A probiotic yeast, colorectal cancer, and the gut microbiome

A rare correlative microbiome study careful enough to think with, and an arrow or two I would redraw.

miscellaneous Sat, Jul 04, 2026
publication human-microbiome

Five Postdocs, Five Questions: An Experiment in Transdisciplinary Thinking at HIFMB

Some personal notes on what we are trying to achieve, and how we are planning to achieve that

miscellaneous Sun, Jun 28, 2026
social science

Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study

The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

miscellaneous Wed, Apr 15, 2026
opinion science human-microbiome

Lost and Found in Modern Microbiology: An Ethnography of Modern Microbiologists

A paper on how microbiologists navigate the tension between reductionism and complexity in their everyday practices, and my 2 cents on it.

miscellaneous Mon, Dec 15, 2025
opinion science

The Next 50 Years of Ocean 'Omics: Reflections from MMOFF 2025

Marine Microbial Observatories for the Future - From Samples to Data to Legacy in the Era of Integrated ‘Omics

miscellaneous Mon, Nov 17, 2025
workshop ocean metagenomics

ECR connection: Meet Meren when you need to

A means for ECRs to get advice from a senior scientist outside of their support network

miscellaneous Sun, Nov 16, 2025
social ecr

The Weight of a Honey Pot: Memory, Belonging, and the Passage of Time

Meren's pilgrimage to Barhal

miscellaneous Mon, Sep 01, 2025
personal

We do not choose our families but we can choose people who push us

A thought in structures that helps us become who we want to become

miscellaneous Wed, Jul 16, 2025
social personal ecr

Evolution of a cover

From a vague idea to a piece of art

miscellaneous Sun, Sep 22, 2024
publication personal

Research week at BIOS: Getting my hands wet with data

Matt's first time sampling water from a CTD

miscellaneous Sat, Apr 08, 2023
field-work ocean

Binning giant viruses and their close relatives with anvi'o

A journey into the genomics of giant viruses and their close relatives

miscellaneous Mon, Jan 03, 2022
metagenomics binning

Targeted binning of a novel nitrogen-fixing population from the Arctic Ocean

Using metabolism estimation to go fishing in some ocean metagenomes.

miscellaneous Wed, Oct 20, 2021
metagenomics binning ocean

From Boats to Bits: Evolution of a study on marine microbes

Or, Meren's personal notes from a 48 hours, high-resolution, diel sampling effort in Hawai'i.

miscellaneous Mon, Sep 13, 2021
field-work metagenomics ocean

Mentorship in life sciences: voices of mentees

An attempt to learn from the experiences of ECRs with their mentors

miscellaneous Tue, Jun 01, 2021
social ecr

A reading list for scientists to recognize and confront anti-Black racism

miscellaneous Mon, Oct 05, 2020
social

The history of metagenomics: An incomplete summary

A personal and directed look at the past of an exciting discipline.

miscellaneous Mon, Jul 27, 2020
opinion metagenomics

Estimating per-residue binding frequencies with InteracDome

A blog post detailing InteracDome's integration into anvi'o

anvio Wed, Jul 22, 2020
tutorial population-genetics technical

Welcome to the dark side of genomes and metagenomes

On how we unified the known and unknown CDS-space in genomes and metagenomes

miscellaneous Wed, Jul 01, 2020
opinion metagenomics technical

Online seminar series on Microbial 'Omics for beginners

Socially isolated community discussions on key concepts and stuff.

miscellaneous Sat, Jun 27, 2020
workshop

Visualizing the fate of contigs across metagenomic binning algorithms

Don't click. Run away. Don't see what you don't want to see.

miscellaneous Thu, Jan 02, 2020
reanalysis binning visualization

To dereplicate or not to dereplicate?

Inflating the number of near-identical genomes versus losing potentially key genetic information in genome-resolved metagenomics studies.

miscellaneous Thu, Dec 12, 2019
opinion metagenomics technical

Visualizing contig coverages to better understand microbial population structures

Ways to visualize mapping results in anvi'o to make informed statements about environmental populations and to generate high-quality figures)

anvio Mon, Nov 25, 2019
tutorial visualization metagenomics

Extract loci from genomes and metagenomes with anvi'o

A flexible and scalable approach to locate and extract target genetic loci from larger genetic contexts.

anvio Thu, Oct 17, 2019
tutorial metagenomics

Genome / metagenome / MAG taxonomy with anvi'o

An attempt at alchemy combining the magic of GTDB and single-copy core genes in anvi'o.

