Anahid (Ana)

As a phd student coming from “ a country of concern” seems like all the ways to continue my research as a postdoc In the US might get blocked. Absolutely heartbroken. I can’t even think straight. Not to sure what to do or where to find the strength to stay productive.
#phd
#postdoc
#microbiomesky

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years

#phagesky

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

Baym continues to make freakin' art. Must see thread/paper

Rosalind Franklin and the damage of gender harassment Spurred by a recent report on sexual harassment in academia, our columnist revisits a historical case and reflects on what has changed—and what hasn’t

Thinking only of Rosalind Franklin today, and what was stolen from her (and so many other female scientists alongside her).

Rosalind Elsie Franklin was an English chemist and X-ray crystallographer whose work was central to the understanding of the molecular structures of DNA (deoxyribonucleic acid), RNA (ribonucleic acid), viruses, coal, and graphite. Description: Dr. Franklin looks across a checkered table at everyday objects. I think this is in a cafe or a breakroom. Since we know this is Paris, this photo is likely from 1946?

With all she did to make Watson and Crick's discovery possible, Rosalind Franklin was essentially "a de facto collaborator," says Lynne Osman Elkin. Novartis Foundation Dr. Franklin looks to her right, wearing a dark necklace and broad-yoked shirt or blouse. She has short dark hair and eyebrows, and has a look of sharp intelligence, with an edge of weariness.

It's International Women in Science Day ♀️, and I want to talk briefly about Rosalind Franklin.

A conventional choice for unconventional reasons: Dr. Franklin was one of the FIRST STRUCTURAL VIROLOGISTS. Let's talk about her work outside of the Crick & Watson debacle.

R.I.P Hamilton Smith, 1978 Nobel Laureate for the discovery of type II restriction-modification systems (HindII).

Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.

NEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data!

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

🧵⬇️

1/8

Isolation, engineering and ecology of temperate phages from the human gut - Nature Human host-associated cellular products may act as induction agents for bacteriophages.

Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...

PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

UChicago Microbiology is searching for tenured or tenure-track faculty working in host-pathogens interactions, viral and bacterial pathogenesis, and emerging infectious diseases. Come join our vibrant Department! microbiology.uchicago.edu
Apply here apply.interfolio.com/174404

AllTheBacteria - all bacterial genomes assembled, available and searchable The bacterial sequence data publicly available via the global DNA archives is a vast potential source of information on the evolution of bacteria. However, most of this sequence data is unassembled, o...

Wow, more than 2.4M of assembled bacteria in the new release of ABT! We plan to index these using our efficient colored De Bruijn graph index, Fulgor. We recently conducted experiments with nearly 1M genomes…getting there :)
www.biorxiv.org/content/10.1...

First time seeing someone else experiencing this. It’s usually happens when I’m extremely tired. But for me instead of feeling it in my core, I mostly feel it in my head and neck. My head starts vibrating, and it usually takes an hour to go away.

We are hiring! The Dept of Microbiology and Molecular Genetics is looking for faculty at the Assistant or Associate professor level (tenure track). Please consider joining our vibrant microbiology and immunology community at the University of Pittsburgh School of medicine

Excited to share new published work on Phaeocystis antarctica microbiomes! Given the world, I was hesitant to self-promote, but a key finding is P. antarctica phycosphere interactions should be studied in situ. Antarctic fieldwork is necessary! onlinelibrary.wiley.com/doi/full/10....
#microbialsky

Department members sit at a very long table in the hallway eating a pre-Thanksgiving potluck feast.

Faculty search announcement 2025: Tenure-Track Assistant Professor in Microbiology at UT Southwestern. We seek candidates working in microbial pathogenesis (some preference may be given to bacterial pathogens). Come join our community! (1/5) www.utsouthwestern.edu/departments/...

