Ronald Davis- PhD
- Managing Director at Stanford University
Ronald Davis
- PhD
- Managing Director at Stanford University
About
820
Publications
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162,470
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Introduction
Current institution
Additional affiliations
January 1994 - June 2015
Publications
Publications (820)
Mimicking metabolic pathways on electrodes enables in vivo metabolite monitoring for decoding metabolism. Conventional in vivo sensors cannot accommodate underlying complex reactions involving multiple enzymes and cofactors, addressing only a fraction of enzymatic reactions for few metabolites. We devised a single-wall-carbon-nanotube-electrode arc...
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and Long COVID are persistent multi-system illnesses affecting many patients. With no known effective FDA-approved treatments for either condition, patient-reported outcomes of treatments are invaluable for guiding management strategies in patient care and generating new avenues for resear...
This pilot study harnessed the power of network medicine to unravel the complex pathogenesis of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). By utilizing a network analysis on whole genome sequencing (WGS) data from the Severely Ill Patient Study (SIPS), we identified ME/CFS-associated proteins and delineated the corresponding netwo...
More than 65 million individuals worldwide are estimated to have Long COVID (LC), a complex multisystemic condition, wherein patients of all ages report fatigue, post-exertional malaise, and other symptoms resembling myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS). With no current treatments or reliable diagnostic markers, there is an...
More than 65 million individuals worldwide are estimated to have Long COVID (LC), a complex multisystemic condition, wherein patients of all ages report fatigue, post-exertional malaise, and other symptoms resembling myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS). With no current treatments or reliable diagnostic markers, there is an...
A scheme that combines optoelectronic tweezers (OET) with spectroscopic analysis is presented. Referred to as spectral tweezers, the approach uses a single focused light beam that acts both as the trapping beam for OET and the probe beam for spectroscopy. Having simultaneous manipulation and spectral characterization ability, the method is used to...
An optoelectronic tweezer (OET) device is presented that exhibits improved trapping resolution for a given optical spot size. The scheme utilizes a pair of patterned physical electrodes to produce an asymmetric electric field gradient. This, in turn, generates an azimuthal force component in addition to the conventional radial gradient force. Stabl...
Significance
The awareness of the individuals’ biological status is critical for creating interactive environments. Accordingly, we devised a multimodal cryptographic bio-human–machine interface (CB-HMI), which seamlessly translates touch-based entries into encrypted biochemical, biophysical, and biometric indices (i.e., circulating biomarkers leve...
Lab-on-a-chip (LOC) devices capable of manipulating micro/nano-sized samples have spurred advances in biotechnology and chemistry. Designing and analyzing new and more advanced LOCs require accurate modeling and simulation of sample/particle dynamics inside such devices. In this work, we present a generalized computational physics model to simulate...
One in four myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) patients are estimated to be severely affected by the disease, and these house-bound or bedbound patients are currently understudied. Here, we report a comprehensive examination of the symptoms and clinical laboratory tests of a cohort of severely ill patients and healthy contr...
Point-of-care testing (POCT) allows physicians to detect and diagnose diseases at or near the patient site, faster than conventional lab-based testing. The importance of POCT is considerably amplified in the trying times of the COVID-19 pandemic. Numerous point-of-care tests and diagnostic devices are available in the market including, but not limi...
Significance
To achieve the mission of personalized medicine, centering on delivering the right drug to the right patient at the right dose, therapeutic drug monitoring solutions are necessary. By devising a surface engineering strategy, we created a voltammetric sensing interface, featuring an “undistorted potential window,” within which the targe...
Background
Polyketide secondary metabolites have been a rich source of antibiotic discovery for decades. Thousands of novel polyketide synthase (PKS) gene clusters have been identified in recent years with advances in DNA sequencing. However, experimental characterization of novel and useful PKS activities remains complicated. As a result, computat...
Red blood cell biomechanics can provide us with a deeper understanding of macroscopic physiology and have the potential of being used for diagnostic purposes. In diseases like sickle cell anemia and malaria, reduced red blood cell deformability can be used as a biomarker, leading to further assays and diagnoses. A microfluidic system is useful for...
