Nanocourses in Biomedical Sciences

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

Course Instructor(s): Mark Schmitt, PhD
Enrollment limit: 10
Brief Description: 4, 2 hour classes over a 4 week period. 涵盖最近关于酵母和哺乳动物细胞在线粒体DNA复制模式上存在分歧的论文. The class will require students to read several papers each week and be ready to discuss them.

Course Instructor(s): Jason Horton, PhD, Sandra Hudson, PhD and Paul Aridgides MD
Enrollment limit: 20
简介:在生物医学应用中，电离辐射被用作细胞毒性剂. 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.

课程讲师:克里斯托弗·保利诺，医学博士，克里斯蒂娜·卢彭，公共卫生硕士，亚伦·格拉斯，博士，丽莎·韦尔
Enrollment limit: 10
Brief Description: Vaccine Development nanocourse will feature 7 one-hour lecture and discussion sessions of the following:

1. 前言:疫苗对疾病流行病学的历史影响和疫苗开发的经济负担
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

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.

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). 学生的任务是测量上述互动的几个例子的绑定亲和力. 学生将设计使用三种仪器进行的结合实验:(1)荧光板阅读器, (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.

Course Instructor(s): Kenneth Mann, PhD
Enrollment limit: 8
简要描述:本课程将涵盖骨骼使用材料和结构框架的机械方面. 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, 并对骨科研究中常用的小骨标本进行生物力学实验分析. 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.

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.

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

Course Instructor(s): Alaji Bah, PhD
Enrollment limit: 10
Brief Description: In this nanocourse, 我们将专注于推荐的策略来表达和纯化折叠和内在无序的蛋白质 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, 我们将探索如何“验证”我们纯化的蛋白质是您感兴趣的蛋白质，并且它是“功能性的”。. 所有这些讨论都将伴随着我的实验室对一种蛋白质的表达/纯化的演示.

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. 微阵列，下一代序列和大数据分析的基本生物信息学工具. 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.

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.

Course Instructor(s): Chunyu Liu, PhD and Chunling Zhang, MS
Enrollment limit: 10
前提条件:学生应携带自己的笔记本电脑(PC或Mac)，可以访问大学的VPN网络, 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. 我们将为学生提供第一手的专业生物信息学家真实工作环境的实践经验. We guide students to plan for their future in the bioinformatics world.

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. 鼓励学生将他们对特定受体或生物过程的兴趣带入讨论. 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)

要求阅读(2篇文章/次)将被分配用于讨论，然后由讲师领导的演示. Additional topics can be included upon request.

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. 我们将对比星形胶质细胞和小胶质细胞在脑炎症中的神经营养和神经毒性作用. Lastly, 我们将考虑外周免疫细胞在加重或可能改善脑组织损伤中的作用. 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)

必读:学生将被要求在课前阅读Edward Bullmore的《推荐最近最火的赌博软件》一书. 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.

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. 噬血节肢动物的独特生物学特性，已进化为促进媒介之间的共存, 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. 将从历史的角度讨论控制病媒传播疾病的各种办法, with a consideration of how modern molecular approaches might be used in the future. Evaluations (s/u) based on final examination and practicum.

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, 体感系统是参与姿势控制和平衡的主要感觉系统. 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. 本课程将以上述技术信号的解释和分析结束.

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. 非学生可在任何时间修读本课程，有或没有作业，请联系博士. Blystone for a course packet.

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. 目标读者是结构生物学爱好者，他们可能是也可能不是结构生物学家. The course will be a combination of lecture presentation, discussion of recent advances, 以及为研究做出贡献、协助外联和知识分享的实际努力. 鼓励学习者将他们对某一特定方面或生物过程的兴趣带入讨论.  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.

不需要任何外部工作，因为练习或使用这些程序完全是自愿的.  我们只是想介绍一下生物信息学工具，并演示如何使用它们来推进科学.  Having any background above the core courses is not required to participate in the course.  The class would be done entirely online.

Course Instructor(s): Alaji Bah, PhD
Enrollment limit: None
简介:本纳米课程是为在生物化学方面有专业知识或兴趣的学生(和教师)设计的, molecular, structural and computational biology, 谁愿意运用他们的技能来了解SARS-CoV-2的蛋白质组生物学, 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. 如果没有可用的结构信息，学生将使用计算工具生成同源模型. 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’, 将确定“读取”和“擦除”这些ptm，以探索针对它们的可行性. Finally, in addition to identifying unique SARS-CoV-2 targets, 我们将调查其他冠状病毒中已知的靶点是否也可以在SARS-CoV-2中利用. 

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

Grade Assessment: Participation

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.

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.

Course Instructor(s): Jessica Ridilla, PhD
Enrollment limit: 10
Brief Description:

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: 如果学生参加了7周的课程并提交了最后的报告，他们将获得及格分数.