Anahid (Ana)
@anahidam.bsky.social
Microbial omic’s and bioinformatics | interested in synthetic biology |
PhD candidate @ Northwestern University CEE | HartmannLab
And most importantly:
A Heterotroph, full of limitations
PhD candidate @ Northwestern University CEE | HartmannLab
And most importantly:
A Heterotroph, full of limitations
Reposted by Anahid (Ana)
Excited to share work I led during my PhD - now out in @cp-cellhostmicrobe.bsky.social 🎉
Using multiomics, we show that microbiome and host expression profiles dynamically shift during pneumonia treatment and track with clinical outcomes 🧪🫁 #MicroSky
www.cell.com/cell-host-mi...
Using multiomics, we show that microbiome and host expression profiles dynamically shift during pneumonia treatment and track with clinical outcomes 🧪🫁 #MicroSky
www.cell.com/cell-host-mi...
www.cell.com
December 10, 2025 at 5:17 PM
Excited to share work I led during my PhD - now out in @cp-cellhostmicrobe.bsky.social 🎉
Using multiomics, we show that microbiome and host expression profiles dynamically shift during pneumonia treatment and track with clinical outcomes 🧪🫁 #MicroSky
www.cell.com/cell-host-mi...
Using multiomics, we show that microbiome and host expression profiles dynamically shift during pneumonia treatment and track with clinical outcomes 🧪🫁 #MicroSky
www.cell.com/cell-host-mi...
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
#phd
#postdoc
#microbiomesky
November 29, 2025 at 6:22 AM
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
#phd
#postdoc
#microbiomesky
Reposted by Anahid (Ana)
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...
#phagesky
www.nature.com/articles/s41...
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–...
www.nature.com
November 26, 2025 at 9:55 PM
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...
#phagesky
www.nature.com/articles/s41...
Reposted by Anahid (Ana)
Baym continues to make freakin' art. Must see thread/paper
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 11:29 PM
Baym continues to make freakin' art. Must see thread/paper
Reposted by Anahid (Ana)
Thinking only of Rosalind Franklin today, and what was stolen from her (and so many other female scientists alongside her).
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
www.science.org
November 7, 2025 at 7:58 PM
Thinking only of Rosalind Franklin today, and what was stolen from her (and so many other female scientists alongside her).
Reposted by Anahid (Ana)
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.
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.
February 11, 2024 at 2:31 PM
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.
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.
Reposted by Anahid (Ana)
R.I.P Hamilton Smith, 1978 Nobel Laureate for the discovery of type II restriction-modification systems (HindII).
October 26, 2025 at 6:54 PM
R.I.P Hamilton Smith, 1978 Nobel Laureate for the discovery of type II restriction-modification systems (HindII).
Reposted by Anahid (Ana)
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
www.nature.com/articles/s41...
🧵⬇️
1/8
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.
www.nature.com
October 23, 2025 at 6:53 PM
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
www.nature.com/articles/s41...
🧵⬇️
1/8
Reposted by Anahid (Ana)
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.
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.
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
nature.com
October 15, 2025 at 9:41 PM
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.
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.
Reposted by Anahid (Ana)
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
Apply here apply.interfolio.com/174404
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
October 5, 2025 at 12:03 PM
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
Apply here apply.interfolio.com/174404
Reposted by Anahid (Ana)
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
August 28, 2025 at 12:16 PM
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...
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.
Unsurprisingly, blood cortisol levels are... not low (tested first thing in the morning in the middle of the shakes, decently outside normal range). Na, Mg, K, all normal.
Advice welcome 🙏 I'm tired of these shakes.
Advice welcome 🙏 I'm tired of these shakes.
Anyone know about anxiety causing body trembles when trying to sleep? It started a few months ago and is getting worse and really interfering with sleep. Just continuous low level trembling from the core, not extremities.
August 21, 2025 at 7:35 AM
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.
Reposted by Anahid (Ana)
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
August 20, 2025 at 7:41 PM
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
Reposted by Anahid (Ana)
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
#microbialsky
August 18, 2025 at 9:57 PM
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
#microbialsky
Reposted by Anahid (Ana)
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/...
August 18, 2025 at 2:31 PM
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🥹🥹🤓🤓
July 28, 2025 at 3:04 AM
Got my first invitation to review a manuscript🥹🥹🤓🤓
Reposted by Anahid (Ana)
‼️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...
careers.peopleclick.com/careerscp/cl...
Postdoctoral Associate
MIT - Postdoctoral Associate - Cambridge MA 02139
careers.peopleclick.com
June 18, 2025 at 2:39 PM
‼️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...
careers.peopleclick.com/careerscp/cl...
Reposted by Anahid (Ana)
Check out this list of awesome #virome tools and be sure to add yours!
github.com/shandley/awe...
#phagesky #microsky
github.com/shandley/awe...
#phagesky #microsky
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
github.com
March 12, 2025 at 8:46 PM
Check out this list of awesome #virome tools and be sure to add yours!
github.com/shandley/awe...
#phagesky #microsky
github.com/shandley/awe...
#phagesky #microsky
Reposted by Anahid (Ana)
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!
Please share!
Postdoc position on computational (meta)genome mining for natural products
www.wur.nl
March 3, 2025 at 10:44 PM
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!
Please share!
Reposted by Anahid (Ana)
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...
"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...
March 2, 2025 at 7:01 AM
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...
"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...
Reposted by Anahid (Ana)
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 🐯
We decided to call them TIGR-Tas systems 🐯
March 1, 2025 at 12:18 AM
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 🐯
We decided to call them TIGR-Tas systems 🐯
Reposted by Anahid (Ana)
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...
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...
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...
www.cell.com
February 27, 2025 at 8:33 PM
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...
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...
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...
#R #Microbiome #SciSky
r-graph-gallery.com/color-palett...
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...
r-graph-gallery.com
February 11, 2025 at 10:30 PM
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...
#R #Microbiome #SciSky
r-graph-gallery.com/color-palett...
Reposted by Anahid (Ana)
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.
🧵
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.
🧵
February 5, 2025 at 1:27 AM
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.
🧵
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.
🧵
Reposted by Anahid (Ana)
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...
cmbio.io/webinars/maa...
Webinar| MaAsLin 3 for Microbiome Statistics and Epidemiology
Join us for an enlightening session with Dr Curtis Huttenhower as he delves into the transformative capabilities of this next-generation statistical tool.
cmbio.io
February 3, 2025 at 8:36 PM
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...
cmbio.io/webinars/maa...