Maude M. David

BioGeoFormer: A deep learning approach to classify unknown genes associated with critical biogeochemical cycles

Jacob H. Wynne, Nima Azbijari, Andrew R. Thurber, Maude M. David

Abstract Remote functional annotation continues to impede progress in microbial ecology, as alignment-based approaches still leave over one-third of microbial sequences functionally unresolved. In contrast, pre-trained natural-language–processing approaches have shown strong potential for inferring functions from diverse biological sequences, and here we …

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Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data

Quintin Pope, Rohan Varma, Christine A. Tataru, Maude M. David et autres

We use open source human gut microbiome data to learn a microbial "language" model by adapting techniques from Natural Language Processing (NLP). Our microbial "language" model is trained in a self-supervised fashion (i.e., without additional external labels) to capture the interactions among …

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Cytokine induced inflammatory bowel disease model using organ-on-a-chip technology

Christine A. Tataru, Maya Livni, Carrie L. Marean‐Reardon, María Clara Franco et autres

Over 2 million people in North America suffer from inflammatory bowel disease (IBD), a chronic and idiopathic inflammatory condition. While previous research has primarily focused on studying immune cells as a cause and therapeutic target for IBD, recent findings suggest that non-immune …

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Sex shapes gut–microbiota–brain communication and disease

Kenton C. Hokanson, Caroline Hernández, Grace E. Deitzler, Maude M. David

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Learning a deep language model for microbiomes: the power of large scale unlabeled microbiome data

Quintin Pope, Rohan Varma, Chritine Tataru, Maude M. David et autres

Abstract We use open source human gut microbiome data to learn a microbial “language” model by adapting techniques from Natural Language Processing (NLP). Our microbial “language” model is trained in a self-supervised fashion (i.e., without additional external labels) to capture the interactions …

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Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism

Christine A. Tataru, Marie Peras, Erica M. Rutherford, Kaiti Dunlap et autres

While healthy gut microbiomes are critical to human health, pertinent microbial processes remain largely undefined, partially due to differential bias among profiling techniques. By simultaneously integrating multiple profiling methods, multi-omic analysis can define generalizable microbial processes, and is especially useful in understanding …

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Multi-level analysis of the gut–brain axis shows autism spectrum disorder-associated molecular and microbial profiles

James T. Morton, Dong-Min Jin, Robert H. Mills, Yan Shao et autres

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in ASD although with limited reproducibility across studies. In this study, we developed a Bayesian differential ranking …

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Supplementation of Clostridiales affects microbial profile and induces sex- specific social behavior deficits in mice following prenatal immune insult

Grace E. Deitzler, Austin Martin, Priyanka Singla, Alexandra Phillips et autres

Abstract Background: Autism spectrum disorder (ASD) is a heritable and complex neurodevelopmental disorder with both genetic and environmental risk factors, with a male:female diagnosis ratio of 3:1. ASD can be modeled in rodents using Maternal Immune Activation (MIA). In this model, pregnant …

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Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism

Christine A. Tataru, Marie Peras, Erica M. Rutherford, Kaiti Dunlap et autres

Abstract While healthy gut microbiomes are critical to human health, pertinent microbial processes remain largely undefined, partially due to differential bias among profiling techniques. By simultaneously integrating multiple profiling methods, multi-omic analysis can define generalizable microbial processes, and is especially useful in …

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Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups

Kiana West, Xiaochen Yin, Erica M. Rutherford, Brendan Wee et autres

Observational studies have shown that the composition of the human gut microbiome in children diagnosed with Autism Spectrum Disorder (ASD) differs significantly from that of their neurotypical (NT) counterparts. Thus far, reported ASD-specific microbiome signatures have been inconsistent. To uncover reproducible signatures, …

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Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism

Christine A. Tataru, Marie Peras, Erica M. Rutherford, Kaiti Dunlap et autres

Abstract While healthy gut microbiomes are critical to human health, pertinent microbial processes remain largely undefined, partially due to differential bias among profiling techniques. By simultaneously integrating multiple profiling methods, multi-omic analysis can define generalizable microbial pro-cesses, and is especially useful in …

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An open-source, low-cost voluntary running activity tracking tool for in vivo rodent studies

Grace E. Deitzler, Nicholas Bira, Joseph R. Davidson, Maude M. David

In vivo rodent behavioral and physiological studies often benefit from measurement of general activity. However, many existing instruments necessary to track such activity are high in cost and invasive within home cages, some even requiring extensive separate cage systems, limiting their widespread …

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