Dr. Luay Nakhleh
Luay Nakhleh, professor and former chair of the Department of Computer Science at Rice University, is the William and Stephanie Sick Dean of the George R. Brown School of Engineering. His research at the intersection of computing and biology focuses on developing new methodologies and software to study the history of both specific genes and entire genomes, and the genetic links between species.
Dr. Huw Ogilvie
Huw Ogilvie is the lead author of StarBEAST2, a widely used method for the joint inference of species and gene trees from sequence data. In addition to StarBEAST2, Huw has collaborated in the development of new methods for the inference of species networks including several methods in PhyloNet, a software package for phylogenetic inference. Huw helps coordinate the development of PhyloNet together with Prof. Nakhleh.
I received my B.S in Electrical Engineering from Sharif University of Technology, Iran, Tehran in 2017. I then started my PhD at Rice University, with Prof. Nakhleh's research group. I am interested in developing new tools for the analysis of single-cell sequencing data from cancer patients. My major works include scVILP (a combinatorial approach for phylogeny-aware single-nucleotide variation detection) and Phylovar (the follow-up of scVILP for large-scale single-cell data).
I received my bachelor’s degree in Electronic Engineering from Tsinghua University, Beijing, China. I am currently a Ph.D. student at Rice University, Co-advised by Dr. Luay Nakhleh and Dr. Ken Chen. I work on single-cell RNA-seq data analysis, innovating machine learning and optimization algorithms to solve biological questions such as trajectory inference, peptide binding prediction, and biomarker selection.
I am a Ph.D student working on phylogenomics.
I am a Ph.D student working on phylogenetic network inferrence.
Hello, I'm Mark and I graduated from Rice in May of 2022 with a B.A in Computer Science. I am currently working on developing this website, improving PhyloNet algorithms and their efficiency, and creating a new Python library. Outside of work I love to golf, play tennis, and be outside with my Golden Retriever.
Xiru Huang 黄玺如
My research focuses on single-cell analysis, especially on single-cell multi-omics integration and clone-specific gene regulatory networks
Yushu Liu 刘宇舒
I am a Ph.D student working on cancer phylogenetics. Specifically, I develop Bayesian methods for inferring the evolutionary history of cancer from single-cell copy number profile.
Yongze (4th year PhD student) obtained a B.S. degree in Computer Science and a B.S. degree in Statistics from the University of North Carolina at Chapel Hill. His research interest lies in the field of bacterial phylogenomics and he designs new tools and pipelines to model the bacterial evolution. Yongze proposed and implemented a more versatile inference unit aiming for a more comprehensive view of bacterial genomes.
Berk Alp Yakici
Berk Alp received his bachelor's degree in computer science from Rice University in May 2022. He is currently a fifth-year master's of science student, working on machine learning methods for tree and network inference. His past work explored distance measures for phylogenetic networks that take branch lengths into account. When he's not working, he loves to cook, travel, and take photos.
I am an undergraduate at Cornell University studying computer science and mathematics. Working under Dr. Ogilvie, I am using genetic data to simulate phylogenetic trees and develop a model to infer changing birth, death, and substitution rates of tumor cells
Josh is a Rice undergraduate who is studying Mathematics and Computer Science. He is working on devising and implementing a novel metric for phylogenetic networks.