Table of Contents
- Current Members (sorted by name)
- A. Murat Eren (Meren) (PI)
- Alexander Henoch (Graduate Student)
- Avril von Hoyningen-Huene (Post-doctoral Scientist)
- Florian Trigodet (Senior Scientist)
- Iva Veseli (Post-doctoral Scientist)
- Kathryn Lambert-Slosarska (Katy) (Graduate Student)
- Raïssa Meyer (Post-doctoral Scientist)
- Sarah Tucker (Post-doctoral Scientist)
- Xi Chen (Xixi) (Post-doctoral Scientist)
- Honorary Members
- Collaborators
- Alumni (sorted by date)
- Matthew Schechter
- Metehan Sever
- Cynthia Wang
- Emily Fogarty
- Isaac Fink
- Samuel Miller
- Matthew Lawrence Klein
- Evan Kiefl
- Karen Lolans
- Andrea Watson
- Jessica Pan
- Abigail Schmid
- Joe Runde
- Alon Shaiber
- Özcan C. Esen
- Mahmoud Yousef
- Quentin Clayssen
- Sonny T. M. Lee
- Steven Cui
- Tom O. Delmont
- Community
- Michael Yu
- Blair G. Paul
- Antonio Fernandez-Guerra
- Chiara Vanni
- Ryan Moore
- Mike Lee
- Veronika Kivenson
- Antti Karkman
- Elaina Graham
- Bryan Merrill
- Julie Reveillaud
- Vincent J. Denef
- Jacob T. Evans
- Jarrod J. Scott
- Visitors
Interested in joining? Please consider reading the lab culture and expectations first. Some information on our location and space is here. Interested in visiting? Please do! We welcome visitors and short-term research stays as long as we are able -- please send an email to any of us to start the conversation.
This is the most current one. We have an archive of them here.
From left-bottom of the photo to the top of the stairs: Alex Henoch, Iva Veseli, Florian Trigodet, Xixi Chen, Kathryn Lambert-Slosarska (Katy), Metehan Sever. The bottom pair, left-to-right: Avril von Hoyningen-Huene, Chris Robinson (who happened to be visiting our group from the University of Indiana at the time). The top pair: Raïssa Meyer, Sarah Tucker. The photograph is missing our colleagues Samuel Miller, Matthew Schechter, Jessika Fuessel, Amy Willis, and Marie Carstensen who couldn't make it for various reasons.
Current Members (sorted by name)
A. Murat Eren (Meren) (PI)
I am a computer scientist with a deep appreciation for the complexity of life. I design algorithms and experiments to better understand microbes and their ecology.
currentProfessor. Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany.currentProfessor. Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany.currentProfessor. Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany.currentGroup Leader (Head of MPI-HIFMB Bridging Group, Marine 'Omics). Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany.pastFellow. Marine Biological Laboratory, Woods Hole, MA 02543, United States.pastAssistant Professor. The Department of Medicine at the University of Chicago, Chicago, IL 60637, United States.pastCommittee on Microbiology. The Biomedical Sciences Cluster at the University of Chicago, Chicago, IL 60637, United States.
- Modern microbiology: Embracing complexity through integration across scales (2024, Cell)
- New isolate genomes and global marine metagenomes resolve ecologically relevant units of SAR11 (2024, bioRxiv)
- Habitat-specificity in SAR11 is associated with a handful of genes under high selection (2024, bioRxiv)
- Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes (2025, Bioinformatics Advances)
- Digital Microbe: A genome-informed data integration framework for collaborative research on emerging model organisms (2024, Scientific Data)
- .. and 56 more ..
- Evolution of a cover (Sun, Sep 22, 2024)
- From Boats to Bits: Evolution of a study on marine microbes (Mon, Sep 13, 2021)
- Mentorship in life sciences: voices of mentees (Tue, Jun 01, 2021)
- Online seminar series on Microbial 'Omics for beginners (Sat, Jun 27, 2020)
- Visualizing the fate of contigs across metagenomic binning algorithms (Thu, Jan 02, 2020)
- .. and 59 more ..
