Meren Lab

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Current (13) Previous (10) Collaborators (6) Community (11)

2020 | 2019

Interested in joining? Please consider reading the lab culture and expectations first. Some information on our location and space is also here.

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. [photos: 1, 2, 3].

MBL Fellow, Marine Biological Laboratory.
Assistant Professor, The Department of Medicine at the University of Chicago.
Committee on Microbiology, The Biomedical Sciences Cluster at the University of Chicago.

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)
Genome / metagenome / MAG taxonomy with anvi'o (Tue, Oct 08, 2019)
Accessing and including NCBI genomes in 'omics analyses in anvi'o (Thu, Mar 14, 2019)
.. and 57 more ..

Andrea Watson (Graduate Student)

I am interested in combining wet lab and computational methods in a complementary way to answer microbiological questions.

Graduate Student, Committee on Microbiology at the University of Chicago.

A reading list for scientists to recognize and confront anti-Black racism (Mon, Oct 05, 2020)

Emily Fogarty (Graduate Student)

I am interested in developing computational and wet lab strategies to study horizontal gene transfer in the human gut microbiome.

Graduate Student, Committee on Microbiology at the University of Chicago.

Visualizing contig coverages to better understand microbial population structures (Mon, Nov 25, 2019)

Evan Kiefl (Graduate Student)

I am interested in uncovering how single nucleotide variants map to functional variation in the genes of naturally-occuring microbial populations.

Graduate Student, The Biophysical Sciences Program at the University of Chicago.

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)

Florian Trigodet (Post-doctoral 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.

Post-doctoral Scientist, The Department of Medicine at the University of Chicago.

Ibrahim Mohamed (Undergraduate Researcher)

“I am a student researcher interested in applying concepts from mathematics and computer science to understand and analyze metagenomes.”

Undergraduate Student, Mathematics.

Isaac Fink (Undergraduate Researcher)

“I am interested in enhancing the power and accessibility of computational tools that analyze the microbiome.”

Undergraduate Student, Computer Science.

Iva Veseli (Graduate Student)

I am a computer scientist/biologist who leverages computational methods to explore biological data. Currently, I am studying microbial metabolism in environmental metagenomes.

Graduate Student, The Biophysical Sciences Program at the University of Chicago.
Fellow, NSF Graduate Research Fellowship Program.

Getting help from the anvi'o community (Mon, Oct 07, 2019)

Karen Lolans (Senior Research Technician)

As a molecular microbiologist, I am interested in the potential that interwoven wet lab and computational strategies play in elucidating complex microbial interactions and processes.

Senior Research Technician, The University of Chicago Section of Gastroenterology, Hepatology and Nutrition.

Kiki Füßel (Mood Regulator)

I am an environmental scientist and a passionate anthropologist who has mastered the use of somatosensory, olfactory, and gustatory systems. I am often quite busy, but if you need to schedule a meeting with me for my services, you can ask anyone in the lab to have access to my calendar.

Therapy Dog.

Matthew Lawrence Klein (Programmer)

“I am interested in technology's role in supporting a more equitable future on planet earth.”

Programmer, The Department of Medicine at the University of Chicago.

Matthew Schechter (Graduate Student)

I am interested in combining comparative genomics and environmental metagenomics to identify genetic determinants of fitness in microbial populations in the human gut and ocean microbiome.

Graduate Student, Committee on Microbiology at the University of Chicago.

Integrating AGNOSTOS gene categories into anvi'o projects (Fri, May 28, 2021)
The history of metagenomics: An incomplete summary (Mon, Jul 27, 2020)
Extract loci from genomes and metagenomes with anvi'o (Thu, Oct 17, 2019)

Samuel Miller (Post-doctoral Scientist)

I study how microbes function in their environments by developing and applying computational tools to interpret data from approaches such as tRNA-sequencing, proteomics, and metagenomics.

Post-doctoral Scientist, The Department of Medicine at the University of Chicago.

Collaborators and Partners in Science

Our partners in science who work closely and actively with our group. Undoubtedly, this list will forever be incomplete. We collaborate with many more scientists and we benefit from the guidance of many of our senior colleagues. This dynamic list is meant to mention our most active collaborators with whom we interact almost daily to weekly (sorted by name, please edit this file if updates necessary).

Amy D. Willis

My lab and I develop statistical and computational methods for the analysis of biodiversity data, with a particular focus on the microbiome. Like the Meren lab, I'm passionate about reproducible science, meaningful data analysis, ecosystem and host health, outreach and education, and collaborating with scientists who share these values.

Principal Investigator, Statistical Diversity Lab, University of Washington.
Assistant Professor, Department of Biostatistics, University of Washington.

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.

Welcome to the dark side of genomes and metagenomes (Wed, Jul 01, 2020)

Arda Söylev

I am a computer scientist, interested in designing algorithms to analyze and understand microbiome and also structural variations in modern and ancient genomes.

Assistant Professor, Konya Food and Agriculture University.

Jessika Fuessel

My aim is to understand the production and fate of microbial metabolites within the context of changing environmental conditions using a multi-omics approaches.

Post-doctoral Scientist, Department of Medicine, University of Chicago.

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.

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.

CNRS, Genoscope - Centre National de Séquençage.

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)
Inspecting the genomic link between Archaea and Eukaryota (Tue, Jan 03, 2017)
.. and 4 more ..

Previous Members (sorted by date)

Those who were officiallly affiliated with our group but now continue their career elsewhere. If you see yourself or someone else below with outdated information, please edit this file.

Jessica Pan

Jessica was a Undergraduate Researcher with us 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, Jessica was an undergraduate student at the Massachusetts Institute of Technology.

Abigail Schmid

Abby was a Undergraduate Researcher with us 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, Abby was a computational modeling Post-Bac student at the Los Alamos National Laboratory.

Joe Runde

Joe was a Physician Researcher with us 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, Joe was an Assistant Professor at the Lurie Children's Hospital, Northwestern University.

Alon Shaiber

Alon was a Graduate Student with us 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, Alon was a Genomics Data Scientist at Weill Cornell Medicine.

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 with us 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.

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 with us 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, Mahmoud was a medical student at the Pritzker School of Medicine, University of Chicago.

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 with us 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, Quentin was a graduate student at the ETH Zurich.

Sonny T. M. Lee

Sonny was a Post-doctoral Scientist with us 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, Sonny was an Assistant Professor of Microbial Ecology (http://www.the-lee-lab.com) at the Kansas State University, Division of Biology.

Tom O. Delmont

Tom was a Post-doctoral Scientist with us 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, Tom was a CNRS scientist at the Genoscope in France.

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)
Inspecting the genomic link between Archaea and Eukaryota (Tue, Jan 03, 2017)
.. and 4 more ..

Steven Cui

Steven was a Summer Student with us 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, Steven was a Software Engineer at Capital One.

Community

Members of our community who generously shared their experiences, opinions and/or computational expertise with others through blog posts. If you see yourself or someone else below with outdated information, please edit this file.