Overview

The minimum requirements for graduation are at least 30 credit hours of graduate-level training, including:  

  • At least 4 research credits of Directed Study  
  • A summer internship or additional Directed Study, worth at least 3 credits  
  • An approved course in Computational Genomics 
  • An approved course in Computational Biophysics 
  • An approved course in Computational Systems Biology 
  • An approved course in Machine Learning 

In addition, all students are required to take the following courses:

  • COBB 2010 : Foundations of Computational Biology (3 credits, Fall)
  • COBB 2110: Faculty Seminar (1 credit, Fall) 
  • COBB 2055: Professional Development (1 credit, Spring)     

Program duration is from 12 to 20 months, depending on the background of the student. To complete the degree in one year, students must demonstrate proficiency in programming, calculus and linear algebra. 

  Directed Study – Gaining hands-on experience in solving problems in computational biology is an essential part of CoBB training. Each student is therefore required to take a minimum of 4 credits of Directed Study with a University of Pittsburgh faculty member. Students select a research mentor for the Directed Study in their first semester, and complete the research requirement in the second and/or third semesters.

 Internship – To gain experience in the professional application of computational biology, students are encouraged to participate in a 2- to 3-month summer internship at a company of their choosing. Acceptable internship sites include industrial labs, biotech/pharma companies, and governmental organizations. CoBB will assist students with identifying corporate partners and potential internship sites, but it is the student’s responsibility to contact the company and secure the internship. Previous internship sites for CoBB students include UPMC Enterprises and Janssen Pharmaceuticals.                            

Detailed Course Listing

The CoBB curriculum was designed to provide students with a strong foundation in essential areas of computational biology, including genomics, structural biology, systems biology, and machine learning.  Descriptions of courses that fulfill CoBB core requirements are below.  

Computational Biophysics
COBB 2030 Computational Structural Biology
(4 credits, Fall)
COBB 2051 Computational Drug Discovery
(4 credits, Spring)
Topics covered include: applying computational and statistical methods to the analysis of DNA and protein structures representing protein, DNA and RNA structure; homology modeling and protein structure prediction; theoretical description of basic interactions, along with computational methods to estimate them; statistical mechanical theory of molecules; molecular dynamics and other sampling methods; modeling protein flexibility, from side chains to loops to slow modes; reaction paths and basics of path sampling; protein-protein and protein-small molecule docking; supramolecular assembly; introduction to Quantitative Structure Activity Relationship (QSAR) in drug design.
This course provides an introduction to the concepts and tools of computational drug discovery, from small molecules to modeling clinical trials. Covered topics include small molecule structural similarity, molecular dynamics and virtual screening, pharmacophore modeling, disease pathway inference and modeling, pharmacokinetics and pharmacodynamics (PK/PD) modeling. The emphasis is on practical application of computational tools and techniques used throughout the drug discovery process.
Computational Systems Biology
COBB 2041 Cell & Systems Modeling
(4 credits, Spring)
COBB 2150 Computational Drug Discovery
(4 credits, Spring)
This course introduces students to the theory and practice of modeling biological systems from the molecular to the population level with an emphasis on intracellular processes. Topics covered include kinetic and equilibrium descriptions of biological processes, systematic approaches to model building and parameter estimation, analysis of biochemical circuits modeled as differential equations, modeling the effects of noise using stochastic methods. A range of biological models and applications are considered, including gene regulatory networks, cell signaling, molecular motors, and developmental biology.
This course provides an introduction to the concepts and tools of computational drug discovery, from small molecules to modeling clinical trials. Covered topics include small molecule structural similarity, molecular dynamics and virtual screening, pharmacophore modeling, disease pathway inference and modeling, pharmacokinetics and pharmacodynamics (PK/PD) modeling. The emphasis is on practical application of computational tools and techniques used throughout the drug discovery process.
Computational Genomics
COBB 2020 Genomics for Systems Biology
(3 credits, Spring)
COBB 2070 Computational Genomics
(3 credits, Spring)
This course introduces students to genomic data and basic analytical principles pertaining  them. Students  will  learn  about  high-throughput  sequencing  methods and applications, genomic variation, transcriptomics and epigenomic data. At the end of the course, the students will be able to analyze efficiently these types of data sets using existing algorithms or algorithms they will develop.
Dramatic advances in experimental technology and computational analysis are fundamentally transforming the basic nature and goal of biological research. The emergence of new frontiers in biology, such as evolutionary genomics and systems biology is demanding new methodologies that can confront quantitative issues of substantial computational and mathematical sophistication. This course introduces classical approaches and the latest methodological advances in the context of the following biological problems: 1) Computational genomics, focusing on gene finding, motifs detection and sequence evolution. 2) Analysis of high throughput biological data, such as gene expression data, focusing on issues ranging from data acquisition to pattern recognition and classification. 3) Molecular and regulatory evolution, focusing on phylogenetic inference and regulatory network evolution, and 4) Systems biology, concerning how to combine sequence, expression and other biological data sources to infer the structure and function of different systems in the cell. From the computational side this course focuses on modern machine learning methodologies for computational problems in molecular biology and genetics, including probabilistic modeling, inference and learning algorithms, pattern recognition, data integration, time series analysis, active learning, etc.
Machine Learning
COBB 2066 Scalable Machine Learning for Big Data Biology
(4 credits, Spring)
Machine learning (ML) has become an integral part of computational thinking in the era of big data biology. This course focuses on understanding the statistical structure of large-scale biological datasets using ML algorithms. We cover the basics of ML and study their scalable versions for implementation on a distributed computing framework. We pursue distributed ML algorithms for matrix factorization, convex optimization, dimensional reduction, clustering, classification, graph analytics and deep learning, among others. This course is project driven (3 to 4 small projects) with source material from genomic sciences, structural biology, drug discovery, systems modeling and biological imaging. Students are expected to design, implement and test their ML solutions in Apache Spark.
Electives

