Daniel Davila
@fddavila.bsky.social
Computational Biologist | Arctic and Gut microbiome @ University of Calgary
Reposted by Daniel Davila
Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome - @rockefelleruniv.bsky.social go.nature.com/4606ozA
September 12, 2025 at 3:03 PM
Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome - @rockefelleruniv.bsky.social go.nature.com/4606ozA
Reposted by Daniel Davila
Online now! In this Perspective members of the Aging Biomarker Consortium (ABC) outline the X-Age project, an ABC plan for building standardized aging clocks in China. (rdcu.be/eGFV0)
doi.org/10.1038/s435...
doi.org/10.1038/s435...
The X-Age Project to construct a Chinese aging clock
Nature Aging - In this Perspective, members of the Aging Biomarker Consortium outline the X-Age Project, an Aging Biomarker Consortium plan for building standardized aging clocks in China. The...
rdcu.be
September 16, 2025 at 11:41 AM
Online now! In this Perspective members of the Aging Biomarker Consortium (ABC) outline the X-Age project, an ABC plan for building standardized aging clocks in China. (rdcu.be/eGFV0)
doi.org/10.1038/s435...
doi.org/10.1038/s435...
Reposted by Daniel Davila
Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome www.nature.com/articles/s41... #jcampubs
Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome - Nature Biotechnology
Optimized long-read sequencing constructs megabase-scale genome assemblies from complex soil samples.
www.nature.com
September 15, 2025 at 4:12 PM
Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome www.nature.com/articles/s41... #jcampubs
Reposted by Daniel Davila
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Nanopore's getting accurate, but
1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?
with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social
1 / N
Reposted by Daniel Davila
Tomorrow begins #GloMiNe2025 organized by @microbiotavault.bsky.social & #MVIF
Atlantic session will be open by Gloria Dominguez-Bello & @cpavloud.bsky.social
Pacific session by Safarina Malik & Célio Dias Santos Júnior
Both sessions will be LIVE!
Check the details: cassyni.com/s/mvif-glomi...
Atlantic session will be open by Gloria Dominguez-Bello & @cpavloud.bsky.social
Pacific session by Safarina Malik & Célio Dias Santos Júnior
Both sessions will be LIVE!
Check the details: cassyni.com/s/mvif-glomi...
September 8, 2025 at 10:16 AM
Tomorrow begins #GloMiNe2025 organized by @microbiotavault.bsky.social & #MVIF
Atlantic session will be open by Gloria Dominguez-Bello & @cpavloud.bsky.social
Pacific session by Safarina Malik & Célio Dias Santos Júnior
Both sessions will be LIVE!
Check the details: cassyni.com/s/mvif-glomi...
Atlantic session will be open by Gloria Dominguez-Bello & @cpavloud.bsky.social
Pacific session by Safarina Malik & Célio Dias Santos Júnior
Both sessions will be LIVE!
Check the details: cassyni.com/s/mvif-glomi...
Reposted by Daniel Davila
Applied Computational Genomics Course at UU: Spring 2024
github.com/quinlan-lab... by the almighty Aaron Quinlan, author of bedtools and many other great tools for genomics analysis.
github.com/quinlan-lab... by the almighty Aaron Quinlan, author of bedtools and many other great tools for genomics analysis.
August 25, 2025 at 2:15 PM
Applied Computational Genomics Course at UU: Spring 2024
github.com/quinlan-lab... by the almighty Aaron Quinlan, author of bedtools and many other great tools for genomics analysis.
github.com/quinlan-lab... by the almighty Aaron Quinlan, author of bedtools and many other great tools for genomics analysis.
Reposted by Daniel Davila
@hansenlab.bsky.social et al. study the evolution of bacterial symbionts of Pariaconus psyllids in Hawaii, demonstrating that island biogeography and host plant ecology shape symbiont losses and codiversification patterns.
🔗 doi.org/10.1093/gbe/evaf153
#genome #evolution #symbiont
🔗 doi.org/10.1093/gbe/evaf153
#genome #evolution #symbiont
August 21, 2025 at 11:38 AM
@hansenlab.bsky.social et al. study the evolution of bacterial symbionts of Pariaconus psyllids in Hawaii, demonstrating that island biogeography and host plant ecology shape symbiont losses and codiversification patterns.
🔗 doi.org/10.1093/gbe/evaf153
#genome #evolution #symbiont
🔗 doi.org/10.1093/gbe/evaf153
#genome #evolution #symbiont
Reposted by Daniel Davila
Read the associated news and views:
Microbial chocolatiers of fine flavour 🍫
by Pablo Cruz-Morales
www.nature.com/articles/s41...
Microbial chocolatiers of fine flavour 🍫
by Pablo Cruz-Morales
www.nature.com/articles/s41...
August 18, 2025 at 3:37 PM
Read the associated news and views:
Microbial chocolatiers of fine flavour 🍫
by Pablo Cruz-Morales
www.nature.com/articles/s41...