Alexander Henoch (Graduate Student)
I am a biologist-turned-computer scientist interested in understanding the influence of the environmental change on the genetic composition of microbial populations.
currentGraduate Student. Helmholtz Institute for Functional Marine Biodiversity.currentGraduate Student. Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research.
Avril von Hoyningen-Huene (Post-doctoral Scientist)
I am a microbiologist and bioinformatician delving into the dynamics of phytoplankton communities in response to environmental changes.
currentPost-doctoral Scientist. Helmholtz Institute for Functional Marine Biodiversity.pastPost-doctoral Scientist. Institute for General Microbiology at Kiel University (CAU).pastPhD Student. General and Applied Microbiology at the University of Göttingen.
Florian Trigodet (Senior Scientist)
I am a microbiologist by training, and as a postdoctoral researcher I am using advanced computational strategies to make sense of the microbial ecology of complex habitats.
currentSenior Scientist. Alfred Wegener Institute for Polar and Marine Research.currentSenior Scientist. Helmholtz Institute for Functional Marine Biodiversity.pastPost-doctoral Scientist. Helmholtz Institute for Functional Marine Biodiversity.pastPost-doctoral Scientist. The Department of Medicine at the University of Chicago.
- Assemblies of long-read metagenomes suffer from diverse errors (2025, bioRxiv)
- Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities (2025, bioRxiv)
- Metabolic independence drives gut microbial colonization and resilience in health and disease (2023, Genome Biology)
- Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples (2023, Nature Methods)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- .. and 1 more ..
Iva Veseli (Post-doctoral Scientist)
I am a computer scientist/biologist who leverages computational methods to explore biological data. Currently, I am studying microbial metabolism in environmental metagenomes.
currentPost-doctoral Scientist. Helmholtz Institute for Functional Marine Biodiversity.pastGraduate Student. The Biophysical Sciences Program at the University of Chicago.pastFellow. NSF Graduate Research Fellowship Program.
- Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities (2025, bioRxiv)
- Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes (2025, Bioinformatics Advances)
- Digital Microbe: A genome-informed data integration framework for collaborative research on emerging model organisms (2024, Scientific Data)
- A cryptic plasmid is among the most numerous genetic elements in the human gut (2024, Cell)
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress (2023, eLife)
- .. and 2 more ..
- Targeted binning of a novel nitrogen-fixing population from the Arctic Ocean (Wed, Oct 20, 2021)
- Getting help from the anvi'o community (Mon, Oct 07, 2019)
Kathryn Lambert-Slosarska (Katy) (Graduate Student)
I am a marine (micro)biologist utilising computational approaches to understand the dynamism and impact of diversity-generating retroelements in microbial lifestyles within changing marine ecosystems.
currentGraduate Student. Helmholtz Institute for Functional Marine Biodiversity.currentMarMic Graduate Student. Max Planck Institute for Marine Microbiology.pastMarMic Master's Student. Max Planck Institute for Marine Microbiology.
Raïssa Meyer (Post-doctoral Scientist)
I am a marine microbiologist interested in data interoperability. I work with (meta)data, people, and the systems and standards needed for global 'omics observing of marine microbes.
currentPost-doctoral Scientist. Helmholtz Institute for Functional Marine Biodiversity.pastGraduate Student. Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research.pastGraduate Student. University of Bremen.pastGraduate Student. Max-Planck-Institute for Marine Microbiology.
Sarah Tucker (Post-doctoral Scientist)
I am a marine microbiologist interested in the genomic, metabolic, and physiological diversity of microorganisms and how this diversity impacts ecological interactions and ocean processes. Currently, I am using computational approaches to examine how marine microbes respond to environmental change.
currentPost-doctoral Scientist. Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory.currentFellow. Simons Postdoctoral Fellowship in Marine Microbial Ecology.pastFellow. John A. Knauss Marine Policy Fellowship Program.pastPhD Student. Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Mānoa.
