Genetics Department News
November 2024
Xiaojie Qiu, PhD receives NIH Director's New Innovator Award
Funding from this award supports his Project: Towards Foundational 3D In Silico Models of Whole Mouse Embryogenesis.
Xiaojie's innovative 'Spateo' model is highlighted this month in a news article by Nature and published in Cell , describing the creation of a cellular ‘hologram’ of a mouse embryo which could be used to visualize development in any species.
Xiaojie's lab focuses on single-cell genomics, mathematical modeling, and machine learning to bridge the gap between the “big data” from single-cell and spatial genomics and quantitative/predictive modeling, seeking to address fundamental questions in mammalian cell fate transitions, especially those of heart evolution, development and disease.
Welcome Ruth Schade!
Ruth Schade, PhD, is a recent Stanford biosciences graduate and the new Genetics Department Community Engagement Program Officer. In this role she will be overseeing the Stanford at The Tech Program, which she participated in as a graduate student in 2022. Ruth is enthusiastic about science education, and she is excited about finding ways to expand education outreach opportunities at The Tech Interactive in San Jose.
October 2024
Jennifer Ortiz Cárdenas, PhD has been named a Stanford Postdoc JEDI Champion Award winner.
Jedi Champions are a recognized current Stanford University postdoctoral scholars who have championed initiatives, activities, or efforts that advance justice, equity, diversity, and inclusion at Stanford and beyond.
Jennifer Ortiz Cárdenas, PhD
Faculty Mentor: Polly Fordyce, PhD
As a first-generation Latinx student, I cherish the opportunities higher education and scientific research have provided me. Research has broadened my perspective, showing me how people from diverse backgrounds collaborate to tackle global challenges.
At the Stanford Microfluidics Foundry, I’m passionate about offering underrepresented minority students their first research opportunities and the support they need to succeed.
My goal is to ensure science captures crucial perspectives and that talented students don’t go unnoticed due to lack of access or connections. This way, groundbreaking discoveries won’t be missed simply because the right minds weren’t in the room where they belonged.
July 2024
Three Stanford Genetics Professors Win Prestigious Awards
Altemose, an assistant professor in genetics, has been named a 2024 Pew Scholar in the Biomedical Sciences. The Pew Scholars program recognizes young investigators of promise in advancing human health and supports their research. Altemose will receive $300,000 over four years to investigate how specific proteins help maintain the function of centromeres, chromosomal structures that play a key role in cell division.
The professor of hematology and of genetics has been awarded the 2024 William Dameshek Award from the American Society of Hematology. The award is for researchers no older than 50 years who have made contributions leading to a new fundamental understanding of hematology. The society is recognizing Bhatt for pioneering the development and application of genomic approaches to studying the microbiome — work that has provided the basis for improving outcomes for many human diseases.
Hernández-López, an assistant professor of bioengineering and of genetics, has been named a 2024 Pew Scholar in the Biomedical Sciences. The Pew Scholars Program recognizes young investigators of outstanding promise in science relevant to the advancement of human health and supports their independent research. Hernández-López will receive $300,000 over four years for his research into novel approaches for designing synthetic protein receptors for engineering cellular communication.
Lars Steinmetz, PhD, professor of genetics, appointed new chair of the department of genetics
Dr. Steinmetz, the Dieter Schwarz Foundation Endowed Professor, steps into this new role as an innovative and influential genetics researcher, a successful entrepreneur, a highly productive leader of laboratories here and in Europe, and with a proven ability to facilitate productive collaborations across sites and disciplines. Learn More
June 2024
Amir Bahmani, Ph.D. has received the Walter J. Gores Award, which is Stanford University’s highest award for excellence in teaching. It recognizes faculty and teaching staff who have made special contributions to teaching in its broadest sense, including lecturing, tutoring, advising, and discussion leading.
