids Res
PMID: 39997215

Conformational dynamics in specialized C2H2zinc finger domains enable zinc-responsive gene repression in S. pombe.
Wadhwa V, Jamshidi C, Stachowski K, Bird AJFoster MP
Protein Sci
PMID: 39865413

Cardiac transcriptional enhancer is repurposed during regeneration to activate an anti-proliferative program.
Rao A, Russell A, Segura-Bermudez J, Franz C, Dockery R, Blatnik A, Panten J, Zevallos M, McNulty C, Pietrzak M, Goldman JA
Development
PMID: 39803985

Sustained release of RNA nanoparticles from reservoir implant for ocular delivery.
Shi Z, Zhong C, Binzel DW, Jin K, Guo P, Li SK. 
J Pharm Sci
PMID: 39725224

Structural basis for aminoacylation of cellular modified tRNALys3 by human lysyl-tRNA synthetase.
Devarkar SC, Budding CR, Pathirage C, Kavoor A, Herbert C, Limbach PA, Musier-Forsyth K, Xiong Y. 
Nucleic Acids Res
PMID: 40036503

An AT-hook transcription factor promotes transcription of histone, spliced-leader, and piRNA clusters.
Wang YH, Hertz HL, Pastore B, Tang W
Nucleic Acids Res
PMID: 39945323

Infectious Subgenomic Amplicon Strategies for Japanese Encephalitis and West Nile Viruses.
Singh PP, Le NPK, Karniychuk U
J Med Virol. 2025 Feb
PMID: 39895481                                                                                                           

Proteomic Profiling of Medullary Thyroid Cancer Identifies CAPN1 as a Key Regulator of NF1 and RET Fueled Growth.
Khan E, Hylton H, Rajan N, Bouley SJ, Siddiqui JK, Rajasekaran S, Koshre GR, Storts H, Valenciaga A, Khan M, Liyanarachchi S, Fernandez F, Zheng X, Phay J, Dedhia PH, Wang J, Walker JA, Ringel MD, Miles WO.
Thyroid
PMID: 39868924.
 

March 2025

Protein and DNA Conformational Changes Contribute to Specificity of Cre Recombinase.
Montgomery JS, Judson ME, Foster MP.
Biochemistry
PMID: 39957070

Role of the sarcin-ricin loop of 23S rRNA in biogenesis of the 50S ribosomal subunit.
Aval SF, Seffouh A, Moon KM, Foster LJ, Ortega J, Fredrick K
RNA. 2025 Mar 18;31(4):585-599. doi: 10.1261/rna.080335.124. 
PMID: 39875174

YTHDF1 and YTHDC1 m6A reader proteins regulate HTLV-1 tax and hbz activity.
King EM, Midkiff A, McClain K, Kim S, Panfil AR
J Virol. 2025 Mar 18
PMID: 39902961

Recent advances in viroid research.
Zhang Y, Bisaro DM, Wu J. 
Virology. 2025 Mar
PMID: 39889478

Metal ion requirement for catalysis by 3'-5' RNA polymerases.
Iwaniec BWJ, Allegretti MM, Jackman JE
bioRxiv [Preprint]. 2025 
PMID: 40166239

Five things to consider before proposing that a circular RNA is a viroid
Wu J, Bisaro DM. March 2025. 
PLOS Pathogens
E1012958

Significant roles in RNA-binding for the amino-terminal regions of Drosophila Pumilio and Nanos.
Wharton TH, Marhabaie M, Wharton RP
PLoS Genet. 2025 Mar 31
PMID: 40163518
 

April

Plasma proteomic profiles correlate with organ dysfunction in COVID-19 ARDS.
Eltobgy M, Klamer B, Farkas D, Londino JD, Englert JA, Horowitz JC, Mallampalli RK, Brock G, Bednash JS
Physiol Rep. 2025 Apr;13
PMID: 40170544

Unexpected enzymatic function of an ancient nucleic acid-binding fold.
Watkins RR, Bockelman S, Vradi A, Grabarkewitz K, Pyun A, Stark J, Wysocki VH, Alfonzo JD, Musier-Forsyth K
Nucleic Acids Res. 2025 Apr 22
PMID: 40274265

