Making science faster with algorithms. Assistant prof CU Boulder, Computer Science and BioFrontiers.
Boulder, CO
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Congrats to Murad Chowdhury! His #ASHG22 poster got a Reviewers Choice Award. Check it out for yourself how he is using population-scale data to improve samplot #SV visualization. PB2317 Thursday 10/27 3-445. github.com/ryanlayer/samplot
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Apps are open for Interdisciplinary Quantitative Biology #PhD Program at @CUBoulder @BioFrontiers Learn both sides of #quantitative #biology with funded rotations through wet and dry labs among 11 departments. colorado.edu/certificate/iqb…
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Our work on integrating population data into SV analysis can be found at github.com/ryanlayer/stix and github.com/ryanlayer/samplot If you missed the talk check out this recording piped.video/TsekM1VjFrA #GI2022
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A proud PI moment when @michael_boulder got Bio-Ontologies Best Poster at @iscb #ISMB2022 he also gave a hell of a talk piped.video/P0r1CkY7V3A
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.@dailycamera has an article saying Broomfield, unlike EVERYWHERE else, didn’t have a post-thanksgiving surge. Any ideas on how they attribute their early Dec spike? dailycamera.com/2020/12/18/t…
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I'll go first. It's pretty tame. I used this one to find lncRNA that could be involved in muscle differentiation in this paper mcb.asm.org/content/35/3/498
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When your #COVID19 numbers start looking scary (see Fig 1), just make a new graph (see Fig 2)!!
ALT Fig 1
ALT Fig 2
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I have heard about how the demographics of #COVID19 infections are shifting. This plot drove it home. X gives dates Y gives # of infections in Boulder Co. Orange is assoc w/ long term care Blue is not. The shift is like an on/off switch. Also, stack bar charts were a bad choice.
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Here is a talk I gave to @BioFrontiers about our work (@DanLarremore @baileyfosdick @TheMikeyBrad and more) on monitoring social distancing at the county/city/campus scale piped.video/watch?v=2lhvKg1t… Obligory interruption by child at 17:15
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@UtahCoronavirus here is an example of how activity has changed (or not) in SLC cities over the past few weeks versus a baseline. We have other metrics too
@UtahEmergency here is an example of how activity has changed (or not) in SLC cities over the past few weeks versus a baseline. We have other metrics too. Happy to share.
In this ever changing world where the “new normal” is still just new, one thing has remained constant. Twitter’s news alert algorithm is the worst. I am pretty sure it’s a bug where they accidentally reverse sort the news by interest then send you the top hit.
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Here is the #COVID2019 #SARSCoV2 plot w/ cases (using @COVIDtracker ht @jxchong) and so you don't have to do math in your head positive hit rates and hit rate distribution. 1.0 hit rate is for the states not reporting negatives (removed from hist). The median rate is 0.08.
As @CUBoulder moves everything online, this is the component that I will miss the most. Yes we are using trello, and yes it is terrible in comparison.
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If you don't use bedtools groupby to make your holiday shopping list, you are doing it wrong. I am thinking about submitting a pull request for a cooking-related summation operator. Thanks @aaronquinlan #needsmorebutter
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After patiently adding equations into MS word, they now all look like this. Like Sisyphus, I am bound to hell.
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Talking what we are doing with samplot github.com/ryanlayer/samplot at the Rocky Mountain Genomics HackCon, including our first foray into some machine learning piped.video/watch?v=-2Iyq3gk…
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Struggling to viz SVs? We have MAJOR updates to samplot 1. split view for translocations and big SVs (see imgs) 2. SV/VCF browser (e.g. layerlab.org/assets/2019-06-… ) More here layerlab.org/2019/06/04/Samp… code/README here github.com/ryanlayer/samplot Big thanks to @brwn_j @jon_belyeu @brent_p
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Are you a ugrad or grad scientist at @CUBoulder who writes code? Do you want to write better code? Check out Software Engineering for Scientists CSCI 2830/7000 The class is NOT domain specific @CUEngineering @BioFrontiers @CUArtsSciences @cuatlas @JILAscience @CU_ICS @LASPatCU
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What's the over/under on how many times I hit refresh waiting for these fields to change? #cantmakemyselfstop #firstr01
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Thanks to @b0rk, @oritpeleg and I can make the our @BioFrontiers comp bio lab a more attractive and more informative
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GIGGLE made the Extramural Research Highlights at the NHGRI’s directors report! My favorite part was when Eric Green said “... entitled, and I don’t kid you, GIGGLE …” My not so favorite part was when he called me “Ryan Lauer” piped.video/watch?v=s0znOz10… github.com/ryanlayer/giggle
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Day 38 at @BioFrontiers Furniture for the new lab space has arrived. Next step, get people in those desks. Maybe you? Grad applications are due Dec 15. colorado.edu/certificate/iqb… colorado.edu/cs/why-cu
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Great story on @NaturePodcast about how @oritpeleg et al modeled bee swarm cooperation in response to stress itunes.apple.com/us/podcast/… Also a nice video at piped.video/watch?v=jswSJzny…
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My academic career has had quite the view. A PhD along the Blue Ridge at @UVA, a post doc tucked into the Wasatch at @UUtah, and now my lab staring at the Font Range at @BioFrontiers @CUBoulder
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This is a disappointing result with respect to how mentors view trainees. Things are gonna get worse, maybe much worse.
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Feeling nostalgic after a great hike at @BrightonResort today. It was our first hike ever in Utah (top) and 3 years and 1 kid later it was our last (bottom) before our move to to @CUBoulder and @BioFrontiers.
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If you are still on the fence about long reads, note that the @nanopore flow cell shipping boxes are _very_ reusable.
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SAMPLOT now supports simultanious visualization of short reads, long reads (@PacBio and @nanopore), linked and phased reads (@10xgenomics), and gene and annotation tracks. Thanks @jon_belyeu for these images and @GenomeInABottle for the data
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Proper send off at a tiki bar for @edchuong (@BioFrontiers) and @kelsey_cone (@ARUPLabs) from @ElEarlyBird
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