About

Enrique Valera is a Research Assistant Professor in the Department of Bioengineering at the University of Illinois Urbana-Champaign. He received his Ph.D. in Electronic Engineering from the Universitat Politècnica de Catalunya (UPC) in Barcelona, Spain, in 2008. His research has focused on biosensor technology, microfluidic platforms, and the development of electrochemical and optical point-of-care devices for clinical diagnostics. Valera has extensive experience in designing microfabrication processes, optics, impedance spectroscopy, and surface chemistry, as well as synthesizing and functionalizing nanoparticles for biosensing applications. His work aims to contribute to the development of medical tools that support personalized medicine and global health solutions, especially in resource-limited settings. He is dedicated to advancing faster, more precise diagnostics and developing adaptable platforms for detecting biomarkers and pathogens. Valera's research spans electronics, chemistry, and applied sciences, with a focus on creating sensitive, portable, and cost-effective diagnostic devices that can be translated from laboratory research to clinical and environmental applications.

Research topics

• Computer Science
• Virology
• Medicine
• Pathology
• Artificial Intelligence
• Telecommunications
• Biology
• Nursing
• Genetics
• Risk analysis (engineering)
• Nanotechnology
• Intensive care medicine
• Data science
• Business
• Molecular biology
• Environmental health
• Materials science

Selected publications

• Data for "Kinetic Modeling of Target-Amplification-Free CRISPR-Cas-Based Autocatalysis Reactions"

  Zenodo (CERN European Organization for Nuclear Research) · 2026-03-12

  datasetOpen access

  This folder contains the experimental data for the publication "Kinetic Modeling of Target-Amplification-Free CRISPR-Cas-Based Autocatalysis Reactions". The MATLAB library used for generating the modeling-based plots is provided in a separate Zenodo deposit.

  PublisherDOI

• Advances in muscle-driven biohybrid robots: electrical, optical and neuromuscular junction-based stimulations

  Interface Focus · 2026-04-24 · 1 citations

  articleOpen access

  Abstract Muscle-driven biohybrid robotics has gained substantial attention for its potential to enable advanced mechanical systems with flexibility, high energy efficiency, self-healing capability and adaptability. Autonomous or stimulated muscle contractions have been used as driving forces of mechanical functions and have successfully demonstrated walking, swimming and crawling behaviours of biohybrid robots. Despite these advances, many opportunities exist to achieve greater actuation, precise control, longer-term viability, and programmability. This review provides insights into the next generation of biohybrid systems by examining prior studies on locomotive biohybrid robots specifically designed for walking and crawling locomotion. We introduce diverse biohybrid walker and crawler models and describe their design principles and operating mechanisms, and discuss key factors for optimal engineering strategies. Furthermore, we classify these models according to three primary muscle-stimulation techniques, i.e. electrical field, optical, and neuromuscular junction, and discuss their unique characteristics, including their advantages and limitations. We also highlight approaches for multi-directional locomotion and wireless control, which can contribute to achieving higher dynamic control of biohybrid robots.

  PublisherOA PDFDOI

• CRISPR-Cas-Based Autocatalysis Reaction Modeling

  Zenodo (CERN European Organization for Nuclear Research) · 2026-03-12

  otherOpen access

  This project provides tools for modeling CRISPR-Cas-based autocatalysis reactions, plotting simulated assay results, and optimizing reaction conditions. The MATLAB library was developed for the publication "Kinetic Modeling of Target-Amplification-Free CRISPR-Cas-Based Autocatalysis Reactions" by Wester et al.

  PublisherDOI

• Data for "Kinetic Modeling of Target-Amplification-Free CRISPR-Cas-Based Autocatalysis Reactions"

  Zenodo (CERN European Organization for Nuclear Research) · 2026-03-12

  datasetOpen access

  This folder contains the experimental data for the publication "Kinetic Modeling of Target-Amplification-Free CRISPR-Cas-Based Autocatalysis Reactions". The MATLAB library used for generating the modeling-based plots is provided in a separate Zenodo deposit.

  PublisherDOI

• CRISPR-Cas-Based Autocatalysis Reaction Modeling

  Zenodo (CERN European Organization for Nuclear Research) · 2026-03-12

  otherOpen access

  This project provides tools for modeling CRISPR-Cas-based autocatalysis reactions, plotting simulated assay results, and optimizing reaction conditions. The MATLAB library was developed for the publication "Kinetic Modeling of Target-Amplification-Free CRISPR-Cas-Based Autocatalysis Reactions" by Wester et al.

