Nicolas Robine

Director, Computational Biology

NYGC Publications

• Evolution of structural rearrangements in prostate cancer intracranial metastases
• African Ancestry Associated Gene Expression Profiles in Triple Negative Breast Cancer Underlie Altered Tumor Biology and Clinical Outcome in Women of African Descent
• Retromer dysfunction in amyotrophic lateral sclerosis
• Gene expression signatures of individual ductal carcinoma in situ lesions identify processes and biomarkers associated with progression towards invasive ductal carcinoma
• Somatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression
• Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
• New York’s Polyethnic-1000: a regional initiative to understand how diverse ancestries influence the risk, progression, and treatment of cancers
• A field guide to cultivating computational biology
• Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway
• Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs
• Genome-wide Cell-Free DNA Mutational Integration Enables Ultra-Sensitive Cancer Monitoring
• Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms.
• SCANVIS: a tool for SCoring, ANnotating and VISualizing splice junctions
• Sequencing and curation strategies for identifying candidate glioblastoma treatments
• Immunogenic neoantigens derived from gene fusions stimulate T cell responses
• Genetic mechanisms of primary chemotherapy resistance in pediatric acute myeloid leukemia
• Human papillomavirus and the landscape of secondary genetic alterations in oral cancers
• Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer
• Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient Derived Tumors Clinical Application of Whole-Genome Sequencing for Reporting Targetable Variants in Cancer
• YES1 amplification is a mechanism of acquired resistance to EGFR inhibitors identified by transposon mutagenesis and clinical genomics.
• taxMaps: Comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.
• Genome-wide somatic variant calling using localized colored de Bruijn graphs
• Identification of Three Rheumatoid Arthritis Disease Subtypes by Machine Learning Integration of Synovial Histologic Features and RNA Sequencing Data
• ATRX is a regulator of therapy induced senescence in human cells
• Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma
• Next-Generation Rapid Autopsies Enable Tumor Evolution Tracking and Generation of Preclinical Models
• Structural insights into mis-regulation of protein kinase A in human tumors
• Prognostic value of miR-375 and miR-214-3p in early stage oral squamous cell carcinoma
• Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences.
• Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma

Software

• Lancet
• taxMaps
• SCANVIS
• NYGC Cancer Pipeline