BIOL4536 - 2023
 Undergraduate Computational Biology / Bioinformatics
 University of Pennsylvania
 Course Materials

Table Of Contents

  1. Syllabus
  2. Lecture Slides
  3. Exams
  4. Quizzes
  5. Homework
  6. Student Evaluations

Professors: Gregory R. Grant, Junhyong Kim
Instructor: Nicholas Lahens
TA's: Chetan Vadali, Jianing Yang
57 registered students

Syllabus

Lecture Slides

no.
Topic
Slides
1
Prob/Stat, hypothesis testingslides
2
Regressionslides
3
Genome Browserslides
4
UNIXslides
5
Nucleic Acid, Sequencing, Global Alignmentslides
6
Local Alignment, Multiple Alignment, Phylogeneticsslides
7
Protein Alignment, Substitution Matrices, Markov Modelsslides
8
The BLAST Algorithmslides
9
Cluster Computeslides
10
DNA Sequencing, SNP/Variant Calling, Phasing, ChIP-Seq, ATAC-Seqslides
11
RNA and RNA-Seqslides
12
Multiple Testing, FDR/FWER, q-valuesslides
13
Pathway Enrichment (GO) Analysisslides
14
Dimensionality Reductionslides
15
Non-Parametric Methodsslides
16
GWASslides
17
Motivating Exampleslides
18
Machine Learningslides

Exams

Exam 1Prob/Stat, Regression, Genome Browser,
Unix, Global DNA Alignment		Practice 1ExamSolutions
Practice 2ExamSolutions
ActualExamSolutions
MakeupExamSolutions
Exam 2Protein Alignment, Local, Multiple,
Substitution Matrices, BLAST,
DNA-Seq, ChIP-Seq, Multiple Testing		Practice ProblemsExamSolutions
Practice 2ExamSolutions
Practice 3ExamSolutions
ActualExamSolutions
MakeupExamSolutions
FinalPathway Enrichment, Dimensionality Reduction
Non-Parametric Methods, GWAS, R, Machine Learning		Practice ProblemsExamSolutions
Practice 1ExamSolutions
Practice 2ExamSolutions
Practice 3ExamSolutions
ActualExamSolutions

Quizzes

Quiz 1Prob/Stat, RegressionActualQuizSolutions
MakeupQuizSolutions
Quiz 2Genome BrowserActualQuizSolutions
MakeupQuizSolutions
Quiz 3AlignmentActualQuizSolutions
MakeupQuizSolutions
Quiz 4BLAST, DNA-SeqActualQuizSolutions
MakeupQuizSolutions

Homework

HW #1Hypothesis TestingAssignmentSolutions
HW #2RegressionAssignmentSolutions
HW #3Genome BrowserAssignmentSolutions
HW #4UNIXAssignmentSolutions
HW #5AlignmentAssignmentSolutions
HW #6BLASTAssignmentSolutions
HW #7ChIP-SeqAssignment
HW #8RNA-SeqAssignment
HW #9R
HW #10R
HW #11R