Bioinformatics

About the Bioinformatics Shared Resource

Bioinformatics supports the interpretation of Big Data collected in a broad range of cancer research. Massey’s Bioinformatics Shared Resource (BISR) provides comprehensive, high-quality and cost-efficient bioinformatics services to support Massey researchers in basic science, clinical research and population science.

Through collaborative interactions with Massey members, the BISR supports the analysis of high-throughput multi-omics data with state-of-the-art bioinformatics algorithms and pipelines, facilitates the access and mining of public cancer datasets, supports grant applications and provides consultation and training to cancer center members and trainees.

Services and software

Services

Service Category	Service/Analysis Type	Description
Data Analysis	RNA-seq Analysis	Differential gene expression profiling, differential splicing analysis, detection of abnormal RNA transcripts
	Single Cell (Nucleus) Analysis	Cell clustering, cell type identification, cell trajectory analysis, pseudo-time analysis, cell-cell communication
	Spatial Omics Data Analysis	Analysis of GeoMx and 10x Visium to reveal the spatial organization of gene expression and cellular interactions within tissues
	Genome Analysis	Analysis of WGS/WES, ChIP-seq, ATAC-seq and other relevant genomic sequencing
	Mining Cancer Genomic Repositories	Access and analysis of cancer data from public genomic databases such as Data Genomic Data Commons (GDC) and Gene Expression Omnibus (GEO)
	Pathway and Ontology Enrichment Analysis	Gene Ontology (GO) enrichment analysis, pathway analysis with Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA), protein-protein interaction network inference and visualization with Cytoscape
	Multi-omics Analysis	Multi-omic analysis and pathway enrichment analysis of proteomics, metabolomics, lipidomics and other omics, integrated across datasets
	Microbiome Analysis	Taxa identification and diversity analysis from 16S rRNA data and metagenomics shotgun sequencing
AI for Genomics	Advanced Data Analysis	Machine learning, statistical analysis and association studies involving genomic datasets, predictive modeling, and AI-driven insights
Consultation	Experimental Design & Bioinformatics	Assistance with experimental design and consulting on bioinformatics services and project planning
Grant Preparation	Bioinformatics Sections	Assistance with grant writing for bioinformatics analyses and computational components
Manuscript Writing	Methods & Results Sections	Assistance with manuscript writing for the description of bioinformatics analysis; consultation on genomic data submission requirements
Other Services	Custom Project Support	If your project needs don't fit the above categories, we are happy to schedule a consultation to determine the scope and requirements

Software

The VCU license provides access to QIAGEN IPA, a powerful platform for biological interpretation of 'omics data. All VCU faculty and trainees would be eligible to obtain an account. Please contact BISR for account creation. Accessible features include:

Core IPA Analysis: Perform fundamental pathway, network, upstream regulator, and disease/function analysis using the extensive Ingenuity Knowledge Base.
Land Explorer: Contextualize your experimental results by comparing them against a large collection of curated public omics datasets from diverse tissues and conditions.
RNA-seq Analysis Portal: A cloud-based tool for streamlined processing of raw RNA-seq data (FASTQ files) to generate results ready for IPA interpretation.
IPA Interpret: Get AI-powered summaries and interactive, shareable web reports highlighting key biological insights from your analyses.
OmicSoft Explorer: Explore and visualize large-scale omics datasets, integrating with IPA for deeper data navigation and insight generation.

Data storage

BISR will transfer and store data for analysis only. Investigators are responsible for obtaining a copy of the raw data to comply with data retention policies as the BISR is unable to provide long-term archival storage services.

Submit a service or software request

A meeting is required to discuss the feasibility of the requested service to make sure the request can be achieved within the core’s resource budget.

