Our BYU CS 704R class will discuss the following papers (to be updated throughout the semester):
| Date | Paper | Presenter |
|---|---|---|
| Wed Jan 7 | Aligning gene trees with family trees. Andrii Serdiuk, Claudia Moreau, Jean Mathieu et al. bioRxiv 2025. | Amy |
| Mon Jan 12 | Ancestral haplotype reconstruction in endogamous populations using identity-by-descent. Kelly Finke, Michael Kourakos, Gabriela Brown, et al. PLOS Computational Biology 2021. | Rebekah |
| Wed Jan 14 | Effects of ancestry, agriculture, and lactase persistence on the stature of prehistoric Europeans. Samantha L. Cox, Kaeli Kaymak-Loveless, Carson Shin, et al. Current Biology 2025. | Chahyun |
| Mon Jan 19 | No class: Martin Luther King Day | N/A |
| Wed Jan 21 | Polygenic prediction of educational attainment within and between families from genome-wide association analyses in 3 million individuals. Aysu Okbay, Yeda Wu, Nancy Wang, et al. Nature Genetics 2022. | Wesley |
| Mon Jan 26 | Estimating the size of long tandem repeat expansions from short reads with ScatTR. Rashid Al-Abri and Gamze Gürsoy. Genome Research 2025. | Jason |
| Wed Jan 28 | Advances in haplotype phasing and genotype imputation. Quan Sun and Yun Li. Nature Reviews Genetics 2025. | Kepler |
| Mon Feb 2 | Nucleotide Transformer: building and evaluating robust foundation models for human genomics. Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza-Revilla, et al. Nature Methods 2024. | Jeff |
| Wed Feb 4 | Sequence context and methylation interact to shape germline mutation rate variation at CpG sites. Sheel Chandra and Ziyue Gao. bioRxiv 2025. | Parker |
| Mon Feb 9 | Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations. Michael Elgart, Genevieve Lyons, Santiago Romero-Brufau, et al. Communications Biology 2022. | Seth |
| Wed Feb 11 | A forest is more than its trees: haplotypes and ancestral recombination graphs. Halley Fritze, Nathaniel Pope, Jerome Kelleher, Peter Ralph. Genetics 2026. | Rebekah |
| Tue Feb 17 | Modeling the European Neolithic expansion suggests predominant within-group mating and limited cultural transmission. Troy M. LaPolice, Matthew P. Williams, Christian D. Huber. Nature Communications 2025. | Gilyeon |
| Wed Feb 18 | Mapping genomic loci implicates genes and synaptic biology in schizophrenia. Vassily Trubetskoy, Antonio F. Pardiñas, Ting Qi, et al. Nature 2022. | Wesley |
| Mon Feb 23 | Genome-wide association study of long COVID. Vilma Lammi, Tomoko Nakanishi, Samuel E. Jones, et al. Nature Genetics 2025. |
Jason |
| Wed Feb 25 | Parental haplotypes reconstruction in up to 440,209 individuals reveals recent assortative mating dynamics. Robin J. Hofmeister, Davide Marnetto, Théo Cavinato, et al. bioRxiv 2025. | Seth |
| Mon Mar 2 | A draft human pangenome reference. Wen-Wei Liao, Mobin Asri, Jana Ebler, et al. Nature 2023. | Kepler |
| Wed Mar 4 | Revisiting the lineages of the Cohanim using data from next-generation sequencing. J. Lipson, S.G. Bohrer, S. Cohen-Weinstein, et al. bioRxiv 2025. | Parker |
| Mon Mar 9 | Shared Ancestors and the Birthday Problem. Lily Agranat-Tamira, Kennedy D. Agwamba, Jazlyn A. Mooney, Noah A. Rosenberg. The American Statistician 2026. | Chahyun |
| Wed Mar 11 | Complex Trait Prediction from Genome Data: Contrasting EBV in Livestock to PRS in Humans: Genomic Prediction. Naomi R Wray, Kathryn E Kemper, Benjamin J Hayes, Michael E Goddard, Peter M Visscher. Genetics 2019. | Amy |
| Mon Mar 16 | Parent-of-origin effects on complex traits in up to 236,781 individuals. Robin J. Hofmeister, Théo Cavinato, Roya Karimi, et al. Nature 2025. | Jeff |
| Wed Mar 18 | Insights into human genetic variation and population history from 929 diverse genomes. Anders Bergström, Shane A. McCarthy, Ruoyun Hui, et al. Science 2020. | Gilyeon |
| Mon Mar 23 | Reconstructing parent genomes using siblings and other relatives. Ying Qiao, Ethan M. Jewett, Kimberly F. McManus, William A. Freyman, et al. bioRxiv 2024. | Seth |
| Wed Mar 25 | No class: canceled | N/A |
| Mon Mar 30 | Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin analyses. Cole M. Williams, Jared O’Connell, Ethan Jewett, et al. HGG Adv 2025. | Rebekah |
| Wed Apr 1 | Multi-ancestry genome-wide association study of major depression aids locus discovery, fine mapping, gene prioritization and causal inference. Xiangrui Meng, Georgina Navoly, Olga Giannakopoulou, et al. Nature Genetics 2024. | Wesley |
| Mon Apr 6 | Surviving the Squeeze: Genomic Analysis of a Successful Invasion by European Common Wall Lizards (Podarcis muralis) in North America (Ohio, USA). Emily R. Bode, Andrew J. Mason, Peri E. Bolton, et al. Molecular Ecology 2026. | Jason |
| Wed Apr 8 | Sequence diversity lost in early pregnancy. Gudny A. Arnadottir, Hakon Jonsson, Tanja Schlaikjær Hartwig, et al. Nature 2025. | Kepler |
| Mon Apr 13 | Adaptive admixture at ACKR1, the Duffy blood group locus, may have shaped Plasmodium vivax prevalence in Oman. Paige E. Haffener, Arwa Z. Al-Riyami, Shoaib Al-Zadjali, et al. AJHG 2026. | Gilyeon |
| Wed Apr 15 | Identity inference of genomic data using long-range familial searches. Yaniv Erlich, Tal Shor, Itsik Pe’er, and Shai Carmi, Science 2018. | Amy |
Approach to presenting papers
See this slide for how to structure your presentation. If you’d like more specific guidance, contact Amy Williams to find a time to discuss your presentation before class.
Potential papers to discuss
- Family-GWAS reveals effects of environment and mating on genetic associations. Tammy Tan, Hariharan Jayashankar, Junming Guan, et al. medRxiv 2026.
- Fine-scale structure of a whole regional population through genetics and genealogies. Gilles-Philippe Morin, Claudia Moreau, Amadou Barry, Simon L. Girard. bioRxiv 2025.
- Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes. Jonathan Judd, Jeffrey P. Spence, Nikhil Milind, et al. bioRxiv 2025.
- A family portrait of the genomic factors shaping tandem repeat mutagenesis. Thomas A. Sasani, Michael E. Goldberg, Akshay K. Avvaru, et al. bioRxiv 2026.
- Modeling the length distribution of gene conversion tracts in humans from the UK Biobank sequence data. Nobuaki Masaki and Sharon R. Browning. PLOS Genetics 2025.
- Estimating gene conversion rates from population data using multi-individual identity by descent. Sharon R. Browning, Brian L. Browning. Am J Hum Genet 2025.
- A Transparent and Generalizable Deep Learning Framework for Genomic Ancestry Prediction. Camille Rochefort-Boulanger, Matthew Scicluna, Raphaël Poujol, et al. bioRxiv 2025.
- Bayesian inference of population structure using identity-by-descent-based stochastic block models. Steven J. Micheletti, Katarzyna Bryc, Samantha G. Ancona Esselmann, et al. bioRxiv 2025.
- FLARE2: local ancestry inference with poorly-matched reference panels. Sharon R Browning, Seth D Temple, Brian L Browning. bioRxiv 2025.
- Improving Local Ancestry Inference through Neural Networks. Jazeps Medina Tretmanis, María C. Ávila-Arcos, Flora Jay, Emilia Huerta-Sanchez. bioRxiv 2026.
- Tracing the origin of Finnish gelsolin amyloidosis using haplotype sharing trees. Osma S. Rautila, Sari Atula, Tuuli Mustonen, et al. bioRxiv 2026.
- The shifting dynamics of ancestry and culture at a post-Roman crossroads. Deven N. Vyas, István Koncz, Tina Milavec, et al. bioRxiv 2025.
- Ancient DNA sheds light on the mating strategies and genetic identity of Han nobles during the Northern and Southern Dynasties. Youyang Qu, Zhanrui Zhao, Chao Ning, et al. Archaeological and Anthropological Sciences 2026.