Molecular Biology and Biochemistry Courses
01:694:390 Introductory Computational Biology
- Introductory Computational Biology is a hands-on, computer-intensive course designed for students interested in exploring the intersection of biology and data science. It is suitable for students with a basic understanding of molecular biology who aspire to scientific or biomedical careers. The curriculum progresses from Unix and Cloud file management to practical bioinformatics analyses, such as DNA mutation mapping (module I), RNA-seq data analysis (module II), and ChIP-seq data analysis (module III). Each module is centered around real-world research questions, with instruction through R/Python coding examples. Assignments and a final project are designed to solidify students' skills in applying computational programs to biological inquiries, preparing them for advanced study or career development in this evolving discipline.
- Semester Offered: Spring
- Credits: 3
- Course URL: canvas
Prerequisites: 01:447:380 Genetics or 01:447:384 Genetic Analysis I
Co-requisites: None
Stop Point (enrollment): 27 (limit due to capacity of a life science computer teaching lab)
Course Syllabus
Spring 2024 (subject to change)
Course satisfies Learning Goals:
After completing this course, students will be able to :
- Explain the basic principles and concepts of computational biology research;
- Appraise the application of computational techniques in current molecular biology;
- Independently utilize Python and R programming languages to analyze DNA and RNA sequences.
These goals aim to provide students with both the theoretical framework and practical expertise necessary for the pursuit of advanced studies or professional opportunities in modern biology.
Course Materials
No textbook is required as most of the needed material is available during class.
Weekly readings on the applications of omics analyses will be posted at the Canvas course site.
Students are encouraged to study R and Python with the following sources:
R for Data Science by Hadley Wickham and Garrett Grolemund
Focus: Data science techniques using the tidyverse package.
Link: https://r4ds.had.co.nz/index.html
An Introduction to R
Focus: Basics of R, official manual from The R Project.
Link: https://cran.r-project.org/doc/manuals/r-release/R-intro.html
Automate the Boring Stuff with Python by Al Sweigart
Focus: General Python automation and scripting.
Link: https://automatetheboringstuff.com/
Course Closed?: If the course is closed, contact Dr. Yang Lyu (Coordinator)
Course Instructors:
Course Coordinator: Dr. Yang Lyu ,
For office hours or discussion, times are open. Email to set up a time to meet or talk after class. You can also ask questions through emails. You can expect us to reply to emails within 1 business day, not including weekends or holidays.
Academic Integrity:
Students are expected to be familiar with Rutgers’ Code of Academic Integrity and the possible penalties (including suspension and expulsion) for violating the policy. Academic dishonesty includes (but is not limited to):
- Cheating
- Plagiarism
- Aiding others in committing a violation or allowing others to use your work
- Failure to cite sources correctly, including artificial intelligence-based tools
- Fabrication
- Using another person’s ideas or words without attribution, including re-using a previous assignment
- Unauthorized collaboration
- Sabotaging another student’s work
We have a zero-tolerance policy for cheating, and all violations will result in substantial penalties. If you have any doubts or questions about what constitutes academic misconduct, please do not hesitate to contact Dr. Lyu.
Student Support and Mental Wellness Services
- Student Success Essentials: https://success.rutgers.edu
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- Counseling, Alcohol and Other Drug Assistance Program & Psychiatric Services (CAPS): http://health.rutgers.edu/medical-counseling-services/counseling
- UWill: free immediate access to teletherapy; you can choose a therapist based on your preferences including issue, gender, language, ethnicity: http://health.rutgers.edu/uwill
- Office for Violence Prevention and Victim Assistance: www.vpva.rutgers.edu
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- Basic Needs Assistance (food, housing, and other essentials): https://ruoffcampus.rutgers.edu/basic-needs
- Rutgers Student Food Pantry: https://ruoffcampus.rutgers.edu/food-pantry
Disability Services
(848) 445-6800 / Lucy Stone Hall, Suite A145, Livingston Campus, 54 Joyce Kilmer Avenue,
Piscataway, NJ 08854 / https://ods.rutgers.edu/
The Office of Disability Services works with students with a documented disability to determine the eligibility of reasonable accommodations, facilitates and coordinates those accommodations when applicable, and lastly engages with the Rutgers community at large to provide and connect students to appropriate resources.
