Research Interests

Mass spectrometry guided analysis of the products and pathways of Earth’s biological systems

Ben Bowen, a Staff Scientist at Lawrence Berkeley National Laboratory, develops capabilities for mass spectrometry-centered projects that empower advanced analysis, modeling, and data integration. This work involves the development of high-performance computing workflows and advanced integration of mathematics and chemistry. At the Joint Genome Institute, Dr. Bowen is the Computational Metabolomics Lead, focusing on delivering the highest quality analysis to users and developing new capabilities. These highly collaborative projects support the Department of Energy’s (DOE) Biological and Environmental Research (BER) user community in their bioenergy and environmental objectives.

When analyzed by cutting-edge mass spectrometry workflows, the molecular composition of a sample may appear disordered and overwhelming. Through Dr. Bowen’s expertise in spectral alignment, molecular networking, chemoinformatics, and bioinformatics, he can typically identify approaches that simplify this complex data, enabling impactful scientific discoveries. This expertise has led to publications on new workflows, software ecosystems, and algorithms. 

Scientific Background. Ben Bowen’s journey began in the field of Chemical Engineering at the University of Arkansas, where he developed a strong foundation in analytical and technical skills while performing three separate research internships and earning his BS in 1998. His interest in science was sparked during high school and grew during his undergraduate training, ultimately leading him to pursue advanced studies and a deep desire to perform cutting-edge research. During graduate school at Arizona State University, under the direction of Neal Woodbury, he obtained his PhD in 2003, in the field of single molecule biophysics, gaining invaluable experience in multidisciplinary research. This diverse training has equipped him with a unique perspective and a versatile skill set, enabling him to excel in the complex and dynamic field of computational metabolomics and its applications in environmental science and human health.

Computational Metabolomics. Dr. Bowen’s primary research focus lies in computational metabolomics, where he has made significant contributions to advancing the field. Notable works include the development of innovative tools and platforms such as Metabolite Atlas, a computational ecosystem for targeted metabolomics, and OpenMSI, a high-performance web-based platform for mass spectrometry imaging. He has also led the creation of powerful algorithms including MAGI, for metabolite annotation and gene integration, BLINK, an ultrafast tandem mass spectrometry cosine similarity scoring tool, and SIMILE, which has advanced the alignment of tandem mass spectra with statistical significance. His work with the GNPS Dashboard has enabled collaborative exploration of mass spectrometry data at unprecedented scale and reusability. He contributed to MIDAS, a database-searching algorithm for metabolite identification and redesigned the MIDAS algorithm into Pactolus.  These contributions have collectively enhanced the capabilities of metabolomics research, facilitating more accurate and efficient analysis of complex datasets.

Plants, Microbes, and the Environment. Dr. Bowen’s research includes applying computational metabolomics to understand plants, microbes, and the environment. He has collaborated on projects to understand the intricate relationships between soil biology and chemistry, as demonstrated in studies linking soil biology and chemistry in biological soil crusts using exometabolomics. His work on dynamic root exudate chemistry and microbial substrate preferences has shed light on rhizosphere microbial community assembly. Additionally, he has contributed to uncovering the potential of anaerobic gut fungi as a reservoir of natural products. These studies highlight the importance of metabolomics in elucidating ecological interactions and advancing environmental science.

Human Health. Although Dr. Bowen’s focus on human health has diminished in recent years, he has made substantial contributions to the field through his earlier work. His research has delved into the impact of diet on the gut microbiome, exemplified by the study on how cooking shapes the structure and function of the gut microbiome. He has also investigated the proteomic analysis of human skeletal muscle, revealing novel abnormalities in obesity and type 2 diabetes. His work has extended to exploring the sensitivity of cancer cells to HAMLET-induced death and the identification of metabolic signatures linked to anti-inflammatory effects of gut bacteria. These contributions have provided valuable insights into the molecular underpinnings of human health and disease.

Other Applications of Mass Spectrometry. Beyond his primary focus areas, Dr. Bowen has explored various other applications of mass spectrometry. He has contributed to the quantitative tracking of isotope flows in microbial community proteomes and developed high-throughput enzyme activity assays using acoustic deposition with NIMS. His work has also included the innovative “replica-extraction-transfer” nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria. These studies demonstrate the versatility and broad applicability of mass spectrometry in diverse scientific disciplines, further highlighting its potential to drive scientific discovery and innovation.

Selected Publications

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