Quantitative Biosciences and Engineering

Advising Faculty

Joel Bach, Associate Professor of Mechanical Engineering

Cecilia Diniz Behn, Associate Professor of Applied Mathematics & Statistics

Nanette Boyle, Associate Professor of Chemical and Biological Engineering

Kevin Cash, Assistant Professor of Chemical and Biological Engineering

Anuj Chauhan, Professor of Chemical and Biological Engineering

Dylan Domaille, Assistant Professor of Chemistry

Christopher Higgins, Professor of Civil and Environmental Engineering

Melissa Krebs, Co-Director, QBE Graduate Program and Associate Professor of Chemical and Biological Engineering

Ramya Kumar, Assistant Professor of Chemical and Biological Engineering

Karin Leiderman, Co-Director, QBE Graduate Program and Associate Professor of Applied Mathematics & Statistics

Terry Lowe, Research Professor of Materials and Metallurgical Engineering

David Marr, Professor of Chemical and Biological Engineering

Christine Morrison, Assistant Professor of Chemistry

Alexander Pak, Assistant Professor, Chemical and Biological Engineering

Steve Pankavich, Associate Professor of Applied Mathematics & Statistics

Anthony Petrella, Associate Professor of Mechanical Engineering

Andrew Petruska, Assistant Professor of Mechanical Engineering

Matthew Posewitz, Professor of Chemistry

James Ranville, Professor of Chemistry

Susanta Sarkar, Assistant Professor of Physics

Jonathan Sharp, Associate Professor of Civil and Environmental Engineering

Anne Silverman, Associate Professor of Mechanical Engineering

E. Dendy Sloan, Emeritus Professor of Chemical and Biological Engineering

John Spear, Professor, Civil and Environmental Engineering

Jeff Squier, Professor of Physics

Amadeu Sum, Professor of Chemical and Biological Engineering

Brian Trewyn, Associate Professor of Chemistry

Shubham Vyas, Associate Professor of Chemistry

Hua Wang, Associate Professor of Computer Science

Kim Williams, Professor of Chemistry

Xiaoli Zhang, Associate Professor of Mechanical Engineering

Teaching Faculty

Linda Battalora, Teaching Professor of Petroleum Engineering

Suzannah Beeler, Assistant Teaching Professor of Chemical and Biological Engineering

Kristine Csavina, Teaching Professor of Mechanical Engineering

Alina Handorean, Teaching Professor of Engineering, Design & Society

Cynthia Norrgran, Teaching Associate Professor of Chemical and Biological Engineering

Josh Ramey, Director of the QBE Undergraduate Program and Teaching Associate Professor of Chemical and Biological Engineering

Justin Shaffer, Teaching Associate Professor of Chemical and Biological Engineering

Quantitative Biosciences and Engineering (QBE) Program Requirements

For admission, students may enter with biology or health-related undergraduate degrees or with a technical degree, e.g., in engineering, mathematics, or computer science. 

Current Mines undergraduate students have the option to apply to the Office of Graduate Studies for the combined program while pursuing their undergraduate degree (see information below).

Each of the three degrees (non-thesis Master of Science, thesis-based Master of Science, and Doctor of Philosophy) require the successful completion of four core courses for a total of 13 credits, as detailed below. 

QBE Core Courses
BIOL500CELL BIOLOGY AND BIOCHEMISTRY4.0
BIOL510BIOINFORMATICS3.0
BIOL520SYSTEMS BIOLOGY3.0
CHGN535PHYSICAL BIOCHEMISTRY3.0
Total Semester Hrs13.0

QBE Graduate Seminar

Full-time graduate students in the QBE program are expected to maintain continuous enrollment in BIOL 590, QBE Graduate Seminar, a 1 credit course. A maximum of 2 credits will be granted toward the MS degree requirements while a maximum of 4 credits will be granted toward PhD requirements, as shown below. Students who are concurrently enrolled in a different degree program that also requires seminar attendance may have this requirement waived at the discretion of the QBE Program Director.

Master of Science in Quantitative Biosciences and Engineering (Non-Thesis Option)

The Master of Science Non-Thesis (MS-NT) degree requires a minimum of 30 credits of acceptable coursework.

QBE Core Courses13.0
QBE Electives (see list below)15.0
BIOL590QUANTITATIVE BIOSCIENCES & ENGINEERING GRADUATE SEMINAR (*)2.0
Total Semester Hrs30.0

*While full-time MS-NT students are expected to maintain continuous enrollment in BIOL 590, the QBE Graduate Seminar; a maximum of 2 credits will be granted toward the MS-NT degree requirements.

Master of Science in Quantitative Biosciences and Engineering (Thesis Option)

The thesis-based Master of Science (MS-T) requires a minimum of 30 semester hours of acceptable coursework and thesis research credits. Students conduct an in-depth research project with one of the participating faculty members who are currently accepting masters degree students. The student must also submit a thesis and pass the thesis defense examination before the thesis committee.

