Pubs

Journals

See Sebastian’s webpage for an up-to-date list of these.

EMIL Technotes

51. S. Magierowski, “SeqSoC: An All-In-One DNA Sequencing Chip,EMIL Tech. Rep., pp. 1–10, June 30, 2022.
50. S. Magierowski, “Flappie Neural Network Basecaller,EMIL Tech. Rep., pp. 1–18, June 26, 2021.
49. S. Magierowski, “Front-End Nanopore Signal Chain Design (v.4),EMIL Tech. Rep., pp. 1–23, May 15, 2021.
48. Y. Dawji and S. Magierowski, “Interfacing EMIL DROIC Hardware to NNI Hardware: An Introduction,EMIL Tech. Rep., pp. 1–3, March 20, 2021.
47. S. Magierowski, “DROIC1 Details,EMIL Tech. Rep., pp. 1-5, March 20, 2021.
46. S. Magierowski, “Writing DNA,EMIL Tech. Rep., pp. 1-5, Apr. 9, 2020.
45. K. Hammad, M. Abbaszadegan, Z. Wu, S. Naushad, D. Ogunremi, S. Magierowski, “Final Report: Bioinformatics and Hardware for 3rd Generation DNA Sequencers in the Services of Field-Based Microbial Threat Detection,EMIL Tech. Rep., pp. 1–23, Mar. 30, 2020.
44. S. Magierowski and E. Ghafar-Zadeh, “End-to-End DNA Storage: A Short-Term Proposal,EMIL Tech. Rep., pp. 1–8, Nov. 8, 2019.
43. S. Magierowski, “End-to-End DNA Storage Device,EMIL Tech. Rep., pp. 1–4, July 29, 2019.
42. S. Magierowski, K. Hammad, Z. Wu, M. Abbaszadegan, “Bioinformatics and Hardware for 3rd Generation DNA Sequencers in the Services of Field-Based Microbial Threat Detection,EMIL Tech. Rep., pp. 1–8, Apr. 1, 2019.
41. S. Magierowski, “A 64-State HMM Basecaller Architecture,EMIL Tech. Rep., pp. 1–7, Feb. 28, 2019.
40. S. Magierowski, “Scrappie Neural Network Basecaller,EMIL Tech. Rep., pp. 1–18, Feb. 8, 2019.
39. S. Magierowski, “Mixed-Signal ICs for High-Speed DNA-Processing,EMIL Tech. Rep., pp. 1–2, Nov. 23, 2018.
38. S. Magierowski, “Front-End Nanopore Signal Chain Design (v.3),EMIL Tech. Rep., pp. 1–11, Sep. 29, 2018.
37. S. Magierowski, “ONT Nanopore Signal Analysis (v.2),EMIL Tech. Rep., pp. 1–5, Sep. 28, 2018.
36. S. Magierowski, “DNA Storage Based on Illumina Technology,EMIL Tech. Rep., pp. 1–8, Sep. 12, 2018.
35. S. Magierowski, “DNA Storage,EMIL Tech. Rep., pp. 1–10, Aug. 31, 2018.
34. S. Magierowski, “Software/Hardware Components for a Rapid Genome-Based Bacterial Detection System,EMIL Tech. Rep., pp. 1–8, July 10, 2018.
33. S. Magierowski, “FPGA Acceleration via PCIe,EMIL Tech. Rep., pp. 1–7, Mar. 15, 2018.
32. S. Magierowski, “Blockchain Overview,EMIL Tech. Rep., pp. 1–8, Feb. 1, 2018.
31. S. Magierowski, “Machine Learning in DNA Sequencing,EMIL Tech. Rep., pp. 1–23, Dec. 31, 2017.
30. S. Magierowski, “HMM Nanopore Basecalling Trellis Arrangements,EMIL Tech. Rep., pp. 1–6, Dec. 15, 2017.
29. S. Magierowski, “MinION Sequencing,EMIL Tech. Rep., pp. 1–8, Nov. 26, 2017.
28. S. Magierowski, F. Abbasian, and Z. Wu, “The MinION: Structure, Operation, Potential
for Genomic Water Quality Assessment,
EMIL Tech. Rep., pp. 1–10, Oct. 26, 2017.
