Ecosyste.ms: Papers

10.1038/s41598-020-60654-7

Pesticide pollution in freshwater paves the way for schistosomiasis transmission
Cited by: 25
Author(s): Jeremias Martin Becker, Akbar Ganatra, Faith Jebiwot Kandie, Lina Mühlbauer, Jörg Ahlheim, Werner Brack, Baldwyn Torto, Eric L. Agola, Francis McOdimba, Henner Hollert, Ulrike Fillinger, Matthias Liess
Software Mentions: 10
Published: over 4 years ago

10.1093/molbev/msu269

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci
Cited by: 488
Author(s): Simon H. Martin, John W. Davey, Chris D. Jiggins
Software Mentions: 10
Published: about 10 years ago

10.1002/ece3.3261

Evolutionarily significant units of the critically endangered leaf frog<i>Pithecopus ayeaye</i>(Anura, Phyllomedusidae) are not effectively preserved by the Brazilian protected areas network
Cited by: 16
Author(s): Rafael Félix de Magalhães, Priscila Lemes, Arley Camargo, Ubirajara Oliveira, Reuber Albuquerque Brandão, Hans Thomassen, Paulo Christiano de Anchieta Garcia, Felipe Sá Fortes Leite, Fabrício R. Santos
Software Mentions: 7
Published: about 7 years ago

10.1186/s12859-020-03945-0

mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes
Cited by: 1
Author(s): Bing Song, August E. Woerner, John V. Planz
Software Mentions: 7
Published: almost 4 years ago

10.1093/bioinformatics/bty646

Automated workflow composition in mass spectrometry-based proteomics
Cited by: 37
Author(s): Magnus Palmblad, Anna‐Lena Lamprecht, Jon C. Ison, Veit Schwämmle
Software Mentions: 6
Published: over 6 years ago

10.1186/1471-2156-13-27

EggLib: processing, analysis and simulation tools for population genetics and genomics
Cited by: 139
Author(s): Stéphane De Mita, Mathieu Siol
Software Mentions: 6
Published: almost 13 years ago

10.1534/g3.112.002527

Alignment-Free Population Genomics: An Efficient Estimator of Sequence Diversity
Cited by: 9
Author(s): Bernhard Haubold, Peter Pfaffelhuber
Software Mentions: 6
Published: over 12 years ago

10.1186/s12915-016-0283-0

Secondary structure impacts patterns of selection in human lncRNAs
Cited by: 39
Author(s): Cinta Pegueroles, Toni Gabaldón
Software Mentions: 6
Published: over 8 years ago

10.1093/molbev/msy198

Phylotranscriptomic Insights into the Diversification of Endothermic<i>Thunnus</i>Tunas
Cited by: 13
Author(s): Adam Ciezarek, Owen G. Osborne, Oliver N. Shipley, Edward J. Brooks, S Tracey, Jaime D. McAllister, Luke D. Gardner, Michael J.E. Sternberg, Barbara A. Block, Vincent Savolainen
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0158691

Single-Locus versus Multilocus Patterns of Local Adaptation to Climate in Eastern White Pine (Pinus strobus, Pinaceae)
Cited by: 28
Author(s): Om P. Rajora, Andrew J. Eckert, John W. R. Zinck
Software Mentions: 5
Published: over 8 years ago

10.1186/s12859-020-03862-2

Mixed logistic regression in genome-wide association studies
Cited by: 2
Author(s): Jacqueline Milet, David Courtin, André Garcia, Hervé Perdry
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0015925

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals
Cited by: 526
Author(s): Robert Kofler, Pablo Orozco‐terWengel, Nicola De Maio, Ram Vinay Pandey, Viola Nolte, Andreas Futschik, Carolin Kosiol, Christian Schlötterer
Software Mentions: 5
Published: almost 14 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.pcbi.1003480

GAGA: A New Algorithm for Genomic Inference of Geographic Ancestry Reveals Fine Level Population Substructure in Europeans
Cited by: 9
Author(s): Oscar Lao, Fan Liu, Andreas Wollstein, Manfred Kayser
Software Mentions: 4
Published: over 10 years ago

