Donia Lab
Department of Molecular Biology
Guyot Hall, Moffett Laboratory
Washington Road
Princeton, NJ 08544
Washington Road
Princeton, NJ 08544
(609)-258-3841
Faculty Assistant
Karen E. Plantarich
217 Schultz Laboratory
(609)-258-5028
Human Microbiome & Marine Symbiosis
DIVERSE SYSTEMS + DIVERSE SCIENTISTS = AMAZING DISCOVERIES
Overview
Much like human beings, microbes often live in diverse communities interacting with both collaborators and competitors. Small molecule natural products mediate a significant portion of these interactions. As expected, the more complex a microbial community is, the richer its small molecule chemical arsenal becomes.
The Donia Lab brings together a diverse and talented group of scientists at the intersection between multiple disciplines: microbiology, molecular biology, biochemistry, pharmacology, small molecule chemistry and biosynthesis, metagenomics, and computational biology, aiming to answer basic biological questions and to develop new therapeutics.
Research
Microbiome-derived metabolism of administered drugs
Small-molecule mediated interactions in marine symbiosis
Small-molecule mediated interactions in the human microbiome
Microbiome-derived metabolism of administered drugs
In addition to the de novo production of small molecules, the human gut microbiome encodes a large repertoire of biochemical enzymes that can metabolize exogenous small molecules – whether they are derived from the human host, or from dietary or therapeutic sources. This concept has been explored for decades by using single isolates of the human microbiome against a common set of human-, drug-, or diet-derived chemicals, but has not been explored systematically. We aim to expand this area of research by developing high-throughout, unbiased approaches for defining the space of biochemical transformations that can be exerted by the collective human gut microbiome against a wide variety of chemicals, and the pharmacological consequences of these transformations.
Small-molecule mediated interactions in marine symbiosis
In the case of marine organisms (e.g., sponges, tunicates, mollusks, algae) and their symbionts, small-molecule-mediated interactions can provide the host with indispensable means of chemical defense, allowing it to survive in a predator-rich environment. We characterize these interactions by first determining the true microbial producers of the defensive molecules and the molecular mechanisms of their production, then we study the evolution of the symbiosis in light of the production of these molecules, and finally, we study the ecological consequences of their production for all interacting partners.
Small-molecule mediated interactions in the human microbiome
With respect to the human body and its microbial inhabitants (the human microbiome), small-molecule-mediated interactions can define the difference between commensals and pathogens, and thus between health and disease states. We are interested in studying these interactions at three main levels: a) identifying the chemical repertoire of the human microbiome; b) characterizing the biological activities and functional roles of the identified molecules in mediating microbiome-host interactions in health and disease states; and finally c) using this knowledge to aid the diagnosis and treatment of human diseases via microbiome-targeted therapies.
Selected Publications
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People
Associate Professor
Dr. Donia received his B.Sc in Pharmacy from the Faculty of Pharmacy, Suez Canal University, Egypt in 2004. He moved to the US in 2005 to study for his Ph.D. at the Medicinal Chemistry Department, School of Pharmacy, University of Utah. He worked in Dr. Eric Schmidt’s laboratory where he studied the chemistry and biology of small molecules produced by bacterial symbionts of marine animals. He used chemical, microbiological, and metagenomic techniques to study the role of small molecules in mediating microbe-host and microbe-microbe interactions in marine invertebrates. In 2010, he joined Dr. Michael Fischbach’s laboratory at the Department of Bioengineering and Therapeutic Sciences at the University of California, San Francisco. There, he studied small molecules produced by members of the human microbiome and their role in mediating microbe-host and microbe-microbe interactions in humans. In particular, he focused on antibiotics produced by human pathogens and commensals, and their role in shaping the composition and dynamics of the human vaginal and oral microbiota. Dr. Donia is a recipient of the NIH Director’s New Innovator Award, the Kenneth Rainin Foundation Innovation and Breakthrough Awards, and is named a Pew Biomedical Scholar. Dr. Donia is a member of the Scientific Advisory Board for Deepbiome Therapeutics.
