University of Maryland
Algorithms, Data Structures and Inference for High-Throughput Genomics
Fall 2019
  • Event
    Date
    Description
    Course Material
  • Lecture
    2019-08-27 00:00:00 +0000
    Tuesday
    Introduction
    [slides]
  • Lecture
    2019-08-29 00:00:00 +0000
    Thursday
    Sequencing Technologies
    [slides]
  • Lecture
    2019-09-03 00:00:00 +0000
    Tuesday
    Introduction to Alignment, Mapping and Indexing
    [slides]
  • Assignment
    2019-09-03 00:00:00 +0000
    Tuesday
    Read Suffix Arrays Paper released!
    [Read Suffix Arrays Paper]
  • Assignment
    2019-09-03 00:00:00 +0000
    Tuesday
    Read TwoPaCo Paper released!
    [Read TwoPaCo Paper]
  • Lecture
    2019-09-05 00:00:00 +0000
    Thursday
    The Suffix Array and Its Construction
    [slides]
  • Lecture
    2019-09-12 00:00:00 +0000
    Thursday
    The FM index and it's use in short-read alignment
    [slides]
  • Lecture
    2019-09-20 00:00:00 +0000
    Friday
    The FMD and Graph FM Indices
    [slides]
  • Lecture
    2019-09-24 00:00:00 +0000
    Tuesday
    The Practical Application of Full-text Indices
    [slides]
  • Lecture
    2019-10-01 00:00:00 +0000
    Tuesday
    Primitives for succinct data structures
    [slides]
  • Lecture
    2019-10-08 00:00:00 +0000
    Tuesday
    K-mer counting, cardinality estimation, AMQs and MPHFs (oh my!)
    [slides]
  • Assignment
    2019-10-14 00:00:00 +0000
    Monday
    Homework 1 released!
    [Homework 1]
  • Lecture
    2019-10-17 00:00:00 +0000
    Thursday
    Large-scale sequence search, part 1
    [slides]
  • Lecture
    2019-10-24 00:00:00 +0000
    Thursday
    Efficient de Bruijn graph representation
    [slides]
  • Lecture
    2019-10-31 00:00:00 +0000
    Thursday
    Efficient colored de Bruijn graph representation
    [slides]
  • Lecture
    2019-11-05 00:00:00 +0000
    Tuesday
    Efficient compacted colored de Bruijn graph construction
    [slides]
  • Lecture
    2019-11-12 00:00:00 +0000
    Tuesday
    Efficient indexing of the (compacted) colored de Bruijn graph
    [slides]
  • Assignment
    2019-11-12 00:00:00 +0000
    Tuesday
    Homework 2 released!
    [Homework 2]
  • Lecture
    2019-11-19 00:00:00 +0000
    Tuesday
    Analysis of transcriptomes with RNA-seq
    [slides]
  • Lecture
    2019-11-21 00:00:00 +0000
    Thursday
    Analysis of transcriptomes with RNA-seq (II)
    [slides]
  • Exam
    2019-12-09 00:00:00 +0000 00:00
    Monday
    Final

    Topics:
    - All
    - The
    - Things