The use of molecular probe technology is demonstrated for routine identification and tracking of cultured and uncultured microorganisms in an activated sludge bioreactor treating domestic wastewater. A key advantage of molecular probe technology is that it can interrogate hundreds of microbial species of interest in a single measurement. In environ...
Multidrug resistance is highly conserved in mammalian, fungal, and bacterial cells, is characterized by resistance to several unrelated xenobiotics, and poses significant challenges to managing infections and many cancers. Eukaryotes use a highly conserved set of drug efflux transporters that confer pleiotropic drug resistance (PDR). To interrogate...
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is arguably the last major disease we know almost nothing about. It is a multi-systemic illness of unknown etiology affecting millions of individuals worldwide, with the capacity to persist for several years. ME/CFS is characterized by disabling fatigue of at least 6 months, accompanied se...
Purpose:
Improved second-tier tools are needed to reduce false-positive outcomes in newborn screening (NBS) for inborn metabolic disorders on the Recommended Universal Screening Panel (RUSP).
Methods:
We designed an assay for multiplex sequencing of 72 metabolic genes (RUSPseq) from newborn dried blood spots. Analytical and clinical performance...
Our understanding of how genotype controls phenotype is limited by the scale at which we can precisely alter the genome and assess the phenotypic consequences of each perturbation. Here we describe a CRISPR–Cas9-based method for multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) in Saccharomyces cerev...
Eukaryotes utilize a highly-conserved set of drug efflux transporters to confer pleiotropic drug resistance (PDR). Despite decades of effort interrogating this process, multiple aspects of the PDR process, in particular PDR regulation, remain mysterious. In order to interrogate the regulation of this critical process, we have developed a small-mole...
For decades, fungi have been a source of U.S. Food and Drug Administration–approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth, with each genome encoding pathways capable of generating as many as dozens of natural products. However...
Background:
Viral infections are a major cause of complications and death in solid organ and hematopoietic cell transplantation.
Methods:
We developed a multiplex viral sequencing assay (mVseq) to simultaneously detect 20 transplant-relevant DNA viruses from small clinical samples. The assay uses a single-tube multiplex PCR to amplify highly con...
Significance
Quantitative detection of protein biomarkers over a wide concentration range from minute amounts of blood is essential for clinical diagnostics. Proximity ligation assay combines antibody–oligo conjugates, enzymatic ligation, and PCR amplification into a sensitive method for quantitative protein detection from small volumes. This repor...
For decades, fungi have been a source of FDA-approved natural products such as penicillin, cyclosporine, and the statins. Recent breakthroughs in DNA sequencing suggest that millions of fungal species exist on Earth with each genome encoding pathways capable of generating as many as dozens of natural products. However, the majority of encoded molec...
Expanded View Figures PDF
Review Process File
Many cellular functions are mediated by protein–protein interaction networks, which are environment dependent. However, systematic measurement of interactions in diverse environments is required to better understand the relative importance of different mechanisms underlying network dynamics. To investigate environment‐dependent protein complex dyna...
Methods of error filtration and correction post-gene assembly are a major bottleneck in the synthetic biology pipeline. Current oligonucleotide purification strategies, including polyacrylamide gel electrophoresis and high-performance liquid chromatography, are often expensive and labor-intensive, give low mass recovery, and contain hazardous chemi...
Significance
The inherent inaccessibility of sweat in sedentary individuals in large volume (≥10 µL) for on-demand and in situ analysis has limited our ability to capitalize on this noninvasive and rich source of information. Through devising an electrochemically enhanced, programmable, and miniaturized iontophoresis interface, integrated in a wear...
Journal of Antibiotics, official journal of the Japan Antibiotics Research Association, is a print and online publication that focuses on research on antibiotics and related types of medicinal substances
Review Process File
Expanded View Figures PDF
Significance
Point-of-care diagnostics in the developing world and resource-limited areas require numerous special design considerations to provide effective early detection of disease. Of particular need for these contexts are diagnostic technologies featuring low costs, ease of use, and broad applicability. Here we present a nanoparticle-inkjet-p...
