Postdoctoral scholars | Georgi Marinov
From Univ. of Indiana
May 2017 - Present
BMI 4050
Email: marinovg @ stanford . edu
Jointly advised by Prof. Will Greenleaf
Research focus: Long-read epigenomic profiling, single cell epigenomic profiling, chromatin architecture in exotic species | | Akshay Balsubramani
From Yoav Freund's lab,
UCSD Computer Science and Engineering
Jan 2017 - Present
BMI 4050
Email: abalsubr @ stanford dot edu
Research Focus: Computational methods for single cell transcriptomics and single cell epigenomics |
| Mahfuza Sharmin
From Héctor Corrada Bravo and Sridhar Hannenhalli's labs, Computer Science, University of Maryland College Park
Sept 2017 - Present
BMI 4050
Email: msharmin @ stanford dot edu
Research Focus: Cross-species models of gene regulation
| | Eran Kotler
Gruss Lipper Fellowship
From Eran Segal's lab,
Weizmann Institute
Jan 2019 - Present
BMI 4050
Email: ekotler @ stanford dot edu
Jointly advised by Prof. Christina Curtis
Research Focus: Regulation and evolution of cancer, tumor-immune microenviroment, cell-free DNA
| | Caleb Lareau
Stanford Science Fellow
From Vijay Sankaran/Jason Buenrosto lab, Harvard University
July 2020 - Present
BMI 4050
Email: clareau @ stanford dot edu
Jointly advised by Prof. Ansuman Satpathy
Research Focus: single cell genomics, immunology |  | Jacob Schreiber
From Bill Noble's lab, Univ. of Washington
Sept 2020 - Present
BMI 4050
Email: jmschr @ stanford dot edu
Research Focus: single cell cis-trans models of gene regulation | | Vivek Ramalingam
From Julia Zeitlinger's lab, Stower's Institute
Nov 2020 - Present
BMI 4050
Email: vir @ stanford dot edu
Research Focus: TF binding models | | |
Graduate Students
| Jin-Wook Lee
(Scientific Programmer)
Jan 2017 - Present
Email: leepc12 @ stanford dot edu
Lane L329A
Research Focus: Pipelines for large-scale genomic analysis | | Zahoor Zafrulla
(Machine learning engineer)
Sept 2019 - Present
Email: zahoor @ stanford dot edu
Lane L329A
Research Focus: Scalable machine learning for genomics |
Research Assistants  | Kristy Mualim
(BS in CS, McGill University)
April 2019 - Present
Email:
Lane L329A
Research Focus: Enhancer-gene linking |
| |
Alumni in Academia  | Daniel Kim
Status: Residency, Internal Medicine, Stanford Medicine
Lab Affiliation: PhD, Biomedical Informatics (MSTP, MD/PhD program)
Sept 2013 - May 2021
(BioX Fellow)
Jointly advised by Prof. Paul Khavari
Research focus: Regulatory dynamics of skin differentiation |  | Avanti Shrikumar Status: Postdoc, Stanford Data Science Fellow
Lab Affiliation: PhD, Computer Science
Sept 2014 - Sept 2020
(HHMI International Student Fellow, Microsoft Women's Fellow, Stanford BioX Fellow) Research focus: Interpretable deep learning models for genomics | 
| Jianrong Wang
Status: Assistant Professor,
Department of Computational Mathematics, Science and Engineering, Michigan State University Lab Affiliation: Postdoctoral Associate
Mar 2016 - Dec 2016 Research Focus: 3D genome architecture | 
| Oana Ursu
Status: Postdoc, Aviv Regev lab, Broad Institute
Lab Affiliation: PhD, Genetics Dept., Co-advised by Mike Snyder
Sept 2013 - Mar 2018
(HHMI International Fellow)
Research focus: 3D genome organization, enhancer-gene linking, regulatory variation |  | Irene Kaplow
Status: Postdoc, Andreas Pfenning Lab, Carnegie Mellon University
Lab Affiliation: PhD, Computer Science Dept,
Co-advised by Hunter Fraser
Mar 2014 - Sept 2017
(CEHG Fellow)
Research focus: DNA methylation QTLs, C2H2 Zinc Finger TF binding models
|  | Michael Wainberg
Status: Postdoc, Tripathy lab, University of Toronto
Lab Affiliation: PhD, Computer Science
Co-advised by Prof. Michael Bassik
Sept 2015 - Mar 2019
(BioX Fellow)
Research focus: TWAS, analysis of CRISPR screens |  | Pang Wei Koh
Status: Graduate Student, Percy Liang lab, CS, Stanford Lab Affiliation: Data Analyst
Jul 2015 - Aug 2016 Research focus: Data imputation, integrative analysis of mesodermal differentiation, Deep learning | |
| | | | | |
 | Johnny Israeli
Status: Nvidia Corp.
