AMI S. BHATT, M.D., PH.D.

Associate Professor, Departments of Medicine (Hematology & BMT) and Genetics

Ami S. Bhatt is an Associate Professor of Medicine & Genetics at Stanford University. She received her MD and PhD (Biochemistry & Molecular Biology) at UCSF. There she received the Fineberg Award for Excellence in Teaching and was inducted into Alpha Omega Alpha. She completed residency and chief residency in Internal Medicine at Brigham & Women’s Hospital and was a fellow in Hematology/Oncology at the Dana-Farber Cancer Institute. Thereafter, she carried out her post-doctoral studies at the Broad Institute of Harvard and MIT.

Ami’s lab seeks to improve outcomes in patients with hematological malignancies by exhaustively characterizing the dynamics of the microbiome in immunocompromised individuals, and exploring how changes in the microbiome are associated with idiopathic diseases in this population. She loves working with trainees and is excited about the application of new molecular and computational technologies to solve complicated metagenomic puzzles. Learning how to organize piles of shotgun metagenomic sequencing data into orderly lists of genomes and genes of potential clinical/biological importance is her passion.

In addition to her academic efforts, Ami is committed to improving cancer care, education and research in resource-limited settings. She is the Director of Global Oncology for the Center for Innovation in Global Health at Stanford University and has served as a visiting lecturer at the Tokyo Medical and Dental University, Trinity College in Dublin, Ireland and the University of Botswana. She, along with Franklin Huang, is a co-founder and co-president of the non-profit organization Global Oncology (www.globaonc.org).

Outside of work, Ami enjoys reading fiction, cooking/baking, dancing, travel, and hiking in the great outdoors. She makes a batch of limoncello or vin de citron yearly and is the recipient of many "stool"-centered joke gifts.

FOR UNDERGRADUATE AND HIGH SCHOOL STUDENTS WHO ARE INTERESTED IN A SUMMER RESEARCH EXPERIENCE IN OUR LAB: We take undergraduate students through the SSRP program: https://biosciences.stanford.edu/prospective/diversity/ssrp/

We will consider high school students who are admitted to the Stanford Gene Camp program: http://med.stanford.edu/genecamp.html

FOR STANFORD UNDERGRADUATE STUDENTS WHO ARE INTERESTED IN A RESEARCH EXPERIENCE IN OUR LAB: We require a minimum commitment of a full year (including full-time work in the lab for at least one summer). If you are interested, please send your CV/resume to Dr. Bhatt

Graduate Students

Matthew Owen Gill

Stanford Graduate Student, 2026

I studied Biology at Santa Clara University and, after graduating in 2019, worked for two years at a biotech startup in the Bay Area developing point-of-care microbial diagnostics. In addition to investigating designed-protein thermostability using molecular dynamics simulations as an undergraduate in the McCully Lab, I also worked in the Hess Lab exploring the natural phenotypic and genomic diversity of E. coli with an emphasis on plasmid variation, antibiotic resistance, and carbon metabolism. I joined Stanford's Genetics department as a PhD student in the Fall of 2021, and I am super excited to continue exploring the wonderful world of (gut) microbes and microbiota in the Bhatt Lab - especially their evolution, ecology, and reciprocal host-microbe relationship.

In my free time I love to hike around the beautiful Bay Area, play puzzle & strategy games, watch (only the best) reality TV, and make guacamole. I aspire to once again take the stage in a musical but that day has yet to come.

mogill[at]stanford[dot]edu

Angela Shang-mei Hickey

Stanford Graduate Student, 2026

I graduated University of Washington in 2019 with a degree in Molecular, Cellular and Developmental Biology. While there, I worked in the lab of Maitreya Dunham studying genome evolution in interspecies hybrids of budding yeast. After graduation, I continued similar work as the lab manager of the Gresham lab at NYU working with Saccharomyces cerevisiae in order to understand evolutionary dynamics of copy number variants in different environments. In the Bhatt lab, I am excited to continue exploring mechanisms of adaptation in microbes, specifically in the dynamic environment of the human gut. I am also interested in understanding how these adaptations affect human health.

Outside of lab, I enjoy travel, board games, watercolor, and just about anything as long as I’m spending time with my friends.

angelah8[at]stanford[dot]edu

Nora Enright

Stanford Graduate Student, 2024

I graduated from MIT in 2019 with a degree in Biological Engineering. While there, I worked with Jacquin Niles developing genetic tools to facilitate study of gene regulation in malaria. I received my Master's in Bioengineering at Stanford while working on engineered skin commensals to study host-microbe interactions in the Fischbach lab. I'm interested in understanding bacterial gene regulation and using newly discovered bacterial enzymes to develop synthetic biology tools.

