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Nanocourses in Biomedical Sciences

Nanocourses are short courses that meet for a total of ~7-8 hours and typically address a new or evolving area that is not covered by the standard graduate curriculum. The course could be given in a week or two days or even over 7 weeks.

To register for a nanocourse, please refer to the schedule of classes on MyUpstate. Nanocourses offered for the respective semester will be listed and can be enrolled in during the registration period. 

To request a nanocourse not listed on the semester schedule, please submit the Nanocourse Request form to Cheryl Small in the College of Graduate Studies, Room 3122 WH. At least 3 students' names must be on the request form for the course to be offered. Following submission of the form, faculty will work with students to arrange timing of the course.

Each Nanocourse is worth 0.5 credits.
Grading is Satisfactory/Unsatisfactory.

Nanocourses Offered

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GS647-002 Nanocourse: Introduction to Flow Cytometry

Course Instructor(s): Steven Taffet, PhD, Aaron Glass, PhD, Lisa Phelps
Enrollment limit: 6
Brief Description: Classes will include: Introduction to flow, Design of antibody panels, Hands on training on the cytometer, Analysis of Flow Data (FloJo), New trends in flow cytometry

GS647-003 Nanocourse: Mitochondrial DNA Replication- Un muddling the field

Course Instructor(s): Mark Schmitt, PhD
Enrollment limit: 10
Brief Description: 4, 2 hour classes over a 4 week period. Cover recent papers in yeast and mammalian cells that disagree on the mode of DNA replication in mitochondria. The class will require students to read several papers each week and be ready to discuss them.

GS647-004 Nanocourse: Radiobiology

Course Instructor(s): Jason Horton, PhD, Sandra Hudson, PhD and Paul Aridgides MD
Enrollment limit: 20
Brief Description: Ionizing radiation is used as a cytotoxic agent in biomedical applications. This course will review the unique aspects of ionizing radiation as physical entity, and its atomic, molecular and physiological effects on living cells and tissues. Topics to be discussed will include radiation effects on cellular biology, oxidative stress and free radical chemistry, applications in cancer therapy, experimental model systems, adverse events and toxicity associated with radiation exposure, and clinical translation of basic radiobiology to the practice of radiation oncology. The course will be presentation/discussion based, and supplemented by readings assigned by the instructors. Student performance will be assessed on the basis of participation in in-class discussion and completion of two home-work assignments.

GS647-005 Nanocourse: Vaccine Development

Course Instructor(s): Kristopher Paolino, MD, Christina Lupone, MPH, Aaron Glass, PhD, Lisa Ware
Enrollment limit: 10
Brief Description: Vaccine Development nanocourse will feature 7 one-hour lecture and discussion sessions of the following:

  1. Introduction: The Historical Impact of Vaccines on Disease Epidemiology and the Economic Burden of Vaccine Development
  2. The History of Regulatory Affairs and Oversight of Vaccine Development
  3. Vaccines and Immunological Memory
  4. Vaccines as Therapeutics: How to fight Cancer with Vaccines
  5. Advances in Vaccine and Immunization Technologies
  6. Debate Arguments on Vaccine Safety: Anti-Vaxxer versus Pro-Vaxxer
  7. New Vaccines: Challenges and Prospects in Development

GS647-006 Nanocourse: What Do I do next?

Course Instructor(s): Mark Schmitt, PhD
Enrollment limit: 8
Brief Description: The class will have 4, 2 hour sessions over a four week period. Each week 1-3 papers will be assigned. In class student will discuss the papers and will work on where the research is going, how one would decide the best course of action to progress the field further. Topics will delve down into what experiments should be done next, how those experiments should be set up, expected results, etc.

GS647-007 Nanocourse: Measuring binding affinities of biomolecules using multiple techniques

Course Instructor(s): Stewart Loh, PhD and Thomas Duncan, PhD
Enrollment limit: 10
Brief Description: This is primarily a laboratory course in which students will receive hands-on training on how to detect and quantify interactions between biomolecules (proteins, nucleic acids) and their binding partners (proteins, peptides, nucleotides, small molecules, and drugs). Students will be tasked with measuring binding affinities of several examples of the above interactions. Students will design binding experiments to be carried out using three types of instruments: (1) fluorescence plate reader, (2) isothermal titration calorimeter, and (3) biolayer interferometer. Students will prepare samples, perform the experiments on each of the three instruments, and analyze the binding data using the manufacturer’s software. This course is meant to provide students with theoretical knowledge as well as practical experience that will help them in their own research projects.

