John W. Rooney Experience

John W. Rooney has been employed at the following positions:


Associate, Aquilla Patents & Marks, PLLC, Center Harbor, NH


  • Trademark and Patent Prosecution and Litigation
  • Trade Secrets Litigation


Associate Professor (Adjunct) and Curriculum Developer, Franklin Pierce University (Portsmouth, NH), The Saylor Foundation (Washington, DC), Community College System of New Hampshire (Manchester, NH and Concord, NH), Hesser College (Manchester, NH),  South University (online)


  • Teaching:  courses in Science, Liberal Arts, Paralegal, and ABA-Certified Legal Nurse Consulting Programs
  • Curriculum Development:  Science, Intellectual Property Law, Health Law, Legal Ethics, Risk Management


Research Associate, Department of Physiology, Dartmouth College, Lebanon, NH


  • Project:  Investigating the role of transcriptional co-activators and chromatin remodeling in steroid hormone-regulated gene expression in breast cancer cells.
  • Responsibilities:  Responsible for designing, implementing and managing multiple research projects.  Reviewing grant proposals and manuscript submissions.  Training and supervising of technical and research staff.  Representation of laboratory at scientific research conferences.
  • Methodologies:  Chromatin Immunoprecipitation (“ChIP”) assays, multiplex real time PCR, large scale protein purification for mass spectrophotometric analysis of post-translational modifications, site-directed mutagenesis and over-expression, and siRNA inhibition of expression, of said proteins in human breast cancer cells.

Legal Intern, Office of Integrity and Compliance, Fletcher Allen Healthcare, Burlington, VT

September-December, 2007

  • Project:  Performed a comprehensive analysis of Fletcher Allen Healthcare-affiliated hospitals and academic medical centers for compliance with Federal Medicare/Medicaid laws, rules and regulations (Stark, Anti-kickback, Anti-Fraud, etc…).  Also assisted Offices of General Counsel, Risk Management and Institutional Review Board (oversees clinical trials) with a wide variety of legal projects.  Accompanied representatives on lobbying visits at Vermont State House hearings on State Healthcare legislation reform.
  • Responsibilites:  Oral and memoranda-based legal analysis provided under severe time constraints.  These analyses and recommendations were relied upon by legal counsel.
  • Methodologies:  Extensive legal research of state and federal case law, statutes, rules and regulations.  Extensive legal analyses and memo writing.

Senior Scientist, AtheroGenics, Inc., Alpharetta, GA


  • Project:  Validated small molecule therapeutics for arteriosclerosis, asthma, COPD, and other inflammatory diseases.
  • Responsibilities:  Established Research Division of Cellular and Molecular Immunology.  Trained and assisted other researchers in methods of Molecular Immunology.  Set up Florescent Activated Cell Sorter (FACS) facility.  Implemented and managed multiple research projects.  Reviewed grant proposals and manuscript submissions.  Represented company at scientific research conferences.  Assisted in compliance with FDA clinical trial rules and regulations.
  • Methodologies:  Attended several FACS training courses at Becton-Dickenson FACS facility and learned to use the BD FACS VantageSE high-speed sorter, BD FACS Calibur flow analyzer, and BD FACScan flow analyzers, using multiple software platforms, including FloJo, CellQuest, ModFit, and Cytometric Bead Assay.  Established purified primary mast cell and T helper cell cultures for use in drug validation.

Scientist, EpiGenesis Pharmaceuticals, Inc., Cranbury, NJ


  • Project:  Validated aerosol-delivered antisense therapeutics for asthma, COPD, and other pulmonary diseases.
  • Responsibilities:  Implemented and managed multiple research projects.  Trained others in methods of Molecular Immunology including basic FACS use.  Reviewed grant proposals and manuscript submissions.  Assisted in compliance with FDA clinical trial rules and regulations.  Established blood born pathogen training course.
  • Methodologies:  Designed and implemented complex combinatorial primary human cell culture models of pulmonary disease states using B cells, antigen-specific T helper cells, mast cells, macrophages, pulmonary smooth muscle cells, and endothelial cells.  Constructed several phagemid cDNA libraries from rabbit, mouse and cynomologous monkey tissues.  Cloned antisense target genes.   Assisted with cynomologous monkey surgery and tissue collection.

