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Selected Publications
- Zhang, Yichang; Castro-Mejía, Josué L; Deng, Ling; Shah, Shiraz A; Thorsen, Jonathan; Leal Rodríguez, Cristina; Jessen, Leon E; Dion, Moïra B; Chawes, Bo; Bønnelykke, Klaus; ,The influence of early life exposures on the infant gut virome,Gut microbes,2025
- Redgwell, Tamsin A; Thorsen, Jonathan; Petit, Marie-Agnès; Deng, Ling; Vestergaard, Gisle; Russel, Jakob; Chawes, Bo; Bønnelykke, Klaus; Bisgaard, Hans; Nielsen, Dennis S; ,Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts,npj Biofilms and Microbiomes,2025
- Dion, Moira B; Shah, Shiraz A; Deng, Ling; Thorsen, Jonathan; Stokholm, Jakob; Krogfelt, Karen A; Schjorring, Susanne; Horvath, Philippe; Allard, Antoine; Nielsen, Dennis S; ,Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages (vol 18, wrae005, 2024),ISME JOURNAL,2025
- Boulund, Ulrika; Thorsen, Jonathan; Larsen, Frej; Poulsen, Casper S; Widdowson, Michael; Jiang, Jie; Tranæs, Kaare; Deng, Ling; Rasmussen, Morten Arendt; Chawes, Bo; ,Infant gut anellovirus composition associates with early life factors and childhood atopic disease,Nature Communications,2025
- Leal Rodríguez, Cristina; Shah, Shiraz A; Rasmussen, Morten Arendt; Thorsen, Jonathan; Boulund, Ulrika; Pedersen, Casper-Emil Tingskov; Castro-Mejía, Josué L; Poulsen, Christina Egeø; Poulsen, Casper Sahl; Deng, Ling; ,The infant gut virome is associated with preschool asthma risk independently of bacteria,Nature medicine,2024
- Dion, Moïra B; Shah, Shiraz A; Deng, Ling; Thorsen, Jonathan; Stokholm, Jakob; Krogfelt, Karen A; Schjørring, Susanne; Horvath, Philippe; Allard, Antoine; Nielsen, Dennis S; ,Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages,The ISME journal,2024
- Li, Zhaojie; Peng, Chuantao; Sun, Zhihong; Deng, Ling; Lukasz, Krych; ,Preparation, function and application of postbiotics,Frontiers in Microbiology,2024
- Zhai, Xichuan; Gobbi, Alex; Kot, Witold; Krych, Lukasz; Nielsen, Dennis Sandris; Deng, Ling; ,A single-stranded based library preparation method for virome characterization,Microbiome,2024
- Zhang, Weijia; Bhoobalan-Chitty, Yuvaraj; Zhai, Xichuan; Hui, Yan; Hansen, Lars Hestbjerg; Deng, Ling; Peng, Xu; ,Replication protein Rep provides selective advantage to viruses in the presence of CRISPR-Cas immunity,The CRISPR Journal,2023
- Rasmussen, Torben Sølbeck; Koefoed, Anna Kirstine; Deng, Ling; Muhammed, Musemma K; Rousseau, Geneviève M; Kot, Witold; Sprotte, Sabrina; Neve, Horst; Franz, Charles MAP; Hansen, Axel Kornerup; ,CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice,The ISME Journal,2023
- Zhai, Xichuan; Castro-Mejía, Josué L; Gobbi, Alex; Aslampaloglou, Antonios; Kot, Witold; Nielsen, Dennis S; Deng, Ling; ,The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analysis,Microbiome,2023
- Shah, Shiraz A; Deng, Ling; Thorsen, Jonathan; Pedersen, Anders G; Dion, Moïra B; Castro-Mejía, Josué L; Silins, Ronalds; Romme, Fie O; Sausset, Romain; Jessen, Leon E; ,Expanding known viral diversity in the healthy infant gut,Nature microbiology,2023
