Explanipedia

Altered gut microbial functional pathways in people with irritable bowel syndrome enable precision health insights Open

Eric Patridge, Anmol Gorakshakar, Matthew M. Molusky, Grant Antoine, Guruduth Banavar · 2025

Rather than waiting to diagnose IBS after symptoms appear, these functional pathway scores can help to provide early health insights into molecular pathways that may contribute to IBS. These molecular endpoints could also assist with measu…

Manhattan Projects for Preventive Medicine Open

Momchilo Vuyisich, Ryan Toma, Holiday Goodreau, Emmanuel Hanon, Damon Tanton , et al. · 2025

In this opinion article, we argue that the requisite scientific knowledge and technological capabilities to elucidate the fundamental causes of chronic diseases—and to develop strategies for their prevention, reversal, and cure—already exi…

Data-Driven Personalized Nutrition Reduces HbA1c in a Prediabetic and Diabetic Population – a Pilot, Randomized, Placebo-Controlled Clinical Trial Open

Momchilo Vuyisich, Grant Antoine, Morvarid Mehrtash, Hilary Keiser, Janelle Connell , et al. · 2024

Type 2 Diabetes (T2D) is a major public health concern. We have previously shown that the biochemical functions of the gut microbiome contribute to the postprandial glucose response and built a machine learned (ML) model that can personali…

Salivary Transcriptome and Mitochondrial Analysis of Autism Spectrum Disorder Children Compared to Healthy Controls Open

Mark Cannon, Ryan Toma, Sri Ganeshan, Emmery de Jesus Alvarez Varela, Momchilo Vuyisich , et al. · 2024

Autism rates have been reported to be increasing rapidly in industrialized societies. The pathology most often combines neurological symptoms associated with language and social impairments with gastrointestinal symptoms. This study aimed …

Manhattan Projects for Preventive Medicine Open

Momchilo Vuyisich, Ryan Toma, Holiday Goodreau, Emmanuel Hanon, Damon Tanton , et al. · 2024

In this opinion article, we argue that the requisite scientific knowledge and technological capabilities to elucidate the fundamental causes of chronic diseases - and to develop strategies for their prevention, reversal, and cure - already…

Altered gut microbial functional pathways in people with Irritable Bowel Syndrome enable precision health insights Open

Eric Patridge, Anmol Gorakshakar, Matthew M. Molusky, Oyetunji Ogundijo, Cristina Julián , et al. · 2024

Functional gastrointestinal disorders present diagnostic and therapeutic challenges, and there is a strong need for molecular markers that enable early health insights and intervention. Herein, we present an approach to assess the gut micr…

A Novel Method for Sampling Subgingival Microbiome: A Comparative Metatranscriptomic Study Open

Diana Demusaj, Ryan Toma, Tanveer Khan, Lan Hu, Guruduth Banavar , et al. · 2024

The subgingival microbiome has been implicated in oral and systemic diseases such as periodontitis and Alzheimer's disease. However, subgingival sampling is challenging. We developed a novel method of sampling the subgingival microbiome by…

Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness Open

Eric Patridge, Anmol Gorakshakar, Matthew M. Molusky, Oyetunji Ogundijo, Angel Janevski , et al. · 2024

It is increasingly recognized that an important step towards improving overall health is to accurately measure biomarkers of health from the molecular activities prevalent in the oral cavity. We present a general methodology for computatio…

An accurate aging clock developed from large-scale gut microbiome and human gene expression data Open

Vishakh Gopu, Francine R. Camacho, Ryan Toma, Pedro J. Torres, Ying Cai , et al. · 2023

Microbial functional pathways based on metatranscriptomic profiling enable effective saliva-based health assessments for precision wellness Open

Eric Patridge, Anmol Gorakshakar, Matthew M. Molusky, Oyetunji Ogundijo, Angel Janevski , et al. · 2023

It is increasingly recognized that an important step towards improving overall health is to accurately measure biomarkers of health from the molecular activities prevalent in the oral cavity. We present a general methodology for computatio…

The effectiveness of precision supplements on depression symptoms in a US population Open