Postdoctoral Fellow (Recipient of Cancer Research Institute Fellowship award.), Columbia College for Physicians and Surgeons, Department of Microbiology, New York, NY


  • Project:  Discovered and studied novel genes involved in primary macrophage differentiation, activation and microbial pathogenesis.
  • Responsibilities:  Implemented and managed multiple research projects.  Wrote several grant proposals.  Reviewed others’ grant proposals and manuscript submissions.  Attendance and presentation at several scientific conferences.
  • Methodologies:  Cloned cDNAs using the PCR-based technique, Representational Difference Analysis (“RDA”).  Established primary macrophage, monocyte, granulocyte and neutrophil cultures using human hematopoietic stem cells.  Retroviral infection of human stem cells, using multiple variations of the Phoenix retrovirus system.  Designed (using molecular modeling software) and successfully used antisense-hammerhead ribozymes to knock-down endogenous gene expression.  Extensive cDNA cloning and subcloning.  Muliplex RNase protection assays for gene expression.  Construction of inducible EBV episomal plasmid expression system.  Established and employed several microbial pathogenic cell models including HIV, Legionella pneumophila, Mycobacterium tuberculosis, Staphylococcus aureus, and Entamoeba histolytica (amoebic dysentery).  Extensive use of FACS including cell cycle analysis by BrdU and propidium iodide, phagocytosis of fluorescent beads, and expression/cell sorting of cDNA-IRES-GFP/YFP positive infected cells.  Affymatrix microarray and bioinformatic analyses.  Also briefly worked on v-abl infection of mouse bone marrow-derived B cell cultures (“Whitlock-Witte” cultures).  Independently initiated collaborations with multiple labs at Columbia, Albert Einstein, Sloan-Kettering, and Princeton.

Postdoctoral Fellow, University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA


  • Project:  Discovered and studied novel genes involved in negative and positive selection of thymocytes in transgenic mice.
  • Responsibilities:  Implemented and managed multiple research projects.  Wrote several grant proposals.  Reviewed others’ grant proposals and manuscript submissions.
  • Methodologies:  Created thymus cDNA libraries from transgenic antigen-specific mouse models of positive and negative T cell selection.  Employed multiple apoptosis and proliferation assays to validate genes;  TUNEL, BrdU, propidium idodide, Caspase C, and Annexin V.

Travelling Scholar/Researcher, Tularik, Inc., South San Francisco, CA (a subsidiary of Genentech, Inc)


  • Project:  Isolated and characterized cytokine promoter DNA-binding proteins as part of Harvard graduate thesis work (see below).
  • Responsibilities:  Implemented and managed multiple research projects.
  • Methodologies:  Large scale (10-20 liter) primary cell cultures.  Large scale protein isolation, fractionation, purification and identification (by micro-peptide sequencing).

Graduate Student, Harvard University, Department of Genetics, Boston, MA


  • Project:  Studied the transcriptional regulation of cytokine genes in primary T helper 1 and T helper 2 cell clones.  Helped to identify c-Maf as the master regulatory factor for T helper 2 fate commitment.
  • Responsibilities:  Implemented and managed multiple research projects.  Reviewed grant proposals and manuscript submissions.  Attendance and presentation at several scientific conferences.
  • Methodologies:  Establishment and transfection of primary mouse T helper 1 and T helper 2 cell clones.  Mutational analysis of Interleukin 2 (IL-2), Interleukin 4 (IL-4), and MHC class II promoters and transient transfection reporter assays.  Identification and analysis of transcription factors.  DNase I and in vivo footprinting.  Creation of hybridomas and antibody purification.  Cell proliferation assays.  Cell fusion studies.  ELISA assays.  Immunoprecipitations, co-immunoprecipitations, and Western analyses.  In vivo metabolic protein labeling and phospho-amino acid analysis.  Transgenic mice studies.  Quantitative RT-PCR.  Gel Shift assays.
  • Projects during two years of lab rotations:
    •  Yeast genetics in the lab of Fred Winston, Ph.D.  Complementation analysis of the transcription factors TFIID and SPT3.  Reverse genetics/mutational analysis.
    • Role of the transcription factor, MyoD, in muscle cell differentiation and embryogenesis in the lab of Andrew Lassar, Ph.D.
    • Genes expressed during E. coli stationary phase in the lab of Roberto Kolter, Ph.D.

Research Technologist, University of Washington, Department of Genetics, Seattle, WA


  • Project:  Transcriptional regulation of Immunoglobulin genes in human B cells.
  • Responsibilities:  Carried out several research projects.  Trained graduate students.  Managed daily lab operations.
  • Methodologies:  PCR.  DNA sequencing. Northern (RNA) and Southern (DNA) analyses.  Creation and complementation analysis of mutated human B cell lines (“reverse genetics”).  Isolation and analysis of primary B cells.  Also briefly worked on molecular biology of Plasmodiumfalciparum (malaria) and Leishmaniasp.

See John W. Rooney’s complete background, here.


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