Lab Affiliation: PhD, Biophysics
Jan. 2015 - June 2018
(BioX Fellow)
Research focus: TF binding models, Deep learning |  | Anna Shcherbina
Status: InSitro Inc.
Lab Affiliation: PhD, Biomedical Informatics
Jan 2016 - Sept. 2020
(BioX Fellow, Nvidia Fellow)
Research focus: Regulatory variation in disease
|  | Nathan Boley
Status: CTO, RavelBio Inc.
Lab Affiliation: Postdoctoral Fellow
Jan. 2015 - Aug 2016
Research focus: TF binding models, ENCODE-DREAM Challenge |  | Chuan Sheng Foo
Status: Programme Head, Precision Medicine, Scientist, Deep Learning Department Institute for Infocomm Research, A-STAR, Singapore
Lab Affiliation: PhD, Computer Science,
Sept 2013 - Sept 2017
(A-STAR Fellow)
Research focus: Deep learning models of chromatin state, nucleosome positioning and accessibility | | Nadine Hussami
Status: Data scientist, Healthcare division, Wolters Kluwer
Lab Affiliation: PhD, Electrical Engineering, Sept. 2015 - Dec 2017
Research focus: Boosting algorithms for gene regulation | | Maryna Taranova
Status: Group Leader, Roche
Lab Affiliation: Postdoctoral Fellow
Sept. 2014 - Dec 2017
Research focus: 3D genome organization and long-range regulatory interactions |  | Sofia Kyriazopoulou-Panagiotopoulou
Status: Scientist at ArsenalBio
Lab Affiliation: PhD, Computer Science, 2014
Co-advised by Serafim Batzoglou
Research focus: Boosting models for gene regulation |  | Chris Probert
Status: Scientist at InSitro
Lab Affiliation: Graduate student, Genetics
Sept 2014 - May 2021
Co-advised by Prof. Christina Curtis
Research focus: Cancer regulatory genomics, predictive models from cell-free DNA | | Anvita Gupta
Status: Startup founder
Lab Affiliation: Master's Research Assistant
June 2018 - August 2019
Research Focus: Generative models for regulatory DNA |  | Peyton Greenside
Status: CSO, BigHat Biosciences
Lab Affiliation: PhD, Biomedical Informatics
Mar 2014 - June 2018
(BioX Fellow, Schmidt Foundation Fellow)
Research focus: Interpretable, deep learning models of regulatory DNA and non-coding variants |  | Aaditya Shidham
Lab Affiliation: Research Assistant
Jan 2015 - June 2015
Research Focus: Data imputation | | |
Administrative AssistantLily Leung Phone: (650) 723-1073
Email: lleung2 at stanford dot edu
Lane L301
Lab Affiliates- Prateek Verma (Research Assistant) - March 2021 - Present - Transformer and graph neural network architectures for genomics
- Casey Hanson (Postdoc, Snyder lab) - Dec 2019 - Present
- Amy X Lu (Visiting student from University of Toronto) (Sept 2019 - Jan 2020) - Domain adaptation methods for generalizing deep learning models of TF binding across cell types
- Ziga Avsec (Visting Student from Technical University of Munich) (Summer 2018) - Deep learning models of ChIP-exo and ChIP-nexus data
- Glenn Markov (Graduate Student, Genetics, Blaulab@Stanford) - Regulation of reprogramming in heterokaryons
- Oana Carja (Postdoc, Emma Lundberg lab) - Dec 2017- Dec 2018
Undergraduate studentsPresent - Aditya Girish (IIT-Kharagpur) - Summer 2021 - Present
Project: Cross cell type prediction of TF binding profiles
Mentor: Alex Tseng - Yangyuan Zhang (Tsinghua) - Summer 2021 - Present
Project: Base-resolution epigenomic imputation models
Mentor: Jacob Schreiber - Juan Elenter (UdelaR, Uruguay) - Spring 2021 - Present
Project: Predicting causal variants in T2D
Mentor: Soumya Kundu - Yanyi Zhang (UoT) - Summer 2021
Project: Smart genome browsers