Jie Liu
I received my PhD in Microbiology at Rutgers University studying the eco-physiology of organohalide respiring bacteria from marine environments. My broad research interests encompass the interactions of microorganisms with its environment/hosts. In the Donia lab, I study chemical sequestration and kleptoplasty in a complex tripartite marine symbiosis.
Paola Estrada
I obtained my B.S in Forensic Science from John Jay College of Criminal Justice. I then went to Hunter College where I worked in the Kawamura Lab isolating small molecules from soil bacteria. For my PhD I went to the University of Illinois (UIUC) and worked in the Nair Lab on the biochemical and structural characterization of enzymes involved small molecule biosynthesis. In the Donia Lab I will be investigating small molecules from the human microbiome.
Moamen Elmassry
I received my Bachelor of Pharmaceutical Sciences from the Faculty of Pharmacy, Cairo University, Egypt. Then, I obtained my Ph.D. in Biology from Texas Tech University, Lubbock, Texas. In my dissertation, I focused on Pseudomonas aeruginosa pathogenesis during sepsis in trauma patients. In the Donia Lab, I study the contribution of the gut microbiota to the human metabolome (and health). I value collaborative research and teaching. I enjoy reading, humanities talks, Tai Chi, sports, and video games.
Ruojun Wang
I grew up in Shanghai, China, and received my B.S. from Fudan University. I then received my Ph.D. in Immunology and Microbial Pathogenesis from Weill Cornell Medical College before joining the Donia Lab. My top interests are host-microbe interactions in health and disease. Outside of the lab, I enjoy birdwatching, photography, and traveling.
Laura Ióca
I received my BSc in Physical and Biomolecular Sciences and my MSc and PhD in Organic and Biological Chemistry at the University of São Paulo, Brazil. In the Donia Lab, I am investigating the biosynthesis machinery of marine symbionts that produce unique natural products scaffolds. Outside of the lab I enjoy listening podcasts and doing puzzles together with a nice cup of tea.
Luis Jesus Linares-Otoya
I received my BSc and MSc in Animal Science at the National University of Trujillo (Peru) and Bonn University (Germany), respectively. Later I obtained my PhD at the University of Bonn / JLU- Giessen (Germany) studying the biosynthesis of natural products from marine bacteria. I am interested in understanding the role of secreted metabolites in microbial communities. In the Donia Lab I study the regulation and biosynthesis of small molecules produced by obligated bacterial endosymbionts and marine bacteroidetes. Outside of the lab I enjoy watching/reading Sci-FI, swimming and cooking.
Sunghoon Hwang
I am from South Korea. I received my BS in Pharmacy from Seoul National University. For my PhD, I studied microbial natural product chemistry, specifically structure elucidation. In the Donia Lab, I am interested in the expression of genes and discovery of the compounds from the human microbiome. In my free time I enjoy exercising, reading, and traveling around.
Bhuwan Khatri Chhetri
I graduated from Kathmandu University, Nepal with a bachelor’s degree in pharmacy. My master’s degree is in chemistry where I worked under Dr. William N. Setzer at University of Alabama, Huntsville on plant natural products-based drug discovery. I moved to University of Texas, San Antonio for a year as a postmaster researcher to work under Dr. Oleg Larionov on synthetic organic chemistry. I completed my PhD in organic chemistry under the supervision of Dr. Julia Kubanek at Georgia Institute of Technology working on the exploration of marine macroorganisms for drug discovery. In the Donia lab, I am interested in unraveling the molecular mechanisms involved in the chemical sequestration in marine symbioses. In my spare time, I enjoy being with my family, cooking, and music composition.
Jeffrey Lee
Mol Bio Graduate Student
I received my B.A. in Biology as well as an MPH in Global Health and an MEng in Energy, Environment, and Chemical Engineering from Washington University in St. Louis. Currently my work is focused on the capture and characterization of peptides from the human microbiome with a particular focus on examining the roles these peptides may have in microbe-microbe and host-microbe interactions. I am interested in how peptides can be harnessed to improve human health in addition to issues of biosecurity, therapeutics, and science policy.
