Genetics Courses
01:447:303 Computational Genetics for Big Data
- Semester Offered: Spring
- Credits: 3
- Course URL: Canvas
Pre-requisites
Students must have previously completed Genetic Analysis I (01:447:384) or Genetics (01:447:380), and Statistics I and II (01:960:211-212).
Course Restrictions
This course is limited to Genetics majors (and graduate students in a number of departments). Other students can be added by special permission number pending computer space availability.
Course Description
The focus of this course is the application of R programming (with independent verification by other methods) to the analysis of genetic data, particularly “big data” sets with multiple measurements. The primary data sets will contain multiple Single-Nucleotide-Polymorphism genotypes, DNA methylation, conservation, eQTLs, RNA-sequence and/or other data for multiple/all genes in a set of individuals.
Computational analysis will be performed on such data, with the goal of determining whether certain genes are causal for given phenotypes.
This course is for junior or senior students who are thinking of careers relating to life sciences, statistics, and/or computer science. Specifically, this course is for students who major in Genetics. The course fulfills the laboratory requirement for the Genetics major.
Students will learn how to acquire such data, format it for R, plot the data, and perform computational analyses. In addition, students will learn how to simulate data under different hypotheses, and how to perform power and sample size calculations for different statistical methods applied to real or simulated data.
Each class consists of a mixture of lecture and computer-based demos and/or exercises. There will be time for students to work on assignments. Guest investigators will make short presentations (in person or virtually) to provide illustrations of how programming and informatics is critical for their research. The course provides the introductory skills needed to conduct basic computational research in the life sciences, including many aspects of computer programming and data analysis.
Course Goals
The goals of Honors Computational Genetics reflect the learning goals of the Department of Genetics, and include:
- Knowledge specific goals: know the terms, concepts, and theories in genetics.
- Integrate the material from multiple courses and research.
- Participate in Discussion Forums with other students. These forums are based on current events in genetics. Students will write scientific opinions and respond to other students’ opinions.
Specific itemized goals include:
- Learning R programming, specifically methods for acquisition and analysis of big data from genomics repositories.
- Discovering online repositories for genomic data sets.
- Learning the fundamentals of statistical analysis for such data sets.
- Performing empirical type I and power evaluations for different statistics applied to expression data by writing R programs that can simulate data with mathematical models; and,
- Determining the fundamentals of experimental design for expression-data statistics.
Core Curriculum Learning Goals Met by this Course: Info Tech & Research [ITR]
- Goal Y: Employ current technologies to access information, to conduct research, and to communicate findings.
- Goal Z: Analyze and critically assess information from traditional and emergent technologies.
Course Materials
The computer lab has Windows computers. Class materials and files may be copied after each class to a portable USB flash drive (Windows formatted) to continue working at home. No textbook is required as most of the needed material is made available during class. However, there will be journal articles that will be provided for discussion forums.
A useful resource to have on hand if you prefer to have a printed book is:
R Cookbook, 2nd Edition, Authors: James Long and Paul Teetor
https://rc2e.com/
Exams, Assignments, and Grading Policy
Attendance is expected at all classes; in-class demos and exercises are an integral part of this class and it is difficult to make-up work when class is missed. If a student must miss a class, please use the University absence reporting website to indicate the date and reason for your absence. An email is automatically sent to the instructors. Completion of all assignments is required, including any that may have been missed due to absence in class.
Students will be assigned weekly projects based on current material. The final grade is based on the grades received on these projects, quizzes, and a final exam.
Course Closed?
If you are a non-Genetics major or if this course is closed, please add your name to request an spn for the course under the Department of Genetics section of the SPN Request Page. Please note the system does not notify students unless they can be accommodated in the course. SPNs are distributed throughout the remainder of the semester and through the drop/add period. If you have any questions, please contact the genetics department at
Faculty:
Dr. Derek Gordon
Office: B-414, Nelson Biological Labs, 604 Allison Road, Busch Campus
** All information is subject to change at the discretion of the course coordinator.
01:447:302 Quantitative Biology & Bioinformatics
- Semester Offered: Fall
- Credits: 3
- Course URL: canvas
Prerequisites
Genetics 01:447:380 or Genetic Analysis I 01:447:384
Course Restrictions
This course is limited to Genetics majors. Other students may be added by special permission number pending space availability.