** All information is subject to change at the discretion of the course coordinator.
01:694:316 Honors Introduction to Research in Molecular Biology
- The main goal of this course is to encourage undergraduate students to conduct independent projects in biomedical research laboratories at Rutgers and RWJMS. The course is designed to introduce students to many of the modern techniques used in genetics, molecular biology, and biochemistry that they may use in research by giving them as much "hands on" experience as possible. Students will carry out a research project for which the results are unknown. The topics covered in this course will provide students with a very good foundation for taking upper level genetics and biochemistry courses in subsequent years.
- Semester Offered: Fall
- Credits: 4
- Course URL: canvas
Prerequisites
Registration will only be allowed to second or third year Honors MBB or Genetics students. Registration is by SPN only. Contact
The Project
After some initial training in techniques commonly used in biomedical research labs, students will work on their main research project. The project involves analyzing mutants in a transcriptional regulatory protein in yeast. Students will analyze the data from different assays to determine how the mutations affect transcriptional silencing and repression of genes in yeast. The DNA sequences of the mutants will be determined and the students will derive the predicted change in the protein sequence. Students will then map their mutation on a model of the protein structure and hypothesize how it will affect the protein's activity. There will also be discussions about finding a research lab to do independent research projects as an undergraduate at Rutgers.
Week Topic
1 Introduction; Why is transcription important for biology and human diseases? Review of the general process of gene expression.
2 Why do we work in yeast? Review of yeast biology and genetics.
3 Eukaryotic chromatin structure and the role of Sir2 in transcriptional silencing
4 Vectors and plasmid DNA purification
5 Analyzing DNA - Restriction enzymes, PCR, and gel electrophoresis
6 DNA sequencing and analysis
7 Exam
8 Genetic and biochemical analysis of transcriptional regulatory sites
9 Genetic and biochemical analysis of transcriptional regulatory proteins
10 Silencing vs repression, PCR Mutagenesis and genetic screens for mutants
11 Principals of protein structure
12 Protein structure modeling using jMo,l Results, problems and interpretations
13 Finding a Lab, Careers in Biomedical Sciences
14 Exam
In Fall 2022 the course will be given in a "flipped" manner. All of the content will be posted in videos and lecture notes on the course Canvas. Students will be expected to work through the chapters and take review quizzes on their own. There will be at least two 80 minute discussion periods each week where we will quickly review the content and then work through problems.
Course URL
Canvas site
Learning Goals
This course satisfies learning goals 1, 2, 3, and 4 of the MBB Department.
Core Curriculum Learning Goals Met by This Course:
NS e. Understand and apply basic principles and concepts in the physical or biological sciences.
NS f. Explain and be able to assess the relationship among assumptions, method, evidence, arguments, and theory in scientific analysis.
IRT y. Employ current technologies to access information, to conduct research, and to communicate findings.
IRT z. Analyze and critically assess information from traditional and emergent technologies.
Exams, Assignments, and Grading Policy
Exams: 30%
Quizzes: 40%
Assignments: 30%
Exams will be timed asynchronous over a 10 hr period and will account for 30% of the grade. The exams will focus on the material covered in the lectures, data analysis, and assigned reading. There will be a midterm and a final (cumulative).
Quizzes
There will be three forms of quizzes:
- Chapter Review Quizzes: After watching the video or reading the lecture notes on a chapter student will take quizzes posted on Canvas on the material. These will be used for the students to gauge their basic understanding of the material. These will be self-paced, but must be completed before the topics are discussed in the on-line meetings. These will represent 10% of the grade.
- Analysis Quizzes will be given over a 10 hr period to gauge the understanding of the material that was presented in the lecture notes and videos and then covered in the online discussion sections in the previous week. These quizzes will account for 20% of your grade.
- Lab Quizzes: After watching the video and reading the protocol notes on a lab students will take quizzes posted on Canvas on the material. These are mainly used to ensure that students are prepared to conduct the lab procedures. The purpose it to avoid mistakes and to allow students to complete the lab more efficiently. These will be due before the lab. These will represent 10% of the grade.
