Ecosyste.ms: Papers

10.1038/s42003-021-02620-1

Past environmental changes affected lemur population dynamics prior to human impact in Madagascar
Cited by: 11
Author(s): Helena Teixeira, Vincent Montade, Jordi Salmona, Julia Metzger, Laurent Brémond, Thomas Kasper, Gerhard Daut, Sylvie Rouland, Sandratrinirainy Ranarilalatiana, Romule Rakotondravony, Lounès Chikhi, Hermann Behling, Ute Radespiel
Software Mentions: 1
Published: about 3 years ago

10.1098/rsos.201229

Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding
Cited by: 3
Author(s): William Amos
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-15-164

WinHAP2: an extremely fast haplotype phasing program for long genotype sequences
Cited by: 5
Author(s): Weihua Pan, Yanan Zhao, Yun Xu, Fengfeng Zhou
Software Mentions: 1
Published: over 10 years ago

10.2174/138920208784340759

Simulation of Genomes: A Review
Cited by: 57
Author(s): Antonio Carvajal-Rodríguez
Software Mentions: 1
Published: over 16 years ago

10.1038/srep31791

Recent evolution of the salivary mucin MUC7
Cited by: 30
Author(s): Duo Xu, Pavlos Pavlidis, Supaporn Thamadilok, Emilie Redwood, Sara Fox, Ran Blekhman, Stefan Rühl, Ömer Gökçümen
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-016-1269-1

In the light of deep coalescence: revisiting trees within networks
Cited by: 47
Author(s): Jiafan Zhu, Yun Yu, Luay Nakhleh
Software Mentions: 1
Published: about 8 years ago

10.1002/ece3.1846

A simulation study of sample size for DNA barcoding
Cited by: 25
Author(s): Arong Luo, Haiqiang Lan, Cheng Ling, Aibing Zhang, Lei Shi, Simon Y. W. Ho, Chao‐Dong Zhu
Software Mentions: 1
Published: almost 9 years ago

10.1002/ece3.5123

Invasion origin, rapid population expansion, and the lack of genetic structure of cotton bollworm ( <i>Helicoverpa armigera</i> ) in the Americas
Cited by: 24
Author(s): Rogério Martins Gonçalves, Thiago Mastrangelo, J. C. V. Rodrigues, Daniel F. Paulo, Celso Omoto, Alberto Soares Corrêa, Ana Maria Lima de Azeredo-Espin
Software Mentions: 1
Published: over 5 years ago

10.1002/ece3.4436

Effects of cyclic changes in population size on neutral genetic diversity
Cited by: 5
Author(s): Haruna Nakamura, Kenjiro Teshima, Hidenori Tachida
Software Mentions: 1
Published: about 6 years ago

10.1002/ece3.1091

Extremely low nucleotide polymorphism in<i>Pinus krempfii</i>Lecomte, a unique flat needle pine endemic to Vietnam
Cited by: 11
Author(s): Baosheng Wang, Marjan Khalili Mahani, Wei Lun Ng, Junko Kusumi, Hai Hong Phi, Norio Inomata, Xiao Ru Wang, Alfred E. Szmidt
Software Mentions: 1
Published: over 10 years ago

10.1038/srep35004

Identifying molecular signatures of hypoxia adaptation from sex chromosomes: A case for Tibetan Mastiff based on analyses of X chromosome
Cited by: 12
Author(s): Hong Wu, Liu Yan-hu, Guodong Wang, Chun‐Tao Yang, Newton O. Otecko, Fei Liu, Shi-Fang Wu, Lu Wang, Li Yu, Yaping Zhang
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-019-41176-3

A dispersal of Homo sapiens from southern to eastern Africa immediately preceded the out-of-Africa migration
Cited by: 44
Author(s): Teresa Rito, Joana Vieira, Marina Silva, Eduardo Conde-Sousa, Luı́sa Pereira, Paul Mellars, Martin B. Richards, Pedro Soares
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-6-252

