Derek Ruths. Computer Science, Rice University. Joined my group: January 2005. Date of Master’s defense: November 2005. Master’s thesis title: Applications of Phylogenetic Incongruence to Detecting and Reconstructing Recombination and Horizontal Gene Transfer. Date of PhD defense: April 2009. PhD dissertation title: Deriving Executable Models of Biochemical Network Dynamics from Qualitative Data and Network Connectivity. Current position: Associate Professor of Computer Science, McGill University.

Cuong Than. Computer Science, Rice University. Joined my group: January 2006. Date of Master’s defense: May 2008. Master’s thesis title: Reconstruction of Phylogenetic Networks and Their Relationships with Trees and Branches. Date of PhD defense: October 2009. PhD dissertation title: Inference of Parsimonious Species Phylogenies from Multi-locus Data. Current position: Industry.

Jeff Kilpatrick. Computer Science, Rice University. Joined my group: Aug 2007. Date of Master’s defense: December 2009. Master’s thesis title: Methods for Detecting Multi-locus Genotype-phenotype Association. Current position: Industry.

Hyun Jung Park. Computer Science, Rice University. Joined my group: Aug 2007. Master’s thesis: waived (prior MSc degree). Date of PhD defense: Mar 2012. PhD dissertation title: Towards Accurate Reconstruction of Phylogenetic Networks. Current position: Assistant Professor, Department of Human Genetics, University of Pittsburgh.

Natalie Berestovsky. Computer Science, Rice University. Joined my group: Aug 2008. Date of Master’s defense: April 2011. Master’s thesis title: On the Modeling of Signaling Networks with Petri Nets. Date of PhD Defense: April 2013. PhD dissertation title: Toward Integrated Computational Models of Cellular Networks. Current position: Industry.

Wanding Zhou. Bioengineering, Rice University. Joined my group: Jan 2009. Master’s thesis waived (non-CS student). Date of PhD defense: March 2013. PhD dissertation title: Graph-based Modeling and Evolutionary Analysis of Microbial Metabolism. Current position: Assistant Professor, Perelman School of Medicine, University of Pennsylvania.

Troy Ruths. Computer Science, Rice University. Joined my group: Aug 2008. 26 Date of Master’s defense: December 2010. Master’s thesis title: A Sequence-based, Population Genetic Model of Regulatory Pathway Evolution. Date of PhD defense: Aug 2013. PhD dissertation title: Population Regulomics: Applying Population Genetics to the cisRegulome. Current position: Founder and CEO of Petro.ai.

Yun Yu. Computer Science, Rice University. Joined my group: Jul 2009. Date of Master’s defense: November 2011. Master’s thesis title: From Gene Trees to Species Trees: Algorithms for Parsimonious Reconciliation. Date of PhD defense: Mar 2014. PhD dissertation title: Models and Methods for Evolutionary Histories Involving Hybridization and Incomplete Lineage Sorting. Current position: Industry.

Yun (Angela) Zhu. Computer Science, Rice University. Joined my group: Aug 2010. Master’s thesis waived (prior MSc degree). Data of PhD defense: Apr 2014. PhD dissertation title: Computational Analyses of Gene Duplication and Network Evolution. Current position: Industry.

Nikola Ristic. Computer Science, Rice University. Joined my group: Aug 2011. Graduated in May 2014, with a professional Masters degree. Current position: Industry.

Jie Lv. Ecology and Evolutionary Biology, Rice University. I became the committee chair, following the departure of Jie’s advisor. Date of PhD defense: April 2015. PhD dissertation title: Evolution of Genome Organization in Animal and Yeast Species. Current position: Post-doctoral fellow, Methodist Research Institute.

Xian Fan. Computer Science, Rice University. Joined my group: Aug 2012. (co-advised by Prof. Ken Chen, MD Anderson Cancer Center) 27 Date of Master’s defense: December 2014. Master’s thesis title: Calculating Variant Allele Fraction of Structural Variation in Next Generation Sequencing by Maximum Likelihood. Date of PhD defense: April 2018. PhD dissertation title: Detecting Structural Variations with Illumina, PacBio and Optical Maps Data by Computational Approaches. Current position: Assistant Professor, Computer Science, Florida State University.