Catherine Day
Mol Bio Graduate Student
I grew up in northern California and received my B.S. in Biology from the California Institute of Technology. In the Donia Lab, I will be studying antibiotic resistance. Outside of research, I enjoy traveling, playing video games and doing puzzles.
Jongbeom Park
Mol Bio Graduate Student
I grew up in Daegu, South Korea and received my BA in Biology from Grinnell College. I am broadly interested in evolutionary biology and developmental biology. I currently plan to investigate the role of peptides in mammalian development. My hobbies include indoor rock climbing, driving, and eating.
Xuanqi (Ivy) Chen
CBE Graduate Student
I received my B.S. in Chemical Engineering from UW-Madison. I am broadly interested in human health care and biotech. In the Donia Lab, I will be using both computational and experimental approach to study human gut microbiome. Outside of lab, I enjoy city explorations, hiking and occasionally skiing.
I grew up in NYC and received my B.S. in Biological Sciences from Cornell University, where I studied plant pathology. Before joining the Donia Lab, I spent two years working at the Broad Institute developing tools for genetic code expansion. Currently, my work focuses on ecologically and functionally relevant host-microbe interactions in marine symbioses. Outside of research I enjoy gardening and fermenting foods, and by extension I keep the lab stocked with freshly-baked loaves of sourdough!
I grew up in the DC area and attended Dartmouth College in New Hampshire, where I studied biology and anthropology. My interests span the realm of microbiology and human health, including biofilm maintenance, the microbiome, and equity in healthcare. I’m interested in drug metabolism by the gut microbiome. When not at the bench, I enjoy embroidery, being outdoors, and spending time with friends.
I’m a New Jersey Native, having both grown up here and gone to school at Rutgers University-New Brunswick. Before Joining the Donia lab, I did 2 years of medical school at Robert Wood Johnson Medical School through the MD/PhD program. Currently, I’m using a multi-omics approach to investigate host-microbe interactions in the gut microbiome. Outside of the lab, I love coffee, watching formula 1 races, and riding my bike!
I got my B.S. in Biology with a minor in Sociology and Anthropology from Fordham University in NYC. In the Donia Lab, I am interested in understanding how the microbiome affects cancer progression. My hobbies include drawing, gardening, and cooking up a feast for friends and family.
I grew up in Delaware and received my B.S.E. in Chemical & Biomolecular Engineering from the University of Pennsylvania. In the Donia Lab, I’m interested in host-microbe and microbe-microbe interactions in health and disease. Outside of the lab, my hobbies include crochet, baking, and theatre.
Julia Garaffa
Molecular Biology Undergraduate
I am from Montgomery, New Jersey, and a member of the class of 2023. In the Donia Lab, I am exploring metabolism of drugs by bacteria in the gut microbiome. Outside of the lab, I am a Residential College Advisor and involved with music and comedy.
Ye Chen
Molecular Biology Undergraduate
I am from Toms River, New Jersey and am a member of the Class of 2023. In the lab, I am investigating mechanisms of gene regulation through quorum sensing. I enjoy writing, learning new languages, and also work performances for Princeton’s Richardson Auditorium.
Isabella Swartz
Molecular Biology Undergraduate
I’m from Warrington, Pennsylvania, and I’m a member of the Class of 2024. On campus I also volunteer with CONTACT which focuses on emotional support and suicide prevention, and I love baking, reading, and doing puzzles.
Katherine Carroll
Chemical and Biological Engineering Undergraduate
I am from Chicago, Illinois and I am in the class of 2024. I am a part of the Chemical and Biological Engineering department, with a certificate in Computer Science. Outside of classes, I am on the open weight rowing team and am in the Entrepreneurship Club.
Seema Chatterjee
Lab Manager
Karen E. Plantarich
Faculty AssistantName | Current |
| Jaime Lopez (Graduate Student) | Post-doc, Stanford University |
| Mary Davis (Undergraduate Student ’22) | |
| Christian Hernandez (Undergraduate Student ’22) | |
| Anna Schmedel (Faculty Assistant) | |
| Shuo Wang (PhD Graduate Student) | |
| Amira Mira (Postdoctoral Research Fellow) | Assistant Professor, Mansoura University, Egypt |
| Janie Kim (Princeton Undergrad ’21) | Graduate Student, Stanford University |
| Nisha Chandra (Princeton Undergrad ’21) | |
| Jared Balaich (PhD Graduate Student) | |
| Bahar Javdan (MD-PhD Graduate Student) | |
| Amir Erez (Post-doc) | |
| Dani Peters (Princeton Undergrad ’20) | |
| Francine Camacho (PhD Graduate Student) | Viome |
| Yuki Sugimoto (Post-doc) | |
| Zhiyuan Li (Post-doc) | Assistant Professor, Peking University |
| David Romero (Undergrad SURP Intern) | Undergrad, California State University, Northridge (CSUN) |
| Evan Zhao (Visiting Post-doc) | Post-doc, Massachusetts Institute of Technology |
| Lucy Williamson (Princeton Undergrad ’19) | |
| Pranatchareeya Chankhamjon (Post-doc) | Scientist, VL55, Flagship Pioneering |
| Maria Diarey Tianero (Post-doc) | Senior Scientist (Program Lead), Lodo Therapeutics |
| Mohamed Farag (Visiting Associate Professor) | Associate Professor, Cairo University |
| Allison Chang (Princeton Undergrad ’18) | Masters Student, Computer Science, Princeton University |
| Diana Chin (Princeton Undergrad ’18) | Post-bac, Yu lab, Boston Children’s Hospital |
| Anna Posfai (Post-doc) | Post-Doc, Kinney lab, Cold Spring Harbor Laboratory |
| Tanya Tafolla (Summer Undergrad Intern) | Grad Student, University of California, Merced |
| Jindong Zan (Post-doc) | Staff Scientist, Becton Dickinson |
| Arman Odabas (Princeton Undergrad ’17) | Med Student, Washington University in St. Louis |
| Audrey Abend (Princeton Undergrad ’17) | Clinical Research Associate II, OpenBiome |
| Raphaella Hull (Oxford-Princeton Exchange Student) | Grad Student, University of Cambridge |
| Phoebe Huang (Princeton Undergrad ’16) | Med Student, University of Rochester |
| Christian Shema Mugisha (Summer Undergrad Intern) | Grad Student, Washington University in St. Louis |
Mohamed S. Abou Donia
Postdoctoral Researchers
Graduate Students
Undergraduates
Staff
Alumni
Mohamed S. Abou Donia
Mohamed S. Abou Donia
Associate Professor
Dr. Donia received his B.Sc in Pharmacy from the Faculty of Pharmacy, Suez Canal University, Egypt in 2004. He moved to the US in 2005 to study for his Ph.D. at the Medicinal Chemistry Department, School of Pharmacy, University of Utah. He worked in Dr. Eric Schmidt’s laboratory where he studied the chemistry and biology of small molecules produced by bacterial symbionts of marine animals. He used chemical, microbiological, and metagenomic techniques to study the role of small molecules in mediating microbe-host and microbe-microbe interactions in marine invertebrates. In 2010, he joined Dr. Michael Fischbach’s laboratory at the Department of Bioengineering and Therapeutic Sciences at the University of California, San Francisco. There, he studied small molecules produced by members of the human microbiome and their role in mediating microbe-host and microbe-microbe interactions in humans. In particular, he focused on antibiotics produced by human pathogens and commensals, and their role in shaping the composition and dynamics of the human vaginal and oral microbiota. Dr. Donia is a recipient of the NIH Director’s New Innovator Award, the Kenneth Rainin Foundation Innovation and Breakthrough Awards, and is named a Pew Biomedical Scholar. Dr. Donia is a member of the Scientific Advisory Board for Deepbiome Therapeutics.
Postdoctoral Researchers
Jie Liu
jl103[at]princeton.edu
I received my PhD in Microbiology at Rutgers University studying the eco-physiology of organohalide respiring bacteria from marine environments. My broad research interests encompass the interactions of microorganisms with its environment/hosts. In the Donia lab, I study chemical sequestration and kleptoplasty in a complex tripartite marine symbiosis.
