A5079945791- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Cancer Diagnosis and Treatment
- Cancer Genomics and Diagnostics
- Diabetes Management and Research
- Invertebrate Immune Response Mechanisms
- Head and Neck Cancer Studies
- Genetic Mapping and Diversity in Plants and Animals
- Diabetes and associated disorders
- Bioinformatics and Genomic Networks
- Tumors and Oncological Cases
- Metabolism, Diabetes, and Cancer
- Glioma Diagnosis and Treatment
- Molecular Biology Techniques and Applications
- Cancer Mechanisms and Therapy
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Gut microbiota and health
- Radiomics and Machine Learning in Medical Imaging
- Neurological and metabolic disorders
Tempus Labs (United States)
2020-2023
Centre for Genomic Regulation
2014-2022
Stanford University
2018-2021
Barcelona Institute for Science and Technology
2018-2020
Pompeu Fabra University
2014-2020
Institute of Science and Technology
2019-2020
University of Florence
2005
Significance To date, various studies have found similarities between humans and mice on a molecular level, indeed, the murine model serves as an important experimental system for biomedical science. In this study of broad number tissues mice, high-throughput sequencing assays transcriptome epigenome reveal that, in general, differences dominate two species. These findings provide basis understanding phenotypes responses to conditions mice.
A BLUEPRINT of immune cell development To determine the epigenetic mechanisms that direct blood cells to develop into many components our system, consortium examined regulation DNA and RNA transcription dissect molecular traits govern differentiation. By inducing responses, Saeed et al. document changes in genome underlie Cheng demonstrate trained monocytes are highly dependent on breakdown sugars presence oxygen, which allows produce energy needed mount an response. Chen examine transcripts...
Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate impact PMI on expression using data from multiple donors obtained GTEx project. find that many genes change over relatively short PMIs in tissue-specific manner, but this potentially confounding effect biological analysis be minimized taking into account...
Diabetes is an increasing problem worldwide; almost 30 million people, nearly 10% of the population, in United States are diagnosed with diabetes. Another 84 prediabetic, and without intervention, up to 70% these individuals may progress type 2 Current methods for quantifying blood glucose dysregulation diabetes prediabetes limited by reliance on single-time-point measurements or average measures overall glycemia neglect dynamics. We have used continuous monitoring (CGM) evaluate frequency...
We present ggsashimi, a command-line tool for the visualization of splicing events across multiple samples. Given specified genomic region, ggsashimi creates sashimi plots individual RNA-seq experiments as well aggregated groups experiments, feature unique to this software. Compared existing versions programs generating plots, it uses popular bioinformatics file formats, is annotation-independent, and allows even large regions by scaling down segments between splice sites. freely available...
A comparison of transcriptional profiles derived from different tissues in a given species or among assumes that commonalities reflect evolutionarily conserved programs and differences tissue responses to environmental conditions developmental program staging. Apparently conflicting results have been published regarding whether organ-specific patterns dominate over species-specific patterns, vice versa, making it unclear what extent the biology organism can be extrapolated another. These...
Mice have been a long-standing model for human biology and disease. Here we characterize, by RNA sequencing, the transcriptional profiles of large heterogeneous collection mouse tissues, augmenting transcriptome with thousands novel transcript candidates. Comparison in cell lines reveals substantial conservation programmes, uncovers distinct class genes levels expression that constrained early vertebrate evolution. This core set captures fraction output mammalian cells, participates basic...
Cancers assume a variety of distinct histologies, and may originate from myriad sites including solid organs, hematopoietic cells, connective tissue. Clinical decision-making based on consensus guidelines such as the National Comprehensive Cancer Network (NCCN) is often predicated specific histologic anatomic diagnosis, supported by clinical features pathologist interpretation morphology immunohistochemical (IHC) staining patterns. However, in patients with nonspecific morphologic IHC...
We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these reveals that most body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components many tissues organs. Based on gene expression, types redefine histological by been traditionally classified. identified genes whose expression is specific to types, genes, we...
Natural Antisense Transcripts (NATs) are long non-coding RNAs (lncRNAs) that overlap coding genes in the opposite strand. NATs roles have been related to gene regulation through different mechanisms, including post-transcriptional RNA processing. With aim identify with potential regulatory function during fly development, we generated RNA-Seq data Drosophila developing tissues and found bsAS , one of most highly expressed lncRNAs wing. is antisense bs/DSRF a involved wing development neural...
Drosophila l(3)mbt malignant brain tumors present sexual dimorphism.
Abstract Background During development, most cells undergo striking changes in order to develop into functional tissues. All along this process, the identity of each tissue arises from particular combination regulatory transcription factors that specifically control expression relevant genes for growth, pattern formation and differentiation. In scenario, regulation gene turns out be essential determine cell fate specificity. Results To characterize dynamic transcriptional profiles during...
3077 Background: While targeted DNA-seq can detect clinically actionable fusions in tumor tissue samples, technical and analytical challenges may give rise to false negatives. RNA-based, whole-exome sequencing provides a complementary method for fusion detection, improve the identification of variants. In this study, we quantify benefit using large, real-world clinical dataset assess detected from RNA conjunction with DNA profiling. Methods: Using Tempus Research Database, retrospectively...
We characterized by RNA-seq the transcriptional profiles of a large and heterogeneous collection mouse tissues, augmenting transcriptome with thousands novel transcript candidates. Comparison obtained in human cell lines reveals substantial conservation programs, uncovers distinct class genes levels expression across types species, that have been constrained early vertebrate evolution. This core set capture constant fraction output mammalian cells, participates basic functional structural...
Abstract We have produced RNA sequencing data for a number of primary cells from different locations in the human body. The clustering these reveals that most body share few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural and blood cells. These act as basic components many tissues organs. Based on gene expression, types redefine histological by been traditionally classified. identified genes whose expression is specific to...
Abstract Background: Tumors of unknown origin account for up to 5% newly diagnosed cancers and the average survival time is 9 12 months from diagnosis. Establishing tumor type subtype guides standard care treatment several NCCN targeted therapy guidelines. Methods: Targeted DNA sequencing more than 500 cancer-associated genes exome-capture RNA was carried out in 25,000 fresh frozen or paraffin embedded samples, including both primary metastatic tumors. Mutations, copy number variants, viral...
Abstract Cancers assume a variety of distinct histologies and may originate from myriad sites including solid organs, hematopoietic cells, connective tissue. Clinical decision making based on consensus guidelines such as NCCN is often predicated specific histologic anatomic diagnosis, supported by clinical features pathologist interpretation morphology immunohistochemical (IHC) staining patterns. However, in patients with nonspecific morphologic IHC findings—in addition to ambiguous...
The formation of chimeric transcripts (chimeras) has been widely reported [1,2,3]. Some them reflect underlying chromosomal rearrangements [4] or are the results propensity reverse transcriptase to engage in template switching [5]. However, a proportion cases genuinely appear correspond trans-splicing RNAs, as previously described [6,7]. Here, we use ENCODE and mouse deeply sequenced bio-replicated RNaseq data from 18 human 30 samples, ChimPipe program identify chimeras occurring multiple...