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Revision as of 00:42, 21 September 2012

CBB 752

UPDATES

-18 Sept 2012
[Poll results] Poll results are on class wiki.

[Section] The section is confirmed to be on Thursdays 4-5pm in BASS room 405 (same room as before). These are the section dates: 20th Sept, 27th Sept, 4th Oct, 11th Oct, 1st Nov, 8th Nov, 15th Nov, 29th Nov (edited)

So this Thursday will be the next section 4-5pm BASS 405.

[Quiz] Quiz 1 is next week, 24th Sept (Monday). Please note that all materials (including discussion papers) up till and including tomorrow’s lecture will be covered. It will be a 20-minute quiz. You can refer to quizzes from previous years for practice.

[Cluster account] We have signed 12 people up for a cluster account on Bulldog L, these people have included their netIDs in the poll, although only 9 are officially enrolled in cbb/cpsc course code. You should have received an email from the systems admin.

-16 Sept 2012
[LECTURE] Note that there will be NO LECTURE tomorrow (Monday 17th SEPT 2012). The next lecture is on Wednesday 19th SEPT 2012.

[SECTION] According to the new poll results, these people on the mailing list will be your fellow course mates and the section timing is still every Thursday 4-5pm. So the next section is this Thursday 20th SEPT 2012. I will post the venue soon.

-14 Sept 2012
[POLL2] A reminder: PLEASE fill out Poll2 ASAP, in order for Yao and I to expedite the admin process (e.g. reserve the room and get cluster accounts for the people doing the computational assignments and final project) and most importantly to let you guys know when and where the next section will be. So we would greatly appreciate if you guys fill this out by end of TODAY.

EVERYBODY intending to take/audit this course is to fill out this poll. Subsequent mailing list and discussion timing will depend ENTIRELY on this new poll.

[PRESENTATIONS] We have marked the names of those who have volunteered for respective papers on the class wiki, right next to the paper itself. So let us know if you intend to take a stab at any of the other available papers.

1. Kyle M. will be presenting the yeast PPI paper (Ekman et. al.)
2. Nathan P. will be presenting the biomolecular MD paper (Karplus & McCammon).

-13 Sept 2012
1. A huge reminder: PLEASE DO THE POLL 2 BY TOMORROW!! thanks.
2. Shantao L. is presenting the yeast protein landscape paper.

-12 Sept 2012
1. Poll 2 is up. Please fill it out by Friday (14 Sept 2012).
2. Next section is 20 SEPT 2012 (NOT tomorrow).

-08 Sept 2012
1. Sebastian K. will be presenting breast cancer gene expression profile paper.
2. Please note that the next write-up is only due on 20th Sept 2012.

-06 Sept 2012
1. Added papers for section session 6.
2. Please note that the NEXT SECTION is 20th Sept 2012.
3. Rob A. is presenting the NGS paper (Metzker et. al.).
4. Jimi M. is presenting the MEME paper.
5. Paul B. is presenting the Watson genome paper (Wheeler et. al.) for the 4th section.

-01 Sept 2012
1. http://info.gersteinlab.org/Cbb752a12#Timing_.26_location
2. http://info.gersteinlab.org/Cbb752a12#Programming_Assignments_.28CBB_and_CS.29_and_Programming_issues
3. http://info.gersteinlab.org/Cbb752a12#Instructors
4. Nicole T. is presenting the BLAST paper for the first section.
5. Steven B. is presenting the SW paper for the first section. A huge thank you to the 2 volunteers for the quick response!

Course Information

Course Description

Bioinformatics encompasses the analysis of gene sequences, macromolecular structures, and functional genomics data on a large scale. It represents a major practical application for modern techniques in data mining and simulation. Specific topics to be covered include sequence alignment, large-scale processing, next-generation sequencing data, comparative genomics, phylogenetics, biological database design, geometric analysis of protein structure, molecular-dynamics simulation, biological networks, normalization of microarray data, mining of functional genomics data sets, and machine learning approaches for data integration.

Concise undergraduate course description

Techniques in data mining and simulation applied to bioinformatics, the computational analysis of gene sequences, macromolecular structures, and functional genomics data on a large scale. Sequence alignment, comparative genomics and phylogenetics, biological databases, geometric analysis of protein structure, molecular-dynamics simulation, biological networks, microarray normalization, and machine-learning approaches to data integration.

