About

Rashid Bashir is a member of the American Academy of Arts and Sciences, recognized in 2024. He is affiliated with the Grainger College of Engineering and is involved in multiple research units including Bioengineering, Mechanical Science and Engineering, Electrical and Computer Engineering, Materials Science and Engineering, and Materials Research Lab. His work is associated with the Coordinated Science Lab, Biomedical and Translational Sciences, the Beckman Institute for Advanced Science and Technology, the Carl R. Woese Institute for Genomic Biology, and the National Center for Supercomputing Applications (NCSA).

Research topics

• Computer Science
• Biology
• Nanotechnology
• Medicine
• Materials science
• Chemistry
• Virology
• Chromatography
• Optoelectronics
• Pathology
• Genetics
• Engineering
• Data science
• Artificial Intelligence
• Physics
• Neuroscience
• Molecular biology
• Cell biology
• Telecommunications
• Simulation
• Endocrinology
• Bioinformatics
• Optics
• Organic chemistry

Selected publications

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

  Interface Focus · 2026-04-24 · 1 citations

  articleOpen accessSenior author

  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

• The clinician-artificial intelligence partnership in early sepsis identification: Leveraging predictive intelligence for enhanced financial outcomes

  Research Square · 2026-01-06

  preprintOpen access
  PublisherOA PDFDOI

• Detecting DNA translocation through a nanopore using a van der Waals heterojunction diode

  Proceedings of the National Academy of Sciences · 2025-05-01 · 1 citations

  articleOpen accessSenior authorCorresponding

  A long-unrealized goal in solid-state nanopore sensing is to achieve out-of-plane electrical sensing and control of DNA during translocation, which is a prerequisite for base-by-base ratcheting that enables DNA sequencing in biological nanopores. Two-dimensional (2D) heterostructures, with their capability to construct out-of-plane electronics with atomic layer precision, are ideal yet unexplored candidates for use as electrical sensing membranes. Here, we demonstrate a nanopore architecture using a vertical 2D heterojunction diode consisting of p-type WSe 2 on n-type MoS 2 . This diode exhibits rectified interlayer tunneling currents modulated by ionic potential, while the heterojunction potential reciprocally rectifies ionic transport through the nanopore. We achieve concurrent detection of DNA translocation using both ionic and diode currents and demonstrate a 2.3-fold electrostatic slowing of average translocation speed. Encapsulation layers enhance chemical and mechanical stability and durability while preserving the spatial resolution of atomically sharp 2D heterointerface for sensing. These results establish a paradigm for out-of-plane electrical sensing of single biomolecules.

  PublisherDOI

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

  SLAS TECHNOLOGY · 2025-03-23 · 3 citations

  reviewOpen accessSenior author

  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

• The Sepsis ImmunoScore Predicts Sepsis, Mortality, and Deterioration Better than Clinical Scores and Widely Available Biomarkers

  medRxiv · 2025-10-05

  preprintOpen access

  BACKGROUND Early identification of patients at risk for sepsis, mortality, and clinical deterioration is essential for improving outcomes, but existing diagnostic and predictive tools have limited accuracy. The objective was to evaluate the performance of an FDA-authorized AI tool, the Sepsis ImmunoScore, compared to widely available biomarkers and clinical tools for diagnosis of sepsis and prediction of in-hospital mortality and intensive care unit (ICU) admission. METHODS This multicenter observational study included 6,027 adult patients suspected of infection across 7 U.S. hospital sites. The Sepsis ImmunoScore’s predictive performance was compared to the sequential organ failure assessment (SOFA) score, procalcitonin (PCT), C-reactive protein (CRP), Systemic Inflammatory Response Syndrome (SIRS) score, National Early Warning Score (NEWS), and quick SOFA (qSOFA). Primary outcomes included sepsis as defined by Sepsis-3 criteria, in-hospital mortality, and ICU admission. Predictive accuracy was assessed using area under the receiver operating characteristic curve (AUC), and 95% confidence intervals were generated and hypothesis testing conducted using the bootstrap method. RESULTS The Sepsis ImmunoScore demonstrated statistically significant superior performance across all outcomes. For sepsis prediction, the Sepsis ImmunoScore achieved an AUC of 0.82, compared to SOFA (0.72), procalcitonin (PCT) (0.70),C-reactive protein (CRP) (0.61), SIRS (0.59), NEWS (0.69), and qSOFA (0.67). For in-hospital mortality prediction, the Sepsis ImmunoScore achieved an AUC of 0.80, outperforming SOFA (0.72), PCT (0.67), CRP (0.58), SIRS (0.60), NEWS (0.72), and qSOFA (0.69). For ICU admission, the Sepsis ImmunoScore reached an AUC of 0.74, superior to SOFA (0.63), PCT (0.64), CRP (0.54), SIRS (0.60), NEWS (0.70), and qSOFA (0.65). All differences between the Sepsis ImmunoScore and comparators were statistically significant. CONCLUSIONS The Sepsis ImmunoScore significantly improved predictive accuracy for sepsis, in-hospital mortality, and ICU admission compared to six conventional clinical scores and biomarkers. This AI-based tool may enhance risk stratification and clinical decision-making, potentially leading to more timely sepsis interventions and improved outcomes. KEY POINTS Question How does the FDA-authorized Sepsis ImmunoScore compare to conventional sepsis tools at diagnosing and predicting sepsis, clinical deterioration, and in-hospital mortality? Findings In a multicenter observational cohort of 6,027 patients with suspected infection, the Sepsis ImmunoScore demonstrated statistically superior performance compared to PCT, CRP, SOFA, qSOFA, SIRS, and NEWS in predicting all outcomes: sepsis diagnosis, ICU admission, and in-hospital mortality. Meaning Because the Sepsis ImmunoScore outperforms existing sepsis diagnostics, it could potentially enhance risk stratification and clinical decision-making for patients with suspected infection, enabling more appropriate and timely interventions.

