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Articles by Levi Waldron
Faecalibacterium prausnitzii, depleted in the Parkinson’s disease microbiome, improves motor deficits in α-synuclein overexpressing mice - npj Parkinson's Disease
Abstract Gut microbiome composition is altered in Parkinson’s disease (PD), the fastest-growing neurological condition, that is characterized by neurodegeneration, motor dysfunction, and is frequently accompanied by gastrointestinal (GI) symptoms. Notably, microbial taxa with anti-inflammatory properties are consistently depleted in PD patients compared to controls.
Clarivate’s 2025 Highly Cited Researchers include five from CUNY SPH
Five CUNY SPH faculty and senior scholars are featured among Clarivate’s Highly Cited Researchers for 2025. Dean Ayman El-Mohandes, Professor Jeffrey Lazarus, Senior Scholar Kenneth Rabin, Distinguished Lecturer Scott Ratzan, and Professor Levi Waldron made the list among the top 1% of researchers cited in their field of research.
Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?
Main text Shotgun metagenomics is a popular approach to sequence the entire DNA content of a sample with a relevant amount of microbial biomass. This approach has enabled breakthroughs in the understanding of the human1 and non-host-associated microbiomes. However, during the design of the Human Microbiome Project (HMP) in 2007, researchers were already aware of the potential presence of human DNA in metagenomic samples and the associated privacy and ethical risks.
Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders - Nature Communications
Abstract The link between the oral microbiome and neurodevelopmental disorders remains a compelling hypothesis, still requiring confirmation in large-scale datasets. Leveraging over 7000 whole-genome sequenced salivary samples from 2025 US families with children diagnosed with autism spectrum disorders (ASD), our cross-sectional study shows that the oral microbiome composition can discriminate ASD subjects from neurotypical siblings (NTs, AUC = 0.66), with 108 differentiating species (q < 0.005).
Ecological Determinants of Altruism in Prokaryote Antivirus Defense
Abstract Prokaryote evolution is driven in large part by the incessant arms race with viruses. Genomic investments in antivirus defense can be coarsely classified into two categories, immune systems that abrogate virus reproduction resulting in clearance, and altruistic programmed cell death (PCD) systems. Prokaryotic defense systems are enormously diverse, as revealed by an avalanche of recent discoveries, but the basic ecological determinants of defense strategy remain poorly understood.
Machine learning for microbiologists - Nature Reviews Microbiology
Abstract Machine learning is increasingly important in microbiology where it is used for tasks such as predicting antibiotic resistance and associating human microbiome features with complex host diseases. The applications in microbiology are quickly expanding and the machine learning tools frequently used in basic and clinical research range from classification and regression to clustering and dimensionality reduction.
GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases - Nature Communications
Abstract Millions of transcriptomic profiles have been deposited in public archives, yet remain underused for the interpretation of new experiments. We present a method for interpreting new transcriptomic datasets through instant comparison to public datasets without high-performance computing requirements.
Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals - Nature Medicine
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Author notes These authors contributed equally: Francesco Asnicar, Sarah E. Berry. These authors jointly supervised this work: Andrew T. Chan, Curtis Huttenhower, Tim D. Spector, Nicola Segata.
By Francesco Asnicar, Ana M Valdes, Long Nguyen, Long Nguyễn, Gianmarco Piccinno, David Drew, Rachel Gibson, Caroline Le Roy, Lucy Francis, Mireia Valles-Colomer, Francesco Beghini, Joan Capdevila, Levi Waldron, Richard Davies, Jonathan Wolf, Jose M. Ordovas, Christopher Gardner, Andrew Chan, Curtis Huttenhower, Tim Spector, Rachel Hine, Christopher Bonnett, Serge Danzanvilliers, George Hadjigeorgiou
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Nature
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Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data
Abstract Background The correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking.
Levi | CaringBridge
Levi’s Story Site created on April 9, 2019 Welcome to my CaringBridge website. I'm planning to use it to document my experience as a patient of oropharyngeal cancer and to keep family, friends, and colleagues updated. I appreciate your support and words of encouragement. Thank you for visiting. See the Ways to Help page to get even more involved. Personal Fundraiser Support Links Helpful Tasks
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