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BIO405: Computational Biology

Unit 2: Computational Molecular Biology   This unit will deal with molecular biology.  From determining the genetic sequence in a scrap of DNA to creating a 3-D virtual model of a protein, scientists use computer modeling in this field to help us better understand a world far beyond the reaches of the microscope.  Study in molecular biology yields vast amounts of data that must be carefully analyzed and interconnected to construct a realistic picture of this world.  Computers greatly reduce the manual workload and error associated with complex analysis.  In this unit, you will learn how to use computers in order to better understand DNA sequencing, transcriptional regulation, protein structure, and protein interactions.  Upon completion of this unit, you should understand each process and be able to create your own models based upon the principles and procedures studied.

Unit 2 Time Advisory
This unit should take approximately 46 hours to complete.

☐    Subunit 2.1: 1 hour

☐    Subunit 2.2: 18 hours

☐    Introduction: 0.5 hours

☐    Subunit 2.2.1: 0.5 hours

☐    Subunit 2.2.2: 4.5 hours

☐    Subunit 2.2.3: 10.5 hours

☐    Subunit 2.2.4: 2 hours

☐    Subunit 2.3: 10 hours

☐    Subunit 2.3.1: 3 hours

☐    Subunit 2.3.2: 1 hour

☐    Subunit 2.3.3: 6 hours

☐    Subunit 2.4: 17 hours

☐    Subunit 2.4.1: 6 hours

☐    Subunit 2.4.2: 11 hours

Unit2 Learning Outcomes
Upon completion of this unit, the student will be able to: - Describe basic molecular principles. - Describe methods for collecting and analyzing DNA data. - Describe methods for creating phylogenetic trees. - Describe how statistical modeling is used with data on proteins. - Provide a qualitative explanation of Markovian models. - Describe methods for collecting and analyzing data on protein structure.

2.1 Mathematical Treatment of Molecular Biology   2.1.1 Principles of Molecular Biology   - Reading: PDFgeni.org’s “Basic Principles of Molecular Biology 1” The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

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2.2 DNA Sequencing   - Reading: Science Daily News’ “A New Read on DNA Sequencing” Link: Science Daily News’ “A New Read on DNA Sequencing” (HTML)

 Instructions: Read this article on advances in DNA sequencing.
 There are other related articles on this topic on the main page
that you may wish to explore for further information on the
subject.  

 Reading this material should take approximately 30 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.2.1 DNA Structure and Classification   - Reading: University of Arizona: Richard Hallick’s “Introduction to DNA Structure” Link: University of Arizona: Richard Hallick’s “Introduction to DNA Structure” (HTML)

 Instructions: Please read the linked material; it provides a good
introduction to the structure of DNA and the formation of the double
helix.  

 Reading this material should take approximately 30 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.2.2 Data Collection   2.2.2.1 DNA Microarrays   - Web Media: YouTube: Proneural’s “DNA Microarrays” Link: YouTube: Proneural’s “DNA Microarrays” (YouTube)

 Instructions: Please watch this video, which provides an example of
DNA microarrays in plants.  Try and break down the material in to
steps involved in the process.  

 Watching this video and taking notes should take approximately 15
minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.2.2.2 DNA Sequencing Process   2.2.2.2.1 Manual   - Reading: National Diagnostics’ “Manual Sequencing” Link: National Diagnostics’ “Manual Sequencing” (HTML)

 Instructions: This is a brief introduction to manual sequencing.
 Two versions of sequencing (Sanger Sequencing and Maxam & Gilbert
Sequencing) are presented on the pages following the links provided.
 Take note of the process and the differences between the two
methods.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
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2.2.2.2.2 Automated   - Web Media: Cold Spring Harbor Laboratory: DNA Learning Center’s “Cycle Sequencing” Link: Cold Spring Harbor Laboratory: DNA Learning Center’s “Cycle Sequencing” (Flash)

 Instructions: Use the “continue” button to work through the
animation on the process of cycle sequencing.  How is this process
different from manual sequencing above?  