Mentor: Surag Nair - Anudeep Golla (Stanford) - Winter 2021 - Present
Project: Deep learning models for HT-SELEX data - Raghav Samavedam (Stanford) - Winter 2021 - Present
Project: Imputation of cross cell type TF binding landscapes
Mentor: Jacob Schreiber - Ishita Mangla (Stanford) - Winter 2021 - Present)
Project: Sequence models of transcription initiation
Mentor: Kelly Cochran - Jessica Frank (Stanford) - Summer 2020 - Present
Project: Regulatory sequence models in immune cell types
Mentor: Caleb Lareau, Soumya Kundu
Past - Shruti Verma (Computer Science, Columbia University) - Summer 2020 - Spring 2021
Project: Predictive models of variation of chromatin state across individuals
Mentor: Soumya Kundu - Nic Fishman (Computer Science, Stanford) (2017-2020)
Project: Generative models of DNA sequence
Mentor: Avanti Shrikumar, Georgi Marinov - Anvita Gupta (Computer Science, Stanford) (2017-2018)
Project: Generative models for DNA sequence
Mentor: Avanti Shrikumar - Joyce Kang (Computer Science, Stanford) (2017-2018)
Honor's thesis: Read Cloud Sequencing Elucidates Microbiome Dynamics in a Stem Cell Transplant Patient (Primary mentor: Prof. Ami Bhatt)
Winner of Firestone Medal for outstanding Honor's thesis
Rotation Students2021 (Winter)- Ziwei Chen (CS) - Variant effect prediction from deep learning models of single cell ATAC-seq data
2020 (Fall)- Aman Patel (CS) - Sequence models of nucleosome profiles
- Austin Wang (CS) - Deep learning models for differential analysis of regulatory profiles
2020 (Summer)- Anusri Pampari (CS)
- Peter Du (Cancer Biology) - joint rotation with Bassik lab
- Micah Olivas (Genetics)
2019 (Fall)- Surag Nair (CS)
- Kelly Cochran (CS)
- Sanket Gupte (CS)
2019 (Summer)2018 (Winter)- Amr Alexandari (CS) - Base pair resolution deep learning models for profile prediction
- Soumya Kundu (CS) - Cross-species models for enhancer prediction
2018 (Spring)- Laksshman Sundaram (CS) - Deep learning models for chromatin marks
- Ananthakrishnan Ganeshan (ICME) - Predicting gene expression from chromatin accessibility
- Victoria Hernandez (Neuroscience)
2018 (Winter)- Ben Siranosian (Genetics) - Deep learning models for regulatory evolution
2017 (Fall)- Daniel Sosa (BMI) - cfDNA analysis
2017 (Winter)- Joe Paggi (CS)- The transcriptome of skin differentiation, time series trajectories
- Omer Hazon (Physics)- Chromatin accessibility changes due to mechanical stress
- Abhimanyu Banerjee (Physics)- Methylation sensitive TF binding models
- Ron Shenderson (Stell Cell Program)- Ectopic enhancer gene linking
- Raunaq Rewari (Mech Engg) - ChIP-nexus models
- Naveen Arivazhagan (CS) - Advanced deep learning architectures for chromatin accessibility dynamics
2016 (Spring)- Anna Scherbina (BMI, Stanford) - Deep learning regulatory chromatin dynamics during nuclear reprogramming
- Timothy Lee (BMI, Stanford) - Deep learning the regulatory code of the C. elegans developing embryo
2016 (Winter)- Anna Scherbina (BMI, Stanford) - Deep learning regulatory chromatin dynamics during nuclear reprogramming
2015 (Fall)- Emma Pierson (CS, Stanford) - Probabilistic models for long-range QTLs
- Michael Wainberg (CS, Stanford) - Deep learning for disease variant prediction
- Boyoung Yoo (CS, Stanford) - chromatin dynamics in Alzheimers disease progression
- Nicholas Sinnott-Armstrong (Genetics, Stanford) - Deep learning for predicting nucleosome positioning and chromatin states
2015 (Spring)- Ragini Phansalkar (BMI (MSTP), Stanford) - QTLs in colorectal cancer
