Courses in Systems Biology and Computational Biology

 

Advanced Statistical and Computational Methods in Genetics and Genomics

Faculty: Iuliana Ionita-Laza
Email: il2135 [at] columbia.edu
Department: Biostatistics
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BIST/P8119-20161-001/
Semester: Spring 2016
Place: TBA (Medical Center Campus)
Schedule: F 1:00-3:50
Description: Design and analysis of high-dimensional genetic studies. Genome-wide linkage and association analyses, next-generation sequencing studies, and network genetics.

 

 

Biological Sequence Analysis

Faculty: Richard Friedman
Email: friedman [at] c2b2.columbia.edu
Department: Biomedical Informatics, and Integrated Program in Cellular, Molecular, and Biomedical Studies
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BINF/G4013-20161-001/
Semester: Spring 2016
Place: Hammer Health Sciences Center, 2nd Floor Microcomputer Classroom
Schedule: W 9:00-12:00
Description: A lecture/laboratory course for experimental biologists in running bioinformatics programs

 

 

Computational Genomics

Faculty: Itsik Pe'er
Email: itsik [at] c2b2.columbia.edu
Department: Computer Science
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/CBMF/W4761-20161-001/
Semester: Spring 2016
Place: TBA (Morningside Heights Campus)
Schedule: MW 4:10-5:25
Description: Provides comprehensive introduction to computational techniques for analyzing genomic data including DNA, RNA and protein structures; microarrays; transcription and regulation; regulatory, metabolic and protein interaction networks. The course covers sequence analysis algorithms, dynamic programming, hidden Markov models, phylogenetic analysis, Bayesian network techniques, neural networks, clustering algorithms, support vector machines, Boolean models of regulatory networks, flux based analysis of metabolic networks and scale-free network models. The course provides self-contained introduction to relevant biological mechanisms and methods.

 

 

Computational Systems Biology: Proteins, Networks, Function

Faculty: Dennis Vitkup
Email: dev7003 [at] dbmi.columbia.edu
Department: Systems Biology
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BINF/G4015-20161-001/
Semester: Spring 2016
Place: ICRC 817 (Medical Center Campus)
Schedule: TR 2:00-4:00
Description: Structural and functional proteomics and cellular network biology.

 

 

Design Principles for Biological Circuits

Faculty: Predrag R. Jelenkovic
Email: predrag [at] ee.columbia.edu
Department: Electrical Engineering
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/ELEN/E6010-20161-001/
Semester: Spring 2016
Place: TBA (Morningside Heights Campus)
Schedule: T 4:10-6:40
Description: Beyond bioinformatics, cells as systems. Metabolic networks, transcription regulatory networks, signaling networks. Deterministic and stochastic kinetics. Mathematical representation of reconstructed networks. Network motifs. Signal transduction and neuronal networks. Robustness. Bacterial chemotaxis and patterning in fruit fly development. Kinetic proofreading. Optimal gene circuit design. Rules for gene regulation. Random networks and multiple time scales. Biological information processing. Numerical and simulation techniques. Major project(s) in Matlab.

 

 

Genomics of Gene Regulation

Faculty: Harmen J. Bussemaker
Email: hjb2004 [at] columbia.edu
Department: Biological Sciences
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BIOL/W4510-20161-001
Semester: Spring 2016
Place: 601 Sherman Fairchild Life Sciences Building
Schedule: M 2:40-5:25
Description: This course will provide students with a quantitative understanding of the ways in which molecular interactions between nucleotides and proteins give rise to the behavior of gene regulatory networks. The key high-throughput genomics technologies for probing the cell at different levels using microarrays and next-generation sequencing will be discussed. Strategies for interpreting and integrating these data using statistics, biophysics, and genetics will be introduced. In computer exercises, student will learn the basics of the R language, and use it to perform analyses of genomics data sets.

