Postdoctoral researcher – Arkin Laboratory

bearded postdoctoral fellow in blue shirt with blue and gray striped background

Avery Noonan

Avery is a postdoctoral researcher in the Environmental Genomics & Systems Biology Division at LBNL. Avery completed his BSc at the University of Toronto in Genetics and Geosciences in 2015 and his PhD at the University of British Columbia in the Genome Sciences and Technology program in 2023. His doctoral research related to the development of high-throughput screening paradigms for the study of photosynthetic microorganisms, as well as the application of computational tools to investigate microbial community structure and dynamics in natural and engineered environments, including photobioreactors and the human lung. In his role in the Arkin lab, Avery is using statistical and machine learning approaches to predict phage-host interactions with the goal of selecting or engineering phages to target specific human pathogens.

Shekhar Mishra

Shekhar obtained his B.Tech and M.Tech in Chemical Engineering from the Indian Institute of Technology, Bombay in 2014. He discovered the joy of research through an internship in computational fluid dynamics, before moving into the field of systems biology with research on modeling the human cholesterol metabolism. After working as a Project Engineer for 9 months on fermentation technology at the DBT-ICT at Mumbai, India, Shekhar started his Ph.D. research at the University of Illinois, Urbana-Champaign in Chemical & Biomolecular Engineering. His doctoral research, in the lab of Huimin Zhao, involved the interdisciplinary application of computational modeling, CRISPR editing and mass spectrometric techniques to design rational strategies for metabolic engineering in yeast. Shekhar joined the Arkin Lab in September 2023 as a postdoctoral researcher with an eye on employing the toolkits of metabolic engineering for improving predictive microbial ecology within the ENIGMA project. Shekhar’s goal is to pursue advances in research that inform strategies for mitigating the adverse effects of anthropogenic climate change. In his spare time, Shekhar volunteers with the Citizen’s Climate Lobby, plays the guitar, goes rock climbing, does some gardening, and tries to catch up to an ever-growing list of books to read.

Lucas Morinière

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

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 combined her expertise in computational genomics and data science to design synthetic microbial consortia for bioremediation of nitrate and heavy metals.

Bradley Biggs

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.

David Bernstein

As of 2023 David is an Assistant Professor, Electrical and Biomedical Engineering at the University of Vermont. David was 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 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.

Fangchao Song

Fangchao Song is a scientist at LLNL. He was a postdoctoral fellow in Arkin Lab at Lawrence Berkeley National Laboratory. Fangchao worked 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.

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.

Yolanda (Yue) Huang

Yolanda is currently assistant professor at SUNY Buffalo. She was 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 worked to identify phage factors that influence bacterial physiology through multiple approaches – computational tools, data mining, and functional genomics.

Denish Piya

Denish is currently a project scientist in the Mutalik Lab. He was 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.

Principal Investigator