10.3390/genes11070775

Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population
Cited by: 2
Author(s): Risa L. Iwasaki, Koji Ishiya, Hideaki Kanzawa-Kiriyama, Yosuke Kawai, Jun Gojobori, Yoko Satta
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.24836

Minimal-assumption inference from population-genomic data
Cited by: 21
Author(s): Daniel B. Weissman, Oskar Hallatschek
Software Mentions: 4
Published: over 7 years ago

10.1111/tpj.15278

An Arabidopsis lipid map reveals differences between tissues and dynamic changes throughout development
Cited by: 17
Author(s): Cheka Kehelpannala, Thusitha Rupasinghe, Asher Pasha, Eddi Esteban, Thomas Hennessy, David Bradley, Berit Ebert, Nicholas J. Provart, Ute Roessner
Software Mentions: 4
Published: over 3 years ago

10.1111/tpj.14795

The genetic and functional analysis of flavor in commercial tomato: the <i>FLORAL4</i> gene underlies a QTL for floral aroma volatiles in tomato fruit
Cited by: 30
Author(s): Yury Tikunov, Raana Roohanitaziani, Fien Meijer‐Dekens, Jos Molthoff, João Paulo, Richard Finkers, Iris Capel, Fátima Carvajal Moreno, Chris Maliepaard, Mariska Nijenhuis-de Vries, C.W. Labrie, W. Verkerke, A.W. van Heusden, Fred van Eeuwijk, R.G.F. Visser, Arnaud Bovy
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.1910

Reconstructing the demographic history of divergence between European river and brook lampreys using approximate Bayesian computations
Cited by: 25
Author(s): Quentin Rougemont, Camille Roux, Samuel Neuenschwander, Jérôme Goudet, Sophie Launey, Guillaume Evanno
Software Mentions: 4
Published: over 8 years ago

10.1186/s13742-016-0114-9

Scalable linkage-disequilibrium-based selective sweep detection: a performance guide
Cited by: 15
Author(s): Nikolaos Alachiotis, Pavlos Pavlidis
Software Mentions: 4
Published: over 8 years ago

10.1111/tpj.14454

Metabolic diversification of nitrogen‐containing metabolites by the expression of a heterologous lysine decarboxylase gene in Arabidopsis
Cited by: 10
Author(s): Y. Shimizu, Amit Rai, Yuko Okawa, Hajime Tomatsu, Masaru Satô, Kota Kera, Hideyuki Suzuki, Kazuki Saito, Mami Yamazaki
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-015-0721-y

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees
Cited by: 32
Author(s): Sha Zhu, J.H. Degnan, Sharyn J. Goldstien, Bjarki Eldon
Software Mentions: 4
Published: about 9 years ago

10.1093/gbe/evaa053

Divergence-Based Introgression Polarization
Cited by: 8
Author(s): Evan S. Forsythe, Daniel B Sloan, Mark A. Beilstein
Software Mentions: 4
Published: over 4 years ago

10.1111/j.1365-294X.2010.04838.x

Multiple hybridization events between <i>Drosophila simulans</i> and <i>Drosophila mauritiana</i> are supported by mtDNA introgression
Cited by: 37
Author(s): Maria D. S. Nunes, Pablo Orozco-ter Wengel, Michaela Kreissl, Christian Schlötterer
Software Mentions: 4
Published: about 14 years ago

10.7554/eLife.12081

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
Cited by: 141
Author(s): Álvaro Martínez Barrio, Sangeet Lamichhaney, Guangyi Fan, Nima Rafati, Mats E. Pettersson, He Zhang, Jacques Dainat, Diana Ekman, Marc P. Höppner, Patric Jern, Marcel Martin, Björn Nystedt, Xin Liu, Wenbin Chen, Xinming Liang, Chengcheng Shi, Yuanyuan Fu, Kailong Ma, Xiaowei Zhan, Chungang Feng, Ulla Gustafson, Carl-Johan Rubin, Markus Sällman Almén, Martina Blass, Michèle Casini, Arild Folkvord, Linda Laikre, Nils Ryman, Simon Ming‐Yuen Lee, Xun Xu, Leif Andersson
Software Mentions: 4
Published: over 8 years ago