 Viewing this material should take approximately 30 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.2.2.3 Alignment   2.2.2.3.1 Pairwise Alignment   - Reading: University of Wisconsin: Mark Craven’s “Pairwise Alignment” Link: University of Wisconsin: Mark Craven’s “Pairwise Alignment” (PDF)

 Instructions: Click on the “pairwise-alignment-1.pdf” link to
download the PDF.  This PowerPoint will introduce you to alignments,
edits, and gaps and define the concept of pairwise alignment.  The
PowerPoint also connects sequence alignment to dynamic computer
programming.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.2.2.3.2 Multiple Sequence Alignment   - Reading: Wikipedia’s “Multiple Sequence Alignment” Link: Wikipedia’s “Multiple Sequence Alignment” (HTML)

 Instructions: The reading describes multiple sequence alignments
and how they relate to dynamic programming.  You should also view
the picture of a multiple sequence alignment found on the same
page.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.2.2.3.3 Whole Genome Alignment   - Reading: Universität des Saarlandes: Center for Bioinformatics’ “Whole Genome Alignment” Link: Universität des Saarlandes: Center for Bioinformatics’ “Whole Genome Alignment” (PDF or PPT)

 Instructions: Click on the “V4-Alignment.pdf” or “V4-Alignment.ppt”
link to download the presentation.  This presentation explains why
whole genome alignments are used, presents a few different ways of
aligning sequences, and addresses local versus global alignments.
 For information in the presentation that needs more clarification,
refer directly to the citations at the bottom of each slide.  

 Reading this material should take approximately 1 hour.  

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2.2.3 Comparisons   2.2.3.1 Comparison with Sequence Databases   2.2.3.1.1 FASTA   - Reading: State University of New York – Stony Brook: Steven Skiena’s “FASTA” Link: State University of New York – Stony Brook: Steven Skiena’s “FASTA” (HTML)

 Instructions: The resource describes FASTA and presents a
step-by-step process for using it.  FASTA is the first widely used
method of using a known sequence to search a database for similar
sequences.  The best approach for understanding this is to actually
create a fictitious sequence and use the search engine to analyze
it.  

 Reading this material should take approximately 30 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.2.3.1.2 BLAST   - Reading: National Center for Biotechnology Information’s “BLAST” Link: National Center for Biotechnology Information’s “BLAST” (HTML)

 Instructions: The link will take you to the BLAST website, where
you will find a description of its capabilities and be able to use
this search tool.  Please try the search tool to see how it
performs.  

 Studying this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.2.3.1.3 Finding Sequence Motifs   - Reading: Nature Biotechnology: Patrik D'haeseleer’s “What Are DNA Sequence Motifs?” Link: Nature Biotechnology: Patrik D'haeseleer’s “What Are DNA Sequence Motifs?” (HTML)

 Instructions: This article discusses varies topics related to
sequence motifs, including logos and searching for novel sites.  You
should make note of key terms and use Google or a similar search
engine to identify unknown terms in the reading.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
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2.2.3.2 Genome Comparison   - Reading: ScienceDaily News’ “Multi-Species Genome Comparison Sheds New Light On Evolutionary Processes, Cancer Mutations” Link: ScienceDaily News’ “Multi-Species Genome Comparison Sheds New Light On Evolutionary Processes, Cancer Mutations” (HTML)

 Instructions: The article summarizes the findings of recent work
comparing genome sequences from multiple species.  Use this example
as a basis for identifying other uses of multi species genome
comparisons.  

 Reading this material should take approximately 30 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.2.3.3 Molecular Phylogenetic Analysis   - Reading: Wikipedia’s “Molecular Phylogenetics” Link: Wikipedia’s “Molecular Phylogenetics” (HTML)

 Instructions: This article describes the history, techniques,
theoretical background, and limitations associated with Molecular
Phylogenetics.  Familiarize yourself with any unfamiliar terms in
the reading by using the links provided.  

 Reading this material should take approximately 45 minutes.  

 Terms of Use: Please respect the copyright and terms of use
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  • Reading: Proceedings of the National Academy of Sciences: Michael A. Thomas et al’s “Molecular Phylogenetic Analysis of Evolutionary Trends in Stonefly Wing Structure and Locomotor Behavior” Link: Proceedings of the National Academy of Sciences: Michael A. Thomas et al’s “Molecular Phylogenetic Analysis of Evolutionary Trends in Stonefly Wing Structure and Locomotor Behavior” (PDF)

    Instructions: At the PNAS webpage, click on the PDF link to see the PDF version of the file.  Read this paper and pay attention to the phylogenetic methods that are used to address the hypotheses presented in the paper.  This paper is a good example of how molecular phylogenetics can be used and should be viewed as one of many ways to apply phylogenetic methods.

