article-journal

A complete genome for the common marmoset
The common marmoset is a New World monkey widely used to study primate evolution and human disease. We present a telomere-to-telomere …
Prajna Hebbar, Tamara Potapova, Hailey Loucks, Karina Ray, Murillo F Rodrigues, Fedor Ryabov, Joanna Malukiewicz, DongAhn Yoo, Leonardo Gomes de Lima, Annat Haber, Sonal Kumar, Swati Banerjee, Matthew Borchers, Gage H. Garcia, Joshua Gardner, Stephanie Hachem, Harrison D. Heath, Seung Kwon Ha, Mira Mastoras, Brandy McNulty, Julian Menendez, Katherine M. Munson, Karol Pal, JungEun Park, Simon Plösch, Christian Roos, William E. Seligmann, Valery Shepelev, Catrina Spruce, Ivo Violich, Lutz Walter, Kateryna D. Makova, Amantha Thathiah, Stacey J. Sukoff Rizzo, Afonso C. Silva, Gregory W. Carter, Karen H. Miga, Evan E. Eichler, Donald F. Conrad, Jennifer L. Gerton, Ivan A. Alexandrov, Benedict Paten
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Census and genetic analysis of the United States marmoset population
The common marmoset (Callithrix jacchus), a small monkey native to Brazil, has been used as a biomedical model in the United States …
Murillo F Rodrigues, Philberta Leung, Jamie A. Ivy, Alexandra Stendahl, Karina Ray, Jenna Castro, Samuel M. Peterson, Ricardo C. H. del Rosario, Simon Ploesch, Joanna Malukiewicz, Katinka A. Vigh-Conrad, Benjamin N. Bimber, Jeffrey D. Wall, Donald F. Conrad
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Accessible, Realistic Genome Simulation with Selection Using stdpopsim
Selection is a fundamental evolutionary force that shapes patterns of genetic variation across species. However, simulations …
Graham Gower, Nathaniel S Pope, Murillo F Rodrigues, Silas Tittes, Linh N Tran, Ornob Alam, Maria Izabel A Cavassim, Peter D Fields, Benjamin C Haller, Xin Huang, Ben Jeffrey, Kevin Korfmann, Christopher C Kyriazis, Jiseon Min, Inés Rebollo, Clara T Rehmann, Scott T Small, Chris C R Smith, Georgia Tsambos, Yan Wong, Yu Zhang, Christian D Huber, Gregor Gorjanc, Aaron P Ragsdale, Ilan Gronau, Ryan N Gutenkunst, Jerome Kelleher, Kirk E Lohmueller, Daniel R Schrider, Peter L Ralph, Andrew D Kern
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Inbreeding and deleterious variation in South Asian populations
Consanguinity (or inbreeding) refers to the offspring of unions between closely related individuals. It is associated with a wide range …
Jeffrey D. Wall, Murillo F Rodrigues
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SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution
SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution
Benjamin C. Haller, Chase W. Nelson, Murillo F Rodrigues, Philipp W. Messer
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Shared evolutionary processes shape landscapes of genomic variation in the great apes
For at least the past 5 decades, population genetics, as a field, has worked to describe the precise balance of forces that shape …
Murillo F Rodrigues, Andrew D Kern, Peter L Ralph
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Neofunctionalization driven by positive selection led to the retention of the loqs2 gene encoding an Aedes specific dsRNA binding protein
Mosquito borne viruses, such as dengue, Zika, yellow fever and Chikungunya, cause millions of infections every year. These viruses are …
Carlos F. Estevez-Castro, Murillo F Rodrigues, Antinéa Babarit, Flávia V. Ferreira, Elisa G. de Andrade, Eric Marois, Rodrigo Cogni, Eric R. G. R. Aguiar, João T. Marques, Roenick P. Olmo
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Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that …
M Elise Lauterbur, Maria Izabel A Cavassim, Ariella L Gladstein, Graham Gower, Nathaniel S Pope, Georgia Tsambos, Jeffrey Adrion, Saurabh Belsare, Arjun Biddanda, Victoria Caudill, Jean Cury, Ignacio Echevarria, Benjamin C Haller, Ahmed R Hasan, Xin Huang, Leonardo Nicola Martin Iasi, Ekaterina Noskova, Jana Obsteter, Vitor Antonio Correa Pavinato, Alice Pearson, David Peede, Manolo F Perez, Murillo F Rodrigues, Chris CR Smith, Jeffrey P Spence, Anastasia Teterina, Silas Tittes, Per Unneberg, Juan Manuel Vazquez, Ryan K Waples, Anthony Wilder Wohns, Yan Wong, Franz Baumdicker, Reed A Cartwright, Gregor Gorjanc, Ryan N Gutenkunst, Jerome Kelleher, Andrew D Kern, Aaron P Ragsdale, Peter L Ralph, Daniel R Schrider, Ilan Gronau
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Efficient ancestry and mutation simulation with msprime 1.0
Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation …
Franz Baumdicker, Gertjan Bisschop, Daniel Goldstein, Graham Gower, Aaron P Ragsdale, Georgia Tsambos, Sha Zhu, Bjarki Eldon, E Castedo Ellerman, Jared G Galloway, Ariella L Gladstein, Gregor Gorjanc, Bing Guo, Ben Jeffery, Warren W Kretzschumar, Konrad Lohse, Michael Matschiner, Dominic Nelson, Nathaniel S Pope, Consuelo D Quinto-Cortés, Murillo F Rodrigues, Kumar Saunack, Thibaut Sellinger, Kevin Thornton, Hugo van Kemenade, Anthony W Wohns, Yan Wong, Simon Gravel, Andrew D Kern, Jere Koskela, Peter L Ralph, Jerome Kelleher
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Clinal and seasonal changes are correlated in Drosophila melanogaster natural populations
Spatial and seasonal variations in the environment are ubiquitous. Environmental heterogeneity can affect natural populations and lead …
Murillo F Rodrigues, Maria D. Vibranovski, Rodrigo Cogni
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