Microbial chocolatiers of fine flavour 🍫
by Pablo Cruz-Morales
www.nature.com/articles/s41...
Reposted by Daniel Davila
Applied HPC with R book-hpc.ggvy.cl/ #rstats
August 17, 2025 at 1:45 PM
Applied HPC with R book-hpc.ggvy.cl/ #rstats
Reposted by Daniel Davila
Scientists have found instances of sex reversal—where an individual has the physical features of one sex but the genetic makeup of the other—in five different Australian bird species. https://scim.ag/41Dvamo
‘Sex reversal' is surprisingly common in birds, new study suggests
Survey of five Australian avians finds numerous discordant individuals, including a genetically male bird that had laid an egg
scim.ag
August 15, 2025 at 1:35 PM
Scientists have found instances of sex reversal—where an individual has the physical features of one sex but the genetic makeup of the other—in five different Australian bird species. https://scim.ag/41Dvamo
Reposted by Daniel Davila
In mice, maternal antibodies ingested in breast milk in the first week after birth help to regulate immune responses in the newborn gut, according to a new study in Science.
Learn more: scim.ag/45yW4Nq
Learn more: scim.ag/45yW4Nq
Breast milk IgG engages the mouse neonatal immune system to instruct responses to gut antigens
Maternal antibodies fundamentally regulate gut immunity in the developing infant, yet the mechanisms underlying this process remain elusive. We found that maternal immunoglobulin G (IgG), ingested in ...
scim.ag
August 14, 2025 at 7:55 PM
In mice, maternal antibodies ingested in breast milk in the first week after birth help to regulate immune responses in the newborn gut, according to a new study in Science.
Learn more: scim.ag/45yW4Nq
Learn more: scim.ag/45yW4Nq
Reposted by Daniel Davila
Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
STEPS To It
Announcing a new program, called STEPS, to simulate the dynamics of evolving microbial populations.
telliamedrevisited.wordpress.com
August 12, 2025 at 3:53 PM
Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
telliamedrevisited.wordpress.com/2025/08/12/s...
STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.
Reposted by Daniel Davila
#Throwback 🧪
PERSPECTIVE | Emerging tools and best practices for studying gut microbial community metabolism
@cecilianoecker.bsky.social & P Turnbaugh
PERSPECTIVE | Emerging tools and best practices for studying gut microbial community metabolism
@cecilianoecker.bsky.social & P Turnbaugh
Emerging tools and best practices for studying gut microbial community metabolism - Nature Metabolism
In this Perspective, Noecker and Turnbaugh provide a detailed guide for studying microbial community metabolism and discuss the best practices in the field.
bit.ly
August 12, 2025 at 4:01 PM
#Throwback 🧪
PERSPECTIVE | Emerging tools and best practices for studying gut microbial community metabolism
@cecilianoecker.bsky.social & P Turnbaugh
PERSPECTIVE | Emerging tools and best practices for studying gut microbial community metabolism
@cecilianoecker.bsky.social & P Turnbaugh
Reposted by Daniel Davila
August 8, 2025 at 2:15 PM
Reposted by Daniel Davila
#NatMicroPicks
Hidden microbial world in trees🌳
Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.
#PlantMicro #MicroSky
www.nature.com/articles/s41...
Hidden microbial world in trees🌳
Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.
#PlantMicro #MicroSky
www.nature.com/articles/s41...
A diverse and distinct microbiome inside living trees - Nature
Microbiome analyses of living trees show that a single tree can host approximately one trillion bacteria, with microbial communities distinctly partitioned between heartwood and sapwood and with minim...
www.nature.com
August 8, 2025 at 2:28 PM
#NatMicroPicks
Hidden microbial world in trees🌳
Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.
#PlantMicro #MicroSky
www.nature.com/articles/s41...
Hidden microbial world in trees🌳
Living wood hosts trillions of bacteria making trees a complex ecosystems with major roles in forest health and function.
#PlantMicro #MicroSky
www.nature.com/articles/s41...
Reposted by Daniel Davila
The successful integration of Indian immigrants in the Western culture is reflected in their gut microbiota! 😄
#MicrobiomeSky
www.nature.com/articles/s41...
#MicrobiomeSky
www.nature.com/articles/s41...
The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation - npj Biofilms and Microbiomes
npj Biofilms and Microbiomes - The adoption of a westernized gut microbiome in Indian Immigrants and Indo-Canadians is associated with dietary acculturation
www.nature.com
August 8, 2025 at 2:23 PM
The successful integration of Indian immigrants in the Western culture is reflected in their gut microbiota! 😄
#MicrobiomeSky
www.nature.com/articles/s41...
#MicrobiomeSky
www.nature.com/articles/s41...
Reposted by Daniel Davila
#NatMicroPicks
Synthetic evolution overdrive 🦠🔧🚅
A highly mutagenic DNA replication system speeds up evolution in Escherichia coli, without harming the host, opening a new way to accelerate protein engineering.
