Maria Nattestad
@marianattestad
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6,381
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301
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, Circa. DeepVariant+DeepConsensus at Google. PhD from @CSHL w/ Mike Schatz, made Ribbon, Assemblytics, SplitThreader.
Mountain View, CA
Joined January 2010
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Now I'm on sabbatical I finally have time to make more OMGenomics videos! Starting with this one:
Please watch and leave comments about where you are at in your skill-building journey :)
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I’m excited to announce that I am joining Google Brain Genomics! 💻🧠🧬
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Just launched Circa! Powerful GUI software for making circos plots from genomic data
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Nice Nature article on visualization in genomics! Some nice discussion from
@asiepel
of disseminating results through creating new browser tracks, and even a few nuggets at the end from yours truly 😅
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Bioinformatics students and teachers, what command line skills are hard to learn or lack good tutorials?
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Does anyone have project ideas for undergrads or early grad students in bioinformatics/genomics? Maybe interesting papers where the data is actually available to reproduce the results?
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DeepVariant 1.0 is released!
Notably: "Compared to DeepVariant v0.10, these changes reduce Illumina WGS errors by 24%, exome errors by 19%, and PacBio errors by 52%."
Plus a new hybrid PacBio+Illumina model:
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I finally got around to making a new OMGenomics video! (I know it's been way too long)
"Five steps for getting started with bioinformatics":
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Want to learn R quickly? Download the Quick Wins in R -- Ultimate Beginner's Cheat Sheet at
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Exciting news!
@RobAboukhalil
and I have just launched The OMGenomics Podcast! 🥳
Featuring casual conversations about the non-scientific parts of life in the biotech industry.
Episode 1: Sabbaticals
➡️Apple Podcasts:
➡️Spotify:
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The "DeepVariant 1.0" talk I gave at the
@CSHL
BioData meeting is now on YouTube!
It covers how DeepVariant's pileup images and shows some of the many improvements in accuracy, runtime, and new models the team has made since it was open-sourced in 2017.
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Just published a new blog post: "One Genome Browser to Rule Them All" based on a great discussion session at
@VIZBI
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Just released a big update to Circa with new features! See them all in action in 2 minutes -- with another awesome soundtrack :)
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Just released my first ever Medium article: "Making genomic data come alive with circos plots"
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Learning bioinformatics? Check out my OMGenomics show on YouTube:
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"Real" bioinformatics is done using the right tool for the job. R is great for most biologists' needs and a huge step in the right direction
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Just launched Chordial! Powerful, fast, easy-to-use software for creating chord diagrams. . If you're following along, yes, Chordial is Circa's little sister (and I will love them both equally) :)
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Just released a new video:
It’s about doing PCA on population genotypes, a quick bioinformatics project you can play with and build on.
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Wow I'm a finalist for the The Benjamin Franklin Award for Open Access in the Life Sciences! I guess this is the part where I humbly ask for your vote? 😅
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I made a tutorial on *GNU parallel* -- a new video on my OMGenomics channel covering everything you need to know to use GNU parallel painlessly, including an example of using parallel for launching bioinformatics jobs to a cloud or compute cluster.
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The paper for our genomic visualizer Ribbon is now on the BioRxiv. !
Thanks to
@infoecho
,
@mike_schatz
, and
@PacBio
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What are interesting small businesses in the bioinformatics space? Looking for bootstrapped (not VC funded), profitable businesses. We may want to interview them for the OMGenomics podcast 🧐
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Today is my last day at Google. Starting Monday I’ll be on sabbatical. Thank you
@acarroll_ATG
,
@pichuan
,
@kishwarshafin
,
@AlexeyKolesni18
,
@daniel_e_cook
, Howard Yang,
@belyaeva_ana
, and the whole Genomics team for a great 4 years! You are all awesome!
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I used some time over the winter break to make a new video with "5 tips for better bioinformatics software" mostly based on things I have learned to do differently over time (a.k.a. my own mistakes).
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We just released the latest
#DeepVariant
blog post! 🥳 Take a look through DeepVariant’s eyes. It’s interactive... 😎
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Ribbon () now officially uses WebAssembly-compiled samtools for reading local bam files! Thanks to
@RobAboukhalil
!
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I just released a new OMGenomics video:
How to edit files on the command line with vim
I cut the tutorial down to just the most practical features I can’t get by without.
Not gonna lie, I learned several new things myself just by making this video…
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Scientists of Twitter, I need your help! What visualization tools are you using in your bioinformatics research?
