Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: ms
https://packages.ecosyste.ms/registries/pypi.org/packages/ms
ms
2 versions
Latest release: about 8 years ago
209 downloads last month
Papers Mentioning ms 308
10.1371/journal.pone.0205396
Probing the ecological and evolutionary history of a thermophilic cyanobacterial population via statistical properties of its microdiversityCited 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.0081977
Both Positive and Negative Selection Pressures Contribute to the Polymorphism Pattern of the Duplicated Human CYP21A2 GeneCited 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.pone.0170701
Coalescence computations for large samples drawn from populations of time-varying sizesCited by: 7
Author(s): Andrzej Polański, Agnieszka Szczęsna, Mateusz Garbulowski, Marek Kimmel
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0253618
Delftia acidovorans secretes substances that inhibit the growth of Staphylococcus epidermidis through TCA cycle-triggered ROS productionCited by: 5
Author(s): Tomotaka Ohkubo, Yasuhiko Matsumoto, Otomi Cho, Yuki Ogasawara, Takashi Sugita
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0002411
Patterns of Polymorphism and Demographic History in Natural Populations of Arabidopsis lyrataCited 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
10.1038/s42003-018-0085-8
RAiSD detects positive selection based on multiple signatures of a selective sweep and SNP vectorsCited by: 84
Author(s): Nikolaos Alachiotis, Pavlos Pavlidis
Software Mentions: 2
Published: over 6 years ago
10.5936/csbj.201303001
CHROMATOGATE: A TOOL FOR DETECTING BASE MIS-CALLS IN MULTIPLE SEQUENCE ALIGNMENTS BY SEMI-AUTOMATIC CHROMATOGRAM INSPECTIONCited by: 9
Author(s): Nikolaos Alachiotis, Emmanouella Vogiatzi, Pavlos Pavlidis, Alexandros Stamatakis
Software Mentions: 2
Published: over 11 years ago
10.1002/ece3.722
Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0Cited by: 16
Author(s): Lisha Mathew, Paul Staab, Laura Rose, Dirk Metzler
Software Mentions: 2
Published: about 11 years ago
10.1002/ece3.2014
Incongruent range dynamics between co-occurring Asian temperate tree species facilitated by life history traitsCited 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/ece3.3190
A neutral view of the evolving genomic architecture of speciationCited by: 6
Author(s): Laura Southcott, Marcus R. Kronforst
Software Mentions: 2
Published: over 7 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/ece3.3993
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
10.1002/evl3.81
Positive and balancing selection on<i>SLC18A1</i>gene associated with psychiatric disorders and human-unique personality traitsCited by: 14
Author(s): Daiki X. Sato, Masakado Kawata
Software Mentions: 2
Published: about 6 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) TreefrogCited 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 RecombinationCited by: 15
Author(s): Miguel Arenas
Software Mentions: 2
Published: almost 12 years ago
10.3389/fgene.2012.00173
Localization of Association Signal from Risk and Protective Variants in Sequencing StudiesCited 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
10.1534/g3.112.004473
Evidence for Population-Specific Positive Selection on Immune Genes of<i>Anopheles gambiae</i>Cited by: 16
Author(s): Jacob E. Crawford, Emmanuel Bischoff, Thierry Garnier, Awa Gnémé, Karin Eiglmeier, Inge Holm, Michelle M. Riehle, Wamdaogo M. Guelbeogo, N’Falé Sagnon, Brian P. Lazzaro, Kenneth D. Vernick
Software Mentions: 2
Published: almost 12 years ago
10.1534/g3.113.007294
Comparative Analyses Identify the Contributions of Exotic Donors to Disease Resistance in a Barley Experimental PopulationCited by: 11
Author(s): Zhou Fang, Amber Eule-Nashoba, Carol Powers, Thomas J. Y. Kono, Shohei Takuno, Peter L. Morrell, Kevin P. Smith
Software Mentions: 2
Published: about 11 years ago
10.1534/g3.118.200462
Complex Haplotypes of <i>GSTM1</i> Gene Deletions Harbor Signatures of a Selective Sweep in East Asian PopulationsCited by: 8
Author(s): Marie Saitou, Yoko Satta, Ömer Gökçümen
Software Mentions: 2
Published: about 6 years ago
10.3390/genes9090452
Recent Selection on a Class I ADH Locus Distinguishes Southwest Asian Populations Including Ashkenazi JewsCited by: 9
Author(s): Shuangshuang Gu, Hui Li, Andrew J. Pakstis, William C. Speed, David Genevieve, Judith R. Kidd, Kenneth K. Kídd
Software Mentions: 2
Published: about 6 years ago
10.1002/gepi.20541
A simple and fast two-locus quality control test to detect false positives due to batch effects in genome-wide association studiesCited by: 32
Author(s): Sang Lee, Dale R. Nyholt, Stuart MacGregor, Anjali K. Henders, Krina T. Zondervan, Grant W. Montgomery, Peter M. Visscher
Software Mentions: 2
Published: almost 14 years ago
10.1186/s13059-016-1098-6
Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humansCited by: 107
Author(s): Aaron J. Sams, Anne Dumaine, Yohann Nédélec, Vania Yotova, Caroline Alfieri, Jerome E. Tanner, Philipp W. Messer, Luis B. Barreiro
Software Mentions: 2
Published: almost 8 years ago
10.1186/s13059-020-02196-9
Stairway Plot 2: demographic history inference with folded SNP frequency spectraCited by: 98
Author(s): Xiaoming Liu, Yunxin Fu
Software Mentions: 2
Published: almost 4 years ago
10.1093/gbe/evu266
Constraint and Adaptation in newt Toll-Like Receptor GenesCited by: 34
Author(s): Wiesław Babik, Katarzyna Dudek, Anna Fijarczyk, Maciej Pabijan, Michał Stuglik, Rafał Szkotak, Piotr Zieliński
Software Mentions: 2
Published: almost 10 years ago
10.1089/cmb.2020.0375
Estimating Genetic Similarity Matrices Using PhylogeniesCited by: 3
Author(s): Shijia Wang, Shufei Ge, Caroline Colijn, Priscila Biller, Liangliang Wang, Lloyd T. Elliott
Software Mentions: 2
Published: over 3 years ago
10.1098/rsos.191900
Signals interpreted as archaic introgression appear to be driven primarily by faster evolution in AfricaCited by: 11
Author(s): William Amos
Software Mentions: 2
Published: over 4 years ago
10.1126/sciadv.abh2419
Ancient genomics reveals tripartite origins of Japanese populationsCited by: 19
Author(s): Niall P. Cooke, Valeria Mattiangeli, Lara M. Cassidy, Ken Okazaki, Caroline A. Stokes, Shin Onbe, Satoshi Hatakeyama, Katsunosuke Machida, Kenji Kasai, Naoto Tomioka, Akihiko Matsumoto, Masafumi Ito, Yoshitaka Kojima, Daniel G. Bradley, Takashi Gakuhari, Shigeki Nakagome
Software Mentions: 2
Published: about 3 years ago
10.1038/srep32689
A HTML5 open source tool to conduct studies based on Libet’s clock paradigmCited by: 10
Author(s): Pablo Garaizar, Carmelo P. Cubillas, Helena Matute
Software Mentions: 2
Published: about 8 years ago
10.1038/s41598-021-99396-5
A prediction model using 2-propanol and 2-butanone in urine distinguishes breast cancerCited by: 3
Author(s): Shoko Kure, Sera Satoi, T Kitayama, Yuta Nagase, Nobuo Nakano, Marina Yamada, Noboru Uchiyama, Satoshi Miyashita, S. Iida, Hiroyuki Takei, Masao Miyashita
Software Mentions: 2
Published: about 3 years ago
10.1007/s00439-016-1651-0
Refining the Y chromosome phylogeny with southern African sequencesCited by: 39
Author(s): Chiara Barbieri, Alexander Hübner, Enrico Macholdt, Shengyu Ni, Sebastian Lippold, Roland Schröder, Sununguko Wata Mpoloka, Josephine Purps, Lutz Roewer, Mark Stoneking, Brigitte Pakendorf
Software Mentions: 2
Published: over 8 years ago
10.1007/s11548-020-02160-9
Learned optical flow for intra-operative tracking of the retinal fundusCited by: 5
Author(s): Claudio S. Ravasio, Theodoros Pissas, Edward Bloch, Blanca Flores, Sepehr Jalali, Danail Stoyanov, M. Jorge Cardoso, Lyndon da Cruz, Christos Bergeles
Software Mentions: 2
Published: over 4 years ago
10.1186/s13323-015-0019-x
Detecting individual ancestry in the human genomeCited by: 20
Author(s): Andreas Wollstein, Oscar Lao
Software Mentions: 2
Published: over 9 years ago
10.7554/eLife.35468
Gene flow mediates the role of sex chromosome meiotic drive during complex speciationCited by: 64
Author(s): Colin D. Meiklejohn, Emily L. Landeen, Kathleen E Gordon, Thomas Rzatkiewicz, Sarah B. Kingan, Anthony J. Geneva, Jeffrey Vedanayagam, Christina A. Muirhead, Daniel Garrigan, David L. Stern, Daven C. Presgraves
Software Mentions: 2
Published: almost 6 years ago
10.1128/JVI.00919-14
