Berkeley Phylogenomics Group

Principal Investigator
	Kimmen Sjölander, Ph.D.

PhD Students
	Bushra Samad PhD Student Phylogenomic methods for microbial (meta)genome functional and taxonomic annotation	“Tree of Life” painting courtesy of Nathan Bennett
	Curt Hansen PhD Student Simultaneous co-estimation and refinement of phylogenetic trees and multiple sequence alignments

PhD Students

Bushra Samad

PhD Student

Phylogenomic methods for microbial (meta)genome functional and taxonomic annotation

“Tree of Life” painting courtesy of Nathan Bennett

Curt Hansen

PhD Student

Simultaneous co-estimation and refinement of phylogenetic trees and multiple sequence alignments

Associated Students

Mohammad Azimi

Graduate Researcher

Hybrid Protein Nucleotide Phylogenetic Trees

Nima Cyrus Emami

Undergraduate Researcher

Hybrid Protein Nucleotide Phylogenetic Trees

Programmers
	Cyrus Afrasiabi Programmer Algorithms	“The King of Limbs” from DIY

Programmers

Cyrus Afrasiabi

Programmer

Algorithms

“The King of Limbs” from DIY

Lab Alumni
	Ajith Warrier Associate Specialist Algorithms, Web programming with Django, Python and Javascript programming
	Yaoqing Shen, Ph.D. Postdoctoral Scholar Metagenome Analysis
	Ruchira Datta, Ph.D. Postdoctoral Scholar Ortholog identification, Pathway inference, Hyperdimensional network
	Shailen Tuli Programmer Algorithm design, Web programming, Python and Ruby programming, Open source software
	Grant Shoffner Research Associate Domain Architecture Rearrangement
	Glen Jarvis Programming Associate Bioinformatics programming, Linux/Web/Database Administration
	John Davidson Programmer Bioinformatics programming, Open source software development, Web programming and design
	Christoph Neyer Undergraduate Student Assessing methods for orthology detection
	Sriram Sankararaman Graduate Student, EECS Probabilistic models for enzyme active sites and specificity determinates
	Dean Starrett, Ph.D. Postdoctoral Scholar Muliple alignment, Phylogeny inference, Protein interaction prediction Webserver
	Bryan Kolaczkowski, Ph.D. Postdoctoral Scholar Reconstructing the evolutionary history of Apicomplexa Webserver Paper
	Nandini Krishnamurthy, Ph.D. Postdoctoral Scholar FlowerPower phylogenomic clustering Webserver Paper
	Duncan Brown, Ph.D. Graduate Student, BioE Automating subfamily classification and subfamily HMM development Webserver Paper
	Carolina Dallett Graduate Student, PMB Identification of evolutionarily conserved regions in proteins
	Raffi Hagopian Undergraduate Student Multiple Sequence Alignment/SATCHMO development Webserver Paper
	Jake Gunn Glanville Undergraduate Student Phylobuilder and other webserver development Webserver Paper
	Christopher Meacham, Ph.D. Programmer PhyloScope phylogenetic tree visualization software and other software development Webserver Paper
	Terry Farrah Programmer Protein structure prediction
	Xia Jiang PhD student Protein structure prediction
	Yannet Interian Postdoctoral scholar Protein-protein interaction prediction