Xi Chen (Xixi) (Post-doctoral Scientist)
I am a bioinformatician and microbial ecologist. I enjoy tailoring computational methods to explore the diversity and dynamics of microbes. My current focus is on those that live in the ocean.
currentPost-doctoral Scientist. Helmholtz Institute for Functional Marine Biodiversity.pastPhD student. Department of Computer Science, University of Tübingen.
Honorary Members
Juniper Veseli (Food Safety Officer)
When I'm not investigating biofilms on food and kitchen counters, I am a social scientist studying the efficacy of different human manipulation techniques. To participate in my research study on cuddling, please contact my study coordinator, Iva.
currentCat.
Kiki Füßel (Mood Regulator)
I am an environmental scientist and a passionate anthropologist who has mastered the use of somatosensory, olfactory, and gustatory systems. If you need to schedule a meeting with me for my services, feel free to reach my personal assistant, Meren.
currentTherapy Dog.
Princess Peach Trigodet (Princess)
In addition to ruling over my domain (and my sister, Juniper), I dabble in materials research by investigating the durability of materials to dental stress. My specialty is cardboard and silicone. If you must be graced by my presence, you may arrange an audience through Florian.
currentHer Majesty.
Collaborators
Those who work closely and actively with our group. It is a fact that we collaborate with many more researchers than what is shown below. The individuals below are those with whom we interact almost daily, who publish with our group very frequently, and with whom we always have something active. They are almost a member of our group with their contributions to our work, but they are just elsewhere.
Jessika Füssel
My aim is to understand the production and fate of microbial metabolites within the context of changing environmental conditions using multi-omics approaches.
currentPost-doctoral Scientist. Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg.
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress (2023, eLife)
- Metabolic independence drives gut microbial colonization and resilience in health and disease (2023, Genome Biology)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
Tom O. Delmont
I am a microbial ecologist who seeks to understand small and large-scale ecological patterns in the microbial world. My most recent investigations focused on humans, pristine soils, and the Southern Ocean.
currentCNRS. Genoscope - Centre National de Séquençage.
- Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities (2025, bioRxiv)
- Bioprospecting marine microbial genomes to improve biotechnology (2024, Nature)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome (2020, Genome Biology)
- Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade (2019, eLife)
- .. and 12 more ..
- Binning giant viruses and their close relatives with anvi'o (Mon, Jan 03, 2022)
- Assessing the completion of eukaryotic bins with anvi'o (Sat, May 05, 2018)
- DWH O. desum v2: Most abundant Oceanospirillaceae population in the Deepwater Horizon Oil Plume (Sat, Nov 25, 2017)
- Ca. Bermanella macondoprimitus is not a strain variant of the oil plume (Reply to Probst et al.) (Mon, Oct 16, 2017)
- A thousand microbial genomes from the TARA Oceans metagenomes (Sun, May 21, 2017)
- .. and 5 more ..
Alumni (sorted by date)
Those who were officiallly affiliated with our group and continued their career elsewhere. If you see yourself or someone else below with outdated information, please edit this file.
Matthew Schechter
Matt was a Graduate Student in our group between 10/2019 and 02/2025. During his time with our group, he developed methods to leverage the growing number of environmental genomes and metagenomes to study the phylogeography of individual proteins. His work led to the creation of EcoPhylo, an easy-to-use computational workflow that integrates ecological and evolutionary perspectives on gene families de novo. The last time we checked (which was in 2025), Matt was A postdoctoral researcher in Luis Barreiro's group at UChicago.
- Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities (2025, bioRxiv)
- Digital Microbe: A genome-informed data integration framework for collaborative research on emerging model organisms (2024, Scientific Data)
- A cryptic plasmid is among the most numerous genetic elements in the human gut (2024, Cell)
- Dietary- and host-derived metabolites are used by diverse gut bacteria for anaerobic respiration (2024, Nature Microbiology)
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress (2023, eLife)
- .. and 1 more ..
