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Dr. Sarah Chen
Stanford · Interpretability · NLP
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Dr. Marcus Holloway
MIT · Robotics · RL
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Dr. Aisha Okonkwo
CMU · Fairness · HCI
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Nova · Professor Researcher · re-ranking top 20…
Chi Chen

Chi Chen

· ProfessorVerified

University of Minnesota · Ecology, Evolution, and Natural Resources

Active 1962–2026

h-index80
Citations24.5k
Papers526165 last 5y
Funding$762k
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Research topics

  • Biology
  • Biochemistry
  • Cell biology
  • Gastroenterology
  • Food science
  • Medicine
  • Internal medicine
  • Environmental science
  • Environmental engineering
  • Engineering
  • Organic chemistry
  • Chemistry
  • Waste management

Selected publications

  • Plasma Neurofilament Light Chain as a Potential Biomarker of Presymptomatic Spinal Muscular Atrophy

    Muscle & Nerve · 2026-01-20 · 1 citations

    article

    INTRODUCTION/AIMS: While neurofilament light chain is a promising biomarker in spinal muscular atrophy (SMA), its dynamics in presymptomatic patients have not yet been determined. This study aimed to analyze the plasma neurofilament light chain (pNfL) as a treatment response biomarker in patients with presymptomatic spinal muscular atrophy (SMA) undergoing nusinersen treatment. METHODS: Eight 5q-SMA patients with three SMN2 copies (four presymptomatic patients from newborn screening and four symptomatic patients) were prospectively enrolled from August 2022 to June 2023. All patients received nusinersen treatment and were followed up for 660 days. pNfL levels were measured at baseline and throughout the treatment, analyzing their temporal changes and correlation with motor function outcomes. RESULTS: At baseline, presymptomatic patients exhibited higher pNfL levels than symptomatic patients (388.74 ng/L vs. 113.60 ng/L). During the loading phase, pNfL levels decreased markedly in both groups, with greater reductions in presymptomatic patients (94.64% vs. 79.50%). All presymptomatic patients achieved age-appropriate motor milestones. Decreased pNfL levels correlated moderately with motor function improvements, as measured by CHOP INTEND (r = -0.548, p < 0.01) and HINE-2 scores (r = -0.635, p < 0.01). DISCUSSION: pNfL is a promising biomarker for monitoring treatment response in patients with presymptomatic SMA, highlighting the importance of early diagnosis and treatment through newborn screening.

  • AbrB knockout not positively affecting bacillomycin D production in Bacillus amyloliquefaciens fmbJ analyzed by metabolomics

    Journal of Biotechnology · 2026-03-27

    article
  • Diet-dependent effects of kombucha on the gut microbiome and its neuroactive potential: Associations with reduced anxiety and depressive-like behaviors in mice

    bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-12

    article

    ABSTRACT Fermented foods are increasingly recognized for their health-boosting potential, yet the mechanisms involved are not fully resolved. Here, we tested whether kombucha reshapes the gastrointestinal microbiome and whether these changes are associated with stress-related behaviors under contrasting dietary backgrounds. Male C57BL/6 mice were fed either a total Western diet (TWD) or a control diet (CTRL) supplemented with kombucha or water three times weekly for seven weeks. Depressive-like and anxiety-related behaviors were evaluated using the forced swimming (FST) and marble burying tests (MBT). Ileum, cecum, and colon microbiomes were profiled via 16S rRNA, ITS2, and shotgun metagenomics, while feces and whole brains were profiled by LC-MS metabolomics. Serum cytokines were measured by ELISA. Results highlight diet-dependent effects of Kombucha on behavioral, microbial and metabolic outcomes. Kombucha reduced immobility in the FST under both diets, whereas fewer marbles buried were observed only under TWD. Kombucha intake enriched Bifidobacterium pseudolongum in the ileum under CTRL and TWD diets, while cecal microbial functions related to amino acid metabolism were stimulated mainly under CTRL. Only CTRL mice receiving kombucha showed higher fecal acetate and butyrate together with lower fecal levels of neurochemically relevant amino acids, including glutamine, phenylalanine, tryptophan, and tyrosine. Under TWD, kombucha was associated with lower spleen weight and altered brain tryptophan/kynurenine profiles. These findings identify kombucha as a food intervention that can remodel gastrointestinal microbial and neuroactive metabolism in a diet depending manner. Associations with reduced depressive and anxiety-related behaviors are promising but warrant further exploration. Key Highlights Kombucha supplementation reshaped the mice gastrointestinal microbiome and its neuroactive potential Kombucha intake was associated reduced depressive and anxious like behaviors The potential of kombucha to modulate microbial, metabolic and behavioral outcomes may be dependent on subject dietary background

