IAMP: Curriculum

Trainees must exhibit a solid understanding of the quantitative fields emphasized in this program, especially around analyzing metabolomics and microbiome data. We rely on required coursework to ensure that all students have basic quantitative skills in computing, statistics, and metabolomics/genomics (see course list) and on experiential learning (e.g., workshops, interaction with the facility directors) activities to develop and apply these skills.

Computational skills: Trainees should be able to understand scientific software and use existing tools for data mining, processing, and alignment. This includes a fundamental understanding of tools available for studying the metabolome and microbiome. Data analysis workshops like DAWG and hands-on laboratory training will teach computational skills and reinforce best practices.

Statistical skills: Trainees must understand the basic theory underpinning standard and Bayesian statistics as well as machine learning approaches and be able to apply these approaches using scripting languages packages (such as R or Python) to perform exploratory data analysis, hypothesis testing, effect size estimation, classification, clustering, and predictive modeling. Statistical skills will be introduced in coursework (Block 4, see below) through the instrument and data analysis groups and reinforced during the R&R discussions.

Trainees should be able to ask questions related to metabolism (host and microbiome) that are enabled by data of the magnitude and complexity now available from modern metabolomics and genomics tools available through our technology cores. We rely on required coursework to ensure all students understand research design, metabolism, microbiology, and analytical chemistry.

Research design: Trainees must demonstrate advanced research skills concerning questions in the life sciences, including designing a proposal to test a hypothesis and critically evaluating data generated in light of this hypothesis. Coursework, bi-weekly meetings, instrument and data analysis groups, and laboratory training will be integrated to guide and assist with developing trainee research design expertise.

Metabolism: Trainees must demonstrate their knowledge of metabolism and apply it to their interpretation, for example, of metabolomics and microbiome data. IAMP trainees will gain knowledge through coursework (Block 5, see below), the Metabolomics Users Group, seminars, trainee meetings, and hands-on training.

Technology: Trainees must understand the molecular basis behind methods used to study the metabolome and microbiome, such as mass spectrometry, NMR, and sequencing-based analysis. Coursework (Block 6), instrument user groups, and hands-on training will disseminate information on state-of-the-art technology used for metabolism research.

Scientists have an obligation to clearly explain their research to diverse audiences that include the public, business persons, and policymakers, as well as scientific peers and colleagues. The trainee will gain communication experience through coursework, summer research projects, teaching, and experiential learning exercises to improve their ability to communicate effectively and persuasively to multiple audiences.

Basic research communication: All trainees must demonstrate their capacity for critical thinking, listening, generating ideas, and communicating their research in written and oral presentations. Presentations will occur during bi-weekly trainee meetings, coursework presentations, research lab meetings, and required graduate program exams and committee meetings, all of which will allow IAMP training faculty to provide feedback and guidance to trainees in best practices for communicating their research.

BMMB 581 Advances in Biochemistry (3): This core-required course introduces a broadened understanding of biochemical and biophysical principles and the basic aspects of eukaryotic and prokaryotic cell biology.

BMMB 582 Advances in Genetics and Genomics (3): This core-required course introduces genetic information, how it is stored and used by cells, and how it can be manipulated and analyzed to answer research questions.

BIOL/MCIBS/VBSC 503 Critical Elements of Genetics and Molecular and Cellular Biology (3): This course will cover selected topics in genetics and molecular and cellular biology. The goals of the course will include increasing student understanding of cellular organization, cellular differentiation, and fundamentals of genetics and evolution. Students will also become familiar with major approaches to probe cellular and genetic questions and become comfortable interpreting data generated in these studies.

BMMB 502 Critical Analysis of Biochemical, Microbiology, and Molecular Biology Scientific Literature (1): This course is designed to improve the student’s ability to read and interpret the primary scientific literature in biochemistry, microbiology, and molecular biology.

MCIBS 592 Research Seminar (2): This course aims to 1) familiarize students with the wide variety of questions and approaches being addressed in current life science disciplines and 2) learn how to successfully science presented in talks and papers. Students will develop the ability to understand how a scientific paper fits into a broader field, develop the ability to interpret a wide variety of data types, learn how to communicate scientific objectives, data, and conclusions, and develop the ability to understand speakers from a variety of disciplines.

NUTR 508 Critical Readings in Molecular Nutrition (1): Understanding approaches, methods, and current concepts in molecular biology and nutrition through critical readings of current primary literature.

BIOL 592 Critical Analysis (1): This course contains 8 hrs of RCR instruction, and students must complete and pass the online CITI and SARI training programs offered by Penn State.

MCIBS 591 Ethics, Rigor, Reproducibility, and Conduct of Research in the Life Sciences (2): This class covers ethics, scientific rigor, data reproducibility,y and transparency in research. The course involves didactic lectures, policy reviews, case studies, student-led discussions, and reflective writing around these topic areas.

