A5020438925- Single-cell and spatial transcriptomics
- Genetics, Aging, and Longevity in Model Organisms
- CRISPR and Genetic Engineering
- Cancer Genomics and Diagnostics
- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Cancer Cells and Metastasis
- Gene expression and cancer classification
- RNA Research and Splicing
- Gene Regulatory Network Analysis
- bioluminescence and chemiluminescence research
- Cell Image Analysis Techniques
- Chromosomal and Genetic Variations
- Evolution and Genetic Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Immune cells in cancer
- Bacterial biofilms and quorum sensing
- Molecular Biology Techniques and Applications
- Pluripotent Stem Cells Research
- Fungal and yeast genetics research
- Antimicrobial Resistance in Staphylococcus
- Bacillus and Francisella bacterial research
- RNA modifications and cancer
New York University
2016-2024
Institute for Systems Biology
2022-2024
NYU Langone Health
2017-2024
Indiana University School of Medicine
2019-2024
NYU Langone’s Laura and Isaac Perlmutter Cancer Center
2021-2024
Technion – Israel Institute of Technology
2010-2023
Institute of Genetics and Developmental Biology
2023
University of California, Berkeley
2023
Chinese Academy of Sciences
2023
University of Vienna
2023
High-throughput sequencing has allowed for unprecedented detail in gene expression analyses, yet its efficient application to single cells is challenged by the small starting amounts of RNA. We have developed CEL-Seq, a method overcoming this limitation barcoding and pooling samples before linearly amplifying mRNA with use one round vitro transcription. show that CEL-Seq gives more reproducible, linear, sensitive results than PCR-based amplification method. demonstrate power studying early...
Genes are often characterized dichotomously as either housekeeping or single-tissue specific. We conjectured that crucial functional information resides in genes with midrange profiles of expression.To obtain such novel genome-wide, we have determined the mRNA expression levels for one largest hitherto analyzed set 62 839 probesets 12 representative normal human tissues. Indeed, when using a newly defined graded tissue specificity index tau, valued between 0 and 1 tissue-specific genes,...
Single-cell transcriptomics requires a method that is sensitive, accurate, and reproducible. Here, we present CEL-Seq2, modified version of our CEL-Seq method, with threefold higher sensitivity, lower costs, less hands-on time. We implemented CEL-Seq2 on Fluidigm's C1 system, providing its first single-cell, on-chip barcoding detected gene expression changes accompanying the progression through cell cycle in mouse fibroblast cells. also compare Smart-Seq to demonstrate CEL-Seq2's increased...
Olfactory receptors likely constitute the largest gene superfamily in vertebrate genome. Here we present nearly complete human olfactory subgenome elucidated by mining genome draft with discovery algorithms. Over 900 receptor genes and pseudogenes (ORs) were identified, two-thirds of which not annotated previously. The number extrapolated ORs is good agreement previous theoretical predictions. sequence at least 63% disrupted what appears to be a random process pseudogene formation. 17...
Abstract During tumor progression, cancer cells come into contact with various non-tumor cell types, but it is unclear how tumors adapt to these new environments. Here, we integrate spatially resolved transcriptomics, single-cell RNA-seq, and single-nucleus RNA-seq characterize tumor-microenvironment interactions at the boundary. Using a zebrafish model of melanoma, identify distinct “interface” state where contacts neighboring tissues. This interface composed specialized microenvironment...
The testis expresses the largest number of genes any mammalian organ, a finding that has long puzzled molecular biologists. Our single-cell transcriptomic data human and mouse spermatogenesis provide evidence this widespread transcription maintains DNA sequence integrity in male germline by correcting damage through mechanism we term transcriptional scanning. We find expressed during display lower mutation rates on transcribed strand have low diversity population. Moreover, effect is...
Abstract The loss of the tail is among most notable anatomical changes to have occurred along evolutionary lineage leading humans and ‘anthropomorphous apes’ 1–3 , with a proposed role in contributing human bipedalism 4–6 . Yet, genetic mechanism that facilitated tail-loss evolution hominoids remains unknown. Here we present evidence an individual insertion Alu element genome hominoid ancestor may contributed evolution. We demonstrate this element—inserted into intron TBXT gene 7–9 —pairs...
KRASG12C inhibitors (adagrasib and sotorasib) have shown clinical promise in targeting KRASG12C-mutated lung cancers; however, most patients eventually develop resistance. In with adenocarcinoma STK11/LKB1 co-mutations, we find an enrichment of the squamous cell carcinoma gene signature pre-treatment biopsies correlates a poor response to adagrasib. Studies Lkb1-deficient KrasG12D cancer mouse models organoids treated KRAS reveal tumors invoke lineage plasticity program, adeno-to-squamous...
Recent experiments revealed large-scale differences in the transcription programs of related species, yet little is known about genetic basis underlying evolution gene expression and its contribution to phenotypic diversity. Here we describe a modulation yeast program that connected emergence capacity for rapid anaerobic growth. Genes coding mitochondrial cytoplasmic ribosomal proteins display strongly correlated pattern Candida albicans, but this correlation lost fermentative Saccharomyces...
Olfactory receptors (ORs) are the largest gene family in human genome. Although they expected to be expressed specifically olfactory tissues, some ectopic expression has been reported, with special emphasis on sperm and testis. The present study systematically explores patterns of OR genes a large number tissues assesses potential functional implication such expression.We analyzed hundreds mouse transcripts, via EST microarray data, several dozens tissues. Different had specific, relatively...
High-throughput single-cell RNA-Seq (scRNA-Seq) is a powerful approach for studying heterogeneous tissues and dynamic cellular processes. However, compared to bulk RNA-Seq, expression profiles are extremely noisy, as they only capture fraction of the transcripts present in cell. Here, we propose k-nearest neighbor smoothing (kNN-smoothing) algorithm, designed reduce noise by aggregating information from similar cells (neighbors) computationally efficient statistically tractable manner. The...