anvio Tue, Oct 08, 2019
tutorial annotation

Getting help from the anvi'o community

A primer on how to find your way through the maze of microbial 'omics and anvi'o

anvio Mon, Oct 07, 2019

Accessing and including NCBI genomes in 'omics analyses in anvi'o

How to download, process, and combine genomes from NCBI in your phylogenomic, pangenomic, and/or other 'omics analyses

anvio Thu, Mar 14, 2019
tutorial metagenomics

An interdisciplinary Wolbachia story through connections across the Atlantic: Metagenomics, long-read sequencing, and other things

After 24 months of work, our study describing the discovery of a plasmid for Wolbachia appeared in Nature Communications. I thought that this would be a good moment to take a break and think through everything that led to this proud moment and learn from it.

miscellaneous Tue, Mar 05, 2019
metagenomics

Fantastic Data and How to Share Them: A Plea to Journal Editors and Reviewers

A small checklist for reviewers to follow to make public data sources public and forever

miscellaneous Sun, Feb 24, 2019
opinion

My unpopular two cents on the 'Face on a Turd'

One of those 'I can not believe you are even considering reading this' posts

miscellaneous Mon, Dec 17, 2018
opinion social

Combining reference genome annotations with your own in pangenomes

Mike Lee heroically combines reference annotations with new annotations

anvio Sat, Dec 01, 2018
tutorial pangenomics annotation

Microbial 'Omics Workshop

A light introduction to questions of microbial ecology and microbial omics through the story of crassphage

anvio Sun, Sep 09, 2018
workshop

Integrating sequence variants and predicted protein structures

A discussion on the practical and theoretical aspects of using anvi'o structure

anvio Tue, Sep 04, 2018
tutorial population-genetics technical

Anvi'o snakemake workflows

Bringing the magic of anvi'o together with the wonders of snakemake.

anvio Mon, Jul 09, 2018
tutorial metagenomics technical

Assessing the completion of eukaryotic bins with anvi'o

A preliminary set of 83 HMMs from BUSCO. -Lol is anvi'o doing picoeuks now fam? -Why yes, yes it does.

anvio Sat, May 05, 2018
tutorial genome-quality

Running remote anvi'o interactive interfaces on your local computer

A hacker's guide to anvi'o networking. Are you scared? You should be!

anvio Wed, Mar 07, 2018
tutorial

Amino acid color coding by conservation in anvi'o gene clusters

Details of a beautiful algorithm.

anvio Tue, Feb 13, 2018
tutorial pangenomics visualization

Importing VirSorter annotations into anvi'o to study phages

Anvi'o projects meet the underappreciated owners of this planet.

anvio Thu, Feb 08, 2018
tutorial annotation

Getting ribosomal RNA gene sequences from a MinION run

We just started playing with this, we have no idea what we are doing. Kthxbye.

miscellaneous Thu, Jan 18, 2018
tutorial metagenomics

Importing GhostKOALA/KEGG annotations into anvi'o

KEGG modules, meet anvi'o. Anvi'o, meet KEGG modules.

anvio Wed, Jan 17, 2018
tutorial annotation

Working with anvi'o additional data tables

Getting additional data in an out of pan and profile databases like a pro.

anvio Mon, Dec 11, 2017
tutorial

DWH O. desum v2: Most abundant Oceanospirillaceae population in the Deepwater Horizon Oil Plume

Dotting i's and crossing t's with this Deepwater Horizon oil plume drama.

miscellaneous Sat, Nov 25, 2017
population-genetics metagenomics ocean

<i>Ca.</i> Bermanella macondoprimitus is not a strain variant of the oil plume (Reply to Probst et al.)

Ca. Bermanella macondoprimitus is not a strain variant of the oil plume (Reply to Probst et al.)

Continuing to investigate how good that simulation was to simulate the oil spill. With a killer poem.

miscellaneous Mon, Oct 16, 2017
reanalysis metagenomics ocean

Gender Gap at an International Conference on Bioinformatics

And a realization of my own unintentional conformism that is part of a bigger problem

miscellaneous Thu, Sep 14, 2017
social

Candidate Phyla Radiation in Human Blood?

