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CIHMID-relevant Course Listing

The following is a list of Cornell courses in host-microbe biology that may be of interest to advanced undergraduate and graduate students.



Microbes, the Earth, and Everything
BIOMI 1120 / PLSC 1120
Instructor: K. Hefferon
Fall (3 credits) – Student option grading
We live on a microbial earth. If we happen to consider microbes in our daily lives most people conjure images of disease, but in reality we depend on microbes to sustain our world. This course showcases the vast microbial world that hides in plain sight all around us and use microbial examples to explore both fundamental biological principles and the scientific method. Course modules emphasize basic concepts from evolution, molecular biology and genetics, diversity, and ecology. Learn about the tiny titans and miniature monsters that are the life support system of our planet, how they have shaped human civilizations, and how they reveal the unifying principles of life.

BIOMI 2100
Instructor: S. Chatterjee, L. Kaltenegger, S. Winans
Fall, Spring (2 credits) – Student option grading
Prerequisite: one semester of general biology. 
This class will explore the current theories about the chemical origins of life on earth, and will then use these insights to discuss the search for life on other planets, inside the Solar system and outside. Topics will include origin of the Sun, the Big Bang, the formation of Earth, the origin of life, from the prebiotic synthesis of amino acids, nucleobases, and other building blocks of life, the evolution of primitive protocells, the earliest RNA-based catalysts, the evolution of protein synthesis machinery, and the origins of eukaryotic cells. We will conclude with strategies and progress in identifying life on other planets in our solar system and on planets orbiting other stars.

Public Health Microbiology
BioMI 2500
Instructors: S. Winans
Fall (3 credits) – Student option grading
Prerequisite: the equivalent of two semesters of majors-level biology and one semester general chemistry.
This course will use a variety of teaching methods (including historical and current case studies and databases) to help students understand basic principles of microbiology as they apply to the emergence, transmission, pathogenicity, and control of infectious human disease. Major topics include water and food borne disease, zoonotic diseases, sexually transmitted diseases and antibiotic resistance.

General Microbiology Lectures
BioMI 2900
Instructor: T. Doerr & K. Hefferon
Fall, Spring (3 credits) – Letter grades only
Prerequisite: two semesters majors-level biology and two semesters college-level chemistry, or equivalent. Highly recommended corequisite: BIOMI 2911. The four-credit option adds one discussion section per week designed to promote active learning and enhance engagement with subjects covered in lecture.
Comprehensive overview of the biology of microorganisms, with emphasis on bacteria. Topics include microbial cell structure and function, physiology, metabolism, genetics, diversity, and ecology. Also covers applied aspects of microbiology such as biotechnology, the role of microorganisms in environmental processes, and medical microbiology.

Biology and Management of Plant Diseases
PLPPM 3010
Instructor: K. Cox
Fall ​(4 credits)
Prerequisite: one year of biology. Co-meets with PLPPM 5010. Lab portion of the course starts the second week of classes.
Introduction to the biology of the pathogens that cause plant diseases, and the diagnosis and management of plant diseases. Topics include the biology of bacteria, fungi, oomycetes, viruses, and nematodes; disease cycles; plant disease epidemiology; and the principles and practices of plant disease management. Intended for students who want a practical knowledge of plant diseases and their control, as well as for students preparing for advanced courses in plant pathology and plant-microbe biology.

The Gut Microbiome
BioMI 3210
Instructor: A. Hay
Fall (3 credits)
Prerequisite: BIOMI 2900 or permission of instructor.
The microbes on and in our bodies are as abundant as our own cells. These diverse microorganisms provide us with metabolic capacities beyond our own and are essential to good health, but can also play a role in disease. This course will introduce the microbes of the human body, discuss their origins, adaptations to the body, molecular interactions, and associations with health and disease.

Principles of Virology
BioMS 4090 / BioMI 4090
(BioMS 6090/ BioMi 6090 option)
Instructors: J. Parker, L. Schang, D. Diel
Fall (3 credits)
Prerequisite: BIOMI 2900 or permission of instructor. Recommended prerequisite: BIOMG 3300.
Covers principles of virology that will give a broad understanding of how viruses infect and cause disease.  Topics include the classification of viruses, virus entry, genome replication and assembly, and virus pathogenesis. Particular emphasis is placed on virus-host cell interactions and common features between different viral families. Recommended for those planning to attend medical school, graduate school or Veterinary college, or just interested in what viruses are and how they cause disease.

