Author

N. Deng

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Biophysics· 3 Cancer Biology· 3 Cell Biology· 3 Pharmacology & Toxicology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:human· 7 Approach:statistical model· 6 Research Focus:cell type annotation· 5 Research Focus:differential expression· 5 Approach:experimental assay· 5 Research Focus:gene regulatory network inference· 4 Organism:mouse· 4 Assay:bulk RNA-seq· 3

Frequent Co-Authors

A. Burman· 3 shared C. Yao· 3 shared D. Jiang· 3 shared G. Huang· 3 shared J. Belperio· 3 shared J. Liang· 3 shared S. S. Weigt· 3 shared T. Xie· 3 shared

Activity by Year

2018-2023 · peak 5/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

3 shared papersCell Biology

A. Burman

Mutual co-authors in cluster

Author profile →

10 papers

Recent·Most cited

Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization

Q. Sun, A. Biswas, D. Lyumkis, R. Levy, N. Deng

This study identifies molecular determinants of binding modes for a third-generation HIV-1 integrase inhibitor, showing that side chain and solvent reorganization, along with conformational entropy, influence ligand binding preferences in closely related viral intasomes.

bioRxiv · Nov 29, 2023 · PreprintBiophysics

Mechanisms of HIV-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug Resistant Variants

M. Li, D. Passos, Z. Shan, S. J. Smith, Q. Sun, A. Biswas, I. Choudhuri, T. Strutzenberg, A. Haldane, N. Deng, Z. Li, X.-Z. Zhao, T. R. Burke, R. M. Levy, S. H. Hughes, , D. Lyumkis

The paper investigates mechanisms of HIV-1 integrase resistance to Dolutegravir and shows that 4d is more effective against resistant variants.

bioRxiv · Dec 4, 2022Biophysics

Comparative Molecular Genomic Analyses of a Spontaneous Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer

N. Ozirmak Lermi, S. B. Gray, C. M. Bowen, L. Reyes-Uribe, B. K. Dray, N. Deng, R. A. Harris, M. Raveendran, F. Benavides, C. L. Hodo, M. W. Taggart, K. Colbert Maresso, K. M. Sinha, J. Rogers, E. Vilar

This study characterizes a spontaneous MMRd CRC model in rhesus macaques, finding high MSI levels and gene expression patterns similar to human CRC, supporting their use as an animal model.

bioRxiv · Aug 19, 2021 · PreprintCancer Biology

DNA barcoding reveals ongoing immunoediting of clonal cancer populations during metastatic progression and in response to immunotherapy

L. A. Baldwin, N. Bartonicek, J. Yang, S. Z. Wu, N. Deng, D. L. Roden, C.-L. Chan, G. Al-Eryani, D. J. Zanker, B. S. Parker, A. Swarbrick, S. Junankar

This study uses DNA barcoding to track clonal evolution in breast cancer during metastasis and immunotherapy, finding ongoing immunoediting and identifying potential therapeutic targets.

bioRxiv · Jan 11, 2021Cancer Biology

Zinc Metabolic Defect of Aging Alveolar Progenitors in Progressive Pulmonary Fibrosis

J. Liang, G. Huang, X. Liu, F. Taghavifar, N. Liu, Y. Wang, N. Deng, C. Yao, A. Burman, T. Xie, S. Rowan, S. S. Weigt, J. BELPERIO, B. Stripp, W. Parks, , P. Noble

The paper identifies a zinc metabolic defect in alveolar progenitor cells in IPF and aged mice, linked to impaired renewal and fibrosis through ZIP8 downregulation.

bioRxiv · Jul 30, 2020 · PreprintCell Biology

Single-Cell Transcriptomics Identifies Dysregulated Metabolic Programs of Aging Alveolar Progenitor Cells in Lung Fibrosis

J. Liang, G. Huang, X. Liu, F. Taghavifar, N. Liu, C. Yao, N. Deng, Y. Wangy, A. Burman, T. Xie, S. C. Rowan, P. Chen, C. M. Hogaboam, B. Stripp, S. S. Weigt, , D. Jiang

This study identifies metabolic defects in alveolar progenitor cells during aging and lung injury that impair their renewal capacity.

bioRxiv · Jul 30, 2020Cell Biology

Definition and Signatures of Lung Fibroblast Populations in Development and Fibrosis in Mice and Men

X. Liu, S. C. Rowan, J. Liang, C. Yao, G. Huang, N. Deng, T. Xie, D. Wu, Y. Wang, A. Burman, T. Parimon, Z. Borok, P. Chen, W. C. Parks, C. M. Hogaboam, , D. Jiang

This study identifies fibroblast subpopulations in mouse and human lungs using scRNA-seq, revealing conserved transcriptomic signatures and their roles in fibrosis.

bioRxiv · Jul 15, 2020 · PreprintCell Biology

Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein AssociationAssociation: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor

N. Deng, C. Tse, L. Wickstrom, M. Kvaratskhelia, E. Gallicchio, R. Levy

This paper investigates the thermodynamics and free energy landscape of HIV-1 integrase multimerization induced by an allosteric inhibitor, revealing short-range interactions and enthalpy-driven binding.

bioRxiv · Jun 29, 2020Biophysics

Effects of rhein on bile acid homeostasis in rats

Z. Xian, J. Tian, L. Wang, Y. Zhang, J. Han, N. Deng, S. Liu, Y. Zhao, C. Li, Y. Yi, D. Wang, J. Meng, C. Pan, A. Liang

This study examines the effects of rhein on bile acid homeostasis in rats, showing dose-dependent changes in bile acid levels and transporter expression without liver or kidney toxicity.

bioRxiv · Jan 29, 2020Pharmacology & Toxicology

MicroRNAs as potential therapeutics to enhance chemosensitivity in advancedprostate cancer

H.-M. Lin, I. Nikolic, J. Yang, L. Castillo, N. Deng, C.-L. Chan, N. K. Yeung, E. Dodson, B. Elsworth, C. Spielman, B. Lee, Z. Boyer, K. Simpson, R. J. Daly, L. G. Horvath, A. Swarbrick

This study identifies microRNA mimics that enhance taxane-induced apoptosis in CRPC cell lines, suggesting potential therapeutic use to improve chemosensitivity.

bioRxiv · Feb 28, 2018Cancer Biology