The low costs of array‐synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. However, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost‐effective method called Recombinase Dire...
The Yeast Knockout Collection is a complete set of gene deletion strains for the budding yeast, Saccharomyces cerevisiae. In each strain, one of approximately 6000 open-reading frames is replaced with a dominant selectable marker flanked by two DNA barcodes. These barcodes, which are unique to each gene, allow the growth of thousands of strains to...
Chemical–genetic interactions (CGIs) describe a phenomenon where the effects of a chemical compound (i.e., a small molecule) on cell growth are dependent on a particular gene. CGIs can reveal important functional information about genes and can also be powerful indicators of a compound’s mechanism of action. Mapping CGIs can lead to the discovery o...
Homeostasis of ionized calcium in biofluids is critical for human biological functions and organ systems. Measurement of ionized calcium for clinical applications is not easily accessible due to its strict procedures and dependence on pH. pH balance in body fluids greatly affects metabolic reactions and biological transport systems. Here, we demons...
The origin of replication complex subunit ORC1 is important for DNA replication. The gene is known to encode a meiotic transcript isoform (mORC1) with an extended 5'-untranslated region (5'-UTR), which was predicted to inhibit protein translation. However, the regulatory mechanism that controls the mORC1 transcript isoform is unknown and no molecul...
DNA sequencing by imaging in an electron microscope is an approach that holds promise to deliver long reads with low error rates and without the need for amplification. Earlier work using transmission electron microscopes, which use high electron energies on the order of 100 keV, has shown that low contrast and radiation damage necessitates the use...
Peak-fitted high-resolution N 1s XPS spectra for single-stranded homopolymeric 20mers.
The data for all samples are fit with one peak for single-bonded nitrogen at 400.6 eV. In addition the Adenine, Cytosine and Guanine samples are fit with a second peak at 399.5 eV corresponding to double-bonded nitrogen.
(DOCX)
High-resolution P 2p XPS spectra for single-stranded homopolymeric 20mers.
All spectra have been peakshifted to 133.6 eV and scaled to the same height. The obtained peakshift and scaling factor were used for normalization of all other elements throughout each sample.
(DOCX)
Background
Genome-scale CRISPR interference (CRISPRi) has been used in human cell lines; however, the features of effective guide RNAs (gRNAs) in different organisms have not been well characterized. Here, we define rules that determine gRNA effectiveness for transcriptional repression in Saccharomyces cerevisiae.
Results
We create an inducible si...
Newborn screening for cystic fibrosis enables early detection and management of this debilitating genetic disease. Implementing comprehensive CFTR analysis using Sanger sequencing as a component of confirmatory testing of all screen-positive newborns has remained impractical due to relatively lengthy turnaround times and high cost. Here, we describ...
Applications of a 3D printing process are presented. This process integrates liquid-state printed components and interconnects with IC chips in all three dimensions, various orientations, and multiple printing layers to deliver personalized system-level functionalities. As an example application, a form-fitting glove is demonstrated with embedded p...
Wearable sensor technologies play a significant role in realizing personalized medicine through continuously monitoring an individual’s health state. To this end, human sweat is an excellent candidate for non-invasive monitoring as it contains physiologically rich information. Previously reported sweat-based and other non-invasive biosensors either...
The improvements in our ability to sequence and genotype DNA have opened up numerous avenues in the understanding of human biology and medicine with various applications, especially in medical diagnostics. But the realization of a label free, real time, high-throughput and low cost biosensing platforms to detect molecular interactions with a high l...
There is an emerging need for portable, robust, inexpensive, and easy-to-use disease diagnosis and prognosis monitoring platforms to share health information at the point-of-living, including clinical and home settings. Recent advances in digital health technologies have improved early diagnosis, drug treatment, and personalized medicine. Smartphon...
Thousands of mutations across more than 50 genes have been implicated in inherited cardiomyopathies. However, options for sequencing this rapidly evolving gene set are limited as many sequencing services and off-the-shelf kits suffer from slow turnaround, inefficient capture of genomic DNA, and/or high cost. Furthermore, customization of these assa...