Essential Immunology
BioMS 4150 / BioMS 6150
Instructor: B. Rhoades
Fall (3 credits) – Student option grading
Highly recommended to have background courses in microbiology, genetics, and cell biology: undergraduates register for 4150; graduate students register for 6150
Course introduces the immune system and key concepts in immunology. Focuses on the human system and medically relevant pathogens and immunization. Course delves into the cell biology of signaling, genetic recombination & gene expression. Students will learn how immune cells develop, communicate and carry out immune responses. Students will learn how vaccines work and use clinical cases to apply knowledge of immune concepts. Course ends with a brief survey of immune-mediated diseases, cancer immunology and immunotherapies. Recommended for those planning to pursue careers in health-related fields, graduate or veterinary studies or those interested in how the body defends itself against diverse threats.

PLPPM 4300
Instructor: T. Pawlowska
Fall (3 credits) – Student option grading
Prerequisite: two semesters of general biology. Co-meets with PLPPM 6300
Fungi are one of the major lineages of eukaryotes and the sister group of animals.  We will consider evolutionary relationships among different groups of fungi, their ecology and significance to humans.  We will explore fungal lifestyles, their reproduction, and the ways that fungi use to communicate with each other and with their symbiotic partners.  In addition to true fungi, we will study several distantly related groups of organisms that share with fungi absorptive nutrition, filamentous somatic structures, and spore-based reproduction.  We will reconstruct fungal phylogenies using molecular evolution methods.  We will also isolate fungi from the environment and identify them using morphological and molecular approaches.

Principles of Infectious Disease for Public Health
VtPEH 6111
Instructors: G. Whittaker, L. Goodman
Fall (3 credits)
Enrollment limited to MPH students and, in rare cases, upper-level undergraduates and graduate students with permission of instructor.
Prerequisite: undergraduate biology and chemistry suggested. 
This course comprises two parts. The lecture section will cover viral, bacterial and parasitic agents important for public health, as well as infectious disease epidemiology, surveillance, and infectious disease countermeasures. The discussion section will address similar topics using cases and professional experiences to drive small-group discussion and applied learning.

Seminar in Ecology and Evolution of Disease
Entom 6900 / BioEE 6900
Instructor: M. Greischar & C. Murdock
Fall, Spring (1 credit)
Graduate-level discussion of the ecology, epidemiology, genetics, and evolution of infectious disease in animal and plant systems. Weekly discussion of research papers published in the primary scientific literature. Participation in discussion and presentation of at least one paper required for course credit.



Locker Rooms, Kitchens and Bedrooms: The Microbiology of College Life
BIOMI 1100
Instructor: K. Hefferon
Spring, Summer (3 credits)
Microbial habitats are literally everywhere on a college campus – and college students interact with microorganisms daily. From the athlete locker room, to the kitchen, to the bathroom, to between the sheets, college students are exposed to a plethora of microorganisms that are benign, beneficial, and pathogenic. The goal of this class is for students to learn about microbiology and microbial ecology as it relates to them – in the college campus environment. Students will learn about viruses, bacteria, eukaryotes and metazoans that cause common illnesses (i.e. gastroenteritis, influenza and STDs), the microbially-driven elemental cycling of alcohol production, and ecology of microorganism that spoil food. Students will take away a practical understanding of the microorganisms that they can apply to their own lives.

Microbiology of Human Contagious Diseases
BioMI 2600
Instructor: S. Winans
Spring, Summer (3 credits) – Student option grading
Prerequisite: one semester of introductory biology or equivalent
This course provides an introduction to the microbiology of microbial diseases. The primary focus is on molecular mechanisms of pathogenesis, including detection of the host environment, binding of pathogenic microbes to host cell surfaces and their invasion of host cells and tissues, and the delivery and functions of microbial toxins. It will include host defenses and microbial countermeasures against these defenses. We will also study the evolution of pathogens and the co-evolution of their hosts.