- Larsen, Frej; Offersen, Simone Margaard; Li, Viktoria Rose; Deng, Ling; Nielsen, Dennis Sandris; Rasmussen, Torben Sølbeck; ,Choice of ultrafilter affects recovery rate of bacteriophages,Viruses,2023
- Zachariassen, Line Fisker; Ebert, Maria Bernadette Bergh; Mentzel, Caroline Märta Junker; Deng, Ling; Krych, Lukasz; Nielsen, Dennis Sandris; Stokholm, Jakob; Hansen, Camilla Hartmann Friis; ,Cesarean section induced dysbiosis promotes type 2 immunity but not oxazolone-induced dermatitis in mice,Gut Microbes,2023
- Larsen, Frej; Jakobsen, Rasmus Riemer; Mao, Xiaotian; Castro-Mejia, Josue; Deng, Ling; Nielsen, Dennis S; ,Purification and up-concentration of bacteriophages and viruses from fecal samples,Bacteriophages: Methods and Protocols,2023
- Hui, Yan; Vestergaard, Gisle; Deng, Ling; Kot, Witold Piotr; Thymann, Thomas; Brunse, Anders; Nielsen, Dennis Sandris; ,Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs,npj Biofilms and Microbiomes,2022
- Johansen, Joachim; Plichta, Damian R; Nissen, Jakob Nybo; Jespersen, Marie Louise; Shah, Shiraz A; Deng, Ling; Stokholm, Jakob; Bisgaard, Hans; Nielsen, Dennis Sandris; Sørensen, Søren J; ,Genome binning of viral entities from bulk metagenomics data,Nature communications,2022
- Brunse, Anders; Deng, Ling; Pan, Xiaoyu; Hui, Yan; Castro-Mejía, Josué L; Kot, Witold; Nguyen, Duc Ninh; Secher, Jan Bojsen-Møller; Nielsen, Dennis Sandris; Thymann, Thomas; ,Fecal filtrate transplantation protects against necrotizing enterocolitis,The ISME journal,2022
- Kihl, Pernille; Krych, Lukasz; Deng, Ling; Hansen, Lars H; Buschard, Karsten; Skov, Søren; Nielsen, Dennis S; Kornerup Hansen, Axel; ,Effect of gluten-free diet and antibiotics on murine gut microbiota and immune response to tetanus vaccination,PLoS One,2022
- Brunse, Anders; Offersen, Simone Margaard; Mosegaard, Josefine Juliane; Deng, Ling; Damborg, Peter; Nielsen, Dennis Sandris; Sangild, Per Torp; Thymann, Thomas; Nguyen, Duc Ninh; ,Enteral broad-spectrum antibiotics antagonize the effect of fecal microbiota transplantation in preterm pigs,Gut Microbes,2021
- Mathieu, Aurélie; Dion, Moïra; Deng, Ling; Tremblay, Denise; Moncaut, Elisabeth; Shah, Shiraz A; Stokholm, Jakob; Krogfelt, Karen A; Schjørring, Susanne; Bisgaard, Hans; ,Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages,Nature Communications,2020
- Rasmussen, Torben Sølbeck; Koefoed, Anna Kirstine; Jakobsen, Rasmus Riemer; Deng, Ling; Castro-Mejía, Josué L; Brunse, Anders; Neve, Horst; Vogensen, Finn Kvist; Nielsen, Dennis Sandris; ,Bacteriophage-mediated manipulation of the gut microbiome–promises and presents limitations,FEMS Microbiology Reviews,2020
- Jakobsen, Rasmus Riemer; Haahr, Thor; Humaidan, Peter; Jensen, Jørgen Skov; Kot, Witold Piotr; Castro-Mejia, Josue Leonardo; Deng, Ling; Leser, Thomas Dyrmann; Nielsen, Dennis Sandris; ,Characterization of the vaginal DNA virome in health and dysbiosis,Viruses,2020
