Algorithms in Bioinformatics


Publications of the Huson lab.


Anupam Gautam, Wenhuan Zeng, Daniel H Huson, MeganServer: facilitating interactive access to metagenomic data on a serverBioinformatics, 2023, btad105,

Rajveer Singh, Shivani Chandel, Arijit Ghosh, Anupam Gautam, Daniel H. Huson, V. Ravichandiran, Dipanjan Ghosh, Easy efficient HDR-based targeted knock-in in Saccharomyces cerevisiae genome using CRISPR-Cas9 system, Bioengineered, 2023

Wenhuan Zeng, Anupam Gautam, Daniel H. Huson, MuLan-Methyl - Multiple Transformer-based Language Models for Accurate DNA Methylation Prediction, preprint bioRxiv, 2023


Isabella Casini, Tim McCubbin, Sofia Esquivel-Elizondo, Guillermo G. Luque, Daria Evseeva, Christian Fink, Sebastian Beblawy, Nicholas D. Youngblut, Ludmilla Aristilde, Daniel H. Huson, Andreas Dräger, Ruth E. Ley, Esteban Marcellin, Largus T. Angenent, Bastian Molitor, An integrated systems-biology platform for power-to-gas technology, Preprint bioRxiv, 2022

Monika Zeller, Daniel H. Huson, Comparison of functional classification systems, NAR Genomics and Bioinformatics, 2022, Iqac090,

Anupam Gautam, Wenhuan Zeng, Daniel Huson Megan Server: facilitating interactive access to metagenomic data on a server, Preprint bioRxiv, 2022

Wenhuan Zeng, Anupam Gautam, Daniel H Huson, DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome, Bioinformatics, 2022;, btac584. 

Yvonne Becker, Sascha Patz, Stephanie Werner, Björn Hoppe, Stephanie Feltgen, Beatrice Berger,  Adam Schickora, René Glenz, Stephan König, Silvio Erler, Gritta Schrader, Daniel Huson, Matthias Becker Bacteria producing contractile phage tail-like particles (CPTPs) are promising alternatives to conventional pesticides  Journal für Kulturpflanzen, 74 (03-04). S. 85-93, 2022 | DOI: 10.5073/JfK.2022.03-04.06 | Becker et al.

Gabriela Fiori da Silva, Anupam Gautam, Iolanda Cristina Silveira Duarte, Tiago Palladino Delforno, Valéria Maia de Oliveira, Daniel H. Huson Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN Scientific Reports 12, Article number: 7769 (2022)

Samad Ashrafi, Nemanja Kuzmanovic, Sascha Patz, Ulrike Lohwasser, Boyke Bunk, Cathrin Spröer, Maria Lorenz, Anja Frühling, Meina Neumann-Schaal, Susanne Verbarg, Matthias  Becker, Torsten Thünen Two new Rhizobioales species isolated from root nodules of common sainfoin (Onobrychis viciifolia) show different plant colonization strategies bioRXiv (pre-print 2022)

Anupam Gautam, Hendrik Felderhoff, Caner Bagci, Daniel H. Huson, Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis, mSystems Vol. 7 No.1.


S. Patz, A. Gautam, M. Becker, S. Ruppel, P.Rodriguez-Palenzuela, D. H. Huson.  PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria bioRXiv (pre-print 2021)

Caner Bağcı, David Bryant, Banu Cetinkaya, Daniel H.Huson. Microbial Phylogenetic Context Using Phylogenetic Outlines, Genome Biology and Evolution, Volume 13, Issue 9, September 2021, evab213,

Rüdiger Zeller, Olaf Delgado Friedrichs, Daniel H. Huson. Tegula - exploring a galaxy of two-dimensional periodic tilings, Computer Aided Geometric Design, Volume 90, October 2021, 1020727 (2021)

Andrew Francis, Daniel H. Huson, Mike Steel, Normalising phylogenetic networks, Molecular Phylogenetics and Evolution, Volume 163, 2021.

Krithika Arumugam, Irina Bessarab, Mindia A. S. Haryono, Xianghui Liu, Rogelio E. Zuniga–Montanez, Samarpita Roy, Guanglei Qiu, Daniela I. Drautz–Moses, Ying Yu Law, Stefan Wuertz, Federico M. Lauro, Daniel H. Huson & Rohan B. H. Williams.  Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencingnpj Biofilms Microbiomes 7, 23 (2021).

