| 2011 | RECOMB | Constrained De Novo Sequencing of Peptides with Application to Conotoxins. | Swapnil Bhatia, Yong J. Kil, Beatrix Ueberheide, Brian T. Chait, Lemmuel Lara Tayo, Lourdes J. Cruz, Bingwen Lu, John R. Yates III, Marshall W. Bern |
| 2011 | UIC | Ubiquitous Meeting Facilitator with Playful Real-Time User Interface. | Ying Zhang, Marshall W. Bern, Juan Liu, Kurt Partridge, Bo Begole, Bob Moore, Jim Reich, Koji Kishimoto |
| 2010 | CHI | Facilitating meetings with playful feedback. | Ying Zhang, Marshall W. Bern, Juan Liu, Kurt Partridge, Bo Begole, Bob Moore, Jim Reich, Koji Kishimoto |
| 2008 | CHI | Escape: a target selection technique using visually-cued gestures. | Koji Yatani, Kurt Partridge, Marshall W. Bern, Mark W. Newman |
| 2008 | LATIN | Origami Embedding of Piecewise-Linear Two-Manifolds. | Marshall W. Bern, Barry Hayes |
| 2008 | RECOMB | Spectrum Fusion: Using Multiple Mass Spectra for De Novo Peptide Sequencing. | Ritendra Datta, Marshall W. Bern |
| 2007 | RECOMB | Improved Ranking Functions for Protein and Modification-Site Identifications. | Marshall W. Bern, David Goldberg |
| 2006 | NCA | SecLEACH - A Random Key Distribution Solution for Securing Clustered Sensor Networks. | Leonardo B. Oliveira, Hao Chi Wong, Marshall W. Bern, Ricardo Dahab, Antonio Alfredo Ferreira Loureiro |
| 2005 | RECOMB | Avoiding Local Optima in Single Particle Reconstruction. | Marshall W. Bern, Jindong Chen, Hao Chi Wong |
| 2005 | RECOMB | EigenMS: De Novo Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning. | Marshall W. Bern, David Goldberg |
| 2004 | ISMB | Automatic Quality Assessment of Peptide Tandem Mass Spectra. | Marshall W. Bern, David Goldberg, W. Hayes McDonald, John R. Yates III |
| 2003 | SODA | Mbius-invariant natural neighbor interpolation. | Marshall W. Bern, David Eppstein |
| 2002 | ICIP | An image signature for any kind of image. | Chi Wong, Marshall W. Bern, David Goldberg |
| 2001 | ICDAR | Document Image Matching and Annotation Lifting. | Ming Ye, Marshall W. Bern, David Goldberg |
| 2001 | SODA | Computing the depth of a flat. | Marshall W. Bern |
| 2001 | WADS | Optimal Mbius Transformations for Information Visualization and Meshing. | Marshall W. Bern, David Eppstein |
| 2001 | WADS | Optimization over Zonotopes and Training Support Vector Machines. | Marshall W. Bern, David Eppstein |
| 2000 | ICIP | Scanner-Model-Based Document Image Improvement. | Marshall W. Bern, David Goldberg |
| 1998 | SIGGRAPH | A New Voronoi-based Surface Reconstruction Algorithm. | Nina Amenta, Marshall W. Bern, Manolis Kamvysselis |
| 1997 | SODA | Optimal Point Placement for Mesh Smoothing. | Nina Amenta, Marshall W. Bern, David Eppstein |
| 1996 | SODA | The Complexity of Flat Origami. | Marshall W. Bern, Barry Hayes |
| 1996 | STOC | Pushing Disks Together - The Continuous-Motion Case. | Marshall W. Bern, Amit Sahai |
| 1995 | ESA | The Centroid of Points with Approximate Weights. | Marshall W. Bern, David Eppstein, Leonidas J. Guibas, John Hershberger, Subhash Suri, Jan Wolter |
| 1995 | SODA | Dihedral Bounds for Mesh Generation in High Dimensions. | Marshall W. Bern, L. Paul Chew, David Eppstein, Jim Ruppert |
| 1993 | STOC | On-line algorithms for cache sharing. | Marshall W. Bern, Daniel H. Greene, Arvind Raghunathan |
| 1993 | WADS | Parallel Construction of Quadtrees and Quality Triangulations. | Marshall W. Bern, David Eppstein, Shang-Hua Teng |
| 1992 | LATIN | Edge Insertion for Optional Triangulations. | Marshall W. Bern, Herbert Edelsbrunner, David Eppstein, Scott A. Mitchell, Tiow Seng Tan |
| 1991 | ICALP | The Expected Extremes in a Delaunay Triangulation. | Marshall W. Bern, David Eppstein, F. Frances Yao |
| 1990 | FOCS | Provably Good Mesh Generation | Marshall W. Bern, David Eppstein, John R. Gilbert |
| 1990 | SODA | Visibility with a Moving Point of View. | Marshall W. Bern, David P. Dobkin, David Eppstein, Robert L. Grossman |
| 1990 | STOC | Online Algorithms for Locating Checkpoints | Marshall W. Bern, Daniel H. Greene, Arvind Raghunathan, Madhu Sudan |
| 1986 | STOC | Two Probabilistic Results on Rectilinear Steiner Trees | Marshall W. Bern |
| 1985 | FOCS | Why Certain Subgraph Computations Require Only Linear Time | Marshall W. Bern, Eugene L. Lawler, A. L. Wong |