CoaSim: A flexible environment for simulating genetic data under coalescent models
Cited by: 67
Author(s): Thomas Mailund, Mikkel H. Schierup, Christian N. S. Pedersen, Peter J. M. Mechlenborg, Jesper N. Madsen, Leif Schauser
Software Mentions: 1
Published: about 19 years ago

10.1186/s12862-016-0606-3

Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions
Cited by: 12
Author(s): Mitsuhiko Sato, Takashi Makino, Masakado Kawata
Software Mentions: 1
Published: almost 9 years ago

10.1002/ece3.2152

Genomic heterogeneity of historical gene flow between two species of newts inferred from transcriptome data
Cited by: 21
Author(s): Michał Stuglik, Wiesław Babik
Software Mentions: 1
Published: over 8 years ago

10.1530/EJE-17-0293

In-frame seven amino-acid duplication in AIP arose over the last 3000 years, disrupts protein interaction and stability and is associated with gigantism
Cited by: 11
Author(s): Roberto Salvatori, Șerban Radian, Yoan Diekmann, Donato Iacovazzo, Alessia David, Plamena Gabrovska, Giorgia Grassi, Anna Marie Bussell, Karen Stals, Astrid Weber, Richard Quinton, Elizabeth Crowne, Valentina Corazzini, Louise A. Metherell, Tara Kearney, Daniel du Plessis, Ajay Sinha, Atik Baborie, Anne Lise Lecoq, Philippe Chanson, Olaf Ansorge, Sian Ellard, Peter Trainer, David J. Balding, Mark G. Thomas, Márta Korbonits
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-2148-12-196

Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model
Cited by: 417
Author(s): Noah M. Reid, Bryan C. Carstens
Software Mentions: 1
Published: almost 13 years ago

10.1111/j.1752-4571.2012.00256.x

Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests
Cited by: 51
Author(s): Elena Mosca, Andrew J. Eckert, John D. Liechty, Jill L. Wegrzyn, Nicola La Porta, Giovanni G. Vendramin, David B. Neale
Software Mentions: 1
Published: over 12 years ago

10.1111/eva.12110

History of the invasive<scp>A</scp>frican olive tree in<scp>A</scp>ustralia and<scp>H</scp>awaii: evidence for sequential bottlenecks and hybridization with the<scp>M</scp>editerranean olive
Cited by: 33
Author(s): Guillaume Besnard, Jérémy Dupuy, Maximilian Larter, Peter Cuneo, D. E. L. Cooke, Lounès Chikhi
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-020-75980-z

Catalytic liquefaction of sewage sludge to small molecular weight chemicals
Cited by: 0
Author(s): Yue‐Hu Wang, Feihong Tian, Peimei Guo, Dazhen Fu, Hero J. Heeres, Taotao Tang, Huayu Yuan, Bing Wang, Li Jiang
Software Mentions: 1
Published: about 4 years ago

10.1002/evl3.159

Assessing biological factors affecting postspeciation introgression
Cited by: 41
Author(s): Jennafer A. P. Hamlin, Mark S. Hibbins, Leonie C. Moyle
Software Mentions: 1
Published: over 4 years ago

10.1002/2211-5463.12074

Identification of protein interfaces within the multi‐aminoacyl‐<scp>tRNA</scp>synthetase complex: the case of lysyl‐<scp>tRNA</scp>synthetase and the scaffold protein p38
Cited by: 11
Author(s): Azaria Rémion, Fawzi Khoder-Agha, David Cornu, Manuela Argentini, Virginie Redeker, Marc Mirande
Software Mentions: 1
Published: over 8 years ago

10.3389/fgene.2020.601439

AdmixSim: A Forward-Time Simulator for Various Complex Scenarios of Population Admixture
Cited by: 4
Author(s): Yan Xiong, Kai Yuan, Xumin Ni, Ying Zhou, Wei Guo, Shuhua Xu
Software Mentions: 1
Published: almost 4 years ago

10.3389/fgene.2015.00150

PopPlanner: visually constructing demographic models for simulation
Cited by: 5
Author(s): Gregory Ewing, Pauline Alberte Reiff, Jeffrey D. Jensen
Software Mentions: 1
Published: over 9 years ago

