Headshot of Lucas Moriniere

Lucas Morinière

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Lucas Morinière joined the Arkin Lab in April 2023 as a postdoctoral researcher in the EDGE project to work on phage-host interactions under Adam Arkin’s and Vivek Mutalik’s supervision. He completed his education at the University Claude Bernard Lyon 1 in France by earning his PhD in 2021 at the Microbial Ecology Lab of Lyon (UMR 5557). His thesis research was focused on the
ecology, genomics, and taxonomy of Xanthomonas hortorum pv. vitians (Xhv), the causal agent of the bacterial leaf spot of lettuce disease. As part of his research, he first conducted a thorough polyphasic taxonomical study which allowed to reshape the entire X. hortorum species. Then, he used transposon insertion sequencing (TnSeq) and comparative genomics to describe the in vitro and in planta essential genomes of this non-model plant-pathogenic bacterium. Afterwards, he pursued as a Temporary Lecturer and Research Assistant (ATER) for a year and used TnSeq to elucidate the molecular determinants of the interaction between Xhv and a new lytic phage. As part of the new NSF funded project, his present research in the Arkin Lab in collaboration with Mutalik lab focuses on uncovering the genetics of phage-host interactions by submitting large collections of Escherichia coli and coliphages to high-throughput susceptibility assays and high-throughput genetic screens (RB-TnSeq, DubSeq) based on a machine-learning-driven experimental workflow.

Manoshi Sen Datta

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Manoshi is a computational microbial ecologist interested in harnessing the power of microbial consortia for sustainability.  During her academic training, Manoshi explored how microscale eco-evolutionary dynamics in wild microbial ecosystems drive ecosystem-level properties. She employed a variety of approaches, including novel experimental model systems (with Otto Cordero), mathematical modeling of laboratory ecosystems (with Jeff Gore), and comparative genomics of wild bacteria (with Martin Polz and Roy Kishony).  Manoshi then joined Boost Biomes, an agtech start-up, where she developed data science approaches to accelerate microbial interaction discovery in complex soil communities.  In the Arkin Lab, she aims to combine her expertise in computational genomics and data science to design synthetic microbial consortia for bioremediation of nitrate and heavy metals.
2021 Bradley Biggs photo

Bradley Biggs

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Bradley completed his B.S. in Chemical Engineering at the University of Southern California, where he worked on silicon-based optical biosensors. As his research interests evolved, he pursued an M.S. in Biotechnology at Northwestern University, and subsequently worked for a time at a metabolic engineering startup based in Cambridge, MA called Manus Bio. He later returned to Northwestern University to pursue his Ph.D. in Chemical Engineering working with advisor Keith Tyo in synthetic biology and metabolic engineering, with his thesis work focusing on engineering the soil bacterium Acinetobacter baylyi for applications in lignin upgrading. In the Arkin Lab, Bradley’s work focuses on integrating synthetic biology and systems biology approaches to the ENIGMA project, continuing to explore soil bacterium and their relevance to engineering applications and the environment.

IMG 7301 David Bernstein

David Bernstein

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David is a postdoctoral researcher in the Arkin Laboratory at UC Berkeley. He received his Bachelor’s degree in Mechanical Engineering from the University of Vermont. He then earned his PhD in Biomedical Engineering from Boston University working in the lab of Daniel Segrè where he developed computational approaches to study the metabolic properties of microbes and microbial communities. In the Arkin lab, he is focused on combining genome-scale metabolic modeling and machine learning to predict microbial phenotype from genotype. Outside of the lab, David enjoys spending time outdoors skiing (both downhill and cross-country) and hiking.

XBD201808 00430 029 Fangchao Song

Fangchao Song

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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.

Jacob Hilzinger

Jacob Hilzinger

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Jake received his Bachelor’s degree in Genetics from the University of Wisconsin-Madison where he was introduced to the world of scientific research through the study of the evolution of gene expression regulation in the yeast Saccharomyces cerevisiae. Upon graduation, Jake began his graduate work in Marine Studies at the University of Delaware where he studied the regulation of energy metabolism in green sulfur bacteria (the Chlorobiaceae). Being a microbiologist that had always admired synthetic biology, and one that was enamored with space exploration, Jake joined the Arkin Lab at the University of California-Berkeley as a postdoc to pursue applications of microbial engineering to space exploration. Jake’s research interests include environmental microbiology, microbial physiology/systems biology, genetics, synthetic biology, and space bioengineering.

Kyle Sander

Kyle Sander

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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.

Yolanda Yue Huang

Yolanda (Yue) Huang

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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.

Denish Piya

Denish Piya

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Denish Piya is a postdoctoral scholar in the Arkin Laboratory at UC Berkeley. He completed his PhD from Texas A&M University focusing on phage research. He is applying CRISPR and Dubseq technologies to study how genes affect fitness in context of phage infection.

Ruoshi Yuan

Ruoshi Yuan

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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.