27. S. Magierowski, “An Automated DNA Sample Loader for Real-Time Genomic Analysis,EMIL Tech. Rep., pp. 1–5, July 24, 2017.
26. S. Magierowski, “2D-Basecalling Algorithm: Basics,EMIL Tech. Rep., pp. 1–5, June 15, 2017.
25. S. Magierowski, “Nanopore ASIC Readout Part III: Embedded Systems,EMIL Tech. Rep., pp. 1–6, Feb. 1, 2017.
24. S. Magierowski, “Nanopore ASIC Readout Part II: Array Design, Control and Programming,EMIL Tech. Rep., pp. 1–6, Jan. 31, 2017.
23. S. Magierowski, “Nanopore Basecaller Analysis: Computations, Comparisons, Costs,EMIL Tech. Rep., pp. 1–4, Dec. 02, 2016.
22. S. Magierowski, “Nanopore ASIC Readout Part I: Overview, System Design, Pre-Amp Specifications,EMIL Tech. Rep., pp. 1–13, Nov. 30, 2016.
21. B. Mittmann and S. Magierowski, “BCall — C Language Basecalling for Nanopore Systems,EMIL Tech. Rep., pp. 1–5, Oct. 23, 2016.
20. S. Magierowski, “ONT Nanopore Signal Analysis,EMIL Tech. Rep., pp. 1–5, Oct. 8, 2016.
19. S. Magierowski, “Everybody’s Basecalling What’s What,EMIL Tech. Rep., pp. 1–5, Sept. 26, 2016.
18. S. Magierowski, “Biological Nanopore Circuit Model,EMIL Tech. Rep., pp. 1–4, Sept. 19, 2016.
17. S. Magierowski, “Abstract Models of Pore Behaviour,EMIL Tech. Rep., pp. 1–6, Aug. 28, 2016.
16. S. Magierowski, “2D-Basecalling on Nanopore Measurements,EMIL Tech. Rep., pp. 1–9, Aug. 5, 2016.
15. S. Magierowski, “HMM-Based Basecalling for Nanopore Systems,EMIL Tech. Rep., pp. 1–12, July 26, 2016.
14. S. Magierowski, “MinION Notes,EMIL Tech. Rep., pp. 1–4, July 6, 2016.
13. S. Magierowski, “Nanocall Notes,EMIL Tech. Rep., pp. 1–24, June 30, 2016.
12. S. Magierowski, “Nanopore Size and Amplitude Numbers (v.4),EMIL Tech. Rep., pp. 1–6, May 16, 2016.
11. S. Magierowski, “The Oxford Nanopore Technologies Nanopore Model,EMIL Tech. Rep., pp. 1–4, Sept. 24, 2015.
10. S. Magierowski, “Simulation: Digital Receivers and Filtering,EMIL Tech. Rep., pp. 1–3, Sept. 10, 2015.
9. S. Magierowski, “The Reshaper Detector in More Detail,EMIL Tech. Rep., pp. 1–6, July 4, 2015.
8. S. Magierowski, “Front-End Nanopore Signal Chain Design,EMIL Tech. Rep., pp. 1–9, June 20, 2015.
7. S. Magierowski, “Nanopore Size and Amplitude Numbers (v.3),EMIL Tech. Rep., pp. 1–5, June 18, 2015.
6. S. Magierowski, “Ion Torrent in a Little Detail,EMIL Tech. Rep., pp. 1–4, July 6, 2014.
5. S. Magierowski, “Some Notes on Sequencing,EMIL Tech. Rep., pp. 1–2, June 12, 2014.
4. S. Magierowski, “Nanopore Signals for System Simulations,EMIL Tech. Rep., pp. 1–2, May 29, 2014.
3. S. Magierowski, “Nanopore Signal Time Characteristics,EMIL Tech. Rep., pp. 1–2, May 20, 2014.
2. S. Magierowski, “Nanopore Size and Amplitude Numbers (v.2),EMIL Tech. Rep., pp. 1–2, May 17, 2014.
1. S. Magierowski, “Nanopore Noise Thoughts,” EMIL Tech. Rep., pp. 1–2, May 14, 2014.

FISHLab Technotes

 

Sebastian Magierowski
Associate Professor
Department of Electrical Engineering and  Computer Science
Lassonde School of Engineering
York University