This is a list of publications associated with Department of Biochemistry faculty, postdoctoral researchers, and students (noted in bold) published during 2024-25 academic year.
Wang L, Pattnaik A, Sahoo SS, Stone EG, Zhuang Y, Benton A, Tajmul M, Chakravorty S, Dhawan D, Nguyen MA, Sirit I, Mundy K, Ricketts CJ, Hadisurya M, Baral G, Tinsley SL, Anderson NL, Hoda S, Briggs SD, Kaimakliotis HZ, Allen-Petersen BL, Tao WA, Linehan WM, Knapp DW, Hanna JA, Olson MR, Afzali B, Kazemian M. 2024. Unbiased discovery of cancer pathways and therapeutics using Pathway Ensemble Tool and Benchmark. Nat Commun 15(1):7288
Saha D, Gregor JB, Hoda S, Eastman KE, Gutierrez-Schultz VA, Navarrete M, Wisecaver JH, Briggs SD. 2024. Candida glabrata maintains two HAP1 ohnologs, HAP1A and HAP1B, for distinct roles in ergosterol gene regulation to mediate sterol homeostasis under azole and hypoxic conditions. mSphere 9(11): e0052424
Yanagi T, Kikuchi H, Takeuchi K, Susa K, Mori T, Chiga M, Yamamoto K, Furukawa A, Kanazawa T, Kato Y, Takahashi N, Suzuki T, Mori Y, Carter BC, Mori M, Nakano Y, Fujiki T, Hara Y, Suzuki S, Ando F, Mandai S, Honda S, Torii S, Shimizu S, Tanaka H, Fujii Y, Rai T, Uchida S, Sohara E. 2024. ULK1-regulated AMP sensing by AMPK and its application for the treatment of chronic kidney disease. Kidney Int. 106 (5): 887-906
Zhang J, Li H, Li L, Wu J, Song L, Liu X, Pan Z, Zhou C, Li W, Liu Z, Jiao M, Hu M, Dong Z, Zhang H, Shi B, Wang Y, Wang D, Carter B, Zhao S, Ren G, Zhao Y, Zhang Y. 2025. Super RNA Pol II domains enhance minor ZGA through 3D interaction to ensure the integrity of major transcriptional waves in late-ZGA mammals. Cell Genom online ahead of print
Simpson JP, Kim CY, Kaur A, Weng JK, Dilkes B, Chapple C. 2024. Genome-wide association identifies a BAHD acyltransferase activity that assembles an ester of glucuronosylglycerol and phenylacetic acid. Plant J 118(6): 2169-2187
Sorg A, Luo ZW, Li QB, Roy K, Basset GJ, Kim J, Hunter C, Chapple C, Rering C, Block AK. 2025. The airborne herbivore-induced plant volatile indole is converted to benzoxazinoid defense compounds in maize plants. New Phytol 246 (2):718-728
Long J, Sliger S, Luo ZW, Pascuzzi PE, Chapple C, Ogas J. 2025. A semidominant point mutation of Mediator tail subunit MED5b in Arabidopsis leads to altered enrichment of H3K27me3 and reduced expression of targets of MYC2. G3 (Bethesda) 15 (3):jkae301
Cottrell KA, Ryu S, Donelick H, Mai H, Young AA, Pierce JR, Bass BL, Weber JD. 2024. Activation of PKR by a short-hairpin RNA. Sci Rep 14(1): 23533
Young AA, Bohlin HE, Pierce JR, Cottrell KA. 2024. Suppression of double-stranded RNA sensing in cancer: molecular mechanisms and therapeutic potential. Biochem Soc Trans 52(5): 2035-2045
Alkhalaf LM, Arrowsmith C, Balskus EP, Bergamini G, Bhandari R, Chang CJ, Chen P, Chen X, Ciulli A, Cricco JA, Davis BG, Delbianco M, Dudareva N, Dueber E, Ferguson F, de Giuseppe PO, Hamachi I, Hammond MC, Hatzios SK, Do Heo W, Janet JP, Kamat SS, Knapp S, Krishnan Y, Lang K, Laraia L, Leveson-Gower RB, Li XD, Liu DR, Liu MF, London N, Mahanta N, Mayor-Ruiz C, Muir T, Murakami MT, Rhee HW, Robers M, Satz A, Schulman BA, Shen B, Shoichet B, Strauss E, Suzuki T, Tiwary P, Waldmann H, Ward TR, Weeks A, Weerapana E, Winter G. 2024. Thoughts for the future. Nat Chem Biol 21 (1):6-15
Rhee SY, Anstett DN, Cahoon EB, Covarrubias-Robles AA, Danquah E, Dudareva N, Ezura H, Gilbert KJ, Gutiérrez RA, Heck M, Lowry DB, Mittler R, Muday G, Mukankusi C, Nelson ADL, Restrepo S, Rouached H, Seki M, Walker B, Way D, Weber APM. 2025. Resilient plants, sustainable future. Trends Plant Sci 30(4):382-388
Bergman ME, Dudareva N. 2024. Plant specialized metabolism: Diversity of terpene synthases and their products. Curr Opin Plant Biol 81:102607
Bergman ME, Kortbeek RWJ, Gutensohn M, Dudareva N. 2024. Plant terpenoid biosynthetic network and its multiple layers of regulation. Prog Lipid Res 95:101287
Bergman ME, Huang XQ, Baudino S, Caissard JC, Dudareva N. 2025. Plant volatile organic compounds: Emission and perception in a changing world. Curr Opin Plant Biol 27:85-102
Huang XQ, Yahyaa M, Kongala PR, Maoz I, Dudareva N, Ibdah M. 2025. Biosynthesis of elemicin and isoelemicin in Daucus carota leaves. Plant J 121(2): e17201
Mensah IK, Gowher H. 2024. Signaling Pathways Governing Cardiomyocyte Differentiation. Genes (Basel) 15(6):798.