Got my first invitation to review a manuscript🥹🥹🤓🤓

Postdoctoral Associate MIT - Postdoctoral Associate - Cambridge MA 02139

‼️I'm looking for a postdoc‼️ Come join effort in using metagenomes to quantify microbial catabolic potential and carbon substrate availability at the ecosystem level. We seek to understand evolutionary forces shaping the carbon cycle. Part of ccomp-stc.org

careers.peopleclick.com/careerscp/cl...

GitHub - shandley/awesome-virome: A listing of software, tools and databases useful for virome analysis A listing of software, tools and databases useful for virome analysis - shandley/awesome-virome

Check out this list of awesome #virome tools and be sure to add yours!

github.com/shandley/awe...

#phagesky #microsky

Postdoc position on computational (meta)genome mining for natural products

Exciting opportunity to join our group as postdoc! Apply now for this project on computational (meta)genome mining as part of a collaborative European research consortium: www.wur.nl/en/vacancy/p...

Please share!

Looks interesting, plasmid assembly from multiple metagenomes
"On synthetic benchmark datasets, PlasMAAG reconstructed 50-121% more near-complete plasmids than competing methods and improved the Matthews Correlation Coefficient of geNomad contig classif. by 28-106%

www.biorxiv.org/content/10.1...

we recently found some really neat RNA-guided DNA-cutting systems in phages. Despite remarkable similarities to CRISPR systems, including encoding guide RNAs in arrays, they appear entirely evolutionarily distinct (but definitely related to snoRNAs 🤓)
We decided to call them TIGR-Tas systems 🐯

The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns With long-term space travel and extraterrestrial habitation becoming feasible, understanding how space environmental exposures, microbial communities, and molecular profiles differ from Earth is cruci...

the microbiome and metabolome is out of this world 🌏 🚀 🌏 🚀 🌏 🚀 🌏 🚀

congratulations to my UC San Diego colleagues in the Knight, Dorrestein, and Chu laboratories — led by Rodolfo Salido and Nina Zhao

www.cell.com/cell/fulltex...

R Color Palette Finder The ultimate tool for finding the perfect color palette for data visualization with R and paletteer. Explore over 2000 palettes, see them in action on various charts, simulate color blindness, and exp...

This is such a cool website for seeing and choosing color palettes for R. You can also put different filters on your color palette ( like Protanopia) to ensure it is accessible to all!
#R #Microbiome #SciSky
r-graph-gallery.com/color-palett...

So I was peer reviewing a manuscript...

Authors cited me - cool.

But wait... the paper they cite does not exist.

It lists coauthors who are real people I have published with, and a real journal that I have published in, with a title that sounds plausible - but is completely made up.

🧵

Curtis will be giving a free webinar on our new tool MaAslin3 on February 20th. Come check out what's new and the changes we made to improve differential abundance testing in microbiome data!

cmbio.io/webinars/maa...

Want to learn more about genetic tools for studying bacteria and phage, check out the summer ABG Course at CSHL. This will be the 80th anniversary of the original CSHL Phage course, so you'll also meet many additional visiting genetics gurus! <https://meetings.cshl.edu/courses.aspx?course=C-ABG>

Grad student funding - Apply for the ASN Student Research Awards. $2k each for research that advances the conceptual unification of ecology, evolution, or behavior. Applications due March 14 www.amnat.org/announcement...

I just searched for plasma sequencing services. Of course there’s a range of services, but I just saw that you can get the same day results- whole plasma sequencing - for just $15!
Mind blowing in an awesome way!
#Microbiome #Ganomics #SciSky

I don’t know how this is gonna be received, but here we go:
As an international student from Iran that came to the US for four years ago, it still blows my mind how fast and accessible sequencing technologies can be./

Last chance to apply for the Emerging Leaders Seminar series! We start going over applications later this month!

It's interesting how various versions of a tool can be so different. I was using StrainPhlAn 4.0 before, and for my dataset, it took more than 48 hours to create the consensus-marker files. Updated to 4.1.1, the same dataset took less than an hour!