See entry from undergraduate catalog: http://students.yale.edu/oci/resultDetail.jsp?course=11937&term=201203 , viz:

MB&B 452 01 (11937) /MCDB452/MB&B752/MB&B753/MB&B754/CB&B752/MCDB752/CPSC752
Bioinformatics: Practical Application of Simulation and Data Mining 
Mark Gerstein
MW 1.00-2.15 BASS 305
Fall 2012 
No regular final examination
Areas Sc
Prerequisites: MB&B 301b and MATH 115a or b, or permission of instructor.
MCDB 120a or 200b is a prerequisite for courses numbered MCDB 202 and above.

Different headings for this class

MB&B452/MCDB452

This version of the course consists of lectures, written problem sets, and a final (semi-computational section and a literature survey) project.

MB&B752/MCDB752

This version of the course consists of lectures, written problem sets, and a final (semi-computational section and a literature survey) project.

CB&B752/CPSC752

This version of the course consists of lectures, programming assignments, and a final programming project.

For graduate students the course is broken up into two "modules" (each counting 0.5 credit towards MB&B course requirement):

MB&B 753a3, Bioinformatics: Practical Application of Data Mining (1st half of term)

MB&B 754a4, Bioinformatics: Practical Application of Simulation (2nd half of term)

Each module consists of lectures, written problem sets, and a final, graduate level written project that is half the length of the full course's final project.

For the grade weighting schemes of each course version, see Class Requirements section.

Prerequisites

The course is keyed towards CBB graduate students as well as advanced MB&B undergraduates and graduate students wishing to learn about types of large-scale quantitative analyses that whole-genome sequencing will make possible. It would also be suitable for students from other fields such as computer science or physics wanting to learn about an important new biological application for computation.

Students should have:

A basic knowledge of biochemistry and molecular biology. A knowledge of basic quantitative concepts, such as single variable calculus, some probability and statistics, and basic programming skills. These can be fulfilled by the following prerequisites statement: "Prerequisites: MBB 200 and Mathematics 115 or permission of the instructor."

Timing & location

Class: Meeting from 1:00-2:15 pm on Monday and Wednesday, in Bass 305. (First meeting will be on 29 Aug 2012 (Wed) and the next meeting will be 31 Aug 2012 (Fri).)

Discussion section: Every Thursday 4-5pm First section: 6th Sept 2012 (Thurs) @ Bass 405 4-5pm

Each section will include discussion of papers assigned (below) and each paper will be presented by a student. Each presentation should be approx. 10 min. Powerpoint slides are optional. Please note the presentation is separate from the write-up, i.e. you still need to do the write-up.

Instructors

Consultation is available UPON REQUEST or according to times stipulated by the individual instructors.

Instructor-in-Charge

Name	Office	Email
Mark Gerstein	Bass 432A	mark.gerstein(at)yale.edu

Guest Instructors

Name	Office	Email
Corey O'Hern	Mason Laboratory	corey.ohern(at)yale.edu
Jesse Rinehart	300 George St	jesse.rinehart(at)yale.edu
James Noonan	333 Cedar St	james.noonan(at)yale.edu
Kei Cheung	300 George St	kei.cheung(at)yale.edu
Steven Kleinstein	300 George St	steven.kleinstein(at)yale.edu
Dov Greenbaum	--	dov.greenbaum(at)aya.yale.edu

Teaching Fellows

Name	Office	Email
Jieming Chen	Bass 437, Bass 323	jieming.chen(at)yale.edu
Yao Fu	Bass 437	yao.fu(at)yale.edu
Wendell Smith (selected lectures)	Mason Laboratory 313	wendell.smith(at)yale.edu

Topics/Class Schedule

Class Schedule (including a list of topics and quiz dates)

Polls

Poll for students' sign up and good times for the weekly discussion section Result

Poll2 Result2

Discussion Section Readings

Session 1

T.F. Smith and M.S. Waterman. (1981) Identification of common molecular subsequences. Journal of Molecular Biology,147(1): 195-7. PMID: 7265238. PDF [Nicole T.]

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215(3):403-10. PMID: 2231712. PDF [Steven B.]

Session 2

Metzker ML. "Sequencing technologies - the next generation” Nature Reviews Genetics. 11 (2010) PDF [Rob A.]

Bailey TL, Williams N, Misleh C, Li WW. (2006) MEME: discovering and analyzing DNA and protein sequence motifs, Nucl Acids Res.34:W369-373 PDF [Jimi M.]

Session 3

Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks.Cell. 2006 Nov 3;127(3):635-48. PDF [Qian W.]

Nevan J. Krogan et al (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 440, 637-643 (30 March 2006) PDF [Shantao L.]

