Quantitative Biology JC - kr-colab/colab_wiki GitHub Wiki

Spring 2024

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)

Winter 2023

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

Fall 2023

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 🍕 🍻

Spring 2023

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 🍕 🍕 🍕

ProtVec?

Winter 2023

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)

Fall 2022

"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

Spring 2022

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

Winter 2022

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:

Fall 2021

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:

Spring 2021

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:

Winter 2021

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

Fall 2020

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?

Summer 2020

Readings on coevolution. Monday at 12pm (PDT) via Zoom.

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)
July 21 Gene-for-gene coevolution between plants and parasites. JN Thompson & JJ Burdon. 1992 (Andy)
July 28 Molecular phylogenies of figs and their pollinator wasps. 1996 (Jeff)
August 11 Statistical properties of polymorphism in host—parasite genetics. SA Frank. 1996 (Andy)
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)
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)
September 8 When is correlation coevolution? SL Nuismer et al. 2010 (Clara)
September 15 Rules of Engagement: Molecular Insights from Host-Virus Arms Races 2012 (Gabby, Victoria)
September 22 The evolution within us 2015 (Saurabh)
September 29 A phylogenetic comparative method for evaluating trait coevolution across two phylogenies for sets of interacting species. 2017 -- (Vince, Matt)
October 6 Host-pathogen coevolution increases genetic variation in susceptibility to infection. 2019 -- Murillo

Spring 2020

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

Winter 2020

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)

Fall 2019

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: