Reference

This reference collection highlights peer-reviewed publications, research protocols, theses, dissertations, and preprints relevant to peptide synthesis, peptide applications, chemical biology, molecular research, drug discovery, and biomedical science.

Original DOI, journal, preprint, or institutional links are provided where available for independent source verification.

Note: Inclusion in this reference collection does not imply endorsement of Alan Scientific by the listed authors, journals, publishers, universities, or research institutions.

2026

Harnessing toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs

Troian, E. A., Barth, V. C., Chauhan, U., Zheng, H., Zhao, C., Zeng, J., Husson, R. N., & Woychik, N. A. (2026). Nucleic Acids Research, 54(7).

Research Area: Microbiology & Molecular Biology
Reference Topic: Synthetic peptides, bacterial ORFs, ribosome stalling
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Expanding the Genetic Code with Lysine Aminoacylation

Li, X., Gan, Q., & Fan, C. (2026). Journal of the American Chemical Society, 148(11), 12411–12422.

Research Area: Chemical Biology
Reference Topic: Lysine aminoacylation, genetic code expansion, amino acid chemistry
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Dpep, a Cell-Penetrating Peptide Targeting ATF5, CEBPB and CEBPD, Synergistically Combines with ABT-263 and Decitabine to Inhibit Cancer Cell Growth and Overcome Dpep Resistance

Zhou, Q., Nguyen, T. T. T., Angelastro, J. M., Siegelin, M. D., & Greene, L. A. (2026). Cells, 15(9), 826.

Research Area: Cancer Research
Reference Topic: Cell-penetrating peptides, Dpep, cancer therapy, drug combinations
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Post-Translational Modifications Modulate the HLA-DR3 Restricted Epitope Landscape of Sjögren’s Associated Autoantigens

Li, D., Voigt, A., & Nguyen, C. Q. (2026). Medicina, 62(6), 1030.

Research Area: Autoimmunity & Immunology
Reference Topic: PTM peptides, HLA-DR3 epitopes, Sjögren’s disease, autoantigens
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Coupling Far-Western Blotting with Peptide Microarrays Reveals Novel E-Cadherin Spore-Surface Ligands in Clostridioides difficile

Lopez-Garcia, O. K., Pizarro-Guajardo, M., Kocurek, K. I., Rezenom, Y. H., Paredes-Sabja, D., et al. (2026). Journal of Proteome Research, 25(7), 3487–3506.

Research Area: Microbiology & Proteomics
Reference Topic: Peptide microarrays, E-cadherin binding, Clostridioides difficile, protein–peptide interactions
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2025

Identification of small signaling peptide-encoding genes modulated by host and nonhost bacterial pathogens in Arabidopsis

Fonseca, J. P., Boschiero, C., Pant, P., Banakar, R., Oh, S., Hussain, A., Zhao, P., & Mysore, K. S. (2025). Journal of Experimental Botany, 76(22), 7123–7134.

Research Area: Plant Biology
Reference Topic: Small signaling peptides, peptide-encoding genes, plant–pathogen interactions
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Protocol for the coculture of murine vaginal epithelial organoids and T cells to induce resident memory CD8 T cell differentiation

Ramprashad, J. C., Lin, Y., & Beura, L. K. (2025). STAR Protocols, 6(3), 104054.

Research Area: Immunology & Cell Biology
Reference Topic: CD8 T cells, epithelial organoids, resident memory T cells
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An enzyme-linked immunosorbent assay (ELISA)-based activity assay for AMP-activated protein kinase (AMPK)

Nguyen, T. P., Lyu, S., & Liu, Y. (2025). FEBS Open Bio.

Research Area: Enzymology & Cell Signaling
Reference Topic: AMPK, kinase assays, ELISA, peptide substrates
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Determining the Substrate Specificity of Lysine Methyltransferases

Hanquier, J. N., Berryhill, C. A., & Cornett, E. M. (2025). In Gaudreau, L. & Guillemette, B. (Eds.), Histones. Methods in Molecular Biology, Vol. 2919. Humana.

Research Area: Epigenetics & Chemical Biology
Reference Topic: Lysine methyltransferases, peptide substrates, histone modification
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Synthetic helical peptides on nanofibers to activate cell-surface receptors and synergistically enhance critical-sized bone defect regeneration

Zhou, T., Cavalcante, R. C., Ge, C., Franceschi, R. T., & Ma, P. X. (2025). Bioactive Materials, 43, 98–113.

