@jfoox

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

 New York City
Joined June 2012
  • Tweets148
  • Following0
  • Followers186
15Media
Jonathan Foox retweeted
Chris Mason
@mason_lab9 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.
3
25
5
86
Jonathan Foox retweeted
Chris Mason
@mason_lab10 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

Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies...

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the...

biorxiv.org
1
14
1
59
Jonathan Foox retweeted
Sagi Shapira@ShapiraLab3 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

Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection

Nature Medicine - A combination of clinical and molecular analyses supports an association between disorders of immune complement or coagulation with poor outcome in patients with SARS-CoV-2...

nature.com
2
13
1
23
Jonathan Foox retweeted
Chris Mason
@mason_lab24 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/…

Multi-Platform Assessment of DNA Sequencing Performance using Human and Bacterial Reference Genomes...

Massively parallel DNA sequencing is a critical tool for genomics research and clinical diagnostics. Here, we describe the Association of Biomolecular Resource Facilities (ABRF) Next-Generation...

biorxiv.org
2
23
3
59
Jonathan Foox retweeted
Chris Mason
@mason_lab2 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.
9
28
2
105
Jonathan Foox retweeted
Chris Mason
@mason_lab22 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

Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome...

The pandemic from the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) led to hundreds of thousands of deaths, including >15,000 in New York City (NYC). This pandemic highlighted a...

biorxiv.org
7
93
8
191
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

This Parasite Doesn’t Need Oxygen to Survive (Published 2020)

But that’s not the weirdest thing about this jellyfish cousin that turns up in the muscles of salmon.

nytimes.com
1
1
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?

The Multipartite Mitochondrial Genome of Enteromyxum leei (Myxozoa): Eight Fast-Evolving Megacircles

Abstract. Myxozoans are a large group of poorly characterized cnidarian parasites. To gain further insight into their evolution, we sequenced the mitochond

academic.oup.com
Jonathan Foox retweeted
PacBio
@PacBio4 Mar 2020
“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
6
1
18
A major gamechanger!
Jared Simpson@jaredtsimpson3 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….
2
Jonathan Foox retweeted
Chris Mason
@mason_lab1 Mar 2020
Replying to @mitenjain
@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
1
5
17
Jonathan Foox retweeted
Chris Mason
@mason_lab1 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
5
29
3
103
Like Neo, I can read the epi-Matrix... thanks @mason_lab for the photos!
Chris Mason
@mason_lab1 Mar 2020
Replying to @jfoox
@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 ;-)
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…

ABRF_2020_Foox_NanoporeBaseMod.pdf

Shared with Dropbox

dropbox.com
9
13
Always a pleasure to have Scott Tighe take us on a global journey of extreme environments #AGBT20
1
1
Good days for long reads and epigenetics!
Chris Mason
@mason_lab26 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…

Mason_AGBT_2020.pdf

Shared with Dropbox

dropbox.com
1
Jonathan Foox retweeted
Chris Mason
@mason_lab24 Feb 2020
Replying to @jfoox
@jfoox speaking about @NASA twins study and changes in methylation over time with EM-seq #AGBT20
2
4
.@dcdanko talking about building a global metagenomic atlas and the molecular echos of cities at #AGBT20
3
4
Excited to share our recent work on characterizing telomeres with long read data! More to come soon...
Chris Mason
@mason_lab3 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

Haplotype Diversity and Sequence Heterogeneity of Human Telomeres

Telomeres are regions of repetitive nucleotide sequences capping the ends of eukaryotic chromosomes that protect against deterioration, whose lengths can be correlated with age and disease risk...

biorxiv.org
4
Beautiful and flexible R package suite from @guangchuangyu for visualizing phylogenetic trees alongside secondary analyses — yulab-smu.github.io/treedata…

Preface | Data Integration, Manipulation and Visualization of Phylogenetic Trees

Master ggtree package suite to handle tree with data.

yulab-smu.top
7
8
Load more