  PublisherDOI

• Kinetic Modeling of Target-Amplification-Free CRISPR-Cas-Based Autocatalysis Reactions

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-04

  articleOpen access

  Abstract CRISPR-Cas-based diagnostics utilize the Cas enzyme’s trans-cleavage activity to generate signal and have become popular platforms for sensitive nucleic acid detection. Recently, autocatalytic systems have been demonstrated to improve the time to response and sensitivity in some cases. However, mechanistic description of these assays is limited and optimization relies on simple trial-and-error. In this work, we present the first comprehensive kinetic model that integrates all major biochemical processes involved in these assays, including cleavage reactions, nucleic acid equilibrium kinetics, inhibition of trans-cleavage by single-stranded DNA, and degradation of single-stranded reaction components. We discuss the biochemical foundations and implementation of the ordinary differential equation model, which is built for adaptation to different reaction schemes. We use the full model to investigate the role of nucleic acid stability in assay performance for a typical nucleic acid design and show that our model demonstrates inhibition effects consistent with experimental data. We describe the reaction behavior, derive a simplified analytical model and compare its performance to the full analytical model. Finally, we demonstrate tools developed for rapid in silico optimization to guide the rational design of future target-amplification-free CRISPR-Cas-based autocatalysis assays.

  PublisherDOI

• Gram Typing Bacteria Panels in Whole Blood Using a Biphasic Duplex-Loop-Mediated Isothermal Amplification Assay

  ACS Sensors · 2026-02-18

  articleCorresponding

  Timely identification of bacteria in bloodstream infections is critical for guiding appropriate antibiotic treatment. However, current clinical workflows entail blood culture (1-5 days), followed by Gram staining, PCR, and antibiotic susceptibility testing. These steps delay actionable results, often leading clinicians to prescribe broad-spectrum antibiotics without results from the above tests, contributing to the rising threat of antimicrobial resistance. Specifically, rapid information of even presence of Gram-positive and/or Gram-negative bacteria would help clinicians choose a specific antibiotic regimen after bacteremia is suspected. Here, we developed a rapid, culture-free method that identifies bacterial Gram type within a panel of 6 bacteria from whole blood at a sensitivity of 1-5 CFU/μL within 1.5 h. The assay features a duplex probe-based detection of amplification by release of quenching (DARQ) loop-mediated isothermal amplification (LAMP) system targeting six of the most common bloodstream pathogens in blood cultures in published hospital reports. The two DARQ probes distinguish a panel of four Gram-negative bacteria (E. coli, S. marcescens, P. mirabilis, and K. pneumoniae) from two Gram-positive bacteria (methicillin-susceptible S. aureus/methicillin-resistant S. aureus and S. epidermidis). Coupled with our "biphasic" sample preparation technique (reported earlier) in a 4 μL sample volume, the assay could eliminate the need for blood culture, extraction & purification, providing Gram type information to guide clinical treatments.

  PublisherDOI

• Review on biphasic blood drying method for rapid pathogen detection in bloodstream infections

  SLAS TECHNOLOGY · 2025-03-23 · 3 citations

  reviewOpen access

  Rapid and accurate detection of pathogenic microorganisms in blood is critical for diagnosing life-threatening conditions such as bloodstream infections (BSIs). Current methods for the detection and identification of bacteria from large volumes of blood (5 mL) involve culture steps followed by DNA extraction/purification/concentration and Polymerase Chain Reaction (PCR)-based nucleic acid amplification. DNA extraction and amplification directly from blood samples is hampered by the complexity of the blood matrix, resulting in time-consuming and labor-intensive processes. This review delves into recent advancements in molecular diagnostics based on blood drying, coined as 'biphasic reaction', and highlights this new technique that attempts to overcome the limitations of traditional sample preparation and amplification processes. The biphasic blood drying method, in combination with isothermal amplification methods such as loop-mediated isothermal amplification (LAMP) or recombinase polymerase amplification (RPA), has recently been shown to improve the sensitivity of detection of bacterial, viral, and fungal pathogens from ∼1 mL of whole blood, while minimizing DNA loss and avoiding the use of extraction/purification/concentration kits. Furthermore, the biphasic approach in combination with LAMP has been shown to be a culture-free method capable of detecting bacteria in clinical samples with a sensitivity of ∼1 CFU/mL in ∼2.5 h. This represents a significant reduction in detection and identification time compared to current clinical procedures based on bacterial culture prior to PCR amplification. This review paper aims to be a guide to identify new opportunities for future advancements and applications of the biphasic technology.

