Topics in Bioinformatics Spring 2016
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Research
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Center for Health Informatics and Bioinformatics
 
High Performance Computing Facility
NYU Langone Medical Center
NIH
NCI
NIGMS
NIST
Topics in Bioinformatics Spring 2016 (BMSC-GA 4456)

Course Directors:
David Fenyö (David@FenyoLab.org), Professor
Stuart Brown (Stuart Brown@nyumc.org), Associate Professor

Course overview

The course is meant to provide students with an overview of bioinformatics techniques. It consist of 7 modules and each module has the same structure:
1. A lecture introducing the project (Tuesday Week 1).
2. The students present their analysis plans and preliminary analysis results (Friday Week 1).
3. A session for discussion of problems encountered (Tuesday Week 2).
4. The students present their final analysis (Friday Week 2).
5. Final report due (Tuesday Week 3).

Learning objectives

At the conclusion of the course, the student will have hands-on experience with common bioinformatics analysis

Course Assessment

  • Projects (100%): Students will complete 7 projects based on 7 assigned papers and one project selected by each student. For each project an analysis plan, a project presentation, and a final report has to be completed.
General Policies
  • Late/missed work: You must adhere to the due dates for all required submissions. If you miss a deadline, then you will not get credit for that assignment/post. Try to avoid last minute submissions.
  • Incompletes: No “Incompletes” will be assigned for this course unless we are at the very end of the course and you have an emergency.
  • Responding to Messages: I will check e-mails daily during the week, and I will respond to course related questions within 48 hours.
  • Announcements: I will make announcements throughout the semester by e-mail. Make sure that your email address is updated; otherwise you may miss important emails from me.
  • Safeguards: Always back up your work on a safe place (electronic file with a backup is recommended) and make a hard copy. Do not wait for the last minute to do your work. Allow time for deadlines.
  • Plagiarism: Plagiarism, the presentation of someone else's words or ideas as your own, is a serious offense and will not be tolerated in this class. The first time you plagiarize someone else's work, you will receive a zero for that assignment. The second time you plagiarize, you will fail the course with a notation of academic dishonesty on your official record.



Lecture 1 Historical Overview of Bioinformatics (January 26, 2016 TRB 718 4pm)
Lecturer: Brown

Reading List

  • Origins of Bioinformatics
  • Roots of Bioinformatics
  • History of Bioinformatics
  • Bioinformatics Timeline
  • History of Sequencing Informatics


    Lecture 2 Historical Overview of Bioinformatics (January 29, 2016 TRB 718 9am)
    Lecturer: Brown


    Lecture 3 Molecular Classification of Cancer: Introduction to Project (February 2, 2016 TRB 718 4pm)
    Lecturer: Brown

    Reading List
  • Molecular classification of cancer: class discovery and class prediction by gene expression monitoring, Science 286 (1999) 531-537.


    Lecture 4 Molecular Classification of Cancer: Presentation of Analysis Plan (February 5, 2016 TRB 718 9am)
    Lecturer: Brown


    Lecture 5 Molecular Classification of Cancer: Discussion of Problems Encountered (February 9, 2016 TRB 718 4pm)
    Lecturer: Brown


    Lecture 6 Molecular Classification of Cancer: Presentation of Results (February 12, 2016 TRB 718 9am)
    Lecturer: Brown


    Lecture 7 Cancer Genomics: Introduction to Project (February 16, 2016 TRB 718 4pm)
    Lecturer: Wang

    Reading List
  • Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma


    Lecture 8 Cancer Genomics: Presentation of Analysis Plan (February 19, 2016 TRB 718 9am)
    Lecturer: Wang


    Lecture 9 Cancer Genomics: Discussion of Problems Encountered (February 23, 2016 TRB 718 4pm)
    Lecturer: Wang


    Lecture 10 Cancer Genomics: Presentation of Results (February 26, 2016 TRB 718 9am)
    Lecturer: Wang


    Lecture 11 DNA Methylation: Introduction to Project (March 1, 2016 TRB 718 4pm)
    Lecturer: Shen

    Reading List
  • DNA methylation: roles in mammalian development, Nature Reviews Genetics 14, 204-220 (2013)
  • Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications, Bioinformatics 27(11): 1571–1572 (2011)


    Lecture 12 DNA Methylation: Presentation of Analysis Plan (March 4, 2016 TRB 718 9am)
    Lecturer: Shen


    Lecture 13 DNA Methylation: Discussion of Problems Encountered (March 8, 2016 TRB 718 4pm)
    Lecturer: Shen


    Lecture 14 DNA Methylation: Presentation of Results (March 11, 2016 TRB 718 9am)
    Lecturer: Shen


    Lecture 15 Chromosome Conformation Capture: Introduction to Project (March 15, 2016 TRB 718 4pm)
    Lecturer: Tsirigos

    Reading List
  • A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping


    Lecture 16 Chromosome Conformation Capture: Presentation of Analysis Plan (March 18, 2016 TRB 718 9am)
    Lecturer: Tsirigos


    Lecture 17 Chromosome Conformation Capture: Discussion of Problems Encountered (March 22, 2016 TRB 718 4pm)
    Lecturer: Tsirigos


    Lecture 18 Chromosome Conformation Capture: Presentation of Results (March 25, 2016 TRB 718 9am)
    Lecturer: Tsirigos


    Lecture 19 Machine Learning: Introduction to Project (March 29, 2016 TRB 718 4pm)
    Lecturer: Ma

    Reading List
  • Forecasting Seizures in Dogs with Naturally Occurring Epilepsy
  • Project details


    Lecture 20 Machine Learning: Presentation of Analysis Plan (April 1, 2016 TRB 718 9am)
    Lecturer: Ma


    Lecture 21 Machine Learning: Discussion of Problems Encountered (April 5, 2016 TRB 718 4pm)
    Lecturer: Ma


    Lecture 22 Machine Learning: Presentation of Results (April 8, 2016 TRB 718 9am)
    Lecturer: Ma


    Lecture 23 Proteomics: Introduction to Project (April 12, 2016 TRB 718 4pm)
    Lecturer: Ruggles

    Reading List
  • Proteogenomic characterization of human colon and rectal cancer, Nature 513 (2014) 382-387.


    Lecture 24 Proteomics: Presentation of Analysis Plan (April 15, 2016 TRB 718 9am)
    Lecturer: Ruggles


    Lecture 25 Proteomics: Discussion of Problems Encountered (April 19, 2016 TRB 718 4pm)
    Lecturer: Ruggles


    Lecture 26 Proteomics: Presentation of Results (April 22, 2016 TRB 718 9am)
    Lecturer: Ruggles


    Lecture 27 Dynamics of Bacterial Communities: Introduction to Project (April 26, 2016 TRB 718 4pm)
    Lecturer: Fenyo ( Slides )

    Reading List
  • Counteraction of antibiotic production and degradation stabilizes microbial communities, Nature 521 (2015) 516-519.


    Lecture 28 Dynamics of Bacterial Communities: Presentation of Analysis Plan (April 29, 2016 TRB 718 9am)
    Lecturer: Fenyo ( Slides )


    Lecture 29 Dynamics of Bacterial Communities: Discussion of Problems Encountered (May 3, 2016 TRB 718 4pm)
    Lecturer: Fenyo


    Lecture 30 Dynamics of Bacterial Communities: Presentation of Results (May 6, 2016 TRB 718 9am)
    Lecturer: Fenyo


    Lecture 31 Final Presentation (May 20, 2016 TRB 718 9am)

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

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