About

Dr. Erkin Şeker is a Professor of Electrical and Computer Engineering at UC Davis. His research focuses on understanding and controlling nanostructured material properties and their interaction with biological systems to develop effective biomedical tools for both basic and clinical applications. He leads the Şeker Lab, which engineers high-throughput miniaturized screening platforms to study nanoscale material properties and their impact on electrical, biochemical, optical, and biological properties. His work aims to create miniature drug delivery platforms, biosensors, multifunctional neural interfaces, and organ-on-a-chip platforms, contributing to advancements in bio, agriculture, and health technologies, as well as photonic and electronic devices, nanoscale electronics and photonics, and biosensing, biophotonics, and electronics.

Research topics

• Immunology
• Cell biology
• Biology
• Biochemistry
• Neuroscience

Selected publications

• Anomalous morphology evolution in nanoporous gold thin films in response to equivalent thermal treatment doses

  Scripta Materialia · 2026-03-13

  articleSenior authorCorresponding
  PublisherDOI

• Cortical cell culture model for examining cancer extracellular vesicle dynamics and neuroinflammatory response

  Figshare · 2026-01-01

  otherOpen access

  Abstract Understanding the interactions of extracellular vesicles (EVs) with central nervous system (CNS) cells is important for identifying mechanisms of disease and developing EV-based therapies. Yet, such studies are typically limited to single cell assays that lack the ability to probe complex intercellular signaling, such as the processes involved in neuroinflammation. Critically, metastatic niche formation in the brain is hypothesized to be mediated in part by cancer-derived EVs, though details are poorly understood. Here we apply multi-cellular CNS mixed culture models to assess neuroinflammatory response for EVs isolated from brain-metastatic cancer cells as a proof-of-concept for the utility of this model. Using primary cortical tri-culture (neurons, astrocytes, microglia) and contrasting co-culture (neurons and astrocytes, without microglia), we assessed the cellular tropism and neuroinflammatory response of EVs from breast cancer cells (MDA-MB-231) to their brain-tropic variant (231-Br), and non-cancer control (HEK293T). EVs exhibited differential total uptake in neurons and astrocytes depending on EV source and whether microglia were included in culture. Furthermore, addition of tumor EVs in tri-cultures with microglia resulted in significantly higher production of cytokines compared to control. Taken together, these results suggest that EV fate and function may be modulated by complex intercellular communication. This study underscores the novelty and importance of employing a multicellular assay, offering a more comprehensive and physiologically relevant model to dissect the intricate dynamics of EVs in neuroinflammatory responses within the CNS, paving the way for nuanced understanding and therapeutic exploration.

  PublisherDOI

• Additional file 1 of Cortical cell culture model for examining cancer extracellular vesicle dynamics and neuroinflammatory response

  Open MIND · 2026-01-01

  article

  Supplementary Material 1

  DOI

• Cortical cell culture model for examining cancer extracellular vesicle dynamics and neuroinflammatory response

  Figshare · 2026-01-01

  otherOpen access

  Abstract Understanding the interactions of extracellular vesicles (EVs) with central nervous system (CNS) cells is important for identifying mechanisms of disease and developing EV-based therapies. Yet, such studies are typically limited to single cell assays that lack the ability to probe complex intercellular signaling, such as the processes involved in neuroinflammation. Critically, metastatic niche formation in the brain is hypothesized to be mediated in part by cancer-derived EVs, though details are poorly understood. Here we apply multi-cellular CNS mixed culture models to assess neuroinflammatory response for EVs isolated from brain-metastatic cancer cells as a proof-of-concept for the utility of this model. Using primary cortical tri-culture (neurons, astrocytes, microglia) and contrasting co-culture (neurons and astrocytes, without microglia), we assessed the cellular tropism and neuroinflammatory response of EVs from breast cancer cells (MDA-MB-231) to their brain-tropic variant (231-Br), and non-cancer control (HEK293T). EVs exhibited differential total uptake in neurons and astrocytes depending on EV source and whether microglia were included in culture. Furthermore, addition of tumor EVs in tri-cultures with microglia resulted in significantly higher production of cytokines compared to control. Taken together, these results suggest that EV fate and function may be modulated by complex intercellular communication. This study underscores the novelty and importance of employing a multicellular assay, offering a more comprehensive and physiologically relevant model to dissect the intricate dynamics of EVs in neuroinflammatory responses within the CNS, paving the way for nuanced understanding and therapeutic exploration.

  PublisherDOI

• Cortical cell culture model for examining cancer extracellular vesicle dynamics and neuroinflammatory response

  Cell Communication and Signaling · 2026-01-04

  articleOpen access

  Understanding the interactions of extracellular vesicles (EVs) with central nervous system (CNS) cells is important for identifying mechanisms of disease and developing EV-based therapies. Yet, such studies are typically limited to single cell assays that lack the ability to probe complex intercellular signaling, such as the processes involved in neuroinflammation. Critically, metastatic niche formation in the brain is hypothesized to be mediated in part by cancer-derived EVs, though details are poorly understood. Here we apply multi-cellular CNS mixed culture models to assess neuroinflammatory response for EVs isolated from brain-metastatic cancer cells as a proof-of-concept for the utility of this model. Using primary cortical tri-culture (neurons, astrocytes, microglia) and contrasting co-culture (neurons and astrocytes, without microglia), we assessed the cellular tropism and neuroinflammatory response of EVs from breast cancer cells (MDA-MB-231) to their brain-tropic variant (231-Br), and non-cancer control (HEK293T). EVs exhibited differential total uptake in neurons and astrocytes depending on EV source and whether microglia were included in culture. Furthermore, addition of tumor EVs in tri-cultures with microglia resulted in significantly higher production of cytokines compared to control. Taken together, these results suggest that EV fate and function may be modulated by complex intercellular communication. This study underscores the novelty and importance of employing a multicellular assay, offering a more comprehensive and physiologically relevant model to dissect the intricate dynamics of EVs in neuroinflammatory responses within the CNS, paving the way for nuanced understanding and therapeutic exploration.

  PublisherDOI

• Additional file 1 of Cortical cell culture model for examining cancer extracellular vesicle dynamics and neuroinflammatory response

  Figshare · 2026-01-01

  articleOpen access

  Supplementary Material 1

  PublisherDOI

• Label free multimodal optical imaging of metabolic heterogeneity in aging by integrating SRS, MPF, FLIM, and SHG

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-14

  articleOpen access

  ABSTRACT Cellular metabolism is governed by the coordinated organization of macromolecules, including lipids and proteins, together with redox-active cofactors such as NADH and FAD. However, resolving these biochemical features quantitatively and spatially at subcellular resolution remains challenging because no single imaging modality can capture molecular composition, redox state, and tissue architecture simultaneously without labeling. Here, we present MANIFEST ( M ulti-mod A l N onlinear I maging with F luorescence E xcitation and S tatistical T emporal-resolved spectroscopy), a label-free imaging platform that integrates stimulated Raman scattering (SRS), second harmonic generation (SHG), multiphoton fluorescence (MPF), and fluorescence lifetime imaging microscopy (FLIM). The MANIFEST combines chemical imaging of lipids with autofluorescence- and lifetime-based quantification of NADH and FAD metabolism, enabling spatially resolved analysis of metabolic heterogeneity at organelle and tissue-compartment levels. We apply this framework to four distinct aging or disease models: amyloid-beta-treated tri-cultured brain cells, high-fat diet mouse liver, human non-ischemic cardiomyopathy tissue, and aging mouse retina. Across these systems, MANIFEST reveals disease-associated lipid remodeling, redox imbalance, disrupted metabolic zonation, collagen reorganization, and layer-specific metabolic changes. By integrating complementary nonlinear optical modalities into a single label-free platform, MANIFEST provides a generalizable approach for high-resolution metabolic phenotyping in complex biological systems and offers new opportunities for studying disease mechanisms, aging biology, and metabolism-driven tissue pathology.

