PathFinder: reconstruction and dynamic visualization of metabolic pathways. - Alexander Goesmann; Martin Haubrock; Folker Meyer; Jörn Kalinowski; Robert Giegerich (Bioinform., 2002)

Development of joint application strategies for two microbial gene finders. - Alice Carolyn McHardy; Alexander Goesmann; Alfred Pühler; Folker Meyer (Bioinform., 2004)

BRIDGE: a bioinformatics software platform for the integration of heterogeneous data from genomic explorations - Alexander Goesmann (2004)

BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. - Daniela Bartels; Sebastian Kespohl; Stefan P. Albaum; Tanja Drüke; Alexander Goesmann; Julia Herold; Olaf Kaiser; Alfred Pühler; Friedhelm Pfeiffer; Günter Raddatz; Jens Stoye; Folker Meyer; et al. (Bioinform., 2005)

BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. - Alexander Goesmann; Burkhard Linke; Daniela Bartels; Michael Dondrup; Lutz Krause; Heiko Neuweger; Sebastian Oehm; Tobias Paczian; Andreas Wilke; Folker Meyer (Nucleic Acids Res., 2005)

CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data. - Heiko Neuweger; Jan Baumbach; Stefan P. Albaum; Thomas Bekel; Michael Dondrup; Andrea T. Hüser; Jörn Kalinowski; Sebastian Oehm; Alfred Pühler; Sven Rahmann; Jochen Weile; Alexander Goesmann (BMC Syst. Biol., 2007)

MeltDB: a software platform for the analysis and integration of metabolomics experiment data. - Heiko Neuweger; Stefan P. Albaum; Michael Dondrup; Marcus Persicke; Tony Watt; Karsten Niehaus; Jens Stoye; Alexander Goesmann (Bioinform., 2008)

Comparative Pathway Analyzer - a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. - Sebastian Oehm; David R. Gilbert; Andreas Tauch; Jens Stoye; Alexander Goesmann (Nucleic Acids Res., 2008)

Qupe - a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. - Stefan P. Albaum; Heiko Neuweger; Benjamin Fränzel; Sita Lange; Dominik Mertens; Christian Trötschel; Dirk Wolters; Jörn Kalinowski; Tim W. Nattkemper; Alexander Goesmann (Bioinform., 2009)

EDGAR: A software framework for the comparative analysis of prokaryotic genomes. - Jochen Blom; Stefan P. Albaum; Daniel Doppmeier; Alfred Pühler; Frank-Jörg Vorhölter; Martha Zakrzewski; Alexander Goesmann (BMC Bioinform., 2009)

TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. - Naryttza N. Diaz; Lutz Krause; Alexander Goesmann; Karsten Niehaus; Tim W. Nattkemper (BMC Bioinform., 2009)

EMMA 2 - A MAGE-compliant system for the collaborative analysis and integration of microarray data. - Michael Dondrup; Stefan P. Albaum; Thasso Griebel; Kolja Henckel; Sebastian Jünemann; Tim Kahlke; Christiane K. Kleindt; Helge Küster; Burkhard Linke; Dominik Mertens; Virginie Mittard-Runte; Heiko Neuweger; et al. (BMC Bioinform., 2009)

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. - Wolfgang Gerlach; Sebastian Jünemann; Felix Tille; Alexander Goesmann; Jens Stoye (BMC Bioinform., 2009)

Visualizing post genomics data-sets on customized pathway maps by ProMeTra - aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. - Heiko Neuweger; Marcus Persicke; Stefan P. Albaum; Thomas Bekel; Michael Dondrup; Andrea T. Hüser; Jörn Winnebald; Jessica Schneider; Jörn Kalinowski; Alexander Goesmann (BMC Syst. Biol., 2009)

Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format. - Justina Krawczyk; Alexander Goesmann; Ralf Nolte; Martin Werber; Bernd Weisshaar (Source Code Biol. Medicine, 2009)

Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. - Jochen Blom; Tobias Jakobi; Daniel Doppmeier; Sebastian Jaenicke; Jörn Kalinowski; Jens Stoye; Alexander Goesmann (Bioinform., 2011)

Conveyor: a workflow engine for bioinformatic analyses. - Burkhard Linke; Robert Giegerich; Alexander Goesmann (Bioinform., 2011)