Course Description
Quantitative Biology and Bioinformatics is a computer-based laboratory course that introduces students to the use of computers in biological research. The course is a Python programming boot camp designed for students with no prior programming experience (45%) followed by bioinformatics instruction that continues to build on the Python skills (55%). Classes consist of a mixture of lecture and computer-based exercises, as well as time for students to work on assignments. The course provides introductory Data Science skills needed to conduct basic computational research in the life sciences and is of most relevance for students who plan to pursue research careers, attend graduate or medical school, or enter the biomedical/research workforce.
Class will meet for 2.5 hrs. twice per week. No prior programming experience is required- the course is designed specifically for beginners. However, because computer programming concepts can be difficult for some students to master, we strongly recommend you complete an hour or more of an online Python tutorial before the start of class, to get a sense of whether a programming course is a good choice for you. More info is provided on the course Canvas website.
Syllabus
Course Satisfies Learning Goals
1. Knowledge specific goals: Know the terms, concepts and theories in genetics.
2. Integrate the material from multiple courses and research. That is, to think holistically and to see the whole as well as the parts.
Exams, Assignments, and Grading Policy
Students will be assigned weekly projects based on current material. The final grade is based on the grades received on these projects, quizzes, a mid term coding project, and a final coding project.
Course Materials
Python programming manuals are available online.
Course Closed?
If this course is closed, please add your name to request an spn for the course under the Department of Genetics section of the SPN Request Page. Please note the system does not notify students unless they can be accommodated in the course. SPNs are distributed throughout the remainder of the semester and through the drop/add period. We ask that if you are provided an spn for a course and choose not to use it, to please notify our offices at
Faculty
Dr. Tara Matise (Coordinator)
B410 Nelson Biological Laboratories
Email:
Dr. Timothy Stanek
Dr. Vikas Nanda
Dr. Wilma Olson
** All information is subject to change at the discretion of the course coordinator.
01:447:488 Genetic Counseling Rotation
- Semester Offered: Fall, Spring
- Credits: 3
- Course URL: Canvas
Prerequisites
a. Undergraduate student in Department of Genetics
b. Have a minimum 2.8 GPA
c. Application interview with Dr. Gary Heiman
d. Have completed the Rutgers University Human Subjects Certification (IRB)
2) Placement requirements- Each rotation placement has its own requirements and the student may be required to pay any charges. Depending on the rotation, these can include:
a. Pass a 5-panel drug screen (paid by student)
b. Pass a Criminal background check (paid by student)- required by Joint Commission on Accreditation of Healthcare Organizations (JCAHO)
c. Completed the hospital orientation manual (self-study) and passed the quiz.
d. Proof of immunization and physical exam (obtained from Hurtado)
Course Description
The goal of this course is to provide students with an understanding of the genetic counseling career. To make the experience worthwhile for the student, we expect the student to commit a sizable amount of time to the Genetic Counseling Rotation course. Genetic Counseling Rotation is not, and should not, be an easy A. Students will be placed at a local Genetics Counseling clinic to shadow a genetic counselor for one semester. They are expected to spend at least 8 hours a week at the rotation. At the clinic, the student will observe genetic counseling sessions, observe the genetic counselor's role in coordination of care and follow-up with patients and physicians, perform literature searches and research availability of genetic testing, and research studies and patient literature. In addition, students will attend a weekly meeting with the course instructor. At the weekly meetings, the instructor will discuss the Genetic Counseling career and application to the master-level programs. Students will also discuss cases that they observed that their rotation.
Course Syllabus
Course Satisfies Learning Goals
At the end of the program students will:
- Understand Genetic Counseling as a profession
- Understand application requirements for masters-level programs
- Gain experience in a clinical Genetic Counseling clinic
Exams, Assignments, and Grading Policy
Grading will be as follows: A; 90-100; B: 80-89; C: 70-79; D: 60-69; F: 0-59.
The course grade will be based on:
25%- Presentation of one case to the Genetic Counseling group
25%- Ten genetic case logs. To download case log template, click here.
25%- Evaluation by the clinical supervisor
25%- Weekly meeting with professor
Course Materials
None
Course Closed?
This course is reserved for students in the Genetic Counseling Certificate Program. Special permission required. To obtain special permission, students must first complete the departmental guidelines (see above), and if accepted, then complete the placement requirements
Faculty
Dr. Gary Heiman
Email:
** All information is subject to change at the discretion of the course coordinator.
01:447:470 Evolutionary Developmental Biology
- Semester Offered: Spring
- Credits: 3
- Course URL: Canvas
Prerequisites
Genetics (447:380) or Genetic Analysis (447:384). Developmental Genetics (447:370) recommended.
