Nicolas Robine
@notSoJunkDNA
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Director, Computational Biology. [nrobine] @nygenome [.org] RNA-Seq / Cancer Genomics / anything NYC / mostly in English, sometimes in French.
New York City
Joined January 2010
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Pinned Tweet
Somewhere between Oxford and the Pacific,
We work to Illuminate the Singular and Ultimate Elements of Life
#DNADay
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Extreme trolling is citing a
@biorxivpreprint
manuscript by using a
@Sci_Hub
URL (in a paper from the Nature Publishing Group) 😂😂😂
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Watch a single cell become a complete organism in six pulsing minutes of timelapse
(via
@RafaelSchulman
)
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🇫🇷I don’t want to be vaccinated
🧑⚕️A Gentleman would do it.
🇫🇷No
🧑⚕️It’s an order.
🇫🇷 No
🧑⚕️Your neighbor did it.
🇫🇷I don’t care
🧑⚕️Damn, who are you exactly?
🇫🇷I am French
🧑⚕️Ah well you can’t have it, you're not eligible.
🇫🇷WHAT DO YOU MEAN I CAN’T HAVE IT? GIVE IT TO ME RIGHT NOW!
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A doctor is vaccinating 4 people: 🇬🇧,🇩🇪,🇺🇸,🇫🇷
🇬🇧I don’t want to be vaccinated
🧑⚕️A Gentleman would do it.
🇬🇧OK, fine
🇩🇪I don’t want to be vaccinated
🧑⚕️It’s an order
🇩🇪OK, fine
🇺🇸I don’t want to be vaccinated
🧑⚕️Your neighbor did it.
🇺🇸OK, fine
🧑⚕️Now, last one
1/2
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"tSNE is better"
"No way. UMAP rules"
...
OK, kids, you know what: we'll put both. Happy?
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French prime minister associating Charpentier's Nobel Prize to the "excellence and attractivity of France's research sector". For the record, she left after her PhD and never came back...
Sincères et chaleureuses félicitations à Emmanuelle Charpentier.
Pour ce prix Nobel, pour les travaux révolutionnaires qu’elle a conduits avec Jennifer Doudna mais aussi pour la recherche française dont on consacre, à nouveau, l’excellence et l’attractivité internationale.
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Multi-omic measurements of heterogeneity in HeLa cells across laboratories
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Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics
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Apparently, "80% of the cost [for RNASeq] is for sequencing, and the rest for library preparation”. And of course people work for free, analysis is free, no overhead. Welcome to Dreamland.
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Genome-wide analysis of somatic noncoding mutation patterns in cancer
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Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution
@macosko
lab
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Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells
, by the
@nygenome
colleagues:
@NYGCtech
@satijalab
@nevillesanjana
and
@psmibert
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Tumor mutational load predicts survival after immunotherapy across multiple cancer types
By
@sloan_kettering
team
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[fr] c'est quand meme fou la carrière de Michel Blanc. Il commence acteur avec les Bronzés, devient astronaute et vient d'etre élu Sénateur de l'Arizona
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On the left is an American Robin. On the right is an American ROBINE!
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I don’t really care about “computational biologist” vs “bioinformatician”, call us whatever you want.
Just avoid "bioinformaticist"
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Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms
The figures and movies are just awesome...
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Immunogenic neoantigens derived from gene fusions stimulate T cell responses
, by
@sloan_kettering
and
@nygenome
. Glad to have contributed!
@GeneCollector
@xrtGenomics
and Luc Morris (not on Twitter?)
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30X WGS of the 2504 Phase 3 1000 Genome samples, sequenced by
@nygenome
, accessible at
@SFGravel
@LukeAnderTroc
@adamauton
@HennLab
@rdhernand
@ribozyme
@erikgarrison
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If I ever get the chance to name a new gene (won’t happen, don’t worry), I will call it Feb30. Just to see how it messes up Excel automated gene->date conversion
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"Quantitative single-cell transcriptomics” review in Briefings in Functional Genomics
Thank you so much for Figure 3. Super useful!
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Tired of the “landscape” papers in genomics? Here comes the portraits!
#pcawg
Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types
#biorxiv_cancer
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Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements
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.
@genetics_blog
in defense of Celsius: "0C: water freezes. 100C: water boils" (at sea level). Fahrenheit: well, why bother with logic?
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That’s BS. We all know music taste (or lack thereof) is epigenetic.
Ancestry is teaming up with Spotify to create playlists based on their user's DNA
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1K
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"New York’s
@polyethnic1000
: a regional initiative to understand how diverse ancestries influence the risk, progression, and treatment of cancers”
@nygenome
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Limited evolution of the actionable metastatic cancer genome under therapeutic pressure
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A very good explanation on why ERCC spike-ins are not useful for RNA-Seq. By Simon Anders.
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One side comment: most of the time, people tweet their move to industry, and stop tweeting right after.
Are they too busy to tweet, too happy to tweet, or too constrained to tweet the way they did when they were in academia?
Would the last academic in human genomics please remember to turn out the lights as they leave?
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Breast tumor microenvironment structures are associated with genomic features and clinical outcome
@NatureGenet
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When COVID’s over and the BioNTech/Moderna vaccination campaign are complete, will we have too many -80C freezers? Can we then get rid of FFPE and start to flash-freeze every biopsied tumors?