- Research week at BIOS: Getting my hands wet with data (Sat, Apr 08, 2023)
- The history of metagenomics: An incomplete summary (Mon, Jul 27, 2020)
- Extract loci from genomes and metagenomes with anvi'o (Thu, Oct 17, 2019)
Metehan Sever
Mete was a Scientific Programmer in our group between 10/2022 and 02/2025. Mete worked on improving anvi'o interactive interfaces by finetuning existing features or adding new ones. Some of his work, especially on how to display and work with phylogenetic trees made anvi'o much more suitable for such applications. The last time we checked (which was in 2025), Mete was A MSc student at the University of Oldenburg.
Cynthia Wang
Cynthia was a Fulbright Scholar in our group between 09/2022 and 07/2023. She investigated computational means to study the interplay between codon composition in genomes and their metabolic priorities. The last time we checked (which was in 2024), Cynthia was A graduate student at the Biophysical Sciences Graduate Program at the University of Chicago.
Emily Fogarty
Emily was a Graduate Student in our group between 06/2018 and 06/2023. Emily put an effort into understanding the ecology and evolution of naturally occurring plasmids of the human gut microbiome. Her work described the ecology of pBI143, a cryptic plasmid that happens to be one of the most prevalent and numerous extrachromosomal circular elements of the human gut. The last time we checked (which was in 2024), Emily was a Clinical Affairs Associate at the Theralink Technologies, Inc..
- A cryptic plasmid is among the most numerous genetic elements in the human gut (2024, Cell)
- Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess (2024, Nature Microbiology)
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress (2023, eLife)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes (2021, Molecular Ecology Resources)
Isaac Fink
Isaac was a Undergraduate Researcher in our group between 04/2020 and 01/2023. Isaac worked on implementing new capabilities for anvi'o to visualize genomic contexts interactively, and contributed code to improve interactive interfaces of anvi'o. The last time we checked (which was in 2024), Isaac was an Associate Software Engineer at Veeva Systems.
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
Samuel Miller
Sam was a Post-doctoral Scientist in our group between 11/2019 and 9/2022. Sam took on one of the most exciting challenges our group had to offer at that time: taking advantage of the recent advances in high-throughput sequencing of short RNA molecules to make sense of microbial tRNA transcripts in complex habitats. Towards this goal, he developed novel and advanced open-source software tools to study all aspects of chemical modification and relative abundance analysis of tRNA transcripts, and combining them with tRNA genes, codons, and metabolisms found in genomes and metagenomes. The last time we checked (which was in 2024), Sam was a Scientific Programmer for the Center for Chemical Currencies of a Microbial Planet at the Marine Biological Laboratory.
- Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities (2025, bioRxiv)
- Digital Microbe: A genome-informed data integration framework for collaborative research on emerging model organisms (2024, Scientific Data)
- Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution (2023, Science Advances)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
Matthew Lawrence Klein
Matthew was a Programmer in our group between 11/2020 and 10/2022. Matthew focused on improving the anvi'o interactive interface. He has made numerous significant contributions to anvi'o that improved the responsiveness of the interactive interface, addressed many bugs, and added most needed features. The last time we checked (which was in 2024), Matthew was a Software Developer in Los Angeles.
Evan Kiefl
Evan was a Graduate Student in our group between 04/2017 and 06/2022. Evan has made technical and intellectual contributions that allowed us to interpret the genetic diversity within naturally occuring microbial populations in the context of their predicted protein structures. The last time we checked (which was in 2024), Evan was a Protein Bioinformatician at Arcadia Science.
