Chris Mason
@mason_lab
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Professor of Genomics, Physiology, & Biophysics @WeillCornell Medicine. Co-Founder / COI @BiotiaNYC , @UrsaBio & @Onegevity ( @thornehealth ); Advisor @TempusLabs
New York, NY
Joined February 2010
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Today we're elated to release a set of 30 papers on aerospace medicine and the biology of spaceflight; they are simultaneously featured on the covers of
@CellCellPress
,
@CellReports
, &
@iScience_CP
using photos taken by
@StationCDRKelly
while in space: /1
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Previously unconnected (and even embargoed) neurons have just exploded in my brain when I saw this announcement of a BackStreetBoys World DNA Tour. Are they running gels? Are the red bands the secret size of DNA needed for boy band success? Is it pure enough for library prep?!?
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I'm elated to release four
@metasub
papers today, with new species, data interfaces, & online resources. The first is in
@CellCellPress
, "A global metagenomic map of urban microbiomes and antimicrobial resistance" led by
@dcdanko
@Daniela_Bezdan
" a 🧵 /1
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Impressive data rolling off the new
@PacBio
Onso sequencer, with Q-values staying above 50 for the full length of the read with the SBB chemistry, and starting up at 55 in the beginning! From
@GenomeInABottle
sample HG002:
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Very excited our paper is out & the cover of
@sciencemagazine
! "The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight." Thanks to
@ShuttleCDRKelly
&
@StationCDRKelly
for hundreds of samples & work for
#YearInSpace
Mission
@aaas
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Superb: 200K whole genomes from the
@uk_biobank
, linked to clinical records, that we can start to mine starting on Nov. 17th!
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"Relationship between the ABO Blood Group and the COVID-19 Susceptibility." Group O=protective; Group A=high risk. Thus,
#COVID19
deaths likely higher in Europe (more A), but less so in Asia/India (more B) or Latin Americans (more O). thx
@nevillesanjana
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First run on the new
@illumina
Firefly sequencer looks great! 6M 151x151 PF reads, 1.8GBases, >99.8% accuracy in 16 hours. Santa came with SBS candy in a CMOS wrapper this year.
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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. Some highlights: /1
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Cool photo of the heart of a blue whale. Arteries so large, an adult human can swim through. It beats 8-10 times per minute & can be heard >2 miles away. They feed almost exclusively on krill, shrimp-like invertebrates, 4-6 tons/day. thx
@historycoolkids
; ping
@erichjarvis
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For anyone planning their own COVID-19 GWAS or genome association study, remember that the UK BioBank is already doing 20,000 severely ill and 15,000 moderately ill COVID-19 patients for WGS/phenotype analysis in addition to the >120K WGS and health records data already there.
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Thanks for having me,
@lexfridman
! It was a lot of fun to be on your show.
Here's my conversation with
@mason_lab
, biophysicist at Cornell, studying the effects of space travel on the human body and how humans can survive long-term space travel, colonization of other planets, and one day venturing out beyond our Solar System.
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1K
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Our new
@NatureBiotech
paper is out today! "The therapeutic landscape for cells engineered with chimeric antigen receptors (CARs)," led by
@mjdmackay
w/ Ari Melnick, Gail Roboz, Monica Guzman, & Shixiu Wu: thx to
@worldquant
,
@psscra
,
@LLSusa
, &
@NIH
!
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Our lab was just selected by
@NASA
for a project, "Spatiotemporal Mapping of the Impact of Spaceflight on the Heart and Brain," where we will create extensive spatial omics data on tissues before and after spaceflight. Thx! cc
@issop_space
&
@NASAGeneLab
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Best name for new method: TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing.
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Clairvoyant sewage! Wastewater testing and sequencing can predict COVID cases up to 6 days ahead of reported cases.
@CDCgov
and
@NIH
partnerships ramping up for widespread sewage sequencing, including our recent grant between
@UMiamiHealth
and
@WeillCornell
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Our new
@NatureComms
paper is out! "Single-molecule sequencing detection of N6-methyladenine (& 5mC) in microbial reference materials"
@nanopore
base modification detection w/ neural networks on microbial references materials w/
@Daniela_Bezdan
&
@cychiu98
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Exciting times in omics! In our new
@GenomeBiology
paper, "Spatial omics technologies at multimodal and single cell/subcellular level," we detail the wide range of technologies, including some that can now get down to 50nm resolution, led by
@JIWOONPARK_
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Quite a powerful announcement: "
@SpaceX
is looking for exceptional science and research ideas that will enable life in space and on other planets." The RFP is now open!
