Aaron E. Lin
A5033461529- Viral Infections and Outbreaks Research
- Viral Infections and Vectors
- Viral gastroenteritis research and epidemiology
- COVID-19 epidemiological studies
- Epigenetics and DNA Methylation
- Bacteriophages and microbial interactions
- interferon and immune responses
- SARS-CoV-2 and COVID-19 Research
- RNA Research and Splicing
- Immune Cell Function and Interaction
- Disaster Response and Management
- CRISPR and Genetic Engineering
- Natural Language Processing Techniques
- Immune responses and vaccinations
- RNA and protein synthesis mechanisms
- Herpesvirus Infections and Treatments
- Immune cells in cancer
- Cytokine Signaling Pathways and Interactions
- Mosquito-borne diseases and control
- Genomics and Phylogenetic Studies
- Respiratory viral infections research
- Cancer-related molecular mechanisms research
- Gut microbiota and health
- CAR-T cell therapy research
- T-cell and B-cell Immunology
Princeton University
2013-2024
National Institute of Biomedical Imaging and Bioengineering
2022-2024
National Institutes of Health
2022-2024
Broad Institute
2015-2023
Center for Systems Biology
2015-2023
Harvard University
2015-2023
IT University of Copenhagen
2023
Tokyo Institute of Technology
2023
Administration for Community Living
2023
American Jewish Committee
2023
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recently identified that causes the disease known as 2019 (COVID-19). Despite urgent need, we still do not fully understand molecular basis of SARS-CoV-2 pathogenesis. Here, comprehensively define interactions between proteins and human RNAs. NSP16 binds to mRNA recognition domains U1 U2 splicing RNAs acts suppress global upon infection. NSP1 18S ribosomal RNA in entry channel ribosome leads inhibition translation Finally,...
Highlights•Thousands of potential Cas13 target sites are present in ssRNA viral genomes•Cas13 is a potent antiviral against three diverse viruses cell culture•Optimal and design criteria identified via genome-wide screen•Companion Cas13-based diagnostics can be used to assess the effects targetingSummaryThe CRISPR effector could an effective for single-stranded RNA (ssRNA) because it programmably cleaves RNAs complementary its (crRNA). Here, we computationally identify thousands crRNA...
The 2013–2015 Ebola virus disease (EVD) epidemic is caused by the Makona variant of (EBOV). Early in epidemic, genome sequencing provided insights into evolution and transmission offered important information for outbreak response. Here, we analyze sequences from 232 patients sampled over 7 months Sierra Leone, along with 86 previously released genomes earlier epidemic. We confirm sustained human-to-human within Leone find no evidence import or export EBOV across national borders after its...
Phylogenetics of superspreading One important characteristic coronavirus epidemiology is the occurrence events. These are marked by a disproportionate number cases originating from often-times asymptomatic individuals. Using rich sequence dataset early stages Boston outbreak, Lemieux et al. identified events in specific settings and analyzed them phylogenetically (see Perspective Alizon). ancestral trait inference, authors several importation events, further investigated context contribution...
Aging | doi:10.18632/aging.205581. Edwin Lee, Natàlia Carreras-Gallo, Leilani Lopez, Logan Turner, Aaron Lin, Tavis L. Mendez, Hannah Went, Alan Tomusiak, Eric Verdin, Michael Corley, Lishomwa Ndhlovu, Ryan Smith, Varun B. Dwaraka
Abstract Recent outbreaks of viral hemorrhagic fevers (VHFs), including Ebola virus disease (EVD) and Lassa fever (LF), highlight the urgent need for sensitive, deployable tests to diagnose these devastating human diseases. Here we develop CRISPR-Cas13a-based (SHERLOCK) diagnostics targeting (EBOV) (LASV), with both fluorescent lateral flow readouts. We demonstrate on laboratory clinical samples sensitivity assays capacity SHERLOCK platform handle virus-specific diagnostic challenges....
Ebola virus (EBOV) causes epidemics with high mortality yet remains understudied due to the challenge of experimentation in high-containment and outbreak settings. Here, we used single-cell transcriptomics CyTOF-based protein quantification characterize peripheral immune cells during EBOV infection rhesus monkeys. We obtained 100,000 transcriptomes 15,000,000 profiles, finding that immature, proliferative monocyte-lineage reduced antigen-presentation capacity replace conventional monocyte...
Abstract Bacterial populations are highly adaptive. They can respond to stress and survive in shifting environments. How the behaviours of individual bacteria vary during stress, however, is poorly understood. To identify characterize rare bacterial subpopulations, technologies for single-cell transcriptional profiling have been developed. Existing approaches show some degree limitation, example, terms number cells or transcripts that be profiled. Due part these limitations, few conditions...
