Jared Simpson

@jaredtsimpson

Computational Biologist. Principal Investigator at OICR & Assistant Professor .

simpsonlab.github.io
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  1. (e)k Bertxiotua
    abe. 4

    Our preprint introducing >300 Gbp sequencing of microbial community standards is up! Of interest to anyone looking for juicy real data to put tools to the test. Amazing lab work & nice first paper with lab

    4 erantzun 86 bertxio 174 atsegin
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  2. (e)k Bertxiotua
    aza. 28

    Now available from : and with colleagues including and measured over 1,000,000,000 Cas9 editing outcomes, and thoroughly dissected the data. 1/

    5 erantzun 49 bertxio 94 atsegin
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  3. (e)k Bertxiotua
    aza. 28

    lab with a beautiful paper:

    3 bertxio Atsegin 1
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  4. (e)k Bertxiotua
    aza. 26

    High-Throughput Biology: From Sequence to Networks, 6-day course w/. Applications due 1/15. Instructors:

    18 bertxio 28 atsegin
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  5. (e)k Bertxiotua
    aza. 12

    Announcing a first release of methplotlib: a genome browser for methylation data from nanopolish by . Feedback and contributions more than welcome!

    3 erantzun 98 bertxio 165 atsegin
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  6. (e)k Bertxiotua
    urr. 23

    Interested in a long-read assembler with the speed of miniasm and comparable consensus accuracy of canu? Try wtdbg2 by my friend Jue Ruan. A human genome in one day. Also available from bioconda.

    9 erantzun 211 bertxio 342 atsegin
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  7. (e)k Bertxiotua
    urr. 21

    TT position available at U of Toronto in genomics and statistical genetics. Great community and colleagues here in Toronto. Potential opportunities for a link with . Please RT

    Erantzun 1 56 bertxio 28 atsegin
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  8. (e)k Bertxiotua
    urr. 18

    I think this'll be our best promethion run so far! It just blew past 75Gb in 24hours with >2100 pores still sequencing and >96% pore occupancy

    Erantzun 1 18 bertxio 38 atsegin
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  9. (e)k Bertxiotua
    urr. 18

    Sooo good! Using long-read sequencing to detect imprinted DNA methylation

    9 bertxio 14 atsegin
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  10. (e)k Bertxiotua
    urr. 16

    D-NAscent: dynamics by sequencing reveals on single-molecules replication origins, fork direction & fork pausing. Great collaboration

    3 erantzun 34 bertxio 53 atsegin
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  11. urr. 16

    We just posted a preprint on measuring genome replication by detecting nucleotide analogues incorporated into the yeast genome using signals. Work led by , and .

    Erantzun 1 34 bertxio 54 atsegin
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  12. (e)k Bertxiotua
    urr. 15

    Never imagined that the malloc in glibc affects the multithreaded performance by this much! :o Impact of malloc on call-methylation performance ...

    3 erantzun 12 bertxio 29 atsegin
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  13. ira. 11

    New nanopolish release (0.10.2) containing the first public version of our poly-A tail length estimator for direct RNA reads: . Developed by Paul Tang in my group.

    3 erantzun 90 bertxio 158 atsegin
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  14. (e)k Bertxiotua
    abu. 3

    130.6 Gb from our first PromethION flowcell... The most exciting moment was realising we still had 7000 pores after 64 hours so fuelled it up and kicked it off again!

    15 erantzun 54 bertxio 159 atsegin
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  15. uzt. 25

    nanopolish v0.10.1 released: this version changes the interface of the consensus polishing workflow so some pipelines may need to be updated. See the release notes here:

    Erantzun 1 69 bertxio 106 atsegin
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  16. (e)k Bertxiotua
    uzt. 24

    Slides from my talk on "k-mer Data Structures" at :

    2 erantzun 38 bertxio 90 atsegin
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  17. (e)k Bertxiotua
    uzt. 20

    Received a nice NanoPlot feature suggestion from : evolution of sequencing speed across time. Here is an example of one of our PromethION runs. Available in v1.15.0 from PyPI

    12 bertxio 36 atsegin
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  18. (e)k Bertxiotua
    uzt. 20

    Come work with us and help build the foundation for a Canadian approach to national genomics research!

    Backend Developer - CanDIG -
    Erantzun 1 3 bertxio 7 atsegin
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  19. (e)k Bertxiotua
    uzt. 8

    Week end fun : Ecoli consensus and chr22 methylation detection using on my mobile phone for some reads (Includes minimap2 and samtools).

    2 erantzun 14 bertxio 29 atsegin
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  20. (e)k Bertxiotua
    uzt. 5

    Meet us at : talks on diploid assembly () and on using Strand-seq to sort long reads by chromosome prior to assembly (). Two posters: sequence-to-graph alignment and haplotype phasing. Also, we are LOOKING FOR POSTDOCS.

    Erantzun 1 16 bertxio 28 atsegin
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