Jonathan Foox

148 posts

Jonathan Foox

@jfoox

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

New York City Katılım Haziran 2012

0 Takip Edilen188 Takipçiler

Jonathan Foox retweetledi

Chris Mason@mason_lab·10 Eyl

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! rdcu.be/cxs38.

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Jonathan Foox@jfoox·19 Mar

@mason_lab Quantify methyltransferase activity with METTLica

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Chris Mason@mason_lab·19 Mar

This is superb - Megadepth! What other algorithms are like 1980s heavy metal bands?!? Like Bam Sabbath?academic.oup.com/bioinformatics…

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Jonathan Foox retweetledi

Chris Mason@mason_lab·10 Mar

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" biorxiv.org/content/10.110… with @ElementoLab @skimomiks @nanostringtech @illumina and many great scientists from @nygenome

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Jonathan Foox retweetledi

Sagi Shapira@ShapiraLab·3 Ağu

Finally out! Super happy and so grateful for everyone involved -- with a very special thank you to @nicktatonetti and @mason_lab! nature.com/articles/s4159… @ColumbiaMed @ColumbiaScience @Columbia #covid #riskfactors #genomics #virology #complement #coagulation #Immunology

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Jonathan Foox retweetledi

Chris Mason@mason_lab·25 Tem

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! biorxiv.org/content/10.110…

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Jonathan Foox retweetledi

Chris Mason@mason_lab·2 Haz

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

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Jonathan Foox@jfoox·23 Nis

@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

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Jonathan Foox retweetledi

Chris Mason@mason_lab·22 Nis

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. biorxiv.org/content/10.110… Some highlights: /1

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Jonathan Foox@jfoox·7 Mar

This is especially interesting after just a few years ago discovering (in a different species) eight large, circular, largely non-coding mitochondrial chromosomes: academic.oup.com/mbe/article/34… maybe just the tip of the iceberg for myxozoan mitochondrial evolution?

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Jonathan Foox@jfoox·7 Mar

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! nyti.ms/2Ptl9TO

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Jonathan Foox retweetledi

PacBio@PacBio·4 Mar

“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. ow.ly/BKQz50yCOJQ

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Jonathan Foox@jfoox·4 Mar

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: simpsonlab.github.io/2020/03/03/nan….

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Jonathan Foox retweetledi

Chris Mason@mason_lab·1 Mar

@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

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Jonathan Foox retweetledi

Chris Mason@mason_lab·1 Mar

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

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Jonathan Foox@jfoox·2 Mar

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 ;-)

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Jonathan Foox@jfoox·2 Mar

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 dropbox.com/s/uqnohf3auz31…

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Jonathan Foox@jfoox·26 Şub

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

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Jonathan Foox@jfoox·26 Şub

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 dropbox.com/s/7xrnuw67ew6o…

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Jonathan Foox retweetledi

Chris Mason@mason_lab·24 Şub

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

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Jonathan Foox@jfoox·25 Şub

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

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Keşfet

@NatureBiotech @MyABRF @stighe99 @sedlazeck @Genomics_Guy @genomicslab @US_FDA @mason_lab