Outside of lab, I like hiking, reading, skating, drinking coffee, and making stuff.

Contact: nenright[at]stanford[dot]edu

DANICA SCHMIDTKE

Stanford Graduate Student, 2025

Prior to joining the Microbiology and immunology program at Stanford I completed my bachelor’s degree in Microbiology at the University of Washington. After graduation I worked as a junior researcher in Harmit Malik's lab at Fred Hutchinson Cancer Research Center. My research background lies in two models for genetic conflict. First, the type VI toxin secretion system encoded by gut bacteria and the ability of their toxin recipients to steal genes that neutralize toxins in kin cells for protection. Second, the ongoing evolutionary arms race between bacteria and bacteriophages leading to rapid evolution on both sides, specifically, the CRISPR-Cas adaptive immune system in bacteria and CRISPR-Cas neutralizing proteins encoded by phages. I plan to continue researching bacteria-phage dynamics during my PhD.

Outside of the lab I enjoy riding my horse, gardening, baking, cooking, painting, and drawing.

Contact: danicats[at]stanford[dot]edu

MEENA CHAKRABORTY, M.S.

Stanford Graduate Student, 2025

I graduated from MIT in 2019 with a degree in Computer Science and Molecular Biology. There, I worked in the Sharp Lab, combining experimental and computational methods to examine the role of microRNAs in governing stem cell identity. I then completed a Master's in Genetics through the Churchill Scholarship program at the University of Cambridge. There, in the Martinez-Arias lab, I studied human gastruloids, a stem-cell-derived model of the human embryo. In the Bhatt Lab, I am excited to investigate the connection between the microbiome and the brain ("microbiome-gut-brain axis"), especially as it relates to neurodegenerative disorders.

In my free time, I enjoy singing, fitness, traveling, and spending quality time with family and friends!

Contact: mchakra[at]stanford[dot]edu

AARON BEHR

Stanford Graduate Student, 2025

I graduated from Brown University (2015) with a dual degree in Computer Science and Biology. While there, I worked with Sohini Ramachandran to develop new algorithms & software for use in inference of population structure from genomic data. I then spent several years as a software engineer at Oracle, where I worked on the Big Data Discovery team and then on cloud platform development. I’m currently interested in understanding how DNA moves horizontally/vertically through different microbes in different ways and in response to different selective pressures (such as phage, antibiotics, other microbes, and host immune system), and how this affects microbial populations over short (within-host) and long (across-host) evolutionary timescales.

In my free time, I enjoy cooking, crosswords, hiking, backcountry skiing, and being at the ocean with good food

Contact: abehr[at]stanford[dot]edu

SIERRA MORGAN BOWDEN

Stanford Graduate Student, 2024

I graduated from the University of Michigan in 2019 with a degree in Molecular, Cellular, and Developmental Biology before joining the Genetics program at Stanford. My research background is in antibiotic biochemistry and epigenetic regulation. I'm interested in the impact that metabolites and proteins produced by the gut microbiome have on host cells.

Outside of the lab, I love exploring California through trail running and skiing.

Contact: sierrasb[at]stanford[dot]edu

MAI DVORAK

Stanford Graduate Student, 2025

Prior to starting in the Biology program at Stanford, I graduated in 2017 from UNC-Chapel Hill with a degree in Biology. My research background is in studying the epigenetic landscape of immune cells in a range of diseases from infectious to autoimmune. In the Bhatt lab, I am interested in understanding how gut microbes communicate with and modulate the human host.

Outside of the lab, I enjoy ice skating, growing vegetables/eating them, and traveling to new places.

Contact: maidvora[at]stanford[dot]edu

MATTHEW P. GRIESHOP

Stanford MD/PhD Student

I graduated with a degree in biochemistry from the University of Wisconsin in 2016 where I also studied eukaryotic transcriptional regulation. I then completed a master's program in molecular biology through the International Max Planck Research School at Georg-August Universität in Göttingen, Germany in 2019. While there, I studied intrinsically disordered proteins and their subcellular localization. Also in 2019, I started in the Stanford MSTP as an MD/PhD student. In the Bhatt lab, I am interested in studying microbiome community substructure and organization as well as exploring mechanisms of communication between the microbiome and human host.

