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 AJ, Foster 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