10.3389/fgene.2012.00165

Systematic underestimation of the age of selected alleles
Cited by: 7
Author(s): Joanna L. Kelley
Software Mentions: 1
Published: almost 13 years ago

10.1038/s41598-021-89078-7

Peering inside a cough or sneeze to explain enhanced airborne transmission under dry weather
Cited by: 23
Author(s): Kai Li, Majid Allahyari, Jorge S. Salinas, Nadim Zgheib, S. Balachandar
Software Mentions: 1
Published: over 3 years ago

10.3389/fgene.2013.00235

The impact of equilibrium assumptions on tests of selection
Cited by: 65
Author(s): Jessica L. Crisci, Yu Ping Poh, Shivani Mahajan, Jeffrey D. Jensen
Software Mentions: 1
Published: almost 12 years ago

10.7554/eLife.24284

Rapid evolution of the human mutation spectrum
Cited by: 135
Author(s): Kelley Harris, Jonathan K. Pritchard
Software Mentions: 1
Published: over 7 years ago

10.3389/fgene.2013.00013

Poor Man’s 1000 Genome Project: Recent Human Population Expansion Confounds the Detection of Disease Alleles in 7,098 Complete Mitochondrial Genomes
Cited by: 7
Author(s): Hie Lim Kim, Stephan C. Schuster
Software Mentions: 1
Published: almost 12 years ago

10.3389/fgene.2021.664357

Hypothesis Testing With Rank Conditions in Phylogenetics
Cited by: 0
Author(s): Colby Long, Laura Kubatko
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-11-116

ABCtoolbox: a versatile toolkit for approximate Bayesian computations
Cited by: 325
Author(s): Daniel Wegmann, Christoph Leuenberger, Samuel Neuenschwander, Laurent Excoffier
Software Mentions: 1
Published: over 14 years ago

10.3389/fgene.2012.00254

Correcting Principal Component Maps for Effects of Spatial Autocorrelation in Population Genetic Data
Cited by: 28
Author(s): Éric Frichot, Sean D. Schoville, Guillaume Bouchard, F. Ochsenbein
Software Mentions: 1
Published: almost 13 years ago

10.3389/fgene.2020.596662

Selective Sweeps Lead to Evolutionary Success in an Amazonian Hyperdominant Palm
Cited by: 4
Author(s): Warita Alves de Melo, Lucas Donizetti Vieira, Evandro Novaes, Christine D. Bacon, Rosane Garcia Collevatti
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12862-015-0335-z

Varying influences of selection and demography in host-adapted populations of the tick-transmitted bacterium, Anaplasma phagocytophilum
Cited by: 12
Author(s): Matthew L. Aardema, Friederike D. von Loewenich
Software Mentions: 1
Published: over 9 years ago

10.3389/fgene.2017.00139

The Empirical Distribution of Singletons for Geographic Samples of DNA Sequences
Cited by: 12
Author(s): Philippe Cubry, Yves Vigouroux, F. Ochsenbein
Software Mentions: 1
Published: about 7 years ago

10.3389/fgene.2013.00146

GraphML specializations to codify ancestral recombinant graphs
Cited by: 7
Author(s): James McGill, Elizabeth A. Walkup, Mary K. Kuhner
Software Mentions: 1
Published: almost 12 years ago

10.3389/fgene.2015.00291

Simultaneous inference of haplotypes and alleles at a causal gene
Cited by: 0
Author(s): Fabrice Larribe, Mathieu J. Dupont, Gabrielle Boucher
Software Mentions: 1
Published: about 9 years ago

10.1534/g3.111.000539

Polymorphism and Divergence in Two Willow Species,<i>Salix viminalis</i>L. and<i>Salix schwerinii</i>E. Wolf
Cited by: 24
Author(s): Sofia Berlin, Johan Fogelqvist, Martin Lascoux, Ulf Lagercrantz, Ann Christin Rönnberg‐Wästljung
Software Mentions: 1
Published: about 13 years ago