General Microbiology Lectures
BioMI 2900
Instructor: D. Buckley, K. Hefferon
Fall, Spring (3-4 credits) – Letter grades only
Prerequisite: one semester of introductory biology (or AP Biology) and one semester of chemistry (or AP Chemistry). Highly recommended prerequisite: co-requisite in BIOMI 2911.
Comprehensive overview of the biology of microorganisms, with emphasis on bacteria. Topics include microbial cell structure and function, physiology, metabolism, genetics, diversity, and ecology. Also covers applied aspects of microbiology such as biotechnology, the role of microorganisms in environmental processes, and medical microbiology.

Dynamic Models in Biology
BIOEE 3620/MATH 3620
Instructor: S. Ellner, A. Hein, A. Vladimirsky
Spring (4 credits)
Prerequisite: two majors-level biology courses and completion of mathematics requirements for biological sciences major or equivalent.
Introductory survey of the development, computer implementation, and applications of dynamic models in biology and ecology. Case-study format covering a broad range of current application areas such as regulatory networks, neurobiology, cardiology, infectious disease management, and conservation of endangered species. Students also learn how to construct and study biological systems models on the computer using a scripting and graphics environment.

The Ecology and Evolution of Infectious Diseases
ENTOM 4000/BioEE 6000
Instructors: M. Greischar & C. Murdock
Spring (4 credits)
Recommended prerequisite: BIOEE 1610, BIOG 1101, BIOG 1102, or BIOG 1190 and MATH 1106, MATH 1110, MATH 1120, MATH 2210, MATH 1710, or STSCI 2150; or equivalencies; or by instructor permission. Co-meets with BIOEE 6000/ENTOM 6000.
This course introduces students to the field of infectious disease ecology, an area of study that has developed rapidly over the past three decades and addresses some of the most significant challenges to human health and conservation. Students will learn about the incredible diversity of parasitic organisms, arguably the most abundant life forms on the planet, and examine how pathogens invade and spread through host populations. Throughout the course, an emphasis will be placed on understanding of infectious diseases dynamics at the population level, and on quantitative approaches for studying pathogen spread and impacts. Specific topics include types of pathogens and their ecological properties, epidemiology and impacts on host populations, types of transmission, evolution of resistance and virulence, drivers of the emergence of new diseases, parasites in the context of ecological communities, strategies for controlling outbreaks, and the role of parasites in biodiversity and conservation.

Pathogenic Bacteriology
BioMS 4040 / BioMI 4040
Instructor: D. Debbie
Spring (2-3 credits)
Prerequisite: BIOMI 2900 or permission of instructor.
Course in medical microbiology, presenting the major groups of bacterial pathogens important to human and veterinary medicine. Emphasizes infection and disease pathogenesis. Topics include disease causality; interactions of host, pathogen, and environment, including immunity to bacteria; and principles of antimicrobial therapy and drug resistance. Recommended for those planning to attend medical school, graduate school, or veterinary medical school, or those just interested in how bacteria cause disease.  A companion seminar addresses the current and classic literature related to the pathophysiology of medically important bacterial pathogens on the cellular and molecular levels.

Diet and the Microbiome
NS 4200
Instructor: A. Poole
Spring (3 credits)
Prerequisite: one semester introductory biology lecture (BIOMG 1350BIOG 1440, or equivalent) and one semester introductory chemistry (CHEM 1560CHEM 2070CHEM 2090, or equivalent). Recommended: microbiology (BIOMI 2900 or equivalent) and introductory statistics (STSCI 2150PAM 2100AEM 2100, or equivalent). Enrollment limited to: senior, junior, and graduate students.
In this course, students will acquire a present-day overview of the reported effects of diet on the microbiome with an emphasis on host physiology outcomes. The microbiome field is rapidly evolving, and this course has no textbook; we will mainly be assessing primary literature and scientific reviews. Students will learn to critically analyze the conclusions drawn from microbiome studies to empower them to make informed judgements as new research findings are reported.

