pypi: msprime | Projects | Ecosyste.ms: Papers

10.1534/genetics.119.302662

Polygenic Adaptation to an Environmental Shift: Temporal Dynamics of Variation Under Gaussian Stabilizing Selection and Additive Effects on a Single Trait
Cited by: 47
Author(s): Kevin R. Thornton
Software Mentions: 9
Published: almost 5 years ago

10.1038/s41431-020-0699-4

Differences in local population history at the finest level: the case of the Estonian population
Cited by: 22
Author(s): Vasili Pankratov, Francesco Montinaro, Alena Kushniarevich, Georgi Hudjashov, Flora Jay, Lauri Saag, Rodrigo Flores, Davide Marnetto, Marten Seppel, Mart Kals, Urmo Võsa, Cristian Taccioli, Märt Möls, Lili Milani, Anto Aasa, Daniel J. Lawson, Tõnu Esko, Reedik Mägi, Luca Pagani, Andres Metspalu, Mait Metspalu
Software Mentions: 8
Published: over 4 years ago

10.7554/eLife.54967

A community-maintained standard library of population genetic models
Cited by: 96
Author(s): Jeffrey R. Adrion, Christopher B. Cole, Noah Dukler, Jared Galloway, Ariella L. Gladstein, Graham Gower, Christopher C. Kyriazis, Aaron P. Ragsdale, Georgia Tsambos, Franz Baumdicker, Jedidiah Carlson, Reed A. Cartwright, Arun Durvasula, Ilan Gronau, Bernard Kim, Patrick McKenzie, Philipp W. Messer, Ekaterina Noskova, Diego Ortega Del Vecchyo, Fernando Racimo, Travis J Struck, Simon Gravel, Ryan N. Gutenkunst, Kirk E. Lohmueller, Peter L. Ralph, Daniel R. Schrider, Adam Siepel, Jerome Kelleher, Andrew D. Kern
Software Mentions: 7
Published: over 4 years ago

10.1093/molbev/msab175

Geonomics: Forward-Time, Spatially Explicit, and Arbitrarily Complex Landscape Genomic Simulations
Cited by: 10
Author(s): Drew E Terasaki Hart, Anusha P Bishop, Ian Wang
Software Mentions: 7
Published: over 3 years ago

10.1093/g3journal/jkaa036

Visualizing population structure with variational autoencoders
Cited by: 44
Author(s): C. J. Battey, Gabrielle C. Coffing, Andrew D. Kern
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pcbi.1006581

Efficient pedigree recording for fast population genetics simulation
Cited by: 112
Author(s): Jerome Kelleher, Kevin R. Thornton, Jaime Ashander, Peter L. Ralph
Software Mentions: 6
Published: about 6 years ago

10.7554/eLife.64669

Detecting adaptive introgression in human evolution using convolutional neural networks
Cited by: 52
Author(s): Graham Gower, Pablo Iáñez Picazo, Matteo Fumagalli, Fernando Racimo
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pcbi.1004842

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
Cited by: 522
Author(s): Jerome Kelleher, Alison Etheridge, Gil McVean
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pgen.1008867

VolcanoFinder: Genomic scans for adaptive introgression
Cited by: 56
Author(s): Derek Setter, Sylvain Mousset, Xiaoheng Cheng, Rasmus Nielsen, Michael DeGiorgio, Joachim Hermisson
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-61216-7

A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm
Cited by: 72
Author(s): Simone Scalabrin, Lucile Toniutti, Gabriele Di Gaspero, Davide Scaglione, Gabriele Magris, Michele Vidotto, Sara Pinosio, Frederica Cattonaro, Federica Magni, Irena Jurman, Mario Cerutti, F. S. Liverani, Luciano Navarini, Lorenzo Del Terra, Gloria Pellegrino, Manuela Rosanna Ruosi, Nicola Vitulo, Giorgio Valle, Alberto Pallavicini, G. Graziosi, Patricia E. Klein, Nolan Bentley, Seth C. Murray, William Solano, Amin Al Hakimi, Timothy Schilling, Christophe Montagnon, Michèle Morgante, Benoît Bertrand
Software Mentions: 5
Published: over 4 years ago