Paola Estrada
pestrada[at]princeton.edu
I obtained my B.S. in Forensic Science from John Jay College of Criminal Justice. I then went to Hunter College where I worked in the Kawamura Lab isolating small molecules from soil bacteria. For my PhD I went to the University of Illinois (UIUC) and worked in the Nair Lab on the biochemical and structural characterization of enzymes involved small molecule biosynthesis. In the Donia Lab I will be investigating small molecules from the human microbiome.
Moamen Elmassry
elmassry[at]princeton.edu
I received my Bachelor of Pharmaceutical Sciences from the Faculty of Pharmacy, Cairo University, Egypt. Then, I obtained my Ph.D. in Biology from Texas Tech University, Lubbock, Texas. In my dissertation, I focused on Pseudomonas aeruginosa pathogenesis during sepsis in trauma patients. In the Donia Lab, I study the contribution of the gut microbiota to the human metabolome (and health). I value collaborative research and teaching. I enjoy reading, humanities talks, Tai Chi, sports, and video games.
Ruojun Wang
rw6686[at]princeton.edu
I grew up in Shanghai, China, and received my B.S. from Fudan University. I then received my Ph.D. in Immunology and Microbial Pathogenesis from Weill Cornell Medical College before joining the Donia Lab. My top interests are host-microbe interactions in health and disease. Outside of the lab, I enjoy birdwatching, photography, and traveling.
Laura Ióca
li7497[at]princeton.edu
I received my BSc in Physical and Biomolecular Sciences and my MSc and PhD in Organic and Biological Chemistry at the University of São Paulo, Brazil. In the Donia Lab, I am investigating the biosynthesis machinery of marine symbionts that produce unique natural products scaffolds. Outside of the lab I enjoy listening podcasts and doing puzzles together with a nice cup of tea.
Luis Jesus Linares-Otoya
luisjl[at]princeton.edu
I received my BSc and MSc in Animal Science at the National University of Trujillo (Peru) and Bonn University (Germany), respectively. Later I obtained my PhD at the University of Bonn / JLU- Giessen (Germany) studying the biosynthesis of natural products from marine bacteria. I am interested in understanding the role of secreted metabolites in microbial communities. In the Donia Lab I study the regulation and biosynthesis of small molecules produced by obligated bacterial endosymbionts and marine bacteroidetes. Outside of the lab I enjoy watching/reading Sci-FI, swimming and cooking.
Sunghoon Hwang
sh1646[at]princeton.edu
I am from South Korea. I received my BS in Pharmacy from Seoul National University. For my PhD, I studied microbial natural product chemistry, specifically structure elucidation. In the Donia Lab, I am interested in the expression of genes and discovery of the compounds from the human microbiome. In my free time I enjoy exercising, reading, and traveling around.
Bhuwan Khatri Chhetri
bk1812[at]princeton.edu
I graduated from Kathmandu University, Nepal with a bachelor’s degree in pharmacy. My master’s degree is in chemistry where I worked under Dr. William N. Setzer at University of Alabama, Huntsville on plant natural products-based drug discovery. I moved to University of Texas, San Antonio for a year as a postmaster researcher to work under Dr. Oleg Larionov on synthetic organic chemistry. I completed my PhD in organic chemistry under the supervision of Dr. Julia Kubanek at Georgia Institute of Technology working on the exploration of marine macroorganisms for drug discovery. In the Donia lab, I am interested in unraveling the molecular mechanisms involved in the chemical sequestration in marine symbioses. In my spare time, I enjoy being with my family, cooking, and music composition.
Graduate Students
Jeffrey Lee
Molecular Biology Graduate Student
yjl2[at]princeton.edu
I received my B.A. in Biology as well as an MPH in Global Health and an MEng in Energy, Environment, and Chemical Engineering from Washington University in St. Louis. Currently my work is focused on the capture and characterization of peptides from the human microbiome with a particular focus on examining the roles these peptides may have in microbe-microbe and host-microbe interactions. I am interested in how peptides can be harnessed to improve human health in addition to issues of biosecurity, therapeutics, and science policy.
Catherine Day
Molecular Biology Graduate Student
cday[at]princeton.edu
I grew up in northern California and received my B.S. in Biology from the California Institute of Technology. In the Donia Lab, I will be studying antibiotic resistance. Outside of research, I enjoy traveling, playing video games and doing puzzles.