10.1186/s12862-016-0791-0

How and how much does RAD-seq bias genetic diversity estimates?
Cited by: 54
Author(s): Marie‐Louise Cariou, Laurent Duret, Sylvain Charlat
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-017-1948-6

Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach
Cited by: 1
Author(s): Oyetunji Ogundijo, Xiaodong Wang
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2105-12-265

phenosim - A software to simulate phenotypes for testing in genome-wide association studies
Cited by: 21
Author(s): Torsten Günther, Inka Gawenda, Karl Schmid
Software Mentions: 1
Published: over 13 years ago

10.1534/g3.113.007633

Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference
Cited by: 24
Author(s): Suyash Shringarpure, Eric P. Xing
Software Mentions: 1
Published: over 10 years ago

10.1534/g3.114.010629

A Recent Global Selective Sweep on the<i>age-1</i>Phosphatidylinositol 3-OH Kinase Regulator of the Insulin-Like Signaling Pathway Within<i>Caenorhabditis remanei</i>
Cited by: 12
Author(s): Emmanuel Jovelin, Jennifer S. Comstock, Asher D. Cutter, Patrick C. Phillips
Software Mentions: 1
Published: over 10 years ago

10.1534/g3.116.028233

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR) in the Genomic Era
Cited by: 94
Author(s): Feng Gao, Chi Ming, Wangjie Hu, Haipeng Li
Software Mentions: 1
Published: over 8 years ago

10.1186/s12859-015-0661-6

HaploPOP: a software that improves population assignment by combining markers into haplotypes
Cited by: 7
Author(s): Nicolas Duforet-Frebourg, Lucie M. Gattepaille, Michaël G. B. Blum, Mattias Jakobsson
Software Mentions: 1
Published: over 9 years ago

10.1093/g3journal/jkab128

Effects of single nucleotide polymorphism ascertainment on population structure inferences
Cited by: 5
Author(s): Kotaro Dokan, Sayu Kawamura, Kenjiro Teshima
Software Mentions: 1
Published: over 3 years ago

10.1093/bioinformatics/btab267

Advancing admixture graph estimation via maximum likelihood network orientation
Cited by: 20
Author(s): Erin K. Molloy, Arun Durvasula, Sriram Sankararaman
Software Mentions: 1
Published: over 3 years ago

10.1093/bioinformatics/btab059

<tt>Fur</tt>: Find unique genomic regions for diagnostic PCR
Cited by: 1
Author(s): Bernhard Haubold, Fabian Klötzl, Lars Hellberg, Daniel W. Thompson, Markus Cavalar
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12862-019-1387-2

Patterns of genomic differentiation between two Lake Victoria cichlid species, Haplochromis pyrrhocephalus and H. sp. ‘macula’
Cited by: 4
Author(s): Shohei Takuno, Ryutaro Miyagi, Jun-ichi Onami, Shiho Takahashi-Kariyazono, Akie Sato, Herbert Tichy, Masato Nikaido, Mitsuto Aibara, Shinji Mizoiri, Hillary D. J. Mrosso, Semvua Isa Mzighani, Norihiro Okada, Yohey Terai
Software Mentions: 1
Published: over 5 years ago

10.1016/j.tig.2017.12.005

Supervised Machine Learning for Population Genetics: A New Paradigm
Cited by: 301
Author(s): Daniel R. Schrider, Andrew D. Kern
Software Mentions: 1
Published: over 6 years ago

10.1186/s12936-016-1214-9

Genomic signatures of population decline in the malaria mosquito Anopheles gambiae
Cited by: 14
Author(s): Samantha OʼLoughlin, Stephen Magesa, Charles M. Mbogo, Franklin W. Mosha, Janet Midega, Austin Burt
Software Mentions: 1
Published: over 8 years ago

10.1099/mgen.0.000044

SimBac: simulation of whole bacterial genomes with homologous recombination
Cited by: 34
Author(s): Tom Brown, Xavier Didelot, Daniel J. Wilson, Nicola De Maio
Software Mentions: 1
Published: almost 9 years ago

10.1186/1753-6561-5-S3-S3

QTLMAS 2010: simulated dataset
Cited by: 20
Author(s): M. Szydłowski, Paulina Paczyńska
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-016-3104-5

A performance study of the impact of recombination on species tree analysis
Cited by: 14
Author(s): Zhiwei Wang, Kevin J. Liu
Software Mentions: 1
Published: about 8 years ago

10.1093/molbev/msu078

Simulation of Genome-Wide Evolution under Heterogeneous Substitution Models and Complex Multispecies Coalescent Histories
Cited by: 35
Author(s): Miguel Arenas, David Posada
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-018-4452-0

Identifying genome-wide immune gene variation underlying infectious disease in wildlife populations – a next generation sequencing approach in the gopher tortoise
Cited by: 15
Author(s): Jean P. Elbers, Mary Bomberger Brown, Sabrina S. Taylor
Software Mentions: 1
Published: almost 7 years ago

10.1093/molbev/msy224

The Unreasonable Effectiveness of Convolutional Neural Networks in Population Genetic Inference
Cited by: 141
Author(s): Lex E. Flagel, Yaniv Brandvain, Daniel R. Schrider
Software Mentions: 1
Published: almost 6 years ago

10.1186/1471-2164-16-S10-S10

A maximum pseudo-likelihood approach for phylogenetic networks
Cited by: 154
Author(s): Yu Yun, Luay Nakhleh
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-015-2298-2

Mapping the genomic architecture of adaptive traits with interspecific introgressive origin: a coalescent-based approach
Cited by: 2
Author(s): Hussein A. Hejase, Kevin J. Liu
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-017-3486-z

Evolution of meiotic recombination genes in maize and teosinte
Cited by: 11
Author(s): Gaganpreet Sidhu, Tomasz Warzecha, Wojciech P. Pawlowski
Software Mentions: 1
Published: almost 8 years ago

10.1111/mec.14833

How to estimate kinship
Cited by: 71
Author(s): Jérôme Goudet, Tomas Kay, Bruce S. Weir
Software Mentions: 1
Published: about 6 years ago

10.1111/j.1365-294X.2010.04990.x

Genealogical lineage sorting leads to significant, but incorrect Bayesian multilocus inference of population structure
Cited by: 35
Author(s): Pablo Orozco‐terWengel, Jukka Corander, Christian Schlötterer
Software Mentions: 1
Published: almost 14 years ago

10.7717/peerj.900

Natural variation in teosinte at the domestication locus<i>teosinte branched1</i>(<i>tb1</i>)
Cited by: 13
Author(s): Laura Vann, Thomas J. Y. Kono, Tanja Pyhäjärvi, Matthew B. Hufford, Jeffrey Ross‐Ibarra
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-015-2241-6

A method for positive forensic identification of samples from extremely low-coverage sequence data
Cited by: 18
Author(s): Samuel H. Vohr, Carlos Fernando Buen Abad Najar, Beth Shapiro, Edward Green
Software Mentions: 1
Published: almost 9 years ago

10.7717/peerj.1203

Coalescent: an open-science framework for importance sampling in coalescent theory
Cited by: 0
Author(s): Susanta Tewari, John L. Spouge
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj.5325

Can secondary contact following range expansion be distinguished from barriers to gene flow?
Cited by: 7
Author(s): Johanna Bertl, Harald Ringbauer, Michaël G. B. Blum
Software Mentions: 1
Published: about 6 years ago

10.7717/peerj.4688

Increased chemical acetylation of peptides and proteins in rats after daily ingestion of diacetyl analyzed by Nano-LC-MS/MS
Cited by: 3
Author(s): Letícia Dias Lima Jedlicka, Sheila Barreto Guterres, Aleksandro Martins Balbino, Giuseppe Bruno Neto, Richardt Gama Landgraf, Liliam Fernandes, Emanuel Carrilho, Etelvino José Henriques Bechara, Nilson Antônio Assunção
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-020-6608-y

Integrated likelihood for phylogenomics under a no-common-mechanism model
Cited by: 0
Author(s): Hunter Tidwell, Luay Nakhleh
Software Mentions: 1
Published: over 4 years ago

