Johns Hopkins Mouse Pathobiology and Phenotyping Short Course
♦ Rigor and Reproducibility in Translational Research 


Aiming for hybrid, with in person practical sessions in July 2023

Introductory lecture: Practical mouse pathobiology lecture will be given by Zoom July 8,  12 noon contact to receive a zoom invitation



⇒ GRAD students for full credit would schedule in-lab training at a later date.

Tuition Remission Form (for JHU Faculty & Staff) 
NON JHU Registration Form: 

⇒  EXHIBIT Registration (includes access to course lectures activities throughout the week) email to get more information



Target Audience: Graduate students and postdocs, as well as research faculty and staff, who currently work with, or expect to work with mouse models and genetically engineered mice.

Since 2010 this has been offered in a short course format, largely for continuity of the practical laboratory training experience.
In 2021 we are offering lectures and lab demo sessions online, and will be trying some online interactive sessions as well.

Faculty from JHU School of Medicine and Bloomberg School of Public Health introduce concepts in mouse biology, pathology, genetics, normal ‘phenotypes’, phenotyping concepts, new and established phenotyping capabilities in multiple disciplines.
JHU cores and resources are highlighted. See previous course programs/schedules below.

Up to 29 hr Approved RACE CE credit. [Only sessions attended can be claimed for credit]
In lab training to be scheduled at a later date, after passing exam to include clinical and physical examination of mice, specimen collection, clinical pathology and anatomic pathology
(Familiarity with basic anatomy is EXPECTED for participation in laboratory sessions).

Syllabus material is provided:   Hard copy laboratory manual is provided to all enrolled in laboratory sessions.  Lecture and laboratory syllabus material is provided electronically as pdf’s linked to the program.   It is NOT necessary to purchase a text book.

(JHUSOM graduate school ME 680.712) Course credit and grades are based on:

  1. Attendance and participation in online sessions;
  2. Exam (‘take home’, Open book, JHU honor code applies), distributed Monday at the beginning of the course, and Due Friday, 5pm.The exam is intended to be practical and relevant to diverse research.
  3.  IN LAB training: Planned in 2023

Course Co-Directors: Cory Brayton, DVM, Dip. ACLAM, ACVP, Jason Villano, DVM, MS, DACLAM, Kinta Diven, MS.

Course Administrator: TBD – 410 502 3050
Graduate students and postdocs in JHU institutions OTHER THAN SOM should contact Wendy for assistance.

Expect 5-10 min breaks between sessions 

MONDAY                  Welcome, Introductions

8am    password protected login will begin

845-10am            Brayton  – Introduction: Phenotyping & Famous Mice

10-11    Brayton  –  Common Phenotypes & Disease (Spontaneous /NON infectious)

11-12    Brayton –  External Environmental (X) Factors and Reproducibility


1-2        Keynote Speaker TBD

2-3        Bayton–  Microbial & infectious Research Challenges

3-4        Brayton  –  Immunovariability in (immune sufficient and immune deficient) mice

4-5        Hutchinson – Research relevant social life and behaviors of mice



TUESDAY                     GEM & Multidisciplinary Phenotyping

9-10        Hawkins/Reeves – Making Mice – traditional and new transgenic technologies

10-11      Aja – Metabolic Phenotypes and Phenotyping

11-12      Mitzner – Pulmonary/Respiratory Phenotypes & Phenotyping

12-130   LUNCH &  Meet the Cores, Tours BREAKOUT SESSIONS
CSMR (metabolic), MRB Behavioral, ESC, OTS

130-230   Doyle – Ophthalmic Phenotypes and Phenotyping

230-330   Vicencio/Lauer – Auditory Phenotypes and Phenotyping

330-430   Foss/Gabrielson  – IMAGING for Phenotyping


WEDNESDAY             Practical Phenotyping 1

JH Phenotyping Laboratory Manual 5th ed 2019  (PDF 58p  ~6MB) free to download
REVIEW by Wednesday AM

9-1030    LAB 1: Brayton Villano  et al – Clinical / Physical Exam + DEMO

1030-12  Brayton – Clinical Pathology (Hematology Chemistry, etc for research)

