James Robert Green

Carleton University · Department of Systems and Computer Engineering

The prediction of novel pre-microRNA (miRNA) from genomic sequence has received considerable attention recently. However, the majority of studies have focused on the human genome. Previous studies have demonstrated that sensitivity (correctly detecting true miRNA) is sustained when human-trained methods are applied to other species, however they ha...

All protein-protein interaction (PPI) predictors require the determination of an operational decision threshold when differentiating positive PPIs from negatives. Historically, a single global threshold, typically optimized via cross-validation testing, is applied to all protein pairs. However, we here use data visualization techniques to show that...

Experimental drug development is time-consuming, expensive and limited to a relatively small number of targets. However, recent studies show that repositioning of existing drugs can function more efficiently than de novo experimental drug development to minimize costs and risks. Previous studies have proven that network analysis is a versatile plat...

Many people with hearing loss are unaware of it and do not seek benefit from available interventions such as hearing aids. This is in part due to the limited accessibility to qualified hearing healthcare providers in developing and developed countries alike. Automated audiometry, which has gained in popularity amidst the torrent of advances in tele...

Methods for the de novo identification of microRNA (miRNA) have been developed using a range of sequence-based features. With the increasing availability of next generation sequencing (NGS) transcriptome data, there is a need for miRNA identification that integrates both NGS transcript expression-based patterns as well as advanced genomic sequence-...

microRNAs (miRNAs) are small non-coding ribonucleic acids that post-transcriptionally regulate gene expression through the targeting of messenger RNA (mRNAs). Most miRNA target predictors have focused on animal species and prediction performance drops substantially when applied to plant species. Several rule-based miRNA target predictors have been...

Infant pose monitoring during sleep has multiple applications in both healthcare and home settings. In a healthcare setting, pose detection can be used for region of interest detection and movement detection for noncontact-based monitoring systems. In a home setting, pose detection can be used to detect sleep positions which has shown to have a str...

Monitoring critical infrastructure is of great importance for resilience against current and emerging hazards. In Canada, at the national level, critical infrastructure is strategically classified into the following 10 sectors: energy and utilities, finance, food, transportation, government, information and communication technology, health, water,...

Across many domains, real-world problems can be represented as a network. Nodes represent domain-specific elements and edges capture the relationship between elements. Leveraging high-performance computing and optimized link prediction algorithms, it is increasingly possible to evaluate every possible combination of nodal pairs enabling the generat...

Infant pose monitoring during sleep has multiple applications in both healthcare and home settings. In a healthcare setting, pose detection can be used for region of interest detection and movement detection for noncontact based monitoring systems. In a home setting, pose detection can be used to detect sleep positions which has shown to have a str...

Although the remote sensing (RS) community has begun to pretrain transformers (intended to be fine-tuned on RS tasks), it is unclear how these models perform under distribution shifts. Here, we pretrain a new RS transformer--called SatViT-V2--on 1.3 million satellite-derived RS images, then fine-tune it (along with five other models) to investigate...

A number of private and public insurers compensate workers whose hearing loss can be directly attributed to excessive exposure to noise in the workplace. The claim assessment process is typically lengthy and requires significant effort from human adjudicators who must interpret hand-recorded audiograms, often sent via fax or equivalent. In this wor...

The identification of novel drug-target interactions (DTI) is critical to drug discovery and drug repurposing to address contemporary medical and public health challenges presented by emergent diseases. Historically, computational methods have framed DTI prediction as a binary classification problem (indicating whether or not a drug physically inte...

Engineering peptides to achieve a desired therapeutic effect through the inhibition of a specific target activity or protein interaction is a non-trivial task. Few of the existing in silico peptide design algorithms generate target-specific peptides. Instead, many methods produce peptides that achieve a desired effect through an unknown mechanism....

Antibacterial drugs (AD) change the metabolic status of bacteria, contributing to bacterial death. However, antibiotic resistance and the emergence of multidrug-resistant bacteria increase interest in understanding metabolic network (MN) mutations and the interaction of AD vs MN. In this study, we employed the IFPTML = Information Fusion (IF) + Per...

