@jaredtsimpson

Computational Biologist. Principal Investigator at OICR & Assistant Professor @UofTCompSci.

simpsonlab.github.io/
Joined September 2009
  • Tweets2.3K
  • Following1.6K
  • Followers6.5K
9Media
Congratulations to Dr. Heather Gibling (aka @hgibling) for an amazing PhD defence today! Thank you @ctitusbrown, @AMosesLab, @reimand and @PughLab for being on the examination committee. Great to work with you and @AwadallaLab on the most challenging parts of the genome
2
5
38
4,731
What is the largest publicly available haplotype reference panel? 1000 genomes? I'm looking for a pre-built pbwt index but don't want to go through dbGAP to get the HRC panel
1
4
7
The Donnelly Centre for Cellular and Biomolecular Research at the Univ of Toronto is inviting applications for three tenure track assistant professors. These are broad searches in the area of functional genomics (2x) and computational biology 1/2 thedonnellycentre.utoronto.c…

Current Opportunities

thedonnellycentre.utoronto.ca
2
75
6
84
Jared Simpson retweeted
Artem Babaian@RNA_Life16 Aug 2022
Super stoked to be joining MoGen @UofT as an Assistant Professor in Oct '22! I'm founding "The Laboratory for RNA-Based Lifeforms" to explore the diversity of Earth's RNA entities 🧬🔎🦠🌎! Looking to hire🥰! (Please RT) #RNA #genetics #virology #bioinformatics 1/3
38
73
7
483
Jared Simpson retweeted
Roham Razaghi
@RohamRaz11 Jul 2022
Happy to share our latest work from @timp0 lab, modbamtools: Analysis of single-molecule epigenetic data for long-range profiling, heterogeneity, and clustering 👉manual and tutorial: rrazaghi.github.io/modbamtoo… 👉preprint: biorxiv.org/content/10.1101/… some of the tools to highlight: 1/
2
25
2
67
Jared Simpson retweeted
Adam Phillippy@aphillippy27 Jun 2022
Our next big thing! 🎉 "Verkko: telomere-to-telomere assembly of diploid chromosomes" from @MikkoRautiaine3 @sergeynurk @sergekoren generates beautiful graphs and automatically assembles 20/46 human chromosomes from HG002 #T2T without gaps biorxiv.org/content/10.1101/…
9
148
13
426
Interested in software development for biomedical and imaging data? With @hartjackson we're looking for a developer for an exciting academic/industry collaboration including some world-unique highly multiplexed imaging data Details ➡️ apply.interfolio.com/106773 DMs open!
5
1
5
nanopolish v0.14.0 released, with support for modification bam files (thanks @BonfieldJames and @chrisnrg) and compiling on M1 macs
2
29
113
Jared Simpson retweeted
Adam Phillippy@aphillippy31 Mar 2022
Today is the big day! The #T2T consortium is claiming victory and announcing that we have finally uncovered every last bit of the human genome! The papers are out today 🥳🧬 science.org/toc/science/376/…
58
1,198
149
3,794
Join my team! Challenging but impactful projects, great colleagues, exciting science @OICR_news! recruitingsite.com/csbsites/…
4
3
Rust bioinformatics programmers: is there an idiomatic way of processing records of a bam file in parallel? Examples appreciated!
4
6
42
I've spent several years building software tools in genomics. While the work couldn't be more exciting, there are unique challenges and tensions in the world of scientific software. How does software in the life sciences actually work (and not work)? newscience.org/how-software-…

How Software in the Life Sciences Actually Works (And Doesn’t Work) - …

By Elliot Hershberg. Published 2022-01-30. Elliot is a PhD student at Stanford University. Before graduate school, he worked on a range of problems in biotechnology. He has helped design cancer...

newscience.org
13
172
33
618
Jared Simpson retweeted
Heng Li@lh3lh313 Jan 2022
Kar-Tong Tan found @nanopore basecallers often systematically call telomere repeats (TTAGGG)n into other repeats with similar signal profiles. He tuned the bonito basecaller and developed a pipeline to greatly reduce such errors. Read the thread and our preprint for details.
Kar-Tong Tan@kartong8813 Jan 2022
Happy to share our work on repeat-calling errors in nanopore sequencing of telomeres with @lh3lh3 and #matthewmeyerson biorxiv.org/content/10.1101/…

Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres

Nanopore long-read genome sequencing is emerging as a potential approach for the study of genomes including long repetitive elements like telomeres. Here, we report extensive basecalling induced...

biorxiv.org
1
33
114
Thank you to my lab for the amazing nanopolish socks! I hope there's no bugs in this code, it would be very hard to fix now
4
8
3
168
Join us at @UofTCompSci! We are now hiring for tenure-stream faculty positions in multiple areas. We will start reviewing applications on December 6, and we will give full consideration to all applications submitted by January 10. Get the details: uoft.me/7jH
Graphic with the words "Now Hiring: Tenure-stream faculty positions in multiple areas" over a photo of downtown Toronto

ALT Graphic with the words "Now Hiring: Tenure-stream faculty positions in multiple areas" over a photo of downtown Toronto

4
62
13
83
Jared Simpson retweeted
Jim Shaw@jim_elevator22 Nov 2021
Me and @YunWilliamYu's work on local k-mer selection techniques is now accepted to Bioinformatics! We investigate both practically and theoretically the properties of different local k-mer selection techniques, the most well-known being the minimizer. academic.oup.com/bioinformat…
3
8
1
26
Very excited to announce that we are recruiting a colleague for a full-time tenure stream position in the area of computational biology in the Donnelly Centre for Cellular and Biomolecular Research, in the Temerty Faculty of Medicine at the University of Toronto. 1/2
1
52
1
76
The CS department at Penn State is looking to fill several(!) faculty positions in bioinformatics. Initial deadline is Dec 1st, but we will consider all applications until the positions are filled. tinyurl.com/3znd5yws. Please RT if relevant to your followers. 1/3
2
107
7
95
Jared Simpson retweeted
Winston Timp@timp019 Oct 2021
Interested in a #postdoc position to develop new sequencing methods? Come work with us! Work includes but is not limited to epigenetics, RNA mods, and single-cell/spatial transcriptomics. docs.google.com/document/d/1…

211018_timp_postdoc_ad

Winston Timp (https://timplab.org/) is searching for new postdoctoral fellows to join his research lab at Johns Hopkins. This position would focus on projects involving sequencing technology develo...

docs.google.com
43
5
60
Jared Simpson retweeted
Matt Loose@mattloose8 Sep 2021
An ultra-long read update. Since @circulomics is "no longer available" for @nanopore people might be interested in these protocols from @longreadclub @NininUon and @DrT1973 - a toolkit of options here dx.doi.org/10.17504/protocol… including monarch from @NEBiolabs - 🧵below with more.
5
81
9
156
Load more