Spring 2021 Schedule
- Week 1: Hallmarks of Cancer
- Paper: Hallmarks of Cancer: The Next Generation (Hanahan & Weinberg, Cell 2011). [Publisher Link]
- Week 2: How to Read a Paper
- Paper: Pan-Cancer Analysis of Whole Genomes (PCAWG Consortium, Nature 2020). [Publisher Link]
- Week 3: Group Discussion
- Paper: The repertoire of mutational signatures in human cancer (Alexandrov et al., Nature 2020). [Publisher Link]
- Week 4: Group Discussion
- Paper: Patterns of somatic structural variation in human cancer genomes (Li et al., Nature 2020). [Publisher Link]
- Week 5: Group Discussion
- Paper: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (Rheinbay et al., Nature 2020). [Publisher Link]
- Week 6: Cancer in the News Milestone
- Week 7: No Class (Mid-Term Break)
- Week 8: Group Discussion
- Paper: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (Cortés-Ciriano et al., Nature 2020). [Publisher Link]
- Week 9: Group Discussion
- Paper: Pathway and network analysis of more than 2500 whole cancer genomes (Reyna et al., Nature 2020). [Publisher Link]
- Week 10: Group Discussion
- Paper: The evolutionary history of 2,658 cancers (Gerstung et al., Nature 2020). [Publisher Link]
- Week 11: Cancer in the News Milestone
- No Class -- Spring Break
- Week 12: TBD
- Week 13: TBD
Spring 2018 Schedule
- Week 1: Hallmarks of Cancer
- Paper: Hallmarks of Cancer: The Next Generation (Hanahan & Weinberg, 2011). [Publisher Link]
- Week 2: Theme: Driver Mutations
- Paper: Somatic mutation in cancer and normal cells (Martincorena and Campbell, 2015). [Publisher Link] [Library Link]
- See also Figures 1 & 2 from Key Principles and Clinical Applications of "Next-Generation" DNA Sequencing (Rizzo & Buck, 2012). [Publisher Link]
- Summary due Monday Feb 5 for students not presenting in Weeks 3 and 4
- Week 3: Technical Presentation
- Discussion Leaders: Gwen & Krishna
- Paper: MuSiC: Identifying mutational significance in cancer genomes (Dees et al., 2012). [Publisher Link]
- Google Form: Week 3 Discussion (complete by Tuesday night; requires Reed email address)
- Week 4: Technical Presentation
- Discussion Leaders: Eli & Zia
- Computational Paper: Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome (Quinlan et al., 2010). [Publisher Link]
- This paper presents HYDRA, the core method used by the application paper.
- SV Identification with HYDRA (Results)
- Panels A-C from Figure 1
- Structural Variation Discovery with HYDRA (Methods)
- Application Paper: Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms (Malhotra et al., 2013). [Publisher Link]
- Google Form: Week 4 Discussion (complete by Tuesday night; requires Reed email address)
- Week 5: No Class, Anna at SIGCSE
- Optional: Re-submit the first summary for a bit of additional credit
- Week 6: Theme: Dysregulated Signaling
- Networks Review Paper: Interactome Networks and Human Disease. (Vidal, Cusick & Barabasi, 2011). [Publisher Link]
- Computational Review Paper: Pathway and Network Analysis of Cancer Genomes. (Creixell et. al, 2015). [Publisher Link]
- Summary due on Friday Mar 2 for students not presenting in Weeks 7 and 8
- Week 7: Technical Presentation
- Discussion Leaders: Ava & Dorothy
- Paper: Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes (Leiserson et al., 2014). [Publisher Link]
- Google Form: Week 7 Discussion (complete by Tuesday night; requires Reed email address)
- Spring Break!
- Optional: Re-submit the second summary for a bit of additional credit by Mon 3/19
- Week 8: Technical Presentation
- Discussion Leaders: Cam & Petra
- Paper: NetSig: network-based discovery from cancer genomes (Horn et al., 2018). [Publisher Link]
- Google Form: Week 8 Discussion (complete by Tuesday night; requires Reed email address)
- Week 9: Theme: Clonal Reconstruction
- Review Paper 1: Evolution of the cancer genome (Yates & Campbell, 2012). [Library Link]
- Review Paper 2: Tumor Evolutionary Principles: How Intratumor Heterogeneity Influences Cancer Treatment and Outcome (Venkatesan & Swanson, 2016). [PDF] [EBook]
- A more recent review (optional): The evolution of tumour phylogenetics: principles and practice (Schwartz & Schaafer, 2017). [Library Link]
- Summary due on Friday Mar 30 for students not presenting in Weeks 10 and 11
- Week 10: Technical Presentation
- Discussion Leaders: Charles & Hayden
- Computational Paper: Estimation of rearrangement phylogeny for cancer genomes (Greenman et al., 2012). [Publisher Link]
- Application Paper: The Life History of 21 Breast Cancers (Nik-Zainal et al., 2012). [Publisher Link]
- Google Form: Week 10 Discussion (complete by Tuesday night; requires Reed email address)
- Week 11: Theme: Single Cell Sequencing
- Review Paper 1: Single-cell sequencing-based technologies will revolutionize whole-organism science (Shapiro et al., 2013). [Publisher Link]
- Review Paper 2: Unravelling biology and shifting paradigms in cancer with single-cell sequencing (Basian et al., 2017). [PDF on Google Drive; bio431 students have access]
- The final summary is due for all students on the last Wednesday of the semester.
- Week 12: The Current State of the Field and Student Evaluations
- No paper assigned; bring your laptop. [Google Document Link]
- Week 13: Final Wrap-Up
- Final Summary (one page) and Reflection Essay (one page max) due on Wednesday, April 25 before seminar.
- For the Reflection Essay, write about why computational methods are useful for studying cancer. What are the limits of such approaches? In the long term, will we be able to completely understand the mechanisms that underlie cancer? Why or why not?
Spring 2017 Schedule (see Moodle for details)
If you are not a discussion leader, fill out the Discussion Participant Form by noon the day of the seminar.
- Week 1: Overview (Anna)
- Slides posted on Moodle.
- Paper (for background):Somatic mutation in cancer and normal cells (Martincorena and Campbell, 2015). Publisher Link.
- Week 2: Hallmarks of Cancer
- Paper: Hallmarks of Cancer: The Next Generation (Hanahan & Weinberg, 2011). Publisher Link.
- For Discussion: Be prepared to summarize each hallmark. We will select three hallmarks to investigate over the course of the semester.
- Week 3: Hallmark #1: Genome Instability
- Discussion Leader: Karl
- Paper: Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms (Malthotra et al., 2013). Publisher Link.
- Week 4: Biology Seminar Practice Talk (Ibrahim)
- Title: Disease Outcome Analysis via Dynamic Imaging and Multi-Platform Molecular Data Integration
- Abstract: A "disease outcome" can refer to a behavior, event, state, or condition for some aspect of a patient's health status. For example, a behavior may correspond to drug efficacy and treatment responsiveness, while an event may correspond to patient survival. In tumors, one way to evaluate behavior is by monitoring tumor angiogenesis (formation of new blood vessels necessary for tumor to nourish itself and sustain its existence) and its vasculature permeability through dynamic imaging, in which a series of images at different time instances are acquired for a specific tumor site after injecting a contrast agent to examine tumor vasculature patterns based on accumulation and washout of the contrast agent. Observing this activity over time can reflect the tumor drug responsiveness and efficacy of the treatment plan. As for evaluating patient survival, accurate estimation of patient prognosis fosters the new era of personalized medicine through health planning, treatment strategies, and drugs customized to the individual patient rather than being chosen based on their average effect on broader population cohorts. Incorporating the underlying biology in designing the survival prediction models can provide biologically relevant insights rather than relying only on the statistical significance of the outputs. In this talk, I present my previous work on characterizing tumor angiogenesis and on designing biologically informed and integrative approaches for survival analysis by considering the integration of a set of interacting multi-platform molecular data and the underlying biology.
- Week 5: Hallmark #1: Genome Instability
- Discussion leader: Vikram
- Computational Paper: Mutational heterogeneity in cancer and the search for new cancer-associated genes. (Lawrence et al., 2013). Reed Library Link.
- Application Paper: Discovery and saturation analysis of cancer genes across 21 tumor types. (Lawrence et al, 2014). Reed Library Link.
- Week 6: Hallmark #2: Activating Mutation and Metastasis
- Discussion leader: Danny
- Paper: Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches (Byrne et al., 2016). Publisher Link.
