Latest Research Publications
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Department of Biochemistry & Molecular Biology
233 S. 10th Street
Bluemle Life Sciences Building
Philadelphia, PA 19107
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BiochemMolBio@jefferson.edu
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Recent Publications from the Department of Biochemistry & Molecular Biology
Jeffrey Benovic, PhD
- The Role of G Protein-Coupled Receptors and Receptor Kinases in Pancreatic β-Cell Function and Diabetes. Pharmacol Rev. 2024 Feb 13;76(2):267-299.
Lin Guo, PhD
- NLS-binding deficient Kapβ2 reduces neurotoxicity via selective interaction with C9orf72-ALS/FTD dipeptide repeats. Commun Biol. 2025 Jan 2;8(1).
- Single Acetylation-mimetic Mutation in TDP-43 Nuclear Localization Signal Disrupts Importin α1/β Signaling. J Mol Biol. 2024 Oct 15;436(20).
- Engineered NLS-chimera downregulates expression of aggregation-prone endogenous FUS. Nat Commun. 2024 Sep 10;15(1).
Ya-Ming Hou, PhD
- Genome-wide profiling of tRNA modifications by Induro-tRNAseq reveals coordinated changes. Nat Commun. 2025 Jan 26;16(1).
- A kinetic model for compound heterozygous pathogenic variants in Tyrosyl-tRNA synthetase gene YARS2-Associated neonatal phenotype. J Biol Chem. 2025 Jan;301(1).
- m6A modification is incorporated into bacterial mRNA without specific functional benefit. Nucleic Acids Res. 2025 May 22;53(10).
- Unraveling RNA Conformation Dynamics in Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-like Episode Syndrome with Solid-State Nanopores. ACS Nano. 2024 Jul 2;18(26).
- Post-transcriptional methylation of mitochondrial-tRNA differentially contributes to mitochondrial pathology. Nat Commun. 2024 Oct 18;15(1).
- Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons Journal of Molecular Biology.2022;434(8).
Fadia Ibrahim, PhD
- Defining the True Native Ends of RNAs at Single-Molecule Level with TERA-Seq. Methods Mol Biol. 2025;2863:359-372.
James B. Jaynes, PhD
- The homie insulator has sub-elements with different insulating and long-range pairing properties. Genetics. 2025 Apr 17;229(4).
- Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties. Elife. 2024 Aug 7;13.
- Chromosome structure in Drosophila is determined by boundary pairing not loop extrusion. Elife. 2024 Aug 7;13.
Yohei Kirino, PhD
- Angiogenin-catalyzed cleavage within tRNA anticodon-loops identified by cP-RNA-seq Biosci Biotechnol Biochem. 2025 Feb 20;89(3):398-405.
- A hormone-dependent tRNA half promotes cell cycle progression via destabilization of p21 mRNA PLoS Biology. 2025 Jun 5;23(6).
- cP-RNA-seq for tRNA half sequencing Methods in Enzymology. 2025; 711: 135-153.
- TaqMan RT-qPCR for tRNA half quantification Methods in Enzymology. 2025; 711: 155-170.
- Immunostimulatory short non-coding RNAs in the circulation of patients with tuberculosis infection Molecular Therapy Nucleic Acids. 2024; 35 (1).
- The tRNAVal half: A strong endogenous Toll-like receptor 7 ligand with a 5'-terminal universal sequence signature Proc Natl Acad Sci SA. 2024 May 7;121(19).
- Immunoactive signatures of circulating tRNA- and rRNA-derived RNAs in chronic obstructive pulmonary disease Molecular Therapy Nucleic Acids. 2024; 35 (3).
Qiaoli Li, PhD
- Magnesium Decreases Urine Supersaturation but Not Calcium Oxalate Stone Formation in Genetic Hypercalciuric Stone-Forming Rats. Nephron. 2024;148(7):480-486.