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Amazing the difference a year makes in the SARS-CoV-2 global distribution. Of the two major clades from a year ago, one is almost gone (19A) and the other is now a minority (19B), from the latest
@nextstrain
build:
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A 6-year culmination of work from our lab, several
@US_FDA
labs, the
@MyABRF
& many more is out in
@NatureBiotech
, featured on the cover! The five SEQC2 papers highlight NGS Improvements for cancer and sc-omics, + a nice commentary by the FDA commissioner:
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Announcing the "COVIDgenes" data portal: , an open site for all to mine the RNA-seq expression results from our
@WeillCornell
|
@nyphospital
COVID-19 patient data. This site (v1.0) hosts various visualization, statistics, & normalization options including: /1
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Great summary of all the many, many studies that show no link of vaccines and Autism
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"Long-read sequencing in the era of epigenomics and epitranscriptomics," a nice summary of the field with the ever-wonderful
@EvaMariaNovoa
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Looking at the BioBot SARS-CoV-2 numbers from Boston sewage...and it does NOT look good... but the trend clearly shows the viral dynamics across the city. Such measurements should be standard for civil engineering, city planning, and epidemiology! Data:
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A new treatment for COVID-19, based on fermentation technology:
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Exciting hardware from
@nvidia
. You could theoretically convert a single human genome into protein sequences and then screen the entire proteome for natural product and drug binding, modeled across the whole protein-protein interactome, all in about a day:
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Our new
@NEJM
paper "Viral Dynamics of SARS-CoV-2 Variants in Vaccinated & Unvaccinated Persons" saw similar viral load, but faster clearance, in vaccinated vs. unvaccinated NBA players w/
@TempusLabs
(COI)
@NathanGrubaugh
@JosephFauver
@mjdmackay
@jdudley
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Honored to have been chosen by
@NASA
to leverage the microbes of Earth's extreme environments for plant growth in lunar regolith (soil). A superb proposal built by
@BradenTierney
, James Henriksen,
@twofrontiers
, Rob Ferl, Christie Peebles, &
@geochurch
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“Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance.” 635 authors, 58 cities, 3,741 samples, 4,424 microbes, 10,928 novel viral species, 91.4% accuracy for predicting city-of-origin. . Big
@metasub
data release &
@biorxivpreprint
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A friendly reminder to keep your passion for your science going, no matter what they say. See here- Einstein made it!
#hatersgonnahate
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I'm honored and humbled to get the International Space Station (ISS) Research and Development Award for Compelling Results in Human Health in Space - thanks
@ISS_CASIS
@ISS_Research
#ISSSRDC
! It's a labor of love :-)
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Our new
@NatureComms
paper is out! "Long non-coding RNAs discriminate the stages and gene regulatory states of human humoral immune response." Proud of the work w/ Ari Melnick, Felipe Prosper,
@ElementoLab
, Cem Meydan, Xabier Agirre & many at
@MeyerCancer
@WeillCornell
@CIMA_unav
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Nice: DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP
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We are on the cover of Cell! This was only possible due to amazing collaborators: led by the fun, tenacious, ever-curious
@OdedRechavi
, & Sarit, Moran, Hila, Or, Mattias, Noam,
@dcdanko
,
@jfoox
, Ebrahim
@WeillCornell
@worldquant
@WCM_PhysBio
@TelAvivUni
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Excited for our new paper out today with
@metasub
colleague
@NiranjanTW
in
@NatureMedicine
"Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment." with combined
@nanopore
and
@illumina
reads for mapping.
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I love my lab peeps, part 2. We talked about making a flag to represent the lab, almost in jest, but they came through with quite a candidate:
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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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Elated that our new
@NatureBiotech
paper is out! "Best practices for benchmarking germline small-variant calls in human genomes." Thanks to all
@GenomeInABottle
,
@GA4GH
, and
@usnistgov
scientists and collaborators.
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Our new paper with
@OdedRechavi
came out today in
@CellCellPress
! "Illuminating Genetic Mysteries of the Dead Sea Scrolls" . 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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"NYC Scientists Swab the Subway in Search of SARS-CoV-2." Is it there? So far, nope! Environmental and ongoing clinical
#COVID19
efforts discussed here: thx
@GENbio
@NEBiolabs
@illumina
@TwistBioscience
@nanopore
@nygenome
@metasub
@BenKallos
@ZymoResearch
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Our best
@nanopore
direct RNA sequence yet! 87% sequence identity for Sindbus virus. Also, a pleasure to see "U" in a .fastq file :-)
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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! .
