Lectures
Recorded lectures
- 2021 CSHL course lectues (WUSTL Box)
- 2020 CSHL course lectures (WUSTL Box)
- 2018 CBW course lectures (YouTube)
- 2016 CBW course lectures (YouTube)
- 2015 CBW course lectures (YouTube)
- 2014 CBW course lectures (YouTube)
- 2013 CBW course lectures (YouTube)
Advanced Sequencing Technologies & Bioinformatics Analysis (November 6-19, 2023)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Emerging next-generation sequencing platforms (Elaine Mardis)
- Overview of Next Generation Short Read Sequencing Technologies (Elaine Mardis)
- Epigenomics (Ben Sunkel)
- The Genomic Era is Alive and Well! (John McPherson)
- Research Applications of Single Cell Sequencing (Trevor Pugh)
- Single cell sequencing technology and applications (Jonathan Preall)
- Genomics at scale with the NHGRI AnVIL (Mike Schatz)
- Long read sequencing technology and research applications (Richard McCombie)
- Genomics in agriculture(Zach Lippman)
- Interpreting cis-regulatory mechanisms learned by genomic deep learning (Peter Koo)
- More advanced command line lab and exercise (Jason Kunisaki)
- What’s new in the human (pan)genome?(Adam Phillippy)
- An Overview of Bioinformatics (Chris Miller)
- Intro to cloud computing (My Hoang)
- [Spatial transcriptomics (Sanja Vickovic)]
- Concepts in genome coordinates, intervals, and arithmetic (Jason Kunisaki)
- Using bedtools (and awk) to perform genome arithmetic (Jason Kunisaki)
- Noncoding RNAs (Chris Maher)
- File formats (Felicia Gomez)
- Alignment concepts (Felicia Gomez)
- Ethics and Regulation of Genomic Research (Jessica Mozersky)
- DNA Alignment LAB_CSHL_2023 (Mariam Khanfar)
- Introduction to IGV (Kartik Singhal)
- Intro to concepts in variant calling (Chris Miller)
- VCF Format (Mariam Khanfar)
- Somatic variant calling (Chris Miller)
- Variant Representation and Interpretation (Wes Goar)
- Introduction to epigenomics - ATAC, ChIPseq and Bisulfite approaches (Chris Miller)
- Data Visualization(Chris Miller)
- Data Cleaning (Chris Miller)
- Single cell ATAC-seq (Yang Li)
- Single cell ATAC-seq Part 2 (Yang Li)
- Introduction to bulk RNA-sequencing (Malachi Griffith)
- Alignment and visualization concepts(Arpad Danos)
- Expression and Differential Expression analysis lecture (Obi Griffith)
- Probability and statistics for genomics analysis (Aaron Quinlan)
- Probability and statistics for genomics analysis Part 2 (Aaron Quinlan)
- Introduction to scRNA analysis (Jonathan Preall)
- Epilepsy-affected brain tissues, somatic mosaicism, model organisms (Tracy Bedrosian)
CBW RNA-seq analysis (July 17-19th, 2023. Toronto, ON, Canada))
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Presentations:
- Intructor Introductions
- Introduction to Cloud Computing (lecture)
- Introduction to RNA Sequencing (lecture)
- Introduction to IGV (lecture)
- Fasta, Fastq, GTF (mini lecture)
- Indexing (mini lecture)
- Alignment (mini lecture)
- Alignment, assembly, kmers (mini lecture)
- SAM, BAM, BED (mini lecture)
- Alignment QC (mini lecture)
- Abundance Estimation (mini lecture)
- HTSeq (mini lecture)
- Differential expression (mini lecture)
- Alignment free analysis with Kallisto (mini lecture)
- Alternative expression (mini lecture)
Advanced Sequencing Technologies & Bioinformatics Analysis (November 7-19, 2022)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Overview of Next-generation Short Read Sequencing Technologies (Elaine Mardis)
- Emerging next-generation sequencing platforms (Elaine Mardis)
- ChIP and Epigenomics (Berkley Gryder)
- Research Applications of Single Cell Sequencing (Trevor Pugh)
- Long read sequencing technology and research applications (Richard McCombie)
- Single cell sequencing technology and applications (Jonathan Preall)
- Computational Biology at the New York Genome Center (Mike Zody)
- An Overview of Bioinformatics (Chris Miller)
- Introduction to Cloud Computing (Kelsy Cotto)
- File formats (Felicia Gomez)
- Alignment concepts (Felicia Gomez)
- Introduction to IGV (My Hoang)
- Introduction to epigenomics - ATAC, ChIPseq and Bisulfite approaches (Chris Miller)
