Office of Undergraduate Instruction

This course may also be used to fulfill the elective requirements of the Biological Sciences major.


Offered:  Fall  T/H4 (Tues/Thurs 1:40 - 3:00 PM) SEC-210

Credits:  3

Prerequisites:  General Biology 01:119:115-116 or  01:119:101-102  and  01:640:135 or 01:640:151

Course Description:  This course is targeted at sophomores and juniors interested in learning the mathematical techniques useful in the biological sciences in the emerging era of computational genomics. The course will cover mathematical methods and tools of computational biology, including Probability Theory, Bayes Theorem, the Binomial, Poisson and Normal distributions, limit theorems, error analysis, tests of statistical significance, parameter estimation, curve fitting, sampling techniques, random number generation and Monte Carlo methods. We will also study mathematical methods useful in the analysis of sequencing and microarray data, such as sequence alignment, phylogeny inference, methods to infer population structure, selection and human migration patterns, methods used in GWAS studies, and methods to identify functional SNPs and pathways.  Concepts will always be explained in the simplest possible way and in the context of biological examples, many of which will be worked out in detail in class. We will often use Matlab as a tool to analyze and plot data, do statistical inference and perform numerical simulations. The overall goal of this course is to give the students the mathematical tools and programming skills necessary to analyze and interpret biological and biomedical data correctly and with confidence.

Course URL: Sakai

Course satisfies Learning Goals

MBB Departmental Learning Goals: 1, 2,and 3

Course Learning Goals:  The overall goal of this course is to give the students the mathematical tools and programming skills necessary to analyze and interpret biological and biomedical data correctly and with confidence. 

Exams, Assignments, and Grading Policy

40%: Homework. Homework will be handed out in class each week and is due the following week.

20%: In class-Midterm

40%: In class-Final

Course Materials

1. Notes for each lecture will be handed out at the end of the class. If you attend all classes and pay attention, these should be sufficient.
2. Text book for statistical methods: Mathematical Statistics and Data Analysis, Second edition: John A. Rice. The book is available as a DjVu document and will be emailed to all students. You will need to install DjVu Viewer on your computer to see its contents.
3. Text book for Matlab (recommended but not required): Computational Statistics Handbook with MATLAB, Second Edition (Chapman & Hall/CRC Computer Science & Data Analysis) by Wendy L. Martinez and Angel R. Martinez (Hardcover - Dec 20, 2007).
4. Software: Please make sure you have MATLAB installed on your computer, including the MATLAB Statistics Toolbox. 

Course Closed?  Enrollment is limited to 50 students.

 

Faculty:  Course Coordinator: This email address is being protected from spambots. You need JavaScript enabled to view it.

 


 

** All information is subject to change at the discretion of the course coordinator.

 

 

Note: Registration in MBB research courses is by special permission only. Students must fill out a Special Permission Form for Undergraduate Research and have it signed by their research advisor and MBB academic advisor before they can get a special permission number.

Sophomore Laboratory Research 01:694:281, 282 283 (1-6, 1-6)

Credits in this course cannot be used toward the required research credits for laboratory option. Minimum GPA of 2.8 or better is required for all research courses.  

Research project in the laboratory of a Rutgers faculty member. Written report of research carried out during each term required (see http://mbb.rutgers.edu/Research-Reports.html for more information).

Undergraduate Laboratory Research 01:694:381, 382, 384 (3-6, 3-6)

Research project in the laboratory of a Rutgers faculty member. Minimum GPA of 2.8 or better is required for all research courses.Written report of research carried out during each term required (see http://mbb.rutgers.edu/Research-Reports.html for more information).

Undergraduate Laboratory Research and Writing 01:694:385, (3)

Research project in the laboratory of a Rutgers faculty member. One hour seminar each week on writing scientific papers. Satisfies SAS Corse Wd Goal.  Minimum GPA of 2.8 or better is required for all research courses. Several drafts of a written report of research carried out during each term required (see http://mbb.rutgers.edu/Research-Reports.html for more information).

Advanced Undergraduate Laboratory Research 01:694:481, 482, 485 (3-6, 3-6)

Pre- or Corequisites: 01:694:407 and 383 Minimum GPA of 2.8 or better is required for all research courses.
Research project in the laboratory of a Rutgers faculty member. Written report of research carried out during the each term required (see http://mbb.rutgers.edu/Research-Reports.html for more information). Oral presentation of student research presented in 01:694:484 (Seminar in Molecular Biology and Biochemistry).

Literature Research in Molecular Biology and Biochemistry 01:694:489, 490 (3, 3)

Prerequisites: 01:694:315, 407-408 and 383 Minimum GPA of 2.8 or better is required for all research courses.
Literature research projects on a selected subject under the direction of a Rutgers or UMDNJ faculty member. Written report of research carried out during the each term required (see http://mbb.rutgers.edu/Research-Reports.html for more information). Students present their research results in 01:694:484 (Seminar in Molecular Biology and Biochemistry).

