Computational biologist in the @mason_lab at Weill Cornell Medicine. Long reads, epigenetics, and evolution.
Joined June 2012
- Tweets 148
- Following 0
- Followers 188
- Likes 119
15 Photos and videos
Jonathan Foox retweeted
9 Sep 2021
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 retweeted
10 Mar 2021
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/10.1101/… with @ElementoLab @skimomiks @nanostringtech @illumina and many great scientists from @nygenome
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Jonathan Foox retweeted
3 Aug 2020
Finally out! Super happy and so grateful for everyone involved -- with a very special thank you to @nicktatonetti and @mason_lab!
nature.com/articles/s41591-0…
@ColumbiaMed @ColumbiaScience @Columbia
#covid #riskfactors #genomics #virology #complement #coagulation #Immunology
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Jonathan Foox retweeted
24 Jul 2020
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/10.1101/…
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Jonathan Foox retweeted
2 Jun 2020
Our new paper with @OdedRechavi came out today in @CellCellPress! "Illuminating Genetic Mysteries of the Dead Sea Scrolls" cell.com/cell/fulltext/S0092…. 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 retweeted
22 Apr 2020
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/10.1101/… Some highlights: /1
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6 Mar 2020
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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6 Mar 2020
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… maybe just the tip of the iceberg for myxozoan mitochondrial evolution?
“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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4 Mar 2020
A major gamechanger!
3 Mar 2020
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….
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Jonathan Foox retweeted
1 Mar 2020
@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 retweeted
1 Mar 2020
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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1 Mar 2020
Like Neo, I can read the epi-Matrix... thanks @mason_lab for the photos!
1 Mar 2020
@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 ;-)
1 Mar 2020
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/uqnohf3auz31i7…
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26 Feb 2020
Always a pleasure to have Scott Tighe take us on a global journey of extreme environments #AGBT20
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26 Feb 2020
Good days for long reads and epigenetics!
26 Feb 2020
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/7xrnuw67ew6oby…
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Jonathan Foox retweeted
24 Feb 2020
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11 Feb 2020
Excited to share our recent work on characterizing telomeres with long read data! More to come soon...
3 Feb 2020
Excited to post our new @biorxivpreprint! "Haplotype Diversity and Sequence Heterogeneity of Human Telomeres"
biorxiv.org/content/10.1101/… Thanks to data from @GenomeInABottle and GIAB collaborators as well as leadership from @LankyCyril and @jfoox
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18 Dec 2019
Beautiful and flexible R package suite from @guangchuangyu for visualizing phylogenetic trees alongside secondary analyses — yulab-smu.github.io/treedata…
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