10.1111/eva.12082

Investigating the genetics of<i><scp>B</scp>ti</i>resistance using m<scp>RNA</scp>tag sequencing: application on laboratory strains and natural populations of the dengue vector<i><scp>A</scp>edes aegypti</i>
Cited by: 9
Author(s): Margot Paris, Sébastien Marcombe, Éric Coissac, Vincent Corbel, Jean‐Philippe David, Laurence Després
Software Mentions: 3
Published: about 11 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

10.1186/1471-2164-12-S5-S1

Gene selection and classification for cancer microarray data based on machine learning and similarity measures
Cited by: 73
Author(s): Qingzhong Li, Andrew H. Sung, Zhongxue Chen, Jianzhong Liu, Lei Chen, Mengyu Qiao, Zhaohui Wang, Xudong Huang, Youping Deng
Software Mentions: 3
Published: almost 13 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.1003942

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data
Cited by: 122
Author(s): Krystyna Nadachowska‐Brzyska, Reto Burri, Pall I. Olason, Takeshi Kawakami, Linnéa Smeds, Hans Ellegren
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-8-268

msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation
Cited by: 138
Author(s): Michael J. Hickerson, Eli A. Stahl, Naoki Takebayashi
Software Mentions: 3
Published: over 17 years ago

10.1093/bioinformatics/btv250

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics
Cited by: 30
Author(s): Yasset Perez‐Riverol, Julian Uszkoreit, Aniel Sánchez, Tobias Ternent, Noemí del Toro, Henning Hermjakob, Juan Antonio Vizcaíno, Rui Wang
Software Mentions: 3
Published: over 9 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

10.3389/fgene.2019.01356

The Sole Mycobacterium smegmatis MazF Toxin Targets tRNALys to Impart Highly Selective, Codon-Dependent Proteome Reprogramming
Cited by: 7
Author(s): Valdir C. Barth, Nancy A. Woychik
Software Mentions: 3
Published: over 4 years ago

10.1093/sysbio/syv082

<i>SimPhy</i>: Phylogenomic Simulation of Gene, Locus, and Species Trees
Cited by: 116
Author(s): Diego Mallo, Leonardo de Oliveira Martins, David Posada
Software Mentions: 3
Published: about 9 years ago

10.1093/molbev/msw299

Genome sequencing reveals the origin of the allotetraploid <i>Arabidopsis suecica</i>
Cited by: 49
Author(s): Polina Yu. Novikova, Takashi Tsuchimatsu, Samson Simon, Viktoria Nizhynska, Viktor Voronin, Robin Burns, О. М. Федоренко, Svante Holm, Torbjörn Säll, Elisa Prat, William Marande, Vincent Castric, Magnus Nordborg
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12859-019-2747-z

Estimates of introgression as a function of pairwise distances
Cited by: 16
Author(s): Bastian Pfeifer, Durrell D. Kapan
Software Mentions: 3
Published: over 5 years ago

10.1093/molbev/msab047

Biases in demographic modelling affect our understanding of recent divergence
Cited by: 32
Author(s): Paolo Momigliano, Ann‐Britt Florin, Juha Merilä
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0166162

Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples
Cited by: 13
Author(s): James B. Pettengill, Arthur W. Pightling, Joseph D. Baugher, Hugh Rand, Errol Strain
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2148-8-180

Evolution of a behavior-linked microsatellite-containing element in the 5' flanking region of the primate AVPR1A gene
Cited by: 56
Author(s): Zoe R. Donaldson, Fyodor A. Kondrashov, Andrea S. Putnam, Yaohui Bai, Tara L Stoinski, Elizabeth A. D. Hammock, Larry J. Young
Software Mentions: 3
Published: almost 17 years ago

10.1371/journal.pone.0031972

Heterogeneity in Genetic Diversity among Non-Coding Loci Fails to Fit Neutral Coalescent Models of Population History
Cited by: 27
Author(s): Jeffrey L. Peters, Trina E. Roberts, Kevin Winker, Kevin G. McCracken
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0156018

Proteomic Study of Entamoeba histolytica Trophozoites, Cysts, and Cyst-Like Structures
Cited by: 17
Author(s): Milka Luna-Nácar, José Navarrete-Perea, Bárbara Moguel, Raúl J. Bobes, Juan Pedro Laclette, Julio César Carrero
Software Mentions: 3
Published: over 8 years ago

10.1093/molbev/msx134

Patterns of Genome-Wide Diversity and Population Structure in the Drosophila athabasca Species Complex
Cited by: 16
Author(s): Karen Miller, Ryan Bracewell, Michael B. Eisen, Doris Bachtrog
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.36482

A multispecies coalescent model for quantitative traits
Cited by: 38
Author(s): Fábio K. Mendes, Jesualdo A. Fuentes-González, Joshua G. Schraiber, Matthew W. Hahn
Software Mentions: 3
Published: about 6 years ago

10.1093/sysbio/syv045

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data
Cited by: 95
Author(s): Alexander Nater, Reto Burri, Takeshi Kawakami, Linnéa Smeds, Hans Ellegren
Software Mentions: 3
Published: over 9 years ago

10.1186/s13323-015-0030-2

Early modern human dispersal from Africa: genomic evidence for multiple waves of migration
Cited by: 35
Author(s): Francesca Tassi, Silvia Ghirotto, Massimo Mezzavilla, Sibelle Torres Vilaça, Lisa De Santi, Guido Barbujani
Software Mentions: 3
Published: almost 9 years ago

10.3390/s21124143

Automatic Visual Attention Detection for Mobile Eye Tracking Using Pre-Trained Computer Vision Models and Human Gaze
Cited by: 3
Author(s): Michael Barz, Daniel Sonntag
Software Mentions: 3
Published: over 3 years ago

10.1093/sysbio/syt033

Delimiting Species Using Single-Locus Data and the Generalized Mixed Yule Coalescent Approach: A Revised Method and Evaluation on Simulated Data Sets
Cited by: 1,118
Author(s): Tomochika Fujisawa, Timothy G. Barraclough
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2105-15-273

A new method for modeling coalescent processes with recombination
Cited by: 16
Author(s): Ying Wang, Ying Zhou, Linfeng Li, Xian Chen, Yuting Liu, Zhiming Ma, Shuhua Xu
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pgen.0030217

Localization of Candidate Regions Maintaining a Common Polymorphic Inversion (2La) in Anopheles gambiae
Cited by: 76
Author(s): Bradley J. White, Matthew W. Hahn, Marco Pombi, Bryan J. Cassone, Neil F. Lobo, Frédéric Simard, Nora J. Besansky
Software Mentions: 3
Published: almost 17 years ago

10.1186/1471-2156-11-86

Discovering joint associations between disease and gene pairs with a novel similarity test
Cited by: 3
Author(s): Wan-Yu Lin, Wen‐Chung Lee
Software Mentions: 3
Published: about 14 years ago

10.1186/1471-2164-14-148

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs
Cited by: 47
Author(s): Anna Esteve‐Codina, Yogesh Paudel, Luca Ferretti, Emanuele Raineri, Hendrik‐Jan Megens, L. Silío, M. C. Rodríguez, Martien A. M. Groenen, Sebastián E. Ramos-Onsins, Miguel Pérez‐Enciso
Software Mentions: 3
Published: almost 12 years ago

10.3390/genes10090693

Interspecific Genetic Differences and Historical Demography in South American Arowanas (Osteoglossiformes, Osteoglossidae, Osteoglossum)
Cited by: 10
Author(s): Fernando Henrique Santos de Souza, Manolo F. Perez, Luiz Antônio Carlos Bertollo, Ezequiel Aguiar de Oliveira, Sébastien Lavoué, Carla C. Gestich, Petr Ráb, Tariq Ezaz, Thomas Liehr, Patrik Ferreira Viana, Eliana Feldberg, Marcelo de Bello Cioffi
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-10-S3-S13

MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads
Cited by: 13
Author(s): Hua Bao, Yuanyan Xiong, Hui Guo, Renchao Zhou, Xuemei Lu, Zhen Yang, Yang Zhong, Suhua Shi
Software Mentions: 3
Published: almost 15 years ago

10.1534/genetics.118.301333

Inferring Continuous and Discrete Population Genetic Structure Across Space
Cited by: 199
Author(s): Gideon S. Bradburd, Graham Coop, Peter L. Ralph
Software Mentions: 3
Published: over 6 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

10.1371/journal.pgen.1008896

Learning the properties of adaptive regions with functional data analysis
Cited by: 13
Author(s): Mehreen R. Mughal, Hillary Koch, Jinguo Huang, Francesca Chiaromonte, Michael DeGiorgio
Software Mentions: 3
Published: about 4 years ago

10.3390/genes1010124

Population Genomics of Secondary Contact
Cited by: 8
Author(s): Anthony J. Geneva, Daniel Garrigan
Software Mentions: 3
Published: over 14 years ago

10.1002/evl3.81

Positive and balancing selection on<i>SLC18A1</i>gene associated with psychiatric disorders and human-unique personality traits
Cited by: 14
Author(s): Daiki X. Sato, Masakado Kawata
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2105-9-44

Generating samples for association studies based on HapMap data
Cited by: 46
Author(s): Jing Li, Yixuan Chen
Software Mentions: 2
Published: almost 17 years ago

10.3389/fgene.2019.00728

Signature of the Paleo-Course Changes in the São Francisco River as Source of Genetic Structure in Neotropical Pithecopus nordestinus (Phyllomedusinae, Anura) Treefrog
Cited by: 12
Author(s): Daniel Pacheco Bruschi, Elen Arroyo Peres, Luciana Bolsoni Lourenço, Luiz Filipe de Macedo Bartoleti, Thadeu Sobral‐Souza, Shirlei Maria Recco‐Pimentel
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2013.00009

Computer Programs and Methodologies for the Simulation of DNA Sequence Data with Recombination
Cited by: 15
Author(s): Miguel Arenas
Software Mentions: 2
Published: almost 12 years ago

10.1002/ece3.3190

A neutral view of the evolving genomic architecture of speciation
Cited by: 6
Author(s): Laura Southcott, Marcus R. Kronforst
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-016-1277-1

A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation
Cited by: 39
Author(s): Hussein A. Hejase, Kevin J. Liu
Software Mentions: 2
Published: about 8 years ago

10.1002/ece3.2444

<scp>SNP</scp> s across time and space: population genomic signatures of founder events and epizootics in the House Finch ( <i>Haemorhous mexicanus</i> )
Cited by: 39
Author(s): Allison J. Shultz, Allan J. Baker, Geoffrey E. Hill, Paul M. Nolan, Scott V. Edwards
Software Mentions: 2
Published: about 8 years ago

10.1002/ece3.722

Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0
Cited by: 16
Author(s): Lisha Mathew, Paul Staab, Laura Rose, Dirk Metzler
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2105-15-3

Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences
Cited by: 15
Author(s): Tao Yang, Hong‐Wen Deng, Tianhua Niu
Software Mentions: 2
Published: almost 11 years ago

10.1002/ece3.2014

Incongruent range dynamics between co-occurring Asian temperate tree species facilitated by life history traits
Cited by: 10
Author(s): Yunpeng Zhao, Xiaoqian Yan, G. W. Muir, Qiong-yan Dai, Marcus A. Koch, Chengxin Fu
Software Mentions: 2
Published: over 8 years ago

10.1002/ece3.3993

Upwelling and eddies affect connectivity among local populations of the goldeye rockfish,<i>Sebastes thompsoni</i>(Pisces, Scorpaenoidei)
Cited by: 10
Author(s): Hyo Jae Yu, Jin-Koo Kim
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2012.00173