  PublisherOA PDFDOI

• Interfacing with the Brain: How Nanotechnology Can Contribute

  ACS Nano · 2025-03-10 · 54 citations

  reviewOpen access

  Interfacing artificial devices with the human brain is the central goal of neurotechnology. Yet, our imaginations are often limited by currently available paradigms and technologies. Suggestions for brain-machine interfaces have changed over time, along with the available technology. Mechanical levers and cable winches were used to move parts of the brain during the mechanical age. Sophisticated electronic wiring and remote control have arisen during the electronic age, ultimately leading to plug-and-play computer interfaces. Nonetheless, our brains are so complex that these visions, until recently, largely remained unreachable dreams. The general problem, thus far, is that most of our technology is mechanically and/or electrically engineered, whereas the brain is a living, dynamic entity. As a result, these worlds are difficult to interface with one another. Nanotechnology, which encompasses engineered solid-state objects and integrated circuits, excels at small length scales of single to a few hundred nanometers and, thus, matches the sizes of biomolecules, biomolecular assemblies, and parts of cells. Consequently, we envision nanomaterials and nanotools as opportunities to interface with the brain in alternative ways. Here, we review the existing literature on the use of nanotechnology in brain-machine interfaces and look forward in discussing perspectives and limitations based on the authors' expertise across a range of complementary disciplines─from neuroscience, engineering, physics, and chemistry to biology and medicine, computer science and mathematics, and social science and jurisprudence. We focus on nanotechnology but also include information from related fields when useful and complementary.

  PublisherOA PDFDOI

• NeuralStorm: Training Graduate Students to Take Neuroengineering by Storm

  2025-07-10

  articleOpen access
  PublisherOA PDFDOI

• A Nucleic Acid-Based Electrochemical Detection Method for Post Hoc Sample Analysis

  ChemRxiv · 2025-08-08

  preprintSenior author

  Conventional detection schemes for nucleic-acid based electrochemical sensors involve a layer of single-stranded DNA (ssDNA) capture probe that is attached to the working electrode at one end and labeled with a redox reporter at the opposite end. Upon electrochemical interrogation, the probe layer produces a current, which is attenuated upon hybridization with the target DNA or RNA biomarker due to conformational change of the ssDNA. The decrease in current, referred to as percent signal suppression (%SS), indicates successful hybridization. Since the probe and target signals need to be successively acquired for accurately determining %SS, this method is not suitable for sample collection at a site without electrochemical analysis capabilities. Here, we introduce a new approach, where the sample can be blotted onto an electrode that is pre-functionalized with probe DNA. In this scheme, post-hybridization current is obtained first, followed by melting the hybridized DNA duplex in warm deionized water for subsequent acquisition of the post-melt current. The increase in cur-rent upon melting, which we refer to as percent signal enhancement (%SE), similarly indicates presence of tar-get DNA with comparable performance to a standard electrochemical detection technique at representative 2 µM and 100 nM target concentrations. The performance of planar and nanoporous gold (np-Au) electrodes are compared for DNA detection in complex biological samples where np-Au exhibits biofouling-resilient sensing. Finally, remote sample collection is simulated by blotting the complex sample on np-Au electrodes for %SE de-termination, where target DNA is successfully detected.

  PublisherDOI

Frequent coauthors

• Martin L. Yarmush

  Shriners Hospitals for Children - Boston

  86 shared

• Wei‐Chuan Shih

  University of Houston

  37 shared

• Keith J. Stine

  University of Missouri–St. Louis

  37 shared

• Mingwei Chen

  Johns Hopkins University

  36 shared

• Prachi Patel

  Northwestern University

  36 shared

• Pabitra K. Nayak

  Tata Institute of Fundamental Research

  36 shared

• J. Eckert

  Austrian Academy of Sciences

  36 shared

• Yi Ding

  Ruijin Hospital

  36 shared

Education

• PhD, Electrical Engineering

  University of Virginia

  2007

• MS, Electrical Engineering

  University of Virginia

  2004

• BS, Electrical Engineering

  Virginia Tech

  2002

Awards & honors

• UC Davis Awards Top Honor for Graduate Teaching to Erkin Şek…