GS647-008 Nanocourse: Bone Biomechanics

Course Instructor(s): Kenneth Mann, PhD
Enrollment limit: 8
Brief Description: This course will cover mechanical aspects of skeletal bone using material and structural frameworks. Basic solid mechanics concepts such as stress, strain, deformation, elasticity, plasticity, and visco-elasticity will be explored. Structural mechanics concepts will include simple beam theory and how this can be used with CT image sets and the BoneJ plugin via IMAGEJ. Experimental approaches to determine bone material/structural properties will be introduced to determine bone properties from larger (human) and small laboratory animal tissue. One hour interactive lecture format over seven weeks. At the end of the course, the student will have basic background needed to perform, interpret, and analyze biomechanics experiments on small bone specimens commonly used in orthopaedic research. The course will require student to complete short problem sets to reinforce main concepts. Assessment of student performance will be based on participation during in-class discussion and completion of home-work assignments.

GS647-009 Nanocourse: SURF Journal Club

Course Instructor(s): Bruce Knutson, PhD
Enrollment limit: 6 (or 12)
Brief Description: The main goal of this nanocourse is to give graduate students the opportunity to obtain teaching experience by running a journal club for Summer Undergraduate Research Fellowship (SURF) students. Students will have the opportunity to organize, moderate, and evaluate journal club participation by a small group of 5-6 Fellows. Graduate students will meet with Fellows once a week starting the second week of June and running until all Fellows have presented. Graduate students will also meet with the course instructor at the beginning and end of the journal club program for mentoring, advice, and feedback.

GS647-010 Nanocourse: Manuscript Submission

Course Instructor(s): Julio Licinio, MD,PhD
Brief Description: How to prepare, submit and resubmit...

GS647-012 Nanocourse: Protein Expression & Purification

Course Instructor(s): Alaji Bah, PhD
Enrollment limit: 10
Brief Description: In this nanocourse, we will focus on strategies to recominantly express and purify folded and intrinsically disordered proteins using E. coli and standard chromatographic techniques respectively. We will first discuss how to obtain the cDNA of your gene of interest, the variety of expression vectors available, cloning straties, E. coli strains available, pilot expression schemes, scaling up to meet your needs etc. Then, then we discuss how we can use the physico-chemical properties and the biological function(s) of the protein to guide our purification strategies. We will discuss the concept of protein ‘purity’ (how pure should your protein be?). Finally, we’ll explore how we can ‘verify’ that our purified protein is your protein of interest and that it’s ‘functional’. All these discussions will be accompanied by demonstration of the expression/purification of a protein from my lab.

GS647-013 Nanocourse: Bioinformatics I: Introduction to Bioinformatics

Course Instructor(s): Vladimir Kuznetsov, PhD
Enrollment limit: 3-15
Brief Description: Bioinformatics: The big picture. Definitions and branches. Links to other disciplines: Biotechnologies, Genomics and Systems biology, Big Data Science, Computing, Statistics, Evolution, Integrative and Predictive Medicine. Nomenclature and annotation systems. Gene ontology. Genome, transcriptome and proteome complexity. Bioinformatics database, web tools and software. Major data bases, web sites and software for analyze of DNA, RNA, and protein sequences. Microarrays, the next generation sequences and basic bioinformatics tools for big data analysis. Sequences obtaining and comparison. Paired and multiple alignments software. Data formats. Blast, BLAT, other similar software. Integrative bioinformatics strategies. Basic probability theory and statistical methods in bioinformatics. Enrichment and correlation analyses. Network and pathways analysis tools. Comparative evolution. Aligned sequences as phylogenetic trees.

GS647-014 Nanocourse: Bioinformatics II: Integrative Strategies in Biotechnology and Medicine

Course Instructor(s): Vladimir Kuznetsov, PhD
Enrollment limit: 3-15
Prerequisite: GS647-013
Brief Description: Human genome, The Encyclopedia of DNA Elements(ENCODE), TCGA and other omics projects. Mapping and data integration. Basic functional genomics and transcriptomics tools. Non-coding DNA and RNA. RNA-seq, Chip-Seq, CHIA-PET, CAGE, DRIP-seq methods. Transcription factors and position-specific matrixes. Transcription regulation. Genome and transcriptome structures and complex architectures. Network analysis and pathways. Non-canonical structures and their analysis. RNA-DNA-protein interactome. Disease critical genome regions identification. TCGA Genome portal and tools. Computational biology, bioinformatics, integrative genomics and predictive oncology. Cancer classification, patient’s prognosis, disease prediction and novel biomarker discovery.

GS647-015 Nanocourse: Introduction to computer systems for bioinformatics

Course Instructor(s): Chunyu Liu, PhD and Chunling Zhang, MS
Enrollment limit: 10
Prerequisite: Students should bring their own laptops (PC or Mac) with VPN access to the University networks, and will need to install a few software (to be specified) after registering the class.
Brief Description: We will introduce basic about computer to biologists, who are interested in either becoming professional bioinformaticians, data analysts, or using bioinformatics tools to analyze their own experimental data. In the 7-hour course, we will describe basic concepts of hardware and software, parts of computers, networks and supercomputers, major OS, file systems and directory, file types and contents, network protocols. We will provide students the first hands-on experience on real working environment of professional bioinformaticians. We guide students to plan for their future in the bioinformatics world.

GS647-016 Nanocourse: New Developments in G-protein Coupled Receptor (GPCR) Research

Course Instructor(s): Barry Knox, PhD
Enrollment limit: None
Brief Description: The purpose of this course is to familiarize the student with new developments in the accelerating world of G-protein coupled receptor research. The course will be a combination of lecture presentation and discussion of recent advances. Students are encouraged to bring their interest in a particular receptor or biological process for discussions. The following topics will be covered in separate sessions:

  1. Introduction to GPCRs and their Evolutionary History (1 hour)
  2. New GPCR Methodology: Signaling, Structure and Screening (2 hours)
  3. GPCR in silico (1 hour)
  4. GPCRs: Invertebrates and Orphans (2 hours)
  5. Psychedelic GPCRs (1.5 hours)
  6. Adhesion GPCRs (1.5 hours)

Required reading (2 articles/session) will be assigned for discussion to follow a presentation led by instructor. Additional topics can be included upon request.

GS647-017 Nanocourse: Neuroinflammation of the Human Brain and Mind

Course Instructor(s): Cyndi Shannon Weickert, PhD
Enrollment limit: 12
Brief Description: This course will begin by reviewing the evidence that mental illness (depression and schizophrenia in particular) can be understood as disorders of the immune system. Next, we will cover the evolving terminology used in the field of neuroinflammation from the perspective of the body and the brain. Then, we will discuss examples from known neurodegenerative disorders to better understand how neuronal signals stimulate a glial inflammatory reaction. We will contrast the neurotrophic and neurotoxic roles of astrocytes and microglia in brain inflammation. Lastly, we will consider the role of peripheral immune cells in aggravating or possibly ameliorating brain tissue damage. The course will involve reading outside the classroom, lecture presentations, discussion of several recent journal articles and written assessments.

The following topics will be covered in separate sessions:

  1. Introduction to Innate and Adaptive, Acute, Chronic and “Sterile” Inflammation in Brain (1.5 hour)
  2. Lessons learned from classically defined neuroinflammatory conditions (1.5 hours)
  3. The double-edge sword of brain glia (1.5 hour)
  4. Our changing understanding of microglial and microglial-like cells (1.5 hours)
  5. Just who is getting across the “Berlin Wall” of the brain? And how? (1.5 hours)
  6. What can Immunologist teach Psychiatrists and vice versa? (1.5 hours)

Required reading: Students will be expected to read the book “The Inflamed Mind” by Edward Bullmore prior to class. At least four chapters from the text book “Neuron-Glia Interaction in Neuroinflammation” Edited by Akio Suzumura and Kazuhiro Ikenaka, will be assigned reading prior to a presentation and discussion led by instructor with 1-2 students assigned as co-discussants. Journal articles (n=4) will be assigned reading to supplement the text book. Students are expected to complete the reading and be prepared for in class discussions. To test if basic concepts of neuroinflammation have been learned and can be applied, students are expected to answer 4/6 short essay questions in less than half a page. The set of questions will be given during the first day of class and will be expected to be completed and turned in on the last day of class.

