Ramaboli MC, Ocvirk S, Khan Mirzaei M, Eberhart BL, Valdivia-Garcia M, Metwaly A, Neuhaus K, Barker G, Ru J, Nesengani LT, Mahdi-Joest D, Wilson AS, Joni SK, Layman DC, Zheng J, Mandal R, Chen Q, Perez MR, Fortuin S, Gaunt B, Wishart D, Methé B, Haller D, Li JV, Deng L, Swart R, O’Keefe SJD (2024) Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer. Nat Commun 15 (1):3379. doi:10.1038/s41467-024-46265-0
Thiele Orberg E, Meedt E, Hiergeist A, Xue J, Heinrich P, Ru J, Ghimire S, Miltiadous O, Lindner S, Schwarz A, Janssen K-P, Herhaus P, Verbeek M, van den Brink MRM, Weber D, Edinger M, Wolff D, Kleigrewe K, Herr W, Bassermann F, Gessner A*, Deng L*, Holler E*, Poeck H*, Bacterial and Bacteriophage Consortia are Associated with Protective Intestinal Immuno-modulatory Meta-bolites in Allogeneic Stem Cell Transplantation Patients, Nature Cancer . 2024, Jan 3. doi: 10.1038/s43018-023-00669-x. Epub ahead of print. PMID: 38172339.
Kirk D, Costeira R, Visconti A, Khan Mirzaei M, Deng L, Valdes AM, C Menni (2024) Bacteriophages, gut bacteria, and microbial pathways interplay in cardiometabolic health. Cell Reports 43 (2)
Walter N, Khan Mirzaei M, Deng L, Willy C, Alt V, Rupp M (2024) The potential of bacteriophage therapy as an alternative treatment approach for antibiotic-resistant infections. Medical Principles and Practice 33 (1), 1-9
Luo S, Ru J, Khan Mirzaei M, Xue J, Peng X, Ralser A, Hadi JL, Mejías-Luque R, Gerhard M and Deng L*. Helicobacter pylori infection alters gut virome by expanding temperate phages linked to increased risk of colorectal cancer. Gut. 2023. gutjnl-2023-330362.
Luo S, Ru J, Khan Mirzaei M, Xue J, Peng X, Ralser A, Mejías-Luque R, Gerhard M and Deng L*. Gut virome profiling identifies an association between temperate phages and colorectal cancer promoted by Helicobacter pylori infection. Gut Microbes. 2023. 15(2): 2257291.
Ru J, Khan Mirzaei M, Xue J, Peng X and Peng X, and Deng L*. ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis. Gut Microbes, 2023. 15(1): p. 2192522. doi: 10.1080/19490976.2023.2192522.
Unterer, M., M.K. Mirzaei, and Deng L*. Targeted Single-Phage Isolation Reveals Phage-Dependent Heterogeneous Infection Dynamics. Microbiology Spectrum, 2023. 0(0): p. e05149-22.
Ralser A, Dietl A, Jarosch S, Engelsberger V, Wanisch A, Janssen KP, Middelhoff M, Vieth M, Quante M, Haller D, Busch DH, Deng L, Mejías-Luque R, Gerhard M. Helicobacter pylori promotes colorectal carcinogenesis by deregulating intestinal immunity and inducing a mucus-degrading microbiota signature. Gut. 2023 Apr 4: gutjnl-2022-328075. doi: 10.1136/gutjnl-2022-328075.
