ME:680.712 Mouse Pathobiology and Phenotyping:

Enhancing Rigor and Reproducibility in Translational Research Involving Mice


ME680.712      July 17-21, 2023          In person         East Baltimore Campus.

Graduate Student & Postdoc Registration via  EDUCATION SIS/SEAM

Postdocs and auditors should contact the course director (Dr. Cory Brayton) to waitlist for lab session availability.

SOM post-doc fellows should submit all registration requests via SEAM, using the case reason “Add/Drop” or “Interdivisional Registration”, depending on the course.
The SOM Change of Schedule form, is optional for post-docs and no program director signature is required.

FACULTY/STAFF: TR /Tuition Remission option may become available. For now please register using

Since 2010 this has been offered in a short course format, largely for continuity of the practical laboratory training experience.

Faculty from JHU School of Medicine and Bloomberg School of Public Health introduce concepts in mouse biology, pathology, genetics, normal ‘phenotypes’, concepts, new and established phenotyping capabilities in multiple disciplines.

JHU cores and resources are highlighted. See previous course programs/schedules below.

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

Course Co-Directors: Cory Brayton, DVM, DipACLAM, DipACVP, Jason Villano, DVM, MS, DipACLAM; Jonathan Harrold, ACUC

Course Administrator: Momina  Malik


This course offers up to ~34 contact hours: ~11hr Laboratory sessions and ~23 hr Lectures.

The three hands-on laboratory sessions 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.

SOM graduate students registered to take this course FOR CREDIT must participate in laboratory sessions.

Postdocs and auditors should contact the course director (Dr. Cory Brayton) to waitlist for lab session availability.


Learning objectives/aims:

  1. Provide information, practical tools and skills essential to humane and optimal use of mice and GEM in translational research;
  2. Achieve Rigor, Reproducibility, Validity, Translatability in research involving mice.


Learning Outcomes:

  1. Critically analyze and select mouse models and conditions for research aims;
  2. Select and Implement humane and useful procedures for research aims;
  3. Plan for pathology, special collections, histology, analyses to achieve useful specimens and data.


Credit/grade based on

  1. Lab participation (required)
  2. Quiz A   short take home multi-choice questions based on 3 methods sections
  3. Quiz B   Write your next methods section (animal portion), aligning with NIH STAR FASEB ARRIVE guidance



MONDAY       July 17 2023       Welcome, Introduction

8am                     Registration

845-10                Brayton – Introduction: Phenotyping & Famous Mice

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

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


1-2                       Brayton:      FREE RANGE RODENTS ?? Are we ready?

2-3                       Villano – 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

5-6pm                 Q&A      MEET THE PARTICIPANTS 


TUESDAY            July 18 2023       GEM & Multidisciplinary Phenotyping

9-1                       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 & VIRTUAL Meet the Cores BREAKOUT SESSIONS (CSMR (metabolic), MRB Behavioral, ESC, OTS)

130-230              Doyle – Ophthalmic Phenotypes and Phenotyping

230-330              Vicenzio/Lauer – Auditory Phenotypes and Phenotyping

330-430              Foss/Gabrielson – IMAGING for Phenotyping


WEDNESDAY     July  19 2023       Practical Phenotyping 1

JH Phenotyping Laboratory Manual   Participants should REVIEW by Wednesday AM

9-1030                Villano et al – Clinical / Physical Exam + DEMO

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

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

130-4                   LAB        1   Villano Harrold Cederberg et al Specimen collections and common procedures 

4-5                       Faculty Discussion of participants questions

Brayton              Research Relevant Mouse Phenotypes & Pathology – interactive REVIEW (Quiz format)


THURSDAY         July 20 2023       Practical Phenotyping 2 Pathology

9-1030                Brayton – Practical Pathology – Necropsy, examination, tissue collection trimming Lecture

1030-1130          Brayton – Comparative Anatomy/Pathology (human/mouse)

1130-1230          LUNCH BREAK (on your own)

1230-430            LAB        2    Brayton Villano et al Anatomic Pathology – Necropsy, examination, tissue collection DEMO/video Q&A

4-5                       Faculty Discussion of participants research questions

Brayton               Survey Quiz Part A Review


FRIDAY                July 21 2023       Practical Phenotyping 3 Advanced Pathology

9-1030                LAB        3    BRAYTON et al            trimming for histopathology (& your research aims)

1030-1130          Brayton                Quiz A ( Review

1130-1230          LUNCH on your own

1230-130            D Rao     Practical Pre GLP Pathology (efficacy/safety assessments in academic settings)

130-230              E Edmondson Immunohistochemistry Principles and practice

230-330              B Kang  Digital Pathology: options for image analysis and quantitative pathology   

330-430              J Ward  Embryo and Developmental Phenotyping

430-5                   Pathology Faculty Discussion of participants research questions

5pm                     Quiz part B 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) services-for-metabolism-research

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

JH Phenotyping Laboratory Manual 5th ed 2019  (PDF 58p  ~6MB)

2021 Schedule of Lecture and Laboratory Topics and Faculty (PDF)

2020 Schedule of Lecture and Laboratory Topics and Faculty (PDF)

2019 Schedule of Lecture and Laboratory Topics and Faculty (PDF)

2016 Schedule of Lecture and Laboratory Topics and Faculty (PDF)

2015 Schedule of Lecture and Laboratory Topics and Faculty (PDF)

2013 Schedule of Lecture and Laboratory Topics and Faculty (PDF)

2012 Schedule of Lecture and Laboratory Topics and Faculty (PDF)

2011 Schedule of Lecture and Laboratory Topics and Faculty  (PDF)

2010 Schedule of Lecture and Laboratory Topics and Faculty (PDF)

2008 Schedule of Lecture and Laboratory Topics and Faculty (PDF)

2007 Schedule of Lecture and Laboratory Topics and Faculty (PDF)

2009 Phenotyping Symposium (PDF)

2008 Phenotyping Symposium (PDF)

2007 Phenotyping Symposium (PDF)

2006 Phenotyping Symposium (PDF)


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 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, Pro 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, L 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

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


Immune Relevant and Immune De cient Mice: Options and Opportunities in Translational Research.            Radaelli E, Santagostino SF, Sellers RS, Brayton CF.ILA