10.1186/s12864-015-1469-5

How do SNP ascertainment schemes and population demographics affect inferences about population history?
Cited by: 43
Author(s): Emily Jane McTavish, David M. Hillis
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-15-S6-S10

Explaining evolution via constrained persistent perfect phylogeny
Cited by: 45
Author(s): Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Gabriella Trucco
Software Mentions: 1
Published: about 10 years ago

10.1186/s12862-019-1516-y

Multiple selective sweeps of ancient polymorphisms in and around LTα located in the MHC class III region on chromosome 6
Cited by: 5
Author(s): Michael C. Campbell, Bryan Ashong, Shaolei Teng, Jayla Harvey, Christopher Cross
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pbio.1000600

Exceptional Diversity, Maintenance of Polymorphism, and Recent Directional Selection on the APL1 Malaria Resistance Genes of Anopheles gambiae
Cited by: 67
Author(s): Susan M. Rottschaefer, Michelle M. Riehle, Boubacar Coulibaly, M Sacko, Oumou Niaré, Isabelle Morlais, Sékou F. Traorè, Kenneth D. Vernick, Brian P. Lazzaro
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2148-11-88

Population growth of Mexican free-tailed bats (Tadarida brasiliensis mexicana) predates human agricultural activity
Cited by: 22
Author(s): Amy L. Russell, Murray P. Cox, Veronica A. Brown, Gary F. McCracken
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pbio.0050171

A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome
Cited by: 395
Author(s): Kun Tang, Kevin R. Thornton, Mark Stoneking
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-14-S15-S6

Fast algorithms and heuristics for phylogenomics under ILS and hybridization
Cited by: 29
Author(s): Yu Yun, Nikola Ristic, Luay Nakhleh
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pbio.0020286

Population History and Natural Selection Shape Patterns of Genetic Variation in 132 Genes
Cited by: 479
Author(s): Joshua M. Akey, Michael A. Eberle, Mark J. Rieder, Christopher S. Carlson, Mark D. Shriver, Deborah A. Nickerson, Leonid Kruglyak
Software Mentions: 1
Published: about 20 years ago

10.1371/journal.pbio.2000234

Shedding Light on the Grey Zone of Speciation along a Continuum of Genomic Divergence
Cited by: 359
Author(s): Camille Roux, Christelle Fraïssé, Jonathan Romiguier, Yoann Anciaux, Nicolas Galtier, Nicolas Bierne
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pbio.0040072

A Map of Recent Positive Selection in the Human Genome
Cited by: 2,292
Author(s): Benjamin F. Voight, Sridhar Kudaravalli, Xiaoquan Wen, Jonathan K. Pritchard
Software Mentions: 1
Published: over 18 years ago

10.1371/journal.pbio.0040052

Gene Losses during Human Origins
Cited by: 199
Author(s): Xiaoxia Wang, Wendy E. Grus, Jianzhi Zhang
Software Mentions: 1
Published: almost 19 years ago

10.1371/journal.pbio.0060251

High Rate of Recent Transposable Element–Induced Adaptation in Drosophila melanogaster
Cited by: 175
Author(s): Josefa González, Lenkov Kapa, Mikhail Lipatov, J. Michael Macpherson, Dmitri A. Petrov
Software Mentions: 1
Published: about 16 years ago

10.1186/1297-9686-43-20

The complete linkage disequilibrium test: a test that points to causative mutations underlying quantitative traits
Cited by: 4
Author(s): Eivind Uleberg, Theo H. E. Meuwissen
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-016-3099-y

Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks
Cited by: 2
Author(s): Yun Yu, Christopher Jermaine, Luay Nakhleh
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pcbi.1002495

Simulation of Molecular Data under Diverse Evolutionary Scenarios
Cited by: 57
Author(s): Miguel Arenas
Software Mentions: 1
Published: over 12 years ago

10.1534/genetics.116.198796

The Bacterial Sequential Markov Coalescent
Cited by: 29
Author(s): Nicola De Maio, Daniel J. Wilson
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pcbi.1003649