Localization of Association Signal from Risk and Protective Variants in Sequencing Studies
Cited by: 9
Author(s): Abra Brisbin, Gregory D. Jenkins, Katarzyna A. Ellsworth, Liewei Wang, Brooke L. Fridley
Software Mentions: 2
Published: almost 13 years ago

10.1186/1471-2105-11-65

Haplotype allelic classes for detecting ongoing positive selection
Cited by: 17
Author(s): Julie Hussin, Philippe Nadeau, Jean‐François Lefebvre, Damian Labuda
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2105-14-200

Using ancestral information to detect and localize quantitative trait loci in genome-wide association studies
Cited by: 22
Author(s): Katherine Thompson, Laura Kubatko
Software Mentions: 2
Published: over 11 years ago

10.1038/s42003-018-0085-8

RAiSD detects positive selection based on multiple signatures of a selective sweep and SNP vectors
Cited by: 84
Author(s): Nikolaos Alachiotis, Pavlos Pavlidis
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2156-9-76

Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow
Cited by: 18
Author(s): Murray P. Cox, August E. Woerner, Jeffrey D. Wall, Michael F. Hammer
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pbio.1000082

Accelerated Adaptive Evolution on a Newly Formed X Chromosome
Cited by: 59
Author(s): Doris Bachtrog, Jeffrey D. Jensen, Zhi Zhang
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0002411

Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrata
Cited by: 173
Author(s): Jeffrey Ross‐Ibarra, Stephen I. Wright, John Paul Foxe, Akira Kawabe, Leah DeRose-Wilson, Gesseca Gos, Deborah Charlesworth, Brandon S. Gaut
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2105-8-472

Direct maximum parsimony phylogeny reconstruction from genotype data
Cited by: 13
Author(s): Srikanth Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz
Software Mentions: 2
Published: almost 17 years ago

10.3390/plants2010016

Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations
Cited by: 6
Author(s): James L. Kitchen, Robin G. Allaby
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0253618

Delftia acidovorans secretes substances that inhibit the growth of Staphylococcus epidermidis through TCA cycle-triggered ROS production
Cited by: 5
Author(s): Tomotaka Ohkubo, Yasuhiko Matsumoto, Otomi Cho, Yuki Ogasawara, Takashi Sugita
Software Mentions: 2
Published: over 3 years ago

10.5936/csbj.201303001

CHROMATOGATE: A TOOL FOR DETECTING BASE MIS-CALLS IN MULTIPLE SEQUENCE ALIGNMENTS BY SEMI-AUTOMATIC CHROMATOGRAM INSPECTION
Cited by: 9
Author(s): Nikolaos Alachiotis, Emmanouella Vogiatzi, Pavlos Pavlidis, Alexandros Stamatakis
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0135028

gPGA: GPU Accelerated Population Genetics Analyses
Cited by: 4
Author(s): C. Zhou, Xianyu Lang, Yangang Wang, Chao‐Dong Zhu
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0006366

Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations
Cited by: 49
Author(s): Murray P. Cox, David A. Morales, August E. Woerner, Jesse Sozanski, Jeffrey D. Wall, Michael F. Hammer
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0205396

Probing the ecological and evolutionary history of a thermophilic cyanobacterial population via statistical properties of its microdiversity
Cited by: 13
Author(s): Michael J. Rosen, Michelle Davison, Daniel S. Fisher, Devaki Bhaya
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0018155

Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum
Cited by: 18
Author(s): Aurélien Tellier, Peter Pfaffelhuber, Bernhard Haubold, Lisha Naduvilezhath, Laura Rose, Thomas Städler, Wolfgang Stephan, Dirk Metzler
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0200278

Positive selection on schizophrenia-associated ST8SIA2 gene in post-glacial Asia
Cited by: 13
Author(s): Naoko T. Fujito, Yoko Satta, Masaya Hane, Atsushi Matsui, Kenta Yashima, Ken Kitajima, Chihiro Sato, Naoyuki Takahata, Toshiyuki Hayakawa
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0091924

