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Resources

Affiliated Graduate Programs

Applied Mathematics Program (Ph.D.)

Applied Mathematics Program (Ph.D.)

The Engineering Sciences and Applied Mathematics Ph.D. program is designed for students who want to pursue research in applied math at the highest level. The applied mathematics faculty is involved in research that uses a variety of mathematical methods associated with asymptotic analysis, bifurcation theory, graph theory, scientific computing, ordinary and partial differential equations, probability and statistics, singular perturbations, stability theory, and stochastic processes.

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Interdisciplinary Biological Sciences Graduate Program (Ph.D.)

Interdisciplinary Biological Sciences Graduate Program (Ph.D.)

IBiS provides the resources and training environment necessary to promote the development of Ph.D. students into independent, creative research scientists and teachers. The program includes approximately 60 training faculty from diverse science and engineering departments, who are linked by common interests in addressing fundamental questions in the biological and biomedical sciences.

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Masters in Quantitative and Systems Biology

Masters in Quantitative and Systems Biology

The one-year Quantitative and Systems Biology program is to train students in quantitative and systems biology approaches and techniques that will enable them to directly enter research careers in industry or academia, or to succeed in top Ph.D. and M.D. programs.

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Courses

Applied Linear Algebra: ES_APPM 395

Nearly every discipline with a quantitative component including engineering, physical sciences, social sciences, finance, computer graphics, big data, and machine learning rely on linear algebra. Numerical computation greatly enables modeling the data analysis in these fields. In order to utilize linear algebra and computing for problem solving, it is essential to understand how to set up problems (in the linear framework and numerically), determine when well defined solutions exist, write programs and algorithms in MATLAB to solve these problems, evaluate whether the algorithm will find the solution efficiently, and evaluate the accuracy of the computation.

Professor: Niall Mangan

Bioinformatics: Biological Sequence and Structure Analysis: BIO_SCI 323

BIO_SCI 323 explores through case studies and classroom discussions, the principles and practical applications of computational tools in contemporary molecular and structural biology research. Besides gaining an appreciation for the algorithmic aspects of these tools, students will learn to code with python and R, design and perform experiments in silico, and critically evaluate results.

Professor: Ishwar Radhakrishnan

Models in Applied Mathematics: ES_APPM 421

Applications to illustrate typical problems and methods of applied mathematics. Mathematical formulation of models for phenomena in science and engineering, problem solution, and interpretation of results. Examples from solid and fluid mechanics, combustion, diffusion phenomena, chemical and nuclear reactors, and biological processes.

Professor: Daniel Abrams

Numerical Methods for Random Processes: ES_APPM 448

Analysis and implementation of numerical methods for random processes: random number generators, Monte Carlo methods, Markov chains, stochastic differential equations, and applications.

Professor: Hermann Riecke

Principles and Methods in Systems Biology: IBIS 404

IBIS 404 uses mathematical-based experimental analysis and modeling to study biological problems. The class will introduce quantitative techniques, computational tools and biological systems that help investigators analyze heterogeneous complex data about molecular networks to uncover meaningful relationships about key components.

Professor: Richard Carthew

Quantitative Analysis of Biology: BIO_SCI 354/ ES_APPM 395-0

BIO_SCI 354 will be a course where we cover some the landmark results in quantitative biology. Every module (of which there are 5-6) will end with analysis of a data set acquired from the authors of studies and reanalysis and re-plotting of a central result from the paper. En route to that I will teach you the biology mathematics physics and statistics required to make the plots. The landmark papers will span from studies in gene regulation, developmental biology, sequencing etc.
We will also have various crash courses in coding, image analysis, etc.Introduction to landmark insights into quantitative biology. Random genetic processes, gene expression, cell adaption, cell cycle, developmental morphogens, phylgenomics.

Course website: https://madhavmani.wixsite.com/qbiocourse

Professor: Madhav Mani

Quantitative Biology: IBIS 410

Quantitative approaches to molecular and cell biology, focused on developing an understanding of connections between biomolecule structure and dynamics, and behavior of cells. The course will also include review of topics from statistics of random variables and statistical data analysis relevant to biology and biophysics.

Professor: John Marko

Quantitative Experimentation in Biology: BIO_SCI 359

BIO_SCI 359 is taught in 4 modules, which will involve students repeating experiments from some of the landmark papers in quantitative biology. Groups of students will work together and learn how to do experiments in a wet lab, perform live-imaging, conduct sequencing based studies, analyze their own data, and presentation skills.

