(&, Co-first Author; †, Corresponding Author) ORCID ID: 0000-0002-7269-4342
H-Index: 34; I10-index: 58; Citations: 3978 [Google Scholar, 2025-12-01]

[84] Yuan X, Zheng T, Huang J, Li Z, Lan H, Ji B, Gao X†. Functional Characterization of a Ferritin-Like Transcriptional Regulator in Cyanobacterial Cold Adaptation. Under Review [RESEARCH]

[83] Li Y, Zhang y, Zhang Y, Wang Q, Ji B, Yang H†, Li X†. Spatial Proteomics in Precision Clinical Medicine: Technologies, Bioinformatics, and Translational Applications. Under Review [REVIEW]

[82] Li T, Zhang J, Niu W, Zhang X, Yuan Z, Wang L, Zhang Y, Wang L, Ji B, Qu L, Yin Y, Wei Y†. Anti-obesity Effects of Lactiplantibacillus plantarum ZNFL-1 by Modulating Gut Microbiota and Lipid Metabolism in High-fat Diet-induced Mice. Probiotics and Antimicrobial Proteins 2025 doi: 10.1007/s12602-025-10692-2. [RESEARCH]

[81] Yu Z, Wei Y, Ji B, Fang X†. Editorial: Plant Natural Products: Biosynthesis, Regulation and Function. Frontiers in Plant Science 2025 16:1661170 doi: 10.3389/fpls.2025.1661170. [EDITORIAL]

[80] Han W&, Xiao L&, Sun H&, Xiang G, Jia Q, Wang H, Ji B, Zhang C, Kerkhoven J. E., Nielsen J, Lu H†. AlphaGEM Enables Precise Genome-Scale Metabolic Modelling by Integrating Protein Structure Alignment with Deep-learning-based Dark Metabolism Mining. bioRxiv 2025 doi: 10.1101/2025.07.21.665674 [RESEARCH]

[79] Liu J&, Fang C&, Ji B&, Zhang T, Li L, Zhu Z†, Jiang L†. Predicting Bacterial Radiation Resistance through Identifying Novel Genomic Features. 2025 Under Review. [RESEARCH]

[78] Peng Y, Ji B, Wang Y, Lu H†. Euktect: Enhanced Eukaryotic Sequence Detection and Classification in Metagenomes via the DNA Language Model. bioRxiv 2025 doi: 10.1101/2025.06.19.660294. [RESEARCH]

[77] Chechi K&, Chakaroun R&, Myridakis A&, Forslund-Startceva K. S&, Fromentin S&, Nielsen T, Aron-Wisneswky J, Belda E, Prifti E, Lassen B. P, Falony G, Vieira-Silva S, Chilloux J, Sonomura K, Hoyles L, Martinez-Gili L, Pallotti F, Andrikopoulos P, Puig-Castellvi F, Roume H, Pons N, Le Chatelier E, Quinquis B, Galleron N, Berland M, Olanipekun M, Jia M, Manolias A, Holmes B, Adriouch S, Blüher M, Coelho P. L, Da Silva K, Galan P, Ji B, Neves L. A, Rouault C, Salem Joe-Elie, Tremaroli V, Hansen H. T, Søndertoft B. N, Lewinter C, Pedersen K. H, The MetaCardis Consortium, Mark D. P, Gøtze P.J, Køber L, Vestergaard H, Hansen T, Zucker Jean-Daniel, Sato Taka-Aki, Hercberg S, Bäckhed F, Letunic I, Oppert Jean-Michel, Nielsen J, Raes J, Tzoulaki I, Dehghan A, Zuber V, Bouzigon E, Lathrop M, Raina P, Froguel P, Mastuda F, Demenais F, Gauguier D, Stumvoll M, Bork P, Pedersen O†, Ehrlich S. D†, Clément K†, Dumas Marc-Emmanuel†. A Gut Microbiome-kidney-heart Axis is Predictive of Future Cardiovascular Diseases. 2025. Nature Communications 2025. In Press. doi: 10.21203/rs.3.rs-5843796/v1. [RESEARCH]

[76] Yuan X, Gao X†, Liang W, Wang X, Guo X, Liu M, Qing Y, Zhao Q, Liu C, Zheng T, Huang J, Ji B, Li Z†. Nocturnal Low Temperature Triger Cross-protection of Dryland Cyanobacteria against Multiple Environmental Stressors. 2025. In Submission. [RESEARCH]

