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Posts by Andy Kempchinsky

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The landscape of microbial associations in human cancer Differences between cancer types, infectious disease, and potential prognostic markers are uncovered by studying microbes within cancer DNA.

The landscape of microbial associations in human cancer www.science.org/doi/10.1126/...

TLDR -- most cancers do not have microbiomes...but a few do have consistent microbe associations (i.e., colorectal and oral cancers). Make sense!

7 months ago 64 27 1 3
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New Apple study challenges whether AI models truly “reason” through problems Puzzle-based experiments reveal limitations of simulated reasoning, but others dispute findings.

The results seem to strengthen the case that these systems rely on elaborate pattern-matching rather than the kind of systematic reasoning their marketing might suggest.

10 months ago 204 71 12 14
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PBEEE/Quebec Merit Scholarship for Foreign Postdocs and Visiting Research Student and Visiting Researchers **Note that the FRQ is in the process of revamping their webpages. We will update links soon as we can with the current 2025 year's information. Be sure to check back to see if any eligibility or docu...

Are you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec?

Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together!

www.mcgill.ca/gps/funding/...

10 months ago 50 67 1 4
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A visual–omics foundation model to bridge histopathology with spatial transcriptomics - Nature Methods OmiCLIP is a visual–omics foundation model that integrates histology and spatial transcriptomics. The associated Loki platform offers accurate and robust tools for alignment, annotation, cell-type dec...

Fascinating! Will read the moment Markie stops purring my lap
#caturday
#WorkLifeBalance
www.nature.com/articles/s41...

10 months ago 5 2 0 0
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Trump team pauses new student visa interviews as it weighs expanding social media vetting It’s the latest salvo against universities, many of whom rely heavily on foreign students for funds.

The Republican administration has halted all student (and postdoc etc) VISA interviews.

I've written a lot about soft power here. The attacks on foreign students in the US not only undercuts the funding stream for US universities; they hemorrhage US soft power.

10 months ago 211 59 12 2
Bioengineering needs diversity - Nature Reviews Bioengineering Policies that limit diversity and inclusion undermine evidence-based science by creating gaps in the data, potentially distorting findings and skewing results. When diversity and inclusion are sidelin...

www.nature.com/articles/s44...

11 months ago 0 0 0 0
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Risk of cancer in people with HIV experiencing varying degrees of immune recovery with sustained virological suppression on antiretroviral treatment for more than 2 years: an international, multicentre, observational cohort The impact of long-term virological suppression and CD4 count recovery on non-AIDS defining cancers (NADC) is unclear.

Risk of cancer in people with HIV experiencing varying degrees of immune recovery with sustained virological suppression on antiretroviral treatment for more than 2 years: an international, multicentre, observational cohort

✅ Just Accepted
⭐ Editor's Choice
#IDSky

11 months ago 2 2 0 0
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Emergence of transferable daptomycin resistance in Gram-positive bacteria - npj Antimicrobials and Resistance npj Antimicrobials and Resistance - Emergence of transferable daptomycin resistance in Gram-positive bacteria

This is fascinating, but also terrible news regarding antimicrobial resistance in multidrug-resistant Gram-positives

'Emergence of transferable daptomycin resistance in Gram-positive bacteria'

www.nature.com/articles/s44...

11 months ago 46 18 4 1
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📢 SBMI 2025
Join us at the 8th International Symposium "Systems Biology of Microbial Infection", Sept 18–19, 2025 in Jena

Submit your abstract & consider applying for a Tandem-Talk!

Info & speakers: asb-conference.hki-jena.de

#SystemsBiology #InfectionBiology #BioimageAnalysisTools

1 year ago 20 9 1 0
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CHECK IT OUT 🦠👀

Very cool article by science journalist Carrie Arnold reviewing recent research from leading laboratories on how the unique shape of a microbial #biofilm emerges from interactions of its component microbes with each other and their environment

www.quantamagazine.org/how-a-biofil...

1 year ago 82 20 5 0

Often in English people confused definitely and defiantly, which gives some of their statements a strong rebelliousness.
“I will defiantly finish reading this book today.”

In German I can never remember if it’s lebe or liebe. So I often say, “Ich liebe in Zürich”, which is poetic as hell.

1 year ago 0 0 0 0
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A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome - Nature A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common resistanc...

www.nature.com/articles/s41...

1 year ago 39 16 1 1
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Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii - Nature Communications In this study, authors conduct a genomic analysis of 15,000 Acinetobacter baumannii isolates, revealing a dominant multidrug-resistant super-lineage (accounting for approximately 70% global isolates),...

New work showing that multidrug-resistant 𝘈𝘤𝘪𝘯𝘦𝘵𝘰𝘣𝘢𝘤𝘵𝘦𝘳 𝘣𝘢𝘶𝘮𝘢𝘯𝘯𝘪𝘪 isn’t a scattered threat—it’s a structured epidemic!

A dominant super-lineage and a rising clade (2.5.6) are spreading worldwide, fueled by gene exchange.

Li et al. Nat Commun
#AMR #bacterialgenomics

www.nature.com/articles/s41...

1 year ago 11 5 0 0
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Information storage across a microbial community using universal RNA barcoding - Nature Biotechnology Barcoding microbial ribosomal RNA creates a recording of gene transfer events without requiring translation.