Outside of the lab, I enjoy staying active and exploring all of the nature the bay area and the west coast has to offer.

Contact: mpgriesh[at]stanford[dot]edu

ALVIN HAN

Stanford Graduate Student, 2023

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I graduated from Duke University in 2018 with a degree in Biology and concentration in Computational Biology before starting in the Microbiology and Immunology program at Stanford. My research background is primarily in zebrafish microbiology. I'm broadly interested in the gut microbiome and particularly, how pathogens interact with and shape the ecology of this community.

I try to birdwatch when time permits, am a big fan of nature photography, and I, like most people in the lab, enjoy anything related to the great outdoors (hiking, kayaking, etc.). I also play the clarinet in Stanford's Wind Symphony in my spare time.

Contact: alvinhan[at]stanford[dot]edu

ANN LIN

Stanford Graduate Student, 2024

I graduated in 2018 from Stony Brook University with a duel degree in Biochemistry and Economics. My background is in the field of cancer genomics and drug development. I am currently interested in understanding how the microbiome modulate host biology.

In my free time, I enjoy exploring the local culinary scene, long walks in nature, and reading (with a nice cup of boba).

Contact: annlin[at]stanford[dot]edu

JACK DIAZ SHANAHAN

Stanford Graduate Student, 2026

I graduated from University of California, Irvine in 2021 with a degree in Biology. My research background is primarily in microbiology, antibiotic resistance and computational biology. Between the Fordyce and Bhatt labs, I am currently interested in developing microfluidic platforms to study the binding energy landscape of novel microbial recombinases, as well as advancing single cell techniques to study the genomic complexity of the human gut microbiome in greater detail.

When time permits, I am outside with a digital or medium format film cameras exploring the wilderness by hiking, backpacking and camping. I want to make a film photography book of my travels during graduate school.

Contact: jackshan[at]stanford[dot]edu

Medical Student Scholars

BORYANA DOYLE

Stanford Medical Student

In 2017, I graduated from MIT with a degree in Physics and a minor in Biology. There I did research in Leonid Mirny’s lab modeling the three-dimensional organization of chromosomes and in Laurie Boyer’s lab studying the differentiation of stem cells into cardiomyocytes. After spending several years tutoring and traveling around the Caribbean on a sailboat, I began my MD at Stanford in 2020. In 2021, I joined the Bhatt lab, where I’m interested in the fundamental structure of the gut microbiome and how it influences health outcomes of the human host.

In my free time, I enjoy sailing, paddleboarding, bicycling, and snowboarding.

Contact: boryana[at]stanford[dot]edu

Medical Residents/Fellows

BIANCA PALUSHAJ

Stanford Medical Resident/Fellow

I'm a fourth year Neurology resident and will be completing a clinical fellowship in Movement Disorders. My interest in the microbiome and intestinal permeability was born out of my own experience with autoimmune disease, and I've cultivated a special research interest in the microbiome and Parkinson's Disease.

In my free time, I enjoy being with my husband, daughter, and dog (particularly exploring the outdoors) and doing anything from running, hiking, rock climbing, camping, To no surprise, I love kombucha, sauerkraut, and a good dill pickle. (edited)

Contact: bmoiseff[at]stanford[dot]edu

MARK NASEF RAGHEB

Stanford Medical Resident

Contact: mragheb[at]stanford[dot]edu

Hello everyone! I am a physician-scientist research resident at Stanford, and am co-mentored by the Bhatt and Bassik labs. My current research interests are in leveraging high throughput technologies to better understand host-microbe interactions. I completed my MD/PhD at the University of Washington in 2021. My PhD work focused on basic mechanisms of mutagenesis and DNA repair as it relates to microbial evolution. I have a long-standing interest in understanding how microbes evolve at the mechanistic level in order to link such mechanisms to outcomes in human health and biology.

Outside the lab, I enjoy using my free time to travel, cook, and spend time with our cats!

Undergraduate Students

Carrie Jiayi Chen

Stanford Undergraduate, 2024

I am a current junior pursuing a degree in Computer Science on the biocomputation track. My current research in the lab is focused on developing a computational tool to analyze microbial genomes and predict the genetic codes they use, as well as perform phylogenetic classification.

Outside the lab, I am involved as a member of Stanford Students in Biodesign (SSB) and as co-producer of the Stanford Collaborative Orchestra (SCOr). In my free time, I love playing piano and flute, painting, traveling, and cooking with friends!

