Research & Results
DBDS featured in new Center for Digital Health Landscape Report
November 17, 2020. Stanford's Center for Digital Health (CDH) is excited to announce the release of the Stanford Center for Digital Health Landscape Report, which features DBDS programs, projects and courses, and work by DBDS faculty researchers Euan Ashley, Daniel Rubin, and Russ Altman. A central goal of this report is to highlight the culture of collaboration that is found throughout the broader Stanford community.
The SZS is an efficient statistical method to identify regulated splicing events in droplet-based RNA sequencing
November 11, 2020. Members of Stanford's Salzman Lab, including ICME PhD Student Julia Eve Olivieri (pictured here), Postdoctoral Fellow in Biochemistry Roozbeh Dehghannasiri, and DBDS faculty member Julia Salzman, released their new bioRxiv preprint. This study introduces a novel, robust, and computationally efficient statistical method, the Splicing Z Score (SZS), to detect differential alternative splicing in single cell RNA-Seq technologies including 10x Chromium.
Distance metrics for ranked evolutionary trees
November 2, 2020. DBDS faculty member Julia Palacios (pictured here) and Stanford Biology colleagues Jaehee Kim and Noah Rosenberg published the results of their most recent research in PNAS.
When Algorithms Compete, Who Wins?
October 27, 2020. DBDS faculty member James Zou (pictured here) is featured in this HAI Blog post about how "Over time, prediction algorithms become specialized for an increasingly narrow slice of the population, and the average quality of their predictions declines."
A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank
October 26, 2020. DBDS community members, Yosuke Tanigawa (pictured here), Matthew Aguirre, Rob Tibshirani, Manuel Rivas, and Trevor Hastie, and Stanford and other colleagues including first-author Junyang Qian, published their newest research in PLOS Genetics.
Patient-Specific Induced Pluripotent Stem Cells Implicate Intrinsic Impaired Contractility in Hypoplastic Left Heart Syndrome
October 26, 2020. BMI Graduate Student, Elizabeth Chin (pictured here), co-first authored a new paper, which was published in Circulation. Co-authors include DBDS faculty member Euan Ashley.
Frequency of Routine Testing for Coronavirus Disease 2019 (COVID-19) in High-risk Healthcare Environments to Reduce Outbreaks
October 26, 2020. BMI Graduate Students Elizabeth Chin and Benjamin Huynh (pictured here) released the results of their latest research to Clinical Infectious Diseases. They are co-first authors on this paper, and co-authors include Stanford MD-PhD alum, Nathan Lo.
Discovering our way out: A sampler of COVID-19 research
October 15, 2020. Check out this Stanford Medicine Magazine story featuring COVID-19 research by DBDS faculty Euan Ashley, Carlos D. Bustamante, and Manuel Rivas. So much amazing work being done in DBDS!
All together now: Stanford Medicine takes aim at COVID-19
October 15, 2020. Nigam Shah is featured in this new Stanford Medicine Magazine story about researchers' early responses to the COVID-19 pandemic.
Three new papers from the Zou Group now available
October 12, 2020. Three new papers from the DBDS Zou Group were recently accepted by NeurIPS, which is the main machine learning conference. These papers introduce FrugalML (improving commercial ML efficiency), Neuron Shapley (for identifying important artificial neurons in the network) and MOPO (for improving reinforcement learning on observational data).
Use the links above to access these papers
Fast Lasso method for large-scale and ultrahigh-dimensional Cox model with applications to UK Biobank
October 5, 2020. ICME PhD Student Ruilin Li (pictured here), colleague Christopher Chiang (GRAIL), and DBDS community members Johanne Justesen, Yosuke Tanigawa, Junyang Qiang, Trevor Hastie, Manuel Rivas, and Rob Tibshirani released the results of their recent research in Biostatistics. They developed a scalable and highly efficient algorithm to fit a Cox proportional hazard model by maximizing the L1L1-regularized (Lasso) partial likelihood function, based on the Batch Screening Iterative Lasso (BASIL) method.
ALICE: Active Learning with Contrastive Natural Language Explanations
September 28, 2020. DBDS faculty member James Zou and colleagues shared a new paper with Cornell University's arXiv on how to use natural language explanations to speed up training of machine learning. The paper was just accepted for publication in EMNLP Conference.