Willy C, Bugert JJ, Classen AY, Deng L, Düchting A, Gross J, Hammerl JA, Korf IHE, Kühn C, Lieberknecht-Jouy S, Rohde C, Rupp M, Vehreschild MJGT, Vogele K, Wienecke S, Witzenrath M, Würstle S, Ziehr H, Moelling K, Broecker F. Phage Therapy in Germany—Update 2023. Viruses. 2023; 15(2):588. doi.org/10.3390/v15020588
Sun J, Ru J, Ramos-Mucci L, Qi F, Chen Z, Chen S, Cribbs AP, Deng L* and Wang X*. DeepsmirUD: Prediction of Regulatory Effects on microRNA Expression Mediated by Small Molecules Using Deep Learning. International Journal of Molecular Sciences. 2023; 24(3):1878. doi.org/10.3390/ijms24031878
Bauer A, Pachl E, Hellmuth JC, Kneidinger N, Heydarian M, Frankenberger M, Stubbe HC, Ryffel B, Petrera A, Hauck SM, Behr J, Kaiser R, Scherer C, Deng L, Teupser D, Ahmidi N, Muenchhoff M, Schubert B, Hilgendorff A. Proteomics reveals antiviral host response and NETosis during acute COVID-19 in high-risk patients. Biochim Biophys Acta Mol Basis Dis. 2022. Nov 1;1869(2):166592. doi: 10.1016/j.bbadis.2022.166592. Epub ahead of print. PMID: 36328146; PMCID: PMC9622026. (IF: 6.2)
Elbehery, A. H., & Deng, L. (2022). Insights into the global freshwater virome. Frontiers in Microbiology, 13. doi: 10.3389/fmicb.2022.953500
Chen, W., Ma, J., Jiang, Y., Deng, L., Lv, N., Gao, J., Cheng, J., Liang, J. B., Wang, Y., Lan, T., Liao, X., & Mi, J. (2022). Selective Maternal Seeding and Rearing Environment From Birth to Weaning Shape the Developing Piglet Gut Microbiome. Frontiers in Microbiology, 13. doi: 10.3389/fmicb.2022.795101
Wu, R., Cao, Z., Jiang, Y., Chen, W., Sun, Y., Li, Q., . . . Ma, J. (2022). Early life dynamics of ARG and MGE associated with intestinal Virome in neonatal piglets. Veterinary Microbiology, 109575. doi:https://doi.org/10.1016/j.vetmic.2022.109575
Tiamani K, Luo S, Schulz S, Xue J, Costa R, Khan Mirzaei M & Deng L*. The role of virome in the gastrointestinal tract and beyond. FEMS Microbiology Reviews, 2022. doi:10.1093/femsre/fuac027
Smith SE, Huang W, Tiamani K, Unterer M, Khan Mirzaei M, Deng L *. Emerging technologies in the study of the virome. Current Opinion in Virology 2022. 54:101231. doi: 10.1016/j.coviro.2022.101231. Epub 2022 May 25. PMID: 35643020. (IF 7.09)
Ma T, Ru J, Xue J, Schulz S, Mirzaei MK, Janssen K-P, Quante M, Deng L*. Differences in Gut Virome Related to Barrett Esophagus and Esophageal Adenocarcinoma. Microorganisms. 2021; 9(8):1701.
Huang H, Jiang Y, Zhao J, Li S, Schulz S, Deng L*. BTEX biodegradation is linked to bacterial community assembly patterns in contaminated groundwater ecosystem. Journal of Hazardous Materials,. 2021 May 24;419:126205. doi: 10.1016/j.jhazmat.2021.126205. Epub ahead of print. PMID: 34216964.
Khan Mirzaei M, Deng L*. New technologies for developing phage-based tools to manipulate the human microbiome. Trends Microbiol. 2021 May 18:S0966-842X(21)00118-9. doi: 10.1016/j.tim.2021.04.007. Epub ahead of print. PMID: 34016512.
Unterer M, Khan Mirzaei M, Deng L*. Gut Phage Database: Signal Transduction and Targeted Therapy 2021 May 17;6(1):193. doi: 10.1038/s41392-021-00615-2. PMID: 34001868; PMCID: PMC8128913.
Goettsch W, Beerenwinkel N, Deng L, … , Marz M*. ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics. Viruses. 2021 Apr 27;13(5):766. doi: 10.3390/v13050766. PMID: 33925452; PMCID: PMC8145447.
Khan Mirzaei M, Xue J, Costa R, Ru J, Schulz S, Taranu ZE, Deng L*. Challenges of Studying the Human Virome - Relevant Emerging Technologies. Trends Microbiol. 2021 Feb;29(2):171-181. doi: 10.1016/j.tim.2020.05.021. Epub 2020 Jul 1. PMID: 32622559.
Khan Mirzaei M, Deng L*. Sustainable Microbiome: a symphony orchestrated by synthetic phages. Microb Biotechnol. 2021 Jan;14(1):45-50. doi: 10.1111/1751-7915.13697. Epub 2020 Nov 10. PMID: 33171009; PMCID: PMC7888444.
Jung S, Jacobs KFK, Shein M, Schütz AK, Mohr F, Stadler H, Stadler D, Lucko AM, Altstetter SM, Wilsch F, Deng L, Protzer U*. Efficient and reproducible depletion of hepatitis B virus from plasma derived extracellular vesicles. J Extracell Vesicles. 2020 Dec;10(2):e12040. doi: 10.1002/jev2.12040. Epub 2020 Dec 22. PMID: 33363711; PMCID: PMC7754750.
Kaletta J, Pickl C, Griebler C, Klingl A, Kurmayer R and Deng L*. A rigorous assessment and comparison of enumeration methods for environmental viruses. (2020) Scientific Reports 10(1): 1-12.
Mirzaei MK, Khan AK, Ghosh P, Taranu ZE, Taguer M, Ru J, Chowdhury R, Kabir MD, Li Deng L, Mondal D and Maurice CF. Bacteriophages Isolated from Stunted Children Can Regulate Gut Bacterial Communities in an Age-Specific Manner. (2020) Cell Host & Microbe, 27 (2): 199-212.