  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 accessSenior authorCorresponding

  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

• Optogenetic neuromuscular actuation of a miniature electronic biohybrid robot

  Science Robotics · 2025-09-03 · 10 citations

  articleOpen accessSenior authorCorresponding

  Neuronal control of skeletal muscle function is ubiquitous across species for locomotion and doing work. In particular, emergent behaviors of neurons in biohybrid neuromuscular systems can advance bioinspired locomotion research. Although recent studies have demonstrated that chemical or optogenetic stimulation of neurons can control muscular actuation through the neuromuscular junction (NMJ), the correlation between neuronal activities and resulting modulation in the muscle responses is less understood, hindering the engineering of high-level functional biohybrid systems. Here, we developed NMJ-based biohybrid crawling robots with optogenetic mouse motor neurons, skeletal muscles, 3D-printed hydrogel scaffolds, and integrated onboard wireless micro-light-emitting diode (μLED)-based optoelectronics. We investigated the coupling of the light stimulation and neuromuscular actuation through power spectral density (PSD) analysis. We verified the modulation of the mechanical functionality of the robot depending on the frequency of the optical stimulation to the neural tissue. We demonstrated continued muscle contraction up to 20 minutes after a 1-minute-long pulsed 2-hertz optical stimulation of the neural tissue. Furthermore, the robots were shown to maintain their mechanical functionality for more than 2 weeks. This study provides insights into reliable neuronal control with optoelectronics, supporting advancements in neuronal modulation, biohybrid intelligence, and automation.

  PublisherOA PDFDOI

• Detecting DNA Translocation through a Nanopore using a van der Waals Heterojunction Diode

  Research Square · 2025-04-25 · 1 citations

  preprintOpen accessSenior author
  PublisherDOI

• Detecting DNA Translocation through a Nanopore using a van der Waals Heterojunction Diode

  Research Square · 2025-04-08

  preprintOpen accessSenior author
  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 accessSenior authorCorresponding

  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

Recent grants

• DNA Methylation Analysis Using Solid-State Nanopore Sensors - A Pathway to Early

  NIH · $355k · 2011–2012

• An Integrated Lab-on-a-Transistor for Biological Detection

  NSF · $300k · 2010–2014

• Integrated Nanowire Array Sensors for Biomolecular Detection

  NSF · $240k · 2006–2009

• NIH Grant R21EB007472

  NIH · $520k · 2010

• NIH Grant R21RR015118

  NIH · $213k · 2003

Frequent coauthors

• Enrique Valera

  University of Illinois Urbana-Champaign

  96 shared

• Ali Khademhosseini

  Terasaki Foundation

  91 shared

• Deirdre Meldrum

  Institute of Nanotechnology

  73 shared

• Kenji Sunagawa

  73 shared

• Claudio Cobelli

  University of Padua

  73 shared

• A. M. Russell

  Computational Intelligence and Information Systems Lab

  73 shared

• Henry Hess

  Columbia University

  73 shared

• B Wheeler

  IEEE Computer Society

  72 shared

Labs

• Neuroscience ProgramPI