[75] Zhang F, Fan Y, Phung V.N., Ji B, Jiang X, Yang R, Liu M, Yang J, Chen J, Xu X, Li F†, Ji P†, Yang H†, Li X†. Nervonic Acid can Alleviates Stroke and Its Associated Poststroke Depression Behaviors. hLife 2024 2(11):592-606 doi: 10.1016/j.hlife.2024.08.001. [RESEARCH]

[74] Lin J, Zhang J, Zhu G, Zhang X, Shang H, Ji B, Bai Y, Qu L†, Wei Y†. Enhancing the Nutritional Quality of Defatted Cottonseed Meal by Solid-State Fermentation with Probiotic Microbes. Fermentation 2024 10(8):429. doi: 10.3390/fermentation10080429. [RESEARCH]

[73] Hefny Z, Ji B, Elsemman E.I., Nielsen J†, Dijck V.P†. Transcriptomic Meta-analysis to Identify Potential Antifungal Targets in Candida albicans. BMC Microbiology. 2024 24:66. doi: 10.1186/s12866-024-03213-8. [RESEARCH]

[72] Li P, Ji B, Lappa D, Meijnikman S.A., Tremaroli V, Luo H, Geng J, Krautkramer K.A., Olsson L, Schwartz W.T., Nieuwdorp M, Bäckhed F, Nielsen J†. Systems Analysis of Metabolic Responses to a Mixed Meal Test in an Obese Cohort Reveals Links between Tissue Metabolism and the Gut Microbiota. bioRxiv. 2023 doi: 10.1101/2022.04.26.489057. [RESEARCH]

[71] Limeta A, Gatto F, Herrgård J. M, Ji B†, Nielsen J. Leveraging High-resolution Omics Data for Predicting Responses and Adverse Events to Immune Checkpoint Inhibitors. Computational and Structural Biology Journal. 2023 21:3912-39319. doi: 10.1016/j.csbj.2023.07.032. [REVIEW]

[70] Li P, Ross S, Luo H, Ji B, Nielsen J†. Metabolic Engineering in Human Gut Microbiome: Recent Developments and Future Prospective. Metabolic Engineering. 2023 79:1-13. doi: 10.1016/j.ymben.2023.06.006. [REVIEW]

[69] Wei Y, Ji B†. The Health Effects of Artificial Sweeteners: Towards Personalized Quantification and Prediction through Gut Microbiome. Eco-Environment & Health. 2023 2(3):89-91. doi: 10.1016/j.eehl.2023.05.003. [COMMENTARY]

[68] Shi T†, Darvishi F†, Can M†, Ji B†, Ji X-J†. Editorial: Design and Construction of Microbial Cell Factories for the Production of Fuels and Chemicals. Frontiers in Bioengineering and Biotechnology. 2023 11:1198317. doi: 10.3389/fbioe.2023.1198317. [COMMENTARY]

[67] Zhao Y&, Chen D-Q&, Ji B, Zhang X, Anbo M, Jelsbak L†. Whole-genome Sequencing Reveals High Risk Clones of Pseudomonas aeruginosa in Guangdong, China. Frontiers in Microbiology. 2023 14:1117017. doi: 10.3389/fmicb.2023.11117017. [RESEARCH]

[66] Lv X†, Wang Y†, Ji B†, Ji X-J†. Systems Metabolic Engineering of Industrial Microorganisms. Microorganisms. 2023 11(4):926. doi: 10.3390/microorganisms11040926. [COMMENTARY]

[65] Lappa D†, Meijnikman S.A., Krautkramer A.K., Olsson M.L., Aydin Ö, Rijswijk V Anne-Sophie, Acherman I.Z. Y, Brauw L.D. M, Tremaroli V, Olofsson E.L., Lundqvist A, Hjorth A.S., Ji B, Gerdes E.A. V, Groen K.A., Schwartz W.T., Nieuwdorp M, Bäckhed F, Nielsen J†. Self-organized Metabotyping of Obese Individuals Identifies Clusters Responding Differently to Bariatric Surgery. PLoS ONE. 2023 18(3): e0279335. doi: 10.1371/journal.pone.0279335. [RESEARCH]

