Lab Members

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
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
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
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

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
Johannes Linder
From Georg Seelig's lab, Univ. of Washington

Aug 2021 - Present

BMI 4050
Email: 

Research Focus: Interpretation of deep learning models in genomics,  generative models and design of biological sequences, regulatory evolution

Graduate Students

Laksshman Sundaram 
(Computer Science)
BioX Fellow 
June 2018 - Present
Email: lakss
 @ stanford . edu
BMI 4050
Jointly advised by Prof. William Greenleaf


Research focus: single cell and disease genomics, neurodevelopment, cardiovascular phenotypes


Abhimanyu Banerjee
(Physics)
Sept 2016 - Present
Email:  manyu @ stanford dot edu
BMI 4050

Research Focus: C2H2 Zinc Finger TF binding models
Amr Alexandari
(Computer Science)
BioX Fellow
Sept 2018 - Present
Email: amr1 @ stanford dot edu
BMI 4050
Jointly advised by Prof. Polly Fordyce

Research Focus: in vitro and in vivo TF binding models

 

Surag Nair
(Computer Science)
Jan 2018 - Present
Email: surag @ stanford dot edu
BMI 4050

Research Focus: Cis-trans models of gene regulation, single cell epigenomics

 Alex Tseng
(Computer Science)
Oct 2019 - Present
Email: amtseng
  @ stanford dot edu
BMI 4050

Research focus: Interpretation methods for deep learning, TF binding models


 Soumya Kundu 
(Computer Science)
May 2019 - Present
Email: soumya.kundu
 @ stanford . edu
BMI 4050

Research focus: Genetic and molecular basis of neurodegenerative/psychiatric disorders


Kelly Cochran
(Computer Science)
Stanford Graduate Fellow
June 2020 - Present
Email: kcochran @ stanford dot edu
BMI 4050

Research Focus: Regulation of RNA processing, RNA binding proteins, splicing

 Anusri Pampari
(Computer Science)
August 2020 - Present
Email: anusri @ stanford dot edu
BMI 4050

Research Focus: Long-range sequence and graph models of gene regulation, Natural language processing for genomic hypothesis discovery

Maxim Zaslavsky
(Computer Science)
NSF Graduate Fellow
Aug 2020  - Present
Email: maximz
  @ stanford dot edu
BMI 4050
Jointly advised by Prof. Scott Boyd

Research focus: Immune repertoire analysis for viral infections
Ziwei Chen
(Computer Science)
Stanford Graduate Fellow
May 2021  - Present
Email: 
ziwei75 @ stanford dot edu
BMI 4050

Research focus: Genomic basis of metabolic disease
Aman Patel
(Computer Science)
May 2021  - Present
Email: 
patelas @ stanford dot edu
BMI 4050

Research focus: Regulatory evolution
Austin Wang
(Computer Science)
May 2021  - Present
Email: atwang
 @ stanford dot edu
BMI 4050

Research focus: single cell / spatial transcriptomics

  

Research Staff

 
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


    

Alumni in Industry

 Akshay Balsubramani
Status: Senior scientist,
Octant Bio

Lab Affiliation: Postdoc
Jan 2017 - July 2021

Research Focus: CRISPR co-essentiality screens, TF binding models, single cell data integration
Mahfuza Sharmin
Status: Data Scientist, Thermo-Fisher

Lab Affiliation: Postdoc
Sept 2017 - July 2021

Research Focus: Deep learning models of chromatin accessibility
 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 Assistant

Lily 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 students

Present
  • 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
Past
  • Shruti Verma (Computer Science, Columbia University) - Summer 2020 - Spring 2021
    Project: Predictive models of variation of chromatin state across individuals
    Mentor: Soumya Kundu
  • Jessica Frank (Stanford) - Summer 2020 - July 2021
    Project: Regulatory sequence models in immune cell types
    Mentor: Caleb Lareau, 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 Students

2021 (Summer)

  • Akshat Nigam (CS) - Transformer and graph neural network models for sequence to chromatin and gene expression profiles 

2021 (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)

  • Alex Tseng (CS)

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 Interns

2021

  • Arjun Barrett (Harker High School) - Mentored by Surag Nair
  • Katie Spivakovsky (Menlo Atherton School) - Mentored by Alex Tseng
  • Ittai Nelken-Regev (Menlo Atherton School) - Mentored by Alex Tseng and Surag Nair

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)

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