• PI:

  Yun S. Song 304B Stanley Hall 321 Evans Hall

• Postdocs:

  	Gonzalo Benegas (PhD, UC Berkeley) 378 Stanley Hall
  	Antoine Koehl (PhD, Stanford University) 378 Stanley Hall
  	Jesús Martínez-Gómez [ Homepage ] (PhD, Cornell University) 361 Koshland Hall

• PhD Students:

  	Carlos Albors 378 Stanley Hall
  	Yufan Cao 378 Stanley Hall
  	Milind Jagota 378 Stanley Hall
  	Canal Li [ Homepage ] 378 Stanley Hall
  	Sebastian Prillo [ Homepage ] (Joint with Nir Yosef) 378 Stanley Hall
  	Junhao (Bear) Xiong (Joint with Jennifer Listgarten)
  	Chengzhong Ye (Joint with Bin Yu)
  	Fanding Zhou 378 Stanley Hall

Undergraduate Students:

	Matthew Liu
	Aakarsh Vermani
	Audrey Chun

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

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.

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 and Current Undergraduate Student Researchers:

• 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
• 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
• Frank Liu
• Xurui Chen
• Dasheng Bi

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.)