davian 1

Davian Ho

Davian is an undergraduate student interested in bioengineering and EECS. He previously worked on extracellular contractile injection systems, and now investigates phages in the gut microbiome and makes vector art for synthetic biology. Davian also a member of CUBES, where he is developing the interface for space resource modeling software.

Keith Keller

Keith Keller

Keith Keller is a system administrator for KBase (https://kbase.us). He has been a member of the Arkin lab since 2002.

Marcin Joachimiak

Marcin P. Joachimiak

Marcin Joachimiak is a Staff Researcher and Software Developer in the Environmental Genomics and Systems Biology Division at Lawrence Berkeley National Lab. He studied Mathematics at University of Chicago while creating transgenic yeast strains to enable high throughput herbicide screening for wheat. In 2002 he went West and studied Biophysics at UCSF where he implemented the Evolutionary Trace method and its variants (JEvTrace), identified novel targets and inhibitors for antimalarials, and performed the first genome annotation and contributed to the first gene expression analysis of the malaria parasite. After a year at Five Prime Therapeutics, where he founded the computational infrastructure and used the Riken mouse cDNA collection to discover novel human genes, he returned to academia as a postdoc in the Brenner Group at UC Berkeley. At UCB he developed a popular visualization tool (JColorGrid), performed key sequence and phylogeny analysis for the Global Ocean Survey, and published an affinity-based model for human branch point site prediction. Since 2006 he has been a member of the Arkin Laboratory, first as part of the ENIGMA project where he developed the gene expression analysis pipeline, functional genomics analysis tools in MicrobesOnline, and a novel machine learning algorithm for multi-data type biclustering. Since 2014 he has been part of the DOE KnowledgeBase where he designs and develops applications for statistical and visualization analysis and most recently on components of the system to enable rapid data type modeling, data science and machine learning, and integration with ontologies and knowledge graphs.

morgan rufus Morgan Price 1

Morgan Price

Thanks to cheap DNA sequencing, we are slowly starting to understand the incredible diversity of bacteria. Morgan Price builds computational tools to help us use all this data to understand how diverse bacteria work. This understanding can help us manage our environment, control the bacteria inside us, and develop new biotechnologies.

Kyle Sander

Kyle Sander

Kyle Sander earned a B.S. in Chemical Engineering and an M.S. degree in Biological and Ecological Engineering studying life cycle effects of algae production for fuels and co-products. He also investigated rapid sand filtration as an algal dewatering process step and enzymatic degradation of, and simultaneous saccharification and ethanol production from of algal cell biomass. Kyle earned his PhD from the University of Tennessee, Knoxville conducting his thesis research within the BioEnergy Science Center at Oak Ridge National Laboratory. Kyle characterized regulatory genes and related cellular redox in two candidate lignocellulolytic, ethanol-producing biocatalysts; Clostridium thermocellum and Caldicellulosiruptor bescii. Basic redox metabolism was characterized yielding an expanded view of redox metabolism in these organisms and effected bioprocessing improvements through genetically modifying redox-related regulation. A genotype-phenotype relationship was similarly identified between the FapR local fatty acid biosynthesis repressor and tolerance to elevated osmolarity conditions, a highly complex, bioprocess-limiting, and difficult-to-engineer trait in C. bescii. As a member of the CUBES project, Kyle studies unbalanced growth coupling of polyhydroyalkanoate production in species of Cupriavidus, and rhizosphere microbiome interspecies interactions toward improving reliability of probiotic species ingress in diverse community settings.

Lauren Lui

Lauren Lui

Lauren is interested in how we can use the latest sequencing technology to study environmental microbial communities, particularly nanopore sequencing.  She studied mathematical biology and bioinformatics at UC Davis, and received her PhD in Biomolecular Engineering and Bioinformatics from UC Santa Cruz. Ever since she started doing research, Lauren has sought to integrate quantitative and computational methods with experimental biology.  Currently, her projects include dissecting plant-microbe interactions with transposon mutant libraries, using synthetic microbial communities to understand the ecological and genetic factors of microbial interactions, and metagenomics of environmental microbes. Her ultimate goal is to be able to predict microbial interactions and community assembly from genome content and environmental measurements. In addition to her scientific work, Lauren is the co-secretary for the Women Scientists and Engineers Council at LBNL and loves doing photography, playing the ukulele, and illustrating with graphic arts.

Ruoshi Yuan

Ruoshi Yuan

Ruoshi Yuan is currently a postdoc researcher in the Arkin lab at UC Berkeley/LBNL. He obtained his PhD in 2016 at Shanghai Jiao Tong University, China, supervised by Dr. Ping Ao. Then he did postdoctoral research at Harvard Medical School with Dr. Johan Paulsson. Ruoshi’s research interests include stochastic and nonlinear dynamics, mathematical modeling of biological phenomena, microbial interactions, complex diseases, and synthetic biology. Besides theory, he also works on high-throughput microfluidic experiments to obtain single cell time series data.

Yolanda Yue Huang

Yolanda (Yue) Huang

Yolanda is a postdoc in the Arkin lab and a Life Sciences Research Foundation (LSRF) fellow sponsored by Astellas Pharmaceuticals. She received her Bachelor’s from McGill University in Biochemistry. She completed her PhD in Chemical Biology with Emily Balskus at Harvard University where she characterized a new glycyl radical enzyme responsible for 4-hydroxyproline metabolism that is prevalent among gut anaerobes. In the Arkin lab, she is working to identify phage factors that influence bacterial physiology through multiple approaches – computational tools, data mining, and functional genomics. Outside of the lab, she can be found active in the outdoors, travelling, cooking, and filling up space with plants.

Astrid Terry

Astrid Terry

Astrid Terry is the ENIGMA Project Manager. Her role is to monitor and enable progress of each project and investigator in the program and closely manage the budget. She coordinates and communicates updates, reports & publications to DOE. A major goal is identifying opportunities for collaboration, and increasing awareness of capabilities and resources available across the Science Focus Area.

XBD201808 00430 029 Fangchao Song

Fangchao Song

Fangchao Song is a postdoctoral fellow in Arkin Lab at Lawrence Berkeley National Laboratory. He is working on droplet-based high throughput method to reveal bacterial interactions in complex microbial community and profile the microbial physiology in different nutrients and environments, under the project of Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA). Before joining the lab, Fangchao was a graduate student working on mathematical modeling of polymerization and biodegradable polymer manufacturing. In 2010, he started a new journey in the microbiology world during his Ph.D research on microbial biofilms and their antibiotic resistance. Since then, he is fascinated by the complexity and orderliness of microbiome, and enthusiastic about designing new method by combining experiments and modeling to better understand the function and dynamics of microbiome. Fangchao obtained his B.S. from Shandong University in 2003, M.S. from Zhejiang University in 2010, and Ph.D. from Syracuse University in 2016, all in Chemical Engineering. He wants to be a researcher and educator in the future.