- Novel treatment for PXE: Recombinant ENPP1 enzyme therapy. Mol Ther. 2024 Nov 6;32(11).
- Inorganic pyrophosphate plasma levels in patients with GGCX-associated PXE-like phenotypes. Front Genet. 2024 Sep 27;15.
Alexander M. Mazo, PhD
- Targeting Chemotherapy to Decondensed H3K27me3-Marked Chromatin of AML Cells Enhances Leukemia Suppression. Cancer Res. 2022;82(3):458-471.
Steven B. McMahon, PhD
- Somatic p53 mutations that are markedly overrepresented in lung cancer confer resistance to ROS-induced cell death. Carcinogenesis. 2025 Apr 3;46(2).
- Non-redundant roles for the human mRNA decapping cofactor paralogs DCP1a and DCP1b. Life Sci Alliance. 2024 Sep 10;7(11).
Diane E. Merry, PhD
- Differentially disrupted spinal cord and muscle energy metabolism in spinal and bulbar muscular atrophy. JCI Insight. 2024 Mar 5;9(7).
- Blocking the dimerization of polyglutamine-expanded androgen receptor protects cells from DHT-induced toxicity by increasing AR turnover. J Biol Chem. 2024 May;300(5).
- Mutant androgen receptor induces neurite loss and senescence independently of ARE binding in a neuronal model of SBMA. Proc Natl Acad Sci USA. 2024 Jul 16;121(29).
Anna Pluciennik, PhD
- Structural and molecular basis of PCNA-activated FAN1 nuclease function in DNA repair. Nat Commun. 2025 May 14;16(1).
Richard Pomerantz, PhD
- Structural basis for Polθ-helicase DNA binding and microhomology-mediated end-joining. Nat Commun. 2025 Apr 19;16(1).
- 4'-Ethynyl-2'-Deoxycytidine (EdC) Preferentially Targets Lymphoma and Leukemia Subtypes by Inducing Replicative Stress. Mol Cancer Ther. 2024 May 2;23(5):683-699.
- Discovery of a small-molecule inhibitor that traps Polθ on DNA and synergizes with PARP inhibitors. Nat Commun. 2024 Apr 5;15(1).
- PARG is essential for Polθ-mediated DNA end-joining by removing repressive poly-ADP-ribose marks. Nat Commun. 2024 Jul 11;15(1).
- Structural basis for a Polθ helicase small-molecule inhibitor revealed by cryo-EM. Nat Commun. 2024 Aug 14;15(1).
Zheng Ruan, PhD
- Human Pannexin 1 Channel is NOT Phosphorylated by Src Tyrosine Kinase at Tyr199 and Tyr309. Elife. 2024 May 23;13.
- Inhibition of the proton-activated chloride channel PAC by PIP2. Elife. 2023 Jan 12;12.
Michael Soniat, PhD
- Using the safety scissors: DNA resection regulation at DNA double-strand breaks and telomeres. DNA Repair (Amst). 2025 Jul 23;152.
- The MRN complex and topoisomerase IIIa-RMI1/2 synchronize DNA resection motor proteins. J Biol Chem. 2023 Feb;299(2).
Dmitry Temiakov, PhD
- Structural Basis for Promoter Recognition and Transcription Factor Binding and Release in Human Mitochondria. Mol Cell. 2025 Jul 22:S1097-2765(25).
- Structural basis for intrinsic strand displacement activity of mitochondrial DNA polymerase. Nat Commun. 2025 Mar 11;16(1).
- Maackia amurensis seed lectin structure and sequence comparison with other M. amurensis lectins. J Biol Chem. 2025 May;301(5).
- Structural basis for substrate binding and selection by human mitochondrial RNA polymerase. Nat Commun. 2024 Aug 20:15(1).
Edward Winter, PhD
- The MAPK homolog, Smk1, promotes assembly of the glucan layer of the spore wall in S. cerevisiae. Yeast. 2024 Jul;41(7):448-457.