- Introduction to bulk RNA-sequencing(Malachi Griffith)
- Noncoding RNAs (Chris Maher)
- Introduction to scRNA analysis (Jonathan Preall)
- scRNA analysis notebook (Jonathan Preall)
- Bedtools Introduction (Jason Kunisaki)
- Genomic arithmetic with bedtools (Aaron Quinlan)
- Real world analysis with bedtools (Aaron Quinlan)
- SNP and indel discover (Joshua Mincer)
- Computational Challenges in Rare Disease Analysis (Aaron Quinlan)
- Variant Representation and Interpretation (Alex Wagner)
- Working with clusters, shell profiles, Unix extras
- Central Limit Theorum (Aaron Quinlan)
- t-stat, t-distribution, t-tests, and p-values (Aaron Quinlan)
- The T2T Genome and applications to variant calling (Dylan Taylor)
Advanced Sequencing Technologies & Bioinformatics Analysis (November 11-19, 2021. Virtual due to COVID-19)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Next Generation Sequencing (Short Read) Technologies (Elaine Mardis)
- Long Read Sequencing (Dick McCombie)
- Population sequencing and analysis projects at NYGC (Mike Zody)
- Single Cell Sequencing (Jonathan Preall)
- Introduction to Cloud Computing (Obi Griffith)
- A Brief Intro to the Human Genome and FASTA (Aaron Quinlan)
- A Brief Intro to FASTQ format (Aaron Quinlan)
- DNA sequence mapping and alignment (Aaron Quinlan)
- SAM/BAM format, samtools, and IGV-ish (Aaron Quinlan)
- Brief Intro SNV Discovery (Aaron Quinlan)
- Intro to RNA-sequencing and analysis (Malachi Griffith)
- A complete reference genome improves analysis of human genetic variation (Michael Schatz)
- Analysis and interpretation of single-cell RNA-seq data (Chris Miller)
- Variant Representation, Annotation, and Interpretation (Alex Wagner)
- Metagenomics and Viromics (Scott Handley)
- Multiome experiment (Jonathan Preall)
- Comprehensive Analysis of Single Cell Epigenomic Data (Yang Li)
- The application of epigenomic profiling strategies to study cancer and other common diseases (Peter Scacheri)
CBW RNA-seq analysis (September 8-10th, 2021. VIRTUAL due to COVID-19)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Presentations:
- Intructor Introductions
- Introduction to RNA Sequencing (lecture)
- Introduction to IGV (lecture)
- Fasta, Fastq, GTF (mini lecture)
- Indexing (mini lecture)
- Alignment (mini lecture)
- Alignment, assembly, kmers (mini lecture)
- SAM, BAM, BED (mini lecture)
- Alignment QC (mini lecture)
- Abundance Estimation (mini lecture)
- HTSeq (mini lecture)
- Differential expression (mini lecture)
- Alignment free analysis with Kallisto (mini lecture)
- Alternative expression (mini lecture)
Advanced Sequencing Technologies & Bioinformatics Analysis (November 16-20, 2020. Virtual due to COVID-19)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Next Generation Sequencing (Short Read) Technologies (lecture - Elaine Mardis)
- Long Read Sequencing (lecture - Dick McCombie)
- Single Cell Sequencing (lecture - Jon Preall)
- The application of epigenomic profiling strategies to study cancer and other common diseases (lecture - Peter Schacheri)
- Intructor Introductions
- Introduction to Cloud Computing (lecture)
- Introduction to RNA Sequencing (lecture)
- Fasta, Fastq, GTF (mini lecture)
- Indexing (mini lecture)
- Alignment (mini lecture)
- Alignment, assembly, kmers (mini lecture)
- SAM, BAM, BED (mini lecture)
- Alignment QC (mini lecture)
- Abundance Estimation and Differential Expression (lecture)
- Alignment free analysis with Kallisto (mini lecture)
- Alternative expression (mini lecture)
- Analysis and interpretation of single-cell RNA-seq data (lecture - Allegra Petti)
CBW Informatics for RNA-seq analysis (June 17-19, 2020. Planned for Montreal but VIRTUAL due to COVID-19)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Presentations:
- Intructor Introductions
- Introduction to RNA Sequencing (lecture)
- Fasta, Fastq, GTF (mini lecture)
- Indexing (mini lecture)
- Alignment (mini lecture)
- Alignment, assembly, kmers (mini lecture)
- SAM, BAM, BED (mini lecture)
- Alignment QC (mini lecture)