    Reading this material should take approximately 2 hours.

    Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

2.2.3.3.1 Principles of Molecular Evolution   - Reading: Proceedings of the National Academy of Sciences: Motoo Kimura and Tomoko Ohta’s “On Some Principles Governing Molecular Evolution” Link: Proceedings of the National Academy of Sciences: Motoo Kimura and Tomoko Ohta’s “On Some Principles Governing Molecular Evolution” (PDF)

 Instructions: Click on the PDF link to see the entire article.  The
abstract lists five principles associated with molecular evolution.
 This is a classic article and you should understand and be able to
list the five principles that are presented.  

 Reading this material should take approximately 1 hour.  

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2.2.3.3.2 Methods for Determining Distance   2.2.3.3.2.1 Average Linkage Clustering   - Reading: Statistics.com’s “Average Linkage Clustering” Link: Statistics.com’s “Average Linkage Clustering” (HTML)

 Instructions: This page provides a short paragraph about linkage
clustering and a link for the linkage function that you should click
on and view that information.  Use the additional links to provide a
more complete understanding of how this function is used and where
it can be applied.  

 This reading should take approximately 30 minutes.  

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displayed on the webpage above.

2.2.3.3.2.2 Neighbor-Joining   - Reading: Christian de Duve Institute of Cellular Pathology: Fred R. Opperdoes’ “The Neighbor-Joining Method” Link: Christian de Duve Institute of Cellular Pathology: Fred R. Opperdoes’ “The Neighbor-Joining Method” (HTML)

 Instructions: The webpage includes a description of the method,
advantages and disadvantages, and an example of how it works.  After
reading this material, compare it to other distance-based methods
used in phylogenetic trees such as maximum parsimony.  

 Reading this material should take approximately 45 minutes.  

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2.2.3.3.3 Maximum Parsimony   - Reading: Christian de Duve Institute of Cellular Pathology: Fred R. Opperdoes’ “Maximum Parsimony” Link: Christian de Duve Institute of Cellular Pathology: Fred R. Opperdoes’ “Maximum Parsimony” (HTML)

 Instructions: The webpage demonstrates how parsimony works and ends
with some summary notes on the subject.  Learn this material in
order to compare it to other distance-based methods used in
phylogenetic trees such as neighbor joining.  

 Reading this material should take approximately 45 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.2.3.3.4 Maximum Likelihood   - Reading: University of Alaska Fairbanks: Mark Lindberg’s “Maximum Likelihood Estimation” The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

[Submit Materials](/contribute/)

2.2.4 Statistical Modeling   2.2.4.1 Markov Models   - Reading: Simon Fraser University: Bertille Antoine’s “Markov Chains” The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

[Submit Materials](/contribute/)

2.2.4.2 Hidden Markov Models   - Reading: Monash University: Lloyd Allison’s “Hidden Markov Models” Link: Monash University: Lloyd Allison’s “Hidden Markov Models” (HTML)

 Instructions: This reading covers different types of Markov models
and provides an example of a Hidden Markov model.  This reading will
help reinforce what you learned in subunit 2.2.4.1.  How are hidden
Markov models different from standard Markov models?  Where would
you apply them?  

 Reading this material should take approximately 45 minutes.  

 Terms of Use: Please respect the copyright and terms of use
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2.2.4.3 Bootstrap Analysis   - Reading: Christian de Duve Institute of Cellular Pathology: Fred R. Opperdoes’ “Bootstrapping” Link: Christian de Duve Institute of Cellular Pathology: Fred R. Opperdoes’ “Bootstrapping” (HTML)

 Instructions: This website describes the process of bootstrapping
and explains how it is used in phylogenetic analysis.  Some useful
samples are provided.  Make sure and understand the method and why
it is used.  

 Reading this material should take approximately 30 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.3 Transcriptional Regulation   2.3.1 Transcriptional Regulation Process   - Reading: Wikipedia’s “Transcriptional Regulation” Link: Wikipedia’s “Transcriptional Regulation” (HTML)

 Instructions: The page provides a good overview of transcription
regulation.  It also identifies some of the major differences
between prokaryotes and eukaryotes.  How is transcriptional
regulation more complex in eukaryotes?  