- A cryptic plasmid is among the most numerous genetic elements in the human gut (2024, Cell)
- Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution (2023, Science Advances)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade (2019, eLife)
- Estimating per-residue binding frequencies with InteracDome (Wed, Jul 22, 2020)
- Extract loci from genomes and metagenomes with anvi'o (Thu, Oct 17, 2019)
- Integrating sequence variants and predicted protein structures (Tue, Sep 04, 2018)
- Studying microbial population genetics with anvi'o (Mon, Jul 20, 2015)
Karen Lolans
Karen was a Senior Research Technician in our group between 07/2018 and 10/2021. Karen has made significant contributons to the wet-lab branch of our group at the University of Chicago by creating and benchmarking protocols for tRNA sequencing and high molecular weight DNA extraction for long-read sequencing even from most challenging samples of low-biomass and host contamination. The last time we checked (which was in 2024), Karen was a Senior Technician at the University of Chicago.
- A cryptic plasmid is among the most numerous genetic elements in the human gut (2024, Cell)
- Metabolic independence drives gut microbial colonization and resilience in health and disease (2023, Genome Biology)
- High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes (2021, Molecular Ecology Resources)
- Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome (2020, Genome Biology)
- The Wolbachia mobilome in Culex pipiens includes a putative plasmid (2019, Nature Communications)
Andrea Watson
Andrea was a Graduate Student in our group between 06/2017 and 09/2021. Throughout her graduate work, Andrea investigated the determinants of microbial colonization in the human gut, a critical question of the human microbiome research that has been beyond our reach outside of simplified model systems. Using genome-resolved metagenomics and fecal microbiota transplantation experiments, Andrea has found some answers to discuss the factors that influence microbial biodiversity in stressful gut environments. The last time we checked (which was in 2024), Andrea was a Bioinformatics Scientist II at Vedanta Biosciences.
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress (2023, eLife)
- Metabolic independence drives gut microbial colonization and resilience in health and disease (2023, Genome Biology)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome (2020, Genome Biology)
- Droplet-based high-throughput cultivation for accurate screening of antibiotic resistant gut microbes (2020, eLife)
- .. and 2 more ..
- A reading list for scientists to recognize and confront anti-Black racism (Mon, Oct 05, 2020)
Jessica Pan
Jessica was a Undergraduate Researcher in our group between 06/2019 and 09/2020. Jessica has joined our lab as a high-school student and made significant contributions to the completely brand-new anvi'o help system. The last time we checked (which was in 2024), Jessica was a Computer Science Master's Student at the Massachusetts Institute of Technology.
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis (2018, Nature Communications)
Abigail Schmid
Abby was a Undergraduate Researcher in our group between 10/2017 and 09/2020. Abby joined our group as an undergraduate researcher and used pangenomics and metagenomics for high-throughput characterization on hypervariable genomic islands of some of the most prevalent members of the human microbiome. Her work left behind a treasure trove of insights into some of the most interesting parts of microbial genomes. The last time we checked (which was in 2024), Abby was an Engineering Science PhD student at the University of Colorado Boulder.
Joe Runde
Joe was a Physician Researcher in our group between 07/2018 and 07/2020. In addition to serving as a Physician Researcher at the University of Chicago Medicine, Joe joined our group to study with us the microbial community dynamics in Chron's disease during Exclusive Enteral Nutrition therapy. His dedication and passion had a huge influence on our lab culture and dynamics. The last time we checked (which was in 2023), Joe was an Assistant Professor at the Lurie Children's Hospital, Northwestern University.
Alon Shaiber
Alon was a Graduate Student in our group between 10/2016 and 02/2020. Throughout his studies of the human oral cavity microbiome and its enigmatic members via genome-resolved metagenomics, he served the community with his open code and tutorials. Alon, the very first graduate student to join our group, dramatically influenced the trajectory of our science. The last time we checked (which was in 2024), Alon was the Computational Biology Team Lead at Immunai.
- Metabolic independence drives gut microbial colonization and resilience in health and disease (2023, Genome Biology)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes (2021, Molecular Ecology Resources)
- Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome (2020, Genome Biology)
- Accurate and complete genomes from metagenomes (2020, Genome Research)
- .. and 5 more ..