- Abundance Estimation (mini lecture)
- HTSeq (mini lecture)
- Differential expression (mini lecture)
- Alignment free analysis with Kallisto (mini lecture)
- Alternative expression (mini lecture)
- scRNA pt. 1 (lecture)
- scRNA pt. 2 (lecture)
CSHL Advanced Sequencing Technologies and Applications (November 5-17, 2019. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Introduction to Cloud Computing (lecture)
- Introduction to RNA Sequencing (lecture)
- Fasta, Fastq, GTF (mini lecture)
- Indexing (mini lecture)
- Alignment (mini lecture)
- Alignment, assembly, kmers (mini lecture)
- SAM, BAM, BED (mini lecture)
- Alignment QC (mini lecture)
- Abundance Estimation (mini lecture)
- HTSeq (mini lecture)
- Differential expression (mini lecture)
- Alignment free analysis with Kallisto (mini lecture)
- Alternative expression (mini lecture)
CBW Informatics for RNA-seq analysis (June 11-13, 2019. Toronto, ON, Canada)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Presentations:
- Introduction to Cloud Computing (lecture)
- Fasta, Fastq, GTF (mini lecture)
- Indexing (mini lecture)
- Alignment (mini lecture)
- Alignment, assembly, kmers (mini lecture)
- SAM, BAM, BED (mini lecture)
- Alignment QC (mini lecture)
- Abundance Estimation (mini lecture)
- HTSeq (mini lecture)
- Differential expression (mini lecture)
- Alignment free analysis with Kallisto (mini lecture)
- Alternative expression (mini lecture)
- scRNA-seq (mini lecture)
CBW-CSHL High-Throughput Biology: From Sequence to Networks (March 11-17, 2019. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) and Canadian Bioinformatics Workshops (CBW) - Course Site
Presentations:
- Module 7 - Introduction to RNA Sequencing (lecture)
- Module 8 - RNA-Seq Alignment and Visualization (lecture)
- Module 9 - Expression and Differential Expression (lecture)
- Module 10 - Reference Free Alignment (lecture)
-
Module 11 - Isoform Discovery and Alternative Expression (lecture)
- Fasta, Fastq, GTF (mini lecture)
- Indexing (mini lecture)
- Alignment (mini lecture)
- Alignment, assembly, kmers (mini lecture)
- SAM, BAM, BED (mini lecture)
- Alignment QC (mini lecture)
- Abundance Estimation (mini lecture)
- HTSeq (mini lecture)
- Differential expression (mini lecture)
- Alignment free analysis with Kallisto (mini lecture)
- Alternative expression (mini lecture)
CSHL Advanced Sequencing Technologies and Applications (November 6-18, 2018. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Instructor Introduction (lecture)
- Module 0 - Introduction to cloud computing (lecture/tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Alignment free expression estimation (lecture)
- Module 4 - Alignment free expression estimation (tutorial)
- Module 5 - Isoform discovery and alternative expression (lecture)
- Module 5 - Isoform discovery and alternative expression (tutorial)
- Introduction to IGV Browser (tutorial)
- Genome Analysis Platforms (lecture)
CBW Informatics for RNA-seq analysis (May 28-30, 2018. Toronto, ON, Canada)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Presentations:
- Intructor Introduction (lecture)
- Module 0 - Introduction to cloud computing (lecture/tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Alignment free expression estimation (lecture)
- Module 4 - Alignment free expression estimation (tutorial)
- Module 5 - Isoform discovery and alternative expression (lecture)
- Module 5 - Isoform discovery and alternative expression (tutorial)
- Introduction to IGV Browser (tutorial)
CSHL Advanced Sequencing Technologies and Applications (November 7-18, 2017. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Introduction to cloud computing (lecture/tutorial)
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
- Introduction to Genome Analysis Platforms (lecture)
CBW Informatics for RNA-seq analysis (July 10-12, 2017. Toronto, ON, Canada)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Presentations:
- Introduction to cloud computing (lecture/tutorial)
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
- Introduction to Genome Analysis Platforms (lecture)