Contact: carriec6[at]stanford[dot]edu

NAVAMI JAIN

Stanford Undergraduate, 2023

I am a freshman hoping to study Computer Science and Human Biology. In the lab, I am interested in studying properties of mobile genetic elements, specifically integrated phages, in the human microbiome. Outside the lab, I am involved in Stanford’s Climate and Health group and Stanford Women in Engineering. In my free time, I enjoy dancing with Noopur, Stanford’s Indian classical dance team!

Contact: navajain[at]stanford[dot]edu

RYAN PARK

Stanford Undergraduate, 2023

Aloha! I am currently a Stanford undergraduate studying Biomedical Computation. My primary focus in the lab is utilizing computational tools to study the gut microbiome, especially those of CAR T-Cell therapy patients. Outside of the lab, I am actively involved in Cardinal Free Clinics and Team HBV. In my free time, I love going to the beach and spending time in nature.

Contact: rpark23[at]stanford[dot]edu

EUNICE YANG

Stanford Undergraduate, 2022

I am a current Stanford undergraduate pursuing a degree in Computer Science with a specialization in Biocomputation. My current research in the lab focuses on using metabolomic and genomics approaches to analyze the role of Akkermansia muciniphila in the gut microbiome.

Outside of lab, I’m involved in health++ (Stanford’s health hackathon), Camp Kesem, and taekwondo. I also enjoy hiking, swimming, and dogspotting!

Contact: eunicey[at]stanford[dot]edu

Postdoctoral Fellows

JAKOB WIRBEL, PH.D.

Postdoctoral Fellow

Hi! My name is Jakob and I am a postdoc in the Bhatt lab since September 2022. Before that, I performed my doctoral studies in the team of Georg Zeller at the European Molecular Biology Laboratory in Heidelberg, Germany. There, I focused on machine learning and statistical analysis tools for the comparative analysis of microbiome data, especially in the context of colorectal cancer.

I am excited to combine the skills I learned during my doctoral work with the approaches and techniques in the Bhatt lab to better understand how microbes and their functions contribute to health and disease in the host.

Other than science, I enjoy reading, cooking and everything outdoors, such as hiking, biking, or climbing.

Contact: wirbel[at]stanford[dot]edu

ARAVIND NATARAJAN, PH.D.

Postdoctoral Fellow

I am elucidating the biochemistry of large serine recombinases (LSRs). LSRs can edit genes in microbes and mammalian cells. They have advantages over CRISPR-Cas9 by way of higher efficiency, supporting larger cargo, and not causing double strand breaks. However, they are not modular like Cas9. To make up for the lack of modularity, I am decoding how LSRs bind to DNA, aiming to develop a suite of LSRs to target different DNA sequences. In my doctoral studies at Cornell University, I was a protein engineer and synthetic biologist, and worked on protein secretion and glycosylation. Prior to this, I earned a master’s in science in genomics with a focus on studying protein translation fidelity in E. coli through bacterial genetics from Madurai Kamaraj University. My undergraduate education was in biochemistry at Madras University.

I am passionate about fostering an inclusive space in higher education, thinking deeply about supporting the recruitment and success of people of traditionally underserved identities. This includes the founding of a podcast called Science Blender. I enjoy Contra dancing, playing rugby and squash, and cooking.

CHRIS SEVERYN, M.D., PH.D.

Instructor of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine

Hello! My work focuses on how the microbiome influences clinical outcomes in both malignant and non-malignant hematology, including individuals that require bone marrow transplantation.

I completed my undergraduate work in Molecular & Cell Biology at UC Berkeley, went to OHSU in Oregon for my M.D. and Ph.D. in Biochemistry/Molecular Bio where I studied the transcriptional regulation of a gene involved in iron metabolism. I was a pediatrics resident and clinical faculty in the bone marrow transplant unit at Duke Children’s Hospital, where I also started my interest in the microbiome. Most recently, I completed my fellowship at Lucile Packard Children’s Hospital at Stanford.

I love doing research in the Bhatt lab combining clinical, computational, and fundamental bench science, and the people I work with are amazing.

Outside of the lab or hospital, I can be found outdoors (hiking or cycling) or attempting some delicious concoction in the kitchen with my family (we love exploring Northern California and cooking).

Contact: cseveryn[at]stanford[dot]edu

PATRICK WEST, PH.D.

Postdoctoral Fellow

Before joining Ami's lab, I completed my Ph.D. at the University of California Berkeley under the mentorship of Prof Jill Banfield. My research focused on developing genome-resolved metagenomic methods to study microbial eukaryotes in the context of the human gut and a variety of ecosystems, including groundwater and soil. My current research is centered around characterizing microbial eukaryotes, methyltransferases, and DNA methylation in the microbiome.