Course Description
Evolutionary origins of the vertebrate body plan are major problems in biology. While paleontology and comparative anatomy have revealed the evolutionary trajectories of the organs, recent genetics, genomics and embryology are becoming powerful tools to answer classical questions. The goals of this course are twofold; 1) obtain fundamental knowledge of anatomy, embryology, and the latest genomics and 2) learn how to integrate genetics, genomics and embryology to answer evolutionary questions through active discussion in the classroom. The training to discover and answer scientific questions in animal diversity will be performed at the American Museum of Natural History. This course is conducted in person (no online option).
Course Syllabus
Spring 2022 Syllabus (Spring 2024 Syllabus will be updated soon)
Course Satisfies Departmental Learning Goals
- Knowledge specific goals:
- Study basic concepts and terminology of comparative anatomy, developmental biology, and evolutionary genomics.
- Integrate the material from multiple courses and research:
- Learn how to integrate genomics, genetics, and developmental biology to approach the origin of the vertebrate plan.
Exams, Assignments, and Grading Policy
Daily mini-quiz and three exams. Pre-reading of textbooks and scientific articles before each class is necessary.
Grading Policy
20% for Pre-Class Reading – Quizzes
20% Attendance
15% for AMNH Field Trip Presentation
15% for Exam I
15% for Exam II
15% for Final Exam
Course Materials
Required;
Vertebrates: Comparative Anatomy, Function, Evolution. 7th Edition by Kenneth Kardong
ISBN-13: 978-1259700910
Recommended (but not required);
Vertebrates: Comparative Anatomy, Function, Evolution. 8th Edition by Kenneth Kardong
ISBN-13: 978-1259700910 (required)
Developmental Biology. 13th Edition by Scott F. Gilbert and Michael J.F. Barresi
ISBN: 9780197574591 (recommended, but not required)
Required device for attendance and mini-quiz
Canvas will be used to check attendance and conduct mini-quiz. Students should bring a laptop computer or smartphone to receive points.
Course Closed?
There is no wait list for this course. Please continue to monitor WebReg for openings.
Faculty
Dr. Tetsuya Nakamura
01:447:465 Genetic Approaches and Research Analysis
- Semester Offered: Fall
- Credits: 3
- Course URL: Canvas
Prerequisites
Genetic Analysis I & II 01:447:384-385 or Genetics (447:380)
Course Syllabus
What is this class like?
This class will teach students how to read, interpret and analyze research articles. The class will follow an active learning format, where we will discuss seminal and recent research articles in depth: What was the scientific question or problem? What methods and strategies were used to address it? What were the findings and conclusions? What are the alternative interpretations and methods that could have been applied? What questions are remaining?
This class will expose students to a diverse selection of research literature, involving genetic and molecular analyses in model organisms such as mice, worms, flies and yeast. The class series will begin with a research article presented by the teacher. During the majority of the class series, students will be divided into groups of 4-5. Each group will be assigned one research article and be required to work together to a) interpret, b) analyze and c) present the article in the form of an oral presentation to the class. Students will be graded on their ability to perform each of these tasks and on active participation during presentations by other groups. All groups will also be required to complete and be graded on a written discussion summary assignment at the end of each article discussion. This summary assignment may take many forms, e.g., preparation of a graphical abstract, subway advert, or other creative forms of expression.
- Learn to read, as well as critically and creatively analyze published research articles.
- Learn the concepts and methods involved in genetic and molecular analyses.
- Learn to think deeply about experimental strategies and scientific interpretations.
- Learn to communicate advanced scientific concepts through oral presentations.
Satisfies Departmental Learning Goals
- Use genetic information and ideas to critically analyze published research articles.
- Integrate the material from multiple courses and research.
Exams, Assignments, and Grading Policy
There is no final exam.
Grades in this course are weighted according to the table below
|
Activity or assignment |
Grade (%) |
|
Group presentation: interpretation of article |
20 |
|
Group presentation: analysis of article |
20 |
|
Group presentation: presentation of article |
20 |
|
Discussion worksheet A |
10 |
|
Discussion worksheet B |
10 |
|
Discussion worksheet C |
10 |
|
Active participation |
10 |
|
Total |
100 |
Course Materials
None
Course Closed?
Please continue to monitor Web-Reg for openings.
Faculty
Devanshi Jain, PhD
** All information is subject to change at the discretion of the course coordinator.