Research Area: Regenerative Medicine & Biomaterials
Reference Topic: Synthetic helical peptides, nanofibers, receptor activation, bone regeneration
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Distinct roles of the two BRCA2 DNA-binding domains in DNA damage repair and replication fork preservation

Neal, F. E., Li, W., Uhrig, M. E., Katz, J. N., Syed, S., Sharma, N., et al. (2025). Cell Reports, 44(5), 115654.

Research Area: DNA Repair & Cancer Biology
Reference Topic: BRCA2, DNA-binding domains, DNA repair, replication fork preservation
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Mechanism of client loading from BiP to GRP94 and its disruption by select inhibitors

Azam, T. P., Han, L., Deans, E. E., Huang, B., Hoxie, R., Friedman, L. J., Gelles, J., & Street, T. O. (2025). Nature Communications, 16(1).

Research Area: Protein Biology & Drug Discovery
Reference Topic: BiP, GRP94, molecular chaperones, protein interactions, inhibitors
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Acute infectious mononucleosis generates persistent, functional EBNA-1 antibodies with high cross-reactivity to alpha-crystalline beta

Ganta, K. K., McManus, M., Blanc, R., Wang, Q., Jung, W., Brody, R., et al. (2025). Cell Reports, 44(5), 115709.

Research Area: Immunology & Infectious Disease
Reference Topic: EBNA-1, antibodies, immune epitopes, cross-reactivity
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Running a genetic stop sign accelerates oxygen metabolism and energy production in horses

Castiglione, G. M., Chen, X., Xu, Z., Dbouk, N. H., Bose, A. A., Carmona-Berrio, D., et al. (2025). Science, 387(6741).

Research Area: Genetics & Metabolism
Reference Topic: Translation, genetic variation, oxygen metabolism, energy production
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Targeting ATF5, CEBPB, and CEBPD with cell-penetrating Dpep sensitizes tumor cells to NK-92MI cell cytotoxicity

Zhou, Q., Siegelin, M. D., & Greene, L. A. (2025). Cells, 14(9), 667.

Research Area: Cancer Research & Immunology
Reference Topic: Cell-penetrating peptides, Dpep, NK-cell cytotoxicity, tumor sensitization
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The T cell receptor landscape of childhood brain tumors

Raphael, I., Xiong, Z., Sneiderman, C. T., Raphael, R. A., Mash, M., et al. (2025). Science Translational Medicine, 17(790), eadp0675.

Research Area: Cancer Immunology & Neuro-Oncology
Reference Topic: T-cell receptors, HLA peptides, pediatric brain tumors, antigen recognition
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2024

Epithelial organoid supports resident memory CD8 T cell differentiation

Ulibarri, M. R., Lin, Y., Ramprashad, J. C., Han, G., Hasan, M. H., Mithila, F. J., et al. (2024). Cell Reports, 43(8), 114621.

Research Area: Immunology & Cell Biology
Reference Topic: Resident memory CD8 T cells, epithelial organoids, immune differentiation
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MTS, WST-8, and ATP viability assays in 2D and 3D cultures: Comparison of methodologically different assays in primary human chondrocytes

Martin, F., Neubert, A., Lutter, A.-H., et al. (2024). Clinical Hemorheology and Microcirculation, 88(S1), S3–S19.

Research Area: Cell Biology
Reference Topic: Cell viability assays, chondrocytes, 2D culture, 3D culture
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Influence of postruminal casein infusion and exogenous glucagon-like peptide 2 administration on the jejunal mucosal transcriptome in cattle

Trotta, R. J., Swanson, K. C., Klotz, J. L., & Harmon, D. L. (2024). PLoS ONE, 19(8), e0308983.

Research Area: Animal Physiology & Nutrition
Reference Topic: GLP-2, peptide hormones, intestinal biology, transcriptomics
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DPEP Inhibits Cancer Cell Glucose Uptake, Glycolysis and Survival by Upregulating Tumor Suppressor TXNIP

Zhou, Q., Nguyen, T. T. T., Mun, J.-Y., Siegelin, M. D., & Greene, L. A. (2024). Cells, 13(12), 1025.

