Bioinformatics-Course-2020

Bioinformatics course (MED-121) for 3rd year students, Program of Medical Informatics, Faculty of Computers and Information, Egypt.

Day	Lecture Objectives	Lecture Materials
1	What is Bioinformatics. Bioinformatics Vs. Medical Informatics. Central Dogma of Life. DNA, Genomes. RNA, Transcriptomes. Proteins, Proteomics. Transcriptions and Translation. Omics era.	Lecture 1 Lecture 1 Video
2	Bioinformatics Road. Prepare a sequencing library. Sequencing Technologies. Sequencing by Synthesis. Base Caller. Nanopore Sequencing. Single Molecule Real Time Sequencing.	Lecture 2 Lecture 2 Video
3	Key attributes of Different Sequencing Technologies Sequencing Projects. Egyptian Genome Project. Whole Genome Vs. Whole Exome Vs. Targeted Sequencing Sequencing Services: RNA-seq, Bisulfite, ChIP-seq, Single cell sequencing Paired-end Vs. Single-end reads Genomic Coverage Base Qualities FASTA Vs. FASTQ data files format	Lecture 3 Lecture 3 Video
4	Genome Annotations Genome Annotations Data File Formats: BED, GFF, GFF3	Lecture 4 Lecture 4 Video
5	String Definitions: String, substring, prefix, suffix, subsequence, kmers The exact marching string problem NAÏVE Algorithm for pattern matching NAÏVE Algorithm Running Time Complexity Analysis	Lecture 5 Lecture 5 Video
6	Boyer Moore Algorithm Boyer Moore Algorithm: Bad Character Rule Boyer Moore Algorithm: Good Suffix Rule Boyer Moore Algorithm: Strong Good Suffix Rule Boyer Moore Algorithm: All togther Boyer Moore Algorithm Running Time Complexity Analysis	Lecture 6 Lecture 6 Video Part 1 Lecture 6 Video Part 2
7	Knuth Morris Pratt Algorithm Knuth Morris Pratt Algorithm: LPS Knuth Morris Pratt Algorithm Running Time Complexity Analysis	Lecture 7 Lecture 7 Video
8	Rabin-Karp Algorithm Rabin-Karp Algorithm: string hashing Rabin-Karp Algorithm Running Time Complexity Analysis	Lecture 8 Lecture 8 Video
9	Sequence Alignment Scoring an Alignment Different Scoring Schemes & Scoring Matrics: To be continue in the next lecture	Lecture 9 Lecture 9 Video
10	Different Scoring Schemes & Scoring Matrics Local Vs. Global Sequence Alignments Pairwise Vs. Multiple Sequence Alignments Linear Vs. Affine Gap penality Models. Global Piarwise Sequence Alignment Algorithm: Needleman-Wunsch Local Piarwise Sequence Alignment Algorithm: Smith-Waterman	Lecture 10 Lecture 10 Video
11	Sequence Assembly Sequence Assembly Challenges Sequence Assembly Terminologies Comparative Vs. De Novo Assembly Overlap-Layout-Consensusly Genome Assembly Approach: To be continue in the next lecture	Lecture 11 Lecture 11 Video
12	Overlap-Layout-Consensusly Genome Assembly Approach Greedy Graph Genome Assembly Approach De-Bruijn-Graph Genome Assembly Approach Genome Assembly Evaluation Metrics	Lecture 12 Lecture 12 Video
13	Task1: Code a whole Boyer Moore Algorithm using Good Suffix Rule and Bad Character Rule, prepare a video to explain it. Course Project: up to students to choose thier project ideas and prepare a video to explain its implementation.	Task 1 Winner: Khalid Gad, 3rd year Medical Informatics Student at Mansoura University, Egypt. Project Winner: Gamela Hussien, Amaal Ahmed, Reham El-Baz, Aya Salah, Wessam Ahmed, 3rd year Medical Informatics Students at Mansoura University, Egypt.