Jongbeom Park
Molecular Biology Graduate Student, joint with Ricardo Mallarino
jongbeom[at]princeton.edu
I grew up in Daegu, South Korea and received my BA in Biology from Grinnell College. I am broadly interested in evolutionary biology and developmental biology. I currently plan to investigate the role of peptides in mammalian development. My hobbies include indoor rock climbing, driving, and eating.
Xuanqi (Ivy) Chen
Chemical and Biological Engineering Graduate Student
xc1590[at]princeton.edu
I received my B.S. in Chemical Engineering from UW-Madison. I am broadly interested in human health care and biotech. In the Donia Lab, I will be using both computational and experimental approach to study human gut microbiome. Outside of lab, I enjoy city explorations, hiking and occasionally skiing.
Gavriela Carver Molecular Biology Graduate Student
gcarver[at]princeton.edu
I grew up in NYC and received my B.S. in Biological Sciences from Cornell University, where I studied plant pathology. Before joining the Donia Lab, I spent two years working at the Broad Institute developing tools for genetic code expansion. Currently, my work focuses on ecologically and functionally relevant host-microbe interactions in marine symbioses. Outside of research I enjoy gardening and fermenting foods, and by extension I keep the lab stocked with freshly-baked loaves of sourdough!
Sophia Koval Molecular Biology Graduate Student
koval[at]princeton.edu
I grew up in the DC area and attended Dartmouth College in New Hampshire, where I studied biology and anthropology. My interests span the realm of microbiology and human health, including biofilm maintenance, the microbiome, and equity in healthcare. I’m interested in drug metabolism by the gut microbiome. When not at the bench, I enjoy embroidery, being outdoors, and spending time with friends.
Siddharth Marwaha MD/PhD Student
sm1463[at]princeton.edu
I’m a New Jersey Native, having both grown up here and gone to school at Rutgers University-New Brunswick. Before Joining the Donia lab, I did 2 years of medical school at Robert Wood Johnson Medical School through the MD/PhD program. Currently, I’m using a multi-omics approach to investigate host-microbe interactions in the gut microbiome. Outside of the lab, I love coffee, watching formula 1 races, and riding my bike!
Salma Youssef MD/PhD Student, joint with Yibin Kang
sy4767[at]princeton.edu
I got my B.S. in Biology with a minor in Sociology and Anthropology from Fordham University in NYC. In the Donia Lab, I am interested in understanding how the microbiome affects cancer progression. My hobbies include drawing, gardening, and cooking up a feast for friends and family.
Christina KimChemical and Biological Engineering Graduate Student
csykim[at]princeton.edu
I grew up in Delaware and received my B.S.E. in Chemical & Biomolecular Engineering from the University of Pennsylvania. In the Donia Lab, I’m interested in host-microbe and microbe-microbe interactions in health and disease. Outside of the lab, my hobbies include crochet, baking, and theatre.
Undergraduates
Julia Garaffa
Molecular Biology Undergraduate
garaffa[at]princeton.edu
I am from Montgomery, New Jersey, and a member of the class of 2023. In the Donia Lab, I am exploring metabolism of drugs by bacteria in the gut microbiome. Outside of the lab, I am a Residential College Advisor and involved with music and comedy.
Ye Chen
Molecular Biology Undergraduate
yhc[at]princeton.edu
I am from Toms River, New Jersey and am a member of the Class of 2023. In the lab, I am investigating mechanisms of gene regulation through quorum sensing. I enjoy writing, learning new languages, and also work performances for Princeton’s Richardson Auditorium.
Isabella Swartz
Molecular Biology Undergraduate
iswartz[at]princeton.edu
I’m from Warrington, Pennsylvania, and I’m a member of the Class of 2024. On campus I also volunteer with CONTACT which focuses on emotional support and suicide prevention, and I love baking, reading, and doing puzzles.