- Module 5 - De novo RNA-Seq Assembly and Analysis Using Trinity (lecture)
- Module 6 - Functional Annotation of Assembled Transcripts Using Trinotate (lecture)
CBW-CSHL High-Throughput Biology: From Sequence to Networks (March 20-26, 2017. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) and Canadian Bioinformatics Workshops (CBW) - Course Site
Presentations:
- Introduction to cloud computing (lecture/tutorial)
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
- Introduction to Genome Analysis Platforms (lecture)
CSHL Advanced Sequencing Technologies and Applications (November 7-20, 2016. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Introduction to cloud computing (lecture/tutorial)
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
- Introduction to Genome Analysis Platforms (lecture)
CBW Informatics for RNA-seq analysis (June 16-17, 2016. Toronto, ON, Canada)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Videos of lectures (Youtube)
Presentations:
- Introduction to Cloud Computing (lecture/tutorial)
- Introduction to Genome Analysis Platforms (lecture)
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
CSHL Advanced Sequencing Technologies and Applications (November 10-22, 2015. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Introduction to cloud computing (lecture/tutorial)
- Introduction to IGV Browser (tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
CBW Informatics for RNA-seq analysis (June 8-9, 2015. Toronto, ON, Canada)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
Presentations:
- Module 0 - Introduction to cloud computing (lecture/tutorial)
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
Lecture Videos:
- Module 0 - Introduction to Cloud Computing (lecture)
- Module 1 - Introduction to RNA sequencing and analysis (lecture)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 3 - Expression and Differential Expression (lecture)
- Module 4 - Isoform Discovery and Alternate Expression (lecture)
CSHL-CBW-NYGC High-throughput Biology: From Sequence to Networks (April 29-30, 2015. New York, NY, USA)
Organized by New York Genome Center (NYGC), Canadian Bioinformatics Workshops (CSHL), and Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Module 1 - Introduction to RNA sequencing (lecture)
- Module 1 - Introduction to RNA sequencing (tutorial)
- Module 2 - RNA-seq alignment and visualization (lecture)
- Module 2 - RNA-seq alignment and visualization (tutorial)
- Module 3 - Expression and differential expression (lecture)
- Module 3 - Expression and differential expression (tutorial)
- Module 4 - Isoform discovery and alternative expression (lecture)
- Module 4 - Isoform discovery and alternative expression (tutorial)
CSHL Advanced Sequencing Technologies and Applications (November 11-23, 2014. Cold Spring Harbor, NY, USA)
Organized by Cold Spring Harbor Laboratory (CSHL) - Course Site
Presentations:
- Module 1 - Introduction to cloud computing (lecture/tutorial)
- Module 2 - Introduction to RNA sequencing (lecture)
- Module 2 - Introduction to RNA sequencing (tutorial)
- Module 3 - RNA-seq alignment and visualization (lecture)
- Module 3 - RNA-seq alignment and visualization (tutorial)
- Module 4 - Expression and differential expression (lecture)
- Module 4 - Expression and differential expression (tutorial)
- Module 5 - Isoform discovery and alternative expression (lecture)
- Module 5 - Isoform discovery and alternative expression (tutorial)
- Introduction to Genome Analysis Platforms
CBW Informatics for RNA-seq analysis (June 19-20, 2014. Vancouver, BC, Canada)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
CBW Informatics for RNA-seq analysis (June 2-3, 2014. Montreal, QC, Canada)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
CBW Informatics for RNA-seq analysis (June 3-4, 2013. Toronto, ON, Canada)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site
CBW Informatics on High Throughput Sequencing Data (June 11-12, 2012. Toronto, ON, Canada)
Organized by Canadian Bioinformatics Workshops (CBW) - Course Site