In my free time I'm passionate about painting, hiking, and video game development.

Contact: ptwest10[at]gmail[dot]com

RACHAEL CHANIN, PH.D.

Postdoctoral Fellow

Prior to joining the Bhatt Lab, I earned my PhD in Dr. Sebastian Winter’s Lab at the University of Texas Southwestern Medical Center. My doctoral work focused on understanding the causes of commensal facultative anaerobic outgrowth during episodes of intestinal inflammation. I am currently interested in understanding the mechanisms that drive bacterial community structure changes in the gut and how these alterations relate to disease state and overall health.

In my free time I love hiking, bike riding, and taking my dog for walks.

Contact: rbchanin[at]stanford[dot]edu

SOUMAYA ZLITNI, PH.D.

Postdoctoral fellow

I'm a postdoctoral scholar in the Bhatt lab. I received my PhD in Biochemistry from McMaster University in Canada where my work centered on the discovery and characterization of novel antibacterial inhibitors, particularly those targeting metabolic pathways. Before coming to Stanford, I was a postdoctoral fellow at the University of Toronto where I developed metabolomic platforms for the study of the metabolic consequences of chemical and genetic perturbations in bacteria and yeast. I'm interested in leveraging my training in microbiology, biochemistry and metabolism to address questions about complex microbial communities and host-microbiome interactions in states of health and disease.

Outside the lab, I enjoy reading, watching movies, hiking and weightlifting.

Contact: szlitni[at]standord[dot]edu

YISHAY PINTO, PH.D

Postdoctoral Fellow

I received my PhD in computational biology from Bar-Ilan University in which I studied mechanisms that diversify genomes. Before joining the lab I worked at Wild Biotech where I studied wild animals microbiome and at Omry Koren's lab is where I fell in love in the microbiome field while associating microbiome composition to human diseases. My research interests are to study microbial genomes plasticity, expanding the knowledge of microbial non-coding elements and specifically functional RNAs.

Outside the lab I'm enjoying traveling with my family, watching soccer and reading.

Contact: yishay[at]standord[dot]edu

DYLAN MAGHINI

Postdoctoral Fellow

I graduated in 2018 from Davidson College with a degree in bioinformatics. My research in the Bhatt lab is in two main areas. First, I apply new sequencing technologies to generate complete and comprehensive genomes for gut microbes, which allows us to differentiate the roles of specific microbial strains in the human gut. Second, I work with the Africa Wits-INDEPTH partnership for Genomic Studies to study the relationship between the gut microbiome and human health and disease in African populations. I am passionate about studying and solving research questions that are directly related to pressing human health issues, and conducting this research in a way that supports and engages local stakeholders and communities.

Outside of the lab, I enjoy baking, hiking, and gardening.

Contact: dmaghini[at]stanford[dot]edu

Staff

Ariel Gulasch

Lab Manager

Hello, I am the Bhatt Lab Manager! Before joining the Bhatt Lab, I completed my undergraduate work at San Jose State University in 2017 where I earned a BS in biology with a concentration in microbiology and a minor in chemistry. After graduation, I came to work at Stanford University and then transitioned to Stanford School of Medicine's Department of Hematology in 2019. I am inspired by the Bhatt Lab's culture and research into the microbiome and joined as lab manager in 2023. Studying the gut microbiome is an exciting area of research with the potential to revolutionize our understanding of health and disease. I can't wait to make contributions to this growing field!

In my free time, I enjoy playing RPGs and other games with my husband and friends, scuba diving in chilly kelp forests with my sister, and re-reading Terry Pratchett novels with my foster kitties.

Contact: arielgu[at]stanford[dot]edu

GABRIELLA GREEN

Clinical Research Coordinator

Hi! I graduated from Saint Mary’s College of California in 2019 with a BS in Biochemistry. Before joining the Bhatt lab I spent two years working in clinical research in San Francisco. The trials I was involved with focused on HIV prevention methods ranging from injectable PrEP to vaccinations. I’m excited to leverage both my clinical and laboratory research skills while working to better understand the relationship between the microbiome and vulnerable populations’ long-term health outcomes.

When I’m away from the lab you can find me on a trail (hiking or running), trying the latest sour from a brewery, or crocheting from the comfort of my couch.

Contact: gzmg1[at]stanford[dot]edu

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