Lab Members

Postdocs

Georgi Marinov
From Univ. of Indiana
May 2017 - Present
Lane L329A
Email: marinovg @ stanford . edu
Jointly advised by Prof. Will Greenleaf

Research focus: Chromatin accessibility, Gene regulation models
Akshay Balsubramani
From Yoav Freund's lab,
UCSD Computer Science and Engineering
Jan 2017 - Present
Lane L329A
Email: abalsubr @ stanford . edu

Research Focus: Machine learning models of TF binding models, 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
Lane L329A
Email:  @ stanford . edu

Research Focus: Cross-species models of gene regulation
Oana Carja
From UPenn
Jan 2018 - Present
Lane L329A
Email: ocarja @ stanford . edu
Jointly advised by Prof. Emma Lundberg

Research focus: D
igital pathology, machine learning and evolutionary cancer research

Graduate Students

Avanti Shrikumar
(Computer Science)
HHMI Fellow
Microsoft Women's Fellow
BioX Fellow
Sept 2014 - Present
Email: avanti @ stanford . edu

Lane L303

Research focus: Interpretable deep learning models for genomics
Anna Shcherbina 
(Biomedical Informatics)
Nvidia Fellow
BioX Fellow
Jan 2016 - Present
Email: annashch @ stanf
ord . edu
Lane L329A
Jointly advised by Prof. Euan Ashley 

Research focus: Regulation of cellular reprogramming; regulatory variation in disease and cancer
Chris Probert
(Genetics)
NSF Fellow 
Set 2014 - Present
Email: cprobert @ stanford . edu

Lane L329A
Jointly advised by Prof. Christina Curtis

Research focus: Cancer regulatory genomics, predictive models from cell-free DNA

 

Daniel Kim
(Biomedical Informatics)
BioX Fellow

Sept 2013 - Present
Email: danielskim @ stanford .edu
Lane L303
Jointly advised by Prof. Paul Khavari

Research focus: Regulatory dynamics of skin differentiation, Network analysis
 
Michael Wainberg 
(Computer Science)
BioX Fellow 
Sept 2015 - Present
Email: wainberg 
@ stanford . edu
Lane L329A
Jointly advised by Prof. Michael Bassik


Research focus: TWAS, analysis of CRISPR screens
 Laksshman Sundaram 
(Computer Science) 
June 2018 - Present
Email: lakss
 @ stanford . edu
Lane L329A
Jointly advised by Prof. William Greenleaf


Research focus: Deep learning models of chromatin state, disease-associated coding and non-coding variants
Abhimanyu Banerjee
(Physics)
Sept 2016 - Present
Email:  manyu @ stanford dot edu
Lane L329A
Research Focus: Methylation sensitive binding of transcription factors
  Amr Mohamed
(Computer Science)
Feb 2017 - Present
Email: amr1 @ stanford dot edu
Lane L329A
Research Focus: Uncertainty of predictions and interpretations derived from neural networks for genomics

Research Staff

 
Jin-Wook Lee
(Scientific Programmer)

Jan 2017 - Present
Email: leepc12 @ stanford dot edu
Lane L329A

Research Focus: Computational infrastructure for large-scale genomic analysis

Research Assistants

 

Surag Nair
(Computer Science)
Jan 2018 - Present
Email: surag @ stanford dot edu
Lane L329A
Research Focus: Imputing chromatin accessibility from gene expression data




Alumni in Academia

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

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

 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
 
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


Peyton Greenside

Status: Postdoc, Emma Brunskill lab, Stanford
(Schmidt Foundation Fellow)

Lab Affiliation: PhD, Biomedical Informatics
Mar 2014 - June 2018 
(BioX Fellow)


Research focus: Interpretable, deep learning models of regulatory DNA and non-coding variants
 
 

Alumni in Industry

 Johnny Israeli
Status: NVidia Corp. 

Lab Affiliation: PhD, Biophysics

Jan. 2015 - June 2018
(BioX Fellow)

Research focus: TF binding models, Deep learning 
 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
Nathan Boley
Status: Freenome

Lab Affiliation: Postdoctoral Fellow

Jan. 2015 - Aug 2016

Research focus: TF binding models, ENCODE-DREAM Challenge 
 Chuan Sheng Foo 
Status: Scientist, AI Dept, Institute for InfoComm Research, 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
Sofia Kyriazopoulou-Panagiotopoulou 
Status: Illumina Inc.

Lab Affiliation: PhD, Computer Science, 2014
Co-advised by Serafim Batzoglou

Research focus: Boosting models 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
 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

  • Ziga Avsec (Visting Student) (Summer 2018) - Deep learning models of ChIP-exo and ChIP-nexus data
  • Glenn Markov (Graduate Student, Genetics, Blaulab@Stanford) - Regulation of reprogramming in heterokaryons

Undergraduate students

  • 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
  • Anvita Gupta (Computer Science, Stanford) (2017-2018)
    Project: Generative models for DNA sequence
  • Nic Fishman (Computer Science, Stanford) (2017-2018)
    Project: Interpreting deep learning models of Massively parallel reporter assays (MPRAs)

Rotation Students

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

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)

Lab Discussion Forum

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