#SynBio #MicroSky
www.science.org/doi/10.1126/...
Synthetic evolution overdrive 🦠🔧🚅
A highly mutagenic DNA replication system speeds up evolution in Escherichia coli, without harming the host, opening a new way to accelerate protein engineering.
#SynBio #MicroSky
www.science.org/doi/10.1126/...
An orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coli
Systems that perform continuous hypermutation of designated genes without compromising the integrity of the host genome can substantially accelerate the evolution of new or enhanced protein functions....
www.science.org
August 8, 2025 at 1:35 PM
#NatMicroPicks
Synthetic evolution overdrive 🦠🔧🚅
A highly mutagenic DNA replication system speeds up evolution in Escherichia coli, without harming the host, opening a new way to accelerate protein engineering.
#SynBio #MicroSky
www.science.org/doi/10.1126/...
Synthetic evolution overdrive 🦠🔧🚅
A highly mutagenic DNA replication system speeds up evolution in Escherichia coli, without harming the host, opening a new way to accelerate protein engineering.
#SynBio #MicroSky
www.science.org/doi/10.1126/...
Reposted by Daniel Davila
If you do #qPCR on soils you might be interested in this paper led by @aoifeduff.bsky.social @femsmicro.org which shows the effect of mastermix, sample type, platform and gene target on the inhibition, precision and accuracy of quantification academic.oup.com/femsec/artic...
Counting soil microbial communities: the impact of qPCR platform and mastermix on accuracy and precision
qPCR is used to measure soil microorganisms but can be affected by inhibitors, change in mastermix, and platform. This study measured precision and accurac
academic.oup.com
July 28, 2025 at 8:17 AM
If you do #qPCR on soils you might be interested in this paper led by @aoifeduff.bsky.social @femsmicro.org which shows the effect of mastermix, sample type, platform and gene target on the inhibition, precision and accuracy of quantification academic.oup.com/femsec/artic...
Reposted by Daniel Davila
You can not live without Rmarkdown if you use R for genomics data analysis. Cheatsheet from Posit:
rstudio.github.io/cheatsheets...
rstudio.github.io/cheatsheets...
July 28, 2025 at 2:15 PM
You can not live without Rmarkdown if you use R for genomics data analysis. Cheatsheet from Posit:
rstudio.github.io/cheatsheets...
rstudio.github.io/cheatsheets...
Reposted by Daniel Davila
✨New issue!✨
🧪
Check out the latest in #metabolism research from across all disciplines.
Read about #Triglycerides in the #Brain, #CagriSema, #Exercise, #LipidMetabolism, the #Microbiome - and many more topics!
www.nature.com/natmetab/vol...
🧪
Check out the latest in #metabolism research from across all disciplines.
Read about #Triglycerides in the #Brain, #CagriSema, #Exercise, #LipidMetabolism, the #Microbiome - and many more topics!
www.nature.com/natmetab/vol...
July 24, 2025 at 2:41 PM
✨New issue!✨
🧪
Check out the latest in #metabolism research from across all disciplines.
Read about #Triglycerides in the #Brain, #CagriSema, #Exercise, #LipidMetabolism, the #Microbiome - and many more topics!
www.nature.com/natmetab/vol...
🧪
Check out the latest in #metabolism research from across all disciplines.
Read about #Triglycerides in the #Brain, #CagriSema, #Exercise, #LipidMetabolism, the #Microbiome - and many more topics!
www.nature.com/natmetab/vol...
Reposted by Daniel Davila
I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!
Garud Lab
garud.eeb.ucla.edu
July 22, 2025 at 5:51 PM
I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!
Reposted by Daniel Davila
How our gut microbiome drives sugar cravings
erictopol.substack.com/p/how-our-gu...
erictopol.substack.com/p/how-our-gu...
How Our Gut Microbiome Can Drive Sugar Cravings
More Evidence for Our Gut Taking Center Stage for What We Eat
erictopol.substack.com
July 23, 2025 at 6:39 PM
How our gut microbiome drives sugar cravings
erictopol.substack.com/p/how-our-gu...
erictopol.substack.com/p/how-our-gu...
Reposted by Daniel Davila
Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!
There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...
There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...
AlphaFold - A practical guide
AlphaFold - A practical guide
www.ebi.ac.uk
July 21, 2025 at 3:33 PM
Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!
There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...
There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...
Reposted by Daniel Davila
This week's #substack is a recent podcast conversation, where we chat about the human microbiome, health, and some new work from the lab that involves predicting diet from poop DNA. gibbological.substack.com/p/a-conversa...
A conversation about the human gut microbiome
Still working on my next post, so I thought I’d share a recent conversation with Dr.
gibbological.substack.com
July 22, 2025 at 3:56 PM
This week's #substack is a recent podcast conversation, where we chat about the human microbiome, health, and some new work from the lab that involves predicting diet from poop DNA. gibbological.substack.com/p/a-conversa...
Reposted by Daniel Davila
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
July 16, 2025 at 9:59 PM
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