A5031236248- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Neural dynamics and brain function
- EEG and Brain-Computer Interfaces
- Advanced Memory and Neural Computing
- Nicotinic Acetylcholine Receptors Study
- Click Chemistry and Applications
- Cancer Genomics and Diagnostics
- Synthesis and Biological Evaluation
- Chemical Synthesis and Analysis
- Gene expression and cancer classification
- Receptor Mechanisms and Signaling
- CRISPR and Genetic Engineering
- Monoclonal and Polyclonal Antibodies Research
- Tryptophan and brain disorders
- Bacteriophages and microbial interactions
- Viral gastroenteritis research and epidemiology
- Neuroscience and Neuropharmacology Research
- Biotin and Related Studies
- Animal Vocal Communication and Behavior
- Sports Dynamics and Biomechanics
- Data Visualization and Analytics
- Virus-based gene therapy research
- Molecular Sensors and Ion Detection
California Institute of Technology
2020-2025
Broad Institute
2025
Harvard University
2025
Leiden University
2021-2023
Pasadena City College
2023
ORCID
2022
Despite recent therapeutic advances, metastatic castration-resistant prostate cancer (mCRPC) remains lethal. Chimeric antigen receptor (CAR) T cell therapies have demonstrated durable remissions in hematological malignancies. We report results from a phase 1, first-in-human study of stem (PSCA)-directed CAR cells men with mCRPC. The starting dose level (DL) was 100 million (M) without lymphodepletion (LD), followed by incorporation LD. primary end points were safety and dose-limiting...
Abstract Exploratory spatial data analysis (ESDA) can be a powerful approach to understanding single-cell genomics datasets, but it is not yet part of standard workflows. In particular, geospatial analyses, which have been developed and refined for decades, fully adapted applied analysis. We introduce the Voyager platform, systematically brings ESDA tradition (spatial) -omics, with local, bivariate, multivariate methods commonly united by uniform user interface. Using Voyager, we showcase...
A recurring challenge in interpreting genomic data is the assessment of results context existing reference databases. With increasing number command line and Python users, there a need for tools implementing automated, easy programmatic access to curated information stored diverse collection large, public databases.gget free open-source tool package that enables efficient querying databases, such as Ensembl. gget consists separate but interoperable modules, each designed facilitate one type...
Summary Standard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting raw read data into cell-gene count matrices through sequence alignment, followed by analyses including filtering, highly variable gene selection, dimensionality reduction, clustering, and differential expression analysis. Seurat Scanpy are the most widely-used packages implementing such workflows, generally thought to implement individual steps similarly. We investigate in detail algorithms...
Nicotinic partial agonists provide an accepted aid for smoking cessation and thus contribute to decreasing tobacco-related disease. Improved drugs constitute a continued area of study. However, there remains no reductionist method examine the cellular subcellular pharmacokinetic properties these compounds in living cells. Here, we developed new intensity-based drug-sensing fluorescent reporters (iDrugSnFRs) nicotinic dianicline, cytisine, two cytisine derivatives – 10-fluorocytisine...
Abstract The term “RNA-seq” refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, single cells, or nuclei. kallisto, bustools, and kb-python programs are free, open-source software tools for performing this analysis together can produce gene expression quantification raw reads. quantifications be individualized multiple samples, both. Additionally, these allow values classified as originating nascent mature species, making...
Pathogen genomic analysis is central to tracking, understanding, and containing outbreaks, but complexity high costs of state-of-the-art (SOTA) phylogenetic tools limit global access impact. We introduce Delphy, an exact reformulation Bayesian phylogenetics designed transform its speed, scalability accessibility while retaining SOTA accuracy. Delphy's data structure, Explicit Mutation Annotated Tree, exploits the sequence similarity in large-scale epidemic datasets for efficient tree...
Maintaining motor behaviors throughout life is crucial for an individual’s survival and reproductive success. The neuronal mechanisms that preserve behavior are poorly understood. To address this question, we focused on the zebra finch, a bird produces highly stereotypical song after learning it as juvenile. Using cell-specific viral vectors, chronically silenced inhibitory neurons in pre-motor nucleus called high vocal center (HVC), which caused drastic degradation. However, producing...
Maintaining motor behaviors throughout life is crucial for an individual’s survival and reproductive success. The neuronal mechanisms that preserve behavior are poorly understood. To address this question, we focused on the zebra finch, a bird produces highly stereotypical song after learning it as juvenile. Using cell-specific viral vectors, chronically silenced inhibitory neurons in pre-motor nucleus called high vocal center (HVC), which caused drastic degradation. However, producing...