Schedule

Below is a sample schedule for a typical CoBB student completing the coursework in 16 months. The elective courses (**HUGEN 2022, **MSCBIO 2075, **BIOENG 2340) emphasize genomics and image analysis. Individual students are able to tailor their schedules to emphasize a topic of specialization.

Semester

Course No.

Course Title

Credit

Fall 01

CoBB 2025

Intro to Bioinformatics Programming in Python

3

 

CoBB 2010

Foundations in Computational Biology

3

 

**HUGEN 2022 (or other approved elective)

Human Population Genetics

2

 

CoBB 2110

Faculty Seminar

1

Spring 01

CoBB 2070

Genomics for Systems Biology

3

 

CoBB 2150

Computational Drug Discovery

4

 

CoBB 2066

Scalable Machine Learning for Big Data Biology

3

 

CoBB 2055

Professional Development

1

Summer 01

CoBB 2085

Internship

3

Fall 02

** MSCBIO 2075 (or other approved elective)

Molecular Evolution

3

 

CoBB 2080

Directed Study

4

 

** BIOENG 2340 (or other approved elective)

Intro to Medical Image Analysis

3

TOTAL

   

33

Electives

CS 2056 -INTRODUCTION TO DATA SCIENCE (3)
Fall,Spring -N/A
BIOENG 2340 -INTRODUCTION TO MEDICAL IMAGING AND IMAGE ANALYSIS (3)
Fall – Introduction to Medical Imaging and Image Analysis presents the physics of image formation as well as methods for tomographic image reconstruction for major medical imaging modalities, including X-ray Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). Also introduced are fundamentals of digital image processing, with particular emphasis on medical applications, including basic techniques to enhance image quality, image de-noising, methods for extracting, classifying, and tracking features of and objects in images, etc. Students will learn how to implement these techniques in MATLAB (The MathWorks Inc., Natick, MA) to solve practical image processing problems. MATLAB exercises will demonstrate to students how filtering operations applied in the image domain or the Fourier domain affect medical images. In addition to these fundamentals, more advanced algorithmic approaches for image segmentation and image as well as point-cloud registration techniques will also be reviewed.
BIOENG 2383 -BIOMEDICAL OPTICAL MICROSCOPY (3)
Spring – This course is designed to teach the basic principles and applications of optical microscopy and imaging techniques commonly used in biomedical research. The enormous growth of optical microscopy has become an essential tool to investigate biological processes, diagnose diseases and quantitatively measure the biological system at unprecedented cellular and molecular level. It has become increasingly important for biomedical researchers to learn the proper use of optical microscopy, understand the advantages and limitations of each type of optical microscopy and how to apply them for specific biomedical applications. In this course, we will cover the physical principles involved in basic light, basic and advanced optical microscopy techniques. Strong emphasis will be given to biomedical applications for each type of optical microscopy. At the end of the course, a student will have a thorough understanding of basic principles of optical imaging and optical microscopy, learn how to apply optical microscopy to address biological questions and perform basic quantitative image analysis.
BIOENG 2505 -MULTI MODAL BIOMEDICAL IMAGING TECHNOLOGIES: FUNCTIONAL, MOLECULAR AND HYBRID IMAGING TECHNIQUES (3)
Fall – In this course some newly evolving multi-modal imaging techniques and analysis methods in biomedical applications will be introduced. The course will briefly cover the fundamental physics, core signal processing, image reconstruction of a variety of current standalone imaging modalities such as X-Ray, computer tomography (CT), magnetic resonance imaging (MRI), nuclear imaging (PET, SPECT), optical imaging (fluorescence, optical diffuse tomography, bioluminescence), and ultrasound. Subsequently, the concept, fundamental physics, and image analysis of some exemplary multi-modal imaging techniques and systems will be introduced. Their applications in Biomedicine in different scales from organ to cellular and molecular level, and from structural to functional imaging will be discussed. The course will also briefly address the issues related to image-based diagnosis, intervention and therapy.
BIOST 2079 -INTRODUCTORY STATISTICAL LEARNING FOR HEALTH SCIENCES (2)
Fall – This 2-credit course is a graduate level course to introduce basic concept and methods for statistical learning with emphasis on modern health science applications. The syllabus includes linear regression with regularization, supervised machine learning, unsupervised clustering, dimension reduction and other special topics (e.g. Bayesian network and hidden Markov model). Target audience will be second year Biostatistics master students or early PhD students with interests in statistical learning techniques for health science data. Through homework problem sets, computer labs and a final project, students train with hands-on materials to implement methods and interpret results in real applications.