- Pan, Saifu; Li, Qi; Deng, Ling; Jiang, Suping; Jin, Xuexia; Peng, Nan; Liang, Yunxiang; She, Qunxin; Li, Yingjun; ,A seed motif for target RNA capture enables efficient immune defence by a type III-B CRISPR-Cas system,RNA biology,2019
- Kihl, Pernille; Krych, Lukasz; Deng, Ling; Kildemoes, Anna Overgaard; Laigaard, Ann; Hansen, Lars Hestbjerg; Hansen, Camilla Hartmann Friis; Buschard, Karsten; Nielsen, Dennis Sandris; Hansen, Axel Kornerup; ,Oral LPS dosing induces local immunological changes in the pancreatic lymph nodes in mice,Journal of Diabetes Research,2019
- Deng, Ling; Silins, Ronalds; Castro-Mejía, Josué L; Kot, Witold; Jessen, Leon; Thorsen, Jonathan; Shah, Shiraz; Stokholm, Jakob; Bisgaard, Hans; Moineau, Sylvain; ,A protocol for extraction of infective viromes suitable for metagenomics sequencing from low volume fecal samples,Viruses,2019
- Brunse, Anders; Hui, Yan; Nguyen, Duc Ninh; Deng, Ling; Nielsen, Dennis Sandris; Thymann, Thomas; ,FECAL MICROBIOTA TRANSPLANTATION PROTECTS AGAINST NECROTIZING ENTEROCOLITIS IN A DONOR SPECIFIC MANNER,PEDIATRIC RESEARCH,2019
- Martinez-Alvarez, Laura; Deng, Ling; Peng, Xu; ,Formation of a Viral Replication Focus in Sulfolobus Cells Infected by the Rudivirus Sulfolobus islandicus Rod-Shaped Virus 2 (vol 91, e00486-17, 2017),JOURNAL OF VIROLOGY,2018
- Castro-Mejía, Josué L; Deng, Ling; Vogensen, Finn K; Reyes, Alejandro; Nielsen, Dennis S; ,Extraction and purification of viruses from fecal samples for metagenome and morphology analyses,The Human Virome: Methods and Protocols,2018
- Han, Wenyuan; Li, Yingjun; Deng, Ling; Feng, Mingxia; Peng, Wenfang; Hallstrøm, Søren; Zhang, Jing; Peng, Nan; Liang, Yun Xiang; White, Malcolm F; ,A type III-B CRISPR-Cas effector complex mediating massive target DNA destruction,Nucleic acids research,2017
- Martínez-Alvarez, Laura; Deng, Ling; Peng, Xu; ,Formation of a viral replication focus in Sulfolobus cells infected by the rudivirus Sulfolobus islandicus rod-shaped virus 2,Journal of Virology,2017
- Mousaei, Marzieh; Deng, Ling; She, Qunxin; Garrett, Roger A; ,Major and minor crRNA annealing sites facilitate low stringency DNA protospacer binding prior to Type IA CRISPR-Cas interference in Sulfolobus,RNA biology,2016
- Garrett, Roger A; Shah, Shiraz A; Erdmann, Susanne; Liu, Guannan; Mousaei, Marzieh; León-Sobrino, Carlos; Peng, Wenfang; Gudbergsdottir, Soley; Deng, Ling; Vestergaard, Gisle; ,CRISPR-Cas adaptive immune systems of the Sulfolobales: unravelling their complexity and diversity,Life,2015
- Erdmann, Susanne; Chen, Bo; Huang, Xiaoxing; Deng, Ling; Liu, Chao; Shah, Shiraz A; Le Moine Bauer, Sven; Sobrino, Carlos León; Wang, Haina; Wei, Yunlin; ,A novel single-tailed fusiform Sulfolobus virus STSV2 infecting model Sulfolobus species,Extremophiles,2014
- Deng, Ling; He, Fei; Bhoobalan-Chitty, Yuvaraj; Martinez-Alvarez, Laura; Guo, Yang; Peng, Xu; ,Unveiling cell surface and type IV secretion proteins responsible for archaeal rudivirus entry,Journal of Virology,2014
