Timothy Allen headshot
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Timothy E. Allen

Professor
Unit: School of Engineering and Applied Science
Department: Department of Biomedical Engineering
Office location and address
MR5 2312
415 Lane Rd
Charlottesville, Virginia 22903
Education
B.S. ​Duke University, 1999
​M.S. University of California, San Diego, 2001
Ph.D. ​University of California, San Diego, 2006
Biography

Dr. Timothy E. Allen is an Associate Professor in the Department of Biomedical Engineering at the University of Virginia. He received a B.S.E. in Biomedical Engineering at Duke University and M.S. and Ph.D. degrees in Bioengineering at the University of California, San Diego. Dr. Allen's teaching activities include coordinating the undergraduate teaching labs and the Capstone Design sequence in the BME department at the University of Virginia, and his research interests are in the fields of computational biology and bioinformatics. He is also interested in evaluating the pedagogical approaches optimal for teaching lab concepts and skills, computational modeling approaches, and professionalism within design classes. Dr. Allen is the PI on a new NSF REU site focused on multi-scale systems bioengineering, a collaboration involving 12 faculty in SEAS, SOM, and CLAS at UVa, as well as four partner institutions in the mid-Atlantic and Southeast. He also coordinates the BME DesignLab along with David Chen (Director, UVa Coulter Translational Partnership).