Assignments: Assignments and lab reports will be given out through the semester. These are all posted in the Assignments section on Canvas. These include submitting weekly questions on material that was covered in class and homework assignments such as the Yeast Gene Search and Restriction Mapping Problem set (see Canvas assignments). Lab reports will contain the data (plate and gel figures, sequence alignments and a picture of the structure) that were previously generated during this course and your interpretation of the results. The Assignments & Lab Reports will count for 30% of the grade.
Course Materials: A laboratory and lecture manual is provided on-line with the class. All course materials will be posted on the course Canvas site.
Course Closed? This course is primarily for second year Honors students intending to major in the MBB. Non-Honors MBB or Genetics students interested in this course should contact Dr. Vershon for an SPN or should enroll in 694:214 or 694:315, which will be held in the spring semester.
Faculty: Course Coordinator:
Office Hours: Dr. Vershon’s official hours are 7:00 AM to 10:00 AM (East Coast time) Tuesdays using the meeting software in Canvas. However, since the best time to ask questions and get help is in the laboratory section of the class. Students may also email or call us to make an appointment if you have problems or questions.
** All information is subject to change at the discretion of the course coordinator.
01:694:492 Gene Regulation in Cancer & Development
- Gene Regulation in Cancer and Development (01:694:492) is a course for advanced undergraduate students majoring in the Life Sciences. Molecular biology is an experimental science, and a major goal of this course is to explain not just what molecular biologists know, but how they know it. Thus, while covering selected topics in gene regulation, development, and cancer, we will emphasize the methods, experimental design, history, and deductive reasoning that has led to the current state of understanding of these topics. There are no textbooks. Material taught in this course is based on understanding general concepts, in-depth analysis of selected primary research articles and enhancing critical thinking skills. Topics include, gene therapy, inherited diseases, circadian rhythms, metabolic disorders, microbiome, COVID/vaccines, immunity and cancer resistant animals.
- Semester Offered: Spring
- Credits: 3
Prerequisites:
One semester biochemistry 01:694:407 or 01:694:395 or 01:694:301 or 11:115:301 or 11:115:403 AND one semester 01:447:380 or 01:447:384.
Syllabus:
Spring 2024 Syllabus (Updated Syllabus will be posted soon)
Course Satisfies MBB Departmental Learning Goals
- Students should demonstrate an understanding of the knowledge that is needed to begin biomedical research and that is required for post-graduate exams and studies.
- Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.
Exams, Assignments, and Grading Policy
PowerPoint lecture material and readings for each class will be posted on the relevant Canvas site for this course. Graded assignments in this class consist of three exams, accompanying open-book study guides, two take-home assignments, and in-class participation in active learning activities.
Course Materials
Course delivery format: In-person only. Lecture slides and select recordings will be made available on Canvas. Exams will be given in-person, in hard copy.
Textbook: None. All assigned readings from peer reviewed literature will be available in Canvas.
Course Closed?
f this course is closed, please contact
Course Coordinator
Course Instructors
Prof. Annika Barber (
Prof. Isaac Edery (
Student Support Services
Student Success Essentials: https://success.rutgers.edu
Student Support Services: https://www.rutgers.edu/academics/student-support
The Learning Centers: https://rlc.rutgers.edu/
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Bias Incident Reporting: https://studentaffairs.rutgers.edu/bias-incident-reporting
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Office of Veteran and Military Programs and Services: https://veterans.rutgers.edu
Student Health Services: http://health.rutgers.edu/
Counseling, Alcohol and Other Drug Assistance Program & Psychiatric Services (CAPS): http://health.rutgers.edu/medical-counseling-services/counseling/
UWill: free immediate access to teletherapy; you can choose a therapist based on your preferences including issue, gender, language, ethnicity. http://health.rutgers.edu/uwill/
Office for Violence Prevention and Victim Assistance: vpva.rutgers.edu/Office of Disability Services: https://ods.rutgers.edu/
Basic Needs Assistance (food, housing, and other essentials): https://ruoffcampus.rutgers.edu/basic-needs
