| Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic Y Turakhia, B Thornlow, AS Hinrichs, N De Maio, L Gozashti, R Lanfear, ... Nature Genetics 53 (6), 809-816, 2021 | 331 | 2021 |
| Domain-specific hardware accelerators WJ Dally, Y Turakhia, S Han Communications of the ACM 63 (7), 48-57, 2020 | 286 | 2020 |
| Darwin: A Genomics Co-processor Provides up to 15,000 X Acceleration on Long Read Assembly Y Turakhia, G Bejerano, WJ Dally Proceedings of the Twenty-Third International Conference on Architectural …, 2018 | 207* | 2018 |
| Cherry-picking: Exploiting process variations in dark-silicon homogeneous chip multi-processors B Raghunathan, Y Turakhia, S Garg, D Marculescu 2013 Design, Automation & Test in Europe Conference & Exhibition (DATE), 39-44, 2013 | 145 | 2013 |
| Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape Y Turakhia, B Thornlow, A Hinrichs, J McBroome, N Ayala, C Ye, K Smith, ... Nature 609 (7929), 994-997, 2022 | 141* | 2022 |
| Mutation rates and selection on synonymous mutations in SARS-CoV-2 N De Maio, CR Walker, Y Turakhia, R Lanfear, R Corbett-Detig, ... Genome Biology and Evolution 13 (5), evab087, 2021 | 117 | 2021 |
| Stability of SARS-CoV-2 phylogenies Y Turakhia, N De Maio, B Thornlow, L Gozashti, R Lanfear, CR Walker, ... PLoS genetics 16 (11), e1009175, 2020 | 109 | 2020 |
| A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees J McBroome, B Thornlow, AS Hinrichs, A Kramer, N De Maio, N Goldman, ... Molecular biology and evolution 38 (12), 5819-5824, 2021 | 85 | 2021 |
| HaDeS: architectural synthesis for heterogeneous dark silicon chip multi-processors Y Turakhia, B Raghunathan, S Garg, D Marculescu Proceedings of the 50th Annual Design Automation Conference, 1-7, 2013 | 80 | 2013 |
| A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales A Marcovitz, Y Turakhia, HI Chen, M Gloudemans, BA Braun, H Wang, ... Proceedings of the National Academy of Sciences 116 (42), 21094-21103, 2019 | 61* | 2019 |
| Maximum likelihood pandemic-scale phylogenetics N De Maio, P Kalaghatgi, Y Turakhia, R Corbett-Detig, BQ Minh, ... Nature Genetics 55 (5), 746-752, 2023 | 49 | 2023 |
| Low-power architecture for sparse neural network YG Turakhia, J Jaffari, A Panda, K Chatha US Patent App. 15/377,858, 2018 | 48 | 2018 |
| Darwin-WGA: A co-processor provides increased sensitivity in whole genome alignments with high speedup Y Turakhia, SD Goenka, G Bejerano, WIJ Dally 2019 IEEE International Symposium on High Performance Computer Architecture …, 2019 | 42 | 2019 |
| Architecture for sparse neural network acceleration YG Turakhia, J Jaffari, A Panda, K Chatha US Patent 10,871,964, 2020 | 32 | 2020 |
| SegAlign: A scalable GPU-based whole genome aligner SD Goenka, Y Turakhia, B Paten, M Horowitz SC20: International Conference for High Performance Computing, Networking …, 2020 | 27 | 2020 |
| matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2 C Ye, B Thornlow, A Hinrichs, A Kramer, C Mirchandani, D Torvi, ... Bioinformatics 38 (15), 3734-3740, 2022 | 24 | 2022 |
| Hypercriticality MY Vardi Communications of the ACM 53 (7), 5-5, 2010 | 24* | 2010 |
| Identifying SARS-CoV-2 regional introductions and transmission clusters in real time J McBroome, J Martin, A de Bernardi Schneider, Y Turakhia, ... Virus Evolution 8 (1), veac048, 2022 | 20 | 2022 |
| phastSim: efficient simulation of sequence evolution for pandemic-scale datasets N De Maio, W Boulton, L Weilguny, CR Walker, Y Turakhia, ... PLoS computational biology 18 (4), e1010056, 2022 | 18 | 2022 |
| Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and … AM Kramer, B Thornlow, C Ye, N De Maio, J McBroome, AS Hinrichs, ... Systematic Biology, syad031, 2023 | 15* | 2023 |
Russ Corbett-DetigBiomolecular Engineering and Genomics Institute, UCSCVerified email at ucsc.edu
