A5026426674- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Chromosomal and Genetic Variations
- Developmental Biology and Gene Regulation
- Cancer-related molecular mechanisms research
- Epigenetics and DNA Methylation
- Cancer-related gene regulation
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Animal Genetics and Reproduction
- Plant Molecular Biology Research
- Gene Regulatory Network Analysis
- Genetics and Neurodevelopmental Disorders
- Viral Infectious Diseases and Gene Expression in Insects
- Insect Resistance and Genetics
Princeton University
2020-2022
Cold Spring Harbor Laboratory
2012-2017
Universitat Pompeu Fabra
2012
Dana-Farber Cancer Institute
2012
Pacific Biosciences (United States)
2012
Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because the non-contiguous transcript structure, relatively short read lengths constantly increasing throughput sequencing technologies. Currently available aligners suffer from high mapping error rates, low speed, length limitation biases. Results: To align our large (>80 billon reads) ENCODE Transcriptome dataset, we developed Spliced Transcripts Alignment to Reference (STAR) software...
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue these is not yet available their characteristic localizations also poorly understood. Because RNA represents direct output genetic information encoded by genomes a significant proportion cell's regulatory capabilities focused on its synthesis, processing, transport, modification translation, generation such crucial for...
The classic organization of a gene structure has followed the Jacob and Monod bacterial model proposed more than 50 years ago. Since then, empirical determinations complexity transcriptomes found in yeast to human blurred definition physical boundaries genes. Using multiple analysis approaches we have characterized individual mapping on chromosomes 21 22. Analyses locations 5′ 3′ transcriptional termini 492 protein coding genes revealed that for 85% these extend beyond current annotated...
Past studies offer contradictory claims for the role of genome organization in regulation gene activity. Here, we show through high-resolution chromosome conformation analysis that
Many eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating and deciphering their individual regulatory dynamics is critical for gene profiling applications our understanding of complexity. We introduce RAMPAGE, a novel promoter activity approach that combines extremely specific 5'-complete cDNA sequencing an integrated data analysis workflow, to address the limitations current techniques. RAMPAGE features...
Abstract RNA annotation and mapping of promoters for analysis gene expression (RAMPAGE) is a method that harnesses highly specific sequencing 5′‐complete complementary DNAs to identify transcription start sites (TSSs) genome‐wide. Although TSS has historically relied on detection cDNAs, current genome‐wide approaches typically have limited specificity provide only scarce information regarding transcript structure. RAMPAGE allows stringent selection molecules, thus allowing base‐resolution...
Multicellular development is driven by regulatory programs that orchestrate the transcription of protein-coding and noncoding genes. To decipher this genomic code, to investigate developmental relevance transcription, we compared genome-wide promoter activity throughout embryogenesis in 5 Drosophila species. Core promoters, generally not thought play a significant role, fact impart restrictions on timing gene expression global scale. We propose hierarchical model which core promoters define...
Multicellular development is largely determined by transcriptional regulatory programs that orchestrate the expression of thousands protein-coding and noncoding genes. To decipher genomic code specifies these programs, to investigate globally developmental relevance transcription, we profiled genome-wide promoter activity throughout embryonic in 5 Drosophila species. We show core promoters, generally not thought play a significant role, fact impart broad restrictions on timing gene scale....