Rutgers Student Food Pantry: https://ruoffcampus.rutgers.edu/food-pantry
** All information is subject to change at the discretion of the course coordinator.
01:694:484 Seminar in Molecular Biology and Biochemistry
- The course is designed to give students a chance to present their research projects in front of an audience or their peers. The course will break up into smaller sections each taught and graded by one of the section instructors. These smaller sections will serve as a forum for the oral presentation of student research or literature reports pertinent to the student's research project, regardless of whether the student is following the Laboratory or Non-Laboratory Options in the MBB major. Students will give two 20 minute oral presentation related to their research activities: one in the first half of the semester and one in the second half. Students should also plan for 5 minutes of discussion/ questions for a total of 25 minutes. Note: students should target their presentation for a scientific audience, therefore this is not a "Newsweek Magazine Level" or "New York Times Journalistic Level" type of presentation. Thus the introduction, results, conclusions of the talk should match the level of the audience, which means students should assume everyone has a B.S. degree in molecular biology and biochemistry. One week prior to the talk students must email an abstract (~1 page) to their section instructor. We will critique it and very likely we will ask for students to submit a revised abstract. We will then distribute the revised abstract by email to the students in the section. Students who are presenting are expected to invite their P.I. (or Grad. student or Postdoc) from your lab to sit in on the presentation. Students will present a poster on their research at the MBB Poster session near the end of the semester.
- Semester Offered: Spring
- Credits: 1
Prerequisites: 1:694:408
Syllabus: Spring Syllabus
Course Satisfies Learning Goals
- Students should demonstrate an understanding of the knowledge that is needed to begin biomedical research and that is required for post-graduate exams and studies.
- Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.
- Students should demonstrate the ability to design experiments and critically analyze data.
- Students demonstrate the ability to communicate their research and findings orally through seminar and poster presentations and through written research papers.
Exams, Assignments, and Grading Policy
MBB 484 Guidelines for Grading
|
|
strong A |
A/B+ |
B+ |
B |
C |
|
60% presentation |
excellent |
good |
OK |
poor |
bad |
|
20% participation + discussant |
often |
often to sometimes |
sometimes |
rare |
never |
|
20% attendance |
<1 point |
1-1.5 |
1.5-2.5 |
2.5-3 |
>3.5 |
Explanation of Grading
Presentations are based on several criteria:
1) The instructors' critique sheet (not the students)
2) How well you prepared, your organization, enthusiasm, interest in your subject, understanding and ability to discuss what you are presenting
3) Your timely hand-in of abstracts and revised abstracts
4) Grades will be curved based on end-of-semester distribution
Participation and Discussant:
Your role as a "Discussant" contributes to only part of the "Participation" grade. The remainder of this grade is based on how active you are in asking questions during the other 12 weeks of the course when you are not a participant.
Attendance Point System
Unexcused absence (no prior notification) is minus one point.
Late is minus 0.5 points.
Excused absence (inform us before the class, or provide a doctor’s note for emergency medical absences) no points to minus one point as per instructors’ discretion. But we will still keep track to prevent abuse
Course Materials: All course materials are posted on the course's Canvas site
Course Closed?
If this course is closed please contact the course instructor concerning special permission numbers.
Faculty
Course Coordinator:
Gyan Bhanot
Participating Faculty:
Barth Grant
Nelson Biology Laboratories, Room A231
Isaac Edery
Center for Advanced Biotechnology & Medicine CABM, Room 339
Student Support Services
Student Success Essentials: https://success.rutgers.edu
Student Support Services: https://www.rutgers.edu/academics/student-support
The Learning Centers: https://rlc.rutgers.edu/
Rutgers Libraries: https://www.libraries.rutgers.edu/
Bias Incident Reporting: https://studentaffairs.rutgers.edu/bias-incident-reporting
Dean of Students – Student Support Office: https://success.rutgers.edu/resource/dean-students-student-support-office
Office of Veteran and Military Programs and Services: https://veterans.rutgers.edu
Student Health Services: http://health.rutgers.edu/
Counseling, Alcohol and Other Drug Assistance Program & Psychiatric Services (CAPS): http://health.rutgers.edu/medical-counseling-services/counseling/
UWill: free immediate access to teletherapy; you can choose a therapist based on your preferences including issue, gender, language, ethnicity. http://health.rutgers.edu/uwill/
Office for Violence Prevention and Victim Assistance: vpva.rutgers.edu/Office of Disability Services: https://ods.rutgers.edu/
Basic Needs Assistance (food, housing, and other essentials): https://ruoffcampus.rutgers.edu/basic-needs
Rutgers Student Food Pantry: https://ruoffcampus.rutgers.edu/food-pantry
** All information is subject to change at the discretion of the course coordinator.
01:694:412 Proteomics and Functional Genomics
- This course is a survey of modern techniques of protein biochemistry, bioinformatics, proteomics, and functional genomics. It will include a discussion of basic concepts of protein structure and function, protein characterization and purification, enzyme kinetics, nmr and x-ray crystallography, mass spectrometry, and various techniques of functional and structural genomics.
