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Quantitative Biology JC
- 10/1: Organization
- 10/8: chapter 3 LLM book, Ananya
- 10/15: chapter 4 LLM, Jordan
- 10/22: chapter 5 LLM, Andy
- 10/29: Kevin Msprimeprime
- 11/5: George monosemanticity
- 11/12: Thomas Overview of Deep Gen Models in Functional and Evolutionary Genomics
- 11/19: Angel: Benegas et al. 2024 arXiv Genomic Language Models: Opportunities and Challenges
- 11/26: Ben A guide to machine learning for biologists
- 12/3: Nate GPN-MSA
- 12/10:
- 4/2: ORGANIZATION
- 4/9: Scoot :: Cousins - Deep human population structure (https://www.biorxiv.org/content/10.1101/2024.03.24.586479v1)
- 4/16: Angel :: Groh - Black walnut (https://www.biorxiv.org/content/10.1101/2023.12.23.573205v2)
- 4/23: Nate :: Shchur - Coalescence rates and migration (https://www.biorxiv.org/content/10.1101/2022.06.17.496540v1.full)
- 4/30: Jiseon :: Grundler - Geographic human history (https://www.biorxiv.org/content/10.1101/2024.03.27.586858v1)
- 5/7: Jordon :: Speidel - F-stats on trees (https://www.biorxiv.org/content/10.1101/2024.03.15.585102v1)
- 5/14: Andy :: Riley - GAN for outlier detection (https://www.biorxiv.org/content/10.1101/2023.03.07.531546v2)
- 5/21: ???? :: Terhorst - Fast PSMC score function (https://www.biorxiv.org/content/10.1101/2024.03.25.586640v1)
- 5/28: Scoot :: Odaro - mosquito DDT resistance knockdown (https://www.biorxiv.org/content/10.1101/2024.03.13.584754v1)
- ?/??: ???? :: Huang - IBD inference from treeseqs (https://www.biorxiv.org/content/10.1101/2024.03.07.583855v1)
Recent popgen/ARG methods and theory
- 1/23: M'NateARGWeaver
- 1/30: Jiseon ARGNeedle
- 2/6: Jordan R. Sparse models of LD
- 2/13: Angel CLUES2
- 2/20: Murillo Genealogical likelihood
- 2/27: Scaling DTWF likelihoods to Biobank
- 3/5: ???
- 3/12: Andy Tree sequences as a general-purpose tool for population genetic inference
Protein structure prediction / function / methodologies / ramifications? 💪
- 9/26 Organizational
- 10/3 Jordan R. AlphaFold
- 10/10 Bruce FoldSeek
- 10/17 Nate FoldTree Not fast or accurate!
- 10/24 Clara PrimateAI -fold
- 10/31 Chris PrimateAI-3D!!
- 11/7 Andy LINSIGHT
- 11/14 Angel Deep mutation scanning
- 11/21 Andy GPN-MSA
- 11/28 PIZZA PARTY 🍕 🍻
- 4/11 Jordan A. Deep Learning Based Text Classification: A Comprehensive Review
- 4/18 Chris Domain-adaptive neural networks improve supervised machine learning based on simulated population genetic data
- 4/25 Andy Attention Is All You Need
- 5/2 Improving Language Understanding by Generative Pre-Training
- 5/9 Murillo Temporal Graph Networks for Deep Learning on Dynamic Graphs
- 5/16 Jordan R. DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- 5/30 Silas DNA language models are powerful zero-shot predictors of non-coding variant effects
- 6/6 Michelle Yeoh The frontier of simulation-based inference
- pizza party 🍕 🍕 🍕
Read some awesome popgen together
- 1/10: Planning
- 1/17: Andy Spatial coalescent connectivity through multi-generation dispersal modelling predicts gene flow across marine phyla
- 1/24: Nate Modeling the spatiotemporal spread of beneficial alleles using ancient genomes
- 1/31: Peter IS THE POPULATION SIZE OF A SPECIES RELEVANT TO ITS EVOLUTION?