QBE Core Courses13.0
QBE Elective3.0
BIOL590QUANTITATIVE BIOSCIENCES & ENGINEERING GRADUATE SEMINAR (*)2.0
BIOL707GRADUATE THESIS / DISSERTATION RESEARCH CREDIT12.0
Total Semester Hrs30.0

*While full-time MS-T students are expected to maintain continuous enrollment in BIOL 590, the QBE Graduate Seminar; a maximum of 2 credits will be granted toward the MS-T degree requirements.

Doctor of Philosophy in Quantitative Biosciences and Engineering

The Doctor of Philosophy (PhD)degree requires a minimum of 72 hours of course and research credit including at least 24 credits in coursework and at least 24 credits in research. Doctoral students must also pass a qualifying examination and thesis-proposal defense, complete a satisfactory thesis, and successfully defend their thesis.

QBE Core Courses13.0
QBE Electives11.0
BIOL590QUANTITATIVE BIOSCIENCES & ENGINEERING GRADUATE SEMINAR (*)4.0
BIOL707GRADUATE THESIS / DISSERTATION RESEARCH CREDIT24.0
QBE Electives or BIOL707 Research20.0
Total Semester Hrs72.0

*While full-time PhD students are expected to maintain continuous enrollment in BIOL 590, the QBE Graduate Seminar, a maximum of 4 credits will be granted toward the PhD degree requirements.

QBE Elective Courses:

The current list of available electives is shown below. Because course options are continually expanding, additional complementary courses (beyond those listed here) may be approved on an ad hoc basis by the advisor in consultation with the program director. 

BIOL599INDEPENDENT STUDY0.5-6
CBEN505NUMERICAL METHODS IN CHEMICAL ENGINEERING3.0
CBEN511NEUROSCIENCE, MEMORY, AND LEARNING3.0
CBEN531IMMUNOLOGY FOR SCIENTISTS AND ENGINEERS3.0
CBEN532TRANSPORT PHENOMENA IN BIOLOGICAL SYSTEMS3.0
CBEN570INTRODUCTION TO MICROFLUIDICS3.0
CBEN624APPLIED STATISTICAL MECHANICS3.0
CBEN625MOLECULAR SIMULATION3.0
CEEN501LIFE CYCLE ASSESSMENT3.0
CEEN551ENVIRONMENTAL ORGANIC CHEMISTRY3.0
CEEN560MOLECULAR MICROBIAL ECOLOGY AND THE ENVIRONMENT3.0
CEEN562ENVIRONMENTAL GEOMICROBIOLOGY3.0
CEEN566MICROBIAL PROCESSES, ANALYSIS AND MODELING3.0
CEEN570WATER AND WASTEWATER TREATMENT3.0
CHGN509BIOLOGICAL INORGANIC CHEMISTRY3.0
CHGN507ADVANCED ANALYTICAL CHEMISTRY3.0
CSCI562APPLIED ALGORITHMS AND DATA STRUCTURES3.0
CSCI575ADVANCED MACHINE LEARNING3.0
EBGN525BUSINESS ANALYTICS3.0
EBGN553PROJECT MANAGEMENT3.0
MATH530INTRODUCTION TO STATISTICAL METHODS3.0
MATH572MATHEMATICAL AND COMPUTATIONAL NEUROSCIENCE3.0
MEGN531PROSTHETIC AND IMPLANT ENGINEERING3.0
MEGN532EXPERIMENTAL METHODS IN BIOMECHANICS3.0
MEGN535MODELING AND SIMULATION OF HUMAN MOVEMENT3.0
MEGN536COMPUTATIONAL BIOMECHANICS3.0
MEGN537PROBABILISTIC BIOMECHANICS3.0
MTGN570BIOCOMPATIBILITY OF MATERIALS3.0
MTGN572BIOMATERIALS3.0

Mines' Combined Undergraduate / Graduate Degree Program

Students enrolled in Mines’ combined undergraduate/graduate program may double count up to 6 credits of graduate coursework to fulfill requirements of both their undergraduate and graduate degree programs. These courses must have been passed with B- or better, not be substitutes for required coursework, and meet all other university, department, and program requirements for graduate credit.

Students are advised to consult with their undergraduate and graduate advisors for appropriate courses to double count upon admission to the combined program.

BIOL500. CELL BIOLOGY AND BIOCHEMISTRY. 4.0 Semester Hrs.

This course will provide students with deep biological insight as well as hands-on experience of studying a biological question at the level of the cell, including gene expression and localization of proteins in eukaryotic cells, to the level of the protein, from molecular biology of the gene to characterization of posttranslational modifications, and protein purification and biochemical and biophysical characterization of protein structure and dynamics. These fundamental properties will be linked to protein activity and function. The emphasis of this course is on quantitative biology. Wherever appropriate, advanced concepts of protein chemistry and physics will be integrated into the delivery of the basic concepts. the course includes a 3 credit hour lecture section and a 1 credit hour lab section.