Cristina Julián, Nan Shen, Matthew M. Molusky, Lan Hu, Vishakh Gopu , et al. · 2023

Nutrition plays a pivotal role in depression, but dietary interventions are usually not personalized and do not consider patients’ microbial and human molecular functions. This preliminary study evaluated the effectiveness of precision sup…

Comparison of the Gut Microbiome Composition Between Men with Peyronie’s Disease and A Matched Cohort: A Pilot Study Open

Mohamad M. Osman, Muhammed Hammad, David W. Barham, Ryan Toma, Farouk M. El‐Khatib , et al. · 2023

Objective:To investigate the potential association of the gut microbiome with Peyronie’s disease, as there has been no research to date that has studied these topics together. The goal of our study is to better characterize any potential r…

A novel method for sampling subgingival microbiome - a comparative metatranscriptomic study Open

Diana Demusaj, Ryan Toma, Tanveer Khan, Lan Hu, Guruduth Banavar , et al. · 2023

The subgingival microbiome has been implicated in several oral and systemic diseases, such as periodontitis, arthritis, and Alzheimer’s disease. However, subgingival sampling is challenging and cannot be readily performed outside of primar…

Data from figures in "An accurate aging clock developed from very large gut microbiome and human gene expression datasets reveal molecular associations for aging" Open

Vishakh Gopu, Guruduth Banavar · 2023

Data underlying the figures in the paper "An accurate aging clock developed from very large gut microbiome and human gene expression datasets reveal molecular associations for aging". A ".xlsx" file and a directory containing the individu…

Data from figures in "An accurate aging clock developed from very large gut microbiome and human gene expression datasets reveal molecular associations for aging" Open

Vishakh Gopu, Guruduth Banavar · 2023

Data underlying the figures in the paper "An accurate aging clock developed from very large gut microbiome and human gene expression datasets reveal molecular associations for aging". A ".xlsx" file and a directory containing the individu…

A Clinically Validated Human Saliva Metatranscriptomic Test for Global Systems Biology Studies Open

Ryan Toma, Ying Cai, Oyetunji Ogundijo, Lan Hu, Stephanie Gline , et al. · 2023

The authors report here the development of a high-throughput, automated, inexpensive and clinically validated saliva metatranscriptome test that requires less than 100 μl of saliva. RNA is preserved at the time of sample collection, allowi…

Detecting salivary host-microbiome RNA signature for aiding diagnosis of oral and throat cancer Open

Guruduth Banavar, Oyetunji Ogundijo, Cristina Julián, Ryan Toma, Francine R. Camacho , et al. · 2022

Objectives Oral squamous cell carcinoma (OSCC) and oropharyngeal squamous cell carcinoma (OPSCC) are the two major subtypes of head and neck cancer (HNC) that can go undetected resulting in late detection and poor outcomes. We describe the…

Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses Open

Ryan Toma, Nathan Duval, Nan Shen, Pedro J. Torres, Francine R. Camacho , et al. · 2022

Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses Open

Ryan Toma, Nathan Duval, Nan Shen, Pedro J. Torres, Francine R. Camacho , et al. · 2022

Objective Infectious diseases are common but are not easily or readily diagnosed with current methodologies. This problem is further exacerbated with the constant presence of mutated, emerging, and novel pathogens. One of the most common s…

The salivary metatranscriptome as an accurate diagnostic indicator of oral cancer Open

Guruduth Banavar, Oyetunji Ogundijo, Ryan Toma, Senthilkumar Rajagopal, Yen Kai Lim , et al. · 2021

Despite advances in cancer treatment, the 5-year mortality rate for oral cancers (OC) is 40%, mainly due to the lack of early diagnostics. To advance early diagnostics for high-risk and average-risk populations, we developed and evaluated …

Gut Microbiome Activity Contributes to Prediction of Individual Variation in Glycemic Response in Adults Open

Hal Tily, Eric Patridge, Ying Cai, Vishakh Gopu, Stephanie Gline , et al. · 2021

Limiting postprandial glycemic response (PPGR) is an important intervention in reducing the risk of chronic metabolic diseases and has been shown to impart significant health benefits in people with elevated levels of blood sugar. In this …

