• PI:

  Yun S. Song 304B Stanley Hall 321 Evans Hall

• Postdocs:

  Antoine Koehl (PhD, Stanford University) 378 Stanley Hall

• PhD Students:

  	Carlos Albors 378 Stanley Hall
  	Yufan Cao 378 Stanley Hall
  	Jack Demaray (Joint with Brady Cress) 378 Stanley Hall
  	Canal Li [ Homepage ] 378 Stanley Hall
  	Stephen Lu 378 Stanley Hall
  	Mike Moubarak (Joint with David Savage) 378 Stanley Hall
  	Kohei Sanno 378 Stanley Hall
  	Junhao (Bear) Xiong (Joint with Jennifer Listgarten)
  	Chengzhong Ye (Joint with Bin Yu)
  	Fanding Zhou 378 Stanley Hall
  	Kevin Zhu 378 Stanley Hall

Undergraduate Students:

	Aakarsh Vermani
	Qile Yang

A note to prospective students and postdocs: If you wish to join our group, you need to pass a casual "No Fear" test. Demonstration by Matthias Steinrücken while on a conference trip to Ireland in June 2012: Photos by Anand Bhaskar

Former Postdocs:

• Paul A. Jenkins [ Homepage ] (Postdoc, Nov 2008 – Jun 2012) Associate Professor in the Departments of Statistics and Computer Science, University of Warwick.
• Matthias Steinrücken [ Homepage ] (Postdoc, Feb 2010 – Jan 2015) Assistant Professor in the Department of Ecology and Evolution, University of Chicago.
• Christopher Hallsworth (Postdoc, Oct 2010 – Aug 2011)
• Tzu-Yu Joyce Liu [ Homepage ] (Postdoc, Sep 2013 – Aug 2017) Associate Professor in the Electrical Engineering Department at National Taiwan University.
• Shishi Luo (Postdoc, May 2014 – May 2017) On to Helix
• Ethan Jewett (Postdoc, Oct 2014 – Aug 2017) On to 23andMe
• Miaoyan Wang (Postdoc, Sep 2015 – Aug 2018) Assistant Professor in the Department of Statistics, University of Wisconsin – Madison
• Zvi Rosen (Postdoc, Jan 2016 – Aug 2018) Assistant Professor in the Department of Mathematics, Florida Atlantic University
• Khanh Dao Duc (Postdoc, Jun 2014 – Jun 2019) Assistant Professor in the Department of Mathematics, University of British Columbia
• William DeWitt (Postdoc, May 2022 – Jun 2024) Assistant Professor in the Department of Genome Sciences, University of Washington
• Gonzalo Benegas (Postdoc, Jan 2024 – Jul 2025) Research Scientist, Open Athena
• Jesús Martínez-Gómez (Postdoc, Aug 2022 – June 2025) Assistant Professor in the Department of Ecology, Evolution, and Marine Biology, UCSB.

Former PhD Students:

