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CSCI-4969/6969: Computational Biology, Spring 2019

Class: 10-11:50AM, TF, Low 4040
Instructor Office Hours: 12-1PM, TF


  • April 3: Project posted. Due date 24th Apr, before midnight, with an update due on 17th Apr.
  • April 3: Assign5 posted. Due date 10th Apr, before midnight.
  • Mar 12: Assign4 posted. Due date 20th Mar, before midnight.
  • Feb 16: Assign3 posted. Due date 22nd Feb, before midnight.
  • Feb 7: Assign2 posted. Due date 15th Feb, before midnight.
  • Jan 18: Assign1 posted. Due date 25th Jan, before midnight.
  • Jan 3: Signup on Piazza for class discussion and Q&A.
  • Jan 3: Course website is up, with the calendar and syllabus.

Calendar & Readings

A tentative sequence of topics to be covered in the classes; changes are likely as the course progresses.

Day: Date Topic Readings Lecture Notes
F: Jan 11 Introduction I R1 Attach:intro.pptx
T: Jan 15 Introduction II & Sequence Alignment R1 Attach:lecture2.pdf
F: Jan 18 Sequence Alignment R2 Attach:lecture3.pdf
T: Jan 22 More Alignment R2 Attach:lecture4.pdf
F: Jan 25 Scoring Matrices & Multiple Sequence Alignment R3, R4 Attach:lecture5.pdf
T: Jan 29 Database Search R5 Attach:lecture6.pdf
F: Feb 1 Suffix Trees R6 Attach:lecture7.pdf
T: Feb 5 Genome Alignment, Suffix Arrays R7, R8 Attach:lecture8.pdf
F: Feb 8 Suffix Arrays and BWT R9 Attach:lecture9.pdf
T: Feb 12 BTW & Approximate Matching R10 Attach:lecture10.pdf
F: Feb 15 Motif Discovery R11 Attach:lecture11.pdf
T: Feb 19 NO CLASS (Monday Schedule)
F: Feb 22 HMMs R12 Attach:lecture12.pdf
T: Feb 26 EXAM I
F: Mar 1 HMMs II R12 Attach:lecture13.pdf
T: Mar 5 NO CLASS (spring break)
F: Mar 8 NO CLASS (spring break)
T: Mar 12 Profile HMMs R13 Attach:lecture14.pdf
F: Mar 15 Neural Networks R14 Attach:lecture15.pdf
T: Mar 19 Neural Networks II R14 Attach:lecture16.pdf
F: Mar 22 RNNs R14 Attach:lecture17.pdf
T: Mar 26 LSTMs R14 Attach:lecture18.pdf
F: Mar 29 CNNs R14 Attach:lecture19.pdf
T: Apr 2 Seq2Seq, Word2vec models Attach:lecture20.pdf
F: Apr 5 Word Embeddings, Protein Structure Protein Embeddings; R15 Attach:lecture21.pdf
T: Apr 9 Protein Structure Alignment R15, R16 Attach:lecture22.pdf
F: Apr 12 Protein Structure Alignment II R15 Attach:lecture23.pdf
T: Apr 16 Protein Structure Prediction R17 Attach:lecture24.pdf
F: Apr 19 EXAM II
T: Apr 23 Sequence Assembly
F: Apr 26 Project Presentations
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Page last modified on April 18, 2019, at 06:52 PM