Gut microbiome activity predicts risk of type 2 diabetes and metformin control in a large human cohort Open

Nan Shen, Nevenka Dimitrova, Cleo Han-Chen Ho, Pedro J. Torres, Francine R. Camacho , et al. · 2021

Recognizing and treating the early stages of type 2 diabetes (T2D) is the most cost effective way to decrease prevalence, before heart disease, renal disease, blindness, and limb amputation become inevitable. In this study, we employ high …

PD62-08 DIFFERENCES IN THE GUT MICROBIOME COMPOSITION BETWEEN MEN WITH ERECTILE DYSFUNCTION AND A MATCHED COHORT: A PILOT STUDY Open

Mahdi Osman, Farouk M. El‐Khatib, Jeanie Nguyen, Edward Choi, Joshua T. Randolph , et al. · 2021

You have accessJournal of UrologySexual Function/Dysfunction: Basic Research & Pathophysiology (PD62)1 Sep 2021PD62-08 DIFFERENCES IN THE GUT MICROBIOME COMPOSITION BETWEEN MEN WITH ERECTILE DYSFUNCTION AND A MATCHED COHORT: A PILOT STUDY …

A clinically validated human saliva metatranscriptomic test for global systems biology studies Open

Ryan Toma, Ying Cai, Oyetunji Ogundijo, Stephanie Gline, Diana Demusaj , et al. · 2021

We report here the development of a high throughput, automated, inexpensive, and clinically validated saliva metatranscriptome test that requires less than 100 microliters of saliva. The RNA in the samples is preserved at the time of colle…

Evidence-based precision nutrition improves clinical outcomes by analyzing human and microbial molecular data with artificial intelligence Open

Janelle Connell, Ryan Toma, Cleo Han-Chen Ho, Nan Shen, Pedro Moura , et al. · 2021

Background Current dietary recommendations are often generalized, conflicting, and highly subjective, depending on the source biases. This results in confusion, skepticism, and frustration in the general population. Methods We have develop…

Data-driven precision nutrition improves clinical outcomes and risk scores for IBS, depression, anxiety, and T2D Open

Janelle Connell, Ryan Toma, Cleo Han-Chen Ho, Nan Shen, Pedro Moura , et al. · 2021

Many studies have shown that foods and nutritional ingredients play an important role in healthy human homeostasis, either directly or via the microbiome. We have developed an objective, integrated, and automated approach to personalized f…

An accurate aging clock developed from the largest dataset of microbial and human gene expression reveals molecular mechanisms of aging Open

Vishakh Gopu, Ying Cai, Subha Krishnan, Senthilkumar Rajagopal, Francine R. Camacho , et al. · 2020

Accurate measurement of the biological markers of the aging process could provide an “aging clock” measuring predicted longevity and allow for the quantification of the effects of specific lifestyle choices on healthy aging. Using modern m…

The salivary metatranscriptome as an accurate diagnostic indicator of oral cancer Open

Guruduth Banavar, Oyetunji Ogundijo, Ryan Toma, Senthilkumar Rajagopal, Yenkai Lim , et al. · 2020

Despite advances in cancer treatment, the five-year mortality rate for oral cancers (OC) is 40%, mainly due to the lack of early diagnostics. To advance early diagnostics for high-risk and average-risk populations, we developed and evaluat…

A Clinically Validated Human Capillary Blood Transcriptome Test For Global Systems Biology Studies Open

Ryan Toma, Nathan Duval, Benjamin Pelle, Matthew Parks, Vishakh Gopu , et al. · 2020

To prevent and treat chronic diseases, including cancer, a global application of systems biology is needed. We report here a whole blood transcriptome test that needs only 50 μl of capillary (fingerprick) blood. This test is suitable for g…

A clinically validated human capillary blood transcriptome test for global systems biology studies Open

Ryan Toma, Benjamin Pelle, Nathan Duval, Matthew Parks, Vishakh Gopu , et al. · 2020

Chronic diseases are the leading cause of morbidity and mortality globally. Yet, the majority of them have unknown etiologies, and genetic contribution is weak. In addition, many of the chronic diseases go through the cycles of relapse and…

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