Rachana Banerjee, Narendrakumar M. Chaudhari, Abhishake Lahiri, Anupam Gautam, Debaleena Bhowmik, Chitra  Dutta, Sujay Chattopadhyay, Daniel H. Huson, Sandip Paul Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae Front. Microbiol., 25 June 2021

Caner Bağcı, Sascha Patz, Daniel H. Huson (2021) DIAMOND+MEGAN: Fast and Easy Taxonomic and Functional Analysis of Short and Long Microbiome Sequences CURRENT PROTOCOLS Volume1, Issue 3

Wenhuan Zeng, Anupam Gautam and Daniel H. Huson (2021) On the Application of Advanced Machine Learning Methods to Analyze Enhanced, Multimodal Data from Persons Infected with COVID-19, Computation 9(4)

Sofia Esquivel-Elizondo, Caner Bağcı, Monika Temovska, Byoung Seung Jeon, Irina Bessarab, Rohan BH Williams, Daniel H Huson, Largus T Angenent  (2021) 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, Vol. 11, No. 594524


M Steel, JC Xavier, DH Huson (2020 ) The structure of autocatalytic networks, with application to early biochemistry, Journal of the Royal Society Interface 17 (171), 20200488

B Albrecht, C Bağcı, DH Huson (2020)  MAIRA-real-time taxonomic and functional analysis of long reads on a laptop, BMC Bioinformatics 21 (13), 1-12

Jasmin Fertey, Jörg Hagmann, Hans‐Joachim Ruscheweyh, Christian Munk, Susanne Kjaer, Daniel Huson, Juliane Haedicke‐Jarboui, Frank Stubenrauch, Thomas Iftner,  (2020) 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), 1058-1068

E Tacconelli, A Gorska, G De Angelis, C Lammens, G Restuccia, Jacques Schrenzel, DH Huson, B Carević, L Preoţescu, Y Carmeli, M Kazma, T Spanu, E Carrara, S Malhotra-Kumar, BP Gladstone (2020) Estimating the association between antibiotic exposure and colonization with extended-spectrum β-lactamase-producing Gram-negative bacteria using machine learning methods: a multicentre, prospective cohort study, Clinical Microbiology and Infection, 26(1):87-94


Arumugam, K, Bagci, C, Bessarab, I, Beier, S, Buchfink, B, Gorska, A, Qiu, G, Huson, DH, and Williams, RB (2019). Annotated bacterial chromosomes from frame-shift-corrected long read metagenomic data  Microbiome, 7(61).

Yogesh Sing, Mohamed El-Hadidi, Jakob Admard, Zinah Wassouf, Julia M Schulze-Hentrich, Ursula Kohlhofer, Leticia Quintanilla-Martinez, Daniel Huson, Olaf Riess, Nicolas Casadei, Enriched Environmental Conditions Modify the Gut Microbiome Composition and Fecal Markers of Inflammation in Parkinsons's Disease, Frontiers in neuroscience 13, 1032

Sascha Patz, Yvonne Becker, Katja R. Richert-Pöggeler, Beatrice Berger, Silke Ruppel, Daniel H. Huson, Matthias Becker, Phage tail-like particles are versatile bacterial nanomachines - A mini-review, Journal of advanced research 19, 75-84

Caner Bağcı, Sina Beier, Anna Górska, Daniel H Huson, Introduction to the Analysis of Environmental Sequences: Metagenomics with MEGAN, Evolutionary Genomics, Humana, New York, NY, 591-604 (2019)

Simone Herp, Sandrine Brugiroux, Debora Garzetti, Diana Ring, Lara M Jochum, Markus Beutler, Claudia Eberl, Saib Hussain, Steffi Walter, Roman G Gerlach, Hans J Ruscheweyh, Daniel Huson, Mikael E Sellin, Emma Slack, Buck Hanson, Alexander Loy, John F Baines, Philipp Rausch, Marijana Basic, Andre Bleich, David Berry, Bärbel Stecher, Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis, Cell host & microbe, 681-694. e8 (2019)

Poole, AC, Goodrich, JK, Youngblut, ND, Luque, GG, Ruaud, A, Sutter, JL, Waters, JL, Shi, Q, El-Hadidi, M, Johnson, LM, Bar, HY, Huson, DH, Booth, JG, and Ley, RE (2019). Human Salivary Amylase Gene Copy Number Impacts Oral and Gut Microbiomes. Cell Host & Microbe, 25(4):553 - 564.e7.



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

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

Lange, A, Beier, S, Huson, DH, Parusel, R, Iglauer, F, and Frick, J (2018). 
Genome Sequence of Galleria mellonella (Greater Wax Moth). 
Genome Announc, 6(2).

Vågene, AJ, Herbig, A, Campana, MG, Robles Garcia, NM, Warinner, C, Sabin, S, Spyrou, MA, Andrades Valtueña, A, Huson, D, Tuross, N, Bos, KI, and Krause, J (2018). 
Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico 
Nature Ecology & Evolution, 2(3):520–528.