- Week 7: No Class - Anna is at SIGCSE
- Spring Break!
- Week 8: Hallmark #2: Activating Mutation and Metastasis
- Discussion leader: Karl
- Review Paper: Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks (Samaga and Klamt, 2012). Publisher Link.
- Application Paper: A MAPK-Driven Feedback Loop Suppresses Rac Activity to Promote RhoA-Driven Cancer Cell Invasion (Hetmanski et al., 2016). Publisher Link.
- Week 9: Hallmark #3: Evading Immune Destruction
- Finish Discussion from last week.
- Begin Discussion led by Vikram (no need to fill out Participant Discussion form)
- Review Paper: Computational genomics tools for dissecting tumour–immune cell interactions (Hackl et a., 2016). Publisher Link.
- Week 10: Hallmark #3: Evading Immune Destruction
- Discussion leader: Vikram
- Paper: Gapped sequence alignment using artificial neural networks: application to the MHC class I system (Andreatta and Nielson, 2016). Publisher Link.
- Week 11: Students Talking about Research (STAR) Practice Talk (Karl)
- Week 12: Quantitative Image Analysis
- Discussion leader: Danny
- Paper: Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling (Yuan et al., 2012). Publisher Link.
- Week 13: Final Wrap-Up and Student Evaluations
Fall 2015 Schedule (see Moodle for details)
- Week 1: Overview
- Presenter: Anna
- Summary Papers: (use these to guide your interests while selecting papers for the semester)
- Computational approaches to identify functional genetic variants in cancer genomes (Creixell et al., 2013). Ereserves.
- Pathway and network analysis of cancer genomes (Gonzalez-Perez et al., 2015). Ereserves.
- Week 2: Labor Day - No Class
- Week 3: Cancer Biology Crash Course
- Presenter: Anna
- Reading: Hallmarks of Cancer: The Next Generation (Hanahan & Weinberg, 2011). Ereserves.
- Focus: Summarize each hallmark/characteristic in Figures 1 and 3 in one or two sentences. Write them down and bring them to seminar.
- Week 4: Determining Mutations (Exomes)
- Presenter: Nick
- Paper: Mutational heterogeneity in cancer and the search for new cancer-associated genes (Lawrence et al., 2013). Publisher Link.
- Look over Differential relationship of DNA replication timing to different forms of human mutation and variation (Koren et al., 2012). Publisher Link.
- Week 5: Determining Structural Variants
- Presenter: Heather
- Paper: Gene expression profiling predicts clinical outcome of breast cancer (Van 't Veer et al., 2002). Publisher Link.
- Week 6: Gene Expression Patterns
- Presenter: Philippe
- Paper: Application of artificial neural networks to link genetic and environmental factors to DNA methylation in colorectal cancer (Coppedè et al., 2015) eReserves.
- Week 7: Gene Set Enrichment
- Presenter: Fenner
- Paper: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles (Subgramanian et al., 2005). Publisher Link.
- Week 8: Fall Break - No Class
- Week 9: Mututal Exclusivity
- Presenter: Joewie
- Paper: De novo discovery of mutated driver pathways in cancer (Vandin, Upfal, and Raphael 2012). Publisher Link.
- Week 10: Network Characteristics
- Presenter: Nicole
- Paper: Dynamic modularity in protein interaction networks predicts breast cancer outcome (Taylor et al., 2009). Publisher Link.
- Week 11: Subnetwork Discovery
- Presenter: Barney
- Paper: Sharing information to reconstruct patient-specific pathways in heterogeneous diseases (Gitter et al., 2014). Publisher Link.
- Refer to figures 1 and 3 in this paper: Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem (Tuncbag et al., 2013). Publisher Link.
- Week 12: Network-Based Modeling
- Presenter: Meghan
- Paper: Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes (Leiserson et al., 2014). Publisher Link.
- Week 13: Network-Based Modeling
- Presenter: Kimmie
- Paper: DawnRank: discovering personalized driver genes in cancer (Hou and Ma, 2014). Publisher Link.
- Week 14: PathLinker
- Anna will lead discussion about a manuscript under review.
- Week 15: Final Discussion and TieDIE
- Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE) (Paull et al., 2013). Publisher Link.