New Future of Everything Podcast with host Russ Altman
September 21, 2020. Host and DBDS professor Russ Altman explores how technology, science and medicine are shaping our lives in the "Future of Everything" podcast. A new episode, entitled "Can democracy survive in a digital world?," features Marietje Schaake, HAI International Policy Fellow.
Transcriptomic signatures across human tissues identify functional rare genetic variation
September 11, 2020. BMI Graduate Student Nicole Ferraro (pictured left) and Stanford and other colleagues including Stephen Montgomery (Genetics) had a paper published in Science Magazine, as part of set of GTEx papers.
AI researchers explore solutions for real-life health challenges
September 4, 2020. New AI research by DBDS faculty member Dennis Wall (pictured left) and Stanford colleagues is featured in this Stanford Scope Blog post.
Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx
September 11, 2020. A second study written by DBDS community members as part of the GTEx paper bundle in Science Magazine was also released. Authors included BMI Graduate Students Michael Gloudemans (pictured left) and Margaret Antonio, and Bustamante Lab alumni Alicia Martin and Shaila Mustaroff.
Sex-specific genetic effects across biomarkers
September 1, 2020. DBDS Community members Emily Flynn (pictured left), Yosuke Tanigawa, Russ Altman, and Manuel Rivas and Stanford colleagues released the results of their latest research in the European Journal of Human Genetics.
5 Questions: Alice Popejoy on race, ethnicity and ancestry in science
August 21, 2020. Alice Popejoy, a DBDS postdoctoral scholar who studies biomedical data sciences, speaks to the role — and pitfalls — of race, ethnicity and ancestry in research.
The Surprising Advantages of Virtual Conferences
August 21, 2020. In this Scientific American story, Russ Altman reflects on his experience organizing the COVID-19 and AI Virtual Conference in April.
Serena Yeung named recipient of new CZI award
August 19, 2020. The Chan Zuckerberg Initiative (CZI) released a press release announcing that DBDS faculty member Serena Yeung and Wah Chiu (Stanford Bioengineering) are co-recipients of the CZI Neurodegeneration Challenge Network Collaborative Pairs award.
Artificial intelligence recognizes deteriorating photoreceptors
August 13, 2020. A recent JAMA Ophthalmalogy paper authored by DBDS faculty member Daniel Rubin, postdoctoral fellow Maximilian Pfau and colleagues was featured in a EurekAlert! news release and also on Dr. Rubin's American Institute for Medical and Biological Engineering (AIMBE) College of Fellows Class of 2018 profile page.
A data scientist and former student researcher shares how the Broad Institute helped guide his career
July 28, 2020. DBDS faculty member, Manuel Rivas (pictured to the left) was featured in a Broad Institute News story.
New Op-Ed by Rob Tibshirani published by the New York Times
July 20, 2020. DBDS Faculty Robert Tibshirani and colleague Michael Eisen (UC Berkeley) contributed an Op-Ed, entitled "How to Identify Flawed Research Before It Becomes Dangerous," to the New York Times. They argue, "Scientists and journalists need to establish a service to review research that’s publicized before it is peer reviewed."
VoPo leverages cellular heterogeneity for predictive modeling of single-cell data
July 27, 2020. Members of the Aghaeepour Laboratory--including Natalie Stanley, Ramin Fallahzadeh, Martin Becker, Thanaphong Phongpreecha, Huda Nassar, Sajjad Ghaemi, Anthony Culos, Alan L. Chang, Maria Xenochristou, Camilo Espinosa, and Nima Aghaeepour (pictured left)--contributed their most recent research to Nature Communications.
RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus
June 20, 2020. DBDS members of the Zou Group, including Kevin E. Wu and James Zou, in collaboration with Stanford colleagues, released the results of their recent research in Cell.
Manisha Desai featured in Women in Data Science (WiDS) Podcast
July 17, 2020. On this episode of the WiDS Podcast, DBDS faculty member, Manisha Desai, shares some insights about the challenges and progress of current COVID-19 clinical trials.
Projected geographic disparities in healthcare worker absenteeism from COVID-19 school closures and the economic feasibility of child care subsidies: a simulation study
July 15, 2020. BMI PhD candidates Elizabeth Chin (pictured left) and Benjamin Huynh, as well as DBDS Prof Trevor Hastie, have a new publication in BMC Medicine, entitled "Projected geographic disparities in healthcare worker absenteeism from COVID-19 school closures and the economic feasibility of child care subsidies: a simulation study."