Submit a ticket (Requires RamsVPN for secure remote access)

Utilization policy
Utilization policy

All current or potential BISR users should familiarize themselves with the following expectations:
- Pre-funding services: Support through the BISR during the pre-funding phase is not truly free – members should recognize that bioinformatician effort through the resource is supported and paid for by Massey funds.
Grant submissions that have benefited from BISR services during the pre-funded phase must include bioinformatician effort in the grant:
- Requested effort should as accurately as possible reflect your project’s true need for bioinformatician time.
- For funded projects utilizing BISR services, users should have no expectation of receiving BISR effort in excess of the percentage of effort actually supported by their grants.
- If the budget of a funded grant is reduced, and you, as PI, choose to cut or reduce the level of bioinformatician effort, then you should expect to receive bioinformatician effort commensurate with the adjusted level, not what was originally proposed. If a BISR-affiliated bioinformatician’s effort is needed for your project, you are well advised to adjust your budget elsewhere.
- Including a “lowball” percentage of effort for bioinformaticians on grants is usually inappropriate, and will in any case often be criticized by grant-reviewers as merely “checking a box” rather than securing meaningful bioinformatic support. Again, requested effort should be commensurate with your project’s actual requirements.
- Please understand that inclusion of bioinformatician effort on grants is crucial for increasing overall BISR staffing levels, as when BISR affiliated bioinformaticians effort becomes grant funded, it frees up resource budget to secure additional personnel.
- Percentage of BISR Bioinformatician effort written into grants must be directly negotiated with the BISR Director, Dr. Jinze Liu, prior to grant submission and should reflect the considerations outlined above.
Other considerations

Users should anticipate that services provided by BISR will correspond to actual bona fide bioinformatic analysis, not merely for general assistance with article and grant preparation. While BISR bioinformaticians may contribute select text for methods and figures as appropriate, they are not responsible for drafting other parts of manuscripts and grant submissions.

Bioinformatics is a field with many sub-specializations. BISR staff have diverse experience, skills and training, and will strive to subserve your bioinformatic needs, but there may be legitimate bioinformatic requirements that BISR may be ill-suited or unable to provide. Please consult with BISR director, Dr. Jinze Liu, as early as possible during your project’s development.

Use of the resource in the pre-funding period will be prioritized according to the following rubric, bearing in mind that, for investigators that are already grant-funded, use of the resource is limited to new projects under development, not previously funded projects:
- Early stage investigators prior to their first extramural peer-reviewed award
- NCI funded investigators
- Investigators with other peer-reviewed cancer relevant support
- Other investigators
Grant Language

Suggested grant language

The VCU Massey Comprehensive Cancer Center Bioinformatics Shared Resource (BISR) is located on the 5th floor of Sanger Hall on the Medical College of Virginia campus. The mission of the BISR is to provide a comprehensive, high-quality and cost-efficient bioinformatics service infrastructure to support Massey researchers in basic science, translational research and cancer control. Through collaborative interactions with Massey members, the BISR supports the analysis of high-throughput multi-omics data with state-of-the-art bioinformatics algorithms and pipelines, facilitates the access and mining of public cancer datasets, supports grant applications and provides consultation and training to cancer center members and trainees. The BISR is funded by the VCU Massey Comprehensive Cancer Center in combination with multiple external grants from National Institute of Health.
Education and training
Education and training

The BISR works in collaboration with the Wright Regional Center and VCU Libraries to offer seminars and workshops on a variety of bioinformatics topics. For advanced notification of new course offerings, subscribe to the bioinformatics mailing list by sending an email to mccbioinfo@vcu.edu that includes your name and the email address you would like on the list.
- Monthly Seminars and Workshops (please see current offerings in the "related classes and events" section below)
- Past Seminars and Workshops
- Educational resources
- Internships available to eligible graduate students and postdocs.
Contact

Contact information

Please use the following webpage to submit your service request. Your request will be reviewed by the BISR and a member of the BISR team will follow-up to schedule a meeting to discuss your experimental design and hypothesis.

Submit a ticket (Requires RamsVPN for secure remote access)

Jinze Liu, Ph.D.
Director
Professor, Department of Biostatistics
liuj15@vcu.edu

Expertise: Methodological and applied research expertise in computational biology, machine learning and databases

Katarzyna Tyc, Ph.D.
Assistant Professor, Department of Biostatistics
tyck@vcu.edu

Expertise: Customized NGS data processing workflows, multi-level data integration, germline and somatic variant calling, microbiome data analysis, molecular biology and translational bioinformatics

Amy Olex, Ph.D.
Senior Bioinformatics specialist, Wright Center
alolex@vcu.edu

Expertise: NGS data analysis and pipeline development, biomedical natural language processing and machine learning

Xufeng Qu, MS
Bioinformatics specialist
qux2@vcu.edu

Expertise: NGS data analysis, especially single-cell transcriptomics and single-cell spatial omics data analyses, machine learning

Christiane Carter, MS
Senior Bioinformatics Analyst
morecockcm@vcu.edu

Expertise: NGS data analysis, genomic data mining, multivariate data analysis, and data visualization

Mikail Bala, MS
Bioinformatician
balami@vcu.edu

Expertise: NGS data quality control and data analysis, pipeline automation

Joaquin Reyna, Ph.D.
Research scientist
reynaj@vcu.edu

Expertise: Methodological and applied research in bioinformatics, with a focus on chromatin conformation, transcription factor binding, transcriptomics, and proteomics. Currently expanding into spatial biology and lipidomics. Extensive experience in database and web development for bioinformatics applications. Strong background in machine learning.

Services

Service Category	Service/Analysis Type	Description
Data Analysis	RNA-seq Analysis	Differential gene expression profiling, differential splicing analysis, detection of abnormal RNA transcripts
	Single Cell (Nucleus) Analysis	Cell clustering, cell type identification, cell trajectory analysis, pseudo-time analysis, cell-cell communication
	Spatial Omics Data Analysis	Analysis of GeoMx and 10x Visium to reveal the spatial organization of gene expression and cellular interactions within tissues
	Genome Analysis	Analysis of WGS/WES, ChIP-seq, ATAC-seq and other relevant genomic sequencing
	Mining Cancer Genomic Repositories	Access and analysis of cancer data from public genomic databases such as Data Genomic Data Commons (GDC) and Gene Expression Omnibus (GEO)
	Pathway and Ontology Enrichment Analysis	Gene Ontology (GO) enrichment analysis, pathway analysis with Gene Set Enrichment Analysis (GSEA) and Ingenuity Pathway Analysis (IPA), protein-protein interaction network inference and visualization with Cytoscape
	Multi-omics Analysis	Multi-omic analysis and pathway enrichment analysis of proteomics, metabolomics, lipidomics and other omics, integrated across datasets
	Microbiome Analysis	Taxa identification and diversity analysis from 16S rRNA data and metagenomics shotgun sequencing
AI for Genomics	Advanced Data Analysis	Machine learning, statistical analysis and association studies involving genomic datasets, predictive modeling, and AI-driven insights
Consultation	Experimental Design & Bioinformatics	Assistance with experimental design and consulting on bioinformatics services and project planning
Grant Preparation	Bioinformatics Sections	Assistance with grant writing for bioinformatics analyses and computational components
Manuscript Writing	Methods & Results Sections	Assistance with manuscript writing for the description of bioinformatics analysis; consultation on genomic data submission requirements
Other Services	Custom Project Support	If your project needs don't fit the above categories, we are happy to schedule a consultation to determine the scope and requirements

Software

Core IPA Analysis: Perform fundamental pathway, network, upstream regulator, and disease/function analysis using the extensive Ingenuity Knowledge Base.
Land Explorer: Contextualize your experimental results by comparing them against a large collection of curated public omics datasets from diverse tissues and conditions.
RNA-seq Analysis Portal: A cloud-based tool for streamlined processing of raw RNA-seq data (FASTQ files) to generate results ready for IPA interpretation.
IPA Interpret: Get AI-powered summaries and interactive, shareable web reports highlighting key biological insights from your analyses.
OmicSoft Explorer: Explore and visualize large-scale omics datasets, integrating with IPA for deeper data navigation and insight generation.