10.1534/g3.119.400088

The Effect of Neutral Recombination Variation on Genome Scans for Selection
Cited by: 54
Author(s): Katie E. Lotterhos
Software Mentions: 4
Published: over 5 years ago

10.1016/j.patter.2021.100212

VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples
Cited by: 26
Author(s): Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Carlo Gambacorti‐Passerini, Marco Antoniotti, Alex Graudenzi, Rocco Piazza
Software Mentions: 4
Published: over 3 years ago

10.1534/genetics.120.303460

Extensive Recombination Suppression and Epistatic Selection Causes Chromosome-Wide Differentiation of a Selfish Sex Chromosome in <i>Drosophila pseudoobscura</i>
Cited by: 16
Author(s): Zachary L. Fuller, Spencer Koury, Christopher J. Leonard, Randee E. Young, Kobe Ikegami, Jonathan Westlake, Stephen Richards, Stephen W. Schaeffer, Nitin Phadnis
Software Mentions: 4
Published: about 4 years ago

10.1534/genetics.120.303253

Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes
Cited by: 38
Author(s): Peter L. Ralph, Kevin R. Thornton, Jerome Kelleher
Software Mentions: 4
Published: over 4 years ago

10.1093/molbev/msaa239

Signatures of Introgression across the Allele Frequency Spectrum
Cited by: 15
Author(s): Simon H. Martin, William Amos
Software Mentions: 3
Published: about 4 years ago

10.1186/s13059-021-02382-3

Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression
Cited by: 29
Author(s): Qimin Cheng, Yuanfeng Li, Xinyi Liu, Yahui Wang, Jie Ping, Yiming Lu, Gangqiao Zhou
Software Mentions: 3
Published: over 3 years ago

10.1007/s00285-020-01470-5

Cannings models, population size changes and multiple-merger coalescents
Cited by: 19
Author(s): Fabian Freund
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pgen.1008552

Tracking human population structure through time from whole genome sequences
Cited by: 63
Author(s): Ke Wang, Iain Mathieson, Jared O’Connell, Stephan Schiffels
Software Mentions: 3
Published: over 4 years ago

10.1002/gepi.22264

Population genetic simulation study of power in association testing across genetic architectures and study designs
Cited by: 6
Author(s): Dominic M. H. Tong, Ryan D. Hernández
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1008895

Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph
Cited by: 62
Author(s): Melissa J. Hubisz, Amy L. Williams, Adam Siepel
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1007191

Inferring sex-specific demographic history from SNP data
Cited by: 22
Author(s): Florian Clemente, Mathieu Gautier, Renaud Vitalis
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1008619

Accounting for long-range correlations in genome-wide simulations of large cohorts
Cited by: 39
Author(s): Dominic Nelson, Jerome Kelleher, Aaron P. Ragsdale, Claudia Moreau, Gil McVean, Simon Gravel
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-019-3154-1

Legofit: estimating population history from genetic data
Cited by: 11
Author(s): Alan R. Rogers
Software Mentions: 3
Published: about 5 years ago

10.1002/evl3.229

Mutation load decreases with haplotype age in wild Soay sheep
Cited by: 25
Author(s): Martin Stoffel, Susan E. Johnston, Jill G. Pilkington, Josephine M. Pemberton
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1007741

Deleterious variation shapes the genomic landscape of introgression
Cited by: 90
Author(s): Bernard Kim, Christian D. Huber, Kirk E. Lohmueller
Software Mentions: 2
Published: about 6 years ago

10.1038/s41431-020-0639-3

The exhaustive genomic scan approach, with an application to rare-variant association analysis
Cited by: 2
Author(s): George Kanoungi, Michael Nothnagel, Tim Becker, Dmitriy Drichel
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pgen.1008340

An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations
Cited by: 16
Author(s): Alexander Platt, Alyssa Pivirotto, Jared Knoblauch, Jody Hey
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pbio.3000391

Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Cited by: 97
Author(s): Sean Stankowski, Madeline A. Chase, Allison M. Fuiten, Murillo F. Rodrigues, Peter L. Ralph, Matthew A. Streisfeld
Software Mentions: 2
Published: over 5 years ago