BIOST 2069 - STATISTICAL METHODS FOR OMICS DATA (2)
Fall -This 2-credit course is a graduate level course to cover popular statistical and computational methods for high-throughput omics data analysis. With the rapid advances of many omics technologies, the course will focus on the fundamental concepts of various topics (e.g. data preprocessing, association analysis, causal mediation analysis, differential analysis, statistical learning, pathway analysis, etc.) and their specific applications to different omics data types (e.g. microarray, next-generation sequencing, single cell sequencing, mass spectrometry, microbiome, etc.). The major target audience is graduate students (master or PhD students) interested in omics data analysis and related research. Through homework problem sets, computer labs and a final project, students train with hands-on materials to understand the methods, implement the algorithms and interpret results in real omics applications.
BIOST 2080 - ADVANCED STATISTICAL LEARNING (2)
Fall – This is a 2-credit course in advanced statistical learning, covering topics related to the statistical interpretation and theory behind machine learning models/methods. Emphases will be given to in-depth derivation of models/algorithms from topics covered in BIOST 2079 (Introductory Statistical Learning for Health Sciences) as well as additional topics on modern statistical learning methodologies, with special focus on methods for health science applications.  This course is designed for graduate students in the Department of Biostatistics and other interested graduate students who already have sufficient statistical and programming background. Students are expected to be familiar with R. Experience in C/C++, Python or Matlab may be helpful, but is not required. Programming skills/training shall be demonstrated by previous programming (or programming heavy) courses in R, Python, Matlab, C/C++, etc.
MSCMP 3790 -BASICS OF PERSONALIZED MEDICINE (3)
Fall – Personalized medicine is becoming a reality that is being driven by ongoing discoveries in cell biology, genomics, proteomics, and metabolomics. The translational speed of these discoveries, particularly in the diagnostic, prognostic, and theragnostic arenas, is rapid. We believe that in the future personalized medicine diagnostics will involve both physicians and basic scientists. A major obstacle to this approach is the lack of training components for basic scientists in this area. This course aims to close that gap and provide an appreciation for, and understanding of, key principles of clinical development and testing in order to help bridge this gap. The course will be designed to delve into concepts of personalized medicine using focused topic areas. The first week will introduce the principles and overriding concepts of clinical test development, which differ qualitatively from investigational research. Next there will be six 2-week sessions, with each section focusing on a separate testing modality. Topics will include inherited genetic diseases and predispositions, acquired genetic changes (cancer), metabolomic profiles of endocrine diseases, immune networks for transplant and rejection, proteomic profiling in blood disorders, and proteomic detection of shock and organ failure.
MSMPHL 3360 -MOLECULAR PHARMACOLOGY (2)
Fall – This course examines molecular mechanisms of drug interactions with an emphasis on drugs that modulate cell signaling, cellular responses to drugs, and drug discovery. The course will include student participation through presentations and discussion of relevant contemporary scientific literature. Topics include: cell cycle checkpoints and anti-cancer drugs, therapeutic control of ion channels, and blood glucose, anti-inflammatory agents and nuclear receptor signaling, and molecular mechanisms of drugs used for the treatment of cardiovascular diseases.
MATH 3370 -MATHEMATICAL NEUROSCIENCE (3)
Spring – Course covers computational and mathematical neuroscience. It will do modeling and analysis of complex dynamics of single neurons and large-scale networks. This course is offered every other Spring starting in 2022.
MATH 3375 –COMPUTATIONAL NEUROSCIENCE METHODS (3)
Fall – This course offers an introduction to modeling methods in neuroscience. Topics range from modeling the firing patterns of single neurons to using computational methods to understand neural coding. Some systems level modeling is also done.
MATH 3380 –MATHEMATICAL BIOLOGY (3)