- 2/7: Jordan Simple scaling laws control the genetic architectures of human complex traits
- 2/14: Chris Automatic inference of demographic parameters using generative adversarial networks
- 2/21: Saurabh
- 2/28: Silas Ultra-fast genome-wide inference of pairwise coalescence times
( beware of probgen around now 🚨🚨 )
- 3/7: Titas Population analysis of Legionella pneumophila reveals a basis for resistance to complement mediated killing
- 3/14: Jiseon [On convolutional neural networks for selection inference: revealing the lurking role of preprocessing, and the surprising effectiveness of summary statistics] (https://www.biorxiv.org/content/10.1101/2023.02.26.530156v1.full.pdf)
"Machine Learning with pytorch and scikit-learn" https://github.com/rasbt/machine-learning-book
PDF can be downloaded from slack here
- 9/27: organization
- 10/4: Andy Chp. 11
- 10/11: Jordan R. Chp. 12
- 10/18: Matt Chp. 13
- 10/25: Jordan A. Chp. 14
- 11/1: ??? Chp. 15
- 11/8: Silas Chp. 16
- 11/15: Chp. 17
- 11/22: Chris Chp. 18
- 11/29: Nate Chp. 19
- 12/6: pizza party
John Maynard-Smith's "Evolutionary Genetics, 2nd ed"
- March 29: organizational
- April 5: Chapter 4, Murillo
- April 12: Chapter 5, Aidan
- April 19: Chapter 7, Matt
- April 26: Chapter 8, Saurabh
- May 3: Chapter 9, Gilia
- May 10: Chapter 10, Clara
- May 17: Chapter 11, Andy
- May 24: Chapter 12, Chris
- May 31: Chapter 13, Anastasia
- January 4: Planning, Goal: Pick your favorite journal and select a recently published mathy paper
- January 11: The population genetics of collateral resistance and sensitivity -- Victoria
- January 18: Diffusion approximations in population genetics and the rate of Muller’s ratchet -- Matt
- January 25: Mutation saturation for fitness effects at human CpG sites -- Andy
- February 1: Contemporary Ne estimation using temporally spaced data with linked loci -- Chris
- February 8: Assortative mating and epistatic mating-trait architecture induce complex movement of the crow hybrid zon -- Aidan
- February 15: The estimates of effective population size based on linkage disequilibrium are virtually unaffected by natural selection -- Anastasia
- February 22: Properties and unbiased estimation of F- and D-statistics in samples containing related and inbred individuals -- Saurabh
- March 1: G = E: What GWAS Can Tell Us about the Environment -- Murillo
- March 8:
- September 28: Planning
- October 5: Deep Unsupervised Learning using Nonequilibrium Thermodynamics-- Matt
- October 12: Traffic Graph Convolutional Recurrent Neural Network: A Deep Learning Framework for Network-Scale Traffic Learning and Forecasting-- Andy
- October 19: Diffusion Models Beat GANs on Image Synthesis
- October 26: Attention is All You Need-- Saurabh
- November 2: Probabilistic Deep Learning with Probabilistic Neural Networks and Deep Probabilistic Models -- Anastasia
- November 9: The Specious Art of Single-Cell-- Victoria
- November 16: Disease variant prediction with deep generative models of evolutionary data-- Vince
- November 23: A spatially aware likelihood test to detect sweeps from haplotype distributions-- Chris
- November 30:
Spatial popgen:
- April 6: Bradburd & Ralph review, "It's about time"
- April 13: Slatkin 1973, Gene flow and selection in a cline - Murillo
- April 20: Barton 1979, The dynamics of hybrid zones - Matt
- April 27: Wilkins 2002, Coalescent in a finite linear population - Vince
- May 4: Pless et al 2021, Landscape connectivity of Aedes aegypti - Jeff
- May 11: Champer et al 2021, Gene drive in continuous space - Gilia
- May 18: Marcus et al 2020, EEMS update - chris
- May 25: Slatkin 1978, Spatial patterns of polygenic characters - Peter
- June 1:
- Jan 12 9 Artificial Selection - Matt
- Jan 19 10 Natural Selection - Gabby Whole lab?
- Jan 26 11 Genomic Analysis of Quantitative Traits - Victoria Whole lab?
- Feb 16th - Wang et al "Signatures of mito-nuclear coevolution in a warbler species complex" https://www.biorxiv.org/content/10.1101/2020.04.06.028506v2
- Feb 23rd - Zaidi et al "Demographic history mediates the effect of stratification on polygenic scores" https://elifesciences.org/articles/61548
- Mar 2 - Collins et al "Extending Approximate Bayesian Computation with Supervised Machine Learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest" https://www.authorea.com/users/343084/articles/469772-extending-approximate-bayesian-computation-with-supervised-machine-learning-to-infer-demographic-history-from-genetic-polymorphisms-using-diyabc-random-forest (Jeff)
- Mar 9 - Soni et al "A new test suggests that balancing selection maintains hundreds of non-synonymous polymorphisms in the human genome" https://www.biorxiv.org/content/10.1101/2021.02.08.430226v2
- Oct 12 -- The Genetics Training Grant asks us to do the following RCR Module.
Module 4: Sample Size, Outliers, and Exclusion Criteria
Part 1: NIH Module https://www.nih.gov/research-training/rigor-reproducibility/training NIH Rigor and Reproducibility Training Modules Module 4: Sample Size, Outliers, and Exclusion Criteria Have students watch the video outside of class: https://www.youtube.com/watch?v=Pc0h-GOcBLE and read over the discussion questions.