Naturally Occurring Deletions of Hunchback Binding Sites in the Even-Skipped Stripe 3+7 Enhancer
Cited by: 11
Author(s): Arnar Pálsson, Natalia Wesolowska, Sigrún Reynisdóttir, Michael Ludwig, Martin Kreitman
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0134435

Formal Comment to Pettengill: The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence
Cited by: 2
Author(s): Mark Achtman, Zhemin Zhou, Xavier Didelot
Software Mentions: 2
Published: about 9 years ago

10.1186/s12862-014-0185-0

Demographic history and gene flow during silkworm domestication
Cited by: 29
Author(s): Shaoyu Yang, Minjin Han, Lei Kang, Zi-Wen Li, Yulong Shen, Ze Zhang
Software Mentions: 2
Published: about 10 years ago

10.1186/s12859-021-04265-7

A novel nonlinear dimension reduction approach to infer population structure for low-coverage sequencing data
Cited by: 1
Author(s): Miao Zhang, Yiwen Liu, Hua Zhou, Joseph C. Watkins, Jin Zhou
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pgen.1003938

Co-evolution of Human Leukocyte Antigen (HLA) Class I Ligands with Killer-Cell Immunoglobulin-Like Receptors (KIR) in a Genetically Diverse Population of Sub-Saharan Africans
Cited by: 111
Author(s): Paul J. Norman, Jill A. Hollenbach, Neda Nemat-Gorgani, Lisbeth A. Guethlein, Hugo G. Hilton, Marcelo J. Pando, Kwadwo A. Koram, Eleanor M. Riley, Laurent Abi-Rached, Peter Parham
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0045138

Can Diversifying Selection Be Distinguished from History in Geographic Clines? A Population Genomic Study of Killifish (Fundulus heteroclitus)
Cited by: 31
Author(s): Allan E. Strand, Larissa M. Williams, Marjorie F. Oleksiak, Erik E. Sotka
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0078813

Ancestral Polymorphisms and Sex-Biased Migration Shaped the Demographic History of Brown Bears and Polar Bears
Cited by: 4
Author(s): Shigeki Nakagome, Shuhei Mano, Masami Hasegawa
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12859-017-1613-0

AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data
Cited by: 7
Author(s): Nathan K. Schaefer, Beth Shapiro, Edward Green
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1005896

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting
Cited by: 305
Author(s): Claudia Solís-Lemus, Cécile Ané
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0222004

Genomic analyses reveal an absence of contemporary introgressive admixture between fin whales and blue whales, despite known hybrids
Cited by: 14
Author(s): Michael V. Westbury, Bent Petersen, Eline D. Lorenzen
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0081977

Both Positive and Negative Selection Pressures Contribute to the Polymorphism Pattern of the Duplicated Human CYP21A2 Gene
Cited by: 9
Author(s): J. Szabó, Ágnes Szilágyi, Zoltán Doleschall, Attila Patócs, Henriette Farkas, Zoltán Prohászka, Kristóf Rácz, George Füst, Márton Doleschall
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1006919

Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes
Cited by: 80
Author(s): Emilie J. Richards, Christopher H. Martin
Software Mentions: 2
Published: about 7 years ago

10.1186/s12859-015-0791-x

The Gap Procedure: for the identification of phylogenetic clusters in HIV-1 sequence data
Cited by: 18
Author(s): Irene Vrbik, David A. Stephens, Michel Roger, Bluma G. Brenner
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pgen.1005877

Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach
Cited by: 129
Author(s): Simon Boitard, Willy Rodríguez, Flora Jay, Stefano Mona, Frédéric Austerlitz
Software Mentions: 2
Published: over 8 years ago

10.1093/bioinformatics/btu861

scrm: efficiently simulating long sequences using the approximated coalescent with recombination
Cited by: 108
Author(s): Paul Staab, Sha Zhu, Dirk Metzler, Gerton Lunter
Software Mentions: 2
Published: almost 10 years ago