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

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

Ami S. Bhatt is a 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

Jane Ann Cook

Stanford Graduate Student

I graduated from Trinity College Dublin, Ireland in 2022 with a BA in Biochemistry. My undergraduate thesis research with Dr. Andrei Budanov explored how mutations in the Sestrin proteins allow lung cancer cells to bypass growth inhibition signals. During the summers of 2021 and 2022, I worked in two labs at UT Southwestern, studying the molecular mechanisms of heart failure with preserved ejection fraction (HFpEF) in Dr. Zhao Wang’s lab and related work in metabolism and diabetes in Dr. Phil Scherer’s lab. During and following undergrad, I also worked as a science writer, first as a journalist for my university newspaper and then as lead writer for a bioinformatics company and an AI drug discovery company.

I am excited to be working in the Bhatt Lab to untangle the mysteries of the microbiome using long-read metagenomics and functional validation. I’m curious about host-microbe interactions, and the roles of mobile genetics elements and bacterial epigenetics in bacterial biology. When I’m not in lab, I love exploring the Bay Area, baking, playing tennis, spending time with friends, and curling up with a good coffee and a book. I also enjoy volunteering as a teacher through programs like Stanford Splash.

cookja[at]stanford[dot]edu

Imani Elaine Porter

Stanford Graduate Student, 2028

I attended Hampton University from 2019-2023 where I graduated with a degree in Biochemistry and minor in Leadership Studies. While there, I did research in the realm of protein crystallography and characterizing protein structure for drug discovery. During undergraduate summer research programs, I worked to cultivate my interest in epigenetics and the external or lifestyle factors that influence gene expression pathways. My experiences led me to join the Genetics department at Stanford in the Summer of 2023 (ADVANCE Summer Institute), and I became intrigued by the implications of gut microbe-host interactions being studied in the Bhatt Lab.

When I’m not in the lab, I like to do puzzles, watch TV, and play board games with my sister and friends. I also enjoy volunteering my time for community building and mentorship, and I’m beginning to dabble in podcasting.

iep32501[at]stanford[dot]edu

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

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

Postdoctoral Fellows

YUYA KIGUCHI, PH.D.

Postdoctoral Fellow

I earned a PhD in bioinformatics in the Masahira Hattori group at the Waseda University in Tokyo, Japan, and spent an early postdoc career at the University of Tokyo (Yutaka Suzuki group). During my research career, I developed the experimental and computational method to identify novel mobile genetic elements, such as bacteriophages and plasmids in the human microbiome, by applying long-read sequencing technology. In the Bhatt Lab, I am working on several exciting projects that uncover the hidden adaptation mechanism of the human commensal bacteria. Personally, I love to play volleyball (in the gym, on the grass, and sand)

Contact: ykiguchi{at}stanford[dot}edu

JORDAN LIN, PH.D.

Postdoctoral Fellow

I received a PhD in molecular genetics from the University of Toronto, where I worked in the lab of Dr. Alex Ensminger. My doctoral work focused on characterizing genes related to pathogenesis and antibiotic stress tolerance in the bacterial pathogen Legionella pneumophila. In the Bhatt lab, I am interested in combining approaches from molecular biology, microbiology, and genomics to better understand how bacterial genomes are structured and evolve.

In addition to research, I like to spend my time outdoors exploring the natural beauty of California and the west coast.

Contact: jdolin[at]stanford[dot]edu

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.

Contact: aranat[@]stanford[dot]edu

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

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

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

Ashley Moore

REACH Postbaccalaureate Scholar

Originally from Maryland, I got my degree in Biology from Bowie State University, where I developed a strong passion for research at the intersection of science and healthcare. My research experiences have spanned multiple disciplines, some of which include tracking individual viral particle motion to understand their role in infection spread and optimizing a high-throughput zebrafish screening model to identify potential drug candidates for sepsis. In the Bhatt lab, I am excited to explore the fascinating and complex ways bacteria shape the gut microbiome and influence health and disease outcomes.

Outside the lab, I enjoy staying active at the gym, reading, discovering new music/podcasts, exploring the outdoors, and roller skating. I look forward to expanding my scientific skills, delving deeper into microbiome research, and connecting with like-minded individuals in the field!

Contact: aamoore3[@]stanford[dot]edu

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