Yen-Ru Chin, Jui-Ting Tsai, Ho-Lin Chen, “A Minimal Requirement for Self-Assembly of Lines in Polylogarithmic Time,” Natural Computing, 17(4), 743-757, Dec. 2018
Ho-Lin Chen and David Doty, “Parallelism and Time in Hierarchical Self-Assembly,” SIAM Journal on Computing, 46-2, 661-709, Mar. 2017
H.-L. Chen, R. Cummings, D. Doty, D. Soloveichik, “Speed faults in computation by chemical reaction networks,” Distributed Computing, 30(5), 373-390, 2017
D. Doty, H.-L. Chen, J. Manuch, A. Rafiey, L. Stacho, “Pattern overlap implies runaway growth in hierarchical tile systems,” Journal on Computational Geometry, 7(2), 3-18, 2016
H.-L. Chen, D. Doty, and D. Soloveichik., “ Deterministic Function Computation with Chemical Reaction Networks,” Natural Computing, 13(4), 517-534, Dec. 2014
H. Zhou, H. Chen and J. Bruck, “Synthesis of Stochastic Flow Networks,” IEEE Transactions on Computers, 63(5), 1234-1247, May 2014
H.-L. Chen, D. Doty, S. Seki, “Program Size and Temperature in Self-Assembly,” Algorithmica, 2014
H.-L. Chen, T. Roughgarden and G. Valiant, “Designing network protocols for good equilibria,” SIAM Journal on Computing, 39(5), 1799-1832, Jan. 2010
H.L. Chen and T. Roughgarden, “Network design with weighted players,” Theory of Computing Systems, 45 (2), 302-324, Aug. 2009
H.-L. Chen, H. Jabbari and A. Condon, “An O(n^5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids,” Journal of Computational Biology, 16 (6), 803-815, Jun. 2009
H.-L. Chen, R. Schulman, A. Goel and E. Winfree, “Reducing Facet Nucleation during Algorithmic Self-Assembly,” Nano Letters, 7 (9), 2913-2919, Sept. 2007
Z. Abrams, H.-L. Chen, L. Guibas, J. Liu, and F. Zhao, “Kinetically Stable Task Assignment for Networks of Microservers,” IEEE Information Processing for Sensor Networks, 2006
Conference & proceeding papers:
Y.-R. Chin, J.-T. Tsai, H.-L. Chen, “A Minimal Requirement for Self-assembly of Lines in Polylogarithmic Time,” 23rd International Meeting on DNA Computing and Molecular Programming, 139-154, Austin, Texas, USA, 2017
T.-L. Wang, C.-K. Yeh, H.-L. Chen, “An Improved Tax Scheme for Selfish Routing,” International Symposium on Algorithms and Computation (ISAAC), 61:1-61:12, Sydney, Australia, 2016
H.-L. Chen, D. Doty, J. Maňuch, A. Rafiey, and L. Stacho, “Pattern overlap implies runaway growth in hierarchical tile systems,” 31st International Symposium on Computational Geometry, Eindhoven, the Netherlands, May 2015
H.-L. Chen, R. Cummings, D. Doty, and D. Soloveichik, “Speed faults in computation by chemical reaction networks,” 28th International Symposium on Distributed Computing (Best paper award), Oct. 2014
H.-L. Chen, D. Doty, D. Holden, C. Thachuk, D. Woods, and C.-T. Yang, “Fast algorithmic self-assembly of simple shapes using random agitation,” 20th International Meeting on DNA Computing and Molecular Programming, Sept. 2014
H.-L. Chen, D. Doty, and D. Soloveichik, “Rate-independent computation in continuous chemical reaction networks,” 5th Innovations in Theoretical Computer Science Conference (ITCS), Jan. 2014
N. Dabby and H.-L. Chen*, “Active Self-Assembly of Simple Units Using an Insertion Primitive,” ACM-SIAM Symposium on Discrete Algorithms, New Orleans, LA, USA, Jan. 2013
D. Woods, H.-L. Chen, S. Goodfriend, N. Dabby, E. Winfree, P. Yin, “Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time,” ITCS 2013, Berkeley, CA, USA, Jan. 2013
H.-L. Chen, D. Doty and D. Soloveichik, “Deterministic Function Computation with Chemical Reaction Networks,” 18th International Conference on DNA Computing and Molecular Programming, Aarhus, Denmark, Sept. 2012
H.-L. Chen and D. Doty, “Parallelism and Time in Hierarchical Self-Assembly,” ACM-SIAM Symposium on Discrete Algorithms, Jan. 2012
H.-L. Chen, D. Doty, and S. Seki, “Program Size and Temperature in Self-Assembly,” International Symposium on Algorithms and Computation (ISAAC), Dec. 2011
H.-L. Chen and M.-Y. Kao, “Optimizing Tile Concentrations to Minimize Errors and Time for DNA Tile Self-Assembly Systems,” International Conference on DNA Computing, 2010
H. Zhou, H.-L. Chen, and J. Bruck, “On the Synthesis of Stochastic Flow Networks,” IEEE International Symposium on Information Theory, 2010
H.-L. Chen, J. Marden and A. Wierman, “On the Impact of Heterogeneity and Back-End Scheduling in Load Balancing Designs,” INFOCOM, 2009
H.-L. Chen, A. De and A. Goel, “Towards Programmable Molecular Machines,” Fifth Annual Conference on Foundations of Nanoscience, 2008
H.-L. Chen, T. Roughgarden and G. Valiant, “Design Networks with Good Equilibria,” ACM-SIAM Symposium on Discrete Algorithms, 2008
H.-L. Chen, A. Goel and C. Luhrs, “Dimension augmentation and combinatorial criteria for efficient error-resistant DNA self-assembly,” ACM-SIAM Symposium on Discrete Algorithms, 2008
H.-L. Chen, A. Goel, C. Luhrs and E. Winfree, “Self-Assembling Tile Systems that Heal from Small Fragments,” Thirteenth International Meeting on DNA Computing, 2007
H.-L. Chen and T. Roughgarden, “Network Design with Weighted Players,” Eighteenth ACM Symposium on Parallelism in Algorithms and Architectures, 2006
H.-L. Chen, A. Goel, R. Schulman and E. Winfree, “Error Correction for DNA Self-Assembly: Preventing Facet Nucleation,” Eleventh International Meeting on DNA Computing, 2005
H.-L. Chen and A. Goel, “Error Free Self-Assembly Using Error Prone Tiles,” Tenth International Meeting on DNA Computing, 2004
Z. Abrams and H.-L. Chen, “The Simplified Partial Digest Problem: Hardness and a Probabilistic Analysis,” Fourth Annual RECOMB Satellite Meeting on DNA Sequencing Technologies and Computation, 2004
H.-L. Chen, Q. Cheng, A. Goel, M. Huang and P. Moisset de Espanés, “Invadable Self-Assembly: Combining Robustness with Efficiency,” Fifteenth Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), 2004
H.-L. Chen, H.-I. Lu and H.-C. Yen, “On Maximum Symmetric Subgraphs,” 8th International Symposium on Graph Drawing, 2000
H.-L. Chen and H.-C. Yen, “Orthogonal and Straight-Line Drawings of Graphs with Succinct Representations,” 7th International Symposium on Graph Drawing, 1999