Astonishing if its true. Astonishing if its false. Astonishments all over.

miscellaneous Wed, Aug 23, 2017
reanalysis metagenomics

Recovering ribosomal RNA gene sequences with anvi'o

Use anvi'o to get rRNA genes out of single-cells, clultivars, metagenome-assembled genomes, or even from entire metagenomic assemblies because why not.

anvio Sun, Jul 09, 2017
tutorial metagenomics

Microbial Dark Matter: The mullet of microbial ecology

It may sound cool today, but it will likely be a bit embarrassing to look back and see it in our history in about two decades from now.

miscellaneous Thu, Jun 22, 2017
opinion metagenomics technical

An anvi'o workflow for phylogenomics

That is easy, but not simple

anvio Wed, Jun 07, 2017
tutorial phylogenomics

A thousand microbial genomes from the TARA Oceans metagenomes

On a journey characterizing a thousand population genomes from the surface of oceans and seas

miscellaneous Sun, May 21, 2017
metagenomics binning ocean

Importing Prokka annotations into anvi'o

If Prokka doesn't come to you, you go to Prokka

anvio Thu, May 18, 2017
tutorial annotation

An anvi'o workshop at the Joint Genome Institute

Just for you. Well, also for others. And totally free! Except you pay for your travel. But then it may be a lot of fun. MAYBE.

miscellaneous Wed, May 17, 2017
workshop

The new anvi'o 'news' tab

Is the big brother watching you? If he does, what does he see?

anvio Tue, May 16, 2017
tutorial

Notes on genome refinement with anvi'o

More than just completion and redundancy estimates

anvio Thu, May 11, 2017
tutorial metagenomics

Anvi'o 'views' demystified

Mike Lee heroically demystifies the view options

anvio Mon, May 08, 2017
tutorial visualization

An anvi'o workshop at the University of Chicago

Just for you. Well, also for others. And totally free! Except you pay for your travel. But then it may be a lot of fun. MAYBE.

miscellaneous Thu, Mar 23, 2017
workshop

The new anvi'o BAM profiler

Has decades of suffering of thousands of anvi'o users come to an end?

anvio Tue, Mar 07, 2017
tutorial metagenomics technical

An 800-years-old <i>Salmonella</i> genome, and a lovely anvi'o figure

An 800-years-old Salmonella genome, and a lovely anvi'o figure

From the paper 'Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica'

miscellaneous Sun, Feb 05, 2017
reanalysis visualization

Inspecting the genomic link between Archaea and Eukaryota

Curating the composite metagenome-assembled genome Lokiarchaeum sp. GC14_75 with anvi'o

miscellaneous Tue, Jan 03, 2017
reanalysis phylogenomics

Wavy coverage patterns in mapping results

Coverage, why you do dis?

miscellaneous Wed, Dec 14, 2016
metagenomics visualization technical

Bacteroides Genome Variants, and a reproducible science exercise with anvi'o

The way we made sure everyone has access to the genomes we recovered

miscellaneous Mon, Nov 21, 2016
reanalysis metagenomics human-microbiome

An anvi'o workflow for microbial pangenomics

The user-friendly interface anvi'o provides to work with pangenomes.

anvio Tue, Nov 08, 2016
tutorial pangenomics

Working with SVG files anvi'o generate

In other words, not putting screenshots in papers

anvio Thu, Oct 27, 2016
tutorial visualization

Annotating an anvi'o contigs database with COGs

Yes. Good ol' COGs. Into your contigs db. Just like that. 60% of the time, every time.

anvio Tue, Oct 25, 2016
tutorial annotation

Microbial 'omics and anvi'o workshops

A resource to find out whether we are coming to or you just missed an event close to a location near you.

anvio Thu, Aug 18, 2016
workshop

I dub thee MBL Fellow

Marine Biological Laboratory and I.

miscellaneous Tue, Jul 12, 2016
personal

Assessing completion and contamination of metagenome-assembled genomes

A tale from 4,000+ gold standard bacterial genomes to justify 'max 10% redundancy'

miscellaneous Thu, Jun 09, 2016
reanalysis genome-quality

Chicago Fellows Program

A prestigious post-doc opportunity at a great university environment

miscellaneous Wed, Jun 08, 2016
reanalysis metagenomics

Binning without mapping

So you have an assembly, or a draft genome, or a MAG, but no metagenomic short reads? That's OK.

anvio Mon, Jun 06, 2016
tutorial metagenomics

Making anvi'o use your own HMM collection

Mike Lee demonstrates how to use a custom HMM single-copy gene profile for archaeal genomes

anvio Sat, May 21, 2016
tutorial genome-quality

Predicting CPR genomes in metagenomic bins

A second look at the genomes published by Brown CT. et al

miscellaneous Sun, Apr 17, 2016
reanalysis metagenomics

SF, SD, LA. Going places, meeting people.

Musings from my recent visits to Berkeley, Stanford, USC, and SDSU

miscellaneous Fri, Apr 08, 2016
workshop

The anvi'o interactive interface

Data types, usage tips, and other stuff about the interface

anvio Sat, Feb 27, 2016
tutorial visualization

A short journey into a metagenomic dataset

Musings over a *Nitrospira* genome that can do complete nitrification

anvio Wed, Dec 09, 2015
reanalysis metagenomics technical

How many bacterial genomes do you have in that assembly?