Discuss the questions in JC.
Part 2:
https://elifesciences.org/articles/56626 Science Forum: Addressing selective reporting of experiments through predefined exclusion criteria Have students read this paper before JC and come prepared to talk about how they might use pre-exclusion criteria to determine under which conditions outliers should be rejected from an experiment that they ran or plan to run.
Quantitative Genetics Caballero book Chapters:
- Oct 19 1&2 Continuous Variation, Forces of Change in the Allele Frequencies - Saurabh
- Oct 26 3 Components of Phenotypic Values and Variances - Murillo
- Nov 2 4 Inbreeding and Coancestry - Aidan
- Nov 9 5 Effective Population Size - Jeff
- Nov 16 6 Estimation of Genetic Values, Variances and Covariances - Clara
- Nov 23 7 Mutation - Vince
- Nov 30 8 Consequences of Inbreeding - Peter
- Dec 14 9 Artificial Selection - Matt
- Dec 21 10 Natural Selection - Gabby Whole lab?
- Dec 28 11 Genomic Analysis of Quantitative Traits - Victoria Whole lab?
Readings on coevolution. Monday at 12pm (PDT) via Zoom.
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July 14: A Mathematical Model for the Co-Evolution of Obligate Parasites and Their Hosts. CH Mode. 1958. (Matt) and When is it coevolution?. DH Janzen. 1980 (CJ)
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July 21 Gene-for-gene coevolution between plants and parasites. JN Thompson & JJ Burdon. 1992 (Andy)
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July 28 Molecular phylogenies of figs and their pollinator wasps. 1996 (Jeff)
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August 11 Statistical properties of polymorphism in host—parasite genetics. SA Frank. 1996 (Andy)
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August 25 Parasite local adaptation: Red Queen versus Suicide King. MF Dybdahl & A Storfer. 2003 (Victoria) and Polygenic traits and parasite local adaptation. BJ Ridenhour & SL Nuismer. 2007 (Anastasia)
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September 1 Multiple reciprocal adaptations and rapid genetic change upon experimental coevolution of an animal host and its microbial parasite. RD Schulte et al. 2010 (Peter)
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September 8 When is correlation coevolution? SL Nuismer et al. 2010 (Clara)
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September 15 Rules of Engagement: Molecular Insights from Host-Virus Arms Races 2012 (Gabby, Victoria)
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September 22 The evolution within us 2015 (Saurabh)
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September 29 A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species. 2017 -- (Vince, Matt)
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October 6 Host-pathogen coevolution increases genetic variation in susceptibility to infection. 2019 -- Murillo
Readings centering on polygenic adaptation. Tuesdays at 3pm via Zooooooom
- 4/7 LeCorre and Kremer (Vince)
- 4/14 Sella and Barton Review (Jeff)
- 4/21 Calfee et al (Murillo)
- 4/28 Jain and Stephan (Matt)
- 5/5 Sanjak et al
- 5/12 Thornton (Saurabh)
- 5/26 Wray et al (CJ)
- 6/2 Chevin and Hospital (Vince)
- 6/9 Rotation talks.
- 6/16 Rosas et al
- 6/23 Hollinger et al
Meetings on Tuesdays from 3:00 to 4:00pm in 301 Pacific.
- 01/21 - The GTEx Consortium atlas of genetic regulatory effects across human tissues (Jeff)
- 01/28 - Bayesian analysis of genetic association across tree-structured routine healthcare data in the UK Biobank (Peter)
- 02/04 - A Comprehensive Survey on Graph Neural Networks (Andy)
- 02/11 - Solving inverse-PDE problems with physics-aware neural networks (Matt)
- 02/18 - Causal inference (Mendelian-Randomization) (Vince)
- 02/25 - Practice talk (CJ)
- 03/02 - Causal Interpretations of Black-Box Models (Murillo)
Meetings on Tuesdays from 1:30 to 2:30pm in 301 Pacific.
- 10/1/19: Organizational (L: Kern)
- 10/8/19: The Neural Network Approach to Inverse Problems in Differential Equations (L: Matt)
- 10/15/19: Hidden Markov Models (L: Adrion)
- 10/22/19: CoalHMM (L: Battey)
- 10/29/19: SMC (L: Anastasia)
- 11/5/19: ARGweaver (L: Murillo)
- 11/12/19: Weight Agnostic Neural Networks (L: Kern)
- 11/19/10: Learning the properties of adaptive regions with functional data analysis (L: Matt)
- 11/26/19: no class
- 12/3/19: Adaptation in structured populations and fuzzy boundaries between hard and soft sweeps (L: Andy)
- 12/10/19: