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

Assistant Professor, Departments of Medicine and Genetics, Divisions of Hematology and BMT

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Dr. Bhatt is an Assistant 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.

Dr. Bhatt 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. Her recent work, demonstrating the discovery of a novel bacterium using sequence-based analysis of a diseased human tissue (Bhatt et al, NEJM, 2013), was first presented as a Late-breaking abstract at ASH 2012 and has subsequently been presented nationally and internationally. 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, Dr. Bhatt 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 baking, dancing, travel, rock climbing and hiking in the great outdoors. She makes a batch of limoncello yearly and is the recipient of many "stool"-centered joke gifts. 

OPEN OFFICE HOUR: Mondays, 3-4pm - Center for Clinical Sciences Research, Room 1155b. 

Out of office dates in 2018: 1/29, 2/12, 3/5, 4/9, 7/30 (on service), 8/6 (on service), 9/3, 9/10, 12/24, 12/31

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


RYAN BREWSTER

Stanford Medical Student, 2021

I am a second year medical student originally from Manchester, MA. Before joining the Stanford community, I completed my undergraduate degree at Middlebury College, where I studied Molecular Biology and Spanish, and performed brain tumor pathology research at Harvard Medical School. I hope to apply my clinical and research career towards health disparities, cancer biology and the communication of human health and disease through story telling and the graphic arts. My research with Dr. Bhatt focuses on microbial signatures and the role of pre-biotics in patients with complications of hematopoietic stem cell transplantation. 

Outside the lab, I moonlight as a competitive freestyle ski coach, graphic designer and medical illustrator. Among my other interests include acoustic guitar, swing dancing, backpacking, and mobile app development. 

Contact:  rbrewster[at]stanford[dot]edu 


MATT DURRANT

Stanford Graduate Student, 2021

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I’m a first-year genetics student with a background in bioinformatics and neuroscience. My current research interests include computational methods development, the microbiome, and allele-specific expression analysis to identify gene-environment interactions.

In my free time I enjoy spending time with my wife and 1-year-old son.

Contact: mdurrant[at]stanford[dot]edu


BRAYON FREMIN

Stanford Graduate Student, 2019

I graduated with a degree in Biology from the University of New Mexico in 2014 and started graduate school at Stanford directly after.  Most of my research background is in muscle development using fruit flies as a model. Currently, I am interested in the effects of metabolites produce by the gut microbiota on human host cells.

Outside of lab, I enjoy reading and hiking.

Contact: bfremin[at]stanford[dot]edu

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ELI MOSS

Stanford Graduate Student, 2019

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I graduated in 2011 from Brown University with a B.S. in Computational Biology.  Since then I've worked on synthetic biology at NASA Ames Research Center, biorobotics at Ginkgo Bioworks, and bioinformatic epidemiology at the Broad Institute before winding up here at Stanford in the department of Genetics.  I'm generally interested in solving biomedical mysteries through careful application of bioinformatic analysis. 

When I'm not thinking about science I enjoy playing music, restoring classic motorcycles, building camper trailers, and walking my dog Bear.

Contact: elimoss[at]stanford[dot]edu


JESSICA RIBADO

Stanford Graduate Student, 2019

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I graduated from Florida State University with degrees in Statistics and Biological Science in 2013. From research backgrounds in evolution and genomics, I am interested in understanding host-microbe interactions. I study how these interactions shape the intestinal immune responses and survival following bone marrow transplantation. 

Outside of lab, my interests include hiking, crafting, and cooking. 

Contact: jribado[at]stanford[dot]edu


BEN SIRANOSIAN

Stanford Graduate Student, 2022

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I'm new to the microbiome and metagenomics fields, but very interested in the interplay between gut microbes and the host immune system. I'm also working on developing new methods for sequencing microbes with excessively repetitive genomes, and algorithms to cluster assembled microbial sequences. Before Stanford, I did my undergad in computational biology at Brown University and spent two years working for the Connectivity Map team at the Broad Institute.

In my free time, I race road and mountain bikes, brew beer and try to get outside as much as possible.

Contact: bsiranos[at]stanford[dot]edu

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FIONA TAMBURINI

Stanford Graduate Student, 2019

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I spent my undergraduate years at Boston College, where I graduated in 2014 with a major in Biochemistry and a minor in Computer Science. At BC I worked in a research lab focused on regulation of transposable elements in the fission yeast genome, which sparked my interest in pursuing genetics and genomics research. In the Bhatt lab, I am studying the relationship between the microbiota and infectious outcomes in cancer patients. I'm also interested in genes and pathways in the microbiome that impact drug interactions and disease.

When I'm not in the lab, I love baking, reading, playing soccer, hiking, and exploring the Bay Area!

Contact: ftamburini[at]stanford[dot]edu


Undergraduate Students


HALEY CARLSON

Undergraduate Stanford Summer Research Program Fellow, 2018

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Hi, I am Haley. I am an undergraduate student at The College of Saint Scholastica in Duluth, MN. I am a rising senior biochemistry major and expect to graduate in May 2019. I am interested in using engineered microorganisms to sustainably produce medicines and examining the use of phages as antibiotics to combat antibacterial resistant strains of bacteria. This summer I am doing research in the Bhatt lab as an SSRP Scholar, I am working on the analysis of short-chain fatty acids in the gut microbiome.

Outside of lab, I like to watch shows about the British royal family, hike, and browse Reddit.


PAULINA CHAMELY

Stanford Undergraduate Student, Class of 2018

Hello! My name is Paulina and I am an undergraduate planning on majoring in Bio-medical computation here at Stanford. Though I am not certain what my concentration in this field will be, it will definitely involve studies on the link between disease, our Genome and our Microbiome! The Microbiome is specifically fascinating and exciting to me as, even though it is something we only recently became aware of, it is found to have huge influences on our bodies functioning and health. I'm excited to see what new discoveries will come out of studying the Microbiome and hopefully be apart of unravelling it's importance!

Outside of the lab, I enjoy spending time sharing people's stories through the "Humans of Stanford" project synonymous to the well known "Humans of New York" initiative. I also love photography, playing sports and anything that involves the outdoors!

Contact: pchamely[at]stanford[dot]edu


JOYCE KANG

Stanford Undergraduate Student, Class of 2018

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Howdy! I’m Joyce, an undergraduate planning to major in Computer Science with a specialization in Biocomputation. I am generally fascinated by the intersection between computational biology and human health, and I’m currently investigating the associations between changes in the gut microbiome and outcomes of bone marrow transplant patients, particularly the development of graft-vs-host-disease. I aspire to become a physician one day and am excited by the potential for recent advances in computation to improve lives.

Outside of lab, I enjoy volunteering as an EMT and as a peer counselor at The Bridge, social dancing, and trying different kinds of cheese (yum)!

Contact: joycek[at]stanford[dot]edu


MICHELLE LI

Stanford Undergraduate Student, Class of 2019

Hello! I’m Michelle, an undergrad majoring in Mathematical and Computational Science with a concentration in Biology and an honors focus on Computational Genomics. I am interested in the applications of genomics and microbiology on the study of human susceptibility of diseases. I am currently investigating the role of insertion sequences in the skin microbiome, and intend to expand the scope to the Human Microbiome Project.

Outside of lab, I play taiko (Japanese-style drumming) with Stanford Taiko, and watch Cantonese films to learn more about my culture as well as to practice the language.
 

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Postdoctoral Fellows


TESSA ANDERMANN, M.D., M.PH.

Infectious Disease Medical Fellow

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I am a second year Stanford Infectious Disease fellow who graduated from both medical school and residency at Stanford in addition to earning an MPH from Berkeley with a focus on epidemiology. I have conducted research in many areas of infectious diseases ranging from studying chemotaxis and pathogenesis in mice models of Helicobacter pylori infection, conducting surveys of PTSD and HIV risk behavior in women in Zimbabwe, and evaluating the efficacy and tolerability of oral ribavirin to treat viral respiratory infections in immunocompromised patients. My current research is focused on investigating the safety and efficacy of fecal microbiota transfer (FMT) for Clostridium difficile infection in immunocompromised patients, primarily those who have undergone hematopoietic stem cell transplant (HSCT). I also hope to further elucidate the gut microbiome before and after FMT with a particular focus on the virome of HSCT patients.

Outside of work, I am passionate about dance, in particular West African traditional dance, hip hop, and funk. I also practice yoga and meditation and have a weakness for really good tea.

Contact: tessaa77[at]gmail[dot]com

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KAREN ANDRADE, PH.D.

Postdoctoral Fellow

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I am a Ford Foundation postdoctoral fellow in the Bhatt Lab. As an interdisciplinary scholar, I am searching for innovative ways to re-imagine how our growing knowledge of the microbiome can have a meaningful impact on human health. At the moment I am working on a project investigating the effect of triclosan/triclocarban on the maturation of the infant skin microbiome, and its potential contribution to atopic dermatitis. I am also exploring how we can utilize design-thinking principles to translate results back to communities. My goal is to craft a human microbiome community-engaged research project that utilizes biodesign principles and leverages the strengths of these fields and exemplifies the benefits of the synergy of these methodologies.

I completed a first postdoctoral position at UC Davis, where I learned and applied design thinking to generate tools to help community and university collaborators to navigate research partnerships in an equitable manner. I hold a Ph.D. from the University of California, Berkeley in Environmental Science Policy and Management.

 Outside of lab I am busy being a mom to my two daughters, hiking and hoping I had more time to read more literature.

Contact: kandrade[at]stanford[dot]edu


ALEX BISHARA, PH.D.

Postdoctoral Fellow

I finished my PhD in 2017 under Serafim Batzoglou in the Department of Computer Science at Stanford.  I developed genome assembly methods that leverage long-fragment barcoding and sequencing techniques.  Applications of these assembly techniques to metagenomics yield significantly improved microbial genome drafts from the human gut microbiome over conventional shotgun approaches.  

Outside or work, I cycle and play tennis.

Contact: abishara[at]stanford[dot]edu


HILA SBERRO, PH.D.

Postdoctoral Fellow

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Before joining the lab, I completed my Ph.D. at the Weizmann Institute of Science under the supervision of Prof. Rotem Sorek. In my research I combined the fields of microbiology, genetics and computer science to reveal new ways by which bacteria defend themselves against phages.

I am very much enjoying the multidisciplinary nature of the Bhatt lab. In general, my aim is to expand our knowledge of functions carried out by bacteria in the gut by using comparative genomics and different sequencing methods.

When I am not in the lab, I am most probably with my kids!

Contact: hsberro[at]gmail[dot]com


SOUMAYA ZLITNI, PH.D. 

Postdoctoral fellow

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 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


Staff


EKATERINA (KATIA) TKACHENKO

Lab Manager/Life Science Research Assistant

Ekaterina Tkachenko (Katia) is a UC Berkeley graduate with a BS in Chemical Biology and a minor in Public Policy. She has a strong interest in biomedical sciences and over 5 years of research experience at Children’s Hospital Oakland Research Institute, Novartis Institute for Biomedical Research (NIBR) and Stanford University. Her research projects focused on immunology, viral and bacterial genomics as well as microbiology. In the Bhatt lab, Katia is specializing in application of next generation sequencing techniques for microbiome research.

Katia’s long-term goal is to pursue a doctorate degree serving low-income local and international communities in the field of Global Oncology.

When she is not studying or working, Katia spends her time cycling, snowboarding, painting and traveling as well as volunteering for Global Oncology Inc.

Contact: katiat [at] stanford [dot] edu


THORA BERNDT DE COTERA

Administrative Assistant

I grew up in Berlin, Germany where I obtained a license as a Pharmacist from the FU Berlin. For the last decades, my family and I have lived in Mexico, Canada, and the East Coast of the United States before moving to California last fall. To work with these talented researchers at Stanford University gives me great joy.

When I am not working, I try to stay in touch with family and friends all over the world, take online classes to learn new things, play tennis or work out, love to read a good book, and explore California with my husband.

Contact: tcotera[@]stanford[dot]edu


Bhatt Lab Alumni


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EDGAR ASIIMWE

Medical Student

EMILY CRIBAS

Undergraduate Summer Research Fellow, 2015

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SHANNON FALCONER, PH.D.

Postdoctoral Fellow

Contact: shannon.falconer[at]gmail[dot]com

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VERONICA MANZO

Stanford Medical Student, 2018

Contact: vmanzo31[@]gmail[dot]com

MISBAH SURANI

Gene Camp Summer Research Fellow, 2015

MINGJIE WANG, PH.D.

Computational Biologist