Fresh in @NatureBiotech! We developed a synthetic biology tool for tracking gene transfer in microbial communities and applied it to study plasmid hosts in a wastewater microbiome. Awesome collab with James Chappell & @joffsilberg.bsky.social and incredible students. www.nature.com/articles/s41...

1 year ago 74 32 3 3
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Join us on Friday, March 21 @ 13:00 CET for the #Virtual Pub with Alexander Morrell, King’s College London, @bioimaginguk.bsky.social. He'll give an exciting talk on "Metallomics Imaging: Unlocking Elemental Insights into Human Health & Disease."
Register🔽
www.eurobioimaging.eu/events/metal...

1 year ago 1 2 0 0
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A computational pipeline for spatial mechano-transcriptomics - Nature Methods The authors present a computational framework that leverages mechanical force inference and spatial transcriptomics to enable analyses of the interplay between the transcriptomic and mechanical state.

🚨 Paper Alert 🚨
Absolutely delighted to share our last paper on "spatial mechano-transcriptomics" @naturemethods👇!!
www.nature.com/articles/s41...

1 year ago 139 53 10 3
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The American Society for Microbiology (ASM) is a great example of an organization that is supposed to stand up for science and scientists, but is completely spineless.

They're kowtowing to pressure from the Admin, refusing to stand up at one of the most critical times in U.S. science.

Compare👇

1 year ago 162 52 8 6

Patient partners play a vital role in research but face systemic barriers to fair pay. Institutions must match their equity commitments with action—transparent, equitable compensation is long overdue.

1 year ago 16 8 0 0
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Macrophages recycle phagocytosed bacteria to fuel immunometabolic responses Nature - Phagocytosed bacteria can serve as an alternative nutrient source for macrophages, influencing their metabolic and immune responses through the recycling of microbial components, with the...

Macrophages are just the tireless workhorses of the immune system.... #ImmunoSky 🧪

www.nature.com/artic...

1 year ago 9 2 0 0
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ISME supports students and postdocs to further develop their academic knowledge and skills in a host institution outside of their country of study. Submit your application by 31 March 2025.
🔗isme-microbes.org/isme-scholar-mobility-fu...
#MicrobialEcology #microbes

1 year ago 19 20 0 2
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Cooperative nutrient scavenging is an evolutionary advantage in cancer - Nature Nutrient-starved tumour cells cooperate by secreting aminopeptidases that digest oligopeptides in the microenvironment, creating a shared pool of free amino acids.

Tumor cells help each other out when amino acids are scarce www.nature.com/articles/s41...

1 year ago 18 9 1 0
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‘The Interview’: Ed Yong Wants to Show You the Hidden Reality of the World The Pulitzer Prize-winning science writer talks about burnout from covering the pandemic and how bird-watching gave him a new sense of hope.

The most achingly beautiful explanation of what science is, from @edyong209.bsky.social: “the idea that much of the world is hidden from us, that we don’t perceive it and don’t understand it, and that it is worth understanding and it is necessary to understand.”

www.nytimes.com/2025/02/22/m...

1 year ago 465 129 9 15

It's hard to express how cool this work is, so I'll just say that if you crave beautiful experiments and rigorously done theory to match, @fernpizza.bsky.social is your guy. Go read this amazing paper right now!

1 year ago 5 3 0 0

Has anyone ever hosted a Wiki-write in?

1 year ago 0 0 0 0

Dear federal scientists: If you have been affected by the probationary firings and would be willing to speak with Science, please reach out to me by email (klangin@aaas.org) or on Signal. We can guarantee annonymity.

1 year ago 2464 1295 24 15
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Indonesia launches groundbreaking national AMR survey on bloodstream infections In November 2024 through January 2025 the Indonesian Ministry of Health (MoH) and World Health Organization (WHO) launched the country’s first national survey to tackle antimicrobial resistance (AMR) ...

Indonesia and WHO launched a national survey on AMR in bloodstream infections, targeting 10,000 patients to improve treatment and policy. This initiative strengthens surveillance, laboratory capacity, and hospital preparedness to combat AMR. #AMR #GlobalHealth

www.who.int/indonesia/ne...

1 year ago 36 9 0 2
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Imaging of cellular dynamics from a whole organism to subcellular scale with self-driving, multiscale microscopy - Nature Methods A self-driving multiresolution light-sheet microscope enables the simultaneous observation and quantification of cellular and subcellular dynamics in the context of intact and developing organisms ove...

I have seen lots of flavors of smart/event-driven microscopy, and this builds directly on the shoulders of existing works, but also takes this idea an important step further, both conceptually and in terms of accomplishments. www.nature.com/articles/s41...

1 year ago 27 4 1 0

We really just take turns presenting in lab meeting and it’s just an adult form of “show & tell”

1 year ago 8 1 0 0

Academics: Jevin and I would love to see this course used broadly around the world. Would you recommend publishing some sort of journal article about the course? (We don't need the publication for our CVs, but just want to get the word out.) If so, where would you target it?

Other promotion ideas?

1 year ago 149 34 18 2

For every dollar of federal research funding in the United States, universities generate between $2.30 and $3.00 of economy activity, much of that in local communities.

That doesn’t even include the return on investment of getting a college or graduate degree, which research also dollars support.

1 year ago 474 139 6 8