Dr. Bahmani is a lecturer in computational biology and genetics and director of the Deep Data Research Center (DDRC). Bahmani is also recognized for co-founding the course Cloud Computing for Biology and Healthcare and developing the Stanford Data Ocean project, which integrates cutting-edge technology with education. Learn More
May 2024
Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease
Featured on the cover of April-May Cell Host & Microbe Journal, Xin Zhou, Ph.D. fellow researchers from Snyder Lab, and colleagues from multiple universities tracked the gut, mouth, nose and skin bacteria of 86 people for as long as six years to try to gauge what constitutes a healthy microbiome.
“We found that when you get sick with something like a cold, you have this temporary change in the microbiome; it becomes very dysregulated,” Xin Zhou, Ph.D. said. “With diabetes, that signature is the same in many ways except that it is long-term rather than temporary.” Learn More
Jesse Engreitz, PhD discusses genetics underlying coronary artery disease in an interview with SCOPE.
A new study co-led by researchers at Stanford Medicine and others, published Feb. 7 in Nature, aims to address this challenge by proposing a solution that links disease-causing DNA variants to the deleterious processes they set in motion. Learn More
June 2024
Global Health Equity Scholarship recipient Dylan Maghini conducts microbiome research with her team in South Africa.
Dylan's research focuses on the intersection between the gut microbiome and human health in a large cohort of nearly two thousand women in four countries (Burkina Faso, Ghana, Kenya, and South Africa).
This collaborative project between Stanford University and the University of the Witwatersrand seeks to measure microbiome composition in low- and middle-income populations, identify how the microbiome is shaped by environmental and lifestyle factors, and measure associations between the microbiome and pressing human health concerns in these populations. The project represents one of the largest population-representative gut microbiome studies in LMIC settings to date, and is an excellent example of collaborative, equitable, and community-engaged research.
Learn more
August 2023
First Spatial Maps at the Single-Cell Level
Michael Angelo, PhD and Michael Snyder, PhD worked with Sanjay Jain, PhD, John Hickey, PhD and collaborators to "uncover how cellular interactions reveal new ways cells can communicate with each other".
By combining cellular imaging techniques, machine learning and other methods of molecular analyses, the teams are creating a comprehensive resource for researchers to better understand all human tissue. The data collected will be publicly available through HuBMAP, enabling researchers to study tissue-specific characteristics, understand disease mechanisms, and develop automated annotation tools that identify and characterize cells. Learn More
December 2022
Professor Polly Fordyce is the recipient of the 2023 Eli Lilly Award in Biological Chemistry.
She is being recognized for her significant contributions to biological chemistry, especially her revolutionary work on applying high throughput biochemical techniques and analyses to investigate molecular recognition. Her novel strategies have dissected quantitative relationships that govern biological function. The work has contributed fundamental new insights into genetic variation, enzyme kinetics and thermodynamics.
October 2022
Serena Sanulli is named NIH Director's New Innovator Award Recipient.
Dr. Sanulli's lab studies genome organization across length and time scales with the long-term goal to understand how cells leverage the diverse biophysical properties of chromatin to regulate genome functions. She is the recipient of the Independent Postdoctoral Fellow Award from the program for Breakthrough Biomedical Research, the McCormick and Gabilan Faculty Fellowship, and she was recently named a Searle Scholar.
May 2022
Two Key Types of Genes Identified
The human genome includes millions of "enhancer" sequences that turn genes on and off—but it has been unclear which enhancers can regulate which genes. A new study led by researchers from the Engreitz Lab finds that two types of genes respond differently to enhancers, and that these responses are controlled by specific sequences in gene promoters. Link to article: https://rdcu.be/cNZxa
April 2022
2022 Winners of the FNIH Lurie Prize in Biomedical Sciences Provide Powerful Contributions to Our Understanding of the Aging Process
The Foundation for the National Institutes of Health (FNIH) has named Anne Brunet, Ph.D., and Andrew Dillin, Ph.D., co-winners of the 2022 Lurie Prize in Biomedical Sciences
March 2022
Neighborhood matters
While the effects of regulatory sequences on gene expression have been widely studied, evidence for the importance of genomic context has been anecdotal. The Steinmetz lab has used the SCRaMbLE system of the yeast synthetic genome for a systematic study of transcript expression from multiple genomic contexts. Long-read sequencing of rearranged test genomes now revealed features of transcriptional context that predicts altered transcript isoform expression.