GS647-018 Nanocourse: The Biology of Arthropod Disease Vectors

Course Instructor(s): Saravanan Thangamani, PhD
Enrollment limit: 6
Brief Description: The goal of this course is to introduce students to arthropods that are vectors (Ticks and Mosquitoes) for a wide variety of infectious agents (Dengue virus, Zika virus, Chikungunya virus, Powassan virus, Plasmodium (Malaria agent), and Borrelia (Lyme disease agent) that cause human diseases. The unique biology of hematophagous arthropods that has evolved to facilitate the coexistence between the vectors, pathogens, and the vertebrate host will be illustrated in both lectures and practical sessions. The curriculum will build upon a general introduction to arthropods. Then, using specific examples, the processes of infection, development, and transmission of pathogens will be discussed. This will include vector behaviors involved in location of the host, physiological adaptations to facilitate blood feeding and digestion, and factors that influence the vector-pathogen relationship. Options for controlling vector-borne diseases will be discussed from a historical perspective, with a consideration of how modern molecular approaches might be used in the future. Evaluations (s/u) based on final examination and practicum.

GS647-019 Nanocourse: Quantitative Assessment of the Postural Control System

Course Instructor(s): George Fulk, PT, PhD & Christopher Neville, PT, PhD
Enrollment limit: 10
Brief Description: Postural control is a term used to describe the way our central nervous system (CNS) regulates sensory information from other systems to produce the necessary motor output to maintain upright posture. The visual, vestibular, and somatosensory systems are the main sensory systems involved in postural control and balance. This course will provide a brief background on the organization of the CNS to control posture in static and dynamic conditions. Following this introduction, the focus will be on postural control measurement using a variety of available technologies from both clinical and research environments. The course will conclude with the interpretation and analysis of signals from the technologies reviewed above.

GS647-020 Nanocourse: Introduction to Light Microscopy

Course Instructor(s): Scott Blystone, PhD
Enrollment limit: None
Brief Description: Introduction to Light Microscopy will provide students with a suitable background to responsibly utilize microscopy as an experimental tool for biologic research. The course will cover the history, theory and mechanics of primary developments in microscopy from inception to current day. Equipment and software used for acquisition and analysis of data are described and evaluated along with the provision of resources to understand and adopt new technology and technique as it develops. Fluorescent imaging, optical sectioning, confocal imagery and superresolution approaches are presented in detail along with dynamic imaging including photobleaching and activation techniques. Final sections of the course delve into understanding metadata, ethically sound image processing, quantitation and presentation of microscopic data.

This course is approximately 8.5 hours of self-paced video in 22 segments. The course may be started and finished at any time within semester registration boundaries. Homework accompanying each video segment must be returned for course grade. This course may be taken by non-students at any time, with or without homework, by contacting Dr. Blystone for a course packet.

GS647-021 Nanocourse: Structuring against Coronavirus

Course Instructor(s): Mark Schmitt, PhD
Enrollment limit: None
Brief Description: In this nanocourse, we will focus on strategies to better understand the structural biology of coronavirus. The target audience are structural biology enthusiasts, who may or may not be structural biologists. The course will be a combination of lecture presentation, discussion of recent advances, and hands-on efforts at contributing to research and aiding in outreach and knowledge-sharing. Learners are encouraged to bring their interests in a particular aspect or biological process for discussions.  This class will be done entirely online.

The following topics will be covered in separate sessions: 

  1. Getting involved: Folding@Home , Proteopedia, and other efforts (1 hour)
  2. Introduction to coronavirus structural biology and the limits (1.5 hour)
  3. Overview of structural biology data collecting and formats (1.5 hour)
  4. Use of Python to analyze structural data at scale  (1 hour)
  5. Macromolecular visualization (1.5 hour)
  6. Reports on Folding@Home / visualization / outreach efforts (1.5 hour)

Group discussion and efforts to follow presentations led by instructor. Additional topics can be included upon request.

There would not be any outside work required as practicing with or utilizing these programs is entirely voluntary.  We simply want to give an introduction to bioinformatic tools and demonstrate how they can be used to advance science.  Having any background above the core courses is not required to participate in the course.  The class would be done entirely online.

GS647-022 Nanocourse: Analysis of the Structural and Unstructural Biology of the SARS-CoV-2 Proteome

Course Instructor(s): Alaji Bah, PhD
Enrollment limit: None
Brief Description: This nanocourse is designed for students (and faculty) with expertise or interests in biochemistry, molecular, structural and computational biology, who are would like to employ their skills in understanding the proteome biology of of SARS-CoV-2, with the ultimate goal of using this knowledge to identify therapeutic targets.