[64] Gao X†, Yuan X, Zheng T, Ji B. Promoting Efficient Production of Scytonemin in Cell Culture of Nostoc flagelliforme by Periodic Short-term Solar Irradiation. Bioresource Technology Reports. 2023 21:101352. doi: 10.1016/j.biteb.2023.101352. [RESEARCH]

[63] Hartwig S.T, Ambye L, Petersen F.J, Wronding T, Amato L, Gruhn R.J, Chan C.H.A, Ji B, Bro-Jorgensen H.M, Werge L, Petersen S.B.M, Brinkmann C, Duno M, Bache I, Herrgard J.M, Jorgensen S.F, Hoffmann R.E†, Nielsen S.H†. Cell-free Fetal DNA for Genetic Evaluation in Copenhagen Pregnancy Loss Study (COPL): A Prospective Cohort Study. 2023 The Lancet. 401(10378):762-771. doi: 10.1016/S0140-6736(22)02610-1. [RESEARCH]

[62] Luo H, Li P, Ji B, Nielsen J†. Modeling the Metabolic Dynamics at the Genome-scale by Optimized Yield Analysis. 2023 Metabolic Engineering. 75:119-130. doi: 10.1016/j.ymben.2022.12.001. [RESEARCH]

[61] Li P, Luo H, Ji B, Nielsen J†. Gut Microbiome and Machine Learning Potential for Personalized Medicine. 2022 Microbial Cell Factories. 21:241. doi: 10.1186/s12934-022-01973-4. [REVIEW]

[60] Li P&, Ji B&, Luo H, Sundh D, Lorentzon M, Nielsen J†. One-year Supplementation with Lactobacillus reuteri ATCC PTA 6475 Counteracts a Degradation of Gut Microbiota in in Older Woman with Low Bone Mineral Density. npj Biofilms and Microbiomes. 2022 8:84. doi: 10.1038/s41522-022-00348-2. [RESEARCH]

[59] Wang L&, Zhang Q&, Mei H, Cui X, Wang M, Zhu Y, Ji B†, Wei Y†. Different Distribution of Core Microbiota in Upper Soil Layer in Two Places of North China Plain. The Open Microbiology Journal. 2021 16: e187428582207220. doi: 10.2174/18742858-v16-e2207220. [RESEARCH]

[58] Chen X†, Li X, Ji B, Wang Y, Ishchuk P.O, Vorontsov E, Petranovic D, Siewers V†, Engqvist M. Suppressors of Amyloid-β Toxicity Improve Protein Production by Reducing Oxidative Stress and Globally Tuning Cellular Metabolism. Data in Brief. 2022 doi: 10.1016/j.dib.2022.108322. [RESEARCH]

[57] Chen X†, Li X, Ji B, Wang Y, Ishchuk P.O, Vorontsov E, Petranovic D, Siewers V†, Engqvist M. Suppressors of Amyloid-β Toxicity Improve Protein Production by Reducing Oxidative Stress and Globally Tuning Cellular Metabolism. Metabolic Engineering. 2022 72: 311-324. doi: 10.1016/j.ymben.2022.04.005. [RESEARCH]

[56] Du R, Wang M, Peng J, Ji B, Ji X, Wei Y†. Advances in Discovery of Novel Antibiotic Synthetic Gene Clusters in Uncultured Microorganisms. Chinese Journal of Bioprocess Engineering. 2022 20(2): 172-181. doi: 10.3969/j.issn.1672-3678.2022.02.006. [REVIEW]

[55] Fromentin S&, Forslund K.S&, Chechi K&, Aron-Wisnewsky J&, Chakaroun R&, Nielsen T&, Tremaroli V, Ji B, Prifti E, Alves R, Assmann K, Belda E, Caesar R, Chilloux J, Coelho LP, Falony G, Fellahi S, Galan P, Galleron N, Helft G, Hoyles L, Isnard R, Chatelier E.L, Julienne H, Myridakis A, Olsson L, Pedersen H.K, Pons N, Quinquis B, Rouault C, Roume H, Salem J.E, Schmidt S, Vieira-Silva S, Wu H, Li P, Lewinter C, Fan Y, Søndertoft N.B, Hansen T.H, The MetaCardis Consortium, Gøtze J.P, Køber L, Vestergaard H, Hansen T, Zucker J.D, Hercberg S, Backhed F, Raes J, Oppert J.M, Nielsen J, Letunic I, Bork P, Dumas M.E, Stumvol M, Clément K†, Ehrlich S.D†, Pedersen O†. Microbiome and Metabolome Features of the Cardiometabolic Disease Spectrum. Nature Medicine. 2022 28: 303–314. doi: 10.1038/s41591-022-01688-4. [RESEARCH]

[54] Belda E, Voland L, Tremaroli V, Falony G, Adriouch S, Assmann K, Prifti E, Aron-Wisnewsky J, Debédat J, Roy L.T, Nielsen T, Amouyal C, André S, Andreelli F, Blüher M, Chakaroun R, Chilloux J, Coelho P.L, Dao M-C, Das P, Fellahi S, Forslund S, Galleron N, Hansen T.H, Holmes B, Ji B, Pedersen H.K, Le P, Chatelier E.L, Lewinter C, Mannerås-Holm L, Marquet F, Myridakis A, Pelloux V, Pons N, Quinquis B, Rouault C, Roume H, Salem J.E, Sokolovska N, Sønderskov N.B, Touch S, Vieira-Silva S, The MetaCardis consortium, Galan P, Holst J, Gøtze J.P, Køber L, Vestergaard H, Hansen T, Hercberg S, Oppert J.M, Nielsen J, Letunic I, Dumas M.C, Stumvoll M, Pedersen O.B, Bork P, Ehrlich S.D, Zucker J.D, Bäckhed F, Raes J, Clément K†. Impairment of Gut Microbial Biotin Metabolism and Host Biotin Status in Severe Obesity: Effect of Biotin and Prebiotic Supplementation on Improved Metabolisms. Gut. 2022 doi: 10.1136/gutjnl-2022-325753. [RESEARCH]

[53] Liu M&, Liu X&, Zhang J, Chang Y, Cui Z, Ji B, Nielsen J, Qi Q†, Hou J†. Mapping of Nonhomologous End Joining-Mediated Integration Facilitates Genome-Scale Trackable Mutagenesis in Yarrowia lipolytica. ACS Synthetic Biology. 2022 11(1): 216-227. doi: 10.1021/acssynbio.1c00390. [RESEARCH]

[52] Fosland K.S&, Chakaroun R&, Zimmermann-Kogadeeva M&, Marko L&, Aron-Wisnewsky J&, Nielsen T&, Moitinho-Silva L, Schmidt SB T, Falony G, Vieira-Silva S, Adriouch S, J. Alves J R, Assmann K , Bastard J.P, Birkner T, Caesar R, Chilloux J, Coelho PL, Fezeu L, Galleron N, Helft G, Isnard R, Ji B, Kuhn M, Chatelier E, Myridakis A, Olsson L, Pons N, Prifti E, Quinquis B, Roume H, Salem J.E, Sokolovska N, Tremaroli V, Valles-Colomer M, Lewinter C, Søndertoft B.N, Pedersen K.H, Hansen T.H, The MetaCardis Consortium, Gøtze J.P, Køber L, Vestergaard H, Hansen T, Zucker JD, Hercberg S, Oppert J.M, Letunic I, Nielsen J, Bäckhed F, Ehrlich S.D, Dumas M.E, Raes J, Pedersen O, Clément K†, Stumvoll M†, Bork P†. Combinatorial, Additive and Dose-dependent Drug-microbiome Associations. Nature. 2021 600(7889): 500-505. doi: 10.1038/s41586-021-04177-9. [RESEARCH]

[51] Wei Y†, Ji B†, Ledesma-Amaro R†, Chen T†, Ji X†. Editorial: Engineering Yeast to Produce Plant Natural Products. 2021 Frontiers in Bioengineering and Biotechnology. 2021 9:798097. doi: 10.3389/fbioe.2021.798097. [COMMENTARY]

[50] Zhang X, Miao Q, Xu X, Ji B, Qu L, Wei Y†. Developments in Fatty Acid-derived Insect Pheromone Production using Engineered Yeasts. Frontiers in Microbiology. 2021 12:759975. doi: 10.3389/fmicb.2021.759975. [REVIEW]

[49] Wei Y†, Li X, Ji B, Qu L. Recent Advances on the Recovery, Modulation and Synthetic Biology of Gut Microbiota and Hosts. Scientia Sinica Vitae. 2021 51. doi: 10.1360/SSV-2021-0088. [REVIEW]

[48] Lu H&, Li F&, Yuan L&, Domenzain I, Li G, Chen Y, Ji B, Kerkhoven JE, Nielsen J†. Expanded Metabolic Networks Together with Accelerated Protein Evolution Render Cellular New Traits in Yeast Subphylum. Molecular Systems Biology. 2021 17:e10427. doi: 10.15252/msb.202110427. [RESEARCH]

[47] Ji B†, Herrgård J. M, Nielsen J. Microbial Community Dynamics Revisited. Nature Computational Science. 2021 doi: 10.1038/s43588-021-00144-6. [COMMENTARY]

[46] Gao X†, Liu L, Cui L, Zheng T, Ji B, Liu K. Comparative Characterization of Two β-galactosidases LacZ and WspA from the Terrestrial Cyanobacterium Nostoc flagelliforme with Focus on the Latter’s Central Active Region and Specific N-terminal Role. Scientific Reports. 2021 11:18448. doi: 10.1038/s41598-021-97929-6. [RESEARCH]

[45] Yang Y, Li X, Yang Y, Shoaie S, Zhang C, Ji B†, Wei Y†. Advances on the Relationships between Cow’s Milk Protein Allergy and Gut Microbiome. Frontiers in Microbiology. 2021 12:716667. doi: 10.3389/fmicb.2021.716667. [REVIEW]

[44] Luo H, Li P, Wang H, Roos S, Ji B, Nielsen J†. Genome-scale Insight into the Metabolic Versatility of Lactobacillus reuteri. BMC Biotechnology. 2021 21:46. doi: 10.1186/s12896-021-00702-w. [RESEARCH]

[43] Liu Y, Li X, Yang Y, Liu Y, Wang S, Ji B, Wei Y†. Exploring Potantial Gut Microbiota in Patients with Colorectal Disease based on 16S rRNA Gene amplicon and Metagenomics. Frontiers in Molecular Bioscience. 2021 8:703638. doi: 10.3389/fmolb.2021.703638. [RESEARCH]

[42] Li G&, Zrimec J&, Ji B, Geng J, Larsbrink J, Zelezniak A, Nielsen J, Engqvist K.M M†. Performance of Regression Models as a Function of Experimental Noise. Bioinformatics and Biology Insights. 2021 doi: 10.1177/11779322211020315. [RESEARCH]

[41] Qin J, Krivoruchko A, Ji B, Chen Y, Kristensen M, Özdemir E, Keasling D.J., Jensen K.M., Nielsen J†. Engineering Yeast Metabolism for the Discovery and Production of Polyamines and Polyamine Analogues. Nature Catalysis. 2021 4: 498-509. doi: 10.1038/s41929-021-00631-z. [RESEARCH]

[40] Marcišauskas S, Kim Y, Blasche S, Patil R.K., Ji B, Nielsen J†. Draft Genome Sequences of Five Fungal Strains Isolated from Kefir. Microbiology Resource Announcements. 2021 10(21):e0019521. doi: 10.1128/MRA.00195-21. [RESEARCH]

[39] Geng J, Ji B, Li G, Lopez-Isuza F, Nielsen J†. CODY Enables Quantitatively Spatiotemporal Prediction on in vivo Gut Microbial Variability Induced by Diet-Intervention. Proceedings of the National Academy of Sciences of the United States of America. 2021 118(13): e2019336118 doi: 10.1073/pnas.2019336118. [RESEARCH]

[38] Li P&, Sundh D&, Ji B&, Lappa D, Ye L, Bäckhed F, Nielsen J†, Lorentzon M†. Metabolic Alterations in Older Women with Low Bone Mineral Density and the Effects of Lactobacillus reuteri Supplementation. JBMR Plus. 2021 5(4): e10478. doi: 10.1002/jbm4.10478 [RESEARCH, WILEY Top Cited Article]

[37] Li Y, Wang J, Wang M,  Gao Y, Jin C, Shi X†, Ji B†, Wei Y†, Liu H†. Microbial Profiling Identifies Potential Key Drivers in Gastric Cancer Patients. Biotechnology & Biotechnological Equipment. 2021 35(1): 496-503. doi: 10.1080/13102818.2021.1896384. [RESEARCH]

[36] Gao X†, Zhu Z, Xu H, An J, Ji B†, Ye S†. Cold Adaptation in Dryland: Transcriptomic Insights into Cold-Stressed Nostoc flagelliforme and Characterization of a Hypothetical Gene with Cold and Nitrogen Stress Tolerance. Environmental Microbiology. 2021 23(2): 713-727. doi: 10.1111/1462-2920.15153. [RESEARCH]

[35] Li G, Hu Y, Zrimec J, Wang H, Zelezniak A, Ji B, Nilsen J†. Bayesian Genome Scale Modelling Identifies Thermal Determinants of Yeast Metabolism. Nature Communications. 2021 12: 190. doi: 10.1038/s41467-020-20338-2. [RESEARCH, Featured Articles]

[34] Limeta A, Ji B†, Gatto F, Levin M, Nielsen J†. Meta-analysis of Gut Microbiota in Predicting Response to Cancer Immunotherapy in Metastatic Melanoma. JCI Insights. 2020 5(23): e140940. doi: 10.1172/jci.imsight.140940. [RESEARCH]

[33] Wang M, Wei Y†, Ji B, Nielsen J. Advances in Metabolic Engineering of Saccharomyces cerevisiae for Cocoa Butter Equivalent Production. Frontiers in Bioengineering and Biotechnology. 2020 8: 594081. doi: 10.3389/fbioe.2020.594081. [REVIEW]

[32] Vaga S&, Lee S&, Ji B, Andreasson A, Talley J.N, Agreus L, Bidkhori G, Kovatcheva-Datchary P, Park J, Lee D, Proctor G, Ehrlich D, Nielsen J†, Engstrand L†, Shoaie S†. Compositional and Functional Differences of the Mucosal Microbiota along the Intestine of Healthy Individuals. Scientific Reports. 2020 10: 14977. doi: 10.1038/s41598-020-71939-2. [RESEARCH]

[31] Abdel-Haleem M.A, Ravikumar V, Ji B, Mineta K, Gao X, Nielsen J, Gojobori T†, Mijakovic I†. Integrated Metabolic Modeling, Culturing and Transcriptomics Explains Enhanced Virulence of V. cholerae during Co-infection with ETEC. mSystems. 2020 5: e00491-20. doi: 10.1128/mSystems.00491-20. [RESEARCH]

[30] Shi X, Wei Y†, Ji B†. Systems Biology of Gastric Cancer: Perspectives on the Omics-based Diagnosis and Treatment. Frontiers in Molecular Biosciences. 2020 7: 203. doi: 10.3389/fmolb.2020.00203. [REVIEW]

[29] Wang J, Ledesma-Amaro R, Wei Y, Ji B, Ji X†. Metabolic Engineering for Increased Lipid Accumulation in Yarrowia lipolytica. Bioresource Technology. 2020 313: 123707. doi: 10.1016/j.biortech.2020.123707. [REVIEW]

[28] Chen X, Ji B, Hao X, Li X, Eisele F, Nystrom T, Petranovic D†. FMN Reduces Amyloid-β Toxicity in Yeast by Regulating Redox Status and Cellular Metabolism. Nature Communications. 2020 11: 867. doi: 10.1038/s41467-020-14525-4. [RESEARCH]

[27] Marcišauskas S, Ji B, Nielsen J†. Reconstruction and Analysis of Kluyveromyces marxianus Genome-scale Metabolic Model. BMC Bioinformatics. 2019 20: 551. doi: /10.1186/s12859-019-3134-5. [RESEARCH]

[26] Ye L, Das P, Li P, Ji B, Nielsen J†. Carbohydrate Active Enzymes are Affected by Diet Transition from Milk to Solid Food in Infant Gut Microbiota. FEMS Microbiology Ecology. 2019 95(11): fiz159. doi: 10.1093/femsec/fiz159 [RESEARCH, Editor’s Choice]

[25] Li G, Ji B, Nielsen J†. The Pan-genome of Saccharomyces cerevisiae. FEMS Yeast Research. 2019 7: foz064. doi: 10.1093/femsyr/foz064. [RESEARCH]

[24] Kumar M, Ji B, Zengler K, Nielsen J†. Modeling Approaches for Studying the Microbiome. Nature Microbiology. 2019 4: 1253-1267. doi: 10.1038/s41564-019-0491-9. [REVIEW]

[23] Das P, Marcišauskas S, Ji B, Nielsen J†. Metagenomic Analysis of Bile Acid Metabolic Genes in Human Gut Microbiome. BMC Genomics. 2019 20: 517. doi: 10.1186/s12864-019-5899-3. [RESEARCH]

