Publications of DH Huson

Gemeinhard, K.; Jeon, B.; Ntihuga, J.; Wang, H.; Schlaiß, C.; Lucas, T.; Bessarab, I.; Nalpas, N.; Zhou, N.; Usack, J. et al.; Huson, D.; Williams, R.; Maček, B.; Aristilde, L.; Angenent, L.: Toward industrial C8 production: Oxygen intrusion drives renewable n caprylate production from ethanol and acetate via intermediate metabolite production. Green Chemistry 27 (11), pp. 2931 - 2949 (2025)

Spirito, C.; Lucas, T.; Patz, S.; Jeon, B.; Werner, J.; Trondsen, L.; Guzman, J.; Huson, D.; Angenent, L.: Variability in n-caprylate and n-caproate producing microbiomes in reactors with in-line product extraction. mSystems 9 (8), e0041624 (2024)

Gautam, A.; Bhowmik, D.; Basu, S.; Zeng, W.; Lahiri, H.; Huson, D.; Paul, S.: Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification. Briefings in Bioinformatics 24 (6), bbad325 (2023)

Casini, I.; McCubbin, T.; Esquivel-Elizondo, S.; Luque, G.; Evseeva, D.; Fink, C.; Beblawy, S.; Youngblut, N.; Aristilde, L.; Huson, D. et al.; Dräger, A.; Ley, R.; Marcellin, E.; Angenent, L.; Molitor, B.: An integrated systems-biology approach reveals differences in formate metabolism in the genus Methanothermobacter. iScience 26 (10), 108016 (2023)

Zeng, W.; Gautam, A.; Huson, D.: MuLan-Methyl: Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction. GigaScience 12, giad054 (2023)

Huson, D.; Cetinkaya, B.: Visualizing incompatibilities in phylogenetic trees using consensus outlines. Frontiers in Bioinformatics 3, 1155286 (2023)

Gautam, A.; Zeng, W.; Huson, D.: MeganServer: facilitating interactive access to metagenomic data on a server. Bioinformatics 39 (3), btad105 (2023)

Zeng, W.; Gautam, A.; Huson, D.: DeepToA: An Ensemble Deep-Learning Approach to Predicting the Theater of Activity of a Microbiome. Bioinformatics 38 (20), btac584, pp. 4670 - 4676 (2022)

Singh, R.; Chandel, S.; Ghosh, A.; Gautam, A.; Huson, D.; Ravichandiran, V.; Ghosh, D.: Easy efficient HDR-based targeted knock-in in Saccharomyces cerevisiae genome using CRISPR-Cas9 system. Bioengineered 13 (6), pp. 14857 - 14871 (2022)

Fiori da Silva, G.; Gautam, A.; Silveira Duarte, I.; Palladino Delforno, T.; Delforno, T.; Maia de Oliveira, V.; Huson, D.: Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN. Scientific Reports 12, 7769 (2022)

Gautam, A.; Felderhoof, H.; Bağci, C.; Huson, D.: Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis. mSystems 7 (1), e0140821 (2022)

Banerjee, R.; Chaudhari, N.; Lahiri, A.; Gautam, A.; Bhowmik, D.; Dutta, C.; Chattopadhyay, S.; Huson, D.; Paul, S.: Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae. Frontiers in Microbiology 12, 639995 (2021)

Esquivel-Elizondo, S.; Bağci, C.; Temovska, M.; Jeon, B.; Bessarab, I.; Williams, R.; Huson, D.; Angenent, L.: The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria. Frontiers in Microbiology 11, 33584563 (2021)

Weng, C.; Gautam, A.; Huson, D.: On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19. Computation 9, 4 (2021)

Fertey, J.; Hagmann, J.; Ruscheweyh, H.-J.; Munk, C.; Kjaer, S.; Huson, D.; Haedicke-Jarboui, J.; Stubenrauch, F.; Iftner, T.: Methylation of CpG 5962 in L1 of the human papillomavirus 16 genome as a potential predictive marker for viral persistence: A prospective large cohort study using cervical swab samples. Cancer Medicine 9 (3), pp. 1058 - 1068 (2020)

Arumugam, K.; Bağci, C.; Bessarab, I.; Beier, S.; Buchfink, B.; Górska, A.; Qiu, G.; Huson, D.; Williams, R.: Annotated bacterial chromosomes from frame-shift-corrected long-read metagenomic data. Microbiome 7, 61 (2019)

Górska, A.; Peter, S.; Willmann, M.; Autenrieth, I.; Schlaberg, R.; Huson, D.: Dynamics of the human gut phageome during antibiotic treatment. Computational Biology and Chemistry 74, pp. 420 - 427 (2018)

Huson, D.; Albrecht, B.; Bağci, C.; Bessarab, I.; Górska, A.; Jolic, D.; Williams, R.: MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. Biology Direct 13, 6 (2018)

Huson, D.; Beier, S.; Flade, I.; Górska, A.; El-Hadidi, M.; Mitra, S.; Ruscheweyh, H.-J.; Tappu, R.: MEGAN Community Edition: Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Computational Biology 12 (6), e1004957 (2016)

Buchfink, B.; Xie, C.; Huson, D.: Fast and sensitive protein alignment using DIAMOND. Nature methods 12 (1), pp. 59 - 60 (2015)