The development of omics technologies provides us with an unprecedented opportunity to understand cellular function, and higher levels of organization. In this class, we will focus on big data being generated in biology, and the techniques used to analyze the data. While the course should be self-contained, we assume some mathematical maturity.

Instructors: Vineet Bafna/Sheng Zhong

TA: Jonghun Park, Jessica Au

Class lectures: TR 9:30 am - 10:50 am (DIB121); Zoom link (starting May 18th; password is: beng203)

Lecture podcasts will be available.
We will use Canvas for quick access to course material and other resources
Notes on the lecture material are available here.
All announcements and discussions on Piazza.
Assignments will be handed out on Canvas and submitted using Gradescope (ID:2KVZKJ)
Academic Integrity (Please read)

Office hours

Vineet Bafna office hours (Friday 4-5 pm via zoom. If you plan to join the OH, I will appreciate a note via piazza)
Jonghun Park office hours (Monday 11-12 pm via zoom)
Jessica Au office hours (Thursday 2-3 pm via zoom)
Dr. Sheng Zhong office hours (Thursday 11-12 pm via the same zoom as the lecture.)

Assignment	Due Date	Data and Resources	Comment
Assignment 1	4/17/2023 10:00 pm PT	Hi-C data file (informative reads only)
Assignment 2	5/4/2023 10:00 pm PT	Data file for BF (in fastq format) queries	Please write your own code for bloom filters, and submit your code.
Assignment 3	5/20/2023 10:00 pm PT	CAH Bovine protein Mass spec (mgf)	(mgf format for MS data)

Midterm 2023	5/16/2023 9:30 am (in class)	2022 Midterm exam. (Solutions available in Piazza @53)
Project 2023

Date	Topic	Lecture slides	Optional reading
Week 1		Course Logistics (ppt)
Week 1,2 4/4/2023 4/6/2023 4/11/2023	Topic 1: Sources of molecular data and data pre-processing Next-gen sequencing 10X Hi-C RNA profiling Metagenomic sequencing ChIP-Seq Protein mass spectrometry	Slides: Sources of OMICS Data (ppt) pdf (Sequencing) Mass Spectrometry (ppt) pdf (MS)
Week 2, 3 4/13/2023 4/18/2023	Topic 2: NGS data pre-processing, and feature extraction. Abstract notion of database filtering Pigeonhole principle and db filtering Building protein and transcript expression matrices	2.1.Alignment basics (pptx) 2.3. Database filtering (pptx Video of 4/18 lecture (New) transcript(vtt file)	'Tuxedo 2' Protocol FM index Wiki Aho Corasick Trie Wiki
Week 3, 4 4/20/2023 4/25/2023	Topic 2. Bloom filters Sketching Locality Sensitive Hashing(tentative)	Bloom Filter video Alignment Free, Assembly Free methods	Sequence Bloom Trees Sketching in Mash
Week 4,5 4/27/2023 5/2/2023	Topic 3. Genome segmentation using Hidden Markov Models	HMMs HMM slides (pdf) 5/2 Lecture Zoomcast	Rabiner chromHMM
Week 5 5/2/2023 5/4/2023	Topic 4. Mass spectrometry data preprocessing Peptide identification (de novo and database search) Quantification	5/2 Lecture Zoomcast ms (pptx) (pdf of slides)	Extra Reading MaxQuant Small molecule MS of human skin Database Search using MS-GF+
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Week 6 5/9/2023	Topic 5. A gentle introduction to linear algebra or manipulating high dimensional spaces Dimensionality Rank Inner and outer products Projections Eigenvalues Hyperplane	pptx pdf of slides	Linear discrim. analysis Perceptron Lin. Programming
Week 6 5/11/2023	Classification, regression and scaling Perceptron algorithm Fischer linear discriminant analysis ML separation Linear programming Large margin separation SVM	Classification pptx	Linear discrim. analysis Perceptron Lin. Programming
Week 7A 5/16/2023	2023 Midterm (available at 8am)	2022 Midterm (solutions this weekend)	Submit using gradescope
Week 7B	Classification of recurrence vs. non-recurrence breast cancer patients based on extracellular RNA	Overview of the 2nd half Lecture 0 - Machine Learning Lecture 1 slides	PNAS 2019
Week 8	Classification of Alzheimer’s vs. control subjects. Introduction to longitudinal data: linear model, mixed model, classification.	Lecture 2 slides Lecture 3 slides	Curr Biol 2020
Week 9	Single-cell ATAC-seq in Alzheimer’s brain Single-cell sequencing and time-course clustering	Lecture 4 slides Lecture 5 slides	Genome Res 2014 PNAS 2014
Week 10	Project presentations	Sign-up sheet	Two-people teams are encouraged.