[22] Gao X†, Liu B, Ji B†. Profiling of Small Molecular Metabolites in Nostoc flagelliforme during the Rehydration and Dehydration Processes. Marine Drugs. 2019 17(5): 298. doi: 10.3390/md17050298. [RESEARCH]

[21] Nielsen J.C, Prigent S, Grijseels S, Workman M, Ji B, Nielsen J†. Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi. mSystems. 2019 4: e00012-19. doi: 10.1128/mSystems.00012-19. [RESEARCH]

[20] Wei Y, Ji B, Siewers V, Xu D, Halkier A.B, Nielsen J†. Identification of Genes from Vitellaria paradoxa Fruits Involved in Shea Butter Biosynthesis through Transcriptomics and Functional Expression in Yeast. Applied Microbiology and Biotechnology. 2019 103(9): 3727-3736. doi: 10.1007/s00253-019-09720-3. [RESEARCH]

[19] Kumar M&, Ji B&, Babaei P&, Das P, Lappa D, Ramakrishnan G, Fox T, Haque R, Petri W, Bäckhed F, Nielsen J†. Gut Microbiota Dysbiosis is Associated with Malnutrition and Reduced Plasma Amino Acid Levels: Lessons from Genome-Scale Metabolic Modeling. Metabolic Engineering. 2018 49: 128-142. doi: 10.1016/j.ymben.2018.07.018. [RESEARCH]

[18] Babaei P, Shoaie S, Ji B, Nielsen J†. Challenges in Modeling the Human Gut Microbiome. Nature Biotechnology. 2018 36: 682-686. doi: 10.1038/nbt.4213. [RESEARCH]

[17] Das P, Ji B, Kovatcheva-Datchary P, Bäckhed F, Nielsen J†. In vitro Co-cultures of Human Gut Bacterial Species as Predicted from Co-occurrence Network Analysis. PLoS ONE. 2018 13(3): e0195161. doi: 10.1371/journal.pone.0195161. [RESEARCH]

[16]  Stancik I.A&, Šestak M.S&, Ji B, Axelson-Fisk M, Franjevic D, Jers C, Domazet-Lošo T, Mijakovic I†. Serine/Threonine Protein Kinases from Bacteria, Archaea and Eukarya Share a Common Evolutionary Origin Deeply Rooted in the Tree of Life. Journal of Molecular Biology. 2018 430(1): 27-32. doi: 10.1016/j.jmb.2017.11.004. [RESEARCH]

[15] Chen X&, Bisschops M.M.M&, Agarwal N.R, Ji B, Schanmugavel K.P, Petranovic D†. Interplay of Energetics and ER Stress Exacerbates Alzheimer’s Amyloid-β (Aβ) Toxicity in Yeast. Frontiers in Molecular Neuroscience. 2017 10: 232. doi: 10.3389/fnmol.2017.00232. [RESEARCH]

[14] Kalantari A, Chen T, Ji B, Stancik I.A, Ravikumar V, Franjevic D, Saulou-Berion C, Goelzer A, Mijakovic I†. Conversion of Glycerol to 3-hydroxypropanoic Acid by Genetically Engineered Bacillus subtilis. Frontiers in Microbiology. 2017 8: 638. doi: 10.3389/fmicb.2017.00638. [RESEARCH]

[13] Nielsen J.C, Grijseels S, Prigent S, Ji B, Dainat J, Nielsen K.F, Frisvad J.C, Workman M, Nielsen J†. Global Analysis of Biosynthetic Gene Clusters Reveals Vast Potential of Secondary Metabolite Production in Penicillium Species. Nature Microbiology. 2017 2: 17044. doi: 10.1038/nmicrobiol.2017.44. [RESEARCH]

[12] Motwalli O, Essack M, Jankovic B.R, Ji B, Liu X, Ansari H.R, Hoehndorf R, Gao X, Arold S.T, Mineta K, Archer J.A.C, Gojobori T, Mijakovic I, Bajic V.B†. In silico Screening for Candidate Chassis Strains of Free Fatty Acid-Producing Cyanobacteria. BMC Genomics. 2017 18(1): 33. doi: 10.1186/s12864-016-3389-4. [RESEARCH]