Honors Laboratory Research 01:694:495, 496 (6, 6)

Pre- or Corequisites: 01:694:315, 407-408 and 483, 484
Honors research project in the laboratory of a faculty member. In the fall semester students are required to attend a seminar each week on writing a thesis. Oral presentation of student research presented in 01:694:484 (Seminar in Molecular Biology and Biochemistry). Students write an Honors thesis and present their research results in 01:694:484 (Seminar in Molecular Biology and Biochemistry). To qualify, a student must have attained, at the end of the junior year, an overall cumulative grade-point average of 3.4 or better and a cumulative grade-point average of 3.4 or better in courses required for the major. Exceptional students not meeting these criteria but wishing to apply for honors research may petition the department chairperson at the beginning of their senior year. Students accepted to the program are expected to complete two terms (6 credits per term) of honors course work. For more information please go to: http://mbb.rutgers.edu/Major/honors.html

Thesis

Each student in the Departmental Honors Program is required to write a thesis on their research project by the end of their senior year. In the fall semester students are required to attend a seminar each week on writing a thesis. The format of the thesis uses that of a scientific article. Honors students are also required to have an oral presentation of their thesis research with two faculty members.

These courses fulfill the MBB Departmental Learning Goal(s) as follows:

01:694:281,282 Goals 3,4
01:694:381,382 Goals 3,4
01:694:481, 482 Goals 3,4
01:694:495, 496 Goals 3,4
01:694:489, 490 Goals 3,4

3. Students should demonstrate the ability to design experiments and critically analyze data.

4. Students should demonstrate the ability to communicate their research and findings orally through seminar and poster presentations and through written research papers.

For further information about the research courses and on how to find a lab please go to http://mbb.rutgers.edu/undergraduate/undergraduate-research

This course is intended for Life Science majors or those with a strong background in the Biological Sciences.

This course may be used to fulfill the elective requirements of the Biological Sciences major.


Offered: Not Offered in Fall 2016 

Credits:  3

Prerequisites:  TBA

Course Description: TBA

Course URL: TBA

Course satisfies Learning Goals

1. 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.

2. Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.

3. Students should demonstrate the ability to design experiments and critically analyze data.

 Exams, Assignments, and Grading Policy: TBD

Course Materials: TBA

Course Closed?  TBD

Faculty: TBD

 


** All information is subject to change at the discretion of the course coordinator.

 

Course is only for Juniors majoring in Molecular Biology and Biochemistry


Offered:  Fall W2 (10:35-11:30 AM) Waksman Rm 1001

Credits:  1

Corequisites:  01:694:407

Course Description:  This course is for registered MBB (694) majors only and should be taken in the fall semester of their third year in college. In the first part of the course, students will be instructed on how to find a laboratory on campus to conduct an independent research. Students will also be instructed on how to perform searches of the scientific literature, data, and funding databases. In the second part of the course there will a series of guest lecturers to introduce students to possible career options in the biological sciences, representing both traditional and alternative career tracks. Below is a list of some of the topics and career options that may be discussed, along with the names of previous guest lecturers.


Topics

  • Introduction to the MBB major and requirements (Dr. Gunderson/Vershon)
  • How to find a laboratory to conduct an independent research project (Dr. Gunderson/Vershon)
  • How to perform literature, data, and funding database searches.
  • Graduate School and Admissions (Dr. Gunderson)
  • Applications to Medical School (HPO Office)
  • Physicians in research and the MD-PhD track
  • Physicians Assistant Program (PAP)
  • Academic track - Life as a research professor (Dr. Gunderson)
  • Academic Track - Life as a teaching professor at the college or high school level
  • Big Pharma - Research Track
  • Big Pharma - Shifting from research track to business
  • Small Biotech
  • Patent and Science Law
  • Non-profit Charitable Agencies
  • Non-Governmental Agencies
  • Public Health Policy
  • Science Writing
  • Alternative careers

Course satisfies Learning Goals

1. 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.

2. Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.

3. Students should demonstrate the ability to design experiments and critically analyze data.

Assignments and Grading Policy:  Class attendance will be a component of the grade. The course will also have a required writing component. For students who have not found a lab to do research, they will search for five different professors whose research interests them and write a one-page report of the research of each professor. For students already doing research in a lab, they will be required to write a 5-page report on the research that is being conducted in their lab.

Course Materials:  All course materials are posted on the course Sakai site. 

Course Closed?  If this course is closed please contact the course instructor concerning special permission numbers.

Faculty

Samuel Gunderson
A322 Nelson lab, 445-1016
This email address is being protected from spambots. You need JavaScript enabled to view it.
office hours by appointment only


** All information is subject to change at the discretion of the course coordinator.

 

 

This course may be used to fulfill the elective requirements of the MBB and Biological Sciences majors.


