Alex Crits-ChristophAstonishing diversity and multifaceted biological connections of Type IV restriction-modification systems
To help any migration bots: I was @contaminatedsci on Twitter.
| Lieberman Lab Website | lieberman.science |
Tami Lieberman
- 409 Followers
- 167 Following
- 152 Posts
Microbiology, evolution, genomics. Thinking about the ~10^9 bacterial mutations generated in and on you daily. Asst Prof MIT.
To help any migration bots: I was @contaminatedsci on Twitter.
To help any migration bots: I was @contaminatedsci on Twitter.
Detecting co-selection through excess linkage disequilibrium in bacterial genomes
Tommi MäklinI wrote a short guide on how to build both alignment-free and reference-based prokaryote phylogenetic trees from SNP alignments without using snippy, check it out
Building trees with SKA
SKA is a tool for comparing small and highly similar genomes using split k-mers. This guide will explain how to use SKA to build a phylogenetic tree for different Escherichia coli lineages in a few minutes. Although SKA is tailored more towards analysing variation within a lineage, tree-building ends up working fine for the whole species but requires more memory. Why SKA is good for building phylogenetic trees The basic approach to building a tree with SKA is to generate a SNP alignment using split k-mers and then feed that to a tree building algorithm of choice.
Small Things ConsideredSensing Blue Light: From Bacteria to Birds
by Mechas
That many birds migrate over long distances is a well-known fact. But reading the book "World on the Wing: The Global Odyssey of Migratory Birds" by Scott Weidensaul proved to be a true eye-opener. I also learned a fact that really stuck with me.
Read more → https://schaechter.asmblog.org/schaechter/2023/04/sensing-blue-light-from-bacteria-to-birds.html
Sensing Blue Light: From Bacteria to Birds
<p>by Mechas <br /> That many birds migrate over long distances is a well-known fact. But reading the book "World on the Wing: The Global Odyssey of Migratory Birds" by Scott Weidensaul proved to be a true eye-opener. I also learned a fact that really stuck with me.
The Atlas of Cell Structure
by Roberto
Our knowledge of the structure of microbial cells just keeps getting better as the resolution of imaging techniques continues to increase. A key player in this rapidly evolving technological field is cryo-electron tomography (cryoET) which, aided by powerful computational tools, allows for the generation of three-dimensional images of whole microbial cells...
Read more → https://schaechter.asmblog.org/schaechter/2023/03/the-atlas-of-cell-structure.html
#microbiology
The Atlas of Cell Structure
<p>by Roberto <br />Our knowledge of the structure of microbial cells just keeps getting better as the resolution of imaging techniques continues to increase. A key player in this rapidly evolving technological field is cryo-electron tomography (cryoET) which, aided by powerful computational tools, allows for the generation of three-dimensional images of whole microbial cells...
Anne CarpenterUS citizens or permanent residents from an under-represented group! High school thru postdoc/faculty.
Contact any NIH-funded researcher you admire & suggest applying for this supplement to join their lab! Many, like me, are happy to host! Pls boost
https://grants.nih.gov/grants/guide/pa-files/PA-21-071.html
(side note: women DO count as under-represented in some fields). Eligible groups listed here:
https://www.nigms.nih.gov/Research/mechanisms/Pages/promotediversityFAQ.aspx
#ResearchFunding #BlackInSTEM #Grants #PostdocFellowships #PhDFunding #PhDFellowships @academicchatter
PA-21-071: Research Supplements to Promote Diversity in Health-Related Research (Admin Supp Clinical Trial Not Allowed)
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Research Supplements to Promote Diversity in Health-Related Research (Admin Supp Clinical Trial Not Allowed) PA-21-071. NIH
Sean GibbonsPrior work from @LabSonnenburg found that ~1/3 of participants on a 10-week high-fiber intervention showed an unexpected ⬆️ in inflammation. We built MCMMs for this cohort, and found that the high-inflammation group showed less predicted butyrate/propionate on a high fiber diet.
Talmudic Question #202
Why do bacteria – think Agrobacterium, Streptomyces, Borrelia among others – not care at all if they have linear and circular chromosomes and episomes (plasmids, prophages) side-by-side in one cell?
Read more → https://schaechter.asmblog.org/schaechter/2023/02/talmudic-question-202.html
more TQs → https://schaechter.asmblog.org/schaechter/talmudic_questions/
#microbiology
Ultrahigh-affinity transport proteins from ubiquitous marine bacteria reveal mechanisms and global patterns of nutrient uptake
https://www.biorxiv.org/content/10.1101/2023.02.16.528805v1
Absolutely killer study, we need more work like this at 100x the scale. Need to think about the next generation of genome annotations.... and the data that will go into them
Nonia ParienteRT @PLOSBiology
#Viral #taxonomy: transforming the existing classification of #viruses into a phylogenetic one is an ongoing challenge. This Consensus View explains how such #taxonomy can encapsulate viral diversity & recognize independent biological origins #PLOSBiology https://plos.io/3xnbLqi
#Viral #taxonomy: transforming the existing classification of #viruses into a phylogenetic one is an ongoing challenge. This Consensus View explains how such #taxonomy can encapsulate viral diversity & recognize independent biological origins #PLOSBiology https://plos.io/3xnbLqi
Four principles to establish a universal virus taxonomy
Transforming an existing phenotypic classification of viruses into one based on evolutionary relationships that can accommodate the vast number of viruses characterized in metagenomics and environmental studies is an ongoing challenge. This Consensus View explains how such a taxonomy can be expanded to encapsulate viral diversity and to recognize independent biological origins of different virus groups.