Aaron McGeever
YOU?
Author Swipe
View article: Germline stem cell isolation, lineage tracing, and aging in a protochordate
Germline stem cell isolation, lineage tracing, and aging in a protochordate Open
Germline stem cells (GSCs), the source of gametes, are the only stem cells capable of passing genes to future generations and are therefore considered units of natural selection. Yet, the factors that influence GSC fitness, and thus govern…
Single-nucleus RNA sequencing reveals a preclinical model for the most common subtype of glioblastoma Open
Different glioblastoma (GBM) subtypes have been identified based on the tumor microenvironment (TME). The discovery of new therapies for these hard-to-treat tumors requires a thorough characterization of preclinical models, including their…
View article: Consensus prediction of cell type labels in single-cell data with popV
Consensus prediction of cell type labels in single-cell data with popV Open
Cell-type classification is a crucial step in single-cell sequencing analysis. Various methods have been proposed for transferring a cell-type label from an annotated reference atlas to unannotated query datasets. Existing methods for tran…
View article: A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors
A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors Open
Elucidating organismal developmental processes requires a comprehensive understanding of cellular lineages in the spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, a dynamic atlas of zebrafish embryonic develo…
View article: Consensus prediction of cell type labels with popV
Consensus prediction of cell type labels with popV Open
Cell-type classification is a crucial step in single-cell analysis. To facilitate this, several methods have been proposed for the task of transferring a cell-type label from an annotated reference atlas to unannotated query data sets. Exi…
Zebrahub – Multimodal Zebrafish Developmental Atlas Reveals the State-Transition Dynamics of Late-Vertebrate Pluripotent Axial Progenitors Open
Elucidating the developmental processes of organisms requires a comprehensive understanding of cellular lineages in the spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, a dynamic atlas of zebrafish embryonic …
ortho_seqs: A Python tool for sequence analysis and higher order sequence–phenotype mapping Open
Motivation An important goal in sequence analysis is to understand how parts of DNA, RNA, or protein sequences interact with each other and to predict how these interactions result in given phenotypes. Mapping phenotypes onto underlying se…
View article: Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections Open
Background Antimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently…
View article: Additional file 2 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
Additional file 2 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections Open
Additional file 2: Table S2. mNGS detection of respiratory pathogens compared to a reference standard of clinical microbiological testing.
View article: Additional file 6 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
Additional file 6 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections Open
Additional file 6: Table S4. AMR genes detected by mNGS.
View article: Additional file 8 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
Additional file 8 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections Open
Additional file 8: Table S6. Pathogen AMR genes detected by FLASH-mNGS.
View article: Additional file 3 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
Additional file 3 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections Open
Additional file 3: Dataset 1. AMR gene database utilized for analyses.
View article: Additional file 4 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
Additional file 4 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections Open
Additional file 4: Dataset 2. AMR genes and guide RNAs for FLASH targeted mNGS. AMR genes and guide RNAs for FLASH targeted mNGS. A) AMR genes targeted by FLASH. B) AMR alleles and guide RNA targets. Legend: Bla = beta lactam; MLS = macrol…
View article: Additional file 5 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
Additional file 5 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections Open
Additional file 5: Table S3. Time to return of clinical antimicrobial susceptibility testing results for culture-confirmed bacterial pathogens.
View article: Additional file 9 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
Additional file 9 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections Open
Additional file 9: Table S7. AMR genes detected by FLASH coupled with Nanopore mNGS.
View article: Additional file 7 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections
Additional file 7 of Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections Open
Additional file 7: Table S5. Performance of RNA-seq, DNA-seq and combined RNA-seq + DNA-seq for AMR prediction compared to clinical antimicrobial susceptibility testing.
View article: A high-resolution flux-matrix model describes the spread of diseases in a spatial network and the effect of mitigation strategies
A high-resolution flux-matrix model describes the spread of diseases in a spatial network and the effect of mitigation strategies Open
Propagation of an epidemic across a spatial network of communities is described by a variant of the SIR model accompanied by an intercommunity infectivity matrix. This matrix is estimated from fluxes between communities, obtained from cell…
View article: Genomic Epidemiology and Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Congregate Healthcare Facilities in Santa Clara County, California
Genomic Epidemiology and Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Congregate Healthcare Facilities in Santa Clara County, California Open
Background Outbreaks of SARS-CoV-2 in long-term care facilities (LTCFs) cause significant morbidity and mortality. Mapping viral transmission within and between facilities by combining genomic sequencing with epidemiologic investigations e…
Single-Cell Analysis for Whole-Organism Datasets Open
Cell atlases are essential companions to the genome as they elucidate how genes are used in a cell type–specific manner or how the usage of genes changes over the lifetime of an organism. This review explores recent advances in whole-organ…
Estimation of Secondary Household Attack Rates for Emergent Spike L452R Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants Detected by Genomic Surveillance at a Community-Based Testing Site in San Francisco Open
Background Sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new …
Estimation of secondary household attack rates for emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco Open
Background Sequencing of the SARS-CoV-2 viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities. Methods SARS-Co…
View article: A minimal model for household-based testing and tracing in epidemics
A minimal model for household-based testing and tracing in epidemics Open
In a previous work (Huber et al. 2020 Phys. Biol. 17 065010), we discussed virus transmission dynamics modified by a uniform clustering of contacts in the population: close contacts within households and more distant contacts between house…
Molecular hallmarks of heterochronic parabiosis at single cell resolution Open
Slowing or reversing biological ageing would have major implications for mitigating disease risk and maintaining vitality. While an increasing number of interventions show promise for rejuvenation, the effectiveness on disparate cell types…