- Extract loci from genomes and metagenomes with anvi'o (Thu, Oct 17, 2019)
- Accessing and including NCBI genomes in 'omics analyses in anvi'o (Thu, Mar 14, 2019)
- Microbial 'Omics Workshop (Sun, Sep 09, 2018)
- Anvi'o snakemake workflows (Mon, Jul 09, 2018)
- An anvi'o workflow for microbial pangenomics (Tue, Nov 08, 2016)
Özcan C. Esen
Ozcan was a Programmer in our group between 02/2016 and 02/2020. Ozcan worked on anvi'o since it was nothing more than an idea, and has been one of the most prolific developers of it during the last five years. His remarkable contributions to the interactive capabilities of anvi'o has always been a critical component of the platform, and will continue to help many life scientists who use anvi'o.
- Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution (2023, Science Advances)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome (2020, Genome Biology)
- Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade (2019, eLife)
- The Wolbachia mobilome in Culex pipiens includes a putative plasmid (2019, Nature Communications)
- .. and 5 more ..
- Running remote anvi'o interactive interfaces on your local computer (Wed, Mar 07, 2018)
- An anvi'o workflow for microbial pangenomics (Tue, Nov 08, 2016)
- The anvi'o interactive interface (Sat, Feb 27, 2016)
Mahmoud Yousef
Mahmoud was a Undergraduate Researcher in our group between 05/2017 and 02/2020. Focusing on pangenomics, he developed functional and geometric homogeneity indices so we can interpret the heterogeneity within gene clusters. The last time we checked (which was in 2024), Mahmoud was an MD/PhD student at the Pritzker School of Medicine, University of Chicago.
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome (2020, Genome Biology)
- Amino acid color coding by conservation in anvi'o gene clusters (Tue, Feb 13, 2018)
- An anvi'o workflow for microbial pangenomics (Tue, Nov 08, 2016)
Quentin Clayssen
Quentin was a FACCTS Visiting Scientist in our group between 04/2019 and 10/2019. He contributed to the development of an anvi'o framework for the rapid determination of genome taxonomy. The last time we checked (which was in 2024), Quentin was a Bioinformatician at DNA Script.
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
Sonny T. M. Lee
Sonny was a Post-doctoral Scientist in our group between 05/2016 and 05/2018. He took the responsibility of leading the Fecal Microbiota Transplantation work in our lab. Sonny also was the driving force behind setting up the wet-lab component of our group. The last time we checked (which was in 2024), Sonny was an Associate Professor of Microbial Ecology (http://www.the-lee-lab.com) at the Kansas State University, Division of Biology.
- Metabolic independence drives gut microbial colonization and resilience in health and disease (2023, Genome Biology)
- Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome (2020, Genome Biology)
- Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes (2018, Nature Microbiology)
- Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics (2017, Microbiome)
Steven Cui
Steven was a Summer Student in our group between 07/2016 and 10/2016. He contributed to the development of tRNA-seq tools, a project that bridged Meren's and Tao Pan's interests. The last time we checked (which was in 2024), Steven was a Principal Associate and a Senior Software Engineer Capital One.
- Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis (2018, Nature Communications)
Tom O. Delmont
Tom was a Post-doctoral Scientist in our group between 10/2015 and 05/2018. He contributed to the development of anvi'o and its application to the ocean and gut metagenomes. Tom was the very first member of our lab, and Meren and Tom have spent lots of time together thinking about new ways to make sense of metagenomic data. The last time we checked (which was in 2024), Tom was a CNRS scientist at the Genoscope in France.
- Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities (2025, bioRxiv)
- Bioprospecting marine microbial genomes to improve biotechnology (2024, Nature)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome (2020, Genome Biology)
- Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade (2019, eLife)
- .. and 12 more ..