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In the latest video on my OMGenomics channel, I answered questions from people with CS backgrounds who are interested in moving into bioinformatics.
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Watch
@RobAboukhalil
and me test-drive GitHub copilot for bioinformatics algorithms! The results were impressive and hilarious. Just wait to see how it generates lunch ideas for us at the end 😂 🍎🥕🍇🍅
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Excited to announce the launch of the OMGenomics YouTube show!
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@ClaB85
Have you tried this tutorial?: I recommend it because I learned a few new things myself!
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OMG(enomics 😝)! I just finished porting my website off of WordPress and onto Jekyll+GitHub pages! Oh it feels so good to be able to edit the site just like I'm writing code and committing it to a git repo. 😎
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Celebrating Ribbon's 1 year anniversary on the BioRxiv and >2,400 users! We'd love to hear from you if you use Ribbon (poster pics anyone?!)
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Curious about
#DeepVariant
and whether deep learning works in genomics? My fellow scientists at
@DNAnexus
have insights to share:
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Exciting new genomic visualization work from Noah Spies in Python:
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Just submitted a new release of Circa. With ribbons!
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Another OMGenomics podcast episode is out! We interview
@nilshomer
about his experience and wisdom from co-founding Fulcrum Genomics, a bioinformatics consulting business helping biotechs solve interesting and novel problems.
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Our research using long-read sequencing to find structural variations in breast cancer made the cover of Genome Research! Thanks
@mike_schatz
and everyone else who put countless hours into this project
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Ribbon SV visualizer now has automation! Load a BEDPE file and a BAM file, hit run: Ribbon loads one region after another and takes pictures
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DNAnexus is looking for summer interns with biology and coding experience:
We have a lot of interesting projects going on, including some in genomics data visualization. Please forward to anyone who might be interested!
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Now we not only have a paper but also a fancy article about the paper :) "Massive genome havoc in breast cancer is revealed" via
@genomeresearch
@EurekAlert
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THIS is how you make a genomics cloud platform that is actually specific to genomic data.
Disclaimer: I helped with some visualization and UX ideas for this :)
Excited to launch , a free platform for exploring genomics data (anything public on AWS, GCP)
Featuring:
- Interactive previews
- Sub-sampling
- Grouped indexes for .bam/.bai, etc
- IGV integration
- Interpreted CIGAR strings, SAM flags, quality scores
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🥳I’m so glad our work overhauling half of DeepConsensus for speed optimizations is ready to release today! It took a lot of work from the whole team, but especially thanks to
@daniel_e_cook
for organizing our efforts!
Release of DeepConsensus v0.2. Large speed improvement (>10x). Added GPU support (w/ NVIDIA V100 is ~3.3x faster than CPU-only). Added Docker images and streamlined dependencies for ease of use. Improved CLI interface and one-step execution script.
()
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Check out this new blog post from
@gunjan_baid
about DeepVariant, giving a great overview of all the major changes and improvements the team has made since DV was first open-sourced in 2017.
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New OMGenomics video: "Should you do a PhD?" As always this is just my perspective as someone who's a bit further down that path and has had this conversation with friends and colleagues before!
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Check out this interview Microsoft did with me for their
#WomenInSTEM
blog! We talk about how I got into this wonderfully interdisciplinary field, and about the work we are doing at
@dnanexus
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Wow I’m honored to be on this list!
A
#WomanInScience
who has inspired our Masters student
@LlorenteArmijo
is Maria Nattestad (
@MariaNattestad
).
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What’s your favorite phylogenetic tree visualization tool/library?
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SplitThreader: Exploration and analysis of rearrangements in cancer genomes is now on the BioRxiv!
@mike_schatz
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Learning R? Check out the first episode of the new Quick Wins in R video series from OMGenomics:
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Why genomics needs custom data visualization
5 complicating factors in genomics that make simple plots insufficient
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If you have ever compared two genomes/assemblies to each other, check out our new
#bioRxiv
preprint on Assemblytics
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Sign up to get weekly bioinformatics videos, scripts, and goodies from OMGenomics that I only share in email:
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#GI2016
poster 67: SplitThreader: A tool for rearrangements in cancer with visualization, gene fusion-finding, and copy number analysis
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I just uploaded a video on bioinformatics project ideas to the OMGenomics channel!
(And it only took me a year since starting this thread 😅)
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Well this has never happened to me before. The women's restroom is empty while the men's has a line out the door. It's a tech conference...
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Our new Circa desktop software lets you make circos plots without writing a single line of code!