Katherine Carroll
Chemical and Biological Engineering Undergraduate
ktc3[at]princeton.edu
I am from Chicago, Illinois and I am in the class of 2024. I am a part of the Chemical and Biological Engineering department, with a certificate in Computer Science. Outside of classes, I am on the open weight rowing team and am in the Entrepreneurship Club.
Staff
Seema Chatterjee
Lab Manager
chatsamp[at]princeton.edu
Karen E. Plantarich
Faculty Assistant
kp1804[at]princeton.edu
Alumni
Name | Current |
| Jaime Lopez (Graduate Student) | Post-doc, Stanford University |
| Mary Davis (Undergraduate Student ’22) | |
| Christian Hernandez (Undergraduate Student ’22) | |
| Anna Schmedel (Faculty Assistant) | |
| Shuo Wang (PhD Graduate Student) | |
| Amira Mira (Postdoctoral Research Fellow) | Assistant Professor, Mansoura University, Egypt |
| Janie Kim (Princeton Undergrad ’21) | Graduate Student, Stanford University |
| Nisha Chandra (Princeton Undergrad ’21) | |
| Jared Balaich (PhD Graduate Student) | |
| Bahar Javdan (MD-PhD Graduate Student) | |
| Amir Erez (Post-doc) | |
| Dani Peters (Princeton Undergrad ’20) | |
| Francine Camacho (PhD Graduate Student) | Viome |
| Yuki Sugimoto (Post-doc) | |
| Zhiyuan Li (Post-doc) | Assistant Professor, Peking University |
| David Romero (Undergrad SURP Intern) | Undergrad, California State University, Northridge (CSUN) |
| Evan Zhao (Visiting Post-doc) | Post-doc, Massachusetts Institute of Technology |
| Lucy Williamson (Princeton Undergrad ’19) | |
| Pranatchareeya Chankhamjon (Post-doc) | Scientist, VL55, Flagship Pioneering |
| Maria Diarey Tianero (Post-doc) | Senior Scientist (Program Lead), Lodo Therapeutics |
| Mohamed Farag (Visiting Associate Professor) | Associate Professor, Cairo University |
| Allison Chang (Princeton Undergrad ’18) | Masters Student, Computer Science, Princeton University |
| Diana Chin (Princeton Undergrad ’18) | Post-bac, Yu lab, Boston Children’s Hospital |
| Anna Posfai (Post-doc) | Post-Doc, Kinney lab, Cold Spring Harbor Laboratory |
| Tanya Tafolla (Summer Undergrad Intern) | Grad Student, University of California, Merced |
| Jindong Zan (Post-doc) | Staff Scientist, Becton Dickinson |
| Arman Odabas (Princeton Undergrad ’17) | Med Student, Washington University in St. Louis |
| Audrey Abend (Princeton Undergrad ’17) | Clinical Research Associate II, OpenBiome |
| Raphaella Hull (Oxford-Princeton Exchange Student) | Grad Student, University of Cambridge |
| Phoebe Huang (Princeton Undergrad ’16) | Med Student, University of Rochester |
| Christian Shema Mugisha (Summer Undergrad Intern) | Grad Student, Washington University in St. Louis |
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Outings and Outreach
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Resources
Metagenomic Identifier of Biosynthetic Gene Clusters (MetaBGC)
Expected Number of Detectable Strains (ENDS)
Metagenomic Identifier of Biosynthetic Gene Clusters (MetaBGC)
MetaBGC is a computational algorithm that discovers small-molecule BGCs directly in complex metagenomic sequencing data of the human microbiome.
To download MetaBGC, please visit our GitHub.
For more information about MetaBGC, please refer to our paper: Sugimoto, Y.*, Camacho, F.R.*, et al. (2019) “A metagenomic strategy for harnessing the chemical repertoire of the human microbiome”. Science. 366 (6471): eaax9176.
Expected Number of Detectable Strains (ENDS)
ENDS is a corrected richness metric where the contribution of each ASV is weighed by the probability that its metabolite can be detected while considering total biomass.
For more information on ENDS, please visit our GitHub and refer to our paper: Javdan, B.*, Lopez, J.*, et al. (2020). “Personalized Mapping of Drug Metabolism by the Human Gut Microbiome”. Cell. 7 (1661-1679): e22.