Selective serotonin reuptake inhibitors (SSRIs) are the most prescribed treatment for individuals experiencing major depressive disorder. The therapeutic mechanisms that take place before, during, or after SSRIs bind transporter (SERT) poorly understood, partially because no studies exist on cellular and subcellular pharmacokinetic properties of in living cells. We studied escitalopram fluoxetine using new intensity-based, drug-sensing fluorescent reporters targeted to plasma membrane,...
We examine a series of articles on honeybee odometry and navigation published between 1996 2010, find inconsistencies in results, duplicated figures, indications data manipulation, incorrect calculations. This suggests that redoing the experiments question is warranted.
There are an estimated 300,000 mammalian viruses from which infectious diseases in humans may arise. They inhabit human tissues such as the lungs, blood, and brain often remain undetected. Efficient accurate detection of viral infection is vital to understanding its impact on health make predictions limit adverse effects, future epidemics. The increasing use high-throughput sequencing methods research, agriculture, healthcare provides opportunity for cost-effective surveillance diversity...
Abstract Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput can, in principle, meet these demands, present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, clinical use HMSAs requires overcoming several computational, statistical engineering challenges. Using recently...
Abstract Motivation Eukaryotic linear motifs (ELMs), or Short Linear Motifs, are protein interaction modules that play an essential role in cellular processes and signaling networks often involved diseases like cancer. The ELM database is a collection of manually curated motif knowledge from scientific papers. It has become crucial resource for investigating biology recognizing candidate ELMs novel amino acid sequences. Users can search sequences UniProt Accessions on the web interface....
Abstract Motivation A recurring challenge in interpreting genomic data is the assessment of results context existing reference databases. Currently, there no tool implementing automated, easy programmatic access to curated information stored a diverse collection large, public Results gget free and open-source command-line Python package that enables efficient querying databases, such as Ensembl. consists separate but interoperable modules, each designed facilitate one type database required...
Scalable, inexpensive, accurate, and secure testing for SARS-CoV-2 infection is crucial control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays that rely on high-throughput (HMSAs) can, in principle, meet these demands, present promising alternatives to currently used RT-qPCR-based tests. However, analysis interpretation HMSAs requires overcoming several computational statistical challenges. Using recently acquired experimental data, we validate an...
Maintaining motor skills is crucial for an animal's survival, enabling it to endure diverse perturbations throughout its lifespan, such as those caused by trauma, disease, and aging. What mechanisms orchestrate brain circuit reorganization recovery preserve the stability of behavior despite prolonged presence a disturbance? To investigate this question, we chronically silenced significant fraction inhibitory neurons in nucleus necessary singing zebra finches. Song finches complex, learned...
ABSTRACT Nicotinic partial agonists provide an accepted aid for smoking cessation and thus contribute to decreasing tobacco-related disease. Improved drugs constitute a continued area of study. However, there remains no reductionist method examine the cellular subcellular pharmacokinetic properties these compounds in living cells. Here, we developed new intensity-based drug sensing fluorescent reporters (“iDrugSnFRs”) nicotinic dianicline, cytisine, two cytisine derivatives –...
ABSTRACT Selective serotonin reuptake inhibitors (SSRIs) are the most prescribed treatment for individuals experiencing major depressive disorder (MDD). The therapeutic mechanisms that take place before, during, or after SSRIs bind transporter (SERT) poorly understood, partially because no studies exist of cellular and subcellular pharmacokinetic properties in living cells. We studied escitalopram fluoxetine using new intensity- based drug-sensing fluorescent reporters (“iDrugSnFRs”)...
Maintaining motor behaviors throughout life is crucial for an individual's survival and reproductive success. The neuronal mechanisms that preserve behavior are poorly understood. To address this question, we focused on the zebra finch, a bird produces highly stereotypical song after learning it as juvenile. Using cell-specific viral vectors, chronically silenced inhibitory neurons in pre-motor nucleus called high vocal center (HVC), which caused drastic degradation. However, producing...
Maintaining motor skills is crucial for an animal's survival, enabling it to endure diverse perturbations throughout its lifespan, such as trauma, disease, and aging. What mechanisms orchestrate brain circuit reorganization recovery preserve the stability of behavior despite continued presence a disturbance? To investigate this question, we chronically silenced fraction inhibitory neurons in pre-motor necessary singing zebra finches. This manipulation altered activity severely perturbed...
Abstract Motivation Eukaryotic linear motifs (ELMs), or Short Linear Motifs (SLiMs), are protein interaction modules that play an essential role in cellular processes and signaling networks often involved diseases like cancer. The ELM database is a collection of manually curated motif knowledge from scientific papers. It has become crucial resource for cataloging biology recognizing candidate ELMs novel amino acid sequences. Users can search sequences UniProt IDs on the web interface....