Kurmayer R, Entfellner E, Weisse T, Offterdinger M, Rentmeister A, Deng L: Chemically labeled toxins or bioactive peptides show a heterogeneous intracellular distribution and low spatial overlap with autofluorescence in bloom-forming cyanobacteria. (2020) Scientific Reports, 10(1):2781.
Ma T, Jiang J, Elbehery AHA, Blank S, Kurmayer R, Deng L*. Resilience of planktonic bacterial community structure in response to short-term weather deterioration during the growing season in an alpine lake. (2020) Hydrobiologia, 847: 535–548
Dzunkova M, Low SJ, Daly JN, Deng L, RinkeC, Hugenholtz P. Defining the human gut host-phage network through single-cell viral tagging. (2019) Nature Microbiology, 4(12):2192-2203.
Jiang Y, Huang H, Ma T, Ru J, Blank S, Kurmayer R, Deng L*. Temperature Response of Planktonic Microbiota in Remote Alpine Lakes. (2019). Frontiers in Microbiology 10:1714
Jiang Y, …, Deng L, Li X, Using nano-attapulgite clay compounded hydrophilic urethane foams (AT/HUFs) as biofilm support enhances oil-refinery wastewater treatment in a biofilm membrane bioreactor. (2019) Science of The Total Environment, 646: 606-61
Ibrahim B, McMahon DP, Hufsky F, Beer M, Deng L, Le Mercier P. Palmarini M, Thiel V, Marz M. A new era of virus bioinformatics. (2018) Virus Research251: 86-90.
Simon LM, Karg S, Westermann A J, Engel M, Elbehery AHA, Hense B, Heinig M, Deng L, Theis F J. MetaMap: An atlas of metatranscriptomic reads in human disease-related RNA-seq data. (2018) GigaScience giy070, doi.org:10.1093/gigascience/giy070
Elbehery AHA, Feichtmayer J, Singh D, Griebler C & Deng L*. The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation. (2018). Frontiers in Microbiology9, doi:10.3389/fmicb.2018.01110
Hufsky F, Ibrahim B, Beer M, Deng L, Le Mercier P, McMahon D, Palmarini M, Thiel V and Marz M: Virologists - heroes need weapons. (2018). Plos Pathogens, 14(2): e1006771. doi.org/10.1371/journal.ppat.1006771
Feichtmayer J, Deng L & Griebler, C. (2017). Antagonistic Microbial Interactions: Contributions and Potential Applications for Controlling Pathogens in the Aquatic Systems. Frontiers in Microbiology8, doi:10.3389/fmicb.2017.02192
Entfellner E, Frei M, Christiansen G, Deng L, Blom J, and Kurmayer R. (2017). Evolution of Anabaenopeptin Peptide Structural Variability in the Cyanobacterium Planktothrix. Frontiers in Microbiology 8:219. (IF 5.64)
Kurmayer R, Deng L and Entfellner E. (2016). Role of toxic and bioactive secondary metabolites in colonization and bloom formation by filamentous cyanobacteria Planktothrix. Harmful Algae 54:69-86. (IF 4.27)
Chen Q, Christiansen G, Deng L, Kurmayer R. (2016) Emergence of nontoxic mutants as revealed by single filament analysis in bloom-forming cyanobacteria of the genus Planktothrix. BMC Microbiology 16: 1-12. . (IF 3.605)
Kurmayer R, Blom JF, Deng L, Pernthaler J. (2015)Integrating phylogeny, geographic niche partitioning and secondary metabolite synthesis in bloom-forming Planktothrix, ISME J.9, 909-921. (IF 10.3)
Deng L, Krauss S, Feichtmayer J, Hofmann R, Arndt H and Griebler C. (2014) Grazing of heterotrophic flagellates on viruses is driven by feeding behaviour. Environmental Microbiology Reports6, 325-330. (IF 3.531)
Hurwitz B, Deng L, Poulos BP, Sullivan MB. (2013) Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environmental Microbiology15, 1428-1440.
Deng L, Gregory A, Yilmaz S, Poulos B, Hugenholtz P, Sullivan MB. (2012) Contrasting life strategies of viruses that infect photo- and hetero- trophic bacteria revealed by viral-tagging. mBio3, e00373-12. doi:10.1128/mBio.00373-12. (Recommended by Faculty 1000, 2013)
Duhaime MB, Deng L, Poulos BT, Sullivan MB. (2012) Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method. Environmental Microbiology 14, 2526-37.
John SG, Mendez CB, Deng L, Poulos B, Kauffman AK, Kern SE, Brum J, Polz MF, Boyle EA, Sullivan MB. (2011) A simple and efficient method for concentration of ocean viruses by chemical flocculation. Environmental MicrobiologyReports3, 195-202.
Deng L and Hayes PK. (2008) Evidence for cyanophage active against bloom-forming freshwater cyanobacteria.Freshwater Biology 53, 1240-1252.
