GeneFisher-Software Support for the Detection of Postulated Genes. - Robert Giegerich; Folker Meyer; Chris Schleiermacher (ISMB, 1996)

Generating Benchmarks for Multiple Sequence Alignments and Phylogenic Reconstructions. - Jens Stoye; Dirk Evers; Folker Meyer (ISMB, 1997)

Rose: generating sequence families. - Jens Stoye; Dirk Evers; Folker Meyer (Bioinform., 1998)

GENDB: a second generation genome annotation system - Folker Meyer (2001)

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)

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)

Finding novel genes in bacterial communities isolated from the environment. - Lutz Krause; Naryttza N. Diaz; Daniela Bartels; Robert A. Edwards; Alfred Pühler; Forest Rohwer; Folker Meyer; Jens Stoye (ISMB (Supplement of Bioinformatics), 2006)

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. - Leslie Klis McNeil; Claudia Reich; Ramy K. Aziz; Daniela Bartels; Matthew Cohoon; Terry Disz; Robert A. Edwards; Svetlana Gerdes; Kaitlyn Hwang; Michael Kubal; Gohar Rem Margaryan; Folker Meyer; et al. (Nucleic Acids Res., 2007)

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. - Folker Meyer; Daniel Paarmann; Mark D'Souza; Robert Olson; Elizabeth M. Glass; Michael Kubal; Tobias Paczian; Alexis A. Rodriguez; Rick Stevens; Andreas Wilke; Jared Wilkening; Robert A. Edwards (BMC Bioinform., 2008)

Using clouds for metagenomics: A case study. - Jared Wilkening; Andreas Wilke; Narayan Desai; Folker Meyer (CLUSTER, 2009)

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes. - Florent E. Angly; Dana Willner; Alejandra Prieto-Davó; Robert A. Edwards; Robert Schmieder; Rebecca Vega-Thurber; Dionysios A. Antonopoulos; Katie Barott; Matthew T. Cottrell; Christelle Desnues; Elizabeth A. Dinsdale; Mike Furlan; et al. (PLoS Comput. Biol., 2009)

Predicted Relative Metabolomic Turnover - Predicting Changes in the Environmental Metabolome from the Metagenome. - Peter E. Larsen; Frank Collart; Folker Meyer; Jack A. Gilbert (BIOINFORMATICS, 2011)

Proposal for Open Discussion - Informatics Challenges for Next Generation Sequencing Metagenomics Experiments. - Folker Meyer; Nikos Kyrpides (BIOINFORMATICS, 2011)

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. - Suparna Mitra; Paul Rupek; Daniel C. Richter; Tim Urich; Jack A. Gilbert; Folker Meyer; Andreas Wilke; Daniel H. Huson (BMC Bioinform., 2011)

An experience report: porting the MG-RAST rapid metagenomics analysis pipeline to the cloud. - Andreas Wilke; Jared Wilkening; Elizabeth M. Glass; Narayan Desai; Folker Meyer (Concurr. Comput. Pract. Exp., 2011)

Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. - William L. Trimble; Kevin P. Keegan; Mark D'Souza; Andreas Wilke; Jared Wilkening; Jack A. Gilbert; Folker Meyer (BMC Bioinform., 2012)

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. - Andreas Wilke; Travis Harrison; Jared Wilkening; Dawn Field; Elizabeth M. Glass; Nikos Kyrpides; Konstantinos Mavrommatis; Folker Meyer (BMC Bioinform., 2012)

A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE. - Kevin P. Keegan; William L. Trimble; Jared Wilkening; Andreas Wilke; Travis Harrison; Mark D'Souza; Folker Meyer (PLoS Comput. Biol., 2012)

A scalable data analysis platform for metagenomics. - Wei Tang 001; Jared Wilkening; Narayan Desai; Wolfgang Gerlach; Andreas Wilke; Folker Meyer (IEEE BigData, 2013)

Workload characterization for MG-RAST metagenomic data analytics service in the cloud. - Wei Tang 001; Jared Bischof; Narayan Desai; Kanak Mahadik; Wolfgang Gerlach; Travis Harrison; Andreas Wilke; Folker Meyer (IEEE BigData, 2014)

Data-Aware Resource Scheduling for Multicloud Workflows: A Fine-Grained Simulation Approach. - Wei Tang 001; Jonathan Jenkins; Folker Meyer; Robert B. Ross; Rajkumar Kettimuthu; Linda Winkler; Xi Yang 002; Thomas Lehman; Narayan Desai (CloudCom, 2014)