Variation in Health Care Prices Across Public and Private Payers
July 14, 2020. DBDS Instructor Suzanne Tamang and colleagues studied "a unique all-payer data set spanning 38 states to examine the differences in inpatient reimbursement rates paid by traditional Medicare, Medicare Advantage, Medicaid, and private (under-65) insurers," and released their results to The National Bureau of Economic Research.
Native American gene flow into Polynesia predating Easter Island settlement
July 8, 2020. Members of the Bustamante and Rivas Labs, including first author Alex Ioannidis (pictured left), contributed their recent research to Nature. It has been featured by a number of major publications: links for these stories are provided below.
Integrating spatial gene expression and breast tumour morphology via deep
June 22, 2020. Members of the DBDS Zou Group, including Abubakar Abid and James Zou, released the results of their recent research in Nature Biomedical Engineering.
FasTag: Automatic text classification of unstructured medical narratives
June 22, 2020. Members of the Rivas Lab, including Guhan Vankataraman (pictured left) and Manuel Rivas, and Carlos Bustamante released the findings of their recent research in PLOS One.
Clinical Genetics Lacks Standard Definitions and Protocols for the Collection and Use of Diversity Measures
June 5, 2020. Members of the DBDS Community, including first author Alice Popejoy, Carlos D. Bustamante, James Zou, and the Clinical Genome Resource (ClinGen) Ancestry and Diversity Working Group contributed a new study to AJHG.
CS 472 students tackle COVID-19
June 2, 2020. "CS 472: 'Data Science and AI for COVID-19” is featured, along with DBDS Faculty instructor James Zou, in this Stanford Daily story. This course "allows undergraduate students, graduate students and people around the world to unite in the fight against the novel coronavirus."
A Machine Learning Approach to Identifying Changes in Suicidal Language
June 2, 2020. DBDS Instructor Suzanne Tamang (pictured left) and colleagues published their recent research in Suicide and Life Threatening Behavior.
New publication from the Wall Lab on Common Microdeletions in SARS-CoV-2 Sequences
May 16, 2020. Stanford Wall Lab members Brianna Sierra Chrisman, Kelley Paskov, Nate Stockham, Jae-Yoon Jung, Maya Varma, Peter Washington, and Dennis P. Wall released the results of their recent COVID-19 research on virological.org.
A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk
May 7, 2020. Members of DBDS's Gentles and Plevritis Labs, including PIs Andrew Gentles and Sylvia Plevritis, released the results of their recent research in Genome Biology.
Stanford researchers working on wearables for early detection of infectious diseases
May 5, 2020. DBDS faculty member Russ Altman is featured in this Stanford Daily story about how "Stanford researchers are working with Fitbit and Scripps Research Institute to develop wearables that can detect infectious diseases such as COVID-19 and help contain their spread."
Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma
May 5, 2020. This study from members of the Rivas Lab, including first author Yosuke Tanigawa (pictured left), has been published by PLOS Genetics.
June 8, 2020 Update: This paper was highlighted as Editors' Choice in Science.
Knight-Hennessy Scholars program announces new cohort
May 4, 2020. We are thrilled to announce that two of our incoming BMI students, Misha Baitemirova and Eric Sun, have been awarded Knight-Hennessy Scholarships. Including Juan Manuel Zambrano, a returning BMI PhD scholar who was awarded a KH Fellowship two years ago, we will have three KH scholars in the BMI program!
Specific splice junction detection in single cells with SICILIAN
April 15, 2020. DBDS faculty member Julia Salzman and members of her lab, postdoc Roozbeh Dehghannasiri and graduate student Julia Olivieri (pictured left), released their preprint on bioxRiv!
Why Do Young, Healthy People Die from COVID-19?
April 14, 2020. DBDS faculty member Manuel Rivas contributes to this Proto Magazine story about why young, healthy people die from COVID-19. His genetics work focuses on outliers at the other extreme: people who are highly resistant to the virus despite repeated exposure.
Assessing Digital Phenotyping to Enhance Genetic Studies of Human Diseases
April 9, 2020. DBDS community members and alumni, Christopher DeBoever (pictured left), Yosuke Tanigawa, Matthew Aguirre, Greg McInnes, Adam Lavertu, and Manuel Rivas, published the results from their recent research on digital phenotyping in AJHG.