Session 4

Wheeler DA et al. "The complete genome of an individual by massively parallel DNA sequencing,” Nature. 452:872-876 (2008) PDF [Paul B. ]

Antezana E, Egaña M, Blondé W, Illarramendi A, Bilbao I, De Baets B, Stevens R, Mironov V, Kuiper M. (2009) The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biol. 2009;10(5):R58. Epub 2009 May 29. PDF

Session 5

Sotiriou et al. (2006) Gene Expression Profiling in Breast Cancer: Understanding the Molecular Basis of Histologic Grade To Improve Prognosis. JNCI J Natl Cancer Inst (15 February 2006) 98 (4):262-272.doi: 10.1093/jnci/djj052 PDF [Sebastian K.]

Ekman D, Light S, Björklund AK, Elofsson A. (2006) What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol. 2006;7(6):R45. PDF [Kyle M.]

Session 6

The Assoc. of Mol. Path. v. Myriad Genetics, Inc., (Fed. Cir. 2012) PDF

Brief of Amicus Curiae Chris Holman: The Assoc. of Mol. Path. v. Myriad Genetics, Inc., (Fed. Cir. 2012) PDF

Session 7

ML Connolly. (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science, 221(4612): 709-13. PMID: 6879170.PDF

Martin Karplus and J. Andrew McCammon. (2002) Molecular dynamics simulations of biomolecules. Nature Structural Biology,9, 646-52. PMID: 12198485.PDF [Nathan P]

Session 8

Dill KA, Ozkan SB, Shell MS, Weikl TR. (2008) The Protein Folding Problem.Annu Rev Biophys,9, 37:289-316. PMID: 2443096.PDF

Bowman GR, Beauchamp KA, Boxer G, Pande VS. “Progress and challenges in the automated construction of Markov state models for full protein systems,” J. Chem. Phys. 131 (2009) 124101 PDF

Session 9

Perelson AS. Modelling viral and immune system dynamics. Nat Rev Immunol. 2002 Jan;2(1):28-36. PDF [Caroline B.]

Class Requirements

Discussion Section / Readings

Papers will be assigned throughout the course. These papers will be presented and discussed in weekly 60-minute sections with the TFs. A brief summary (a half-page per article) should be submitted at the beginning of the discussion session.

Bioinformatics quizzes

There will be four short quizzes (25 minutes) in class comprising SIMPLE questions that you should be able to answer from the lectures plus the main readings.

Programming Assignments (CBB and CS) and Programming issues

There will be several short programming assignments required for CBB and CS students taking this course. Acceptable languages and submission requirements will be discussed prior to the first assignment. These assignments are NOT required for students not taking the CBB or CS sections of the course.

These are the programming languages that we permit in the programming assignments and final project: Perl, Python, C, C++, MATLAB and R. If you really feel more comfortable with other languages, please email the TFs to discuss. Also, packages such as BioPerl and BioPython are not allowed in the assignments and final project. If in doubt, please consult the TFs.

We recommend the use of PERL for most of the programming. A useful resource is the following book: Programming Perl, 3rd Edition in the O' Reilly series, by Larry Wall, Tom Christiansen, Jon Orwant. The Yale Library has also older editions, which would work too. We would also recommend the following online resources: http://www.perlmonks.org/ and http://stackoverflow.com/. Otherwise, Google is your best friend.

Assignment postings

TBD

Final Project

TBD

Grade Categories

The following are the approximate grading systems:

CBB and CPSC Sections:

Category	% of Total Grade
Quizzes	33%
Final Project	33%
Discussion Section	9%
Programming Assignments	25%

MBB and MCDB Sections:

Category	% of Total Grade
Quizzes	33%
Final Project	33%
Discussion Section	17%
Problem Sets	17%

Relevant Yale College Regulations

Students may have questions concerning end-of-term matters. Links to further information about these regulations can be found below:

http://yalecollege.yale.edu/content/reading-period-and-final-examination-period

http://yalecollege.yale.edu/content/completion-course-work

Brief presentation on how to cite correctly : http://archive.gersteinlab.org/mark/out/log/2012/06.12/cbb752b12/cbb752_cite.ppt

Misc

Permissions on using website material

Graphic for course homepage

If you're really motivated, take a look at http://gersteinlab.org/jobs for further Research Opportunities

Pages from previous years

2012 quizzes 2012 spring, 2011, 2010, 2009 and earlier (Pointers on finding things on old class pages)

@@ Line 343: / Line 343: @@
 ==Pages from previous years==
+[http://archive.gersteinlab.org/cbb752a/b12quizzes.zip 2012 quizzes]
 [http://info.gersteinlab.org/Cbb752b12 2012 spring],
 [http://info.gersteinlab.org/Cbb752b11 2011],

Cbb752a12