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Simulation of gene family histories

Maribel Hernandez-Rosales, Nicolas Wieseke, Marc Hellmuth, Peter F Stadler
2014 BMC Bioinformatics  
A small example of a gene family history generated by our simulation is shown in Fig. 1 . We also show the gene tree generated from the gene family history embedded in the species tree.  ...  The simulation of gene family histories starts with the generation of species trees. Within these rooted bifurcating trees the nodes represent species and edges their relation.  ... 
doi:10.1186/1471-2105-15-s3-a8 pmcid:PMC4072294 fatcat:onulbfrerraobkper2khazxxkm

Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution

László G. Nagy, Robert Riley, Philip J. Bergmann, Krisztina Krizsán, Francis M. Martin, Igor V. Grigoriev, Dan Cullen, David S. Hibbett
2016 Molecular biology and evolution  
Here, we use phylogenomic comparative methods, which we validate through simulations, to identify shifts in gene family diversification rates that are correlated with evolution of WR, using data from 62  ...  gene families that have no functional annotation.  ...  Acknowledgments We thank Dimitrios Floudas for helpful discussions on wooddecay related gene families and S andor Kocsubé for his help with designing the figures.  ... 
doi:10.1093/molbev/msw238 pmid:27834665 fatcat:h6rv7wn7fjhjfpyzoc7ewxgwta

Methods for Assessing Familial Aggregation: Family History Measures and Confounding in the Standard Cohort, Reconstructed Cohort and Case-Control Designs

Regina Zimmerman, Deb K. Pal, Adrienne Tin, Habibul Ahsan, David A. Greenberg
2009 Human Heredity  
In addition, we test if the definition of family history affects the accuracy of results obtained from either design. We use simulated data, which allows us to know the true data origin.  ...  Neither family size nor age of family members defining family history were confounders in the case-control design.  ...  Acknowledgements Funding to support the preparation of this manuscript was received from T32 MH65213, NS047530, NS27941, MH48858, DK31775, P30 ES09089 and P42 ES10349 from the National Institutes of Health  ... 
doi:10.1159/000224640 pmid:19521102 pmcid:PMC2869073 fatcat:wwcd4aajz5c7fpk2inxlghnayi

Non-phylogenetic identification of co-evolving genes for reconstructing the archaeal Tree of Life [article]

Luiz Thiberio Rangel, Shannon M. Soucy, Joao Carlos Setubal, Johann Peter Gogarten, Gregory P. Fournier
2020 bioRxiv   pre-print
Applying IES to a real dataset of 1,322 genes from 42 archaeal genomes identified eight major clusters of co-evolving gene families.  ...  We identify one strongly connected set of 62 co-evolving genes occurring as both single-copy and multiple homologs per genome, with compatible evolutionary histories closely matching previously published  ...  Results and Discussion 24 Simulated dataset 25 Evolutionary histories between simulated gene families were compared to each other using three 26 distinct metrics: RF, #$% , and !" .  ... 
doi:10.1101/2020.10.16.343293 fatcat:2shqy7vpe5aubd3cjqgasdiykq

A null model for microbial diversification

Timothy J. Straub, Olga Zhaxybayeva
2017 Proceedings of the National Academy of Sciences of the United States of America  
Via a combination of simulations and analyses of core and phylogenetic marker genes, we show that patterns of diversity for the genera Escherichia, Neisseria, and Borrelia are generally indistinguishable  ...  Analyses of gene sequences in various closely related prokaryotic groups reveal that sequence diversity is typically organized into distinct clusters, and processes such as periodic selection and extensive  ...  Ford Doolittle for numerous stimulating discussions of the project and for comments on the manuscript. We also thank Drs.  ... 
doi:10.1073/pnas.1619993114 pmid:28630293 pmcid:PMC5502593 fatcat:gtcwtjby2zhklpnjn7tzrtjrre

An efficient, non-phylogenetic method for detecting genes sharing evolutionary signals in phylogenomic datasets