Research Area: Cancer Research
Reference Topic: Dpep, cell-penetrating peptides, cancer metabolism, TXNIP, glycolysis
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Companion to: A molecular basis for milk allergen immune recognition in eosinophilic esophagitis

Dilollo, J., Hu, A., Qu, H., Canziani, K. E., Clement, R. L., McCright, S. J., et al. (2024). bioRxiv, 2024.11.13.623408.

Research Area: Allergy & Immunology
Reference Topic: Milk allergens, immune recognition, epitopes, eosinophilic esophagitis
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The MYCN oncoprotein is an RNA-binding accessory factor of the nuclear exosome targeting complex

Papadopoulos, D., Ha, S. A., Fleischhauer, D., Uhl, L., Russell, T. J., Mikicic, I., et al. (2024). Molecular Cell, 84(11), 2070–2086.e20.

Research Area: Cancer Biology & RNA Biology
Reference Topic: MYCN, RNA binding, nuclear exosome, synthetic peptides
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Structural Analysis and Client Binding Studies of the ER-Specific Molecular Chaperones BiP and Grp94

Deans, E. E. (2024). Doctoral dissertation, Brandeis University.

Research Area: Protein Biology & Structural Biology
Reference Topic: BiP, GRP94, molecular chaperones, peptide binding, fluorescent peptides
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2023

Postruminal casein infusion and exogenous Glucagon-Like peptide 2 administration differentially stimulate pancreatic α-amylase and small intestinal α-glucosidase activity in cattle

Trotta, R. J., Swanson, K. C., Klotz, J. L., & Harmon, D. L. (2023). Journal of Nutrition, 153(10), 2854–2867.

Research Area: Animal Physiology & Nutrition
Reference Topic: GLP-2, peptide hormones, digestive enzymes, gastrointestinal physiology
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PI(3,5)P2 Controls the Signaling Activity of Class I PI3K

Sun, J., et al. (2023). bioRxiv.

Research Area: Cell Signaling
Reference Topic: PI3K signaling, phosphoinositides, lipid–protein interactions
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Multifunctionalized Cationic Chitosan Polymeric Micelles Polyplexed with pVGF for Noninvasive Delivery to the Mouse Brain through the Intranasal Route for Developing Therapeutics for Alzheimer’s Disease

Gothwal, A., Lamptey, R. N. L., & Singh, J. (2023). Molecular Pharmaceutics, 20(6), 3009–3019.

Research Area: Neuroscience & Drug Delivery
Reference Topic: Brain delivery, intranasal delivery, VGF, Alzheimer’s disease
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SARS-CoV-2 infection establishes a stable and age-independent CD8+ T cell response against a dominant nucleocapsid epitope using restricted T cell receptors

Choy, C., Chen, J., Li, J., Gallagher, D. T., Lu, J., Wu, D., et al. (2023). Nature Communications, 14(1).

Research Area: Immunology & Infectious Disease
Reference Topic: SARS-CoV-2, CD8+ T cells, nucleocapsid epitopes, T-cell receptors
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Dpep Inhibits Cancer Cell Growth and Survival via Shared and Context-Dependent Transcriptome Perturbations

Zhou, Q., & Greene, L. A. (2023). Cancers, 15(22), 5318.

Research Area: Cancer Research
Reference Topic: Dpep, cell-penetrating peptides, transcriptomics, cancer cell survival
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2022

Electrostatics drive the molecular chaperone BiP to preferentially bind oligomerized states of a client protein

Deans, E. E., Kotler, J. L., Wei, W., & Street, T. O. (2022). Journal of Molecular Biology, 434(13), 167638.

Research Area: Protein Biology
Reference Topic: BiP, molecular chaperones, peptide binding, protein oligomerization
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Growing Meat on Plants: Using intermediate CBD-RGD fusion proteins to improve bovine satellite cell attachment on cellulose-based scaffolds

Cohen, J. (2022). Pitzer Senior Theses, 131.

Research Area: Tissue Engineering & Biomaterials
Reference Topic: RGD, fusion proteins, cell adhesion, cellulose scaffolds
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Restricting α-synuclein transport into mitochondria by inhibition of α-synuclein–VDAC complexation as a potential therapeutic target for Parkinson’s disease treatment

Rajendran, M., Queralt-Martín, M., Gurnev, P. A., Rosencrans, W. M., Rovini, A., Jacobs, D. C., et al. (2022). Cellular and Molecular Life Sciences, 79(7).