Nigam Shah: A researcher turns to data to fight the COVID-19 virus
April 8, 2020. DBDS faculty member Nigam Shah joined Russ Altman for this Future of Everything podcast. Shah, "an expert in bioinformatics...describes how better information and modeling can help caregivers stay a step ahead of the new virus."
COVID-19 patients often infected with other respiratory viruses, preliminary study reports
March 29, 2020. DBDS faculty member Nigam Shah is featured in this Stanford Medicine News story about a preliminary analysis that finds that people infected with the virus that causes COVID-19 are often co-infected with other respiratory viruses.
How sick will the coronavirus make you? The answer may be in your genes
March 27, 2020. DBDS faculty member Manuel Rivas is quoted in this Science Magazine story, and his group's recent preprint is also mentioned.
COVID-19 Host Susceptibility Studies Ramp Up Internationally
March 26, 2020. DBDS faculty members Carlos Bustamante (pictured left) and Manuel Rivas are featured in this GenomeWeb article about The COVID-19 Host Genetics Initiative.
Video-based AI for beat-to-beat assessment of cardiac function
March 25, 2020. DBDS faculty member James Zou and colleagues published their most recent research in Nature. This paper presents the first AI system to assess cardiac function. It also makes publicly available one of the largest medical video datasets as a community resource. Stanford Medicine News also published a feature story about this groundbreaking research.
Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes
March 24, 2020. DBDS community members Yosuke Tanigawa (pictured left) and Manuel Rivas wrote a pre-print related on COVID-19 that is now posted on preprints.org.
Healthcare worker absenteeism, child care costs, and COVID-19 school closures: a simulation analysis
March 23, 2020. DBDS community members, Elizabeth Chin (pictured left) and Benjamin Huynh (PhD students in Biomedical Informatics Training Program), and faculty member Trevor Hastie, with UCSF and Harvard Medical School collaborators, wrote this timely preprint, which is now available online.
Peripheral T cell expansion predicts tumour infiltration and clinical response
February 26, 2020. Alumnus of the Biomedical Informatics (BMI) Training Program and Principal Scientist of Bioinformatics and Computational Biology at Genentech, Thomas Wu released the results of his recent research in Nature.
The automatic construction of bootstrap confidence intervals
February 18, 2020. DBDS faculty member Bradley Efron's and, pictured left, Senior Research Scientist Balasubramanian Narasimhan's new paper on automatic construction of bootstrap confidence intervals was recently published in the Journal of Computational and Graphical Statistics.
When AI is watching patient care: Ethics to consider
February 10, 2020. DBDS faculty member Serena Yeung is featured in this Stanford Scope Blog post about her recent Viewpoint, published in JAMA.
Unprecedented exploration generates most comprehensive map of cancer genomes charted to date
February 5, 2020. DBDS faculty members Carlos D. Bustamante and Francisco De La Vega (pictured left) were major contributors to the final publications of a series of papers by the PanCancer Analysis of Whole Genomes (PCAWG) consortium, released this week in Nature publications. They were involved for a number of years in this initiative, mainly working on the analysis of the germline genome of the studys' cancer patients.
Ethical and Legal Aspects of Ambient Intelligence in Hospitals
January 24, 2020. DBDS faculty member Serena Yeung and colleagues published a Viewpoint about “Ethical and Legal Aspects of Ambient Intelligence in Hospitals” on JAMA Network.
Study sheds light on the genetics of hibernation
January 23, 2020. DBDS Communications Manager, Katie M. Kanagawa, worked closely with DBDS faculty member Carlos D. Bustamante and DBDS Bustamante Lab alum, Katharine Grabek, to develop this Stanford Scope blog post, summarizing their recent research on the genetics of hibernation and exploring the significance of their findings for squirrels and humankind.
Single-cell transcriptional diversity is a hallmark of developmental potential
January 23, 2020. DBDS faculty member Aaron Newman and colleagues released the findings from their recent research in Science Magazine. This research is also featured in a Stanford Medicine News story, entitled "A single number helps Stanford data scientists find most dangerous cancer cells."