10.1186/s12915-018-0535-2

Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication
Cited by: 117
Author(s): Amanda L. Pendleton, Feichen Shen, Angela M. Taravella, Sarah B. Emery, Krishna R. Veeramah, Adam R. Boyko, Jeffrey M. Kidd
Software Mentions: 2
Published: over 6 years ago

10.1534/genetics.117.300448

Assessing the Relationship of Ancient and Modern Populations
Cited by: 16
Author(s): Joshua G. Schraiber
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1006963

Composite likelihood method for inferring local pedigrees
Cited by: 22
Author(s): Amy J. Ko, Rasmus Nielsen
Software Mentions: 2
Published: about 7 years ago

10.1186/s12859-017-2002-4

Gene flow analysis method, the D-statistic, is robust in a wide parameter space
Cited by: 60
Author(s): Yichen Zheng, Axel Janke
Software Mentions: 2
Published: almost 7 years ago

10.1016/j.ajhg.2019.08.011

Ancestry-Dependent Enrichment of Deleterious Homozygotes in Runs of Homozygosity
Cited by: 35
Author(s): Zachary A. Szpiech, Angel C. Y. Mak, Marquitta J. White, Donglei Hu, Celeste Eng, Esteban G. Burchard, Ryan D. Hernández
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2020.531218

Hierarchical Modelling of Haplotype Effects on a Phylogeny
Cited by: 5
Author(s): Maria Lie Selle, Ingelin Steinsland, Finn Lindgren, Vladimir Brajković, Vlatka Čubrić-Ćurik, Gregor Gorjanc
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-019-2927-x

ImaGene: a convolutional neural network to quantify natural selection from genomic data
Cited by: 55
Author(s): Luis Torada, Lucrezia Lorenzon, Alice E. Beddis, Ulaş Işıldak, Linda Pattini, Sara Mathieson, Matteo Fumagalli
Software Mentions: 1
Published: about 5 years ago

10.1093/molbev/msx300

Madeiran Arabidopsis thaliana Reveals Ancient Long-Range Colonization and Clarifies Demography in Eurasia
Cited by: 30
Author(s): Andrea Fulgione, M. Koornneef, Fabrice Roux, Joachim Hermisson, Angela M. Hancock
Software Mentions: 1
Published: almost 7 years ago

10.1111/mec.14954

Allele frequency‐free inference of close familial relationships from genotypes or low‐depth sequencing data
Cited by: 59
Author(s): Ryan K. Waples, Anders Albrechtsen, Ida Moltke
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pcbi.1008638

Ancestral haplotype reconstruction in endogamous populations using identity-by-descent
Cited by: 3
Author(s): Kelly Finke, Michael Kourakos, Gabriela Brown, Huyen Trang Dang, Shi Jie Samuel Tan, Yuval B. Simons, Shweta Ramdas, Alejandro A. Schäffer, Rachel L. Kember, Maja Bućan, Sara Mathieson
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1008204

Models of archaic admixture and recent history from two-locus statistics
Cited by: 53
Author(s): Aaron P. Ragsdale, Simon Gravel
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1006549

Inference of Candidate Germline Mutator Loci in Humans from Genome-Wide Haplotype Data
Cited by: 21
Author(s): Cathal Seoighe, Aylwyn Scally
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1007385

Ancestry-specific recent effective population size in the Americas
Cited by: 85
Author(s): Sharon R. Browning, Brian L. Browning, Martha L. Daviglus, Ramón Durazo-Arvizú, Neil Schneiderman, Robert C. Kaplan, Cathy C. Laurie
Software Mentions: 1
Published: over 6 years ago

10.1111/eva.12829

The spatial scale of dispersal revealed by admixture tracts
Cited by: 21
Author(s): Maud Duranton, François Bonhomme, Pierre‐Alexandre Gagnaire
Software Mentions: 1
Published: over 5 years ago

10.1002/evl3.126

Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows
Cited by: 24
Author(s): Jennifer Walsh, Phred M. Benham, Petra E. Deane‐Coe, Peter Arcese, Bronwyn G. Butcher, Yvonne L. Chan, Zachary A. Cheviron, Chris S. Elphick, Adrienne I. Kovach, Brian J. Olsen, W. Gregory Shriver, Virginia L. Winder, Irby J. Lovette
Software Mentions: 1
Published: over 5 years ago

Projects: pypi: msprime

Papers Mentioning msprime 48