Ken Duffy

Contact

Algorithms for communication systems, the life sciences, and DNA forensics

Algorithms for communication systems, the life sciences, and DNA forensics

Information theory, coding, communications:

A. Riaz, A. Yasar, F. Ercan, W. An, J. Ngo, K. Galligan, M. Médard, K. R. Duffy & Rabia T. Yazicigil, A sub-0.8 pJ/bit, 16.3 Gbps/mm^2 universal soft-detection decoder using ORBGRAND in 40 nm CMOS. IEEE International Solid-State Circuits Conference, 2023.
K. R. Duffy, W. An & M. Médard. Ordered reliability bits guessing random additive noise decoding. IEEE Transactions on Signal Processing, 70, 4528–4542, 2022.
W. An, M. Médard & K. R. Duffy. Keep the bursts and ditch the interleavers. IEEE Transactions on Communications, 70 (6), 3655–3667, 2022.
K. R. Duffy, M. Médard & W. An. Guessing random additive noise decoding with symbol reliability information (SRGRAND). IEEE Transactions on Communications, 70 (1), 3–18, 2022.
K. R. Duffy & S. Shneer. MDS coding is better than replication for job completion times. Operations Research Letters, 49 (1), 91–95, 2021.
H. Wang, L. Vo, F. P. Calmon, M. Médard, K. R. Duffy & M. Varia, Privacy with estimation guarantees, IEEE Transactions on Information Theory, 65 (12), 8025-8042, 2019.
K. R. Duffy, J. Li & M. Médard, Capacity-achieving guessing random additive noise decoding (GRAND), IEEE Transactions on Information Theory, 65 (7), 4023-4040, 2019.

Life sciences:

M. B. Horton, H. Cheon, K. R. Duffy, D. Brown, S. H. Naik, C. Alvarado, J. R. Groom, S. Heinzel & P. D. Hodgkin. Lineage tracing reveals B cell antibody class switching is stochastic, cell-autonomous, and tuneable. Immunity, 55 (10), 1843–1855, 2022.
K. Bresser, L. Kok, A. C. Swain, L. A. King, L. Jacobs, T. S. Weber, L. Perié, K. R. Duffy, R. J. de Boer, F. A. Scheeren & T. N. Schumacher, Replicative history marks functional disparity in the CD8+ T cell memory pool. Nature Immunology, 3(5), 791–801, 2022.
H. Cheon, A. Kan, G. Prevedello, S. C. Oostinde, S. J. Dovedi, E. D. Hawkins, J. M. Marchingo, S. Heinzel, K. R. Duffy & P. D. Hodgkin. Cyton2: A model of immune cell population dynamics that includes familial instructional inheritance. Frontiers in Bioinformatics, 1, 1–20, 2021.
T. Tak, G. Prevedello, G. Simon, N. Paillon, C. Benlabiod, C. Marty, J-L. Villeval, I. Plo, K. R. Duffy & L. Perié. HSPCs display within-family homogeneity in differentiation and proliferation despite population heterogeneity. eLife, 10, e60624, 2021.
M. L. R. Haltalli, S. Watcham, N. K. Wilson, K. Eilers, A. Lipien, H. Ang, F. Birch, S. G. Anton, C. Pirillo, N. Ruivo, M. L. Vainieri, C. Pospori, R. E. Sinden, T. C. Luis, J. Langhorne, K. R. Duffy, B. Göttgens, A. M. Blagborough & C. Lo Celso, Manipulating niche composition limits damage to haematopoietic stem cells during plasmodium infection. Nature Cell Biology, 22, 1399–1410, 2020.

DNA Forensics

K. R. Duffy, D. Lun, M. Mulcahy, L. O’Donnell, N. Sheth & C. M. Grgicak. Evidentiary evaluation of single cells renders highly informative forensic comparisons across multifarious admixtures. Forensic Science International: Genetics, 2023.
N. Sheth, K. R. Duffy & C. M. Grgicak. High-quality data from a forensically relevant single-cell pipeline enabled by low PBS and Proteinase K concentrations. Journal of Forensic Sciences, 67, 697–706, 2022.
C. Grgicak, K. R. Duffy, & D. Lun. A posteriori probabilities on the number of contributors when conditioned on a known contributor. Forensic Science International: Genetics, 54, 102563, 2022.
N. Sheth, H. Swaminathan, A. J. Gonzalez, K. R. Duffy & C. M. Grgicak. Towards developing forensically relevant single cell pipelines by incorporating direct-to-PCR extraction: effects on signal quality and allele dropout. International Journal of Legal Medicine, 135 (3), 727–738, 2021.
C. M. Grgicak, S. Karkar, X. Yearwood-Garcia, L. E. Alfonse, K. R. Duffy & D. Lun. A large-scale validation of NOCIt’s a posteriori probability of the number of contributors and its integration into forensic interpretation pipelines, Forensic Science International: Genetics, 47, 102296, 2020.