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  • Students will be familiar with basic terminology of all aspects of biology and will be able to recognize important cellular functions by their names
  • Students will be able to define the chemical building blocks of biomolecules and understand how these connect to biological functions
  • Students will be able to visualize protein and other molecular structures and their interactions using pymol software
  • Students will have gained sufficient insight into different areas of biology and medicine to make informed decisions on their future career path
  • Students will be able to make quantitative statements on the major biological processes
  • Students will be familiar with modern –omics approaches and will know what can and what cannot be learned from them
  • Students will be trained to identify opportunities for studying the interfaces between Mines’ themes of earth, environment and energy and specific applications in biology and health
  • Students will gain an appreciation of the benefits of integrating quantitative, computational approaches and design experimental approaches to test predictions
  • Students will be able to analyze large datasets as a result of the sister course and derive biological hypotheses from them based on current understanding of biomolecules studied in this class
  • Students will be able to critically evaluate existing bio/medical data and derive gaps in knowledge
  • Students will be trained in active thinking and design of future work to address identified gaps

BIOL501. ADVANCED BIOCHEMISTRY. 3.0 Semester Hrs.

Advanced study of the major molecules of biochemistry: amino acids, proteins, enzymes, nucleic acids, lipids, and saccharides- their structure, chemistry, biological function, biosynthesis, and interaction. Stresses bioenergetics and the cell as a biological unit of organization. Advanced discussion of the intertwining of molecular genetics, biomolecule synthesis, and metabolic cycles. Prerequisites: CHGN428 or BIOL500.

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View Course Learning Outcomes
  • Demonstrate a broad knowledge of the fundamental introductory concepts of Chemistry, Biology and Physics
  • Demonstrate a thorough knowledge of the intersection between the disciplines of Biology and Chemistry.
  • Locate, critically analyze, interpret and discuss data, hypotheses, results, theories, and explanations found in the primary literature, applying knowledge from Chemistry and Biology.
  • Appreciate the way in which practitioners in the disciplines of Biology and Chemistry intersect and bring their expertise to bear in solving complex problems involving living systems.

BIOL510. BIOINFORMATICS. 3.0 Semester Hrs.

Bioinformatics is a blend of multiple areas of study including biology, data science, mathematics and computer science. The field focuses on extracting new information from massive quantities of biological data and requires that scientists know the tools and methods for capturing, processing and analyzing large data sets. Bioinformatics scientists are tasked with performing high-throughput, next-generation sequencing. They analyze DNA sequence alignment to find mutations and anomalies and understand the impact on cellular processes. The bioinformatician uses software to analyze protein structure and its impact on cell function. Learning how to design experiments and perform advanced statistical analysis is essential for anyone interested in this field, which is main goal of this course. Prerequisite: CSCI102.

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View Course Learning Outcomes
  • 1. knowledge and awareness of the basic principles and concepts of biology, computer science and mathematics;
  • 2. existing software effectively to extract information from large databases and to use this information in computer modeling;
  • 3. problem-solving skills, including the ability to develop new algorithms and analysis methods;
  • 4. an understanding of the intersection of life and information sciences, the core of shared concepts, language and skills;
  • 5. the ability to speak the language of structure-function relationships, information theory, gene expression, and database queries.

BIOL520. SYSTEMS BIOLOGY. 3.0 Semester Hrs.

This course provides students an introduction to the emerging field of systems biology. It will consist of lectures, group discussion sessions, and problem-solving sessions and/or computational labs. Students will learn strategies and tools to interrogate biological systems using mathematical modeling. Topics of the course will come from typical aspects of biomathematical modeling including, but not limited to: the choice of a modeling framework from various approaches; the design of interaction diagrams; the identification of variables and processes; the design of systems models; standard methods of parameter estimation; the analysis of steady states, stability, sensitivity; numerical evaluations of transients; phase-plane analysis; simulation of representative biological scenarios. All theoretical concepts are exemplified with applications.

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  • At the completion of the course, students will be able to:1. Describe and understand important types of quantitative/mathematical models used in the field of systems biology
  • 2. Explain the basic strengths and limitations of quantitative/mathematical modeling of biological systems
  • 3. Design and implement quantitative/mathematical models of biological systems
  • 4. Apply appropriate techniques for steady-state and dynamical analysis of models
  • 5. Utilize different modeling tools for the analysis of models and their output
  • 6. Assimilate current systems biology literature, extend it in a final project, and communicate results professionally and effectively

BIOL598. SPECIAL TOPICS. 6.0 Semester Hrs.

(I, II, S) Pilot course or special topics course. Topics chosen from special interests of instructor(s) and student(s). Usually the course is offered only once, but no more than twice for the same course content.. Variable credit: 0 to 6 credit hours. Repeatable for credit under different titles.

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BIOL599. INDEPENDENT STUDY. 0.5-6 Semester Hr.

(I, II, S) Individual research or special problem projects supervised by a faculty member, also, when a student and instructor agree on a subject matter, content, and credit hours. Prerequisite: "Independent Study" form must be completed and submitted to the Registrar. Variable credit: 0.5 to 6 credit hours. Repeatable for credit under different topics/experience and maximums vary by department. Contact the Department for credit limits toward the degree.

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BIOL707. GRADUATE THESIS / DISSERTATION RESEARCH CREDIT. 1-15 Semester Hr.

(I, II, S) Research credit hours required for completion of a Masters-level thesis or Doctoral dissertation. Research must be carried out under the direct supervision of the student's faculty advisor. Variable class and semester hours. Repeatable for credit.

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