Skyport: container-based execution environment management for multi-cloud scientific workflows. - Wolfgang Gerlach; Wei Tang 001; Kevin P. Keegan; Travis Harrison; Andreas Wilke; Jared Bischof; Mark D'Souza; Scott Devoid; Daniel E. Murphy-Olson; Narayan Desai; Folker Meyer (DataCloud@SC, 2014)

Do specialized distributed frameworks for bioinformatics applications obtain better performance over generic ones? - Kanak Mahadik; Wei Tang 001; Saurabh Bagchi; Folker Meyer (BCB, 2015)

Shock: Active Storage for Multicloud Streaming Data Analysis. - Andreas Wilke; Wolfgang Gerlach; Travis Harrison; Tobias Paczian; Wei Tang 001; William L. Trimble; Jared Wilkening; Narayan Desai; Folker Meyer (BDC, 2015)

Container Orchestration for Scientific Workflows. - Wolfgang Gerlach; Wei Tang 001; Andreas Wilke; Dan Olson; Folker Meyer (IC2E, 2015)

A RESTful API for Accessing Microbial Community Data for MG-RAST. - Andreas Wilke; Jared Bischof; Travis Harrison; Tom Brettin; Mark D'Souza; Wolfgang Gerlach; Hunter Matthews; Tobias Paczian; Jared Wilkening; Elizabeth M. Glass; Narayan Desai; Folker Meyer (PLoS Comput. Biol., 2015)

A Case Study in Using Discrete-Event Simulation to Improve the Scalability of MG-RAST. - Caitlin Ross; Misbah Mubarak; John Jenkins; Philip H. Carns; Christopher D. Carothers; Robert B. Ross; Wei Tang 001; Wolfgang Gerlach; Folker Meyer (SIGSIM-PADS, 2016)

The MG-RAST metagenomics database and portal in 2015. - Andreas Wilke; Jared Bischof; Wolfgang Gerlach; Elizabeth M. Glass; Travis Harrison; Kevin P. Keegan; Tobias Paczian; William L. Trimble; Saurabh Bagchi; Ananth Grama; Somali Chaterji; Folker Meyer (Nucleic Acids Res., 2016)

Suitability of NoSQL systems - Cassandra and ScyllaDB - For IoT workloads. - Ashraf Mahgoub; Sachandhan Ganesh; Folker Meyer; Ananth Grama; Somali Chaterji (COMSNETS, 2017)

Rafiki: a middleware for parameter tuning of NoSQL datastores for dynamic metagenomics workloads. - Ashraf Mahgoub; Paul Wood; Sachandhan Ganesh; Subrata Mitra; Wolfgang Gerlach; Travis Harrison; Folker Meyer; Ananth Grama; Saurabh Bagchi; Somali Chaterji (Middleware, 2017)

On the way to research objects for environmental genomics (or metagenomics). - Folker Meyer; Robert D. Finn; Wolfgang Gerlach; Alex L. Mitchell; Travis Harrison; Andreas Wilke (RO, 2018)

SOPHIA: Online Reconfiguration of Clustered NoSQL Databases for Time-Varying Workloads. - Ashraf Mahgoub; Paul Wood; Alexander Medoff; Subrata Mitra; Folker Meyer; Somali Chaterji; Saurabh Bagchi (USENIX ATC, 2019)

Federation in genomics pipelines: techniques and challenges. - Somali Chaterji; Jinkyu Koo; Ninghui Li; Folker Meyer; Ananth Grama; Saurabh Bagchi (Briefings Bioinform., 2019)

MG-RAST version 4 - lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. - Folker Meyer; Saurabh Bagchi; Somali Chaterji; Wolfgang Gerlach; Ananth Grama; Travis Harrison; Tobias Paczian; William L. Trimble; Andreas Wilke (Briefings Bioinform., 2019)

The MG-RAST API explorer: an on-ramp for RESTful query composition. - Tobias Paczian; William L. Trimble; Wolfgang Gerlach; Travis Harrison; Andreas Wilke; Folker Meyer (BMC Bioinform., 2019)

Towards a trustworthy, secure and reliable enclave for machine learning in a hospital setting: The Essen Medical Computing Platform (EMCP). - Hendrik F. R. Schmidt; Jörg Schlötterer; Marcel Bargull; Enrico Nasca; Ryan Aydelott; Christin Seifert; Folker Meyer (CogMI, 2021)