Significance
Biosensing technologies have significant impact on medical diagnostics but difficulties in the handling of complex biospecimens, portability, and nonlinearity in dynamic detection range present considerable technical bottlenecks in their translation into clinical settings. Here, we present the nanoplasmonic electrical field-enhanced re...
Human transcriptome arrays (HTA) have recently been developed for high-throughput alternative splicing analysis by measuring signals not only from exons but also from exon-exon junctions. Effective use of these rich signals requires the development of computational methods for better gene and alternative splicing analyses. In this work, we introduc...
Significance
Cells consist of micro- and nanoscale components and materials that contribute to their fundamental magnetic and density signatures. Previous studies have claimed that magnetic levitation can only be used to measure density signatures of nonliving materials. Here, we demonstrate that both eukaryotic and prokaryotic cells can be levitat...
Described in here are design, fabrication, and testing of a miniaturized, rapid, label free, high throughput and inexpensive nanoelectronic array in a microfluidic channel, which can be used to detect and quantify different biomarkers. We have fabricated different geometrical designs of the array and demonstrated label free and real time electrical...
We demonstrate a novel multielectrode sensing method for extracting signal from noise in a microfluidic impedance cytometer through introducing redundancy in our measurements and coding the signal. We use a pair of coplanar interdigitated electrodes (IDEs), where we can sense the change in impedance between any two neighboring fingers of the IDE pa...
Accumulated biological knowledge is often encoded as gene sets, collections of genes associated with similar biological functions or pathways. The use of gene sets in the analyses of high-throughput gene expression data has been intensively studied and applied in clinical research. However, the main interest remains in finding modules of biological...
When conducting high-throughput biological experiments, it is often necessary to develop a protocol that is both inexpensive and robust. Standard approaches are either not cost-effective or arrive at an optimized protocol that is sensitive to experimental variations. Here, we describe a novel approach that directly minimizes the cost of the protoco...
The accurate identification of the true allele frequency of HLA genes in various ethnic groups may be a challenging task. The current methodology to catalog the common and well-documented (CWD) HLA alleles is based on the 3rd or 4th field made from assumptions for gene segments that were not tested by Sanger Sequencing methods. We examined the alle...
Microdroplets are an effective platform for segregating individual cells and amplifying DNA. However, a key challenge is to recover the contents of individual droplets for downstream analysis. This paper offers a method for embedding cells in alginate microspheres and performing multiple serial operations on the isolated cells. Rhodobacter sphaeroi...
Unlabelled:
Diploid budding yeast undergoes rapid mitosis when it ferments glucose, and in the presence of a non-fermentable carbon source and the absence of a nitrogen source it triggers sporulation. Rich medium with acetate is a commonly used pre-sporulation medium, but our understanding of the molecular events underlying the acetate-driven tran...
Significance
We introduce a novel method for controlling orientation of proteins during immobilization on solid-state surfaces using electric fields. Atomic force microscopy measurements and fluorescence-based readout are used to confirm this phenomenon. This method of immobilization has broad implications for improvement in performance of both aff...
A vibrant discussion of the merits and limitations of animal models is long overdue. The limitation of space precludes addressing many of the questionable approaches and statements by Takao and Miyakawa (1).
It was recently reported that the sizes of many mRNAs change when budding yeast cells exit mitosis and enter the meiotic differentiation pathway. These differences were attributed to length variations of their untranslated regions. The function of UTRs in protein translation is well established. However, the mechanism controlling the expression of...
Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA
Background: Circulating tumor cells (CTCs) in blood and disseminated tumor cells (DTCs) in bone marrow are being studied to monitor disease and guide therapy, but the relationship between CTCs and DTCs is weak and may confound clinical decision-making. Because blood sampling is...
Detection of surface charges has various applications in medicine, electronics, biotechnology, etc. The source of surface charge induction may range from simple charge-polarized molecules like water to complicated proteins. It was recently discovered that surface charge accumulation can alter the temperature at which VO2 undergoes a Mott transition...
