| 2023 | CPM | Merging Sorted Lists of Similar Strings. | Gene Myers |
| 2022 | WABI | Accurate k-mer Classification Using Read Profiles. | Yoshihiko Suzuki, Gene Myers |
| 2020 | AAAI | Towards Interpretable Semantic Segmentation via Gradient-Weighted Class Activation Mapping (Student Abstract). | Kira Vinogradova, Alexandr Dibrov, Gene Myers |
| 2020 | WACV | Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy. | Martin Weigert, Uwe Schmidt, Robert Haase, Ko Sugawara, Gene Myers |
| 2018 | MICCAI | Cell Detection with Star-Convex Polygons. | Uwe Schmidt, Martin Weigert, Coleman Broaddus, Gene Myers |
| 2017 | MICCAI | Isotropic Reconstruction of 3D Fluorescence Microscopy Images Using Convolutional Neural Networks. | Martin Weigert, Loc Royer, Florian Jug, Gene Myers |
| 2016 | EuroPar | Seamless HPC Integration of Data-Intensive KNIME Workflows via UNICORE. | Richard Grunzke, Florian Jug, Bernd Schuller, Ren Jkel, Gene Myers, Wolfgang E. Nagel |
| 2015 | MICCAI | Uncertainty-Driven Forest Predictors for Vertebra Localization and Segmentation. | David L. Richmond, Dagmar Kainmueller, Ben Glocker, Carsten Rother, Gene Myers |
| 2014 | MICCAI | Active Graph Matching for Automatic Joint Segmentation and Annotation of C. elegans. | Dagmar Kainmueller, Florian Jug, Carsten Rother, Gene Myers |
| 2014 | WABI | Efficient Local Alignment Discovery amongst Noisy Long Reads. | Gene Myers |
| 2013 | CPM | Discrete Methods for Image Analysis Applied to Molecular Biology. | Gene Myers |
| 2008 | RECOMB | Automatic Recognition of Cells (ARC) for 3D Images of C. elegans. | Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart K. Kim, Gene Myers |
| 2007 | WABI | Computability of Models for Sequence Assembly. | Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno |
| 2006 | HiPC | Imaging-Based Systems Biology. | Gene Myers |
| 2003 | ISMB | ISMB 2003 - Editorial. | Gene Myers |
| 2002 | COCOON | The Assembly of the Human and Mouse Genomes. | Gene Myers |
| 2002 | WABI | Invited Lecture - Accelerating Smith-Waterman Searches. | Gene Myers, Richard Durbin |
| 2001 | RECOMB | Comparing sequence scaffolds. | Gene Myers |
| 2000 | SODA | The whole genome assembly of Drosophila. | Gene Myers |
| 1999 | ISMB | A Dataset Generator for Whole Genome Shotgun Sequencing. | Gene Myers |
| 1999 | RECOMB | Progress toward the whole-genome shotgun sequencing of Drosophila. | Gene Myers |
| 1998 | CPM | A Fast Bit-Vector Algorithm for Approximate String Matching Based on Dynamic Programming. | Gene Myers |
| 1997 | CPM | Estimating the Probability of Approximate Matches. | Stefan Kurtz, Gene Myers |
| 1997 | RECOMB | Progressive multiple alignment with constraints. | Gene Myers, Sanford Selznick, Zheng Zhang, Webb Miller |
| 1995 | SODA | Chaining Multiple-Alignment Fragments in Sub-Quadratic Time. | Gene Myers, Webb Miller |
| 1992 | LATIN | Approximate Matching of Network Expressions with Spacers. | Gene Myers |
| 1990 | SODA | Suffix Arrays: A New Method for On-Line String Searches. | Udi Manber, Gene Myers |