#ASMicrobe
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Watch me make this circos plot in 45 seconds with an awesome soundtrack :)
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How to make heatmaps in R using the ComplexHeatmaps package:
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If I made an OMGenomics podcast where I interviewed people in biotech, what would you want to hear about?
Career stories
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Startup stories
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Industry news
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Answering questions
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"After we've put all this effort into building one assembly for a species, shouldn't the next one be easier?" --
@mike_schatz
advocating for a resurgence of reference-guided genome assembly in a great talk today at
#PAGXXVI
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A Circa user had a question, so I got carried away and made a whole video to answer them: "Circa for RNAseq: Differential expression circos plot"
That was pretty fun actually, I should make more little technical videos like this.
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Learn R in bite-sized pieces with the free Quick Wins in R series. Get the cheat sheet and follow along at
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Just uploaded a new OMGenomics video, a Q&A episode answering 5 questions from the YouTube comments... with a special guest 😆
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Wow, Circa is already getting citations! Just found this one from Nature Scientific Reports:
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🎉DeepConsensus v0.3 is now released! 🎉 Amazing to work with such a great team!
Release of DeepConsensus v0.3. ~5x faster than v0.2. Improved accuracy (yield of Q30 reads on a 24kb dataset increased to +49% relative to pbccs vs. +41% with v0.2).
()
Amazing tech lead job by
@marianattestad
, with
@pichuan
as Eng manager.
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Excited to release a new OMGenomics podcast where we interview
@kajawasik
and dive deep into one of her companies, Variant Bio, whose goal is to develop new therapeutics by studying the genetics of populations with exceptional traits.
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New episode of the OMGenomics podcast just dropped! 🥳
This time with video and a guest: our friend Steve Osazuwa!
We answer the eternal "should I do a PhD?" question and hear what Steve's barber thinks.
(Also find it wherever you listen to podcasts)
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Need to see large structural variants and copy number changes?
Check out this video demo of SplitThreader:
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New video from OMGenomics: The powers of ggplot demonstrated with the Automagical R Plotting script
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CSHL WSBS alumni at
#AGBT18
@CSHL
@wsbsbot
@RobAboukhalil
, Colin Malone,
@kajawasik
,
@erlichya
, and
@marianattestad
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New course: Conquering Data Analysis in R -- only covers the 10% of R skills I learned that I use 90% of the time
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.
@infoecho
@mike_schatz
My first public talk on Ribbon is now on youtube: thanks
@Magdoll
for filming and editing!
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New video on OMGenomics channel:
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The long-awaited SK-BR-3 paper is up on the BioRxiv! This is the monster of a project that inspired Ribbon, SplitThreader, Assemblytics,...
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This week on OMGenomics: Building a minimum viable product for bioinformatics software
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Fun side effect of doing data visualization in my normal work is that I wasn't satisfied with Mint's charts for analyzing my spending habits. So I did it myself in python and made a video about it:
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Check out this quick new video tour we made of visualization tools available right now on
@dnanexus
: Special shout-outs to from
@RobAboukhalil
and from
@ChaseAllnMiller
and
@MarthGabor
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I got to pre-test this and it’s quite fun! If you’ve been meaning to try Rosalind’s exercises, this is a very easy entry point!
🚀 New on : solve Rosalind coding challenges with an IDE and a Python interpreter, directly in your browser!
Check it out:
First 10 exercises are up, more to come! cc
@PhillipCompeau
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.
@RobAboukhalil
and I posing in front of the new
@PacBio
Sequel
#agbt17
(is that you on the right
@mike_schatz
?!)
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Just released the 3rd episode of Quick Wins in R: Linear Regression, including showing fit line on a scatter plot
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To all the people furiously taking pictures of Mike's awesome slides yesterday, (including one with an iPad!) here you go :)
#PAGXXVI
Slides from my talk yesterday: Reference-quality diploid genomes without de novo assembly:
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New from OMGenomics: A practical guide to getting started with bioinformatics.
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What is a perfect genome assembly? Great talk from "measurement geek"
@mike_schatz
at
#JIMB
World Metrology Day Symposium today at
@Stanford
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I wonder if people called Antonie van Leeuwenhoek a "microscopy biologist", just like we are called computational biologists.
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Where has this been all my life?!?
TIL: For saner
#javascript
debugging, you can output an array of objects as a table using console.table() instead of console.log()
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Finally made another video for OMGenomics: How to land your dream job! :D
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We just released episode 3 of the OMGenomics podcast: "Job hopping".
Inspired by opinions seen on Twitter, we discuss whether people should stay much more than 1 year per company to avoid being judged by future employers as a job-hopper.
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