Andrea Watson

Andrea was a Graduate Student with us between 06/2017 and 09/2021. Throughout her graudate 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 microbiata transplantation experiments, Andrea has found some answers to discuss the factors that influence microbial biodiversity in stressful gut environments. The last time we checked, Andrea was a Bioinformatics Scientist at Vedanta Biosciences.

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

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.