| 2016 | ISSAC | Selecting Algorithms for Black Box Matrices: Checking For Matrix Properties That Can Simplify Computations. | Wayne Eberly |
| 2010 | ISSAC | Yet another block Lanczos algorithm: how to simplify the computation and reduce reliance on preconditioners in the small field case. | Wayne Eberly |
| 2007 | ISSAC | Faster inversion and other black box matrix computations using efficient block projections. | Wayne Eberly, Mark Giesbrecht, Pascal Giorgi, Arne Storjohann, Gilles Villard |
| 2006 | ISSAC | Solving sparse rational linear systems. | Wayne Eberly, Mark Giesbrecht, Pascal Giorgi, Arne Storjohann, Gilles Villard |
| 2005 | ISSAC | A reliable block Lanczos algorithm over small finite fields. | Bradford Hovinen, Wayne Eberly |
| 2004 | ISSAC | Reliable Krylov-based algorithms for matrix null space and rank. | Wayne Eberly |
| 2003 | ISSAC | Early termination over small fields. | Wayne Eberly |
| 2000 | FOCS | Computing the Determinant and Smith Form of an Integer Matrix. | Wayne Eberly, Mark Giesbrecht, Gilles Villard |
| 2000 | ISSAC | Black box Frobenius decompositions over small fields. | Wayne Eberly |
| 1997 | ISSAC | On Randomized Lanczos Algorithms. | Wayne Eberly, Erich L. Kaltofen |
| 1996 | ISSAC | Efficient Decomposition of Associative Algebras. | Wayne Eberly, Mark Giesbrecht |
| 1995 | SODA | Efficient Parallel Computations for Singular Band Matrices. | Wayne Eberly |
| 1992 | FOCS | On Efficient Band Matrix Arithmetic | Wayne Eberly |
| 1991 | FOCS | Size-Depth Tradeoffs for Algebraic Formulae | Nader H. Bshouty, Richard Cleve, Wayne Eberly |
| 1984 | FOCS | Very Fast Parallel Matrix and Polynomial Arithmetic | Wayne Eberly |