Neonatal infants in need of advanced care, often require transportation via road ambulance to neonatal intensive care units. The ambulance exposes these vulnerable infants to potentially harmful noise and vibration. To better understand the levels of vibration, this paper maps the magnitude of acceleration due to vibration throughout the cabin of a...

Astroglial cells are key players in the development and maintenance of neurons and neuronal networks. Astroglia express steroid hormone receptors and show rapid responses to hormonal manipulations. However, despite important sex differences in the cortex and hippocampus, few studies have examined sex differences in astroglial cells in telencephalic...

The lived environment, particularly when proximal to roadways, is filled with multi-digit and multi-numbered values corresponding to advertised commodities. The reliable detection of single multi-digit values from natural imagery has been widely studied through the last decade (e.g. Street View House Numbers [SVHN]); however, extraction and assignm...

The development of non-contact patient monitoring applications for the neonatal intensive care unit (NICU) is an active research area, particularly in facial video analysis. Recent studies have used facial video data to estimate vital signs, assess pain from facial expression, differentiate sleep-wake status, detect jaundice, and in face recognitio...

Despite the enormous success of the “pretraining and fine-tuning” paradigm, widespread across machine learning, it has yet to pervade remote sensing (RS). To help rectify this, we pretrain a vision transformer (ViT) on 1.3 million satellite-derived RS images. We pretrain SatViT using a state-of-the-art (SOTA) self-supervised learning (SSL) algorith...

Multiple private and public insurers compensate workers whose hearing loss can be directly attributed to excessive exposure to noise in the workplace. The claim assessment process is typically lengthy and requires significant effort from human adjudicators who must interpret hand-recorded audiograms, often sent via fax or equivalent. In this work,...

Video-based monitoring of patients in the neonatal intensive care unit (NICU) has great potential for improving patient care. Video-based detection of clinical events, such as bottle feeding, would represent a step towards semi-automated charting of clinical events. Recording such events contemporaneously would address the limitations associated wi...

Primary Subject area Neonatal-Perinatal Medicine Background Each year, thousands of newborns are transported by air or ground ambulance to receive specialized medical care. For neurologically immature and physiologically compromised infants, especially preterm infants, the noise and vibration exposure during transport are high despite preventative...

Metabolic Reaction Networks (MRNs) are complex networks produced by thousands of chemical reactions or transformations (links) of metabolites (nodes) in a live organism. An essential goal of chemical biology is to test the connectivity (structure) of these complex MRNs models presented for new microorganisms with promising features. In theory, we c...

Engineering peptides to achieve a desired therapeutic effect through the inhibition of a specific target activity or protein interaction is a non-trivial task. Few of the existing in silico peptide design algorithms generate target-specific peptides. Instead, many methods produce peptides that achieve a desired effect through an unknown mechanism....

The soybean crop, Glycine max (L.) Merr., is consumed by humans, Homo sapiens, worldwide. While the respective bodies of literature and -omics data for each of these organisms are extensive, comparatively few studies investigate the molecular biological processes occurring between the two. We are interested in elucidating the network of protein-pro...

Continuity of care is achieved in the neonatal intensive care unit (NICU) through careful documentation of all events of clinical significance, including clinical interventions and routine care events (e.g., feeding, diaper change, weighing, etc.). As a step towards automating this documentation process, we propose a scene recognition algorithm tha...

Vibration and noise exposure during emergency neonatal ground and air transport are recognized as hazards for the neonate; however, no standardized test environment exists to reliably quantify such exposure with high repeatability. An on-road test was performed to provide a quantitative measurement of on-road vibrations to be used in the deve...

Background Understanding the disease pathogenesis of the novel coronavirus, denoted SARS-CoV-2, is critical to the development of anti-SARS-CoV-2 therapeutics. The global propagation of the viral disease, denoted COVID-19 (“coronavirus disease 2019”), has unified the scientific community in searching for possible inhibitory small molecules or polyp...

Background Checking the connectivity (structure) of complex Metabolic Reaction Networks (MRNs) models proposed for new microorganisms with promising properties is an important goal for chemical biology. Objective In principle, we can perform a hand-on checking (Manual Curation). However, this is a hard task due to the high number of combinations o...