Professor: Richard Carthew

Core Facilities

Biological Imaging Facility

Biological Imaging Facility

The Biological Imaging Facility provides researchers instrumentation to capture high-quality images, then analyze and display them using powerful image analysis and 4D rendering software packages. The photonic capabilities include laser scanning confocal, spinning disk confocal, widefield, deconvolution, photomanipulation, and fluorescence correlation spectroscopy. All the microscopes are equipped with environmental control chambers and users have access to cell culture and animal facilities, as well as a system equipped for microinjection. The facility also offers a number of image analysis software packages including Imaris and Volocity.

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Center for Advanced Microscopy and Nikon Imaging Center

Center for Advanced Microscopy and Nikon Imaging Center

The Center for Advanced Microscopy (CAM) offers state-of-the art instrumentation and services for the study of biological processes at the whole animal, tissue, cellular and subcellular levels. The facility's basic services include electron microscopy, super resolution microscopy (SIM & STORM), fluorescent laser scanning and spinning disk microscopy, fluorescent lifetime imaging, fluorescence correlation spectroscopy microscopy, automated high throughput tissue cytometry, laser capture microdissection, mutliphoton imaging, and whole animal bioluminescent and fluorescent imaging.

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Flow Cytometry Facility

Flow Cytometry Facility

The Flow Cytometry Core Facility provides cell sorting services and access to routine flow cytometry assays such as immunophenotyping and DNA analysis as well as guidance, technical assistance and equipment for the investigators to utilize more complex mult-parametric, multi-laser measurement and cell sorting in their research. The recent acquisition of the MoFlo high-speed sorter has increased the facilities technical capabilities. The facility serves as a focus for studies of cellular heterogeneity in disease. Services range from consultation on experimental design, sample preparation and data analysis to instrument operation and set-up for cell sorting and multilaser operation.

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High Throughput Analysis Lab

High Throughput Analysis Lab

Northwestern’s High Throughput Analysis Lab provides researchers with equipment and expertise for the development and execution of high throughput biological analysis and screening. The facility is fully equipped with state-of-the-art liquid handling, plate detection and automated microbial culture handling capabilities. Services include HTS assay development, Biochemical High Throughput Screening, and Cell-based High Throughput Screening. The HTAL has an BioRad ddSEQ single cell isolator for single-cell RNA-seq that can be coupled to the Illumina sequencing platform.

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NUSeq

NUSeq

NUSeq is a new core facility that provides full next-gen sequencing (NGS) capability to Northwestern University. The core brings together in-house NGS data generation and bioinformatics support in a single integrated operation. As the only Northwestern core facility dedicated to NGS, NUSeq serves all NU researchers on both the Chicago and Evanston campuses, as well as those at external academic and commercial organizations.

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Quest High Performance Computing Cluster

Quest High Performance Computing Cluster

Northwestern's high performance computing (HPC) system is called Quest. Housed at one of the University's secure Data Center facilities, it offers a large, shared computational facility. Quest is used for a variety of projects, including those that require high-performance capability due to computationally intensive tasks, such as intense numerical calculations or dealing with extremely large datasets.

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Affiliated Research Centers

Quantitative Biological Modeling

Quantitative Biological Modeling

The Center's core premise is that what scientists really want through "data analysis" is to understand cause and effect, and ultimately, to discover how to control systems to produce a desired outcome. From an applied mathematical perspective, this desire is a wish for dynamical models that can accurately describe them.

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Northwestern Institute on Complex Systems (NICO)

Northwestern Institute on Complex Systems (NICO)

The Northwestern Institute on Complex Systems was founded in 2004 with the goals of uncovering fundamental principles governing complex systems in science, technology, and human behavior and applying these principles to solve societally relevant problems through the analysis, design, and control of complex systems. Today, NICO serves as a hub and facilitator for pathbreaking research in complexity and data science transcending the boundaries of established disciplines.

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Chemistry of Life Processes Institute

Chemistry of Life Processes Institute

Chemistry of Life Processes Institute (CLP) researchers use the technologies of tomorrow to discover the diagnostic methods and therapies needed to save lives today. Chemists, engineers, and physicists team with life scientists and clinicians to change how we diagnose and treat cancer, cardiovascular and kidney disease, infectious diseases, neurodegenerative diseases, and trauma. This transdisciplinary convergence of knowledge is creating new fields of research that will have a long-lasting impact on human health and disease.

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