Research Area: Neuroscience
Reference Topic: α-Synuclein, VDAC, mitochondria, Parkinson’s disease
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Targeting lipid–protein interaction to treat Syk-mediated acute myeloid leukemia

Singaram, I., Sharma, A., Pant, S., Lihan, M., Park, M., Pergande, M. R., et al. (2022). Nature Chemical Biology, 19(2), 239–250.

Research Area: Cancer Research & Chemical Biology
Reference Topic: Lipid–protein interactions, Syk signaling, acute myeloid leukemia
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Ephrin-B2-expressing natural killer cells induce angiogenesis

Wolf, K., Crawford, E. B., Wartan, N. M., Schneiderman, S., Riehl, V., Dambaeva, S., & Beaman, K. D. (2022). JVS – Vascular Science, 3, 336–344.

Research Area: Immunology & Vascular Biology
Reference Topic: Natural killer cells, Ephrin-B2, angiogenesis
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HSV Tegument Protein pUL51 Interacts with Host Dynactin for Viral Spread

White, S., Tran, M., & Roller, R. J. (2022). bioRxiv.

Research Area: Virology
Reference Topic: Herpes simplex virus, pUL51, dynactin, viral spread
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TLK1-mediated MK5-S354 phosphorylation drives prostate cancer cell motility and may signify distinct pathologies

Khalil, M. I., Singh, V., King, J. A., & De Benedetti, A. (2022). Molecular Oncology, 16(13), 2537–2557.

Research Area: Cancer Research
Reference Topic: TLK1, MK5 phosphorylation, prostate cancer, cell motility
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Herpes simplex virus cytoplasmic assembly center as a tool for viral egress research and therapeutic development

White, S. (2022). Doctoral dissertation, The University of Iowa.

Research Area: Virology
Reference Topic: Herpes simplex virus, viral assembly, viral egress, therapeutic development

2021

Cell-Penetrating CEBPB and CEBPD Leucine Zipper Decoys as Broadly Acting Anti-Cancer Agents

Zhou, Q., Sun, X., Pasquier, N., Jefferson, P., Nguyen, T. H., Siegelin, M. D., Angelastro, J. M., & Greene, L. A. (2021). Cancers, 13(10), 2504.

Research Area: Cancer Research
Reference Topic: Cell-penetrating peptides, leucine zipper decoys, anticancer peptides
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Mitochondrial Unfolded Protein Response Regulator ATF5 in Mitochondrial Targeted Therapies in AML

Zhao, R. (2021). Doctoral dissertation, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 1154.

Research Area: Cancer Research
Reference Topic: ATF5, mitochondrial stress response, acute myeloid leukemia
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The Effect of Heat Stress and Bacteria-Delivered Plant Elicitors on Plant Immunity Against Root-Knot Nematodes

Hamel, K. M. (2021). Washington State University.

Research Area: Plant Biology
Reference Topic: Plant immunity, bacterial elicitors, plant–pathogen interactions, nematodes
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Phosphoinositide-binding activity of Smad2 is essential for its function in TGF-β signaling

Buwaneka, P., Ralko, A., Gorai, S., Phạm, H., & Cho, W. (2021). Journal of Biological Chemistry, 297(5), 101303.

Research Area: Cell Signaling
Reference Topic: Smad2, phosphoinositides, TGF-β signaling, protein–lipid interactions
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Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery

Chiou, S. H., Tseng, D., Reuben, A., Mallajosyula, V., Molina, I. S., Conley, S. D., et al. (2021). Immunity, 54(3), 586–602.e8.

Research Area: Cancer Immunology
Reference Topic: T-cell epitopes, HLA, antigen discovery, non-small cell lung cancer
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About This Reference Collection

This page is maintained as a scientific reference resource. Original DOI, journal, institutional repository, thesis, dissertation, or preprint links are provided where available for independent source verification.

The Research Area and Reference Topic classifications are editorial categories intended to make the collection easier to browse and search. Inclusion in this collection does not imply endorsement of Alan Scientific by the listed authors, journals, publishers, universities, or research institutions.