An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes
Cited by: 51
Author(s): Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn, Luay Nakhleh
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-9-S1-S24

Algorithms to estimate the lower bounds of recombination with or without recurrent mutations
Cited by: 4
Author(s): Xiaoming Liu, Yun Xin Fu
Software Mentions: 1
Published: almost 17 years ago

10.1371/currents.tol.34260cc27551a527b124ec5f6334b6be

Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated conditions
Cited by: 73
Author(s): João Filipe Riva Tonini, Andrew Moore, David B. Stern, Maryia Shcheglovitova, Guillermo Ortı́
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pgen.1000924

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites
Cited by: 261
Author(s): Talia L. Karasov, Philipp W. Messer, Dmitri A. Petrov
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pgen.1005703

A Spatial Framework for Understanding Population Structure and Admixture
Cited by: 103
Author(s): Gideon S. Bradburd, Peter L. Ralph, Graham Coop
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pgen.1005550

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes
Cited by: 49
Author(s): Mark Lipson, Po−Ru Loh, Sriram Sankararaman, Nick Patterson, Bonnie Berger, David Reich
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pgen.1002967

Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
Cited by: 1,819
Author(s): Joseph K. Pickrell, Jonathan K. Pritchard
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pgen.1006489

Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans
Cited by: 62
Author(s): Arbel Harpak, Anand Bhaskar, Jonathan K. Pritchard
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pgen.1003519

The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit
Cited by: 83
Author(s): Miguel Carneiro, Frank W. Albert, Sandra Afonso, Ricardo José Garcia Pereira, Hernán A. Burbano, Rita Campos, José Melo‐Ferreira, José Antonio Blanco‐Aguiar, Rafael Villafuerte, Michael W. Nachman, Jeffrey M. Good, Nuno Ferrand
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pgen.1000674

Inference of Microbial Recombination Rates from Metagenomic Data
Cited by: 34
Author(s): Philip L. Johnson, Montgomery Slatkin
Software Mentions: 1
Published: about 15 years ago

10.1186/s12862-016-0857-z

A genome-wide scan for genes under balancing selection in Drosophila melanogaster
Cited by: 27
Author(s): Myriam Croze, Andreas Wollstein, Vedran Božičević, Daniel Živković, Wolfgang Stephan, Stephan Hütter
Software Mentions: 1
Published: almost 8 years ago

10.1186/gb-2008-9-9-r143

The signature of long-standing balancing selection at the human defensin β-1 promoter
Cited by: 61
Author(s): Rachele Cagliani, Matteo Fumagalli, Stefania Riva, Diego Forni, Giacomo P. Comi, Giorgia Menozzi, Nereo Bresolin, Manuela Sironi
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-8-146

Simple models of genomic variation in human SNP density
Cited by: 13
Author(s): Raazesh Sainudiin, Andrew G. Clark, Richard Durrett
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-11-702

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes
Cited by: 162
Author(s): Eduard Akhunov, Alina Akhunova, Olin D. Anderson, James A. Anderson, N. K. Blake, Michael T. Clegg, Devin Coleman‐Derr, E. J. Conley, Curt Crossman, Karin R. Deal, Jorge Dubcovsky, Bikram S. Gill, Yong Gu, Jakub Hadam, Hwa‐Young Heo, Naxin Huo, Gerard R. Lazo, Ming Luo, Q. Yaqin, David E. Matthews, Patrick E. McGuire, Peter L. Morrell, C. O. Qualset, James Renfro, D. A. Tabanao, L. E. Talbert, Chao Tian, Donna M. Toleno, Marilyn L. Warburton, Frank M. You, Wenjun Zhang, Jan Dvořák
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pgen.1009701

Phylogenomic assessment of the role of hybridization and introgression in trait evolution
Cited by: 6
Author(s): Yaxuan Wang, Zhen Cao, Huw A. Ogilvie, Luay Nakhleh
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pgen.1008175

A statistical model for reference-free inference of archaic local ancestry
Cited by: 27
Author(s): Arun Durvasula, Sriram Sankararaman
Software Mentions: 1
Published: over 5 years ago