- Binning giant viruses and their close relatives with anvi'o (Mon, Jan 03, 2022)
- Assessing the completion of eukaryotic bins with anvi'o (Sat, May 05, 2018)
- DWH O. desum v2: Most abundant Oceanospirillaceae population in the Deepwater Horizon Oil Plume (Sat, Nov 25, 2017)
- Ca. Bermanella macondoprimitus is not a strain variant of the oil plume (Reply to Probst et al.) (Mon, Oct 16, 2017)
- A thousand microbial genomes from the TARA Oceans metagenomes (Sun, May 21, 2017)
- .. and 5 more ..
Community
Those who generously shared their experiences, opinions and/or computational expertise with us and others through blog posts that appeared on our web pages. If you see yourself or someone else below with outdated information, please edit this file.
Michael Yu
I develop new machine learning methods and algorithms to study large biomedical datasets. I'm interested in transferring techniques in computational biology to other fields, including natural language processing.
- Research Assistant Professor. Toyota Technological Institute at Chicago.
- A cryptic plasmid is among the most numerous genetic elements in the human gut (2024, Cell)
- Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess (2024, Nature Microbiology)
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress (2023, eLife)
- Metabolic independence drives gut microbial colonization and resilience in health and disease (2023, Genome Biology)
Blair G. Paul
Our lab investigates the influence of genetic variation on physical and chemical interactions among microorganisms, with additional interest in microbe-virus dynamics.
- Assistant Scientist. Marine Biological Laboratory.
Antonio Fernandez-Guerra
My group and I develop and apply new methodologies to analyze modern and ancient (meta)genomic data. We like to use ancient microbes to reconstruct past environments and make sense of the genes of unknown function in genomes and metagenomes.
- Assistant Professor. Lundbeck Foundation GeoGenetics Centre, The GLOBE Institute, University of Copenhagen.
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Welcome to the dark side of genomes and metagenomes (Wed, Jul 01, 2020)
Chiara Vanni
- Graduate Student. Max Planck Institute for Marine Microbiology.
Ryan Moore
- Graduate Student (Wommack Lab). Center for Bioinformatics and Comp Bio, University of Delaware.
- A cryptic plasmid is among the most numerous genetic elements in the human gut (2024, Cell)
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
Mike Lee
- NASA Space Biology Fellow. NASA Ames Research Center.
- JCVI Research Fellow. J. Craig Venter Institute.
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Combining reference genome annotations with your own in pangenomes (Sat, Dec 01, 2018)
- Anvi'o 'views' demystified (Mon, May 08, 2017)
- Making anvi'o use your own HMM collection (Sat, May 21, 2016)
Veronika Kivenson
- Graduate Student. Earth Science, UC Santa Barbara.
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Notes on genome refinement with anvi'o (Thu, May 11, 2017)
Antti Karkman
- Postdoctoral researcher. University of Helsinki.
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Importing Prokka annotations into anvi'o (Thu, May 18, 2017)
Elaina Graham
- Graduate Student. University of Southern California.
- Importing GhostKOALA/KEGG annotations into anvi'o (Wed, Jan 17, 2018)
Bryan Merrill
- Graduate Student. Department of Microbiology & Immunology, Stanford University.
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Importing VirSorter annotations into anvi'o to study phages (Thu, Feb 08, 2018)
Julie Reveillaud
- Research Scientist. INRA, ASTRE Unit, Montpellier, France.
- The Wolbachia mobilome in Culex pipiens includes a putative plasmid (2019, Nature Communications)
- Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents (2017, Nature Communications)
- Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences (2015, The ISME Journal)
- Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals? (2014, PLoS One)
- Host-specificity among abundant and rare taxa in the sponge microbiome (2014, The ISME Journal)
Vincent J. Denef
- Assistant Professor. Ecology and Evolutionary Biology, University of Michigan.
