Nicolas Robine
A5024606831- Cancer Genomics and Diagnostics
- Pancreatic and Hepatic Oncology Research
- Molecular Biology Techniques and Applications
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Genomics and Rare Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Genetic factors in colorectal cancer
- Cancer-related molecular mechanisms research
- Genetic Associations and Epidemiology
- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Epigenetics and DNA Methylation
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- MicroRNA in disease regulation
- BRCA gene mutations in cancer
- Global Cancer Incidence and Screening
- Cancer Cells and Metastasis
- Acute Myeloid Leukemia Research
- RNA Interference and Gene Delivery
- Lung Cancer Treatments and Mutations
- Protein Degradation and Inhibitors
- Cholangiocarcinoma and Gallbladder Cancer Studies
New York Genome Center
2016-2025
Weill Cornell Medicine
2017-2023
Texas Health Dallas
2023
Lander Institute
2023
Cornell University
2017-2023
ORCID
2021
Memorial Sloan Kettering Cancer Center
2010-2017
Columbia University Irving Medical Center
2017
Howard Hughes Medical Institute
2017
IBM Research - Thomas J. Watson Research Center
2017
From Genome to Regulatory Networks For biologists, having a genome in hand is only the beginning—much more investigation still needed characterize how used help produce functional organism (see Perspective by Blaxter ). In this vein, Gerstein et al. (p. 1775 ) summarize for Caenorhabditis elegans genome, and The modENCODE Consortium 1787 Drosophila melanogaster full transcriptome analyses over developmental stages, genome-wide identification of transcription factor binding sites,...
Pancreatic cancer is the most lethal common solid malignancy. Systemic therapies are often ineffective, and predictive biomarkers to guide treatment urgently needed. We generated a pancreatic patient-derived organoid (PDO) library that recapitulates mutational spectrum transcriptional subtypes of primary cancer. New driver oncogenes were nominated transcriptomic analyses revealed unique clusters. PDOs exhibited heterogeneous responses standard-of-care chemotherapeutics investigational...
Oncogenic Suspect Exposed It can be difficult logistically to study the genomics of rare variants common cancers. Nevertheless, Honeyman et al. (p. 1010 ) studied fibrolamellar hepatocellular carcinoma (FL-HCC), a and poorly understood liver tumor that affects adolescents young adults for which there is no effective treatment. FL-HCCs from 15 patients all expressed chimeric RNA transcript protein containing sequences molecular chaperone fused in frame with catalytic domain kinase A. The...
Canonical animal microRNAs (miRNAs) are generated by sequential cleavage of precursor substrates the Drosha and Dicer RNase III enzymes. Several variant pathways exploit other RNA metabolic activities to generate functional miRNAs. However, all these culminate in cleavage, suggesting that this is a unifying feature miRNA biogenesis. Here, we show maturation miR-451, perfectly conserved among vertebrates, independent Dicer. Instead, structure-function knockdown studies indicate generates...
Human papillomavirus (HPV) is a necessary but insufficient cause of subset oral squamous cell carcinomas (OSCCs) that increasing markedly in frequency. To identify contributory, secondary genetic alterations these cancers, we used comprehensive genomics methods to compare 149 HPV-positive and 335 HPV-negative OSCC tumor/normal pairs. Different behavioral risk factors underlying the two types were reflected distinctive genomic mutational signatures. In OSCCs, signatures APOBEC cytosine...
In this study, we sought to refine histologic scoring of rheumatoid arthritis (RA) synovial tissue by training with gene expression data and machine learning.
Women of sub-Saharan African descent have disproportionately higher incidence triple-negative breast cancer (TNBC) and TNBC-specific mortality across all populations. Population studies show racial differences in TNBC biology, including prevalence basal-like quadruple-negative subtypes Americans (AA). However, previous investigations relied on self-reported race (SRR) primarily U.S. Due to heterogeneous genetic admixture biological consequences social determinants, the true association...
Since the initial annotation of miRNAs from cloned short RNAs by Ambros, Tuschl, and Bartel groups in 2001, more than a hundred studies have sought to identify additional various species. We report here meta-analysis RNA data Drosophila melanogaster , aggregating published libraries with 76 sets that we generated for modENCODE project. In total, began 1 billion raw reads 187 comprising diverse developmental stages, specific tissue- cell-types, mutant conditions, and/or Argonaute...
Piwi proteins, a subclass of Argonaute-family carry approximately 24-30-nt Piwi-interacting RNAs (piRNAs) that mediate gonadal defense against transposable elements (TEs). We analyzed the Drosophila ovary somatic sheet (OSS) cell line and found it expresses miRNAs, endogenous small interfering (endo-siRNAs), piRNAs in abundance. In contrast to intact gonads, which contain mixtures germline types express different Piwi-class OSS cells are homogenous population only PIWI primary piRNAs....
Reliable detection of somatic variations is critical importance in cancer research. Here we present Lancet, an accurate and sensitive variant caller, which detects SNVs indels by jointly analyzing reads from tumor matched normal samples using colored de Bruijn graphs. We demonstrate, through extensive experimental comparison on synthetic real whole-genome sequencing datasets, that Lancet has better accuracy, especially for indel detection, than widely used callers, such as MuTect, MuTect2,...
Abstract Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read offers the advantage of better mappability and long-range phasing, which results substantial improvements germline SV detection. However, long-read detection methods do not generalize well analysis SVs tumor genomes with complex rearrangements, heterogeneity, aneuploidy. Here, we present Severus: a method for accurate different types using phased breakpoint...
The evolution of isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) after standard-of-care therapy remains poorly understood. Here we analyzed matched primary and recurrent GBMs from 59 patients using single-nucleus RNA sequencing bulk DNA sequencing, assessing the longitudinal GBM ecosystem across layers cellular molecular heterogeneity. most consistent change was a lower malignant cell fraction at recurrence reciprocal increase in glial neuronal types tumor microenvironment (TME)....
In isocitrate dehydrogenase wildtype glioblastoma (GBM), cellular heterogeneity across and within tumors may drive therapeutic resistance. Here we analyzed 121 primary recurrent GBM samples from 59 patients using single-nucleus RNA sequencing bulk tumor DNA to characterize transcriptional heterogeneity. First, GBMs can be classified by their broad composition, encompassing malignant nonmalignant cell types. Second, in each type describe the diversity of states pathway activation,...
Abstract Motivation: Microarray-based CGH (Comparative Genomic Hybridization), transcriptome arrays and other large-scale genomic technologies are now routinely used to generate a vast amount of profiles. Exploratory analysis this data is crucial in helping understand the help form biological hypotheses. This step requires visualization meaningful way visualize results perform first level analyses. Results: We have developed graphical user interface for molecular It currently use at Institut...
The extensively studied cAMP-dependent protein kinase A (PKA) is involved in the regulation of critical cell processes, including metabolism, gene expression, and proliferation; consequentially, mis-regulation PKA signaling implicated tumorigenesis. Recent genomic studies have identified recurrent mutations catalytic subunit tumors associated with Cushing's syndrome, a kidney disorder leading to excessive cortisol production, also fibrolamellar hepatocellular carcinoma (FL-HCC), rare liver...
Abstract Senescence is a state of stable cell cycle exit with important implications for development and disease. Here, we demonstrate that the chromatin remodeling enzyme ATRX required therapy-induced senescence. accumulates in nuclear foci senescence multiple types transformed cells exposed to either DNA damaging agents or CDK4 inhibitors. Mobilization into depends on ability interact H3K9me3 histone HP1. Foci form soon after cycle, before other hallmarks appear. Eliminating senescent...