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Jared Simpson
@
jaredtsimpson
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Computational Biologist. Principal Investigator at OICR & Assistant Professor @UofTCompSci.
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2,104
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1,326
ಹಿಂಬಾಲಿಸುತ್ತಿರುವವರು
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5,830
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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Sam Nicholls
@samstudio8
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ಡಿಸೆಂ 4 |
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Our preprint introducing >300 Gbp @nanopore sequencing of @ZymoResearch microbial community standards is up! Of interest to anyone looking for juicy real data to put tools to the test. Amazing lab work @Scalene & nice first paper with @pathogenomenick lab biorxiv.org/content/early/…
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Jared Simpson
@jaredtsimpson
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ಡಿಸೆಂ 1 |
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too late! I’ve just landed back in Toronto
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Jared Simpson
@jaredtsimpson
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ನವೆಂ 30 |
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the signals from the pores are different, so they complement each other
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Jared Simpson
@jaredtsimpson
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ನವೆಂ 29 |
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didn’t make it to blue bottle then?
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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Leopold Parts
@LeopoldParts
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ನವೆಂ 28 |
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Now available from @NatureBiotech : @FelicityRAllen and @luca__crepaldi with colleagues including @vitaliikl @michaelkosicki and @SPJacksonGroup measured over 1,000,000,000 Cas9 editing outcomes, and thoroughly dissected the data. 1/
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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Andy Fraser
@andy_utoronto
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ನವೆಂ 28 |
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@LeopoldParts lab with a beautiful paper:
nature.com/articles/nbt.4…
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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Michael Hoffman
@michaelhoffman
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ನವೆಂ 26 |
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High-Throughput Biology: From Sequence to Networks, 6-day course @cshlmeetings w/@Bioinfodotca. Applications due 1/15. Instructors: @bffo @meyer_ann @mbourgey @fmgcavalli @malachigriffith @obigriffith @robinhaw @quaidmorris @reimand @jaredtsimpson meetings.cshl.edu/courses.aspx?c… pic.twitter.com/TsfjAvZcRE
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Jared Simpson
@jaredtsimpson
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ನವೆಂ 12 |
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this is great - we wanted a set of tools exactly like this!
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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Wouter De Coster
@wouter_decoster
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ನವೆಂ 12 |
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Announcing a first release of methplotlib: a genome browser for @nanopore methylation data from nanopolish by @jaredtsimpson. Feedback and contributions more than welcome! gigabaseorgigabyte.wordpress.com/2018/11/12/ann…
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Jared Simpson
@jaredtsimpson
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ನವೆಂ 9 |
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yeah I thought about trying to output a consensus quality but would have to find a way to represent indel error qualities
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Jared Simpson
@jaredtsimpson
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ನವೆಂ 6 |
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congrats!
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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Heng Li
@lh3lh3
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ಅಕ್ಟೋ 23 |
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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. github.com/ruanjue/wtdbg2
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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Quaid Morris
@quaidmorris
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ಅಕ್ಟೋ 21 |
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TT position available at U of Toronto in genomics and statistical genetics. academicjobsonline.org/ajo/jobs/12432 Great community and colleagues here in Toronto. Potential opportunities for a link with @VectorInst. Please RT
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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Fil Zuzarte
@IdeaAntenna
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ಅಕ್ಟೋ 18 |
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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 @nanopore pic.twitter.com/xFtJ5NUOxn
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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Martin A. Smith
@martinalexsmith
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ಅಕ್ಟೋ 18 |
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Sooo good!
Using long-read sequencing to detect imprinted DNA methylation biorxiv.org/content/early/…
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Jared Simpson
@jaredtsimpson
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ಅಕ್ಟೋ 17 |
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biorxiv.org/content/early/… by @wouter_decoster. Accession IDs are in the paper
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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DNA Replication Lab
@DNARepliLab
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ಅಕ್ಟೋ 16 |
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D-NAscent: #DNAreplication dynamics by @nanopore sequencing reveals on single-molecules replication origins, fork direction & fork pausing. Great collaboration @jaredtsimpson
@MichaelABoemo @Carolin_35 @Dunn_School @Kriaucionis_Lab @Ludwig_Cancer #genomics disq.us/t/37ch5fb pic.twitter.com/chf0Cpgzs7
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Jared Simpson
@jaredtsimpson
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ಅಕ್ಟೋ 16 |
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We just posted a preprint on measuring genome replication by detecting nucleotide analogues incorporated into the yeast genome using @nanopore signals. Work led by @MichaelABoemo, @Carolin_35 and @CNieduszynski. biorxiv.org/content/early/…
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Jared Simpson
@jaredtsimpson
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ಅಕ್ಟೋ 15 |
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Back when I was in games development pre-allocation with custom allocators was standard. Some of my assemblers used that strategy too
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| Jared Simpson ಮರುಟ್ವೀಟಿಸಿದ್ದಾರೆ | ||
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Hasindu Gamaarachchi
@Hasindu2008
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ಅಕ್ಟೋ 15 |
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Never imagined that the malloc in glibc affects the multithreaded performance by this much! :o
Impact of malloc on #nanopolish call-methylation performance ... pic.twitter.com/KF93Kbij77
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