University or Institution

Cummings School of Veterinary Medicine at Tufts University

area of research:

Advancing models of infectious disease through deep learning and artificial intelligence.

PRIMARY MENTOR:

The primary mentor is Gillian Beamer, VMD, PhD, DACVP an assistant professor at Cummings School of Veterinary Medicine (CSVM). She is an NIH-funded scientist with a research program on tuberculosis and a board-certified veterinary anatomic pathologist. The overarching goal of her research is to define the complex genetics of differential host susceptibility to Mycobacterium tuberculosis and accurately predict disease outcomes (i.e., define risk for individual patients). Dr Beamer also collaborates with investigators on many other infectious diseases: cryptosporidiosis, shigellosis, colibacillosis, salmonellosis, helminthiasis, and tick-borne diseases. Dr Beamer uses digital pathology and collaborates with computer scientists in academia and industry to create new digital pathology solutions. Since joining Tufts in 2012, Dr Beamer has mentored: post-doctoral scientists, visiting faculty and veterinarians; veterinary residents (anatomic pathology and ophthalmology); veterinary students; medical students; graduate students; masters students; undergraduates and high school students.

MENTOR TEAM:

  1. Metin Gurcan, PhD is a full professor and Director, Center for Biomedical Informatics at Wake Forest School of Medicine in Winston Salem, NC. His research interests are in algorithms, artificial intelligence, biomedical informatics, computer-assisted image processing and automated pattern recognition. His role is mentoring for anything related to histopathology image processing.
  2. Bulent Yener, PhD is a full professor, and co-Director of Pervasive Computing and Networking Center, in the Department of Computer Science at Rensselaer Polytechnic Institute (RPI) in Troy, New York. His role is mentoring for data mining and analytics.
  3. Amanda Martinot, MPH, PhD, DACVP is an assistant professor in the Department of Infectious Disease and Global Health at CSVM. She is co-director of the newly established Comparative Pathology and Genomics Core. Her diagnostic and research pathology interests encompass tuberculosis, multiple viral pathogens (including SARS-2), and advanced digital histopathology.

Description of Potential Research Projects:

Computer-aided image processing, analysis, deep learning and artificial intelligence are actively being used in medical applications and biomedical research. The field of veterinary anatomic pathology, with support from the American College of Veterinary Pathologists strategic plan, is now exploring and adopting these new technologies (“digital pathology”) to improve data extraction from images used research and diagnostic settings. To our knowledge, this fellowship is the first to actively recruit and support pathologist fellows to train under veterinary pathologists and computer scientists that are currently developing and using deep learning and artificial intelligence to investigate animal models of human infectious disease. This fellowship is open to board-certified veterinary pathologists and board-eligible trainees with a strong interest in learning to use and apply digital pathology to animal models of infectious disease. The goals of this fellowship are to 1) Create and use digital pathology tools to understand host-pathogen interactions that cause disease; 2) Extract and quantify image features for quantitative analyses and predictive modelling; 3) Gain an understanding of how machine learning, deep learning, and artificial intelligence apply to modern pathology and biomedical research images; 4) Develop critical thinking, scientific communication, and grant-writing skills. The overarching goal of Dr Beamer’s laboratory is to understand differential host susceptibility to Mycobacterium tuberculosis and to use that knowledge to produce and test accurate prognostic biomarkers.

Additional Training Opportunities:

Dr Beamer’s laboratory. The fellow will be integrated into Dr Beamer’s bi-weekly laboratory meetings with collaborators at Wake Forest University and at RPI, and their graduate students for presentations, discussions, and data analyses on tuberculosis. Monthly meetings include Dr. Martinot’s group.

Department of Infectious Disease and Global Health IDGH sponsors monthly journal clubs and work-in-progress seminars as part of existing graduate and signature programs: Masters of Infectious Disease and Global Health, Masters of Conservation Medicine, PhD in Biomedical Sciences, and certificate in International Veterinary Medicine.

Comparative Pathology and Genomics Core CSVM was recently awarded a grant from the Massachusetts Life Sciences program to establish a core on campus, which substantially improves capacity to evaluate animal models of infectious disease. The core is directed by co-mentor Dr. Amanda Martinot (MPH, PhD, DACVP) and co-directed by Dr Heather Gardner, DVM, PhD, DACVIM (Oncology) who specializes in genetics. The fellow will participate in all aspects of the core, developing an understanding of equipment, methods, and applications for advanced digital histopathology techniques: tissue cyclic immunofluorescence (t-CyCIF); RNA and DNA spatial profiling; and machine learning/artificial intelligence algorithm development, validation, and application for H&E, IHC, and IF-stained tissues using aiforia’s platform and HALO.

Cummings School of Veterinary Medicine Weekly, monthly, and quarterly seminars at CSVM, Tufts Medical Center, and local partners (i.e., University of Massachusetts Medical Center in Worcester and Harvard School of Public Health) provide a rich scientific and collaborative environment. CSVM has a robust summer research program and seminar series and a dedicated annual Research Day. A fellow with a strong clinical interest can also attend weekly and monthly seminars on clinical topics for small and large animals, and wildlife; weekly histopathology rounds; and monthly “grand rounds” with specialty services (e.g., ophthalmology and neurology).

Tufts University CTSI Tufts has many opportunities for fellows at Grafton, Medford, and Boston campuses. The CTSI, housed on the Boston campus, provides outstanding resources in translational science education and training. The mission of the CTSI is to accelerate translation of research into clinical care. The CTSI provide support in research design & analysis, research collaboration, clinical studies & trials, informatics, one health and medical devices. They sponsor drop-in sessions and events with a calendar here: https://www.tuftsctsi.org/all-events/201906/. The CTSI also has a K-scholar program at https://www.tuftsctsi.org/education/k-scholar-programs/ and each semester offers interactive seminars and workshops for new and experienced researchers affiliated with Tufts. Currently, there are at least 28 courses to address the need for investigators to operate across disciplines and stages in the translational spectrum, and to equip participants with competencies that can truly advance clinical and translational research.

Contact Information for Interested Potential Trainees:

Gillian Beamer, VMD, PhD, DACVP

Cummings School of Veterinary Medicine

508-839-7913

[email protected]