Journals

  1. N. D. Maio, L. Weilguny, C. R. Walker, Y. Turakhia, R. Corbett-Detig, N. Goldman, "phastSim: Efficient simulation of sequence evolution for pandemic-scale datasets", PLOS Computational Biology, April 2022 [paper, code]

  2. J. Schull*, Y. Turakhia*, J. Hemker, W. J. Dally, G. Bejerano, "Champagne: Automated whole-genome phylogenomic character matrix method using large genomic indels for homoplasy-free inference", Genome Biology and Evolution (GBE), February 2022. [paper, code]

  3. A. Kramer, Y. Turakhia, R. Corbett-Detig, "ShUShER: private browser-based placement of sensitive genome samples on phylogenetic trees", Journal of Open Source Software (JOSS), Oct 2021. [paper, code, web tool]

  4. J. McBroome, B. Thornlow, A. S. Hinrichs, A. Kramer, N. D. Maio, N. Goldman, D. Haussler, R. Corbett-Detig^, Y. Turakhia^, "A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees", Molecular Biology and Evolution (MBE), Sep 2021 [paper, code, wiki].

  5. Y. Turakhia^, B. Thornlow, A. S. Hinrichs, N. D. Maio, L. Gozashti, R. Lanfear, D. Haussler, and R. Corbett-Detig^, "Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic", Nature Genetics, May 2021 [paper, slides, code, wiki, video].

  6. N. D. Maio, C. R. Walker, Y. Turakhia, R. Lanfear, R. Corbett-Detig, N. Goldman, "Mutation rates and selection on synonymous mutations in SARS-CoV-2", Genome Biology and Evolution (GBE), April 2021 [paper, code]

  7. Y. Turakhia*, N. D. Maio*, B. Thornlow*, L. Gozashti, R. Lanfear, C. R. Walker, A. S. Hinrichs , J. D. Fernandes, R. Borges, G. Slodkowicz , L. Weilguny, D. Haussler, N. Goldman, R. Corbett-Detig, Stability of SARS-CoV-2 Phylogenies”, PLOS Genetics, Nov 2020. [paper, code].

  8. Y. Turakhia*, H. I. Chen*, A. Marcovitz*, G. Bejerano, “A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals”, Nucleic Acids Research (NAR), Jul 2020 [paper, code].

  9. W. Dally, Y. Turakhia, S. Han, “Domain-Specific Hardware Accelerators”, Communications of the ACM (CACM), Jul 2020 (cover feature) [paper].

  10. A. Marcovitz*, Y. Turakhia*, H. I. Chen*, M. Gloudemans, B. A. Braun, H. Wang, G. Bejerano, “A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales”, Proceedings of the National Academy of Sciences of the United States of America (PNAS), Oct 2019. [paper, code]

  11. Y. Turakhia, G. Bejerano, W. Dally, “Darwin: A Genomic Co-processor”, IEEE Micro (Top Picks), May 2019. [paper]

  12. Y. Turakhia, G. Liu, S. Garg, D. Marculescu, “Thread Progress Equalization: Dynamically Adaptive Power-Constrained Performance Optimization of Multi-threaded Applications”, Transactions on Computers (TC), Apr 2017. [paper]

Conferences

  1. S. D. Goenka*, Y. Turakhia*, B. Paten, M. Horowitz, "SegAlign: A Scalable GPU-Based Whole Genome Aligner", International Conference for High Performance Computing, Networking, Storage and Analysis (SC), 2020. [paper, slides, code]

  2. Y. Turakhia*, S. D. Goenka*, G. Bejerano, W. Dally, “Darwin-WGA: A Co-processor Provides Increased Sensitivity in Whole Genome Alignments with High Speedup” , International Symposium on High-Performance Computer Architecture (HPCA), 2019. [paper, slides, code]

  3. Y. Turakhia, G. Bejerano, W. Dally, “Darwin: A Genomic Co-processor Provides 15,000× Speedup on long read assembly”, Architectural Support for Programming Languages and Operating Systems (ASPLOS), 2018 (Best paper award). [paper, slides, code]

  4. Y. Turakhia, B. Raghunathan, S. Garg, D. Marculescu, “HaDeS: Architectural Synthesis for Heterogeneous Dark Silicon Chip Multi-processors”, Design Automation Conference (DAC), 2013. [paper, slides]

  5. B. Raghunathan, Y. Turakhia, S. Garg, D. Marculescu, “Cherry-Picking: Exploiting Process Variations in Dark-Silicon Homogeneous Chip Multi-Processors”, Design, Automation, and Test in Europe Conference (DATE), 2013. [paper, slides]

Book Chapters

  1. S. Garg, Y. Turakhia, D. Marculescu, “Heterogeneous Dark Silicon Chip Multi-Processors Design and Run-time Management”, The Dark Side of Silicon (Energy Efficient Computing in the Dark Silicon Era), Springer, 2016. [chapter]

Pre-prints

  1. C. Ye, B. Thornlow, A. S. Hinrichs, D. Torvi, R. Lanfear, R. Corbett-Detig, Y. Turakhia, "matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2", bioRxiv preprint 2022. [pre-print, code]

  2. Y. Turakhia^*, B. Thornlow*, A. S. Hinrichs, N. D. Maio, L. Gozashti, R. Lanfear, D. Haussler, and R. Corbett-Detig^, "Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region", bioRxiv pre-print, Aug 2021 [pre-print, code].

  3. B. Thornlow*, A. S. Hinrichs*, M. Jain, N. Dhillon, S. La, J. D. Kapp, I. Anigbogu, M. Cassatt-Johnstone, J. McBroome, M. Haeussler, Y. Turakhia, T. Chang, H. E. Olsen, J. Sanford, M. Stone, O. Vaske, I. Bjork, M. Akeson, B. Shapiro, D. Haussler, A. M. Kilpatrick, R. Corbett-Detig, "A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control", bioRxiv pre-print, Apr 2021 [pre-print]

  4. Y. Turakhia, S. Das, T. Aamodt, W. Dally, “HoLiSwap: Reducing Wire Energy in L1 Caches”, arXiv preprint, Jan 2017. [pre-print]

Workshop papers

  1. R. Snytsar, Y. Turakhia, “Parallel approach to sliding window sums”, International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP), 2019. [paper]

  2. V. Kumar, P. Engineer, M. Datar, Y. Turakhia, S. Agarwal, S. Diwale and S. Patkar, “Framework for Application Mapping over Packet-switched Network of FPGAs : Case studies”, FPGAs for Software Programmers Workshop (FPL) at the International Conference on Field Programmable Logic and Applications, 2015. [paper]

Patents

  1. Y. Turakhia, J. Jaffari, A. Panda, K. Chatha, “An Architecture for Sparse Neural Network Acceleration”, US 10,871,964 B2 (expires 2039-08-09).

(* implies authors made equal contributions)

(^ corresponding authors)