12-130   LUNCH &  Meet the Cores, Tours BREAKOUT SESSIONS
CSMR (metabolic), AIMS Core, MRB Imaging 1230-50, ESC, OTS

130-3    LAB 2: Villano  et al Specimen collections and common procedures 

3-4        Faculty/Core breakout Q&A sessions AND/OR interactive REVIEW (Quiz format)


THURSDAY              Practical Phenotyping 2

9-1030       Brayton/Forbes- Anatomic Pathology Phenotyping  – Necropsy, examination, tissue collection trimming Lecture

1030-1130  LAB 3: Brayton Anatomic Pathology – Necropsy, examinaton, tissue collection DEMO/video Q&A

1130-12      OTS CORE Histology Lab

12-1           LUNCH BREAK (on your own)

1-215         Brayton – Comparative Anatomy/Pathology (human/mouse)

230-330    Meeker  –  Immunohistochemistry – principles and protocol development

330-430       Faculty Discussion of participants research questions AND/OR Brayton – Research Relevant Mouse Phenotypes & Pathology – interactive REVIEW (Quiz format)


FRIDAY                   Practical Phenotyping 3 Advanced Pathology

9-10      TBD   Brayton – Research Relevant Mouse Phenotypes & Pathology – interactive REVIEW (Quiz format)

10-11    TBD – Practical Pre GLP Pathology (efficacy/safety assessments in academic settings)

11-12  TBD – Digital Pathology: options for image analysis and quantitative pathology      

12-1      J Ward – Embryo and Developmental Phenotyping

1-130  pathology Faculty Discussion of participants research questions

5pm        Quizzes Due ! for course ME680.712


Phenotyping Core
Johns Hopkins Phenotyping and Comparative Pathology Core (MRB)
iLAB information and submission

Animal Care and Use Committee (ACUC)

Applied Imaging Mass Spectrometry (AIMS) Core

Behavioral Core School of Medicine
Rodent Behavioral Phenotyping (MRB)

CSMR Centralized Services for Metabolism Research
Indirect calorimetry, food intake (Rangos)

ES Cell and Transgenic Core
Johns Hopkins Transgenic and ES Cell core

MRB Molecular Imaging  Core
MRI, PET, CT, SPECT, IVIS, Optical Imaging, Ultrasound (MRB)

OTS Oncology Tissue Services Core
TMA, IHC, Slide Scanning, Histology core labs at SKCCC
iLAB information and submission

Laboratory Manual and Previous Programs



2022 Brayton Intro Mice 0704

2022 Brayton Reporting Workshop

Research-Relevant Conditions and Pathology of Laboratory Mice, Rats, Gerbils, Guinea Pigs, Hamsters, Naked Mole Rats, and Rabbits.  Cooper TK, Meyerholz DK, Beck AP, Delaney MA, Piersigilli A, Southard TL, Brayton CF. ILAR J. 2022.

Research-Relevant Clinical Pathology Resources: Emphasis on Mice, Rats, Rabbits, Dogs, Minipigs, and Non-Human Primates.       Bau-Gaudreault L, Arndt T, Provencher A, Brayton CF. ILAR J. 2021.

Research Relevant Background Lesions and Conditions: Ferrets, Dogs, Swine, Sheep, and Goats.   Helke KL, Meyerholz DK, Beck AP, Burrough ER, Derscheid RJ, Löhr C, McInnes EF, Scudamore CL, Brayton CF. ILAR J. 2021.

Research-Relevant Background Lesions and Conditions in Common Avian and Aquatic Species.               Mangus LM, França MS, Shivaprasad HL, Wolf JC. ILAR J. 2021.

Research Relevant Conditions and Pathology in Nonhuman Primates.    Saravanan C, Flandre T, Hodo CL, Lewis AD, Mecklenburg L, Romeike A, Turner OC, Yen HY. ILAR J. 2020. Re

Immune Relevant and Immune Deficient Mice: Options and Opportunities in Translational Research.            Radaelli E, Santagostino SF, Sellers RS, Brayton CF.ILAR J. 2018.