 Reading this material should take approximately 30 minutes.  

 Terms of Use: Please respect the copyright and terms of use
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2.3.1.1 Simple Regulation   - Reading: National Center for Biotechnology Information: Griffiths et al’s “Regulation of Gene Expression” Link: National Center for Biotechnology Information: Griffiths et al’s “Regulation of Gene Expression” (HTML)

 Instructions: The reading has several sections that describe
different elements involved in the regulation of gene expression.
 Take note of the different regulatory elements and how they are
involved in gene expression.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
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2.3.1.2 Regulatory Networks   - Reading: French National Institute for Research in Computer Science and Control: Hidde de Jong’s “Mathematical Modeling of Regulatory Networks” Link: French National Institute for Research in Computer Science and Control: Hidde de Jong’s “Mathematical Modeling of Regulatory Networks” (PDF)

 Instructions: Click on the “arc-03-intro.pdf” link to download the
PDF.  This reading provides a mathematical approach to modeling
networks.  

 Reading this material should take approximately 1.3 hours.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.3.2 Data Collection   2.3.2.1 Finding Regulatory Sequence in DNA   - Reading: Nature.com: Nature Immunology Journal’s “Finding Regulatory Sequences” Link: Nature.com: Nature Immunology Journal’s “Finding Regulatory Sequences” (HTML)

 Instructions: Click on the tabs while reading and performing the
operations that are suggested.  This tutorial will give you a
firsthand demonstration of how to find sequence motifs.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
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2.3.3 Statistical Modeling   2.3.3.1 Bayesian Networks   - Reading: Microsoft Research: David Heckerman’s “A Tutorial on Learning with Bayesian Networks” Link: Microsoft Research: David Heckerman’s “A Tutorial on Learning with Bayesian Networks” (PDF)

 Instructions: Click on the PDF link to download the file.  This is
a lengthy reading that introduces Bayesian networks and Bayesian
statistics and terminology.  You should be able to describe what
Bayesian networks are and how they can be used.  You should also
have at least a basic understanding of the math behind them.  

 Reading this material should take approximately 2 hours.  

 Terms of Use: Please respect the copyright and terms of use
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2.3.3.2 Boolean Networks   - Reading: Connexions: Ewa Paszek’s “Boolean Networks” Link: Connexions: Ewa Paszek’s “Boolean Networks” (HTML)

 Introductions: The reading relates Boolean networks to molecular
biology and provides an example of how they are used in biology.
 You should able to describe what a Boolean network is and apply to
the example given of cell cycle regulation.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
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2.3.3.3 Dynamic Modeling   - Reading: Emory University: Peter Thompson’s “Introduction to Dynamic Programming” Link: Emory University: Peter Thompson’s “Introduction to Dynamic Programming” (PDF)

 Instructions: Click on the “Chapter 4: Introduction to Dynamic
Programming” link to download the PDF.  The reading covers
deterministic and stochastic dynamic programming.  You should be
able to compare and contrast the two types of programming.  

 Reading this material should take approximately 2 hours.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.3.3.4 Using Differential Equations   - Reading: Lamar University: Paul Dawkins’ “Differential Equations” Link: Lamar University: Paul Dawkins’ “Differential Equations” (HTML)

 Instructions: This useful webpage defines all terms associated with
differential equations and includes the math associated with
transforms and first and second order equations.  Where can
differential equations be applied in biology?  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.4 Proteins   2.4.1 Protein Structure   2.4.1.1 Protein Structure and Classification   - Reading: Wikipedia’s “Structural Classification of Proteins” Link: Wikipedia’s “Structural Classification of Proteins” (HTML)

 Instructions: The reading covers basic protein classes and links to
further reading about each.  Make sure you understand the different
classes of proteins and be able to provide examples for each class.
 You are strongly encouraged to explore the links and read further
about different types of proteins.  

 Reading this material should take approximately 45 minutes.  

 Terms of Use: Please respect the copyright and terms of use
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2.4.1.2 Data Collection   2.4.1.2.1 Protein Preparation   - Reading: Wikipedia’s “Protein Purification” Link: Wikipedia’s “Protein Purification” (HTML)

 Instructions: The page covers methods of extraction and outlines
the steps of protein purification.  After reading this, you should
be able to describe the steps necessary for extracting and purifying
proteins.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.4.1.2.2 Protein Imaging   2.4.1.2.2.1 X-Ray Crystallography   - Reading: Molecular Station’s “X-ray Crystallography” Link: Molecular Station’s “X-ray Crystallography” (HTML)

 Instructions: Read this explanation of how x-ray crystallography is
used to identify protein structure.  Be able to describe the process
and why it can provide an image of protein structure.  

 Reading this material should take approximately 30 minutes.  

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2.4.1.2.2.2 NMR   - Lecture: Nobelprize.org: Kurt Wüthrich’s “NMR Studies of Structure and Function of Biological Macromolecules” Link: Nobelprize.org: Kurt Wüthrich’s “NMR Studies of Structure and Function of Biological Macromolecules” (Flash)

 Instructions: This is a 55 minute lecture involving Wuthrich’s
Nobel-Prize-winning material on NMR and molecular biology.  Pay
particular attention to the process of NMR and how it differs from
other methods that contribute to our understanding of protein
structure.  

 Viewing this lecture should take approximately 1 hour.  

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2.4.1.3 Structure Modeling   - Reading: New York University’s Bonneau Laboratory: Richard Bonneau and David Baker’s “Ab Initio Protein Structure Prediction” Link: New York University’s Bonneau Laboratory: Richard Bonneau and David Baker’s “Ab Initio Protein Structure Prediction” (PDF)

 Instructions: Click on the link entitled “Bonneau.pdf” to download
the PDF.  This reading covers 2.4.1.3.1.1–2.4.1.3.1.4.  

 Reading this material should take approximately 1.3 hours.  

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2.4.1.3.1 Structure Prediction   2.4.1.3.1.1 Homology Modeling   Note: This subunit is covered by the reading under subunit 2.4.1.3: Structure Modeling.

2.4.1.3.1.2 Fold Recognition   Note: This subunit is covered by the reading under subunit 2.4.1.3: Structure Modeling.

2.4.1.3.1.3 Threading   Note: This subunit is covered by the reading under subunit 2.4.1.3: Structure Modeling.

2.4.1.3.1.4 Ab Initio   Note: This subunit is covered by the reading under subunit 2.4.1.3: Structure Modeling.

2.4.1.3.2 Computational Protein Design   - Reading: ScienceDirect: Arthur G. Street and Stephen L. Mayo’s “Computational Protein Design” Link: ScienceDirect: Arthur G. Street and Stephen L. Mayo’s “Computational Protein Design” (PDF)

 Instructions: Click on the PDF link on the right side of the page
to access and read this article, which presents different
considerations involved in the design of proteins.  It may be useful
to outline the key points throughout the paper or make a list of
things to consider when designing proteins.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
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2.4.1.3.3 Statistical Tests of Structure Accuracy   - Reading: Birkbeck College, University of London: David S. Moss, Ian J. Tickle, and Roman Laskowski’s “Estimation of Precision and Accuracy in Protein Structure Refinement from X-ray Data” Link: Birkbeck College, University of London: David S. Moss, Ian J. Tickle, and Roman Laskowski’s “Estimation of Precision and Accuracy in Protein Structure Refinement from X-ray Data” (HTML)

 Instructions: Read this proposal on protein structure accuracy.
 The reading provides some background on methods of determining
accuracy in protein structure and also provides a list of useful
references.  It may be useful to go directly to the references cited
in the paper to gain more insight into statistical tests for
accuracy.  Note that the references may not be freely accessible.  

 Reading this material should take approximately 30 minutes.  

 Terms of Use: Please respect the copyright and terms of use
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2.4.2 Protein-Protein Interactions   2.4.2.1 Principles of Protein Interactions   - Reading: National Center for Biotechnology Information: Susan Jones and Janet M. Thornton’s “Principles of Protein-Protein Interactions” Link: National Center for Biotechnology Information: Susan Jones and Janet M. Thornton’s “Principles of Protein-Protein Interactions” (PDF)

 Instructions: Download the full-text PDF of this article at the
bottom of the page.  This reading reviews protein-protein
interactions with respect to cell signaling.  It would be useful to
make a list of examples of how proteins interact with other
proteins.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
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2.4.2.2 Methods for Detecting Interactions   - Reading: Darmstadt University of Technology: Frank Krause’s “Detection and Analysis of Protein-Protein Interactions” Link: Darmstadt University of Technology: Frank Krause’s “Detection and Analysis of Protein-Protein Interactions” (PDF)

 Instructions: Click on the link entitled “07\_1\_4artB.pdf” to view
the PDF.  This is a detailed reading that presents a number of
methods for detecting protein interactions.  Be able to describe
several of the methods that are presented in the paper.  

 Reading this material should take approximately 2 hours.  

 Terms of Use: Please respect the copyright and terms of use
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2.4.2.2.1 Gel Electrophoresis   - Reading: The American Electrophoresis Society: Reiner Westermeier and Robert Marchmont’s “Blue Native Gel Electrophoresis” Link: The American Electrophoresis Society: Reiner Westermeier and Robert Marchmont’s “Blue Native Gel Electrophoresis” (HTML)

 Instructions: The article describes a method of detecting
protein-protein interactions using Blue Native PAGE.  You should be
able to accurately describe this method of detecting protein
interactions.  

 Reading this material should take approximately 30 minutes.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.4.2.2.2 Affinity Chromatography   - Reading: Amersham Pharmacia Biotech’s “Affinity Chromatography” Link: Amersham Pharmacia Biotech’s “Affinity Chromatography” (PDF)

 Instructions: Click the first link under “Affinity Chromatography”
to download the PDF.  This is a large and comprehensive manual on
the process of Affinity Chromatography.  You should be able to
describe the general method including how it works and any drawbacks
to the method.  

 Reading this material should take approximately 2 hours.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.4.2.2.3 Mass Spectroscopy   - Reading: University of Arizona: Daniel Figeys, Linda D. McBroom, and Michael F. Moran’s “Mass Spectrometry for the Study of Protein-Protein Interactions” Link: University of Arizona: Daniel Figeys, Linda D. McBroom, and Michael F. Moran’s “Mass Spectrometry for the Study of Protein-Protein Interactions” (PDF)

 Instructions: Click on the link entitled “Protein Interactions” to
download the PDF.  The main page also contains information about
mass spectrometry and genomics that may be of interest to you as you
study.  You should be able to describe the general method including
how it works and any drawbacks to the method.  

 Reading this material should take approximately 1 hour.  

 Terms of Use: Please respect the copyright and terms of use
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2.4.2.3 Modeling   2.4.2.3.1 Bayes’ Theorem   - Reading: Stanford Encyclopedia of Philosophy’s “Bayes’ Theorem” Link: Stanford Encyclopedia of Philosophy’s “Bayes’ Theorem” (HTML)

 Instructions: This reading describes Bayes theorem and then
introduces the mathematical basis for how it works and how it can be
used.  

 Reading this material should take approximately 2 hours.  

 Terms of Use: Please respect the copyright and terms of use
displayed on the webpage above.

2.4.2.3.2 Bayesian Networks   - Reading: PR-OWL’s “What Is a Bayesian Network?” Link: PR-OWL’s “What Is a Bayesian Network?” (HTML)

 Instructions: This is an introduction to the mathematical treatment
of Bayesian networks; it includes limitations and a case study.  

 Reading this material should take approximately 1.3 hours.  

 Terms of Use: Please respect the copyright and terms of use
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2.4.2.3.3 Likelihood Ratios   - Reading: University of Utah’s Virtual Labs in Probability and Statistics: “Likelihood Ratio Tests” Link: University of Utah’s Virtual Labs in Probability and Statistics: “Likelihood Ratio Tests” (HTML)

 Instructions: This reading describes likelihood ratios and provides
several alternative tests for hypothesis testing.  Where could
likelihood ratios be used in biology?  

 Reading this material should take approximately 1 hour.  

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2.4.2.3.4 Clustering Coefficients   - Reading: Wikipedia’s “Clustering Coefficient” Link: Wikipedia’s “Clustering Coefficient” (HTML)

 Instructions: This reading defines clustering coefficients and
describes the different types used in graph theory.  What is the
advantage of using one type over another?  

 Reading this material should take approximately 45 minutes.  

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