EN-BME- REU Site: Multi-Scale Systems Bioengineering and Biomedical Data Sciences
Source: U.S. National Science Foundation (NSF)
April 01, 2020 – March 31, 2023
EN-BME- REU Site: Multi-Scale Systems Bioengineering
Source: U.S. NSF - Directorate For Engineering
December 01, 2016 – November 30, 2019
EN-BME Advanced Design in Biomedical Engineering
Source: Nciia - Lemelson Fdn.
August 01, 2007 – August 31, 2015
PuzzleCast: Designing a Solution to Muscle Atrophy Through a Modular Cast
Source: The National Collegiate Inventors & Innovators All
April 01, 2011 – June 30, 2014
EN-BME-Introducing Simulink and Model-Based Into a Core Sophomore Level Biomedical Engineering Design Course
Source: The MathWorks, Inc.
June 01, 2013 – May 31, 2014
Enhancing Undergraduate Biomedical Engineering Instrumentation Laboratories Using MATLAB
Source: The MathWorks, Inc.
May 01, 2012 – May 31, 2013
BME 3030: Design and Innovation in Medicine
Credits: 3
Project-driven course focusing on biomedical product design with emphasis on marketability, innovation, entrepreneurship and business. Topics include design fundamentals, problem/needs identification, delineation of realistic constraints and product specifications, intellectual property, market analysis, entrepreneurship, specific advanced design, business plan development, venture funding, and medical product testing methods. REQ: BME 2000 or instructor permission.
BME 3080: Biomedical Engineering Integrated Design and Experimental Analysis (IDEAS) Laboratory I
Credits: 4
A year-long course integrating concepts and skills from prior courses to formulate and solve problems in biomedical systems, including experimental design, performance and analysis. Testing in tissues/cells & manipulation of molecular constituents to determine structural and functional characteristics for design of therapeutic or measurement systems. Methods incl biochemical, physiological, cell biology, mechanical, electrical and computer, systems, chemical, imaging, and other approaches. Prerequisite: 3rd Year standing in Biomedical Engineering major
BME 3090: Biomedical Engineering Integrated Design and Experimental Analysis (IDEAS) Laboratory II
Credits: 4
Second half of a year-long course to integrate the concepts and skills from prior courses in order to formulate and solve problems in biomedical systems, including experimental design, performance, and analysis. Lab modules include testing in tissues/cells and manipulation of molecular constituents of living systems to determine their structural and functional characteristics and to design measurement or therapeutic systems. Methods include biochemical, physiological, cell biology, mechanical, electrical and computer, systems, chemical, imaging, and other approaches. Prerequisite: BIOM 3080 or instructor permission.
BME 4063: Biomedical Engineering Capstone Design I
Credits: 3
A year-long design project required for BME majors. Students select, formulate, and solve a design problem related to a device or a system. Projects use conceptual design, skills obtained in the integrated lab and substantial literature and patent reviews. Projects are sponsored by faculty, physicians and/or companies. Students may work on their own with outside team members when appropriate or with other students in integrative teams. Prerequisite: 4th year standing in the Biomedical Engineering major or instructor permission.
BME 4064: Biomedical Engineering Capstone Design II
Credits: 3
Second half of a year-long design project in biomedical engineering required for BME majors. Students select, formulate, and solve a biomedically relevant design problem whose deliverables include a device, therapeutic, and/or system. Projects may be sponsored by BME faculty, medical doctors, and/or companies. Students may work on their own with outside team members when appropriate or with other SEAS students in integrative teams. Prerequisite: APMA 2120, 2130, 3110, BME 2101, 2104, 3080, 3310, fourth-year standing in BME major, or instructor permission.
BME 4550: Special Topics in Biomedical Engineering
Credits: 3
Applies engineering science, design methods, and system analysis to developing areas and current problems in biomedical engineering. Topics vary by semester. Recent topics include Medical Imaging Systems Theory, BME Advanced Design, BME Electronics Lab, and Systems Biology Modeling and Experimentation. Prerequisite: third- or fourth-year standing and instructor permission.
BME 4995: Biomedical Engineering Advanced Projects
Credits: 1–3
A year-long research project in biomedical engineering conducted in consultation with a department faculty advisor; usually related to ongoing faculty research. Includes the design, execution, and analysis of experimental laboratory work and computational or theoretical computer analysis of a problem. Requires a comprehensive report of the results. Prerequisite: third- or fourth-year standing, and instructor permission.
BME 6030: Design and Innovation in Medicine
Credits: 3
A project-based grounding in biomedical product design, with emphasis on clinical immersion and topics including design fundamentals, problem/needs identification, delineation of realistic constraints and product specifications, intellectual property, market analysis, entrepreneurship, specific advanced design topics, business plan development, venture funding, and medical product testing methods. Prerequisite: Instructor Permission
BME 6101: Physiology I for Engineers
Credits: 3
Introduces fundamental concepts of cellular physiology; applies quantitative engineering analysis to intra- and intercellular signaling and mechanical systems relevant to organ physiology and pathology; teaches students to learn to think critically about the physiology and cell biology literature. Prerequisite: BME 2104 or equivalent; proficiency with ODEs.
BME 6102: Engineering Physiology II
Credits: 3
Second part of physiology sequence for engineering students; focuses on physiology of the cardiovascular, pulmonary, renal, and nervous systems; emphasizes quantitative analysis of organ function, particularly the use of mathematical models to identify and understand key underlying mechanisms. Prerequisite: BME 6101
BME 6311: BME Measurement Principles
Credits: 3
Students will gain a fundamental understanding of the theoretical principles underlying biomedical measurements. Topics are organized sequentially from signal initiation through signal processing to downstream statistical analysis of measurements. Students will be exposed to the practical implementation of general principles through homework assignments that involve the analysis and evaluation of molecular, cellular, and clinical measurements. Prerequisites: 1. BME 6101: Physiology I (or equivalent) 2. SEAS graduate student status 3. Some previous exposure to probability-statistics, Fourier analysis, and linear systems 4. Or Instructor Permission
BME 6315: Systems Bioengineering
Credits: 3
Introduces techniques for constructing mathematical and computational models of biological processes at many levels of organizational scale from genome to whole-tissue. Topics include choice of techniques, quantitative characterization of biological properties, assumptions and model simplification, parameter estimation and sensitivity analysis, model verification and validation and integration of computational modeling w/experimental approaches. Prerequisites: BME 6101, and BME 2104 or BME 7806 (or equivalent).
BME 8995: M.E. Supervised Project Research (M.E. STUDENTS ONLY)
Credits: 1–6
FOR M.E. STUDENTS ONLY. A research project in biomedical engineering conducted in consultation with a faculty advisor. Includes the design, execution, and analysis of experimental laboratory work and computational or theoretical computer analysis of a problem. Fulfills the project requirement for the Biomedical Engineering Masters of Engineering degree. Prerequisites: Instructor Permission Required.
BME 8999: Master's Research
Credits: 1–12
Master's Research
BME 9999: Dissertation
Credits: 1–12
Formal record of student commitment to doctoral research under the guidance of a faculty advisor. May be repeated as necessary.

All-University Teaching Award 2017

Faculty Banner Carrier for SEAS Class of 2017 at Final Exercises 2017

The Society of P.R.I. Recognition for Commitment to Students 2016

Jefferson Scholars Foundation Faculty Fellow 2014-PRESENT

Hartfield-Jefferson Teaching Prize 2014

Most Dedicated BME Professor Award 2011

Award for Excellence in Biomedical Engineering Undergraduate Education 2008, 2010, & 2011

Seven Society 20th Annual Monticello Dinner Series 2010

Thomas E. Hutchinson Faculty Award for Dedication and Excellence in Teaching 2009