MeltDB 2.0-advances of the metabolomics software system. - Nikolas Kessler; Heiko Neuweger; Anja Bonte; Georg Langenkämper; Karsten Niehaus; Tim W. Nattkemper; Alexander Goesmann (Bioinform., 2013)

ReadXplorer - visualization and analysis of mapped sequences. - Rolf Hilker; Kai Bernd Stadermann; Daniel Doppmeier; Jörn Kalinowski; Jens Stoye; Jasmin Straube; Jörn Winnebald; Alexander Goesmann (Bioinform., 2014)

AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization. - Daniel Langenkämper; Alexander Goesmann; Tim W. Nattkemper (BMC Bioinform., 2014)

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) Open. - Juliane C. Dohm; André E. Minoche; Daniela Holtgräwe; Salvador Capella-Gutiérrez; Falk Zakrzewski; Hakim Tafer; Oliver Rupp; Thomas Rosleff Sörensen; Ralf Stracke; Richard Reinhardt; Alexander Goesmann; Thomas Kraft; et al. (Nat., 2014)

ReadXplorer 2 - detailed read mapping analysis and visualization from one single source. - Rolf Hilker; Kai Bernd Stadermann; Oliver Schwengers; Evgeny Anisiforov; Sebastian Jaenicke; Bernd Weisshaar; Tobias Zimmermann; Alexander Goesmann (Bioinform., 2016)

EDGAR 2.0: an enhanced software platform for comparative gene content analyses. - Jochen Blom; Julian Kreis; Sebastian Spänig; Tobias Juhre; Claire Bertelli; Corinna Ernst; Alexander Goesmann (Nucleic Acids Res., 2016)

ReferenceSeeker: rapid determination of appropriate reference genomes. - Oliver Schwengers; Torsten Hain; Trinad Chakraborty; Alexander Goesmann (J. Open Source Softw., 2020)

ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. - Oliver Schwengers; Andreas Hoek; Moritz Fritzenwanker; Linda Falgenhauer; Torsten Hain; Trinad Chakraborty; Alexander Goesmann (PLoS Comput. Biol., 2020)

EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure. - Marius A. Dieckmann; Sebastian Beyvers; Rudel Christian Nkouamedjo-Fankep; Patrick Harald Georg Hanel; Lukas Jelonek; Jochen Blom; Alexander Goesmann (Nucleic Acids Res., 2021)

Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning. - Yunxiao Ren; Trinad Chakraborty; Swapnil Doijad; Linda Falgenhauer; Jane Falgenhauer; Alexander Goesmann; Anne-Christin Hauschild; Oliver Schwengers; Dominik Heider (Bioinform., 2022)

The Aruna Object Storage A Distributed Multi Cloud Object Storage System for Scientific Data Management. - Marius A. Dieckmann; Sebastian Beyvers; Jannis Hochmuth; Anna Rehm; Frank Förster; Alexander Goesmann (CoRDI, 2023)

Towards a Research Data Commons in the German National Research Data Infrastructure NFDI: Vision, Governance, Architecture. - Michael Diepenbroek; Ivaylo Kostadinov; Bernhard Seeger; Frank Oliver Glöckner; Marius A. Dieckmann; Alexander Goesmann; Barbara Ebert; Sonja Schimmler; York Sure-Vetter (CoRDI, 2023)

Embedding the de.NBI Cloud in the National Research Data Infrastructure Activities. - Nils Hoffmann; Irena Maus; Sebastian Beier; Peter Belmann; Jan Krüger; Andreas Tauch; Alexander Goesmann; Roland Eils; Peer Bork; Oliver Kohlbacher; Ursula Kummer; Rolf Backofen; et al. (CoRDI, 2023)

Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data. - Patrick Blumenkamp; Max Pfister; Sonja Diedrich; Karina Brinkrolf; Sebastian Jaenicke; Alexander Goesmann (BMC Bioinform., 2024)

Towards FAIR and federated Data Ecosystems for interdisciplinary Research. - Sebastian Beyvers; Jannis Hochmuth; Lukas Brehm; Maria Hansen; Alexander Goesmann; Frank Förster (CoRR, 2025)