L Thibério Rangel, Shannon M Soucy, João C Setubal, Johann Peter Gogarten, Gregory P Fournier, Mario dos Reis
2021 Genome Biology and Evolution  
Analyses of simulated gene family datasets show that I E S 's accuracy is on par with popular tree-based methods while also less susceptible to noise introduced by sequence alignment and evolutionary model  ...  Applying I E S to an empirical dataset of 1,322 genes from 42 archaeal genomes identified eight major clusters of gene families with compatible evolutionary trends.  ...  compared to the number of perturbations between simulated gene families.  ... 
doi:10.1093/gbe/evab187 pmid:34390574 pmcid:PMC8483891 fatcat:2kz44r7acjat7osqdtgpreovtm

The Influence of Screening for Precancerous Lesions on Family-Based Genetic Association Tests: An Example of Colorectal Polyps and Cancer

Stephanie L. Schmit, Jane C. Figueiredo, Victoria K. Cortessis, Duncan C. Thomas
2015 American Journal of Epidemiology  
The content of this report does not necessarily reflect the views or policies of the National Cancer Institute or any of the collaborating centers in the CCFRs, nor does mention of trade names, commercial  ...  Conflict of interest: none declared.  ...  CRC, colorectal cancer; FH, family history; G 1-G 3 , simulated genes related to CRC development through risk of polyps, risk of CRC but not polyps, and progression from polyps to CRC, respectively; ln  ... 
doi:10.1093/aje/kwv128 pmid:26306664 pmcid:PMC4597802 fatcat:mlvedtokh5btfla6ulochflnzy

Leveraging Family History in Case-Control Analyses of Rare Variation [article]

Claudia R. Solis-Lemus, S. Taylor Fischer, Andrei Todor, Cuining Liu, Elizabeth J. Leslie, David J. Cutler, Debashis Ghosh, Michael P. Epstein
2019 bioRxiv   pre-print
We use simulated data to show that, when family history information is available, our new method outperforms standard rare-variant association methods like burden and SKAT tests that ignore family history  ...  However, both theoretical and experimental studies have demonstrated that subjects with a family history of disease can be enriched for risk variation relative to subjects without such history.  ...  This simulated dataset 262 comprises of 1000 controls, 1000 cases without family history, and 1000 cases with family history for three 263 levels of conditional recurrence risk ratios (columns: λ = 2,  ... 
doi:10.1101/665075 fatcat:62ibycgefnbu7chfpwqgmc2jym

Application of a Polygenic Model of Breast and Ovarian Cancer to Critical Illness Insurance

A. S. Macdonald, K. R. McIvor
2006 Annals of Actuarial Science  
Mutations in the BRCA1 and BRCA2 genes confer very high risk of breast cancer (BC) but only account for about 25% of the observed familial clustering of BC.  ...  We use this model to find premium rates for critical illness insurance: (a) given knowledge of an applicant's polygenotype; and (b) given knowledge of a family history of BC or ovarian cancer.  ...  We would like to thank the sponsors for funding, and members of the Steering Committee for helpful comments at various stages. KM is funded by the Engineering and Physical Sciences Research Council.  ... 
doi:10.1017/s174849950000018x fatcat:6qfehfdqtzh4rk3s24vgja42rm

RecPD: A Recombination-aware measure of phylogenetic diversity

Cedoljub Bundalovic-Torma, Darrell Desveaux, David S. Guttman, Luis Pedro Coelho
2022 PLoS Computational Biology  
., genetic variants, gene families, metabolic capabilities, or taxa) is assessing their diversity and distribution among a sample of individuals.  ...  We used simulation studies to show that RecPD reliably reconstructs feature evolutionary histories under diverse recombination and loss scenarios.  ...  Acknowledgments We would like to thank all members of the Guttman and Desveaux labs for their insight input to this project.  ... 
doi:10.1371/journal.pcbi.1009899 pmid:35192600 pmcid:PMC8896707 fatcat:pnwe6sgtbja3bgk7uy3j5ygzdq

Mirage: A phylogenetic mixture model to reconstruct gene-content evolutionary history using a realistic evolutionary rate model [article]

