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.
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.
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.
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.
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.
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.”
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.
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.
Those we miss (sorted by date)
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.
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.
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.
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.
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.
Ryan Moore
- Graduate Student (Wommack Lab), Center for Bioinformatics and Comp Bio, University of Delaware.
Mike Lee
- NASA Space Biology Fellow, NASA Ames Research Center.
- JCVI Research Fellow, J. Craig Venter Institute.
- 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.
- Notes on genome refinement with anvi'o (Thu, May 11, 2017)
Antti Karkman
- Postdoctoral researcher, University of Helsinki.
- 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.
- Importing VirSorter annotations into anvi'o to study phages (Thu, Feb 08, 2018)
Julie Reveillaud
- Research Scientist, INRA, ASTRE Unit, Montpellier, France.
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.
- Visualizing the fate of contigs across metagenomic binning algorithms (Thu, Jan 02, 2020)
Antonio Fernandez-Guerra
- 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)