- Semester Offered: Spring
- Credits: 3
- Course URL: canvas
Prerequisites
One semester of Biochemistry (01:694:407 or 01:694:395 or 01:694:301 or 11:115:301 or 11:115:403) AND one semester of Genetics (01:447:380 or 01:447:384).
Course Syllabus
Spring 2025 (Subject to change)
Course Description
This course is an exploration of the cutting-edge techniques and technologies used in protein biochemistry, proteomics, and functional genomics. Students will gain a deep understanding of protein structure, purification methods, enzyme kinetics, genome editing, and the vast field of genomics. The course will cover topics such as:
- Introduction to genomics and proteomics
- Advancements in DNA sequencing technologies and their applications
- Chromatin structure and genome organization
- Single-cell analysis approaches
- Mass spectrometry in proteomics
- Protein folding and interactions
- Macromolecular assemblies and condensates
- CRISPR-based genome editing
- Next-generation sequencing technologies
- Student-led presentations on genetic diseases
For 2025: This year's course will also feature two lectures by Dr. Kevin Monahan on single-cell analysis approaches and 3D chromatin folding.
Course URL
Canvas
Course Satisfies Learning Goals
- Students will gain a comprehensive understanding of the knowledge and skills required to conduct biomedical research in proteomics and functional genomic.
- Students will develop the ability to independently research and evaluate information about specific biological systems or problems.
Exams, Assignments, and Grading Policy
- Take-home Exam I: 30%
- Take-home Exam II: 30%
- Student Presentation: 25%
- Take-home Exam III: 15%
- Class participation will also be taken into account, particularly during student presentations.
There will be no final exam. Late submissions will only be accepted if prior notice is given, and a further extension will not be granted. Late submissions without notice may result in a grade deduction based on the length of the delay, up to a maximum of 30%.
Course Materials
Instructors will supply the necessary readings. For conducting next-generation sequencing analysis, students must have access to a personal computer with a physical keyboard and an internet connection.
Course Closed?
This course is by special permission only, with priority given to MBB majors. The majority of the class will be juniors and seniors. To obtain a special permission number or to get on the waiting list if you are not an MBB major, CALL 848-445-2075. If the course is closed, please use the following link: Wait List Sign Up for Spring 2025 Courses
If you have any questions, please contact the Division of Life Sciences - Office of Undergraduate Instruction at 848-445-2075 or visit our office at Nelson Biological Laboratories B112, Busch Campus.
Faculty
Dr. Jia Fei
E-mail:
Dr. Stephen Anderson
E-mail:
Student Support Services
Student Success Essentials: https://success.rutgers.edu
Student Support Services: https://www.rutgers.edu/academics/student-support
The Learning Centers: https://rlc.rutgers.edu/
Rutgers Libraries: https://www.libraries.rutgers.edu/
Bias Incident Reporting: https://studentaffairs.rutgers.edu/bias-incident-reporting
Dean of Students – Student Support Office: https://success.rutgers.edu/resource/dean-students-student-support-office
Office of Veteran and Military Programs and Services: https://veterans.rutgers.edu
Student Health Services: http://health.rutgers.edu/
Counseling, Alcohol and Other Drug Assistance Program & Psychiatric Services (CAPS): http://health.rutgers.edu/medical-counseling-services/counseling/
UWill: free immediate access to teletherapy; you can choose a therapist based on your preferences including issue, gender, language, ethnicity. http://health.rutgers.edu/uwill/
Office for Violence Prevention and Victim Assistance: vpva.rutgers.edu/Office of Disability Services: https://ods.rutgers.edu/
Basic Needs Assistance (food, housing, and other essentials): https://ruoffcampus.rutgers.edu/basic-needs
Rutgers Student Food Pantry: https://ruoffcampus.rutgers.edu/food-pantry
** All information is subject to change at the discretion of the course coordinator.