February 2022
“90 Seconds with Lisa Kim”: Genome sequencing sets Guinness World Record
A new ultra-rapid genome sequencing approach developed by Stanford Medicine scientists sets the first Guinness World Record for the fastest DNA sequencing technique, producing results for one study participant in just over five hours. See the video on StanfordMed TODAY.
January 2022
Sorting cells by intracellular features
Fluorescence-activated cell (FACS) sorting has revolutionized biomedical research, giving us the ability to isolate cells according to the expression of labeled proteins. So far, however, FACS has been blind to spatial processes such as protein localization. The Seinmetz lab, in collaboration with BD Biosciences, combined ultrafast microscopy and image analysis with a flow cytometric cell sorter to unlock spatial phenotypes for high-throughput sorting applications.
https://www.science.org/doi/10.1126/science.abj3013
April 2021
Genome-wide enhancer maps link risk variants to disease genes
Genome-wide association studies (GWAS) have identified thousands of noncoding loci that are associated with human diseases and complex traits, each of which could reveal insights into the mechanisms of disease1. Many of the underlying causal variants may affect enhancers2,3, but we lack accurate maps of enhancers and their target genes to interpret such variants. Read more...
Image credit: Zayna Sheikh
April 2020
Fitbit detecting oncoming sickness
Dr. Michael Snyder discovered that among the millions of measurements they make every day, subtle variances in a Fitbit's data could be a predictor of an oncoming illness.
April 2020
Department of Genetics COVID-19 Research
Our scientists from the Department of Genetics have launched research projects as part of the global response to COVID-19.
April 2020
Stanford Medicine scientists hope to use data from wearable devices to predict illness, including COVID-19
Researchers from Stanford Medicine and their collaborators aim to predict the onset of viral infection through data provided by wearable technology. What they need now are participants.
September 2018
We are bombarded by thousands of diverse species and chemicals
We are all exposed to a vast and dynamic cloud of microbes, chemicals and particulates that, if visible, might make us look something like Pig-Pen from Peanuts.
September 2018
Researchers can forecast risk of deadly vascular condition from genome sequence
A new approach that distills deluges of genetic data and patient health records has identified a set of telltale patterns that can predict a person’s risk for a common, and often fatal, cardiovascular disease, according to a new study from the Stanford University School of Medicine.
July 2018
Diabetic-level glucose spikes seen in healthy people
A study out of Stanford in which blood sugar levels were continuously monitored reveals that even people who think they’re “healthy” should pay attention to what they eat.
May 2018
New center sets out to stop disease before it starts
At the Precision Health and Integrated Diagnostics Center, scientists turn the norms of disease research on their head, searching not for treatments but for ways to prevent disease entirely.
It’s not often that world-class scientists band together to investigate disease with no intention of curing it. Yet upward of 55 scientists at Stanford’s Precision Health and Integrated Diagnostics Center are doing just that in a push to get researchers and physicians off their heels and onto their toes in the battle against disease..
April 2018
CRISPR used to genetically edit coral
In a proof-of-principle study, Stanford scientists and their colleagues used the CRISPR-Cas9 gene-editing system to modify genes in coral, suggesting that the tool could one day aid conservation efforts.
Coral reefs on the precipice of collapse may get a conservation boost from the gene-editing tool known as CRISPR, according to researchers at the Stanford University School of Medicine and their collaborators.
January 2018
Weight flux alters molecular profile
Stanford scientists have found links between changes in a person’s weight and shifts in their microbiome, immune system and cardiovascular system.