A quick way to get an insight into the number of genomes your contigs represent.

anvio Mon, Dec 07, 2015
tutorial metagenomics technical

Running the interactive interface through an SSH tunnel

For people who does not have time to download stuff.

anvio Sat, Nov 28, 2015
tutorial

An anvi'o workflow for microbial pangenomics (old version)

The user-friendly interface anvi'o provides to work with pangenomes.

anvio Sat, Nov 14, 2015
tutorial pangenomics

Docker image for anvi'o

Fresh anvi'o builds for the lazy.

anvio Sat, Aug 22, 2015
tutorial

OS X installer for anvi'o

Do you want to try anvi'o? Do you have a MAC computer? We got you covered.

anvio Thu, Aug 20, 2015
tutorial

Studying microbial population genetics with anvi'o

Exploring micro-diversity patterns using for deeper insights into ecology

anvio Mon, Jul 20, 2015
tutorial population-genetics

Removing contaminants from cultivars with anvi'o

Anvi'o provides an interface to screen for possible contaminants and curate individual genomes

anvio Thu, Jun 25, 2015
tutorial metagenomics

Comparing different mapping software using anvi'o

Bowtie, Bowtie2, BWA, CLC, GSNAP, BBMap, Novoalign, and SMALT.

anvio Tue, Jun 23, 2015
tutorial metagenomics

Combining metagenomics with metatranscriptomics

Tricks for people who like to go deeper.

anvio Wed, Jun 10, 2015
tutorial metagenomics

Post-doc opportunity in France at LM2E

Life at the extremes: microbial EcoGenomics of deep-sea extremophiles

miscellaneous Fri, May 22, 2015
job-opportunity ecr

Refining a bin using anvi'o

Dealing with heavily contaminated bins identified in an unsupervised manner.

anvio Mon, May 11, 2015
tutorial metagenomics

High-Resolution Microbiome Informatics Meeting, 2015

A small-scale meeting to make a statement about high-resolution.

oligotyping Sat, Mar 14, 2015
workshop oligotyping

New insights into microbial ecology through subtle nucleotide variation

A summary of the oligotyping special topic in Frontiers In Microbiology

oligotyping Thu, Feb 12, 2015
publication oligotyping

Minimum Entropy Decomposition: A new clustering algorithm

1nt resolution at marker gene analyses!

Tue, Nov 04, 2014
publication oligotyping

From QIIME to Oligotyping

A solution by James Meadow

oligotyping Thu, Oct 16, 2014
tutorial oligotyping

Oligotyping and alignment

Answers to some of the questions that have been asked frequently

oligotyping Sun, Sep 14, 2014
tutorial oligotyping

A Docker image for oligotyping

For people who does not want to install the pipeline

oligotyping Tue, Sep 02, 2014
tutorial oligotyping

Installing the oligotyping pipeline

Installing the pipeline shall not be a PITA.

oligotyping Sat, Aug 16, 2014
tutorial oligotyping

Oligotyping analysis of the human oral microbiome

In which we oligotyped the entire oral microbiome data generated by the HMP...

oligotyping Wed, Jun 25, 2014
publication human-microbiome oligotyping

Frontiers in Microbiology Special Topic

A special topic for oligotyping

oligotyping Thu, Dec 12, 2013
publication oligotyping

How to oligotype: Best practices

Flowchart of oligotyping...

oligotyping Mon, Nov 04, 2013
tutorial oligotyping

Methods paper for oligotyping is out!

It is published in Methods in Ecology and Evolution...

oligotyping Wed, Oct 16, 2013
publication oligotyping

Network analysis of the human oral microbiota using oligotypes

The oligotyping pipline generates Gephi-compatible network descriptions.

oligotyping Fri, Mar 29, 2013
publication human-microbiome oligotyping

Sewage reflects the distribution of human faecal Lachnospiraceae

A study that shows the connection between human microbiome and the sewage

oligotyping Thu, Feb 28, 2013
publication human-microbiome oligotyping

Basic sample mapping with oligotyping

If you have a categorical mapping file, the oligotyping pipeline can deliver more

oligotyping Mon, Feb 04, 2013
tutorial oligotyping

Oligotyping Pipeline Explained

How to install, and how to start using the oligotyping pipeline

oligotyping Fri, May 11, 2012
tutorial oligotyping

A Success Story: Gardnerella Vaginalis Profiles Among Sexual Partners

The first story we recovered using oligotyping

oligotyping Wed, May 02, 2012
publication human-microbiome oligotyping