2015 (Winter)- Avanti Shrikumar (CS, Stanford) - Multi-tissue prediction of enhancer activity
2014 (Fall)- Avanti Shrikumar (CS, Stanford) - Multi-tissue prediction of enhancer activity
- Johnny Israeli (Biophysics, Stanford) - Predicting chromatin state from ATAC-seq data
- Alejandro Schuler (BMI, Stanford) - Regulatory dynamics in reprogramming fibroblasts to NPCs
- Chris Probert (Genetics, Stanford) - Enhancer sequence grammars
- Kris Sankaran (Statistics, Stanford) - Imputing chromatin variation from genetic variation
2014 (Summer)- Alex Han (Genetics, Stanford) - Statistical models for enhancer-gene linking
2014 (Spring)- Peyton Greenside (BMI, Stanford) - Chromatin variation in Pulmonary Hypertension
2014 (Winter)- Bo Wang (CS, Stanford) - Regulatory basis of coronary heart disease
Summer High School Interns2021- Arjun Barrett (Harker High School) - Mentored by Surag Nair
- Katie Spivakovsky (Menlo Atherton School) - Mentored by Alex Tseng
2020- Harsh Deep (Harker High School)
- Shray Alag (Harker High School)
- Chloe Jeon (High School Student)
- Tarun Chirovolu (High School student)
- Avyay Varadarajan (High School student)
2019- Eileen Li (High School student)
- Avyay Varadarajan (High School student)
- Hannah Zhou (High School student)
- Tarun Chirovolu (High School student)
- Mallika Parulekar (High School student)
2018- Jocelin Su (High School student) - In vivo TF binding models
- Rajiv Movva (High school student) - Computational models for MPRAs
- Katherine Tian (High school student) - In vivo TF binding models
- Eva Prakash (High School student) - In vivo TF binding models
2017- Rajiv Movva (High school student) - Computational models for MPRAs (Top 40 finalist in the Regeneron Science Talent Show)
- Arian Raje (High School student) - Computational models for MPRAs
- Bryan Chiang (High School student) - TF binding models
- Eva Prakash (High School student) - Architecture search for neural networks
2016- Nikhil Cheerla (High School student) - Deep learning models for detection regulatory variants
2015- Rahul Mohan (Sophomore, Bellarmine College Preparatory in San Jose) - Recurrent neural networks and LSTMs for modeling DNA sequence
2014- Anirudh Mathukumilli (High School Student, Mountain Vista High School, Colorado) - Relationship between enhancer variation across cell-types and individuals
- Pranav Reddy (High School Student, Harker School, San Jose) - Regulatory analysis of GWAS hits in Alzheimer's disease
- Aathira Menon (High School Student, Harker School, San Jose) - Statistical analysis of ChIP-seq data
- Neha Sunil (High School Student, Harker School, San Jose) - Design of RNA guides for CRISPR/CAS9
- Kayla McCue (Undergraduate, Caltech) - Statistical models for reproducibility of histone ChIP-seq data
Collaborators
- William Greenleaf (Genetics, Stanford)
- Christina Curtis (Genetics, Stanford)
- Michael Bassik (Genetics, Stanford)
- Michael Snyder (Genetics, Stanford)
- Paul Khavari (Dermatology, Stanford)
- Helen Blau (Stem Cell Institute, Stanford)
- Anne Brunet (Genetics, Stanford)
- Serafim Batzoglou (CS, Stanford)
- Howard Chang (Dermatology, Stanford)
- Eugene Butcher (Pathology, Stanford)
- Jonathan Pritchard (Genetics, Stanford)
- Dana Pe'er (Biology, Columbia)
- Anthony Oro (Dermatology, Stanford)
- Jin Hyung Lee (Neuroscience, Stanford)
Lab Discussion Forum (Private) |
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