Jonathan Foox

Computational biologist in the @mason_lab at Weill Cornell Medicine. Long reads, epigenetics, and evolution.

[Chris Mason @mason_lab]

Elated to release our new @NatureBiotech paper, "Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study" led by @jfoox & @MyABRF, @stighe99 @sedlazeck, Don Baldwin, @Genomics_Guy, @genomicslab & @US_FDA's SEQC2! https://t.co/sYP5ZXNNtH.

[Jonathan Foox @jfoox]

@mason_lab Quantify methyltransferase activity with METTLica

[Chris Mason @mason_lab]

Our new preprint is out! "Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps" https://t.co/KcPkiJQuX9 with @ElementoLab @skimomiks @nanostringtech @illumina and many great scientists from @nygenome

[Sagi Shapira @ShapiraLab]

Finally out! Super happy and so grateful for everyone involved -- with a very special thank you to @nicktatonetti and @mason_lab!

https://t.co/NwOmwcwBCy

@ColumbiaMed @ColumbiaScience @Columbia
#covid #riskfactors #genomics #virology #complement #coagulation #Immunology

[Chris Mason @mason_lab]

Our @biorxivpreprint "Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes" w/ human @GenomeInABottle & @MyABRF @officialatcc samples on @illumina @nanopore @MGI_BGI @GenapSys @PacBio @thermofisher platforms! https://t.co/dCN4brESGN

[Chris Mason @mason_lab]

Our new paper with @OdedRechavi came out today in @CellCellPress! "Illuminating Genetic Mysteries of the Dead Sea Scrolls" https://t.co/hu7DqFgMlK. 7 years in the making with tireless work from Oded to get it right; sets a precedent for genetically-driven artifact reconstruction.

[Jonathan Foox @jfoox]

@NYCuratrix @DrShaena @RGGSatAMNH @sebastian_kvist @SnorriSigur @DrScanley @pedro_peloso @SpencerGalen @KellySpeer @bernardo_santos I'm bad at Twitter and just saw this. Can this still happen sometime? I've got my McAleer's virtual background all ready to go

[Chris Mason @mason_lab]

Our new @biorxivpreprint is up! "Host, Viral, and Environmental Transcriptome Profiles of SARS-CoV-2." COVID-19 patients (n=338) examined w/ qRT-PCR, RT-LAMP, & total RNA-seq, host responses (e.g. ACE2) & new diagnostic methods. https://t.co/lsPfzh8cOq Some highlights: /1

[Jonathan Foox @jfoox]

This is especially interesting after just a few years ago discovering (in a different species) eight large, circular, largely non-coding mitochondrial chromosomes: https://t.co/AHb7Ezh0KG maybe just the tip of the iceberg for myxozoan mitochondrial evolution?

[Jonathan Foox @jfoox]

Amazing new work from the Huchon lab showing evolutionary loss of mitochondria in a myxozoan species -- in other words, an animal that doesn't need oxygen to survive. Featured in the NYT! https://t.co/TdgbXj3ZKl

[PacBio @PacBio]

“We find that long telomeric stretches can be accurately captured with long-read sequencing.” Learn how @LankyCyril @jfoox @mason_lab & co were able to discover novel & known non-canonical motifs w/ new edgeCase framework & @GenomeInABottle seq data. https://t.co/cep5XKPzW9

[Jonathan Foox @jfoox]

A major gamechanger!

[Jared Simpson @jaredtsimpson]

Nanopolish v0.12 supports live methylation calling, while the sequencer is running. An update worthy of dusting off the old blog for: https://t.co/8ETJlj5OUX.

[Chris Mason @mason_lab]

@mitenjain showing the fast Shasta pipeline for fast human genome assembly, with N50 results in the 20-30Mb, a low error rate (~1%), and reasonable cost ($70) for an @awscloud assembly and MarginPolish and Helen polishing to remove homopolymers #ABRF2020

[Chris Mason @mason_lab]

A 2.44 Mb human read- the longest sequenced DNA molecule to date! @circulomics Kevin Liu shows updates to the @mattloose, @pathogenomenick, and @Scalene long-read protocol, w/ more >1Mb reads (whales) & even “pods of whales” on @nanopore, also helped by a nuclease flush #ABRF2020

[Jonathan Foox @jfoox]

Like Neo, I can read the epi-Matrix... thanks @mason_lab for the photos!

[Chris Mason @mason_lab]

@jfoox rocking an Epigenomics talk and covering all the @nanopore methods and applications. He noted that the hotel art at #ABRF2020 looks at lot like squiggle plots of Pico-amp current data ;-)

[Jonathan Foox @jfoox]

Sharing slides from my #ABRF2020 talk on detecting base modifications in @nanopore data – with a special shout out to all the fish-based software names! Thanks to @mitenjain @stoibs11 and the many awesome members of the ONT informatics community https://t.co/0kRN2y9a9H

[Jonathan Foox @jfoox]

Always a pleasure to have Scott Tighe take us on a global journey of extreme environments #AGBT20

[Jonathan Foox @jfoox]

Good days for long reads and epigenetics!

[Chris Mason @mason_lab]

Slides from my #AGBT20 talk, "Diplotype-resolved, single-molecule telomere sequencing reveals elongation during spaceflight and non-canonical repeats" featuring work w @jfoox @LankyCyril @Daniela_Bezdan @dcdanko @danjbuts @mjdmackay @NEBiolabs #YearinSpace https://t.co/MmCipeB04E

[Chris Mason @mason_lab]

@jfoox speaking about @NASA twins study and changes in methylation over time with EM-seq #AGBT20

[Jonathan Foox @jfoox]

.@dcdanko talking about building a global metagenomic atlas and the molecular echos of cities at #AGBT20