Genetic variation drives seasonal onset of hibernation in the 13-lined ground squirrel
December 20, 2019. This research by DBDS Bustamante Lab alumni, including Katharine Grabek, Thomas Cooke, Kaitlyn Spees, Shirley Sutton, and DBDS faculty Carlos Bustamante, was published in Nature Communications Biology.
Lower BMI means lower diabetes risk, even among non-overweight people
December 10, 2019. Lower body mass index (BMI) is consistently associated with reduced type II diabetes risk, among people with varied family history, genetic risk factors and weight, according to a new study published this week in PLOS Medicine by DBDS faculty Manuel Rivas of Stanford University, and colleagues.
Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution
December 6, 2019. This study, published in Nature Communications, features Stanford research from DBDS Chair Sylvia K. Plevritis, faculty member Robert Tibshirani, members of the Plevritis lab including Benedict Anchang and first-author Loukia Karacosta, and others.
Stanford researchers program cancer-fighting cells to resist exhaustion, attack solid tumors in mice
December 4, 2019. DBDS postdoctoral scholar in the Plevritis Lab, Zinaida Good, and colleagues were featured in a Stanford Medicine News Center story about how “CAR-T cells are remarkably effective against blood cancers, but their effect can be transient as the cells become exhausted. Stanford researchers found a way to keep the cells effective in mice with human tumors.” This story was featured in the 12/5 Stanford Report.
Stanford-led snapshot of artificial intelligence reveals challenges
November 26, 2019. DBDS Faculty member, Russ Altman, is featured in a Stanford News story about how a "A periodic review of the artificial intelligence industry revealed the potential pitfalls of outsourcing our problems for technology to solve rather than addressing the causes, and of allowing outdated predictive modeling to go unchecked." This story was also included in the December 3rd issue of the Stanford Report.
Through Apple Heart Study, Stanford Medicine researchers show wearable technology can help detect atrial fibrillation
November 13, 2019. DBDS Faculty member, Manisha Desai, is featured in this Stanford Medicine News Center story about a "Study [that] shows that Apple Watch app can identify heart rhythm irregularities, which can help catch atrial fibrillation." This story was also included in the November 27th issue of The Brief by Dean Lloyd Minor.
Sex and gender analysis improves science and engineering
November 6, 2019. DBDS Primary Faculty member, Dr. James Zou, and co-authors released results from their research on how to use sex and gender analysis to improve science and engineering in Nature.
Sex and gender analysis improves science, Stanford scholars say
November 6, 2019. Stanford News featured research conducted by co-author, and DBDS faculty member, James Zou on how "a gender and sex analysis in scientific research can open the door to discovery and innovation."
Smartphone app encourages physical activity, study finds
October 31, 2019. DBDS Secondary faculty member, Euan Ashley, was featured in Stanford Medicine News and the Dean's Brief. The story explores how, "Using a smartphone app, Stanford scientists and their colleagues conducted the first entirely digital randomized clinical trial to boost exercise among participants."
Genome-wide Association Studies in Ancestrally Diverse Populations: Opportunities, Methods, Pitfalls, and Recommendations
October 10, 2019. Check out this new Cell Primer on GWAS in diverse populations. Authors, including DBDS Postdoctoral Scholar Alice Popejoy and Bustamante Lab alum Alicia Martin, worked really hard to make sure that race, ethnicity, and ancestry were considered carefully from an interdisciplinary perspective.
Medical device safety in the real world: Tapping EHR data
October 7, 2019. This Stanford Medicine News feature story features DBDS Secondary Faculty member, Dr. Nigam Shah, and explores how "Researchers used artificial intelligence and de-identified data from electronic health records to identify the safest types of hip implants."
Components of genetic associations across 2,138 phenotypes in the UK Biobank highlight adipocyte biology
September 6, 2019. Check out this new study, published today in Nature Communications, featuring research and results from the DBDS Rivas Lab, colleagues, and collaborators!
5 Questions: Tina Hernandez-Boussard on using ‘real-world data’ to inform clinical care
September 3, 2019. "In an interview, computational biologist [and DBDS Secondary Faculty/BMI Faculty] Tina Hernandez-Boussard discusses analyzing the value of electronic health records as a source of information in the clinic."
Rubin Lab Names One of Best Four 2018 Papers on Clinical Decision Support by IMIA!