Applied Immunology
BioMS 4250/BioMS 6250
Instructor: B. Rhoades
Spring (3 credits)
Required prerequisite: BioMS 4150 or BioMS 6150 or permission of the instructor (not the dept. chair). BIOMS 4250 is only for undergraduate students. BIOMS 6250 is only for graduate students.
Applied Immunology builds on knowledge of basic immunology. It picks up where BIOMS 4150 – Essential Immunology left off and covers diseases due to an unbalanced immune system. Topics include tolerance, homeostasis and barrier immunology, allergy, autoimmunity, transplantation, AIDS, and tumor immunology. The course will demonstrate that the field of “applied” immunology is dynamic and continually evolving by demonstrating how new technologies and research findings are “applied” toward designing immune-based therapies. Students will learn how commonly research methods measure immune responses. Recommended for students pursuing careers in medicine, biomedical research, biotechnology and public health, or anyone curious about the immune system and their health.

Plant Behavior and Biotic Interactions, Lecture
BioEE 4460 / BioNB 4460 / PlSci 4460
Instructors: A. Kessler, R. Raguso
Spring (3 credits)
​​​How do plants respond to antagonists, such as herbivores and pathogens? What are the checks and balances that keep mutualist organisms in their tight interactions? How are symbioses organized on molecular, metabolic and ecological levels? What are the molecular, plant hormonal, and metabolic mechanisms mediating plant biotic interactions with other organisms? What ecological and evolutionary consequences do these interactions have for the fitness of the plants and their interactors? This course provides an overview of plants’ myriad interactions with antagonists and mutualists, from microbes to multicellular organisms, and explains the underlying ecological and evolutionary concepts. It gives an introduction to the study of induced plant responses in the light of a behavioral biology framework.

Special Topics in Evolutionary Biology
BioEE 4940
Instructor: A. Lopez Sepulcre
Spring (4 credits)
Part of the department’s ‘Special Topics’ course. The Ecology and Evolutionary Biology Department teaches “trial” courses under this number. Offerings may vary by semester and will be advertised before the semester begins. The same course is not offered more than twice under this number.

Molecular Biology of Plant-Microbe Interactions
PLPPM 6010
Instructor: C. Casteel
Spring ​(3 credits)
Prerequisite: introductory genetics (BIOMG 2800BIOMG 2801 or PLBRG 2250) or biochemistry (BIOMG 3300 or BIOMG 3310, and BIOMG 3320 or equivalent) or PLPPM 3010.
The co-evolutionary molecular battle between microbial pathogens and plants has game-like properties whose rules are emerging from recent genomic, biochemical, and cell biological advances. This course explores the molecular pieces and collective behaviors of pathogen virulence and plant immune systems, similarities between interaction mechanisms in plant and animal pathosystems, and the application of this knowledge to sustainable agriculture. The course emphasizes the development of professional skills, such as the management of scientific literature, creative design and critical evaluation of research, communication of complex scientific concepts to diverse audiences, and discussion of environmental issues associated with transgene-based disease management strategies. Students write and peer review research proposals.

Core Concepts in Molecular Bacteriology
BioMI 6200
Instructor: H. Feaga
Spring (3 credits)
The goal of this course is to prepare students for advanced work in molecular bacteriology, with a special emphasis on experimental design. First year graduate students as well as senior undergraduates with an interest in understanding how bacterial cells work at the molecular level will gain the most from this course. We will cover bacterial growth and metabolism, cell structures, physiology, pathogenesis, and experimental approaches. A background in bacteriology or microbiology is not required, since we will begin each week with a review of fundamental concepts before digging deeper into these concepts using primary literature. Further, we will examine the foundational experiments that led to our current understanding of the bacterial world. We will then critically analyze recent primary literature in this field to advance our knowledge and will use this literature as a basis for generating new hypotheses. Students will also build a foundation in structural, genetic, and biochemical tools used in microbiology laboratories. Foundational knowledge and practical skills learned in this course will help prepare the student for advanced work in the bacteriology laboratory.