Tsukasa Fukunaga, Wataru Iwasaki
2020 bioRxiv   pre-print
Simulation analysis showed that Mirage can accurately estimate complex and heterogeneous gene gain/loss rates and reconstruct gene-content evolutionary history.  ...  Using Mirage, we revealed that gene families of metabolic function-related gene families displayed frequent gene gains and losses in all taxa investigated.  ...  As the evaluation criteria for the reconstructed evolutionary history in the simulated dataset analysis, we used the proportion of gene families whose gene copy numbers were correctly estimated in ancestral  ... 
doi:10.1101/2020.10.09.333286 fatcat:7dilevspy5c33mocm46fmuxzr4

Statistical methods for Mendelian models with multiple genes and cancers [article]

Jane W. Liang, Gregory E. Idos, Christine Hong, Stephen B. Gruber, Giovanni Parmigiani, Danielle Braun
2022 arXiv   pre-print
future, based on family history.  ...  However, the upsurge of multi-gene panel germline testing has spurred the discovery of many new gene-cancer associations that are not presently accounted for in these models.  ...  Acknowledgments We gratefully acknowledge support from the National Cancer Institute at the National Institutes of Health grants 5T32CA009337 (JWL) and 4P30CA006516 (GP).  ... 
arXiv:2108.12504v4 fatcat:vqdsbd6w2nfhzg5dgxe35v2wf4

Preliminary Localization of a Gene for Autosomal Dominant Hypoparathyroidism to Chromosome 3ql3

David N Finegold, Marlene M Armitage, Mae Galiani, Tara C Matise, M R Pandian, Yvette M Perry, Ranjan Deka, Robert E Ferrell
1994 Pediatric Research  
Multipoint linkage analysis gave a lod score of 2.71 for the region flanking D3S1303. Simulation using the computer program SLINK showed that a lod score of 2.71 at O = 0.0 was  ...  The hypocalcemic phenotype in this family was mapped by linkage analysis using short, tandem-repeat polymorphisms to the region of chromosome 3q13.  ...  A 2-mo-old boy was referred to the endocrine clinic of the Children's Hospital of Pittsburgh with a history of hypocalcemia at 1 d of age and a strong maternal family history of hypocalcemia.  ... 
doi:10.1203/00006450-199409000-00024 pmid:7808841 fatcat:dnstesnbyjd3lmhbh2c4uubjqy

Coevolution of gene families in prokaryotes

O. X. Cordero, B. Snel, P. Hogeweg
2008 Genome Research  
We study gene family coevolution on a tree of life based on a large-scale ancestral gene content reconstruction, which includes gene duplication and deletion events.  ...  inevitable consequence of evolution along a tree. (2) Concerted family expansion (gene duplication) and contraction (gene deletion) reflect functional constraints and therefore lead to better function  ...  To infer a map of coevolutionary relationships, we compare the reconstructed evolutionary histories of gene families along a tree of life.  ... 
doi:10.1101/gr.6815508 pmid:18230804 pmcid:PMC2259110 fatcat:lvf3x2lklrghnowctilrcpukuu

Amino acid transporter expansions associated with the evolution of obligate endosymbiosis in sap-feeding insects (Hemiptera: sternorrhyncha)

Romain A Dahan, Rebecca P Duncan, Alex CC Wilson, Liliana M Dávalos
2015 BMC Evolutionary Biology  
Results: By applying a series of methods to reconcile gene and species trees, inferring the size of gene families in ancestral lineages, and simulating the null process of birth and death in multi-gene  ...  Conclusions: Our findings support the influence of obligate endosymbioses on host genome evolution by both inferring significant expansions of gene families involved in symbiotic interactions, and discovering  ...  Yohe and other members of the Dávalos lab for helpful comments on the manuscript and figures, as well as Dannie Durand for help with Notung and Bengt Sennblad for help with GenPhyloData.  ... 
doi:10.1186/s12862-015-0315-3 pmid:25887093 pmcid:PMC4374396 fatcat:o6hlcclrv5hpngs4idx6vao554
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