BMMB 509 Ethics in Biomedical Science (1): Discussion of ethical issues and RCR relevant to scientific research in the biomedical sciences. CHEM 500 (1) contains an eight-meeting RCR module that mirrors the ORI “Introduction to the Responsible Conduct of Research” by Nicholas H. Steneck (ISBN-13: 978-0-16-072285-1). Students complete CITI training offered by Penn State.

BIOL 592 Critical Analysis (1): This course contains 8 hrs of RCR instruction, and students must complete and pass the online CITI and SARI training programs offered by Penn State.

BMMB 852 Applied Bioinformatics (2): The purpose of this course is to provide students with a foundation in the various applications of high-throughput sequencing, including chip-Seq, RNA-Seq, SNP calling, metagenomics, de-novo assembly, and others. Students will understand common bioinformatics data formats and standards, become familiar with analyzing sequencing data from various instruments, and develop computationally oriented thinking necessary to take on large-scale data analysis projects.

BMMB 554: Foundations in Data Driven Life Sciences (3): This course aims to fill gaps related to a wide range of logistical problems related to data handling and processing, a widespread disconnect between developers and consumers of biomedical analysis software, and a lack of accessible, well-developed curricula and active learning opportunities necessary for the development of key data analysis skills in the next generation of researchers and clinicians. This course aims at filling these gaps.

STAT 555 Statistical Analysis of Genomics Data (3): This course will introduce students to statistical analysis and experimental design for high-throughput "omics" data. Topics include an introduction to the biology of gene and protein expression, experimental design for high throughput measurement platforms, data pre-processing, differential expression analysis, peak finding, clustering and classification, and data reduction techniques. Trainees will become familiar with statistical and bioinformatics software.

STAT 500 Applied Statistics (3): introduces the basic concepts of probability, standard distributions, statistical methods, and data analysis. It is intended for graduate students who have one undergraduate statistics course and wish to review the fundamentals before taking additional 500-level statistics courses.

STAT 501: Regression Methods (3): offers an introduction to regression analysis using statistical software in Minitab. Topics include simple and multiple linear regression, inference, diagnostics, regression model building, and correlation.

NUTR 445 Nutrient Metabolism I (3): Nutrients, their sources, metabolism, interrelationships, and requirements with a focus on carbohydrates, lipids, and proteins. This course is designed to provide a foundation in the chemistry and metabolism of the macronutrients. Building on a knowledge base in biochemistry, physiology, and nutrition, this course will focus on the metabolism of proteins, carbohydrates, and lipids and integrating these metabolic pathways.

NUTR 501 Regulation of Nutrient Metabolism I (3): Integration of nutritional, biomedical, biochemical, physiological, and hormonal processes involved in carbohydrate, lipid, and protein metabolism.

NUTR 502 Regulation of Nutrient Metabolism II (3): Complementary to NUTR 501, emphasizing metabolic roles of vitamin and mineral elements.

FDSC 500D: Fundamentals of Food Science, Nutrition (3): An overview of nutrition research and recommendations' role in labeling regulations and product development of manufactured foods. Students will acquire a basic understanding of human carbohydrate, protein, and fat metabolism and how public health concerns about chronic disease have influenced the Nutrition Facts panel and health claims.

VBSC 514 Prostaglandins and Leukotrienes (3): Biochemical, physiological, structure-activity relationships, and nutritional aspects of arachidonic acid and related essential fatty acid metabolism.

VBSC 555 Principles of Metabolomics (3): This course teaches the general principles of metabolomics studies and analysis. Course objectives are: 1) demonstrate an understanding of the nature of metabolomics investigations and methods that enter into reproducible, rigorous studies; 2) describe the instrumental and chemical considerations involved in gathering robust data; apply uni- and multivariate statistical analyses to the data; demonstrate an understanding of interpretation strategies and how to relate statistical analyses to the original sample system; and 3) apply knowledge of metabolomics in discussing emerging instrumental and analytical strategies.

BMMB/CHEM 573 (3): NMR Spectroscopy for synthetic and biological chemistry (3) examines nuclear magnetic resonance approaches for characterizing the structure and dynamics of synthetic compounds, natural products, and biological macromolecules.

BMMB 521: Advanced Microbiology (3): This course will allow students to learn from 8 established investigators as they present topics current to their areas of research in the greater fields of microbiology. Students can improve their ability to interpret scientific literature by reading assigned papers. Students can enhance their written communication skills through short reports and oral communication skills by giving presentations.

FDSC 526 Microbial Physiology of Foodborne Organisms (3): A current literature-based course investigating how foodborne bacteria (beneficial and pathogenic) grow, survive and react to environments encountered in foods and during food processing.

MICRB 412 Medical Microbiology (3): Characteristics, methods of identification, and pathogenesis of bacteria that cause human disease; principles of disease dynamics and control.

VBSC 430 Principles of Toxicology (3): Introduction to the biomedical aspects of toxicology with emphasis on the mechanisms and fate of chemical interaction with biological systems.

VBSC 451 Immunotoxicology of Drugs and Chemicals (3): An in-depth discussion of the effect of xenobiotics and drugs on host immune mechanisms.