Computational Approaches to Microbial Systems
BioMI 6300
Instructor: M. Schmidt
Spring (3 credits)
Prerequisites: BioMI 2900/BioMI2911,BioMG 2800.
High-throughput sequencing has revolutionized and become common practice across the field of microbiology. This course will prepare students for analyzing large sequencing datasets through a meaningful biological lens. Via a combination of lectures, discussions of primary literature, and hands-on, data-driven computational labs, we will learn how to organize computational projects, work in the command line, perform cloud computing, and gather, interpret, and analyze amplicon, genomic, and shot-gun metagenomic data to advance our understanding of microbial systems. We will evaluate the distribution of microbial biodiversity and gene abundances and compare the taxonomic and genomic composition of microbial communities. This course is geared towards graduate students and upper-level undergraduate students across biology. We will focus on how to use software for biological analyses while touching on broader concepts of statistical algorithms.

Seminar in Ecology and Evolution of Disease
Entom 6900 / BioEE 6900
Instructor: C. Murdock, M. Greischar
Fall, Spring (1 credit)
Graduate-level discussion of the ecology, epidemiology, genetics, and evolution of infectious disease in animal and plant systems. Weekly discussion of research papers published in the primary scientific literature. Participation in discussion and presentation of at least one paper required for course credit.

Special Topics in Evolution and Ecology
BioEE 7600
Instructor: A, Dhondt, M. Holgerson
Fall, Spring (1 credit)
This course is aimed at first- or second-year students, who will be prepared to include modeling in their PhD research, but later-stage students are also welcome. Each week there will be 3 lectures (75 – 90 min) and 3 computer labs (3hrs). The emphasis of the course is on building deterministic dynamic models and studying them on the computer, including models for single populations, interacting populations (including infectious disease models), and natural selection in simple haploid and diploid models. Time permitting we may also look at evolutionary invasion analysis (e.g., evolution of virulence), stochastic models, or maximum likelihood methods for fitting dynamic models to data.



Plagues and People
ENTOM 2100
Instructors: E. Gray, L. Harrington, C. Murdock
Fall (3 credits) – Student option grading
Human diseases have affected human lives and society through history. This course focuses on the pathogens, parasites, and arthropods causing human plagues through multiple perspectives (biomedical, social, ethical, cultural). Those plagues that have had the greatest impact on human culture and expression are emphasized. Lectures are supplemented with readings and videos . Also addresses emerging diseases, bioterrorism, and future plagues.

Biology of Infectious Disease: From molecules to ecosystems
BIOMI 2950
Instructor: T. Hendry
Fall (3 credits) – Letter grades only
Prerequisite: two of the three core undergraduate biology courses, BIOMG 1350BIOG 1440/BIOG 1445BIOEE 1610, or the equivalent. Enrollment limited to: sophomores or higher.
A broad integration and overview of the origins, nature, and dynamics of infectious disease in humans, plants, and animals. An examination of the historical and contemporary concepts and impacts of infectious agents on hosts at multiple spatial and temporal scales and at different levels of biological organization. The ecology and evolution of pathogens, hosts, and vectors are also discussed. Consideration of newly emerging diseases in human, plant, and animal populations and the influence of human activities on global disease spread. Current and future issues and trends in disease monitoring and mitigation will also be addressed.

Filamentous Fungal Genetics and Genomics
PLPPM 6380
Instructor: L. Huberman
Prerequisite: BIOMG 2800 or PLBRG 2250.
Fungi play a vital role in our ecosystem and are responsible for devastating crop infestations that threaten global food supplies and diseases that result in the death of hundreds of thousands of individuals each year. This course explores fungal biology through the lens of molecular genetics and genomics, including epigenetics, genome defense mechanisms, metabolism, and signaling pathways. We will cover the use of genetic tools in fungi ranging from classical genetics to CRISPR to high-throughput sequencing. This course will also teach skills necessary to analyze genetic and genomic data using Python and publicly available sequencing analysis software. No prior coding experience is necessary. The course will emphasize the development of professional skills, such as critically reading and reviewing scientific literature, experimental design, scientific communication, and data analysis. Students will write and peer review manuscripts based on the analysis of transcriptional profiling of fungi. Classes will include lectures, student-led discussion of the primary literature, presentations, and computer labs. A laptop is necessary for this course.