  • Heyndrickxia coagulans JF1 with potent ethanol-degrading capacity: In vitro screening and functional characterization

    Food Bioscience · 2026-01-22

    article
  • Unlocking subsalt reservoir time-lapse insights with 4D elastic FWI imaging in Atlantis Field

    The Leading Edge · 2025-07-01

    article

    Abstract 4D seismic data have played a critical role in understanding the hydrocarbon habitat, guiding field development, and the targeting and sequencing of injectors and producers in Atlantis Field. In the past two decades, relentless seismic imaging efforts have been made in the 4D seismic study in Atlantis Field, leading to tremendous progress since the acquisition of the first ocean-bottom node survey in 2005. More recent imaging advancements have come primarily from the successful application of acoustic and elastic full-waveform inversion (FWI) and have resulted in significant improvements to the complex salt canopy velocity model and, consequently, improved illumination of subsalt areas of the field. However, the challenge of capturing the elusive 4D signals underneath the complex salt canopy has persisted due to the reliance on conventional imaging methods such as reverse time migration, with the weak imbalanced subsalt illumination being a significant bottleneck. This has resulted in poor subsalt 3D images and even poorer 4D images, with signals lost in the noisy background. In recent years, FWI imaging, especially elastic FWI imaging, has proven to be a superior method for subsalt imaging, with greatly improved illumination, signal-to-noise ratio (S/N), and event focusing over conventional imaging methods. Extending elastic FWI imaging from 3D to 4D, therefore, was the next logical step, although the feasibility had not been tested previously in Atlantis Field. In this study, we present the results of the first application of elastic time-lag FWI (E-TLFWI) imaging to Atlantis 4D data sets. The results showed major uplift in subsalt 4D signals with significantly improved 4D S/N and more accurate and reliable 4D responses. The observed subsalt 4D signals are supported by well data and are in line with subsalt production history, highlighting the potential of 4D E-TLFWI imaging to revolutionize 4D imaging in complex subsalt environments.

  • Correlation of auditory network hyperconnectivity with P3a amplitude and set-shifting in individuals with autism spectrum disorder

    Progress in Neuro-Psychopharmacology and Biological Psychiatry · 2025-11-03 · 1 citations

    article
  • Stellettin B inhibits VEGF-induced angiogenesis in human endothelial progenitor cells in vitro and in vivo

    Phytochemistry Letters · 2025-10-01

    article
  • Associations between hyperketonemia and the rumen metagenome and metabolome in Holstein cows during the first 2 weeks postpartum

    Animal Microbiome · 2025-06-04 · 2 citations

    articleOpen access

    Hyperketonemia (HYK) is characterized by elevated levels of blood ketone bodies in dairy cows. Despite previous research on the physiological events related to HYK, associations between the rumen metagenome, metabolome, and HYK have not been well described. Therefore, the objective of this study was to compare rumen metagenome and metabolome profiles of cows with naturally occurring HYK to those without HYK during the first two weeks postpartum. Blood beta-hydroxybutyrate (BHB) concentrations at d 5, 10 and 14 postpartum were used to classify 16 rumen cannulated Holstein cows as either hyperketonemic (+ HYK; ≥1.2 mmol/L BHB at any of the collection days) or non-hyperketonemic (-HYK). Five + HYK cows were identified and were paired with 5 -HYK cows based on parity and calving date. Microbial DNA was extracted from rumen fluid and sequenced using shotgun metagenomics with the Illumina platform. Kraken2 was used to map reads to microbial taxonomic groups and Humann3.8 was used to predict potential functions. Metabolome profiling of rumen fluid was conducted using high-resolution liquid chromatography-mass spectroscopy. MetaboAnalyst6.0 was used to identify potential changes in metabolic pathways. Metagenomes and metabolomes comparisons were conducted using mixed models that included the fixed effects of group, day, their interaction, and the random effect of cow. There was minimal difference detected in alpha diversity for the metagenome, but differences in the metabolome were detected by HYK status. The concentration of asparagine and p-cresol was greater in + HYK cows compared to -HYK, but citrulline was greater in -HYK cows throughout all days considered. On d5 the concentration of ornithine was greater in + HYK compared to-HYK cows, and on d10 acetate was greater in the -HYK cows. There were no differences detected in the pathway analysis from the metabolites quantified by HYK status. Overall, modest differences in rumen metabolome were observed between + HYK and -HYK cows in early lactation. Future studies should explore associations between the rumen environment and HYK as this could be informative for treatment and management practices.

