Research Collaborations
TBI provides computational methodologies and web-based tools to integrate 'OMIC data management, visualization, and analysis pipelines along with public open-source resources for data sharing, standardized analysis pipeline, and visualization support, using the BRAVO (Biomarker Recognition and Validation Online) system. It includes more than 1,000,000 human disease samples from 58 cancer studies from NCI CPTAC/TCGA for 16 cancer diagnoses (brain, breast, bladder, colorectal, head & neck, glioblastoma, kidney, liver, lung, leukemia, lymphoma, gastric, melanoma, ovarian, pancreatic, and prostate) and Type 1 & Type 2 diabetes public cohort studies. We can assist researchers with characterizing predictive biomarkers for correlative OMICs expressions with clinicopathological phenotype and outcomes.
Our software portfolio extends to more than 100 open-source genomic analysis tools hosted on the HPRCC and POSEIDON platform for customized user support and training. Additional in-house-developed analysis tools are miRNA, scRNA/scDNA, ATAC-seq, ChIP-seq, RNAseq/DNAseq exome- and transcriptome- sequence analysis, BD-Func pathway analysis, and COHCAP methylation epigenomics analysis.
TBI provides support and training for vendor-based software for OMIC data generated/processed from Affymetric, Illumina Genome Studio, 10X Genomics, Life Technologies, PacBio, NanoString, and Mass Spectroscopy to mention a few, such as Partek, Qiagen CLC Bio/IPA Ingenuity Pathway/QCII-T/TRANSFAC, MetaCcore, which incorporate industry-standard data sharing, workflows, and visualization needs for CLIA-certified clinical laboratories.
TBI provides structure-based and ligand-based computer-assisted molecular modeling to predict 3D protein folding and its interactions with DNA/RNA/protein as well as drug complexes for further molecular dynamics simulation using the Schrödinger Suite of software. We can provide pharmacokinetic predictions of absorption, distribution, metabolics, excretion, and toxicity (ADMET) to further refine the qualitative structure activity relationship (QSAR) for lead optimization. We mine literature from NCBI Medline, PubChem, ClinicalTrial.org, and patent databases to assist with selecting the best drug candidate(s) for design of internal clinical trials and patent applications.
A complex sample of gut contents or a body-cavity specimen is filled with numerous known and unknown microorganisms. Only a small fraction of those microorganisms is possible to culture using classical microbiology methods for the purpose of characterizing the microbial community as a whole. Yet, understanding the composition and function of the microbial community is critical for potential diagnostics and research. High throughput sequencing offers an alternative approach to characterizing the microbial community. Specifically, sequencing 16S rRNA amplicons allows profiling the community by discovering the operational taxonomic units (OTUs) – groups of sequences related to known prokaryotic taxa. Quantitative comparison of the counts of sequences belonging to the OTUs between the samples reveals shifts in microbiota composition as a result of affecting disease status and/or associated treatments. From the community functional perspective, a metagenomics approach is used, which implies ALL microbial genes are sequenced and annotated. (Review article)
The Translational Bioinformatics group offers end-to-end microbiome analytics starting from the raw data. We take care of the data processing, storage, statistical analysis, experimental design, manuscript, and grant preparation. We are also open to future challenging microbiome analyses by integrating metagenomic and metaproteome data generated from the host genome, epigenome, transcriptome, and metabolome to attempt uncovering the role of microbes in affecting human health and disease.
The High Performance Research Computing Center (HPRCC) is responsible for supporting the computational biology, genomics, informatics, mathematical oncology, metabolomics, proteomics, and system biology programs. This group provides customized research support for high performance computing clusters and research servers.
City of Hope Data Center is built up on a new Tier 2 state-of-the-art technology. There are four 1.2MW diesel generators that operate in demand with load, backup power for 30 days, and 24/7 network monitoring. A VMWare ESX virtualization farm provides virtual servers that can be spooled up on demand for testing and staging environments for this project. The Data Center is equipped with a Compellent SAN (Storage Area Network) and Isilon Cluster NFS (network file system) for which capacity is constantly increasing and currently amounts to multiple Petabytes (PB) of data storage. The High Performance Computing environments at COH provides ~6000 CPU cores, ~37TB memory and 56 NVIDIA V100 for basic research and translates study. COH telecommunications infrastructure provides network connectivity through a fiber optic network and follows industry standard layout topologies supported by a wide array of Cisco network infrastructure hardware. City of Hope's fiber optics network christened Hopenet-2000 is one of the most advance fiber optics network implemented in a campus setting. All software and electronic information resources are included in the COH institutional backup/disaster recovery plan, with regular backups onto digital tapes stored offsite, an incremental backup daily and full backup weekly. This entire infrastructure is secured with dedicated firewall and VPN appliances from Juniper Networks. COH will use its existing support infrastructure to provide self-service and HelpDesk functions to the end users. COH maintains a 24x7 helpline and RemedyForce helpdesk software to provide support.
The deployed workstation environment consists of recent PCs running a mix of Microsoft Windows, Linux, and OS X. Intranet resources include shared databases and software applications for data pipelining, business intelligence and data visualization, LIMS, and Electronic Lab Notebooks. Linux and Mac workstations are also available for software development and testing. The COH Information Technology Services Department provides training and support for PC hardware and standard desktop software applications. The security and privacy of records and data are further protected using unique login ID and passwords in accordance with the Microsoft Windows Active Directory security framework, conforming to well-established computer security standards. Remote access to electronic information resources is handled via a dual mode solution – a client based Cisco ASA VPN, and a clientless VPN solution from Juniper Networks. All software and electronic information resources, are included in the COH institutional backup / disaster recovery plan. The plan includes regularly scheduled backups onto digital tapes that are stored at an offsite location. An incremental tape backup is created daily for all main COH servers, and a full backup is created weekly.