ABSTRACT Until recently, Ebola virus (EBOV) was a rarely encountered human pathogen that caused disease among small populations with extraordinarily high lethality. At the end of 2013, EBOV initiated an unprecedented outbreak in West Africa is still ongoing and has already thousands deaths. Recent studies revealed genomic changes this particular variant undergoes over time during human-to-human transmission. Here we highlight might negatively impact efficacy currently available...
ABSTRACT Biological aging is a multifactorial process involving complex interactions of cellular and biochemical processes that reflected in omic profiles. Using common clinical laboratory measures ~30,000 individuals from the MGB-Biobank, we developed robust, predictive biological phenotype, EMRAge , balances biomarkers with overall mortality risk can be broadly recapitulated across EMRs. We then applied elastic-net regression to model DNA-methylation (DNAm) multiple omics, generating...
T cells specific for the cytochrome c Ag are widely used to investigate many aspects of TCR specificity and interactions with peptide-MHC, but structural information has long been elusive. In this study, we present structures well-studied 2B4 TCR, as well a naturally occurring variant 5c.c7 226, which is cross-reactive more than half possible substitutions at all three TCR-sensitive residues on peptide Ag. These alone in complex peptide-MHC ligands allow us reassess prior mutagenesis...
Ebola virus is the causative agent of a severe syndrome in humans with fatality rate that can approach 90 %. During infection, host immune response thought to become dysregulated, but mechanisms through which this happens are not entirely understood. In study, we analyze RNA sequencing data determine infection circulating cells. Approximately half 100 genes strongest early increases expression were interferon-stimulated genes, such as ISG15, OAS1, IFIT2, HERC5, MX1 and DHX58. Other highly...
Personalized support for students is a gold standard in education, but it scales poorly with the number of students. Prior work on learnersourcing presented an approach learners to engage human computation tasks while trying learn new skill. Our key insight that students, through their own experience struggling particular problem, can become experts optimizations they implement or bugs resolve. These then generate hints fellow based expertise. We present workflows harvest and organize...
Abstract SARS-CoV-2 has caused a severe, ongoing outbreak of COVID-19 in Massachusetts with 111,070 confirmed cases and 8,433 deaths as August 1, 2020. To investigate the introduction, spread, epidemiology Boston area, we sequenced analyzed 772 complete genomes from region, including nearly all within first week epidemic hundreds major outbreaks at conference, nursing facility, among homeless shelter guests staff. The data reveal over 80 introductions into predominantly elsewhere United...
Abstract Lassa fever, a hemorrhagic fever caused by virus (LASV), is endemic in West Africa. It difficult to distinguish febrile illnesses that are common Africa from based solely on patient’s clinical presentation. The field performance of recombinant antigen-based immunoassays was compared quantitative polymerase chain assays (qPCRs) using samples subjects meeting the case definition presenting Kenema Government Hospital Sierra Leone. (ReLASV) enzyme-linked immunosorbant assay (ELISA) for...
Abstract Background Geroscience focuses on interventions to mitigate molecular changes associated with aging. Lifestyle modifications, medications, and social factors influence the aging process, yet complex mechanisms require an in-depth exploration of epigenetic landscape. The specific clock predictor effects a vegan diet, compared omnivorous remain underexplored despite potential impacts aging-related outcomes. Methods This study examined impact entirely plant-based or healthy diet over 8...
Much like the host cells they infect, viruses must also regulate their life cycles. Herpes simples virus type 1 (HSV-1), a prominent human pathogen, uses promoter-rich genome in conjunction with multiple viral trans-activating factors. Following entry into cells, virion-associated outer tegument proteins pUL46 and pUL47 act to increase expression of immediate-early (α) genes, thereby helping initiate infection cycle. Because has gone largely unstudied, we employed hybrid mass...
Abstract Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and pivotal mediators of the immune response, yet little is known about their properties at single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from Ebola virus (EBOV) infected not-infected rhesus macaques identified 3979 novel lncRNAs. To profile lncRNA expression dynamics circulating single-cells during EBOV infection, design metric, Upsilon, to estimate cell-type specificity. Our...
Viral infections can alter the cellular epigenetic landscape, through modulation of either DNA methylation profiles or chromatin remodeling enzymes and histone modifications. These changes act to promote viral replication host defense. Herpes simplex virus type 1 (HSV‐1) is a prominent human pathogen, which relies on interactions with factors for efficient spread. Nevertheless, knowledge regarding its remains limited. Here, we used fluorescently‐labeled viruses in conjunction immunoaffinity...
In one patient over time, we found that concentration of Ebola virus RNA in semen during recovery is remarkably higher than blood at peak illness. Virus replication-competent with no change viral genome time. Presence sense suggests replication cells present semen.