Mensah IK, Gowher H. 2024. Epigenetic Regulation of Mammalian Cardiomyocyte Development. Epigenomes 8(3):25
Wang S, Siddique R, Hall MC, Rice PA, Chang L. 2024. Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition. Cell 187(24): 6865-6881
DeMarco AG, Dibble MG, Hall MC. 2024. Inducible degradation-coupled phosphoproteomics identifies PP2A(Rts1) as a novel eisosome regulator. Front Cell Dev Biol. 12:1451027
Dong J, Jassim BA, Milholland KL, Qu Z, Bai Y, Miao Y, Miao J, Ma Y, Lin J, Hall MC, Zhang ZY. 2024. Development of Novel Phosphonodifluoromethyl-Containing Phosphotyrosine Mimetics and a First-In-Class, Potent, Selective, and Bioavailable Inhibitor of Human CDC14 Phosphatases. J Med Chem 67(11):8817-8835
Milholland KL, Waddey BT, Velázquez-Marrero KG, Lihon MV, Danzeisen EL, Naughton NH, Adams TJ, Schwartz JL, Liu X, Hall MC. Cdc14 phosphatases use an intramolecular pseudosubstrate motif to stimulate and regulate catalysis. J Biol Chem 300(9):107644
Kenny S, Iyer S, Gabel CA, Tegenfeldt N, DeMarco AG, Hall MC, Chang L, Davisson VJ, Pol SV, Das C. 2025. Structure of E6AP in complex with HPV16-E6 and p53 reveals a novel ordered domain important for E3 ligase activation. Structure 33(3): 504-516
Cooper PO, Yang J, Wang HH, Broman MM, Jayasundara SM, Sahoo SS, Yan B, Awdalkreem GD, Cresswell GM, Wang L, Goossens E, Lanman NA, Doerge RW, Zheng F, Cheng L, Alqahtani S, Crist SA, Braun RE, Kazemian M, Jerde TJ, Ratliff TL. 2024. Inflammation impacts androgen receptor signaling in basal prostate stem cells through interleukin 1 receptor antagonist. Commun Biol 7(1):1390
Li Z, Kim W, Utturkar S, Yan B, Lanman NA, Elzey BD, Kazemian M, Yeo Y, Andrisani O. 2024. DDX5 deficiency drives non-canonical NF-κB activation and NRF2 expression, influencing sorafenib response and hepatocellular carcinoma progression. Cell Death Dis 15(8):583
Li Z, Rahman N, Bi C, Mohallem R, Pattnaik A, Kazemian M, Huang F, Aryal UK, Andrisani O. 2024. RNA Helicase DDX5 in Association With IFI16 and the Polycomb Repressive Complex 2 Silences Transcription of the Hepatitis B Virus by Interferon. J Med Virol 96(12):e70118
Lin JX, Du N, Li P, Kazemian M, Gebregiorgis T, Spolski R, Leonard WJ. 2025. Critical functions for STAT5 tetramers in the maturation and survival of natural killer cells. Nat Commun 16(1):894
Kwizera R, Xie J, Nurse N, Yuan C, Kirchmaier AL. 2024. Impacts of Nucleosome Positioning Elements and Pre-Assembled Chromatin States on Expression and Retention of Transgenes. Genes (Basel) 15(9):1232
Xie C, Zhang C, Liu X, Zhou Y. 2025. The cellular basis of meristem development in fern gametophytes. Biochem Soc Trans 53(1):BST20240728
Geng Y, Xie C, Zhang C, Liu X, Zhou Y. 2025. Functions and Regulation of HAM Family Genes in Meristems During Gametophyte and Sporophyte Generations. Plant Cell Environ 48(3): 2125-2131
Geng Y, Xie C, Yan A, Yang X, Lai DN, Liu X, Zhou Y. 2024. A conserved GRAS-domain transcriptional regulator links meristem indeterminacy to sex determination in Ceratopteris gametophytes. Curr Biol 34(15):3454-3472
Wang K, Li L, Kenny S, Gan D, Reitsma JM, Zhou Y, Das C, Liu X. 2025. Molecular mechanisms of CAND2 in regulating SCF ubiquitin ligases. Nat Commun 16(1):1998
Yang X, Yan A, Liu X, Volkening A, Zhou Y. 2025. Single cell-derived multicellular meristem: insights into male-to-hermaphrodite conversion and de novo meristem formation in Ceratopteris. Development 152(3): DEV204411
Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N, Pache L, Burgstaller-Muehlbacher S, De Jesus PD, Teriete P, Hull MV, Chang MW, Chan JF, Cao J, Poon VK, Herbert KM, Cheng K, Nguyen TH, Rubanov A, Pu Y, Nguyen C, Choi A, Rathnasinghe R, Schotsaert M, Miorin L, Dejosez M, Zwaka TP, Sit KY, Martinez-Sobrido L, Liu WC, White KM, Chapman ME, Lendy EK, Glynne RJ, Albrecht R, Ruppin E, Mesecar AD, Johnson JR, Benner C, Sun R, Schultz PG, Su AI, García-Sastre A, Chatterjee AK, Yuen KY, Chanda SK. 2024. Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature 631(8019): E3
Ibrahim IM, Lee JH, Weaver S, Kwizera R, Lohman JR, Puthiyaveetil S. 2025. Cysteine residues contribute to the regulation of Arabidopsis state transition 7 kinase. FEBS Lett 599(3): 436-446
McKenzie SD, Puthiyaveetil S. 2025. Protein phosphorylation and oxidative protein modification promote plant photosystem II disassembly for repair. Plant Commun 6(3):101202
Deshpande A, Marsing M, Singla V, Ibrahim IM, Puthiyaveetil S, Morgan JA. 2025. Introduction of a phenylalanine sink in fast growing cyanobacterium Synechococcus elongatus PCC 11801 leads to improved PSII efficiency, linear electron transport, and carbon fixation. Plant J 122(2):e70129
Yan W, Li Y, Xie S, Tao WA, Hu J, Liu H, Zhang G, Liu F, Nie Y, Chen X, Zhang X, Liu Y, Wei D, Ma C, Zhang H, Xu H, Wang S. 2024. Chondrocyte-Targeted Delivery System of Sortase A-Engineered Extracellular Vesicles Silencing MMP13 for Osteoarthritis Therapy. Adv Healthc Mater 13(16):e2303510
Feng X, Shen A, Zhang W, Jia S, Iliuk A, Wang Y, Zhang W, Zhang Y, Tao WA, Hu L. 2025. High-throughput capture and in situ protein analysis of extracellular vesicles by chemical probe-based array. Nat Protoc 20 (4):1057-1081.
Cornejo KG, Venegas A, Sono MH, Door M, Gutierrez-Ruiz B, Karabedian LB, Nandi SG, Hadisurya M, Tao WA, Dykhuizen EC, Saha RN. 2024. Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA polymerase II productive elongation. Cell Rep 43(11):114877
Zhang G, Ding Y, Zhang H, Wei D, Liu Y, Sun J, Xie Z, Tao WA, Zhu Y. 2024. Assessment of urine sample collection and processing variables for extracellular vesicle-based proteomics. Analyst 149(12):3416-3424
Snyder M, Liu YK, Shang R, Xu H, Thrift C, Chen X, Chen J, Kim KH, Qiu J, Bi P, Tao WA, Kuang S. 2024. LETMD1 regulates mitochondrial protein synthesis and import to guard brown fat mitochondrial integrity and function. iScience 27(10):110944
Bockorny B, Muthuswamy L, Huang L, Hadisurya M, Maria Lim C, Tsai LL, Gill RR, Wei JL, Bullock AJ, Grossman JE, Besaw RJ, Narasimhan S, Tao WA, Perea S, Sawhney MS, Freedman SD, Hildago M, Iliuk A, Muthuswamy SK. 2024. A large-scale proteomics resource of circulating extracellular vesicles for biomarker discovery in pancreatic cancer. Elife 12:RP8737369
Sang T, Chen CW, Lin Z, Ma Y, Du Y, Lin PY, Hadisurya M, Zhu JK, Lang Z, Tao WA, Hsu CC, Wang P. 2024. DIA-Based Phosphoproteomics Identifies Early Phosphorylation Events in Response to EGTA and Mannitol in Arabidopsis. Mol Cell Proteomics 23(8): 100804
Zhao R, Hadisurya M, Ndetan H, Xi NM, Adduri S, Konduru NV, Samten B, Zhang J, Tao WA, Singh KP, Ji HL. 2024. Regenerative Signatures in BAL of Acute Respiratory Distress Syndrome. Am J Respir Cell Mol Biol 71(6): 740-742
Lihon MV, Tuchscherer NA, Tao WA. 2025. Isolation and Identification of Brain Tissue Extracellular Vesicles for Translational Proteomics. Methods Mol Biol 2884:225-239
Das S, Zea Rojas MP, Tran EJ. 2024. Novel insights on the positive correlation between sense and antisense pairs on gene expression. Wiley Interdiscip Rev RNA 15 (4):e1864
Das S, Zea MP, Russon MP, Xing Z, Torregrosa-Allen S, Cervantes HE, Harper HA, Elzey BD, Tran EJ. 2025. Supinoxin blocks small cell lung cancer progression by inhibiting mitochondrial respiration through DDX5. iScience 28(4): 112219