Data storage

Submit a service or software request

A meeting is required to discuss the feasibility of the requested service to make sure the request can be achieved within the core’s resource budget.

Submit a ticket (Requires RamsVPN for secure remote access)

Utilization policy

All current or potential BISR users should familiarize themselves with the following expectations:

Pre-funding services: Support through the BISR during the pre-funding phase is not truly free – members should recognize that bioinformatician effort through the resource is supported and paid for by Massey funds.

Grant submissions that have benefited from BISR services during the pre-funded phase must include bioinformatician effort in the grant:

Requested effort should as accurately as possible reflect your project’s true need for bioinformatician time.
For funded projects utilizing BISR services, users should have no expectation of receiving BISR effort in excess of the percentage of effort actually supported by their grants.
If the budget of a funded grant is reduced, and you, as PI, choose to cut or reduce the level of bioinformatician effort, then you should expect to receive bioinformatician effort commensurate with the adjusted level, not what was originally proposed. If a BISR-affiliated bioinformatician’s effort is needed for your project, you are well advised to adjust your budget elsewhere.
Including a “lowball” percentage of effort for bioinformaticians on grants is usually inappropriate, and will in any case often be criticized by grant-reviewers as merely “checking a box” rather than securing meaningful bioinformatic support. Again, requested effort should be commensurate with your project’s actual requirements.
Please understand that inclusion of bioinformatician effort on grants is crucial for increasing overall BISR staffing levels, as when BISR affiliated bioinformaticians effort becomes grant funded, it frees up resource budget to secure additional personnel.
Percentage of BISR Bioinformatician effort written into grants must be directly negotiated with the BISR Director, Dr. Jinze Liu, prior to grant submission and should reflect the considerations outlined above.

Other considerations

Users should anticipate that services provided by BISR will correspond to actual bona fide bioinformatic analysis, not merely for general assistance with article and grant preparation. While BISR bioinformaticians may contribute select text for methods and figures as appropriate, they are not responsible for drafting other parts of manuscripts and grant submissions.

Bioinformatics is a field with many sub-specializations. BISR staff have diverse experience, skills and training, and will strive to subserve your bioinformatic needs, but there may be legitimate bioinformatic requirements that BISR may be ill-suited or unable to provide. Please consult with BISR director, Dr. Jinze Liu, as early as possible during your project’s development.

Use of the resource in the pre-funding period will be prioritized according to the following rubric, bearing in mind that, for investigators that are already grant-funded, use of the resource is limited to new projects under development, not previously funded projects:

Early stage investigators prior to their first extramural peer-reviewed award
NCI funded investigators
Investigators with other peer-reviewed cancer relevant support
Other investigators

Suggested grant language

The VCU Massey Comprehensive Cancer Center Bioinformatics Shared Resource (BISR) is located on the 5th floor of Sanger Hall on the Medical College of Virginia campus. The mission of the BISR is to provide a comprehensive, high-quality and cost-efficient bioinformatics service infrastructure to support Massey researchers in basic science, translational research and cancer control. Through collaborative interactions with Massey members, the BISR supports the analysis of high-throughput multi-omics data with state-of-the-art bioinformatics algorithms and pipelines, facilitates the access and mining of public cancer datasets, supports grant applications and provides consultation and training to cancer center members and trainees. The BISR is funded by the VCU Massey Comprehensive Cancer Center in combination with multiple external grants from National Institute of Health.

Education and training

The BISR works in collaboration with the Wright Regional Center and VCU Libraries to offer seminars and workshops on a variety of bioinformatics topics. For advanced notification of new course offerings, subscribe to the bioinformatics mailing list by sending an email to mccbioinfo@vcu.edu that includes your name and the email address you would like on the list.