A paper describing the work was published online Jan. 17 in Cell Systems. The lead authors are Stanford postdoctoral scholars Wenyu Zhou, PhD, and Hannes Röst, PhD; staff scientist Kévin Contrepois, PhD; and former postdoctoral scholar Brian Piening, PhD. Senior authorship is shared by Michael Snyder, PhD, professor of genetics at Stanford; Tracey McLaughlin, MD, professor of medicine at Stanford; and George Weinstock, PhD, professor and director of microbial genomics at the Jackson Laboratory, an independent, nonprofit biomedical research institution.
October 2017
Study uncovers mutation that supercharges tumor-suppressor
Cancer researchers have long hailed p53, a tumor-suppressor protein, for its ability to keep unruly cells from forming tumors. But for such a highly studied protein, p53 has hidden its tactics well.
Now, researchers at the Stanford University School of Medicine have tapped into what makes p53 tick, delineating a clear pathway that shows how the protein mediates anti-tumor activity in pancreatic cancer. The team’s research also revealed something unexpected: A particular mutation in the p53 gene amplified the protein’s tumor-fighting capabilities, creating a “super tumor suppressor.”
Tissue-specific gene expression uncovered, linked to disease
Understanding how a person’s DNA sequence affects gene expression in various tissues reveals the molecular mechanisms of disease. Stanford scientists involved in the National Institutes Health’s GTEx project have published some of their insights.
May 2017
John Pringle and Anne Villeneuve elected to National Academy of Sciences
Three Stanford researchers are among the 84 newly elected members of the National Academy of Sciences.
The new members from Stanford are Dominique Bergmann, PhD, professor of biology; John Pringle, PhD, professor of genetics; and Anne Villeneuve, PhD, professor of developmental biology and of genetics. Full story..
February 2017
$10.5 million awarded to researchers to work on DNA encyclopedia
Stanford’s William Greenleaf, Michael Bassik, Michael Snyder, Jonathan Pritchard and Michael Cherry have won grants to work on the federally funded Encyclopedia of DNA Elements. Full story..
January 2017
Wearable sensors can tell when you are getting sick
New research from Stanford shows that fitness monitors and other wearable biosensors can tell when an individual’s heart rate, skin temperature and other measures are abnormal, suggesting possible illness. Full story..
Interested in applying to the Ph.D. Program?
The Ph.D. program in the Department of Genetics provides opportunities for graduate study in all major areas of modern genetics, including identification and analysis of human disease genes, molecular evolution, gene therapy, statistical genetics, application of model organisms to problems in biology and medicine, and computational and experimental approaches to genome biology.
Learn more about the Genetics Ph.D. Program here.
Stanford Genetics PhD Program Interest Webinar Slides
Department Chair
"Driven by curiosity, our mission as a leader in genetics and genomics is to engineer state-of-the-art technologies to unravel genetic complexity and transform groundbreaking research into life-changing innovations.”
Lars Steinmetz, PhD
Dieter Schwarz Foundation Endowed Professor and Chair, Department of Genetics. Co-director, Stanford Genome Technology Center (SGTC)
Incoming & Outgoing Department Chairs
Lars Steinmetz, PhD, and Michael Snyder, PhD celebrate Sndyer's extraordinary 15 years and usher in a new era with Steinmetz at the helm.
Show Your Support
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About Us
An underlying theme in our Department is that genetics is not merely a set of tools but a coherent and fruitful way of thinking about biology and medicine. To this end, we emphasize a spectrum of approaches based on molecules, organisms, populations, and genomes.
We provide training through laboratory rotations, dissertation research, seminar series, didactic and interactive coursework, and an annual three-day retreat of nearly 200 students, faculty, postdoctoral fellows, and research staff.
The mission of the Department includes education and teaching as well as research; graduates from our program pursue careers in many different venues including research in academic or industrial settings, health care, health policy, and education. We are especially committed to increasing diversity within the program, and to the training of individuals from traditionally underrepresented minority groups to apply.
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