After an introduction to Coronaviruses in general, we will focus specifically on the proteome of SARS-CoV-2, and we will identify virus’ proteins and their potential biological functions. We will determine whether the structures of these proteins (or their homologs and/or their complexes) have solved and deposited in protein databases. If no structural info is available, students will generate homology models using computational tools. These structures could be starting points for structure-based drug designs.

We all also identify regions of the viral proteome that cannot fold in isolation i.e the so called Intrinsically Disordered Proteins or Protein Regions (IDPs/IDRs), which are normally sites targeted for post translational modifications (PTMs). Viral or host proteins that are involved in ‘writing’, ‘reading’ and ‘erasing’ these PTMs will be identified to explore the feasibility of targeting them. Finally, in addition to identifying unique SARS-CoV-2 targets, we will investigate whether previous known targets in other Coronavirus can also be exploited in SARS-CoV-2. 

Contact Time : ~1 hr WebEx on Mondays and on Thursdays for three weeks 

Grade Assessment: Participation

GS647-023 Nanocourse: Introduction to Machine Learning

Course Instructor(s): Stephen Faraone, PhD; Stephen Glatt, PhD; Yanli Zhang-James, MD, PhD; Jonathan Hess, PhD
Enrollment limit: None
Brief Description:
Into to ML-1: Faraone
Into to ML-2: Faraone
Random Forests & application to imaging: Zhang-James
Support Vector Machines: Hess/Glatt
Ensemble Learning & Applications to Neuroimaging: Zhang-James/Faraone
Neural Networks & application to Covid-19: Faraone & Zhang-James
Convolutional Neural Networks & Applications to Genomics: Faraone
SVM and applications to transcriptomics: Hess/Glatt
Ensemble Learning: Zhang-James
Multi-task learning and application to imaging data: Faraone/Zhang-James
The student's grade will be based on class participation.

GS647-024 Nanocourse: Principles of Single Cell RNAseq

Course Instructor(s): Adam Waickman, PhD
Enrollment limit: 15
Brief Description:
Expected contact hours: 8 hours of contact time, split over 2 days.
Proposed schedule
Day 1 (2-3 hours)
- Overview of scRNAseq (history)
- Principles of Next Generation Sequencing
- What is scRNAseq good for
- What isn't scRNAseq good for
- Experimental design considerations
- Wet-work overview and equipment review
Day 2 (5-6 hours)
- Data analysis part I: raw sequencing data analysis in a linux environment (requires HPC)
- Data analysis part II: data visualization and statistical analysis in R
- Hands-on data analysis
- Final close-out: recap and new technologies in development
Students will be given a hands-on component to analyze some datasets.

The student's grade will be based on class participation.

GS647-026 Nanocourse: Social Media and Science Communication

Course Instructor(s): Jessica Ridilla, PhD
Enrollment limit: 10
Brief Description:
This course will bridge traditional scientific communication approaches with nouveau social media-based campaigns. We will discuss how scientists use social media platforms to disseminate and discuss science. We will develop and post scientific content to social media platforms (specifically: Twitter, Instagram, and TikTok), using a course specific handle. Course Activities: Create scientific social media posts. Assessment/Evaluation: 40% of the grade will be in class assignments (i.e., developing and performing a 30s elevator pitch, Tweetorial of a published scientific paper).
40% will be posting/tagging five course assignments on appropriate social media platforms. 20% will be on discussion-based participation (participation = a comment/question per lecture). Bonus: if a (positive) student post goes viral, students will be rewarded with a taco party.

GS647-027 Nanocourse: Coding in R for Neuroscientists

Course Instructor(s): Yingxi Lin, PhD
Enrollment limit: none
Brief Description:
This nanocourse is designed to teach beginners how to code with R in a context that is relevant to the demands of biology/neuroscience. The course with cover the basics of R functionality and data types and structures and will expand on that knowledge to enable statistical and graphical examination of data. Example datasets used will include histological quantifications, electrophysiological measurements, behavioral assessments, and RNA sequencing results. RStudio will be used to implement base R functions as well as dplyr and ggplot2 packages.
Assessment/Evaluation: Students will receive a passing grade if they attend 7 weeks of class and submit the final presentation.