• Junming Yin (PhD, 2010. Jointly advised by Mike Jordan) On to CMU as a Lane Fellow in Computational Biology. Now an Assistant Professor at the University of Arizona.
  PhD Thesis Title: Computational Methods for Meiotic Recombination Inference
• Wei-Chun Kao (PhD, 2011) On to Unisonic Technologies (VP Operations). Now at Omniscient Cloud Technologies (Founder).
  PhD Thesis Title: Algorithms for Next-Generation High-Throughput Sequencing Technologies
• Joshua S. Paul (PhD, 2012) On to InVitae.
  PhD Thesis Title: Conditional Sampling Distributions for Coalescent Models Incorporating Recombination
• Andrew H. Chan (PhD, 2013) On to Google Inc. Now at Airbnb.
  PhD Thesis Title: Scalable Statistical Methods for Ancestral Inference from Genomic Variation Data
• Anand Bhaskar (PhD, 2013) On to Stanford University as a CEHG Postdoctoral Fellow in Jonathan Pritchard's lab. Now at Facebook.
  PhD Thesis Title: Statistical, Algorithmic, and Robustness Aspects of Population Demographic Inference from Genomic Variation Data
• Ma'ayan Bresler (PhD, 2014) On to Google Inc.
  PhD Thesis Title: Statistical Methods for Genome Assembly
• Sara Sheehan (PhD, 2015) On to Smith College as an Assistant Professor of Computer Science. Now an Assistant Professor of Computer Science at Haverford College.
  PhD Thesis Title: Scalable Algorithms for Population Genomic Inference
• Kelley Harris (PhD, 2015. Jointly advised by Rasmus Nielsen) On to Stanford University as a Kirschstein-NRSA Postdoctoral Fellow in Jonathan Pritchard's lab. Now an Assistant Professor of Genome Sciences at the University of Washington, Seattle.
  PhD Thesis Title: Inference of population history and mutation biology from human genetic variation
• John A. Kamm (PhD, 2015) On to the Sanger Institute & the University of Cambridge as an HFSP Postdoctoral Fellow in Richard Durbin's lab.
  PhD Thesis Title: One and Two Locus Likelihoods under Complex Demography
• Jonathan Terhorst (PhD, 2017) On to the University of Michigan as an Assistant Professor in the Department of Statistics.
  PhD Thesis Title: Demographic Inference from Large Samples: Theory and Methods
• Jonathan Fischer (PhD, 2018) Now a Clinical Assistant Professor in the Department of Biostatistics at the University of Florida.
  PhD Thesis Title: Statistical Methods and Analyses in Computational Genomics: Explorations of Eukaryotic Transcription
• Jeffrey P. Spence (PhD, 2019) On to Stanford University as a Postdoc in Jonathan Pritchard's lab.
  PhD Thesis Title: Probabilistic Models and Statistical Inference in Population Genetics
• Jane Yu (PhD, 2019) On to Facebook AI as Research Scientist.
  PhD Thesis Title: Computational Tools for Immune Repertoire Characterization and Primer Set Design
• Jeffrey Chan (PhD, 2021) Machine Learning Scientist, Dyno Therapeutics.
  PhD Thesis Title: Scalable Machine Learning Algorithms for Biological Sequence Data
• Dan Daniel Erdmann-Pham (PhD, 2021) On to Stanford University as a Stein Fellow in the Department of Statistics
  PhD Thesis Title: Probabilistic Models and Statistical Tools for Gene Expression Analysis
• Nicholas Bhattacharya (PhD, 2022)
  PhD Thesis Title: Making Sense of Protein Representation Learning in the Wild
• Sanjit Batra (PhD, 2022) On to Optum Labs as Senior Machine Learning Scientist.
  PhD Thesis Title: Computational methods for regulating transcription and translation
• Neil Thomas (PhD, 2022) On to Google X as Machine Learning Research Scientist.
  PhD Thesis Title: Browsing in the Library of Babel: Leveraging Evolutionary Information to Improve Protein Modeling
• Alan Aw (PhD, 2023) On to U Penn as postdoc.
  PhD Thesis Title: Statistical Genomics Through the Lens of Exchangeability, Stability and Stratification
• Gonzalo Benegas (PhD, 2023) Staying on as postdoc in the lab.
  PhD Thesis Title: Computational and Machine Learning Methods for Understanding Gene Regulation and Variant Effects
• Yutong Wang (PhD, 2024) On to UCSF as postdoc.
  PhD Thesis Title: Statistical and Machine Learning Methods for Understanding Spatial Biology and Cellular Communication.
• Yun Deng (PhD, 2024. Jointly advised by Rasmus Nielsen)) On to Stanford as postdoc.
  PhD Thesis Title: Advanced statistical and algorithmic methods for Ancestral Recombination Graph.
• Sebastian Prillo (PhD, 2025. Jointly advised by Nir Yosef) On to Voleon.
  PhD Thesis Title: Scalable and Accurate Models of Molecular Evolution.
• Milind Jagota (PhD, 2025.) On to Columbia University as postdoc.
  PhD Thesis Title: Modeling and Interpreting Genome Evolution at Multiple Timescales

Former Master's Students:

• Peter McMahon (2008. Master's student from the University of Cape Town.
  On to Stanford University as a PhD student in EE.)
  Master's Thesis Title: Accelerating Genomic Sequence Alignment using High Performance Reconfigurable Computers.
• Nanheng (Alex) Wu (2009. Master's student in EECS, UC Berkelely. Jointly advised by Satish Rao)
  Master's Thesis Title: Preliminary Studies on de novo Assembly with Short Reads.
• Justin Hong (2020. 5th Year Master's student in EECS, UC Berkelely. Jointly advised by Kannan Ramchandran)
  Master's Thesis Title: A Likelihood-based Deconvolution of Bulk Gene Expression Data Using Single-Cell References.
• Julian Faust (2022. 5th Year Master's student in EECS, UC Berkelely.)
  Master's Thesis Title: Machine Learning Prediction of TCR-Epitope Binding.
• Frank Liu (2023. 5th Year Master's student in EECS, UC Berkelely.)
  Master's Thesis Title: Codon Usage Bias Regulates the Dynamics of Protein Translation.
• Emaad Khwaja (2023. Master's student in EECS, UC Berkelely.)
  Master's Thesis Title: Text-to-Image Model for Protein Localization Prediction.

Past Undergraduate Student Researchers:

• Aileen Chen
• Jerry Hong
• Fulton Wang (2009) On to MIT as a PhD student in EECS.
• Jonas Mueller (2011--2013) On to MIT as a PhD student in EECS.
  Honor's Thesis Title: Statistical inference of recombination-inducing genic features in Drosophila melanogaster
• Jeffrey Chan
• Tyler Brabham (2014) On to YouTube.
• Yun Park
• Emilia Wieczorek
• Kawin Swaddiwudhipong
• Harry Dong
• Andrew Chen (2019--2020)
  Honor's Thesis Title: Conservation and Variation in Human Ribosomal DNA as Characterized by Long-Reads
• Micah Carroll
• Frank Liu
• Xurui Chen
• Dasheng Bi
• Alex Fung
• Ashley (Danyao) Chen
• Yiqin Wang
• Lillian Weng
• Audrey Chun
• Matthew Liu

Past Visitors:

• Jesper Nielsen (Aug 2009 -- Mar 2010, Visiting PhD student from Aarhus University, Denmark)
• Paula Cristina Tataru (Jan 2013 -- Jul 2013, Visiting PhD student from Aarhus University, Denmark)
• Daniel Živković (April 2013 -- Jul 2013, Visiting postdoc from LMU Munich)
• Jeffrey Chan (May 2013 -- Aug 2013, Visiting undergraduate student from MIT. Amgen Scholar.)