  • Development of an evaluation index system for intelligent minimally invasive tumor ablation based on telemedicine

    Journal of Cancer Research and Therapeutics · 2025-09-01 · 2 citations

    articleOpen accessCorresponding

    OBJECTIVE: This study aimed to establish an evaluation index system for intelligent minimally invasive tumor ablation based on telemedicine, thereby providing theoretical support for the assessment, application, and promotion of remote intelligent ablation therapies. METHODS: An expert consultation questionnaire was developed based on a review of the literature. Purposive sampling was performed to select 16 experts specializing in minimally invasive oncology, telemedicine management, and healthcare informatics. Two rounds of Delphi questionnaire surveys were conducted. The index system was finalized through iterative discussions based on expert feedback. The analytical hierarchy process (AHP) was utilized to determine the indicator weights. RESULTS: Both rounds of the questionnaire achieved 100% response rates. The expert authority coefficient reached 0.789, while the Kendall's W coefficients for the two rounds were 0.138 (P < 0.001) and 0.224 (P < 0.001), respectively. The finalized system comprised 6 first-level indicators, 13 second-level indicators, and 45 third-level indicators, establishing a comprehensive management framework for telemedicine-based intelligent tumor ablation. CONCLUSION: The evaluation system established in this study demonstrated scientific validity and reliability. It identified critical success factors for implementing remote ablation procedures, offering a practical reference for advancing telemedicine-enabled minimally invasive cancer therapies.

  • Programmable DNA‐Peptide Hybrid Nanostructures for Potent Neutralization of Multiple Influenza a Virus Subtypes

    Advanced Functional Materials · 2025-12-23

    articleOpen access

    ABSTRACT The continued emergence of antigenic drift and drug‐resistant viral strains highlights the need for antiviral strategies that deliver robust efficacy, broad subtype coverage, and minimal off‐target toxicity. We demonstrate a potent and broad‐spectrum strategy that employs hybrid biomaterials of Urumin (a host defense peptide) and a honeycomb (HC) DNA origami through spatially organized multivalent presentation for enhanced antiviral efficacy. Molecular dynamics simulations reveal that Urumin penetrates and destabilizes the hemagglutinin (HA) trimer core, disrupting influenza A viral (IAV) entry. Arranging Urumin in trimeric clusters on the HC enables potent multivalent binding to trimeric HAs on IAV, enhancing antiviral efficacy at nanomolar concentrations, ∼1000‐fold more effective than free Urumin. In vitro assays confirm HC‐Urumin outperforms free Urumin in blocking viral entry and preserving cell viability in more IAV subtypes. In vivo studies show that compared to free Urumin, HC‐Urumin treatment reduces disease severity, preserves physiological behavior, and decreases mortality in infected mice, while maintaining virus‐specific adaptive immune responses without altering humoral immunity. Our study offers an advanced and effective materials platform and strategy for broad‐spectrum, low‐dose intervention against human and animal IAVs, which can be adapted to combat other viruses by patterning corresponding host defense peptides on custom designed DNA nanostructures.

Recent grants

Frequent coauthors

  • Donna P. Ankerst

    Technical University of Munich

    119 shared
  • Ian M. Thompson

    Christus Health

    116 shared
  • Phyllis J. Goodman

    116 shared
  • Charles A. Coltman

    114 shared
  • M. Scott Lucia

    University of Colorado Anschutz Medical Campus

    114 shared
  • Howard L. Parnes

    National Cancer Institute

    113 shared
  • Frank J. Gonzalez

    Colciencias

    110 shared
  • Catherine M. Tangen

    Cancer Research And Biostatistics

    89 shared

Education

  • PhD, Pharmaceutical Science

    Rutgers University New Brunswick

    2004
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