High-throughput metabolomics can be used to optimize cell growth for enhanced production or for monitoring cell health in bioreactors. It has applications in cell and gene therapies, vaccines, biologics, and bioprocessing. NMR metabolomics is a method that allows for fast and reliable experimentation, requires only minimal sample preparation, and c...

Antimicrobial resistance has prompted research and the development of new antibiotic treatments. Efforts to discover new drugs with antibacterial activity have generated large data sets from multiple preclinical trials with different experimental conditions. Predicting the activity of new chemical compounds on pathogenic microorganisms with differe...

Speed humps are an effective means to moderate the speed of traffic but can have adverse effects on the circulation of emergency vehicles. This study aims to use various comfort and injury risk metrics to evaluate the effects of speed hump traversal on the comfort of the passengers. Studies of human comfort during ambulance transport typically cons...

Protein lysine methylation mediates a variety of biological processes, and their dysregulation has been established to play pivotal roles in human disease. A number of these sites constitute attractive drug targets. However, systematic identification of methylation sites is challenging and resource intensive. Here, we present a protocol combining M...

BACKGROUND Clinical decision support systems (CDSS) have the potential to lower patient mortality and morbidity rates. However, signal artifacts present in physiologic data affect the reliability and accuracy of CDSS. Moreover, patient monitors and other medical devices generate false alarms while processing artifactual data. This leads to alarm fa...

Background Clinical decision support systems (CDSS) have the potential to lower the patient mortality and morbidity rates. However, signal artifacts present in physiological data affect the reliability and accuracy of the CDSS. Moreover, patient monitors and other medical devices generate false alarms while processing physiological data, further le...

Premature infants or neonates in need of advanced clinical care must be transported to specialized hospitals. Past studies have examined vibrations experienced by patients during transport; however, multiple confounding factors limit the utility of on-road data. Hence, the development of a standardized test environment is warranted. The overall pur...

MicroRNAs (miRNAs) are short, non-coding RNAs that interact with messenger RNA (mRNA) to accomplish critical cellular activities such as the regulation of gene expression. Several machine learning methods have been developed to improve classification accuracy and reduce validation costs by predicting which miRNA will target which gene. Application...

Protein Lys methylation plays a critical role in numerous cellular processes, but it is challenging to identify Lys methylation in a systematic manner. Here we present an approach combining in silico prediction with targeted mass spectrometry (MS) to identify Lys methylation (Kme) sites at the proteome level. We develop MethylSight, a program that...

Newborns admitted to the neonatal intensive care unit (NICU) require a high level of care due to their precarious condition. Nurses typically monitor their vital signs continuously using wearable sensors such as electrocardiogram (ECG) electrodes placed on their chest and a pulse oximeter on a limb. When the patient moves, this can cause motion art...

Rare or orphan diseases affect only small populations, thereby limiting the economic incentive for the drug development process, often resulting in a lack of progress towards treatment. Drug repositioning is a promising approach in these cases, due to its low cost. In this approach, one attempts to identify new purposes for existing drugs that have...

Interfacility transport to tertiary care for high-risk neonates has become an integral part of equitable access to optimal perinatal healthcare. Excellence in clinical care requires expertise in transport medicine and the coordination of safe transport processes. However, concerns remain regarding environmental stressors involved in the transportat...

A bstract Understanding the disease pathogenesis of the novel coronavirus, denoted SARS-CoV-2, is critical to the development of anti-SARS-CoV-2 therapeutics. The global propagation of the viral disease, denoted COVID-19 (“coronavirus disease 2019”), has unified the scientific community in searching for possible inhibitory small molecules or polype...

Recent mobile and automated audiometry technologies have allowed for the democratization of hearing healthcare and enables non-experts to deliver hearing tests. The problem remains that a large number of such users are not trained to interpret audiograms. In this work, we outline the development of a data-driven audiogram classification system desi...

The need for larger-scale and increasingly complex protein-protein interaction (PPI) prediction tasks demands that state-of-the-art predictors be highly efficient and adapted to inter- and cross-species predictions. Furthermore, the ability to generate comprehensive interactomes has enabled the appraisal of each PPI in the context of all prediction...

Background: MicroRNAs (miRNAs) are a family of short, non-coding RNAs that have been linked to critical cellular activities, most notably regulation of gene expression. The identification of miRNA is a cross-disciplinary approach that re