September 3, 2019. The Rubin Lab's paper,* on AI modeling to predict survival of metastatic cancer patients to enable personalized treatment decision making, was named one of the 4 best papers (among 1,148 papers reviewed) published in 2018 on Clinical Decision Support by the International Medical Informatics Association (IMIA)!
16 new gene-based abnormalities found to increase risk for autism
August 8, 2019. The Wall Lab has released a new study in Cell, entitled "Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks. " This is the largest whole genome sequencing study of its kind in this space, with some great discoveries including a new syndrome for autism.
Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells
July 29, 2019. This study, published in Nature Biotechnology, features work by DBDS Faculty member, James Zou, and members of the Zou Group.
Wall Lab research featured in New York Times!
July 17, 2019. Read more about how "Google Glass May Have an Afterlife as a Device to Teach Autistic Children."
5 Questions: Genevieve Wojcik on the need for diversity in genome-based studies
June 20, 2019. DBDS Research Scientist, Dr. Gen Wojcik, "speaks about the lack of diversity in genomewide association studies, why it’s a problem and how increasing diversity in these studies can elevate the entire population."
Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features
May 28, 2019. This PLoS Computational Biology publication features the results of research conducted by DBDS Department Chair, Sylvia Plevritis, and members/alumni of her lab, Gina Bourchard and David Knowles.
Determining cell type abundance and expression from bulk tissues with digital cytometry
May 6, 2019. Stanford researchers, including Assistant Professor of Biomedical Data Science, Aaron Newman, have developed a computational platform for analyzing the molecular behavior of individual cells in tissue samples, opening the door for new discoveries, diagnostics and treatments.
An open resource for accurately benchmarking small variant and reference calls
April 1, 2019. This piece, authored by Francisco De La Vega, Adjunct Professor of Biomedical Data Science, and collaborators, was published in Nature Biotechnology!
Opportunities and Challenges for transcriptome-wide association studies
April 2019- This is a new study released by Nature Genetics, authored by members of the Rivas lab, Anshul Kundaje, David Knowles, and others.
Effect of Wearable Digital Intervention for Improving Socialization in Children With Autism Spectrum Disorder
March 25, 2019- Members of the Desai and Wall Labs, including Secondary BDS Faculty members Drs. Manisha Desai and Dennis Wall, published the results from a Randomized Clinical Trial in JAMA Pediatrics.
Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands
March 20, 2019- This publication is co-authored by Bustamante Lab alumna, Rosa Fregel-Lorenzo, and lab PI Carlos Bustamante, among others.
New publication in Nature Biotechnology on benchmarking germline, small-variant calls in human genomics
March 12, 2019. As part of the Global Alliance for Genomics and Health (GA4GH), BDS Adjunct Professor Francisco De La Vega and others present a benchmarking framework for variant calling.
New Publication in Genome Medicine on PRS
December 27, 2018. BDS faculty, Drs. Carlos D. Bustamante and Francisco De La Vega published a new study on Polygenic Risk Scores: A Biased Prediction” in Genome Medicine.
New publication from the Wall Lab in PLoS Medicine
November 27, 2018. Felicitations to the Wall Lab for yesterday's publication of a super exciting paper (IMHO) in PLoS Medicine on mobile, machine-learning based detection of autism, which received top spot/front page billing!
New primer on deep learning in Nature Genetics and paper from the Zou Group in npg Digital Medicine
November 26, 2018. Congratulations to James Zou, et al, for today's publication of a primer on deep learning in genomics in Nature Genetics, with an accompanying interactive online tutorial. We hope this will be a useful resource for the community.
Also, felicitations on the feature story released last week by Stanford Medicine's New Center about a recent DeepTag paper (published in late October in npg Digital Medicine) Study authors included BDS members, Allen Nie, Ashley Zehnder, Arturo Lopez Pineda, Manuel Rivas, Carlos D. Bustamante, and James Zou, among others.
New publication in PLOS Genetics from the Rivas Lab
May 28, 2018. BDS faculty member Dr. Manuel Rivas's work, entitled "Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population," has been published today in PLOS Genetics.
UK Biobank data opens up window into genetics of disease
April 25, 2018. "A trove of genetic records from the UK Biobank was unleashed last July, and after mining the immense data set, scientists at Stanford have found strong evidence for 27 direct links between specific genetic mutations and a variety of human diseases.
