Lab Members

Postdocs

Maryna Taranova
From UC Irvine Theoretical and Computational Biophysics
Sept. 2014 - Present
Lane L329A
Email: mtaranova @ stanford .edu

Research focus: 3D genome organization and long-range regulatory interactions
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 
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
 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

Oana Ursu 
(Genetics)
HHMI Fellow
Email: oursu @ stanford .edu
Lane L303
Jointly advised by Prof. Mike Snyder

Research focus: 3D genome organization, enhancer-gene linking, regulatory variation
Peyton Greenside
(Biomedical Informatics)
BioX Fellow

Email: pgreens @ stanford . edu
Lane L303

Research focus: Disease genomics. Interpretable, deep learning models of hematopoietic differentiation
Avanti Shrikumar
(Computer Science)
HHMI Fellow
Microsoft Women's Fellow
BioX Fellow
Email: avanti @ stanford . edu
Lane L303

Research focus: Interpretable deep learning models for genomics

 

Daniel Kim
(Biomedical Informatics)
BioX Fellow

Email: danielskim @ stanford .edu
Lane L303
Jointly advised by Prof. Paul Khavari

Research focus: Regulatory dynamics of skin differentiation, Network analysis
Anna Shcherbina 
(Biomedical Informatics)
Nvidia Fellow
BioX Fellow
Email: annashch @ stanford . edu
Lane L329A
Jointly advised by Prof. Euan Ashley 

Research focus: Regulation of cellular reprogramming; regulatory variation in disease and cancer

 

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

Research focus: TF binding models, Deep learning
 
Michael Wainberg 
(Computer Science)
BioX Fellow 
Email: wainberg @ stanford . edu
Lane L329A
Jointly advised by Prof. Michael Bassik


Research focus: TWAS, analysis of CRISPR screens
 Chris Probert
(Genetics)
NSF Fellow 
Email: cprobert @ stanford . edu
Lane L329A
Jointly advised by Prof. Christina Curtis

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

Research Staff

 
Jin-Wook Lee
(Scientific Programmer)

Email: leepc12 @ stanford dot edu
Lane L329A

Research Focus: Computational infrastructure for large-scale genomic analysis


Alumni in Academia

Jianrong Wang

Status: Assistant Professor,
Department of Computational Mathematics, Science and Engineering, Michigan State University

Lab Affiliation: Postdoctoral Associate
March 2016 - Dec 2016

Research Focus: 3D genome architecture

Pang Wei Koh

Status: PhD program in Computer Science at Stanford

Lab Affiliation: Data Analyst
July 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, 2017 (CEHG Fellow)


Research focus: DNA methylation QTLs, C2H2 Zinc Finger TF binding models
  

Alumni in Industry

Nathan Boley

Status: Driver Group

Lab Affiliation: Postdoctoral Fellow

Jan. 2015 - Aug 2016

Research focus: TF binding models, ENCODE-DREAM Challenge 
 Aaditya Shidham

Lab Affiliation: Research Assistant
Jan 2015 - June 2015

Research Focus: Data imputation
Sofia Kyriazopoulou-Panagiotopoulou 

Status: Illumina Inc.

Lab Affiliation: PhD, Computer Science, 2014


Research focus: Boosting models for gene regulation
 Chuan Sheng Foo 

Status: Scientist, Artificial Intelligence Department, Institute for InfoComm Research, Singapore

Lab Affiliation: PhD, Computer Science, 2017 (A-STAR Fellow)


Research focus: Deep learning models of chromatin state, nucleosome positioning and accessibility

Administrative Assistant

Tara Trim
Email: ttrim @ stanford . edu
Lane L301


Lab Affiliates

  • Bo Wang (Graduate Student, Computer Science, BatzoglouLab@Stanford) - Deep Learning, Network analysis
  • Nadine Hussami (Graduate Student, Statistics, TibshiraniLab@Stanford) - Multi-task Boosting models for regulatory network inference
  • Aaron Daugherty (Graduate Student, Genetics, Brunetlab@Stanford) - Chromatin accessibilty in C. elegans
  • Glenn Markov (Graduate Student, Genetics, Blaulab@Stanford) - Regulation of reprogramming in heterokaryons
  • Noah Spies (Postdoc, Genetics, Sidowlab@Stanford) - Cancer evolution

Rotation Students

2017 (Winter)

  • Joe Paggi - The transcriptome of skin differentiation, time series trajectories
  • Omer Hazon - Chromatin accessibility changes due to mechanical stress
  • Abhimanyu Banerjee - Methylation sensitive TF binding models
  • Ron Shenderson - Ectopic enhancer gene linking
  • Raunaq Rewari - ChIP-nexus models
  • Naveen Arivazhagan - 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
  • 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

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