New York Medical College

Research

Systems Biology Core Laboratory

Systems Biology Core Laboratory

 

Mass Spec FacilityComprehensive understanding of normal physiology, disease-associated alterations and recovery following a treatment requires synergizing “omic” and pathophysiological data to identify and quantify the molecular mechanisms responsible for patient outcomes. By quantifying thousands to millions genomic characteristics at a time the microarray and next generation sequencing technologies offer the opportunity to understand the biological system as a whole. SBC combine the theoretical and experimental skills of two faculty members to provide resources and expertise to design, perform, understand and analyze a wide variety of pathophysiological and “omics” studies.

Available Experimental Services

SBC  2A. Preparatory techniques:
- DNA, RNA and protein extraction, purification,
- RNA reverse transcription and fluorescent labeling
- DNA and proteins fluorescent labeling
- DNA, RNA and protein concentration (NanoDrop)
- DNA, RNA, proteins concentration and QC (Bioanalyzer)
- Western blotting
- SpeedVac concentration of proteins, DNAs and RNAs
- Controlled PCR amplification

SBC 3B. Hybridization of Agilent microarrays:
- Whole Genome Gene Expression microarrays for 30+ species
- Exon microarrays (human, mouse, rat)
- miRNA microarrays
- CGH (Comparative Genomic Hybridization) microarrays
- CGH+SNP (Single Nucleotide Polymorphism) microarrays
- CNV (Copy Number Variant) microarrays
- ChIP-on-chip (Chromatin ImmunoPrecipitation) microarrays
- DNA methylation (CpG islands) microarrays

C. Hybridization of Illumina beadchips:
- Whole Genome Expression BeadChips: human, mouse, rat
- Infinium iSelect HD custom genotyping BeadChips for
virtually all species
- Infinium HumanMethylation450 BeadChip
- Infinium HumanCytoSNP-FFPE-12 BeadChips
- Infinium Human Omni Express-FFPE BeadChips

SBC 4D. Hybridization and scanning of custom arrays:
- cDNA microarrays
- oligonucleotide microarrays
- protein/antibody arrays

 

Theoretical Services

A. Computational Genomics:
- Noise analysis of various ‘omics’ platforms
- Feature extraction, primary analysis, export in selective formats, organization of searchable
dbases and deposit into NCBI, NYMC and other public data repositories
- Normalization and filtration of ‘omics’ data
- Determination of expression level, control and coordination of individual genes
- Regulome
- Prominent Gene Analysis
- Pair-Wise Relevant Analysis
- Transcriptomic Distance Analysis
- Transcriptomic Recovery Analysis

SBC 5B. Bioinformatics:
- Agilent Feature Extraction, Axon GenePix + Acuity, Illumina Genome Studio
- Gene ontology (GO) analysis
- Pathway analysis (KEGG, Amigo, Ingenuity, GeneMap, DAVID)
- Identification and quantification of significantly altered functional pathways
- Determine composition, topology and interplay of functional genomic fabrics
- Determine remodeling of functional genomic fabrics and their interplay during development/hormonal cycle/disease progression/treatment
- Quantify the overall transcriptomic recovery in response to a therapy

SBC 6C. Biostatistics:
- Optimize information-to-cost experimental design, select study population, define outcomes and determine sample size and number of technical and biological replicas;
- Perform various statistical tests on experimental data
- Normalize, filter and perform statistical analysis of pathophysiological and ‘omic’ data;
- Collect, perform primary analysis, export in selective formats, organize in searchable dbases and prepare data for deposit into NCBI, NYMC and other public repositories;
- Assistance with Origin Pro, GraphPad Office, Excel and Mathematica

D. Computational Biology/Mathematical modeling:
- Develop (classical/quantum) physics and (continuous/discrete, deterministic/stochastic) mathematical models of complex biological systems/phenomena
- Run numerical simulations of mathematical models
- Determine the dynamics of the overall pathophysiological and transcriptomic changes during development, hormonal cycle, progression of a disease and recovery in response to a therapy.

Assistance to write grant applications, reports, articles and book chapters.

Contacts:

Dumitru A Iacobas, PhD, Core Director
Basic Sciences Building, Rm. 410
Phone: 914-594-3997; Email: dumitru_iacobas@nymc.edu

Dr. John T. Fallon III, MD, PhD
Chairman of Pathology
Basic Sciences Building, Rm. 413
Phone: 914-594-4150; Fax: 914-594-4163; Email: john_fallon@nymc.edu

Page updated: October 28, 2014