[11] Ji B, Zhang Sheng-Da, Rouy Z, Zhang Wei-Jia, Murat D, Alberto F, Santini Claire-Lise, Philippe N, Pradel N, Zhang L, Tempel S, Li Y, Médigu C, Barbe V, Talla E†, Wu Long-Fei†. The Chimeric Nature of the Genomes of Marine Magnetotactic Coccid-Ovoid Bacteria Defines a Novel Group of Proteobacteria. Environmental Microbiology. 2017 19: 1103-1119. doi: 10.1111/1462-2920.13637. [RESEARCH]

[10] Kumar M, Babaei P, Ji B, Nielsen J†. Human Gut Microbiota and Healthy Aging: Recent Developments and Future Prospective. Nutrition and Healthy Aging. 2016 4(1): 3-16. doi: 10.3233/NHA-150002. [REVIEW]

[9] Zhang C, Ji B, Mardinoglu A, Nielsen J† , Hua Q†. Logical Transformation of Genome Scale metabolic Models for Gene Level Applications and Analysis. Bioinformatics. 2015 31(14): 2324-2331. doi: 10.1093/bioinformatics/btv134. [RESEARCH]

[8] Ji B, Nielsen J†. From Next-Generation Sequencing to Systematic Modeling of the Gut Microbiome. Frontiers in Genetics. 2015 6: 219. doi: 10.3389/fgene.2015.00219. [REVIEW]

[7] Ji B, Nielsen J†. New Insight into the Gut Microbiome through Metagenomics. Advances in Genomics and Genetics. 2015 5: 77-91. doi: /10.2147/AGG.S57215. [REVIEW]

[6] Talla E, Hedrich S, Magnenot S, Ji B, Johnson D.B, Barbe V, Bonnefoy V†. Insight into the Pathway of Iron- and Sulfur-Oxidation, and Biofilm Formation from the Hemolithotrophic Acidophile Acidithiobacillus ferrivorans CF27. Research in Microbiology. 2014 165(9): 753-760. doi: 10.1016/j.resmic.2014.08.002. [RESEARCH]

[5] Shi L&†, Ji B&, Kolar-Znika L, Boskovic A, Jadeau F, Combet C, Grangeasse C, Franjevic D, Talla E†, Mijakovic I. Evolution of Bacterial Tyrosine Kinases and Their Relaxed Specificity towards Substrates. Genome Biology and Evolution. 2014 6(4): 800-817. doi: 10.1093/gbe/evu056. [RESEARCH]

[4] Ji B&, Zhang Sheng-Da&, Arnoux P, Rouy Z, Alberto F, Philippe N, Murat D, Zhang Wei-Jia, Rioux Jean-Baptiste, Ginet N, Sabaty M, Mangenot S, Pradel N, Tian J, Yang J, Zhang L, Zhang W, Pan H, Henrissat B, Coutinho P.M, Li Y, Xiao T, Médigue C, Barbe V, Pignol D, Talla E†, Wu Long-Fei†. Comparative Genomic Analysis Provides Insights into the Evolution and Niche Adaptation of Marine Magnetospira sp. QH-2 Strain. Environmental Microbiology. 2014 16(2): 525-544. doi: 10.1111/1462-2920.12180. [RESEARCH]

[3] Ji B, Gimenez G, Barbe V, Vacherie B, Rouy Z, Amrani A, Talla E, Ollivier B, Dolla A, Pradel N†. Complete Genome Sequence of the Piezophilic Mesophilic Sulfate-Reducing Bacterium Desulfovibrio hydrothermalis AM13T. Genome Announcements. 2013 1(1): e00226-12. doi: 10.1128/genomeA.00226-12. [RESEARCH]

[2] Pradel N†, Ji B, Gimenez G, Talla E, Lenoble P, Garel M, Tamburini C, Fourquet P, Lebrun R, Bertin P, Denis Y, Pophillat M, Barbe V, Ollivier B, Dolla A†. The First Genomic and Proteomic Characterization of a Deep-Sea Sulfate Reducer: Insights into the Piezophilic Lifestyle of Desulfovibrio piezophilus. PLoS ONE. 2013 8(1): e55130. doi: 10.1371/journal.pone.0055130. [RESEARCH]

[1] Duquesne K, Prima V, Ji B, Rouy Z, Médigue C, Talla E, Sturgis JN†. Draft Genome Sequence of the Purple Photosynthetic Bacterium Phaeospirillum molischianum DSM120, a Particularly Versatile Bacterium. Journal of Bacteriology. 2012 194(13): 3559-3560. doi: 10.1128/JB.00605-12. [RESEARCH]