A5024923108- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Single-cell and spatial transcriptomics
- MicroRNA in disease regulation
- Gene expression and cancer classification
- Genetic diversity and population structure
- Ubiquitin and proteasome pathways
- Cancer Genomics and Diagnostics
- Genetic Mapping and Diversity in Plants and Animals
- Epigenetics and DNA Methylation
- Chromosomal and Genetic Variations
- Veterinary Oncology Research
- Vascular Tumors and Angiosarcomas
- Cardiac tumors and thrombi
- Heat shock proteins research
- Protein Degradation and Inhibitors
- CRISPR and Genetic Engineering
- Retinoids in leukemia and cellular processes
- Cancer-related Molecular Pathways
- Animal Genetics and Reproduction
Cornell University
2016-2025
Baker Engineering (United States)
2024
Département Santé Animale
2020-2024
New York State College of Veterinary Medicine
2019-2024
Ithaca College
2020-2022
Institute for Systems Biology
2019
University of Connecticut
2014-2019
Cold Spring Harbor Laboratory
2014
Harvard University
2014
SUNY Upstate Medical University
2007-2009
The complete genome sequences of an indigenous hunter-gatherer from Namibia's Kalahari Desert and a Bantu South Africa are presented in this issue, together with protein-coding regions three other groups the Kalahari. Analysis genetic variance what is probably oldest known modern human lineage will contribute to understanding diversity, facilitate inclusion southern Africans medical genomics research projects. Initial observations data include fact that Bushmen seem more different each...
We have integrated and analyzed a large number of data sets from variety genomic assays using novel computational pipeline to provide global view estrogen receptor 1 (ESR1; a.k.a. ERα) enhancers in MCF-7 human breast cancer cells. Using this approach, we defined class primary transcripts (eRNAs) that are transcribed uni- or bidirectionally binding sites (ERBSs) with an average transcription unit length ∼3–5 kb. The majority up-regulated by short treatments estradiol (i.e., 10, 25, 40 min)...
Inferring single-cell compositions and their contributions to global gene expression changes from bulk RNA sequencing (RNA-seq) datasets is a major challenge in oncology. Here we develop Bayesian cell proportion reconstruction inferred using statistical marginalization (BayesPrism), method predict cellular composition individual types RNA-seq, patient-derived, scRNA-seq as prior information. We conduct integrative analyses primary glioblastoma, head neck squamous carcinoma skin cutaneous...
Abstract Programs of gene expression are executed by a battery transcription factors that coordinate divergent from pair tightly linked core initiation regions promoters and enhancers. Here, to investigate how is reprogrammed upon stress, we measured nascent RNA synthesis at nucleotide-resolution, profiled histone H4 acetylation in human cells. Our results globally show the release promoter-proximal paused polymerase into elongation functions as critical switch which gene’s response stress...
Color pattern mimicry in Heliconius butterflies is a classic case study of complex trait adaptation via selection on few large effect genes. Association studies have linked color variation to handful noncoding regions, yet the presumptive cis-regulatory elements (CREs) that control patterning remain unknown. Here we combine chromatin assays, DNA sequence associations, and genome editing functionally characterize 5 gene optix . We were surprised find architecture characterized by pleiotropy...
Heat shock (HS) initiates rapid, extensive, and evolutionarily conserved changes in transcription that are accompanied by chromatin decondensation nucleosome loss at HS loci. Here we have employed situ Hi-C to determine how heat stress affects long-range conformation human Drosophila cells. We found compartments topologically associating domains (TADs) remain unchanged an acute HS. Knockdown of Shock Factor 1 (HSF1), the master transcriptional regulator response, identified HSF1-dependent...
Previous studies have shown that GAGA Factor (GAF) is enriched on promoters with paused RNA Polymerase II (Pol II), but its genome-wide function and mechanism of action remain largely uncharacterized. We assayed the levels transcriptionally-engaged polymerase using global run-on sequencing (GRO-seq) in control GAF-RNAi Drosophila S2 cells found promoter-proximal was significantly reduced a large subset where GAF occupancy by knock down. These show dramatic increase nucleosome upon depletion....
Our genomes encode a wealth of transcription initiation regions (TIRs) that can be identified by their distinctive patterns actively elongating RNA polymerase. We previously introduced dREG to identify TIRs using PRO-seq data. Here, we introduce an efficient new implementation uses data both uni- and bidirectionally transcribed with 70% improvement in accuracy, three- fourfold higher resolution, >100-fold increases computational efficiency. Using novel strategy based on statistical...
Major changes in chromosome number and structure are linked to a series of evolutionary phenomena, including intrinsic barriers gene flow or suppression recombination due chromosomal rearrangements. However, rearrangements can also affect the fundamental dynamics molecular evolution within populations by changing relationships between loci altering rates recombination. Here, we build chromosome-level assembly Eueides isabella and, together with recent Dryas iulia, examine consequences...
Abstract Background The concentrations of distinct types RNA in cells result from a dynamic equilibrium between synthesis and decay. Despite the critical importance decay rates, current approaches for measuring them are generally labor-intensive, limited sensitivity, and/or disruptive to normal cellular processes. Here, we introduce simple method estimating relative half-lives that is based on two standard widely available high-throughput assays: Precision Run-On sequencing (PRO-seq)...
Abstract During meiotic prophase I, spermatocytes must balance transcriptional activation with homologous recombination and chromosome synapsis, biological processes requiring extensive changes to chromatin state. We explored the interplay between accessibility transcription through I of mammalian meiosis by measuring genome-wide patterns accessibility, nascent transcription, processed mRNA. find that Pol II is loaded on maintained in a paused state early during I. In later stages, released...
Global run-on coupled with deep sequencing (GRO-seq) provides extensive information on the location and function of coding non-coding transcripts, including primary microRNAs (miRNAs), long RNAs (lncRNAs), enhancer (eRNAs), as well yet undiscovered classes transcripts. However, few computational tools tailored toward this new type data are available, limiting applicability GRO-seq for identifying novel transcription units.Here, we present groHMM, a tool in R, which defines boundaries units...