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Our new paper, "Haplotype diversity and sequence heterogeneity of human telomeres," is on the cover of
@genomeresearch
! Congrats to
@LankyCyril
@jfoox
@Daniela_Bezdan
@danjbuts
@cemmeydan
and Susan Bailey's lab for the awesome collaboration. A thread... /1
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Our
@nature
paper with
@LabMelnick
@NevinYusufova
is out! Histone1 KO data shows links to lymphoma, epigenetic reprogramming, & silencing of genes in GC B-cells
@ElementoLab
@skimomiks
@artsinyc
@jdlicht
@GCloner
@David_Lab_MSK
@skimomiks
@efapostolou29
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Our new paper "The COVID-19 XPRIZE and the need for scalable, fast, and widespread testing." A big push for new diagnostic technologies and innovation . Of note, we see a >5 log(base 10) difference in the Limit of Detection (LoD) for current FDA EUA tests!
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Congrats to Dr. Pradeep Ambrose! He successfully Zoom-defended his
@WeillCornell
@WeillCornellGS
&
@RockefellerUniv
Ph.D. thesis (470 pages) on RNA viruses, notably during a Pandemic made by an RNA virus! It was a pleasure to have you in the lab and co-mentor with Charlie Rice!
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We're hiring! Looking for (1) Bioinformaticians & (2) NGS scientists for: microbial therapies, extremophiles' BGCs, aerospace medicine, microbial evolution, T-cell engineering, global emerging pathogen/COVID-19 tracking, & several other projects (send to: chm2042
@med
.cornell.edu)
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The
@NEBiolabs
APOBEC-based enzymatic methylation protocol (EM-seq) is out! We see more even coverage across CpG islands & greater detection of CpG sites vs. WGBS; data coming soon from the
@US_FDA
@nygenome
#SEQC2
#EpiQC
study w/
@GenomeInABottle
samples
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DNBSeq-Tx is the system (robot) making $100 genomes, using 200nm DNBs and 500nm pitch and large-scale efficiencies is scale in reagents. 150 genomes per slide, done in 3.5 days. 20TB/day. Three years in the making.
#AGBT20
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Elated that our lab and
@WeillCornell
is now a National Center of Excellence for wastewater mapping and tracking of viruses, bacteria, and other mysteries that float in the waterways under our cities, also as part of
@metasub
and
@Nanotrap
To celebrate National Public Health Week, we are announcing the establishment of 16 Centers of Excellence providing
#wastewater
#epidemiology
services to 40 states! We thank the
@NIH
&
@NIBIBgov
for the support and
@publichealth
workers for their efforts!
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Lots of new developments in RNA modifications and related work profiled in this nice
@sciencemagazine
Feature "Epitranscriptomics: RNA revisited" … (including our lab & Jaffrey Lab, He Lab,
@TheHornerLab
@EvaMariaNovoa
@martinalexsmith
@ElementoLab
)
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We found a novel link between a microbe and multiple sclerosis (MS). Strains of Clostridium perfringens that make an epsilon toxin were enriched in people with MS, linking a bacterial toxin with a neurological disorder. Featured today on the cover of
@jclinicalinvest
!
#Cover
: Altered gut microbiome in multiple sclerosis:
Ma, Sannino & Linden et al. report that Clostridium perfringens producing epsilon toxin occur in high abundance within the gut microbiome in people with MS.
Image credit:
@GHPMedArt
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New collection device for DNA just came out: spider webs! :-) "Spider webs capture environmental DNA from terrestrial vertebrates"
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I'm elated to share the news that our
@BiotiaNYC
&
@TwistBioscience
SARS-CoV-2 hybrid capture NGS test just got
@US_FDA
emergency use authorization (EUA)! Full viral sequencing & analysis of strains, also w/ data and physician portal (note: Co-Founder). .
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Excited to share our latest paper, "The Case for Biotech on Mars" in
@NatureBiotech
, detailing a long-term plan in four key areas: food production, materials synthesis, medical therapeutics, and matter reclamation; w/
@harvardmed
@Ginkgo
@wyssinstitute
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"This your last chance. You take the blue tardigrade, the story ends. You publish, and you eventually forget grad school ever happened. You take the red panda, and I show you how deep the freezer really goes."
Hilarious AI art from
@cemmeydan
. Love my lab!
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There are currently 136 genes with pharmacogenomics guidance from the
@US_FDA
, and more coming! It's not just a cytochrome P450 2D6 world...many more:
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The debate is over: WGS is better for clinical diagnostics than WES.
