BIOL7000 - Advanced Topics in Current Biological Research

Status
A
Activity
SEM
Section number integer
301
Title (text only)
Advanced Topics in Current Biological Research
Term
2024C
Subject area
BIOL
Section number only
301
Section ID
BIOL7000301
Course number integer
7000
Level
graduate
Instructors
David S. Roos
Description
Integrative seminar on current biological research for first-year PhD students.
Course number only
7000
Use local description
No

BIOL5860 - Mathematical Modeling in Biology

Status
A
Activity
LEC
Section number integer
401
Title (text only)
Mathematical Modeling in Biology
Term
2024C
Subject area
BIOL
Section number only
401
Section ID
BIOL5860401
Course number integer
5860
Meeting times
MW 1:45 PM-3:14 PM
Level
graduate
Description
This course will cover various mathematical models and tools that are used to study modern biological problems. Mathematical models may be drawn from cell biology, physiology, population genetics, or ecology. Tools in dynamical systems or stochastic processes will be introduced as necessary. No prior knowledge of biology is needed to take this course, but some familiarity with differential equations and probability will be assumed.
Course number only
5860
Cross listings
MATH5861401
Use local description
No

BIOL5825 - Biochemistry and Molecular Genetics Superlab

Status
A
Activity
LAB
Section number integer
401
Title (text only)
Biochemistry and Molecular Genetics Superlab
Term
2024C
Subject area
BIOL
Section number only
401
Section ID
BIOL5825401
Course number integer
5825
Meeting times
TR 1:45 PM-4:44 PM
Level
graduate
Instructors
Jennifer A Punt
John D Wagner
Description
Intensive laboratory class where open-ended, interesting biological problems are explored using modern lab techniques. Topics may include protein structure/function studies; genetic screens, genomics and gene expression studies; proteomics and protein purification techniques; and molecular cloning and DNA manipulation. The course emphasizes developing scientific communication and independent research skills. Course topics reflect the interests of individual Biology faculty members. This course is recommended for students considering independent research.
Course number only
5825
Cross listings
BIOL4825401
Use local description
No

BIOL5606 - Urban Botany

Status
A
Activity
LAB
Section number integer
401
Title (text only)
Urban Botany
Term
2024C
Subject area
BIOL
Section number only
401
Section ID
BIOL5606401
Course number integer
5606
Meeting times
F 12:00 PM-2:59 PM
Level
graduate
Description
Urban environments present unique challenges and opportunities for plant species. After a review of plant taxonomy and anatomy, this course will examine the ecological impacts of plants in urban settings. We will explore landscapes in and around Penn’s campus to understand how plant communities contribute to ecosystem services in these environments. The applied uses of plants in agriculture, medicine, bioremediation, and other aspects of community health will also be explored.
Course number only
5606
Cross listings
BIOL4606401
Use local description
No

BIOL5536 - Fundamentals of Computational Biology

Status
A
Activity
LEC
Section number integer
401
Title (text only)
Fundamentals of Computational Biology
Term
2024C
Subject area
BIOL
Section number only
401
Section ID
BIOL5536401
Course number integer
5536
Meeting times
MW 1:45 PM-3:14 PM
Level
graduate
Instructors
Junhyong Kim
Description
Introductory computational biology course designed for both biology students and computer science, engineering students. The course will cover fundamentals of algorithms, statistics, and mathematics as applied to biological problems. In particular, emphasis will be given to biological problem modeling and understanding the algorithms and mathematical procedures at the "pencil and paper" level. That is, practical implementation of the algorithms is not taught but principles of the algorithms are covered using small sized examples. Topics to be covered are: genome annotation and string algorithms, pattern search and statistical learning, molecular evolution and phylogenetics, functional genomics and systems level analysis.
Course number only
5536
Cross listings
CIS5360401, GCB5360401
Use local description
No

BIOL5535 - Introduction to Computational Biology & Biological Modeling

Status
A
Activity
LEC
Section number integer
401
Title (text only)
Introduction to Computational Biology & Biological Modeling
Term
2024C
Subject area
BIOL
Section number only
401
Section ID
BIOL5535401
Course number integer
5535
Meeting times
MW 3:30 PM-4:59 PM
Level
graduate
Instructors
Gregory R Grant
Junhyong Kim
Description
The goal of this course is to develop a deeper understanding of techniques and concepts used in Computational Biology. Both theoretical and practical aspects of a range of methods will be covered. Theoretical aspects will include statistical analysis, modeling, and algorithm design. This course cannot provide a comprehensive survey of the field but focuses on a select core set of topics and data types. We will discuss the genome browser, alignment algorithms, classical and non-parametric statistics, pathway analysis, dimensionality reduction, GWAS, multiple testing and machine learning, with primary focus on biomedical data. UNIX, R and Python will be utilized to learn to execute big data analysis pipelines, including RNA-Seq and DNA-Seq. UNIX and R will be taught from first principles but prior experience in Python will be assumed. You will be provided with a computational (cloud based) platform on which to do all programming and assignments.
Prerequisite: Programming experience in Python required.
Course number only
5535
Cross listings
BIOL4536401, CIS4360401
Use local description
No

BIOL5517 - Theoretical Population Biology

Status
A
Activity
SEM
Section number integer
401
Title (text only)
Theoretical Population Biology
Term
2024C
Subject area
BIOL
Section number only
401
Section ID
BIOL5517401
Course number integer
5517
Meeting times
TR 10:15 AM-11:44 AM
Level
graduate
Instructors
Erol Akcay
Description
Introduction to basic theoretical tools to study the evolutionary and ecological dynamics of populations. Topics to be discussed include: basic population dynamics and population genetics theory, evolutionary game theory/adaptive dynamics, social evolution (kin selection/multilevel selection), life-history evolution, and stochastic models. Other topics may be added based on the specific interests of students in the class.
Course number only
5517
Cross listings
BIOL4517401
Use local description
No

BIOL5510 - Statistics for Biologists

Status
A
Activity
LEC
Section number integer
401
Title (text only)
Statistics for Biologists
Term
2024C
Subject area
BIOL
Section number only
401
Section ID
BIOL5510401
Course number integer
5510
Meeting times
TR 10:15 AM-11:44 AM
Level
graduate
Instructors
Joshua Benjamin Plotkin
Description
Introductory probability theory. Principles of statistical methods. Problems of estimation and hypothesis testing in biology and related areas.
Course number only
5510
Cross listings
BIOL2510401
Use local description
No

BIOL5430 - Evolution and Ecology of Infectious Diseases

Status
A
Activity
SEM
Section number integer
401
Title (text only)
Evolution and Ecology of Infectious Diseases
Term
2024C
Subject area
BIOL
Section number only
401
Section ID
BIOL5430401
Course number integer
5430
Meeting times
M 1:45 PM-4:44 PM
Level
graduate
Instructors
Dustin Brisson
Description
This course will focus on fundamental topics related to the ecological and evolutionary processes driving the transmission of pathogenic microbes among hosts including life-history strategies; evolution of pathogenic traits; the impacts of temporal, spatial and host-trait heterogeneity; and factors causing the emergence of an infectious pathogen. Examples will be drawn from human, wildlife, and plant pathogens to illustrate these ecological and evolutionary topics. Students will learn to develop and apply current ecological and evolutionary theory to infectious microbe research and gain practical experience accessing, interpreting and synthesizing the peer-reviewed scientific literature through a combination of popular and scientific readings, discussion, and lecture.
Course number only
5430
Cross listings
BIOL4430401
Use local description
No