Adam Arkin

About

Adam Arkin is the Dean A. Richard Newton Memorial Professor in the Department of Bioengineering at the University of California, Berkeley and a Senior Faculty Scientist at the Lawrence Berkeley National Laboratory. His laboratory develops experimental and computational technologies aimed at the discovery, prediction, control, and design of microbial and viral functions and behaviors within environmental contexts. He serves as the chief scientist of the Department of Energy Scientific Focus Area, ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies), which is designed to understand, at a molecular level, the impact of microbial communities on their ecosystems, with a specific focus on terrestrial communities in contaminated watersheds. Additionally, he directs the Department of Energy Systems Biology Knowledgebase (KBase) program, an open platform for comparative functional genomics, systems and synthetic biology for microbes, plants, and their communities, facilitating the sharing of results and methods among scientists. Arkin also directs the Center for Utilization of Biological Engineering in Space, which seeks microbial and plant-based biological solutions for in situ resource utilization to reduce launch mass and improve the reliability and quality of food, pharmaceuticals, fuels, and materials for astronauts on missions to Mars. Furthermore, he is the Co-Director of the Berkeley Synthetic Biology Institute, which unites scientists from U.C.…

Research topics

• Computer Science
• Biology
• Genetics
• Computational biology
• Evolutionary biology
• Ecology
• Data science
• Artificial Intelligence
• Engineering
• Art history

Selected publications

• A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming

  Nature Communications · 2020-09-18 · 1297 citations

  articleOpen access

  Unraveling the drivers controlling community assembly is a central issue in ecology. Although it is generally accepted that selection, dispersal, diversification and drift are major community assembly processes, defining their relative importance is very challenging. Here, we present a framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93-0.99), precision (0.80-0.94), sensitivity (0.82-0.94), and spe…

  PublisherOA PDFDOI

• Quantifying the local adaptive landscape of a nascent bacterial community

  Nature Communications · 2023 · 435 citations

  The fitness effects of all possible mutations available to an organism largely shape the dynamics of evolutionary adaptation. Yet, whether and how this adaptive landscape changes over evolutionary times, especially upon ecological diversification and changes in community composition, remains poorly understood. We sought to fill this gap by analyzing a stable community of two closely related ecotypes ("L" and "S") shortly after they emerged within the E. coli Long-Term Evolution Experiment (LTEE)…

  DOI

• Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity

  Microbiome · 2020-04-06 · 399 citations

  articleOpen access

  BACKGROUND: The newly defined superphylum Patescibacteria such as Parcubacteria (OD1) and Microgenomates (OP11) has been found to be prevalent in groundwater, sediment, lake, and other aquifer environments. Recently increasing attention has been paid to this diverse superphylum including > 20 candidate phyla (a large part of the candidate phylum radiation, CPR) because it refreshed our view of the tree of life. However, adaptive traits contributing to its prevalence are still not well known. RES…

  PublisherOA PDFDOI

• Redefining fundamental concepts of transcription initiation in bacteria

  Nature Reviews Genetics · 2020 · 154 citations

  DOI

• Towards a Biomanufactory on Mars

  Frontiers in Astronomy and Space Sciences · 2021 · 62 citations

  Senior authorCorresponding

  A crewed mission to and from Mars may include an exciting array of enabling biotechnologies that leverage inherent mass, power, and volume advantages over traditional abiotic approaches. In this perspective, we articulate the scientific and engineering goals and constraints, along with example systems, that guide the design of a surface biomanufactory. Extending past arguments for exploiting stand-alone elements of biology, we argue for an integrated biomanufacturing plant replete with modules f…

  DOI

Recent grants

• NIH Grant R01GM073010

  NIH · $1.5M · 2011

• Engineering Eukaryotic Protein Scaffolds to Reprogram Prokaryotic Signaling and Metabolic Pathways

  NSF · $540k · 2008–2012

• NIH Grant R01GM073058

  NIH · $2.3M · 2016

Frequent coauthors

• Adam M. Deutschbauer

  Lawrence Berkeley National Laboratory

  285 shared

• Terry C. Hazen

  University of Tennessee at Knoxville

  274 shared

• Jeffrey M. Skerker

  University of California, Berkeley

  244 shared

• Morgan N. Price

  Genomics (United Kingdom)

  210 shared

• Jizhong Zhou

  Tsinghua University

  206 shared

• Jay D. Keasling

  Joint BioEnergy Institute

  154 shared

• Vivek K. Mutalik

  126 shared

• Eric J. Alm

  Massachusetts Institute of Technology

  126 shared

Labs

• Arkin LaboratoryPI

Education

• Postdoctoral Fellow, Developmental Biology

  Stanford University

  1997

• Postdoctoral Fellow, Chemistry

  Stanford University

  1995

• Ph.D. Physical Chemistry, Chemistry

  Massachusetts Institute of Technology

  1992

• Bachelor of Art, Chemistry

  Carleton College

  1988

Similar researchers at University of California, Berkeley

• Rasmus Nielsenh-180
• Daniel Rokhsarh-155
• Marc Hellersteinh-105