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)

SAMPI: Protein Identification with Mass Spectra Alignments. - Hans-Michael Kaltenbach; Andreas Wilke; Sebastian Böcker (BMC Bioinform., 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)

Fishing for the Right Words: Decision Rules for Human Foraging Behavior in Internal Search Tasks. - Andreas Wilke; John M. C. Hutchinson; Peter M. Todd; Uwe Czienskowski (Cogn. Sci., 2009)

Exploration and Exploitation in Memory Search Across the Lifespan. - Thomas T. Hills; Rui Mata; Andreas Wilke; Gregory R. Samanez-Larkin (CogSci, 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)

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)

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)

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)

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)

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)

Ensuring Security & Trust in a Post-Quantum Environment. - Manfred Paeschke; Walter Fumy; Andreas Wilke (Datenschutz und Datensicherheit, 2019)

The Relevance of Subjective Benefits in Risky Choice Across ten Domains of Life. - Jana Jarecki; Andreas Wilke (CogSci, 2020)

Fingerprinting Analog IoT Sensors for Secret-Free Authentication. - Felix Lorenz; Lauritz Thamsen; Andreas Wilke; Ilja Behnke; Jens Waldmüller-Littke; Ilya Komarov; Odej Kao; Manfred Paeschke (ICCCN, 2020)

PSI/J: A Portable Interface for Submitting, Monitoring, and Managing Jobs. - Mihael Hategan-Marandiuc; André Merzky; Nicholson T. Collier; Ketan Maheshwari; Jonathan Ozik; Matteo Turilli; Andreas Wilke; Justin M. Wozniak; Kyle Chard; Ian T. Foster; Rafael Ferreira da Silva; Shantenu Jha; et al. (e-Science, 2023)

An Automation Framework for Comparison of Cancer Response Models Across Configurations. - Justin M. Wozniak; Rajeev Jain; Andreas Wilke; Rylie Weaver; Alexander Partin; Thomas S. Brettin; Rick Stevens (e-Science, 2023)

ExaWorks Software Development Kit: A Robust and Scalable Collection of Interoperable Workflow Technologies. - Matteo Turilli; Mihael Hategan-Marandiuc; Mikhail Titov; Ketan Maheshwari; Aymen Alsaadi; André Merzky; Ramon Arambula; Mikhail Zakharchanka; Matt Cowan; Justin M. Wozniak; Andreas Wilke; Ozgur Ozan Kilic; et al. (CoRR, 2024)

Assessing Reusability of Deep Learning-Based Monotherapy Drug Response Prediction Models Trained with Omics Data. - Jamie C. Overbeek; Alexander Partin; Thomas S. Brettin; Nicholas Chia; Oleksandr Narykov; Priyanka Vasanthakumari; Andreas Wilke; Yitan Zhu; Austin Clyde; Sara Jones; Rohan Gnanaolivu; Yuanhang Liu; et al. (CoRR, 2024)

Exascale Workflow Applications and Middleware: An ExaWorks Retrospective. - Aymen Alsaadi; Mihael Hategan-Marandiuc; Ketan Maheshwari; André Merzky; Mikhail Titov; Matteo Turilli; Andreas Wilke; Justin M. Wozniak; Kyle Chard; Rafael Ferreira da Silva; Shantenu Jha; Daniel E. Laney (CoRR, 2024)

Benchmarking community drug response prediction models: datasets, models, tools, and metrics for cross-dataset generalization analysis. - Alexander Partin; Priyanka Vasanthakumari; Oleksandr Narykov; Andreas Wilke; Natasha Koussa; Sara E. Jones; Yitan Zhu; Jamie C. Overbeek; Rajeev Jain; Gayara Demini Fernando; Cesar Sanchez-Villalobos; Cristina Garcia-Cardona; et al. (CoRR, 2025)