| 2025 | IJCAI | Precarity and Solidarity: Preliminary Results on a Study of Queer and Disabled Fiction Writers' Experiences with Generative AI. | Carolyn Elizabeth Lamb, Daniel G. Brown, Maura R. Grossman |
| 2025 | SIGCSE | Self-Disclosure and Beyond: Takeaways from an Online and In-Person Computing Ethics Course. | Helen Weixu Chen, Maura R. Grossman, Daniel G. Brown |
| 2025 | TEI | Helping Popular Musicians Learn by Ear: Analyzing Video Lessons to Inform the Design of Memory-Oriented Human-Recording Interactions. | Christopher Liscio, Daniel G. Brown |
| 2013 | PSB | LSHPlace: Fast Phylogenetic Placement Using Locality-Sensitive Hashing. | Daniel G. Brown, Jakub Truszkowski |
| 2011 | WABI | Towards a Practical O(n logn) Phylogeny Algorithm. | Daniel G. Brown, Jakub Truszkowski |
| 2010 | WABI | Discovering Kinship through Small Subsets. | Daniel G. Brown, Tanya Y. Berger-Wolf |
| 2008 | SPIRE | On the Structure of Small Motif Recognition Instances. | Christina Boucher, Daniel G. Brown, Stephane Durocher |
| 2007 | COCOON | Integer Programming Formulations and Computations Solving Phylogenetic and Population Genetic Problems with Missing or Genotypic Data. | Dan Gusfield, Yelena Frid, Daniel G. Brown |
| 2007 | WABI | A Graph Clustering Approach to Weak Motif Recognition. | Christina Boucher, Daniel G. Brown, Paul Church |
| 2006 | CPM | New Bounds for Motif Finding in Strong Instances. | Brona Brejov, Daniel G. Brown, Ian M. Harrower, Toms Vinar |
| 2005 | APBC | The use of functional domains to improve transmembrane protein topology prediction. | Emily W. Xu, Daniel G. Brown, Paul Kearney |
| 2005 | CPM | Sharper Upper and Lower Bounds for an Approximation Scheme for Consensus-Pattern. | Brona Brejov, Daniel G. Brown, Ian M. Harrower, Alejandro Lpez-Ortiz, Toms Vinar |
| 2005 | ISMB | ExonHunter: a comprehensive approach to gene finding. | Brona Brejov, Daniel G. Brown, Ming Li, Toms Vinar |
| 2004 | CPM | Optimizing Multiple Spaced Seeds for Homology Search. | Jinbo Xu, Daniel G. Brown, Ming Li, Bin Ma |
| 2004 | WABI | The Most Probable Labeling Problem in HMMs and Its Application to Bioinformatics. | Brona Brejov, Daniel G. Brown, Toms Vinar |
| 2004 | WABI | Multiple Vector Seeds for Protein Alignment. | Daniel G. Brown |
| 2004 | WABI | A New Integer Programming Formulation for the Pure Parsimony Problem in Haplotype Analysis. | Daniel G. Brown, Ian M. Harrower |
| 2004 | WABI | New Algorithms for Multiple DNA Sequence Alignment. | Daniel G. Brown, Alexander K. Hudek |
| 2003 | CPM | Optimal Spaced Seeds for Hidden Markov Models, with Application to Homologous Coding Regions. | Brona Brejov, Daniel G. Brown, Toms Vinar |
| 2003 | WABI | Vector Seeds: An Extension to Spaced Seeds Allows Substantial Improvements in Sensitivity and Specifity. | Brona Brejov, Daniel G. Brown, Toms Vinar |
| 2003 | WABI | Optimal DNA Signal Recognition Models with a Fixed Amount of Intrasignal Dependency. | Brona Brejov, Daniel G. Brown, Toms Vinar |
| 2002 | IGARSS | Development of a method for remote sensing of land-cover change 1980-2000 in the USFS North Central Region using heterogeneous USGS LUDA and NOAA AVHRR 1 km data. | Kathleen M. Bergen, Daniel G. Brown, James R. Rutherford, Eric J. Gustafson |
| 2001 | SODA | A probabilistic analysis of a greedy algorithm arising from computational biology. | Daniel G. Brown |
| 2000 | SODA | Selective mapping: a discrete optimization approach to selecting a population subset for use in a high-density genetic mapping project. | Daniel G. Brown, Todd J. Vision, Steven D. Tanksley |