Offered:  Fall  M/H2 (Mon/Thurs. 10:20-11:40 AM) Nelson A237

Credits:  3

Prerequisites:  01:447:384 or 01:694:408 or 01:146:478

Course Description:  The aim of the course is to provide an introduction to chromatin dynamics, particularly the structural and biochemical modifications of chromatin that underlie epigenetic states and their effects on gene expression and development. The importance of epigenetic states is perhaps the major discovery of molecular biology in the past ten years. They are critical to understanding the control of gene expression in development, the programming and reprogramming that takes place in the differentiation of pluripotent stem cells and they provide an accounting for many of the genomic malfunctions that result in human disease. An acquaintance with the concepts of what has come to be known as Epigenomics is essential for a Molecular Biology major.

  1. Epigenetics: concept and examples, Review transcription [by Dr. Sam Gu]
  2. Nucleosome, biochemistry and structure [SG]
  3. Nucleosome positioning and long-range chromatin organization [SG]
  4. Covalent modification of histones, metabolism and chromatin regulation [SG]
  5. Histone variants and Replicating chromatin  [SG]
  6. Epigenetics and diseases [SG]
  7. Epigenomics methods [By Dr. Mikel Zaratiegui]
  8. ATP dependent remodeling [MZ]
  9. DNA methylation [MZ]
  10. Heterochromatin [MZ]
  11. Small RNA and RNAi [MZ]
  12. piRNA [MZ]
  13. Genome organization [By Dr. Vincenzo Pirrotta]
  14. Polycomb mechanisms [VP]
  15. Genomic programming [VP]
  16. Genomic programming [VP]
  17. Chromatin insulators and genome architecture [VP]
  18. Genetic imprinting [VP]
  19. X chromosome dosage compensation [VP]

Additional 3-4 classes dedicated to student presentations (MZ, VP, and SG), 2 Guest lectures and 3 classes for exams

Course satisfies Learning Goals

1. 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.

2. Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.

4. 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

60% Exams (20% each) Each exam will cover one of the sections, as well as the corresponding guest lecture. The format of the exams may vary between instructors. 

10% Participation (In lectures as well as other student presentations)

30% Student presentation Each group (2 students) will be assigned a research article at the beginning of the course.Both members of the team must participate in reading, analyzing and digesting the paper. They (as a team) will submit their written answers to a set of questions (see below) one month before the presentation.

Each group will make an appointment with a faculty member to rehearse their presentation 2 weeks before the scheduled presentation date.  At this meeting, the students will present written answers to a set of questions described below. The faculty member will provide feedback for the students to revise their presentation. The quality of the team preparation for this meeting, and how well the students incorporate faculty feedback into their presentation will become part of the grade for the student presentation section.

Each classroom presentation will consist of 20 minutes to present slides. The two team members will generally alternate in presenting the material. Additional 10 minutes after the presentation will be reserved for questions from the instructors and the other students. We encourage you to rehearse the final presentation to ensure a good time management.

Presentations should introduce the problem the paper is trying to address, give a brief overview of the techniques used (unless they are very common, like RT-PCR or Southern blotting), a rundown of the major results and conclusions, and present a critique of the paper’s strong and weak points. Do not attempt to discuss every single experiment but focus on the major issues. Remember that you only have 10 minutes each to present the paper, so be brief and to the point. The slides or transparencies should be free of superfluous clutter and clear enough to stand on their own. In order to fully understand the paper and the problem the students should be prepared to read and analyze the most important previous literature that the paper refers to. Questions from the audience and instructors may also refer to issues that the paper doesn’t cover directly but are pertinent to their conclusions, especially if they have been covered in class.

Questions (written answers are due three weeks one month before the presentation and should usually involve 4-5 pages):

Introduction:

  • - What are the main questions that the paper is trying to answer?
  • - What information is necessary to understand the main question addressed by the paper?
  • - What system is used by the study? Why?
  • - What are the specific discoveries made by the study? What is the most important finding?
  • - What is the significance to the field?

Methods:

  • - What techniques are used to address the questions?
  • - What are the advantages of the techniques?
  • - Can you think of an alternative technique?

Results:

  • - How do you describe the results that support the major conclusion? (For example: what do the bands in each lane of a gel represent? What are the controls? What are the axes of graphs?)
  • - Do you have any alternative interpretations?

Discussion:

  • - Do the experiments support the stated goals and conclusions?
  • - What models do the authors propose based on the finding?
  • - What are the new questions raised by the finding? 
  • - Are there any medical implications? 

Course Materials:  All  course matetials will be posted on the Sakai site

Course Closed?  If 694:413 is closed please contact This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it.

Faculty

Co-Coordinator: This email address is being protected from spambots. You need JavaScript enabled to view it.
                         Phone: 445-0824
                        Office: Nelson A123
                        Office hours: By Appointment

Co-Coordinator: This email address is being protected from spambots. You need JavaScript enabled to view it.
                         Phone: 445-1497
                        Office: Nelson A133
                        Office hours: By Appointment

Instructor: Dr. Vincent Pirrotta
                Phone: 445-2446
                Office: Nelson A121
                Office hours: By Appointment


** All information is subject to change at the discretion of the course coordinator.

 

 

Contact Us

Nelson Biological Laboratories

Nelson Biological Laboratories
604 Allison Rd
Piscataway, NJ 08854


p. (848) 445-2075
f.  (732) 445-5870