 

 

Human Evolutionary Genetics

Faculty: Molly Przeworski, Guy Sella, and Joseph Pickrell
Email: mp3284 [at] columbia.edu
Department: Biological Sciences
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BIOL/G6560-20161-001/
Semester: Spring 2016
Place: 601B Sherman Fairchild Life Sciences Building
Schedule: TR 2:40-3:55
Description: The course brings together population genetics theory, empirical studies and genetic models of disease to provide an integrated perspective on the evolutionary forces that shape human variation and in particular disease risk. Our goals are to provide you with a basic toolbox with which to approach human variation data and in parallel, to expose you to cutting-edge research and to the forefront of knowledge in human population genetics. To this end, the course includes in-depth discussions of classic papers in these fields coupled with recent findings employing new technologies and approaches.

 

Related Courses

 

Advanced Machine Learning

Faculty: Aurelie Lozano and Lior Horesh
Email: acl2187 [at] columbia.edu
Department: Computer Science
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/COMS/W4772-20161-001/
Semester: Spring 2016
Place: TBA (Morningside Heights Campus)
Schedule: R 12:10-2:00
Description:  

 

 

Algebraic Topology II

Faculty: Mohammed Abouzaid
Email: ma3230 [at] columbia.edu
Department: Mathematics
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/MATH/G4308-20161-001/
Semester: Spring 2016
Place: 307 Mathematics Building
Schedule: MW 2:40-3:55
Description: Continuation of Algebraic Topology I from Fall 2015.

 

 

Biophysical Chemistry

Faculty: Ruben Gonzalez
Email: rlg2118 [at] columbia.edu
Department: Chemistry
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/CHEM/G4170-20161-001/ 
Semester: Spring 2016
Place: TBA (Morningside Heights Campus)
Schedule: TF 4:10 - 5:25
Description: Tactics and techniques for the study of large molecules of biological importance, analysis of the conformation of proteins and nucleic acids; hydrodynamic, scattering, and spectroscopic techniques for examining macromolecular structure.

 

 

Introduction to Algebraic Topology

Faculty: Anton Zeitlin
Email: az2319 [at] columbia.edu
Department: Mathematics
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/MATH/W4053-20161-001/
Semester: Spring 2016
Place: 520 Mathematics Building
Schedule: TR 5:40-6:55
Description: The study of topological spaces from algebraic properties, including the essentials of homology and the fundamental group. The Brouwer fixed point theorem. The homology of surfaces. Covering spaces.

 

 

Introduction to Molecular Modeling

Faculty: Richard Friesner
Email: rich [at] chem.columbia.edu
Department: Chemistry
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/CHEM/G4232-20161-001/ 
Semester: Spring 2016
Place: TBA (Morningside Heights Campus)
Schedule: TR 10:10-11:25
Description: Molecular modeling has become an integral part of research in many areas of chemistry, and in industry in drug discovery and materials design. Many experimental papers in the literature are routinely complemented by molecular modeling calculations. Experimental scientists working in industry have a significant advantage if they know how to optimally use modeling software. The course would consist of a normal lecture part plus a lab session every week in which the students learn to use modeling software by working on projects.

 

 

Machine Learning

Faculty: Satyen Kale
Email: satyen [at] satyenkale.com
Department: Computer Science
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/COMS/W4771-20161-001/
Semester: Spring 2016
Place: TBA (Morningside Heights Campus)
Schedule: TR 10:10-11:25
Description: Topics from generative and discriminative machine learning including least squares methods, support vector machines, kernel methods, neural networks, Gaussian distributions, linear classification, linear regression, maximum likelihood, exponential family distributions, Bayesian networks, Bayesian inference, mixture models, the EM algorithm, graphical models and hidden Markov models.

 

 

Methods in Biomedical Informatics II: Computational Methods

Faculty: Noemie Elhadad
Email: noemie.elhadad [at] columbia.edu
Department: Biomedical Informatics
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BINF/G4002-20161-001/
Semester: Spring 2016
Place: TR: 200 Presbyterian Hospital; F: Location to be announced
Schedule: TR 9:00-10:15; F 10:00-11:15
Description: Survey of the methods underlying the field of medical informatics.  Explores techniques in mathematics, logic, decision science, computer science, engineering, cognitive science, management science and epidemiology, and demonstrates the application to health care and biomedicine.

 

 

Methods in Biomedical Informatics III: Research Methods

Faculty: Lena Mamykina
Email: lena.mamykina [at] dbmi.columbia.edu
Department: Biomedical Informatics
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BINF/G6002-20161-001/
Semester: Spring 2016
Place: 200 Presbyterian Hospital (Medical Center Campus)
Schedule: MTR 2:30-3:45
Description: Formulation of research plans in Biomedical Informatics including grant proposal writing.

 

 

Molecular Biology of Cancer

Faculty: Carol Prives
Email: clp3 [at] columbia.edu
Department: Biological Sciences
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BIOL/W4799-20161-001/
Semester: Spring 2016
Place: 601 Sherman Fairchild Life Sciences Building (Morningside Heights Campus)
Schedule: TR 2:40-3:55
Description: Tracing the discovery of the role of DNA tumor viruses in cancerous transformation. Oncogenes and tumor suppressors are analyzed with respect to their function in normal cell cycle, growth control, and human cancers.

 

 

Principles of Developmental Biology

Faculty: Andrew Tomlinson
Email: at41 [at] columbia.edu
Department: Genetics and Development
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/GEND/G4027-20161-001/
Semester: Spring 2016
Place: TBA (Morningside Campus)
Schedule: M 10:00-11:30; R 3:00-4:30
Description:  

 

 

Research Seminar in Biomedical Informatics

Faculty: Nicholas Tatonetti
Email: nick.tatonetti [at] columbia.edu
Department: Biomedical Informatics
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BINF/G4099-20161-001/
Semester: Spring 2016
Place: 200 Presbyterian Hospital(Medical Center Campus)
Schedule: T 4:00-5:00
Description: Presentations by medical informatics faculty and invited international speakers in medical informatics, computer science, nursing informatics, library science, and related fields.

 

 

Seminar in Computational Neuroscience & Neuroengineering

Faculty: Nima Mesgarani
Email: nm2764 [at] columbia.edu
Department: Electrical Engineering
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/EEBM/E9070-20161-001/
Semester: Spring 2016
Place: TBA (Morningside Heights Campus)
Schedule: R 12:10-2:00
Description: Study of recent developments in computational neuroscience and neuroengineering.  Spring 2016 Topic: Bio-Inspired Computation.

 

 

Statistics for Basic Sciences

Faculty: Fred Loweff and Karen Allis
Email: fl12 [at] columbia.edu
Department: Pharmacology
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/PHAR/G8012-20161-001/
Semester: Spring 2016
Place: TBA (Medical Center Campus)
Schedule: T 1:00-3:00
Description:  

 

 

Stem Cell Biology & Applications

Faculty: Daniel Kalderon
Email: ddk1 [at] columbia.edu
Department: Biological Sciences
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BIOL/W4193-20161-001/
Semester: Spring 2016
Place: TBA (Morningside Heights Campus)
Schedule: TR 10:10-11:25
Description: The course examines current knowledge and potential medical applications of pluripotent stem cells (embryonic stem cells and induced pluripotent stem cells), direct conversions between cell types and adult, tissue-specific stem cells (concentrating mainly on hematopoietic and gut stem cells as leading paradigms).

 

 

Theoretic Genetic Modeling

Faculty: Prakash Gorroochurn
Email: pg2113 [at] columbia.edu
Department: Biostatistics
URL: http://www.columbia.edu/cu/bulletin/uwb/subj/BIST/P8139-20161-001/
Semester: Spring 2016
Place: TBA (Medical Center Campus)
Schedule: M 1:00-3:50
Description: The theoretical foundations underlying the models and techniques used in mathematical genetics and genetic epidemiology. Use and interpretation of likelihood methods; formulation of mathematical models; segregation analysis; ascertainment bias; linkage analysis; genetic heterogeneity; and complex genetic models.