  PublisherDOI

• Amplification-free, OR-gated CRISPR-Cascade reaction for pathogen detection in blood samples

  Proceedings of the National Academy of Sciences · 2025-03-10 · 55 citations

  articleOpen access

  Rapid and accurate detection of DNA from disease-causing pathogens is essential for controlling the spread of infections and administering timely treatments. While traditional molecular diagnostics techniques like PCR are highly sensitive, they include nucleic acid amplification and many need to be performed in centralized laboratories, limiting their utility in point-of-care settings. Recent advances in CRISPR-based diagnostics (CRISPR-Dx) have demonstrated the potential for highly specific molecular detection, but the sensitivity is often constrained by the slow trans-cleavage activity of Cas enzymes, necessitating preamplification of target nucleic acids. In this study, we present a CRISPR-Cascade assay that overcomes these limitations by integrating a positive feedback loop that enables nucleic acid amplification-free detection of pathogenic DNA at atto-molar levels and achieves a signal-to-noise ratio greater than 1.3 within just 10 min. The versatility of the assay is demonstrated through the detection of bloodstream infection pathogens, including Methicillin-Sensitive Staphylococcus aureus (MSSA), Methicillin-Resistant Staphylococcus aureus (MRSA), Escherichia coli , and Hepatitis B Virus (HBV) spiked in whole blood samples. Additionally, we introduce a multiplexing OR-function logic gate, further enhancing the potential of the CRISPR-Cascade assay for rapid and accurate diagnostics in clinical settings. Our findings highlight the ability of the CRISPR-Cascade assay to provide highly sensitive and specific molecular detection, paving the way for advanced applications in point-of-care diagnostics and beyond.

  PublisherOA PDFDOI

• Amplification-Free Dual-Blocking Autocatalytic CRISPR-Cascade for Atto-Molar DNA Detection with Low Nonspecific Signal

  Proceedings of the National Academy of Sciences · 2025-12-03

  articleOpen access

  Autocatalytic CRISPR architecture offers amplification-free nucleic acid detection by directly linking target recognition to self-reinforcing ribonucleoprotein (RNP) generation. However, spontaneous background activation remains a key barrier, because strand invasion or unwinding events can initiate unintended amplification and diminish assay specificity. Here, we introduce a dual-blocking CRISPR-Cascade design that independently cages both the guide RNA and trigger DNA, establishing an intrinsic AND gate to raise the effective kinetic barrier for unintended RNP formation. This strategy suppresses leakage by approximately 3- to 18-fold relative to single blocking configurations in full Cascade reactions, while preserving rapid detection (10 min), achieving single-copy sensitivity, and enabling quantitative detection. When paired with a competitive guide RNA decoy, the system further reduces background signals without affecting true target detection. Finally, we demonstrate robust Methicillin-resistant Staphylococcus aureus (MRSA) detection from whole blood in under 40 minutes including the sample purification and extraction. These results establish dual-blocking as a generalizable molecular gating framework for constructing leakage-resistant, amplification-free CRISPR systems suitable for rapid and decentralized diagnostics. Significance: Amplification-free CRISPR diagnostics are often presented as simple positive feedback circuits, but most existing systems treat leakage, defined as target independent background activation that arises when blocked CRISPR components spontaneously form active ribonucleoprotein (RNP), as an unavoidable side effect rather than as a designable property. In particular, prior work has not explicitly accounted for two key sources of background signal in autocatalytic assays: Cas driven unwinding of blocked constructs and transient breathing of nucleic acid duplexes that intermittently expose trigger sites. Our study directly analyzes these leakage pathways in the context of switchable-cage-gRNA (scgRNA) and Cascade probe design and shows that blocking a single component is fundamentally vulnerable to both enzyme-driven strand invasion and equilibrium breathing. By contrast, we introduce a dual-blocking strategy in which both the guide RNA and the trigger DNA are gated. We further add a decoy guide RNA that competes for Cas12a. This multi-layer architecture demonstrates that robust amplification-free operation requires several coordinated barriers rather than a single switch, providing a new design principle for constructing self-amplifying CRISPR circuits with low background and robust signal-to-noise ratio.

  PublisherDOI

Frequent coauthors

• Rashid Bashir

  University of Illinois Urbana-Champaign

  96 shared

• M.‐Pilar Marco

  Institute of Advanced Chemistry of Catalonia

  40 shared

• Jacob Berger

  University of Illinois Urbana-Champaign

  32 shared

• A. Rodrı́guez

  24 shared

• Karen White

  24 shared

• Tanmay Ghonge

  University of Illinois Urbana-Champaign

  23 shared

• Umer Hassan

  Rutgers, The State University of New Jersey

  20 shared

• Anurup Ganguli

  University of Illinois Urbana-Champaign

  20 shared

Labs

• Enrique Valera LabPI

Education

• PhD, Electronic Engineering Department

  Universitat Politècnica de Catalunya

  2008

Awards & honors

• Four granted patents (two in Spain and two in the United Sta…