PIPELINE Facility Core

Pipeline Facility Core

The PIPELINE (Promoting Impact on Precision EHS by Leveraging Instrumentation, NextGen and Emerging Technologies) Facility Core encompasses world-class expertise and resources in state-of-the-art imaging with continually evolving genomic, epigenomic, metabolic and proteomic, and informatics approaches, applied from the single-cell to population level studies.

The overall goal of the PIPELINE Facility Core is to advance precision environmental health research by providing access to expertise and technologies and facilitating effective utilization of “omic” technologies across the parent organizations of the GC-CPEH. “Omics” data and integrative bioinformatics meet the research needs of Center Members to achieve systems level insights.

PIPELINE Facility Core Leadership

Dr. Chris Amos, Director
Christopher Amos, Ph.D.
Baylor College of Medicine
Dr. Cristian Coarfa, Co-Director
Cristian Coarfa, Ph.D.
Baylor College of Medicine
Aaron Thrift, Ph.D.
Leadership Development Program Participant (LDP)
Baylor College of Medicine

PIPELINE Facility Core Resources

The PIPELINE Facility Core leverages well-established resources that exist across the TMC and parent organizations of the GC-CPEH to bring NextGen technologies to members. The PIPELINE Facility Core serves members with support at all stages of a project, including overall design, execution, data acquisition, and data integration and interpretation.

CellOmics: Integrated Microscopy Core

Navigator: Dr. Michael Mancini, Baylor College of Medicine

  • Light microscopy
  • Super-resolution microscopy (SIM and STORM)
  • Live imaging (ultrafast and long-term)-Multi-dimensional spatial analysis
  • High throughput microscopy
  • Image analytics

Learn more >

Genomic and RNA Profiling

Navigator: Dr. Daniel Kraushaar, Baylor College of Medicine

  • Sample Quality Control
  • NGS
    • RNA-Seq
    • ChIP-Seq
    • Whole genome sequencing
    • Whole genome bisulfite sequencing
    • Targeted Sequencing
    • Sequencing only
  • NanoString Gene Expression Assays

Learn more >

Mass Spectrometry Proteomics

Navigator: Dr. Anna Malovannaya, Baylor College of Medicine

  • Consultation and Project design
  • 365 Proteome Profiling
  • Protein Complex Identification and Affinity Proteomics
  • Post-Translational Modification (PTM) Analysis
  •  “Per-Band” Sequencing
  • Data Analysis

Learn more >


Navigator: Dr. Nagireddi Putluri, Baylor College of Medicine

  • Sample Preparation and Quality Control
  • Targeted Steady-State Analysis
  • Unbiased Steady-State Metabolomics
  • Lipidomics
  • Metabolomic Flux Analysis

Learn more >

Microbiome and Metagenomics

Navigator: Dr. Kristi Hoffman, Baylor College of Medicine

  • DNA and RNA Extraction
  • Targeted Amplicon Sequencing
  • Untargeted Virome Amplicon Sequencing Metagenome and Complete Genome Sequencing
  • Qualitative PCR
  • Data Analysis

Learn more >

MultiOmics Data Analysis

Navigator: Dr. Cristian Coarfa, Baylor College of Medicine

  • Consultation
  • Primary Analysis of Data by Different Tech Platforms
  • Integrative MultiOmics Analysis
  • Data Deposition

Learn more >

Protein and Monoclonal Antibody Production

Navigator: Dr. Dean Edwards, Baylor College of Medicine

  • Monoclonal Antibody Production
  • Protein Expression and Purification
  • Peptide Synthesis (3rd-party fee-for-service)
  • Biochemical Assays (3rd-party fee-for-service)

Learn more >

Single Cell Genomics

Navigator: Dr. Rui Chen, Baylor College of Medicine

  • Single Cell RNA Profiling
  • Single Cell ATAC-seq
  • Smartseq RNA profiling

Learn more >

UTHealth Human Genetics Center

Navigator: Dr. Alanna Morrison, UTHealth Houston

  • Genomics
    • Whole genome, whole exome
  • Epigenomics
    • Whole genome, RRBS, Capture
    • ChIP-Seq
  • Transcriptomics
  • Single Cell Genomics
    • RNA-Seq, ATAC-Seq

Learn more >

UTMB Inhalation Toxicology Core

Navigator: Dr. Bill Ameredes, UTMB Galveston

  • Inhalation/Exposure Laboratories including gaseous and aerosol toxicants; allergens; topical dermal and ocular exposures; intravitreal and systemic exposures
  • Tobacco and e-Cigarette Smoking/Vaping Inhalation
  • Hazardous Chemical-approved Exposure Facility
  • Airway/Lung Physiology Function Assessment
  • Ocular and Skin Response Assessment
  • Cell Culture Exposure Facilities
  • Integration with UTMB Imaging Network for lung and eye toxic responses; fixed and live-cell imaging; microCT-PET-SPEC, molecular optical imaging (IVIS) and Optical Coherence Tomography (OCT) 
  • ITC Facility Brochure

Learn more >

UTMB Mass Spectrometry Proteomics

Navigator: Dr. Bill Russell, UTMB Galveston

  • Intact molecular weight measurement
  • Protein identification from gel bands
  • Protein identification from complex mixtures
  • Identification of post-translational modifications
  • SILAC, iTRAQ, and label-free quantification of peptides and proteins
  • Small molecule quantification
  • Metabolomics

Learn more >

UTMB Next Generation Sequencing

Navigator: Dr. Steven Widen, UTMB Galveston

  • ChIP-Seq
  • De novo assembly
  • Variant identification
  • SNPs
  • Transcriptome (reference-guided or de novo)
  • miRNA and small ncRNA sequencing
  • Quantitative – RNA-Seq expression analysis
  • Exome Sequencing (Cancer or Custom Panels)

Learn more >

UTMB Center for Single-Cell Genomics

Navigator: Dr. Peter McCaffrey, UTMB Galveston

  • 10X Genomics Chromium workflows:
    • Single-cell gene expression on fixed and fresh tissues
    • Single-cell epigenomics (ATAC)
    • Single-cell multi-omics (gene expression + ATAC)
  • 10X Visum and Xenium workflows:
    • Single-cell spatial transcriptomics (via 10X Visium)
    • Single-cell in-situ transcriptomics (via 10X Xenium)
  • Learn More

Request PIPELINE Facility Core Services

GC-CPEH Full members and Pilot Project awardees utilizing the PIPELINE Facility Core Resources are eligible for the Center subsidies to underwrite their costs up to 25 to 50%.

Please submit the GC-CPEH Facility Core Service Request Form to begin your request.

Any Questions?

Contact Dr. Heyreoun An Han for more information.


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“Research reported in this publication was supported by the National Institute of Environmental Health Sciences of the National Institutes of Health under Award Number P30ES030285. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.”