| 2018 | EuroCrypt | Supersingular Isogeny Graphs and Endomorphism Rings: Reductions and Solutions. | Kirsten Eisentrger, Sean Hallgren, Kristin E. Lauter, Travis Morrison, Christophe Petit |
| 2014 | STOC | A quantum algorithm for computing the unit group of an arbitrary degree number field. | Kirsten Eisentrger, Sean Hallgren, Alexei Y. Kitaev, Fang Song |
| 2011 | CRYPTO | Classical Cryptographic Protocols in a Quantum World. | Sean Hallgren, Adam D. Smith, Fang Song |
| 2010 | SODA | Algorithms for Ray Class Groups and Hilbert Class Fields. | Kirsten Eisentrger, Sean Hallgren |
| 2008 | ICALP | Superpolynomial Speedups Based on Almost Any Quantum Circuit. | Sean Hallgren, Aram W. Harrow |
| 2008 | ICALP | Making Classical Honest Verifier Zero Knowledge Protocols Secure against Quantum Attacks. | Sean Hallgren, Alexandra Kolla, Pranab Sen, Shengyu Zhang |
| 2006 | STOC | Limitations of quantum coset states for graph isomorphism. | Sean Hallgren, Cristopher Moore, Martin Rtteler, Alexander Russell, Pranab Sen |
| 2005 | COCOON | Quantum Noisy Rational Function Reconstruction. | Sean Hallgren, Alexander Russell, Igor E. Shparlinski |
| 2005 | STOC | Fast quantum algorithms for computing the unit group and class group of a number field. | Sean Hallgren |
| 2003 | SODA | Quantum algorithms for some hidden shift problems. | Wim van Dam, Sean Hallgren, Lawrence Ip |
| 2002 | STOC | Polynomial-time quantum algorithms for Pell's equation and the principal ideal problem. | Sean Hallgren |
| 2000 | FOCS | An Improved Quantum Fourier Transform Algorithm and Applications. | Lisa Hales, Sean Hallgren |
| 2000 | STOC | Normal subgroup reconstruction and quantum computation using group representations. | Sean Hallgren, Alexander Russell, Amnon Ta-Shma |
| 1999 | STOC | Quantum Fourier Sampling Simplified. | Lisa Hales, Sean Hallgren |