Pretty please?
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I highly recommend “Gene Machine” by Venki Ramakrishnan. I picked it up because I had 1/2h to kill at the bookstore this weekend and got hooked! Really great book!
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RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues.
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That dude just re-invented the CRAM format...
@antonioregalado
@aparanjape
@Rainmaker1973
That’s a good point. One could simply have a few reference human genomes and simply code each individual with a lossless compression delta!
Could probably fit the DNA sequences of all humans alive today in a fairly small data storage system.
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May not be the biggest news of the day in genomics, but it’s actually a big deal (at least for us!)
@nygenome
was granted approval by
@HealthNYGov
to perform whole genome and transcriptome sequencing for oncology. For more details, check out our paper published in
@JMDiagn
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First day in office since March. Exciting and a bit emotional!
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We're often complimented for the
@nygenome
logo, but I once met a guy in the street with this TShirt. He found the logo online, printed it at home and had never heard of the New York Genome Center. Should we start a clothing business on the side?
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10 years ago, under a beautiful sun, I walked into a small office on 57th and Broadway. It was my first day at
@nygenome
.
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Using DNA sequencing data to quantify T cell fraction and therapy response
@CharlesSwanton
@NickyMcGranahan
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"BORIS is overexpressed in several cancers”.
UK friends, this one is for you.
(BORIS stands for "brother of the regulator of imprinted sites")
BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells
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My Friday afternoon contribution to the Genetics/Epigenetics debate
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Genomics of the origin and evolution of Citrus
No “lemon-shaped” Venn diagram, but a surprising picture of “citrons” (which is the word we use in French for lemon)
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Next time you see “change in 7% of DNA”, remember that the most heavily mutated tumors have about 0.1% of the genome mutated (~1000/Mb). Also human and macaque are 93% identical...
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Single-cell genomics identifies cell type–specific molecular changes in autism
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Accurate genotyping across variant classes and lengths using variant graphs
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Flood in Paris: the French Lady Liberty looks a bit more like the NYC one.
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Today is special: 10 years ago, we arrived in the US, with a 4 month old baby and a postdoc position at
@sloan_kettering
. It’s been a great ride, and we’re thankful for everything this city and this country brought us.
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Predicting cancer outcomes from histology and genomics using convolutional networks
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Staff scientists of the world: unite!
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Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
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Manuscript received at 10:42AM, review submitted at 3:16PM. The main reason: I had read the
#preprint
before!
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My favorite Sunday morning activity is to harmonize RNA-seq/RNA-Seq/RNAseq/RNASeq/RNA Seq/RNA seq across 4 documents…
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Evaluation of 2 main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion
"in most cases we strongly recommend polyA+ selection over rRNA depletion for gene quantification in clinical RNA sequencing"
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Now that our paper in
@SciReports
is out, I want to show you all the instructions every author receive before publication.
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#CovidParents
: download “Color with
@CellCellPress
” and start with the virus 🦠 (it’s not
#OpenAccess
but the only price is your email address)
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I can’t wait to see the correlation between the coronavirus map and the kissing map in France
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@DrSidMukherjee
Liquid Biopsy (and mention of clonal hematopoiesis, and general "somatic mutations in normal tissues”)
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Predicting Splicing from Primary Sequence with Deep Learning
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Super happy to announce that
@cziscience
funded our Ancestry Networks project "Multi-omics Maps of the Human Endometrium Across Diverse Ancestries”, with
@GlobalRadOnc
@beyazlab
@NorthwellHealth
@CSHL
@nygenome
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I’m a little surprised that so few of the
#PCAWG
press coverage mention that the papers have been on
@biorxivpreprint
for 2+ years. The data, tools and main conclusions were already out and integrated in the community’s knowledge base
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That day when I had lunch with a future Nobel Prize winner at
@nygenome
(with
@psmibert
@anchetov
@with_stephenson
). Congrats
@doudna_lab
!
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In a moment of weakness, I volunteered to present "What is genomics?" for Bring your kids your work, in 3 weeks. Who has pointers and materials on that, for 7-15 yo kids?
PLEASE HELP!!!😂😂😂
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High-throughput single-nucleus hybrid sequencing reveals genome-transcriptome correlations in cancer
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Elizabeth Holmes
Who should be the next NIH Director? Wrong answers only. (I'll start: Dr. Oz)
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Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics
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Or how a marginal improvement on variant calling algorithms becomes an "AI tool to make sense of your genome”.
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The landscape of genomic alterations across childhood cancers
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Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer
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Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
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I think I can now start to look at the procedure to become a US Citizen....
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"Universal Alternative Splicing Of Noncoding Exons". Deveson, Brunck et al.
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Just received the abstracts for the upcoming cross-county Science Fair and I am so pleased to see many HIGH SCHOOL students using TCGA datasets (and other large-scale publicly accessible genomics datasets). It’s amazing
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Determining cell type abundance and expression from bulk tissues with digital cytometry
#CIBERSORTx
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Rna-Seq aligner: "The most widely cited tool underperforms for most metrics, particularly when using default settings”
#DropTheTopHat
Simulation-based comprehensive benchmarking of RNA-seq aligners
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"Many other long-lived mammalian species display cancer resistance, including whales, grey squirrels, microbats, cows and horses"
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