Endovascular Treatment of Stroke Due to Medium-Vessel Occlusion.
Goyal M, Ospel JM, Ganesh A, Dowlatshahi D, Volders D, Möhlenbruch MA, Jumaa MA, Nimjee SM, Booth TC, Buck BH, Kennedy J, Shankar JJ, Dorn F, Zhang L, Hametner C, Nardai S, Zafar A, Diprose W, Vatanpour S, Stebner A, Bosshart S, Singh N, Sebastian I, Uchida K, Ryckborst KJ, Fahed R, Hu SX, Vollherbst DF, Zaidi SF, Lee VH, Lynch J, Rempel JL, Teal R, Trivedi A, Bode FJ, Ogungbemi A, Pham M, Orosz P, Abdalkader M, Taschner C, Tarpley J, Poli S, Singh RJ, De Leacy R, Lopez G, Sahlas D, Chen M, Burns P, Schaafsma JD, Marigold R, Reich A, Amole A, Field TS, Swartz RH, Settecase F, Lenzsér G, Ortega-Gutierrez S, Asdaghi N, Lobotesis K, Siddiqui AH, Berrouschot J, Mokin M, Ebersole K, Schneider H, Yoo AJ, Mandzia J, Klostranec J, Jadun C, Patankar T, Sauvageau E, Lenthall R, Peeling L, Huynh T, Budzik R, Lee SK, Makalanda L, Levitt MR, Perry RJ, Hlaing T, Jahromi BS, Singh P, Demchuk AM, Hill MD; ESCAPE-MeVO Investigators.
N Engl J Med. 2025 Apr 10
PMID: 39908448

Role of glycosylation mutations at the N-terminal domain of SARS-CoV-2 XEC variant in immune evasion, cell-cell fusion, and spike stability.
Li P, Faraone JN, Hsu CC, Chamblee M, Liu Y, Zheng Y-M, Xu Y, Carlin C, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Li J, Gumina RJ, Bednash JS, Xu K, Liu S-L. 
J Virol.
PMID: 40135879

Myc family proteins: Molecular drivers of tumorigenesis and resistance in neuroendocrine tumors.
Hylton-McComas HM, Cordes A, Floros KV, Faber AC, Drapkin BJ, Miles WO
Biochim Biophys Acta Rev Cancer
PMID: 40280500.
 

May

Pnrc2 promotes rapid mRNA decay and coordinately supports early development with P-body factors Ddx6 and Ddx61.
Gallagher TL, Blatnik MC, Austin CC, Thompson KG, Pvirre DM, Morgan A, Kearse MG, Amacher SL
bioRxiv [Preprint]. 2025 May 14, 2025.
PMID: 40463158

Validation of Duchenne muscular dystrophy candidate modifiers using a CRISPR-Cas9-based approach in zebrafish.
Lerma G, Ryhlick KR, Carraher OM, Beljan JC, Amacher SL
bioRxiv [Preprint]. 2025 May 20:2025
PMID: 40475573

International society of liquid biopsy (ISLB) perspective on minimal requirements for ctDNA testing in solid tumors
Fusco N, Venetis K, Pepe F, Shetty O, Farinas SC, Heeke S, Burnier JV, Patton SJ, Heitzer E, Nigita G, Hofman P, Serrano MJ, Cristofanilli M, Jantus-Lewintre E, Gandara DR, Rolfo C, Malapelle U. 
J Liq Biopsy. 2025 May 24
PMID: 40521567

Predictors of perioperative stroke in patients with Ischemic-type moyamoya disease treated with surgical revascularization: A retrospective multicenter study.
Musmar B, Roy JM, Abdalrazeq H, Atallah E, Naamani KE, Chen CJ, Jabre R, Saad H, Grossberg JA, Dmytriw AA, Patel AB, Khorasanizadeh M, Ogilvy CS, Thomas AJ, Monteiro A, Siddiqui A, Cortez GM, Hanel RA, Porto G, Spiotta AM, Piscopo AJ, Hasan DM, Ghorbani M, Weinberg J, Nimjee SM, Bekelis K, Salem MM, Burkhardt JK, Zetchi A, Matouk C, Howard BM, Lai R, Du R, Abbas R, Sioutas GS, Amllay A, Munoz A, Herial NA, Tjoumakaris SI, Gooch MR, Rosenwasser RH, Jabbour P
J Stroke Cerebrovasc Dis. 2025 May.
PMID: 40057254

Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses.
Warren CJ, Barbachano-Guerrero A, Bauer VL, Stabell A, Dirasantha O, Yang Q, Sawyer SL. 
Elife. 2025 May 14
PMID: 40366257

Neutralization and spike stability of JN.1-derived LB.1, KP.2.3, KP.3, and KP.3.1.1 subvariants.
Li P, Faraone JN, Hsu CC, Chamblee M, Liu Y, Zheng Y-M, Xu Y, Carlin C, Horowitz JC, Mallampalli RK, Saif LJ, Oltz EM, Jones D, Li J, Gumina RJ, Bednash JS, Xu K, Liu S-L.  
mBio
PMID: 40136024
 

June

Mitochondrial tRNA processing: a neutral evolutionary ratchet innovation.
Lai LB, Jackman JE, Daniels CJ, Gopalan V
Trends Biochem Sci.  2025 Jun 27: 
PMID: 40581570

Ribosome deficiency induces Salmonella filamentation within host cells.
Lyu Z, Wilson C, Weiss K, Lewis S, Fredrick K, Margolin W, Ling J. 
mBio. 2025 Jun 30
PMID: 40586582.

Protocol for analyzing tRNA-derived ncRNAs from small RNA-seq data using tRFUniverse functional analyses.
La Ferlita A, Nigita G, Ferro A, Alaimo S, Pulvirenti A. STAR 
Protoc. 2025 Jun 20
PMID: 40503934

An RNA ligase partner for the prokaryotic protein-only RNase P: insights into the functional diversity of RNase P from genome mining.
Seshadri R, Gopalan V
mBio. 2025 Jun 11
PMID: 40298408

Loss of Methyltransferase and Hypomethylated m6A Sarcomere Transcripts Leading to Early-Onset Dilated Cardiomyopathy.
Hand SM, Zhao Y, Li D, Burke S, Lim HW, Yester J, Garg V, Accornero F, Li X, Li D, Jang J
Circulation. 2025 Jun 
PMID: 40489544

Virocell resource manipulation under nutrient limitation.
Lindback MM, Howard-Varona C, Fudyma J, Tfaily M, Sullivan MB, Duhaime MB.  mSystems. 2025 Jun 24
PMID: 40552834

Riluzole in Combination with mFOLFOX6 and Bevacizumab in Treating Patients with Metastatic Colorectal Cancer: A Phase I Clinical Trial.
Li C, Noonan AM, Hays J, Roychowdhury S, Malalur P, Elkhatib R, Manne A, Mittra A, Rahman S, Yan L, Hill K, Abbott N, Phelps M, Na JY, Liang B, Storts H, Khan M, Zhang EH, Miles W, Yildiz V, Wei L, Wang JJ, Jin N. 
Clin Cancer Res
PMID: 40116361
 

July

srp54 promotes motor neuron development and is required for motility in zebrafish. Losievski N, Kamath P, Fox A, Aloi NM, Baird MC, Everest A, Gallagher TL, Amacher SL, Kolb SJ
Neuroscience. 2025 Jul 23;579:24-34
PMID: 40328346.

Acute degradation of nucleolin reveals its novel functions in cell cycle progression and cell division in triple negative breast cancer.
Mills J, Tessari A, Anastas V, Sunilkumar D, Samadi Rad N, Lamba S, Cosentini I, Reers A, Zhu Z, Miles WO, Coppola V, Cocucci E, Magliery TJ, Shive H, Davies AE, Rizzotto L, Croce CM, Palmieri D. 
J Exp Clin Cancer Res
PMID: 40653460

2024 Publications

2023 Publications