Monthly Seminars and Workshops (please see current offerings in the "related classes and events" section below)
Past Seminars and Workshops

October 4, 2023 - Ingenuity Pathway Analysis Workshop (in-person)
September, 14 2022 - Ingenuity Pathway Analysis Workshop (in-person, recording not available)
July 13, 2022 - Introduction to Single Cell Sequencing Analysis (Jinze Liu, Ph.D., Amy Olex, Ph.D., and Xufeng Xu, MS)
Fall 2018 - Introductory Bioinformatics seminars through the Wright Regional Center, organized by Amy Olex, Ph.D.

Bioinformatics and Precision Medicine (Amy Olex, Ph.D.)
Cancer Informatics and Precision Medicine (Tamas Gal, Ph.D.)
High-Throughput Technologies (Amy Olex, Ph.D.)
Bulk RNA Sequencing Pipelines (Amy Olex, Ph.D.)
Pathway and Functional Enrichment Analysis (Mikhail Dozmorov, Ph.D.)
NanoString Technology (Theresa Swift-Scanlan, Ph.D.)

Educational resources

YouTube Channel
Introduction to Bioinformatics Databases is a self-paced online course that is a collaboration between VCU Libraries and the Wright Regional Center. A certificate is issued upon successful completion of all course modules. Open for enrollment every Fall (around October). Register HERE (must be able to log into VCU’s Canvas).

Internships available to eligible graduate students and postdocs.

Contact information

Please use the following webpage to submit your service request. Your request will be reviewed by the BISR and a member of the BISR team will follow-up to schedule a meeting to discuss your experimental design and hypothesis.

Submit a ticket (Requires RamsVPN for secure remote access)

Jinze Liu, Ph.D.
Director
Professor, Department of Biostatistics
liuj15@vcu.edu

Expertise: Methodological and applied research expertise in computational biology, machine learning and databases

Katarzyna Tyc, Ph.D.
Assistant Professor, Department of Biostatistics
tyck@vcu.edu

Expertise: Customized NGS data processing workflows, multi-level data integration, germline and somatic variant calling, microbiome data analysis, molecular biology and translational bioinformatics

Amy Olex, Ph.D.
Senior Bioinformatics specialist, Wright Center
alolex@vcu.edu

Expertise: NGS data analysis and pipeline development, biomedical natural language processing and machine learning

Xufeng Qu, MS
Bioinformatics specialist
qux2@vcu.edu

Expertise: NGS data analysis, especially single-cell transcriptomics and single-cell spatial omics data analyses, machine learning

Christiane Carter, MS
Senior Bioinformatics Analyst
morecockcm@vcu.edu

Expertise: NGS data analysis, genomic data mining, multivariate data analysis, and data visualization

Mikail Bala, MS
Bioinformatician
balami@vcu.edu

Expertise: NGS data quality control and data analysis, pipeline automation

Joaquin Reyna, Ph.D.
Research scientist
reynaj@vcu.edu

Expertise: Methodological and applied research in bioinformatics, with a focus on chromatin conformation, transcription factor binding, transcriptomics, and proteomics. Currently expanding into spatial biology and lipidomics. Extensive experience in database and web development for bioinformatics applications. Strong background in machine learning.

Related Classes & Events

Acknowledgments

To ensure high-quality service, the BISR collaborates with VCU’s High-Performance Research Computing (HPRC) Core to utilize their computing infrastructure for data analysis. The BISR primarily utilizes the Athena and Apollo clusters, which are specifically designed to support research using data that must comply with federal security and privacy requirements. Please refer to the HPRC website to obtain suggested grant language to describe the HPRC facility and the computing infrastructure utilized by the BISR.

Users must appropriately cite and acknowledge the use of the shared resource in any publications or grant submissions using the following suggested language:

"Services in support of the research project were provided by the VCU Massey Comprehensive Cancer Center Bioinformatics Shared Resource. Massey is supported, in part, with funding from NIH-NCI Cancer Center Support Grant P30 CA016059."