WELCOME Norma J. Nowak, PhD Executive Director, NY State Center of Excellence in Bioinformatics and Life Sciences (CBLS) Director, UB Genomics and Bioinformatics Core (GBC)
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Grow Your Business: Assistance for Industry Partners CBLS
UB Genomics and Bioinformatics Core Laboratory Technicians Sujith Valiyaparambil Natalie Waldron Mission Bioinformatics Team Jie (Jessie) Wang, Ph.D Jonathan Bard Brandon Marzullo Strive to offer latest advances in next-generation sequencing and gene expression services to UB, external researchers and private entities to help facilitate research, discovery, and product development.
GBC continued How can High-throughout Sequencing work for you? ChiP-seq DNA-seq (whole genome and exome) RNA-seq mirna-seq 16S Amplicon Kahvejian et.al., Nature biotechnology, 2008
GBC continued Technology Platforms Nucleic Acid Purification, QC, Library preparation QIASymphony automated nucleic acid purification platform Advanced Analytics Fragment Analyzer Biotek Synergy plate reader for picogreen quantitation Sage Biosciences Blue Pippin Prep Diagenode SX-8G Automated system Sequencing and Gene Expression Illumina Hiseq 2500 Illumina Miseq Affymetrix Genechip 450 Biorad digital droplet PCR (QX100)
GBC continued Genomic DNA Illumina Sequencing Workflow RNA/miRNA
Percentage 0.0 0.1 0.2 0.3 GBC continued Bioinformatics Support Initial Data Processing Quality Monitoring Assay Specific Analysis Peak Model forward tags reverse tags shifted tags d=147 600 400 200 0 200 400 600 Distance to the middle Illumina base pipeline generating FASTQ files Sequencing run quality assessment and metrics Automated analysis pipelines dependent on sample type Data Hosting and Visualization Viewable aligned sequence data and analysis via UCSC genome browser
GBC continued Leveraging CCR Resources for Data Storage and Analysis )
The Relevancy of Classic Techniques Differential Gene Expression Northern blotting (1977) : 1 Probe 20 samples Dot Blots (1987) : 100s of probes 1 sample RT-PCR (1992) : 100s of probes 10-100 samples Microarrays (1995 ) : 100,000s of probes 1 sample Next-gen sequencing (2005) : 250 x 10 6 reads 1 sample
Research and Development Product development Lab-on-chip testing and development for Rheonix. Clinical diagnostics Development of diagnostic gene panels for Multiple Sclerosis and Autism Spectrum Disorder in partnership with Lineagen. Translational research Global mirna sequencing of plasma from animals with Traumatic Brain injury. Project led by Sinapis Pharma. Microbiome Sequencing V1-V3 and V3-V4 16S amplification and sequencing of oral microbiota samples
Copyright Rheonix, Inc. 2016 All Rights Reserved
Copyright Rheonix, Inc. 2016 All Rights Reserved
Successful Integration of NGS Library Prep on CARD Copyright Rheonix, Inc. 2016 All Rights Reserved
Copyright Rheonix, Inc. 2016 All Rights Reserved
Copyright Rheonix, Inc. 2016 All Rights Reserved
Using Advanced Proteomic Analysis to Identify Optimal Clinical Applications for Novel Cancer Therapies TREAT CELLS WITH DRUG X ISOLATE TOTAL PROTEIN ADAPT TO CLINICAL PRACTICE VALIDATE WITH PRE-CLINICAL MODELS PATHWAY 1: COMBINE WITH DRUG Z IDENTIFY AND QUANTITATE INDIVIDUAL PROTEINS PATHWAY 2: AVOID DRUG Y PATHWAY 3: NEW INDICATION? PATHWAY 4: NEW DOSING REGIMEN? USE DATA TO REVEAL/DESIGN OPTIMAL THERAPEUTIC APPLICATIONS DEFINE PATHWAYS/PROCESSES AFFECTED BY DRUG X
S TAT E U N I V E R S I T Y AT B U F FA L O UB CCR's Industry Cluster C e n t e r f o r C o m p u t a t i o n a l R e s e a r c h
HPC NY : NYS High Performance Computing Consortium Powered by ESD/NYSTAR
UB Center for Computational Research
The UB CCR industry cluster Industry Cluster Node Rack
Current Industrial Partners (18) genomics data analytics molecular modeling fluid dynamics
Where to go for more information
Webware Infrastructure for Rapid Conversion and Implementation of Predictive Modeling Approaches in a Web-Based Tool Physics-based Model HPC Database HPC Enabled Meta-model Meta-Model Web-based computational lifing tool Engineering components: bearing, gears For general users as well as experts Rapid Meta-model based tests High accuracy physics-based tests Turkey solution for O&M, buy on life High Fidelity High Accuracy Tests DigitalClone TM UX Fast Screening Real Time Tests Introduction to Sentient Science 3/30/2016
Thank You Q&A