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: Transcriptome reconstruction in skin differentiation, 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: Generative models, Semisupervised learning, Ensemble learning, TF binding models 

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: Dynamics gene regulation models
 

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
Peyton Greenside
(Biomedical Informatics)
BioX Fellow

Mar 2014 - Present
Email: pgreens @ stanford . edu
Lane L303

Research focus: Disease genomics. Interpretable, deep learning models of hematopoietic differentiation
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

 

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
 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
 Johnny Israeli
(Biophysics)
BioX Fellow  
Jan 2015 - Present
Email: jisraeli @ stanford . edu
Lane L329A

Research focus: TF binding models, Deep learning
  

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

 

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

Abhimanyu Banerjee
(Physics)
Sept 2016 - Present
Email:  manyu @ stanford dot edu
Lane L329A
Research Focus: Methylation sensitive binding of transcription factors




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: PhD program in Computer Science at 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

Alumni in Industry

Nathan Boley
Status: Driver Group

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
 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
 

Administrative Assistant

Lily Leung

Phone: (650) 723-1073
Email: lleung2 at stanford dot edu
Lane L301


Lab Affiliates

  • Glenn Markov (Graduate Student, Genetics, Blaulab@Stanford) - Regulation of reprogramming in heterokaryons

Rotation Students

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/Undergraduate Interns

2017

  • Rajiv Movva - Computational models for MPRAs (Top 40 finalist in the Regeneron Science Talent Show)
  • Arian Raje - Computational models for MPRAs
  • Bryan Chiang - TF binding models
  • Eva Prakash - Architecture search for neural networks

2016

  • Nikhil Cheerla - 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

Comments