#ABRF2017
with
@genomicslab
on
@illumina
XTen machines at 40X coverage
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I love my lab part
#3
: they re-named the -20C freezers as female scientists/leaders/aerospace pioneers: (1) Rosalind Franklin (chemist, DNA), Katherine Johnson (mathematician, hidden figure!), Mae Jemison (astronaut, engineer), and Marie Curie (physicist).
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Chloroplasts possible in human cells?! This paper, "A plant-derived natural photosynthetic system for improving cell anabolism," shows the "feasibility and applicability of cross-species transplantation of a plant-derived natural photosynthetic system"
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real-time
@illumina
data with LiveKraken "a real-time read classification tool based on Kraken. It uses streams of raw data from Illumina sequencers to classify reads taxonomically...results comparable to those of Kraken the moment the sequencer finishes."
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Elated to share our latest paper, "System-wide transcriptome damage and tissue identity loss in COVID-19 patients," led by
@JIWOONPARK_
@jfoox
in our lab &
@RobSchwartzLab
@RiceLaboratory
@cemmeydan
@RockefellerUniv
@WCMCPathology
@nygenome
🧵 /1
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ChromBPnet model is a dream for all those with ATAC-seq data who want to remove bias and noise from Tn5 transposases
@anshulkundaje
#AGBT24
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"I don't think that any child should die of a disease when we have a technology to make it better." Amen. WGS for the win!
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"Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions" Our paper is out! RNA-seq, LAMP, HLA, viral capture, EMRs, spatial in
@NatureComms
; a 🧵 /1
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@Rainmaker1973
It is not. Rather, it is much like most surfaces you touch. And, it is a bounty of new genetic information! See here: and and
and here
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I am elated to serve on the Steering Committee for
@theNASciences
' &
@NASA
Decadal Survey on Biological and Physical Sciences Research in Space (2023-2032), where we will craft a vision for science at the frontiers of research in space - input is welcome!
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Great paper showing 30% lower adverse drug reactions using pharmacogenomics: “A 12-gene pharmacogenetic panel to prevent adverse drug reactions: an open-label, multicentre, controlled, cluster-randomised crossover implementation study.”
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Excited to be chosen with
@DrDuaneHassane
for a
@NASA
Award today! "NASA Selects 21 Proposals to Support Crew Health and Performance in Astronauts on Missions to the Moon and Mars"
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The cost of launching astronauts and materials to space is continuing to precipitously drop: thanks
@SpaceX
!
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Karen Miga from
@UCSC
showing how to get 11 reference-quality genomes in 9 days on
@nanopore
PromethION, using
@circulomics
short read eliminator kit to get N50 at 44kb for reads
#AGBT19
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Our new
@NatureComms
paper with
@IwijnDeVlaminck
@john__r__lee
and others is out! "A metagenomic DNA sequencing assay that is robust against environmental DNA contamination"
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Cool combo method: Spatial Transcriptomics-correlated Electron Microscopy maps transcriptional and ultrastructural responses to brain injury
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Wastewater is becoming the new "liquid biopsy" of cities! Some of our work profiled here in the
@nytimes
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“By 2023 there will be more single cells sequenced than people on Earth”
@10xgenomics
session at
#AGBT18
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@10xgenomics
has 3 new products: single cell ATAC-seq, single cell CNV mapping for clonal evolution, and myriad single cell feature barcodes
#AGBT18
AND an updated platform for Cell-Beads Gel-Beads (CBGBs), works on current Chromium, w/ protein digestion & alkaline denaturation.
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All COVID-19 data stored at EMBL-EBI are being aggregated into a dedicated page on the Pathogen Portal. By April, a first version of the COVID-19 Portal will be live:
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Our new paper is out! "Sequencing of Circulating Microbial Cell-Free DNA Can Identify Pathogens in Periprosthetic Joint Infections." with amazing work from from
@Donlinlab
,
@dcdanko
and many great colleagues at
@HSpecialSurgery
@WeillCornell
&
@KariusInc
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@JMRothberg
@Dr_Alex_Crimi
Indeed LAMP works! Using
@TwistBioscience
controls and
@NEBiolabs
reagents with some clinical samples too - we see sensitivity range down to 10-100 viral copies. More coming soon...paper in review.
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Nice QC stats on the brand new
@illumina
iSeq100 (we still like to call it Firefly in the lab), as described on
@OmicsOmicsBlog
here . Base composition and Q-values good to >150nt (attached) at
#JPM18
. More data coming soon
@agbt
#AGBT18
.
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We are out swabbing NYC today, along with researchers in 60 other cities as part of global city sampling day (gCSD) 2021
#gCSD21
! Here with
@asierra93
@BenYoung13
@krista_ryon
and so far we are at 810 samples in <24h
@metasub
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