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, Single cell chromatin accessibility 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
  

Graduate Students



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

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

Email: pgreens @ stanford . edu
Lane L303

Research focus: Disease genomics. Computational models of disease-associated genetic and regulatory variation
Chuan Sheng Foo
(Computer Science)
A*STAR Fellow  
Email: csfoo @ cs .stanford .edu
Lane L303

Research focus: Models of chromatin accessibility, chromatin structure, nucleosome positioning and chromatin state dynamics, Deep learning

 

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
Irene Kaplow
(Computer Science)
CEHG Fellow
Email: ikaplow @ stanford . edu
Lane L303 and 317 Herrin Labs
Jointly advised by Prof. Hunter Fraser

Research focus: Computational models for regulatory variation

 

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

Research focus: TF binding models, Deep learning
 Avanti Shrikumar
(Computer Science)
HHMI Fellow
Microsoft Women's Fellow
BioX Fellow
Email: avanti @ stanford . edu
Lane L303

Research focus: Multi-tissue enhancer models, Deep learning, modeling time-series data
 Chris Probert
(Genetics)
NSF Fellow 
Email: cprobert @ stanford . edu
Lane L329A
Jointly advised by Prof. Christina Curtis

Research focus: Cancer regulatory genomics
 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
Michael Wainberg 
(Computer Science)
BioX Fellow 
Email: wainberg @ stanford . edu
Lane L329A
Jointly advised by Prof. Michael Bassik


Research focus: Regulatory variants; analysis of genome editing screens; combinatorial drug-gene interactions 


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

Alumni in Industry

 
Nathan Boley
Lab Affiliation: Postdoctoral Fellow
Jan. 2015 - Aug 2016
Status: Research Scientist at Driver Group

Research focus: TF binding models, Causal regulatory networks, transcriptome assembly and quantification
 Aaditya Shidham
Lab Affiliation: Research Assistant
Jan 2015 - June 2015

Research Focus: Data imputation
Sofia Kyriazopoulou-Panagiotopoulou 
Lab Affiliation: Graduate student jointly advised by Prof. Serafim Batzoglou
Sept 2013 - Sept 2014.
Status: Currently at 10X Genomics

Research focus: Predictive models of gene regulation integrating sequence, expression and chromatin state, regulatory heterogeneity, chromatin variation across individuals
 

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
  • 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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