- To dereplicate or not to dereplicate? (Thu, Dec 12, 2019)
Jacob T. Evans
- Bioinformatician. Ecology and Evolutionary Biology, University of Michigan.
- To dereplicate or not to dereplicate? (Thu, Dec 12, 2019)
Jarrod J. Scott
- Post-doctoral Scientist. Smithsonian Tropical Research Institute.
- Community-led, integrated, reproducible multi-omics with anvi'o (2021, Nature Microbiology)
- Visualizing the fate of contigs across metagenomic binning algorithms (Thu, Jan 02, 2020)
Visitors
Those who visited our laboratory for a period of a week or longer.
Amy D Willis
Amy, who was a Professor at Department of Biostatistics, University of Washington 🇺🇸, arrived on 09/2024 and stayed with us for about 9 months. Amy's visit was more than a visit -- it was a true sabbatical during which we took advantage of the new genomes in public databases to investigate the codon variation landscape throughout the tree of life as a function of microbial ecology, evolution, and metabolism. Members of our group is forever thankful to the members of Amy's group for sharing her with us.Siyu Mei
Mei, who was a Graduate Student at Groningen Institute for Evolutionary Life Science, University of Groningen 🇳🇱, arrived on 03/2025 and stayed with us for about 1 month.Chris Robinson
Chris, who was a Graduate Student at Department of Biology, Indiana University 🇺🇸, arrived on 11/2024 and stayed with us for about 6 weeks.Eeva Eronen-Rasimus
Eeva, who was a Senior Researcher at Marine Reserach Center, Finnish Environmental Institute 🇫🇮, arrived on 10/2024 and stayed with us for about 10 days.
Eeva, Igor, and Tommi during a lunch meeting with the rest of the group :)
Tommi Välikangas
Tommi, who was a Postdoctoral Scientist at , Natural Resources Institute Finland 🇫🇮, arrived on 10/2024 and stayed with us for about 10 days.Igor Pessi
Igor, who was a Postdoctoral Scientist at , Finnish Environment Institute 🇫🇮, arrived on 10/2024 and stayed with us for about 10 days.Stephen J Giovannoni
Steve, who was a Professor at Department of Microbiology, Oregon State University 🇺🇸, arrived on 07/2024 and stayed with us for about 3 months. A large proportion of the logistics of Steve's visit was coordinated by the Hanse-Wissenschaftskolleg (HWK), an independent institute for advanced study and a non-profit foundation. We are extremely lucky in Oldenburg that such an institute exists and supports international collaborators who wish to visit a lab in the region. If you are thinking about coming here for a sabbatical or a for a few months of research stay, please consider visiting the HWK web page.
Journal Club with Steve.
Arthur Cousson
Arthur, who was a Graduate Student at EcoSols Joint Research Unit, Institut Agro Montpellier 🇫🇷, arrived on 05/2024 and stayed with us for about 8 weeks.
Arthur and others.
Oleg Vlasovets
Oleg, who was a Graduate Student at , Helmholtz Zentrum München 🇩🇪, arrived on 01/2024 and stayed with us for about 3 months.
Lunch meeting with Oleg (on the most left), Daan Speth, Tom Delmont, Sarahi Garcia, and others in the lab.
Mary Ann Moran
Mary Ann, who was a Professor at Department of Marine Sciences, University of Georgia 🇺🇸, arrived on 10/2023 and stayed with us for about a week.
Sarahi Garcia, Sandra McLellan, Jessika Fuessel, Meren, and Mary Ann Moran in Bremen.
Sandra McLellan
Sandra, who was a Professor at School of Freshwater Sciences, University of Wisconsin-Milwaukee 🇺🇸, arrived on 10/2023 and stayed with us for about a week.Jed Fuhrman
Jed, who was a Professor at Wrigley Institute for Environmental Studies, University of Southern California 🇺🇸, arrived on 09/2022 and stayed with us for about a week.
Tom Delmont, Jed Fuhrman, Meren, and all the carboard boxes.