pitt_logo

Computational Genomics MSCBIO2070/02-710 (cross-listed as 02-510), Spring 2016

Seyoung Kim (sssykim[AT]cs.cmu.edu)
Office Hours: 3-4 pm Monday after class, PSC103

Maria Chikina (mchikina[AT]pitt.edu)
Office Hours: 3-4 pm Monday after class, PSC103

  • Starting date: January 11, 2016
  • Class lectures: Mondays & Wednesdays from 1:30-2:50 pm
  • Location:  Pittsburgh Supercomputing Center 103.
  • Teaching Assistants:
    Wayne Mao, wem26[AT]pitt.edu; Office hours: Wednesday after class, PSC 103, or by email appointment
  • Textbooks (suggested but not required): Pevsner, J. (2015). Bioinformatics and functional genomics (third edition). John Wiley & Sons. Bioniformatics and functional genomics (third edition)
  • Course Discussion Forum (Piazza), join this! (If you don't have an andrew email address, please send TA an eamil!)
  • Course Summary and grading policies are listed here
  • Course Project page

 

 cmu logo
Date
Instructor
Module
Lecture Topics
Slides
Reading
Homeworks
1/11

Maria

Introduction to molecular biology

Lecture 1
1/13

Maria

Sequence alignment

Genome sequencing and assembly
Lecture 2
  • Compeau, P. E., Pevzner, P. A., & Tesler, G. (2011)
  • Pevzner, P. A., Tang, H., & Waterman, M. S. (2001)
  • Chap 9. Pevsner, J. (2015)
    • 1/18

    		No class, MLK day
    1/20

    Maria
    		Pair-wise sequence alignment I:
  • Global/local/affine gap
  • Scoring matrices
  • Dynamic programming
    • Lecture 3
    HW1 out
    1/20

    Wayne
    Recitation
    		 Python Recitation 5-6pm
    Slides
    1/25
    Maria
    		Pair-wise sequence alignment II:
  • Multiple sequence alignment
  • Profile-profile alignment
    		•
    Lecture 4
    1/27

    Maria
    Evolution

  • HMMs and their applications
  • Predicting CpG islands, genes from DNA sequences
  • HMM variations for higher-order Markov and duration modeling
  • Pair HMMs for alignment

    • Lecture 5
    2/1
    Maria

  • Molecular evolution
  • Molecular clock
  • Selection tests
  • Evolutionary distance calculation using Jukes cantor & Kimura models

    		•
    Lecture 6
    2/3

    Maria

    Phylogeny
    Lecture 7
    2/8

    Maria
    Gene expression

    Microarrays
    Lecture 8
  • Martin Krzywinski & Naomi Altman (2014)
  • Tusher, V. G., Tibshirani, R., & Chu, G. (2001)


    • 2/10

    Maria

  • Normalization
  • Differentially expressed genes

    		•
    Lecture 9
    2/15

    Maria

    Clustering
    Lecture 10
    HW1 due
    2/17

    Maria

    Classification
    Lecture 11
    HW2 out
    2/17

    Wayne
    Recitation
    		 R Recitation 5:20-6:00pm
    Slides
    2/22

    Maria

  • Next generation sequencing
  • RNA-Seq/ChIP-seq

    		•
    Lecture 12
    2/24

    Maria

    Noncoding RNAs and epigenetics I
    Lecture 13

    2/29

    Takis Benos

    Noncoding RNAs and epigenetics II
    Lecture 14
    3/2

    Seyoung
    Population genetics

  • Genetic variants
  • Haplotype inference

    		•
    Lecture 15
    3/7

    Spring Break

    3/9

    Spring Break

    3/14

    Seyoung

  • Hardy-Weinberg equilibrium
  • Genetic drift
  • Population structure

    		•
    Lecture 16
  • Patterson, N., Price, A. L., & Reich, D. (2006)
  • Raj, A., Stephens, M., & Pritchard, J. K. (2014)
    		•
    HW2 due
    3/16

    Seyoung

  • Family-based genetic analysis
  • Linkage analysis

    		•
    Lecture 17
    HW3 out (Autolab)
    3/21

    Seyoung

  • Genome-wide association studies
  • Epistasis
  • Correcting for population stratifications

    		•
    Lecture 18
  • Balding, D. J. (2006)
    		•


    3/23

    Seyoung

  • Structural variants
  • Indels, copy number variants
  • Detecting structural variants from next generation sequencing data

    		•
    Lecture 19
  • Alkan, C., Coe, B. P., & Eichler, E. E. (2011)
    		•
    3/28

    Seyoung

  • Population genetics meets evolution
  • Natural selection
  • Incomplete lineage sorting

    		•
    Lecture 20
  • Siepel, A. (2009)
  • Sabeti, P. C., Schaffner, S. F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., ... & Lander, E. S. (2006)
    • Project proposal due
    3/30

    Seyoung
    Systems Biology
    		 Gene regulatory networks I:
  • Motif discovery
  • Position weight matrices
  • Conditional random fields for motif modeling
    		•
    Lecture 21
    4/4

    Seyoung
    		Gene regulatory networks II:
  • Cis/trans regulatory elements
  • Allele-specific expression
    		•
    Lecture 22
  • Wittkopp, P. J., Haerum, B. K., & Clark, A. G. (2004)
    		•
    HW3 due
    4/6

    Seyoung
    		Gene regulatory networks III:
  • Module network and its various extensions
    		•
    Lecture 23
    HW4 out (Autolab)
    4/8

    Maria, Seyoung

    Exam Review Session (4PM-6PM, GHC 2109)

    Previous Exams
  • Midterm Review
  • Review Sheet
    • 4/11

    Seyoung

    RNA secondary structure prediction
    Lecture 24
  • Eddy, S. R. (2004)
  • Eddy, S. R., & Durbin, R. (1994)
    • 4/13

    Exam (NSH 1507)

    4/18 (PSC 110)

    Seyoung

  • Cancer data analysis
  • Driver/passenger mutations
  • Tumor heterogeneity
  • Tumor subtypes and personalized medicine

    		•
    Lecture 25
    4/20 (PSC 110)

    Seyoung

  • Protein structure prediction
  • Protein-protein interactions

    		•
    Lecture 26
    4/25

    Seyoung

  • Metagenomics
  • Analysis of human microbiome sequencing data

    		•
    Lecture 27
    HW4 due
    4/27

    Maria, Seyoung

    Poster session (GHC 4405 & 4400 loby)
    5/2

    Final project due

     

    Last Updated: 2/17/2016