A5056756087- Single-cell and spatial transcriptomics
- Genetics and Neurodevelopmental Disorders
- Trypanosoma species research and implications
- Neuroinflammation and Neurodegeneration Mechanisms
- Advanced biosensing and bioanalysis techniques
- Lung Cancer Treatments and Mutations
- DNA Repair Mechanisms
- Neural dynamics and brain function
- Biosensors and Analytical Detection
- Mitochondrial Function and Pathology
- Helminth infection and control
- Neuroscience and Neuropharmacology Research
- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- Parasites and Host Interactions
- Genetic factors in colorectal cancer
- Research on Leishmaniasis Studies
- Reproductive Biology and Fertility
- Radiation Effects in Electronics
- Genomic variations and chromosomal abnormalities
- Gene Regulatory Network Analysis
- RNA modifications and cancer
- Chromosomal and Genetic Variations
Broad Institute
2022-2025
National Institute of Diabetes and Digestive and Kidney Diseases
2024-2025
National Institutes of Health
2024-2025
University of Vermont
2021
Ovulation is a spatiotemporally coordinated process that involves several tightly controlled events, including oocyte meiotic maturation, cumulus expansion, follicle wall rupture and repair, ovarian stroma remodeling. To date, no studies have detailed the precise window of ovulation at single-cell resolution. Here, we performed parallel RNA-seq spatial transcriptomics on paired mouse ovaries across an time course to map spatiotemporal profile cell types. We show major types exhibit...
Abstract The mammalian cerebral cortex comprises a complex neuronal network that maintains delicate balance between excitatory neurons and inhibitory interneurons. Previous studies, including our own research, have shown specific interneuron subtypes are closely associated with particular pyramidal neuron types, forming stereotyped local microcircuits. However, the developmental processes establish these precise networks not well understood. Here we show types instrumental in driving...
Abstract Microsatellite instability is responsible for the human repeat expansion diseases (REDs). The mutagenic process differs from classical cancer-associated microsatellite (MSI) in that it requires mismatch repair proteins normally protect against MSI. LIG4, an enzyme essential non-homologous end-joining (NHEJ), major pathway double-strand break (DSBR) mammalian cells, protects mouse models. Thus, NHEJ may compete with access to a common intermediate. This raises possibility involves...
Background: Understanding the biological mechanisms underlying differential responses to immunotherapy is critical for advancing treatment strategies in metastatic melanoma. We analyzed single-nucleus RNA sequencing data from 66 melanoma samples, including 18 with matched spatial transcriptomics via MERFISH, across sites such as lymph nodes, colon, skin, lung, brain, and liver. Our study aimed identify tumor-intrinsic transcriptional programs their association durable clinical benefit....
Abstract Background: Immune checkpoint inhibitor (ICI) therapies have markedly improved the prognosis for patients with stage III & IV metastatic melanoma by prolonging progression-free and overall survival rates. However, variability in immune evasion resistance mechanisms presents significant challenges to clinical efficacy of ICIs. This project aims define drivers immunotherapy response employing advanced genomic, single-cell mRNA analyses, spatial profiling techniques on tissue...
A long CGG-repeat tract in the
The mammalian cerebral cortex comprises a complex neuronal network that maintains delicate balance between excitatory neurons and inhibitory interneurons. Previous studies, including our own research, have shown specific interneuron subtypes are closely associated with particular pyramidal neuron types, forming stereotyped local microcircuits. However, the developmental processes establish these precise networks not well understood. Here we show types instrumental in driving terminal...
Serine/Threonine Kinase 11 (STK11) encodes an important tumor suppressor that is frequently mutated in lung adenocarcinoma. Clinical studies have shown mutations STK11 resulting loss of function correlate with resistance to anti-PD-1 monoclonal antibody therapy KRAS-driven non-small cell cancer (NSCLC), but the molecular mechanisms responsible remain unclear. Despite this uncertainty, functional status emerging as a reliable biomarker for predicting non-response NSCLC patients. The clinical...
More than 100 years since the first description of Chagas Disease and with over 29,000 new cases annually due to vector transmission (in 2010), American Trypanosomiasis remains a Neglected Tropical (NTD). This study presents most comprehensive Trypanosoma cruzi sampling in terms geographic locations triatomine species analyzed date includes both nuclear mitochondrial genomes. addresses gap information from North Central America. We incorporate previously published DNA sequence data two...
Imaging Spatial Transcriptomics techniques characterize gene expression in cells their native context by imaging barcoded probes for mRNA with single molecule resolution. However, the need to acquire many rounds of high-magnification data limits throughput and impact existing methods.We describe Joint Sparse method Transcriptomics, an algorithm decoding lower magnification than that used standard experimental workflows. incorporates codebook knowledge sparsity assumptions into optimization...
Abstract Microsatellite instability is responsible for the human Repeat Expansion Disorders. The mutation differs from classical cancer-associated microsatellite (MSI) in that it requires mismatch repair proteins normally protect against MSI. LIG4, an enzyme essential non-homologous end-joining (NHEJ), major pathway double-strand break (DSBR) mammalian cells, protects expansion mouse models. Thus, NHEJ may compete with access to a common intermediate. This raises possibility involves...
Motivation Imaging Spatial Transcriptomics (iST) techniques characterize gene expression in cells their native context by imaging barcoded probes for mRNA with single molecule resolution. However, the need to acquire many rounds of high-magnification data limits throughput and impact existing methods. Results We describe Joint Sparse method (JSIT), an algorithm decoding lower magnification IT than that used standard experimental workflows. JSIT incorporates codebook knowledge sparsity...