Spring – This course introduces a number of modeling methods for biological systems. We will examine a number of problems from cell biology, immunology, population biology, physiology and molecular genetics. The main tools will be techniques from ordinary and partial differential equations. Discrete and delay-differential equations will also be used however the background for these will not be assumed. We will take models from current and classic papers in the field.
MSCMP 3780 –SYSTEMS APPROACH INFLAMMATION (2)
Fall – This course is focused on particular topics of great biologic complexity in critical illness, where modeling has the potential to translate in improved patient care. Lectures are provided by basic (biological and mathematical sciences) and clinical faculty, in conjunction with members of industry and speakers from outside institutions. This information will be communicated within the framework of defined themes that describe the complexity of inflammation in acute and chronic illnesses.
BIOINF 2118 –PROBABILITY AND STATISTICS IN BIOMEDICAL INFORMATICS (3)
Spring. This is an introductory probability and statistics course intended primarily for biomedical informatics students. The first part of the course covers probability, including basic probability, random variables, univariate and multivariate distributions, transformations, expectation, numerical integration, and approximations. The second part of the course covers statistics, including study design, classical parametric inference, hypothesis testing, Bayesian inference, non-parametric methods, classification, ANNOVA, and regression. We will use r for statistical computing and applications. Examples and applications will focus on biomedical informatics and related discipline.
BIOINF 2018 –INTRODUCTION TO R PROGRAMMING FOR SCIENTIFIC RESEARCH (3)
Summer – Science is increasingly inter-disciplinary, and programming has become a valuable skill in many investigations. This course is designed to empower you with the ability to solve scientific problems through writing computer programs. Emphasis is placed on using the R language to solve biology problems.
HUGEN 2022 –HUMAN POPULATION GENETICS (2)
Fall – This survey course covers the principles of population genetics as applicable to human populations, including (1) the laws of inheritance that govern the organization of the genomes in populations, (2) the evolutionary forces and phenomena that impact genetic diversity in human populations, and (3) the foundational concepts of genetic epidemiology and gene discovery.
BIOSC 2545 –THE MATHEMATICS OF BIOLOGY (3)
This course uses examples from across biology to illustrate how simple mathematical models can increase our understanding of biological systems. We will focus on several foundational modeling approaches, including systems of difference equations, matrix models, probability, and statistical data analysis. Students will discover how these approaches are used, their strengths and limitations, and how they could be extended to more complex problems. Students should be prepared to use both spreadsheet programs and scripts, written in a language such as Python or R, to explore thesemodels.
NROSCI 2012 –NEUROPHYSIOLOGY (3)
This course examines the electrical properties of nerve cells and the mechanisms by which nerve cells communicate. The following topics will be covered: electrical principles used by nerve cells, the basis of the resting potential, the function of voltage-dependent ionic channels, the mechanisms by which action potentials are generated, neurotransmitter receptor function, and the physiology of fast synaptic communication.
BIOSC 2810 –MACROMOLECULAR STRUCTURE AND FUNCTION (3)
Fall – Course is concerned primarily with the structure and functions of proteins and nucleic acids. These are large polymers where structure and function are determined by the sequence of monomeric units. Topics will include the physical and chemical properties of the monomer units (amino acids/nucleotides); the determination of the linear sequence of these units; the size, shape and general properties of the biopolymers in aqueous systems; and the relation between structure and function, particularly in transport (hemoglobin) and in catalysis (enzymes).
MSCBIO 2074 –EVOLUTIONARY BIOLOGY OF HUMAN DISEASE (3)
Spring – Evolution is a fundamental unifying principle of biology. This class takes a broad approach to illustrate how an evolutionary perspective augments medical research and practice. Topics covered range from the evolution of human populations, to antibiotic resistance, and include medical conditions as diverse as diabetes, cardiovascular disease, cancer or aging.
COBB 2100 – COMPUTATIONAL SYSTEMS AND BIOLOGY SEMINAR (1)
Spring/Fall – Students in this course will attend weekly seminars by internationally recognized researchers, and they will provide critical analyses of the talks.