Some of these mutations have never been associated with disease before, and some even seem to confer protection against disease, making them prime drug candidates.
The team's work, published in Nature Communications, focused in on a particular type of genetic oddity that halts proper protein formation before it's complete. It's called a protein-truncating variant, or a PTV. Manuel Rivas, PhD, a biomedical data scientist at Stanford, is the corresponding author."- Hanae Armitage, SCOPE Blog (Stanford School of Medicine)
AI can be sexist and racist — it’s time to make it fair
July 18, 2018. Computer scientists must identify sources of bias, de-bias training data and develop artificial-intelligence algorithms that are robust to skews in the data, argue James Zou (Stanford BDS) and Londa Schiebinger.
BMIR and DBDS Faculty Featured in New PanCan Papers
April 12, 2018. The Cancer Genome Atlas (TCGA) PanCan effort recently released a series of 27 papers. Published in various Cell journals, these papers mark the culmination and completion of the PanCancer Atlas Initiative (PanCan) and The Cancer Genome Atlas (TCGA) consortium. Faculty from Stanford’s Center for Biomedical Informatics Research (BMIR) and the Department of Biomedical Data Science (DBDS) contributed greatly to the completion of this large-scale PanCan initiative, which spanned a decade and analyzed over 11,000 tumors from 33 of the world’s most prevalent cancers.
Germline determinants of the somatic mutation landscape in 2,642 cancer genomes
November 16, 2017- Francisco de la Vega (Adjunct Professor in DBDS) and (DBDS Chair) Carlos D. Bustamante have, for the past few years, been working on a project with the International Cancer Genome Consortium - the Pan-Cancer Analysis of Whole-Genomes (PCAWG) group. The project involves the analysis of whole-genome sequencing data from cancer tumor specimens from over 2,600 cancer patients and matched normal tissue, and hundreds of researchers around the world organized in subgroups over 14 research themes. Drs De La Vega and Bustamante have, more specifically, been participating in the analysis of germline genomes to understand how the germline variants affect, among other things, the cancer somatic mutational process.
A milestone has recently been reached in the project, with the release of the germline team's manuscript at BioRxiv. This manuscript will be submitted soon for review, and will be published in a special issue in 3-4 months, with other consortium papers.
Interpretation of Neural Networks is Fragile
Fake news for AI by AI, in other words.
November 8, 2017- DBDS's Zou group just released a paper which, for the first time, demonstrates that interpretation of machine learning predictions are extremely fragile. The team, led by Ph.D. students Amirata Ghorbani and Abubakar Abid, showed that for two images that are visually identical and that are both predicted to be, for example, malignant, the machine learning algorithm can give two completely different explanations.
This is very disconcerting in practice because in order to trust machine learning predictions, researchers typically rely on its explanation for why certain predictions are made. This work shows that the explanation itself is highly unreliable.
Mosaic Mutations in Blood DNA Sequence Are Associated with Solid Tumor Cancers
July 6, 2017- This is the first of a couple of articles that will be coming out of the Rivas Lab and appearing in npj Genomic Medicine this summer 2017.
The editors of Genomic Medicine summarize the article as follows: "Having some abnormal blood cells with mutations that shorten the coding sequence of their genes increases one’s risk for solid tumors. Mark Daly and colleagues from the Broad Institute in Cambridge, Massachusetts, USA, used large genomic databases to test whether having blood cells both with and without genetic variants predicted to shorten the encoded protein — a phenomenon known as mosaic protein-truncating variants (PTVs) — was associated with developing a range of solid-tumor cancers. They studied DNA from around 8,000 people with cancer and 6,000 healthy controls. They confirmed previous reports linking these variants to breast and ovarian cancer, and extended the association to include tumors of the brain, skin and lungs. (Other studies have also shown that mosaic PTVs precede and predict the development of leukemia.) These results broadly connect cancer to blood DNA changes."
Stanford Daily Interview with DBDS Faculty James Zou
February 3, 2017- "In this series, The Stanford Daily sits down to talk with new faculty members on campus.
Assistant professor James Zou joined Stanford’s newly created biomedical data science department in the fall, teaching CS 273B: “Deep Learning in Genomics and Biomedicine” with Anshul Kundaje, assistant professor of genetics and computer science. The Daily sat down with Zou to discuss joining the Stanford community and his interests beyond his academic discipline."