@nsmarkov

Doing analysis of (sc)RNA-seq and more in pulmonary diseases at @NM_lung. Infrastructure, visualisation, photography, beginner jazz piano

 Chicago
Joined August 2012
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  • Following188
  • Followers142
9Media
Happy to share our work examining lung T cell responses during severe pneumonia—including #COVID19: nature.com/articles/s41590-0…. Huge lift 💪 from The NU SCRIPT Investigators @NM_Lung @NUFeinbergMed. Kudos to @nsmarkov @Ziyou2015 & Karolina Senkow 🧵
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Both major medical journals agree: this decision will kill women. – at Burlington, VT
NEJM
@NEJM24 Jun 2022
The just-announced U.S. Supreme Court decision in Dobbs v. Jackson Women’s Health Organization represents a stunning reversal of precedent that inserts government into the personal lives and health care of Americans. nej.md/3Aa5cKe
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I share same concerns: “truth” won't be enough to make people not act upon lies/misinformation (also because there are no facts). Good to see someone proposing other approaches
Carl Miller@carljackmiller18 Jun 2022
I've heard a lot of people in events and things over the past few weeks calling for a 'western information warfare'. Whilst I understand the sentiment (and the frustration) there are two big, linked reasons why it wouldn't ever work. 1. You don't fight the kind of illicit...
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Я лингвистка и мне надоели мифы,которые используются в пропаганде. Тред с аргументами,вдруг пригодится Структура 1. «рус,укр и бел – диалекты одного языка»(нет) 2. «сограждане на основании языка» (нет) 3. «защита рус языка»(нет) 4. «Зеленский притворяется,что забыл рус»(нет)
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Key takeaway for me: spike of new accounts and account activity since Russia's invasion in Ukraine, apparently correlated with the messages (hard to actually see in the thread). Why important? “The world” is not just US&Europe&China&Japan. Talking with all others is important.
Carl Miller@carljackmiller18 Mar 2022
When we say Kyiv is winning the information war, far too often we only mean information spaces we inhabit. Pulling apart the most obvious RU info op to date (as we did using semantic modelling), very clear it is targeting BRICS, Africa, Asia. Not the West really at all.
I'm Belarusian. Seeing more and more hate against Belarusians as a result of Lukashenko's participation in Putin's atrocious war against Ukraine, I have a few things to say.
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Just in case you want to check daily radiation levels in Europe, visit remap.jrc.ec.europa.eu/Advan…
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Thank you very much for voicing this position, Yann. This is totally true: most talented, educated researchers and students in Russia are appalled by Russian invasion of Ukraine and all other putin's decisions. There are many of them & Russia is facing a humanitarian crisis 1/
Yann LeCun
@ylecun27 Feb 2022
Give a research position to any Russian scientist who wants out, starting with the signatories of this letter: trv-science.ru/2022/02/we-ar… And give a work visa to any Russian tech worker who wants out.
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I am one of those people (omit talented), but I immigrated ~4y ago. I fully support Ukraine and condemn Russian invasion, and many other foul decisions of the Russian government. Yet the outlines of the crisis for that part of russians who do not support the regime are there 2/
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And same goes for Belarus and belarusians. My friend put a lot more about the same into her text, but it is on facebook: facebook.com/sanya.pushkar.3… Please, check it out if you want to know more
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If you work w/ single-cell RNA-seq & are performing RNA velocity analyses, you might find this @GorinGennady et al. preprint w/ Meichen Fang & Tara Chari of interest. It's a deep dive into the method, and navigation of the 67 pages may be aided w/ this🧵1/ biorxiv.org/content/10.1101/…

RNA velocity unraveled

We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a...

biorxiv.org
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More fun publisher surveillance: Elsevier embeds a hash in the PDF metadata that is *unique for each time a PDF is downloaded*, this is a diff between metadata from two of the same paper. Combined with access timestamps, they can uniquely identify the source of any shared PDFs.
[A list of metadata for a PDF, the important field being two "Unknown:<long random character string>" fields that are color coded to indicate that they have been changed between versions.

ALT [A list of metadata for a PDF, the important field being two "Unknown:<long random character string>" fields that are color coded to indicate that they have been changed between versions.

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Our review about zeroes in scRNA-seq data: clarify statistical and biological concepts; introduce 5 mechanisms of adding non-biological zeros for fair method benchmarking; compare 3 input data types: observed, imputed, and binarized counts: tinyurl.com/2p8rtfvd @GenomeBiology
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Someone at @UVALibrary deserves a gold star for this amazing quiz about costs of the Big Four publishing contracts. You have got to see this. “What costs more?” virginia.libwizard.com/f/wha… #OpenAccess #Publishing #BigFour
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I am proud of the work of our team on the flight of the smallest beetles, published in the third issue of @Nature this year. nature.com/articles/s41586-0… 1/9
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Finished reading Authority and american usage last night. It's been a while since I got so much intellectual pleasure and sense of insight from a text. I think it has a lot of valid criticism of academic writing, along with ideas on how to do better, and I hope to follow them.
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📣#NeurIPS2021📄 Why are we still debugging neural nets by staring at loss curves? We present Cockpit, a visual debugger for deep learning. Joint work with @f_dangel & @PhilippHennig5 Paper: arxiv.org/abs/2102.06604 Code: github.com/f-dangel/cockpit Video: youtu.be/wQsjgx3zfkQ 🧵
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Fitting a figure into 400px wide is probably an academic way of doing icon design
Yesterday I came across a moving documentary by @eliehonig on the trial of Adolph Eichmann. This year marks 60 years since it commenced on April 11, 1961. The documentary brought back memories of my visit to La Cumbre near Córdoba, Argentina in 2005.. 1/ xitter.cf/eliehonig/status/14487…
Elie Honig
@eliehonig14 Oct 2021
My first documentary for @cnn, as just aired on @camanpour show. Looking back at the 1961 trial of the Nazi Adolph Eichmann, and the lessons that resonate today. cnn.com/2021/10/14/opinions/…
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Just another reminder about reproducibility: when your paper has a figure such as attached, and then you write in “code availability” that the “paper does not report original code”—this is not true. Parameter choices, outlier filtering, package versions etc are all important
Michael Hoffman @michaelhoffman.bsky.social@michaelhoffman24 Sep 2021
1/Reproducibility standards for machine learning in the life sciences proposed by @autobencoder, me, @markowetzlab, @suinleelab, @GreeneScientist, @stephaniehicks in @naturemethods. nature.com/articles/s41592-0…

Reproducibility standards for machine learning in the life sciences

Nature Methods - To make machine-learning analyses in the life sciences more computationally reproducible, we propose standards based on data, model and code publication, programming best practices...

nature.com
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