- Deng, Ling; Garrett, Roger A; Shah, Shiraz A; Peng, Xu; She, Qunxin; ,A novel interference mechanism by a type IIIB CRISPR‐Cmr module in S ulfolobus,Molecular microbiology,2013
- Okutan, Ebru; Deng, Ling; Mirlashari, Saideh; Uldahl, Kristine; Halim, Mayada; Liu, Chao; Garrett, Roger A; She, Qunxin; Peng, Xu; ,Novel insights into gene regulation of the rudivirus SIRV2 infecting Sulfolobus cells,RNA biology,2013
- Deng, Ling; Kenchappa, Chandra S; Peng, Xu; She, Qunxin; Garrett, Roger A; ,Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus,Nucleic acids research,2012
- Peng, Nan; Deng, Ling; Mei, Yuxia; Jiang, Dongqing; Hu, Yongmei; Awayez, Mariana; Liang, Yunxiang; She, Qunxin; ,A synthetic arabinose-inducible promoter confers high levels of recombinant protein expression in hyperthermophilic archaeon Sulfolobus islandicus,Applied and environmental microbiology,2012
- Gudbergsdottir, Soley; Deng, Ling; Chen, Zhengjun; Jensen, Jaide VK; Jensen, Linda R; She, Qunxin; Garrett, Roger A; ,Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector‐borne viral and plasmid genes and protospacers,Molecular microbiology,2011
- Garrett, Roger A; Shah, Shiraz A; Vestergaard, Gisle; Deng, Ling; Gudbergsdottir, Soley; Kenchappa, Chandra S; Erdmann, Susanne; She, Qunxin; ,CRISPR-based immune systems of the Sulfolobales: complexity and diversity,Biochemical Society Transactions,2011
- Li, Xiyang; Guo, Li; Deng, Ling; Feng, Deqin; Ren, Yi; Chu, Yindi; She, Qunxin; Huang, Li; ,Deletion of the topoisomerase III gene in the hyperthermophilic archaeon Sulfolobus islandicus results in slow growth and defects in cell cycle control,Journal of Genetics and Genomics,2011
- Zhang, Changyi; Guo, Li; Deng, Ling; Wu, Yuanxin; Liang, Yunxiang; Huang, Li; She, Qunxin; ,Revealing the essentiality of multiple archaeal pcna genes using a mutant propagation assay based on an improved knockout method,Microbiology,2010
- Zhao, Shumiao; Huang, Jun; Zhang, Changyi; Deng, Ling; Hu, Nan; Liang, Yunxiang; ,High-level expression of an Aspergillus niger endo-β-1, 4-glucanase in Pichia pastoris through gene codon optimization and synthesis,J Microbiol Biotechnol,2010
- Deng, Ling; Zhu, Haojun; Chen, Zhengjun; Liang, Yun Xiang; She, Qunxin; ,Unmarked gene deletion and host–vector system for the hyperthermophilic crenarchaeon Sulfolobus islandicus,Extremophiles,2009
- She, Qunxin; Zhang, Changyi; Deng, Ling; Peng, Nan; Chen, Zhengjun; Liang, Yun Xiang; ,Genetic analyses in the hyperthermophilic archaeon Sulfolobus islandicus,Biochemical Society Transactions,2009
- She, Q; Deng, L; Zhu, H; Chen, Z; Dreibrøl, M; Awayez, M; Liang, YX; ,Host-vector systems for hyperthermophilic archaeon Sulfolobus,Microbes and the Environment: Perspective and Challenges,2008
- Zhao, Shumiao; Deng, Ling; Hu, Nan; Zhao, Bin; Liang, Yunxiang; ,Cost-effective production of Bacillus licheniformis using simple netting bag solid bioreactor,World Journal of Microbiology and Biotechnology,2008
Achievements
Patent
Honor
Software achievement