Unfixed Endogenous Retroviral Insertions in the Human PopulationCited by: 110
Author(s): Emanuele Marchi, Alexander Kanapin, Gkikas Magiorkinis, Robert Belshaw
Software Mentions: 2
Published: about 10 years ago
10.1186/1471-2164-10-551
Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variationsCited by: 35
Author(s): Aurélie Bonin, Margot Paris, Guillaume Tetreau, Jean‐Philippe David, Laurence Després
Software Mentions: 1
Published: almost 16 years ago
10.1186/1471-2156-11-33
Influence of mutation rate on estimators of genetic differentiation - lessons from Arabidopsis thalianaCited by: 53
Author(s): Ilkka Kronholm, Olivier Loudet, Juliette de Meaux
Software Mentions: 1
Published: over 14 years ago
10.1371/journal.pgen.0020105
Possible Ancestral Structure in Human PopulationsCited by: 258
Author(s): Vincent Plagnol, Jeffrey D. Wall
Software Mentions: 1
Published: over 18 years ago
10.1371/journal.pgen.1006199
Determining the Effect of Natural Selection on Linked Neutral Divergence across SpeciesCited by: 46
Author(s): Tanya N. Phung, Christian D. Huber, Kirk E. Lohmueller
Software Mentions: 1
Published: about 8 years ago
10.1371/journal.pgen.1005987
An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogasterCited by: 39
Author(s): Ana Catalán, Amanda Glaser-Schmitt, Eliza Argyridou, Pablo Duchen, John Parsch
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pgen.1003242
Gene Copy-Number Polymorphism Caused by Retrotransposition in HumansCited by: 85
Author(s): Daniel R. Schrider, Fábio C. P. Navarro, Pedro A. F. Galante, Raphael B. Parmigiani, Anamaria A. Camargo, Matthew W. Hahn, Sandro J. de Souza
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pgen.1002453
Inference of Population Structure using Dense Haplotype DataCited by: 955
Author(s): Daniel J. Lawson, Garrett Hellenthal, Simon Myers, Daniel Falush
Software Mentions: 1
Published: almost 13 years ago
10.1186/gb-2014-15-2-r36
Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genesCited by: 69
Author(s): Nitin Udpa, Roy Ronen, Dan Zhou, Junbin Liang, Tsering Stobdan, Otto Appenzeller, Ye Yin, Yuanping Du, Lixia Guo, Rui Cao, Yu Wang, Xin Jin, Chen Huang, Wenlong Jia, Dandan Cao, Guangwu Guo, Victoria E. Claydon, R. Hainsworth, Jorge L. Gamboa, Mehila Zibenigus, Guta Zenebe, Jin Xue, Siqi Liu, Kelly A. Frazer, Yingrui Li, Vineet Bafna, Gabriel G. Haddad
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pgen.1000695
Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency DataCited by: 1,526
Author(s): Ryan N. Gutenkunst, Ryan D. Hernández, Scott Williamson, Carlos D. Bustamante
Software Mentions: 1
Published: about 15 years ago
10.1371/journal.pgen.1003093
Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis arenosaCited by: 149
Author(s): Jesse D. Hollister, Brian J. Arnold, Elisabeth Svedin, Katherine S Xue, Brian P. Dilkes, Kirsten Bomblies
Software Mentions: 1
Published: almost 12 years ago
10.1002/humu.23121
Increased Population Risk of<i>AIP</i>-Related Acromegaly and Gigantism in IrelandCited by: 22
Author(s): Șerban Radian, Yoan Diekmann, Plamena Gabrovska, Brendan Holland, Lisa Bradley, Helen Wallace, Karen Stals, Anna Marie Bussell, Karen McGurren, Martín Cuesta, Anthony W. Ryan, Maria Herincs, Laura C. Hernández-Ramírez, Aidan Holland, Jade Samuels, Elena Daniela Aflorei, Sayka Barry, Judit Dénes, Ida Pernicova, Craig E Stiles, Giampaolo Trivellin, Ronan McCloskey, Michal Ajzensztejn, Noina Abid, Scott Akker, Moisés Mercado, Mark L. Cohen, Rajesh Thakker, Stephanie E Baldeweg, Ariel Barkan, Mădălina Muşat, Miles Levy, Stephen M. Orme, Martina Unterländer, Joachim Bürger, Ajith Kumar, Sian Ellard, Joseph McPartlin, Ross McManus, Gerard Linden, Brew Atkinson, David J. Balding, Amar Agha, Chris Thompson, Steven Hunter, Mark G. Thomas, Patrick J. Morrison, Márta Korbonits
Software Mentions: 1
Published: about 8 years ago
10.7554/eLife.63753
Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgressionCited by: 20
Author(s): Mark S. Hibbins, Matthew J. S. Gibson, Matthew W. Hahn
Software Mentions: 1
Published: almost 4 years ago
10.1093/gbe/evu042
Increased Substitution Rates Surrounding Low-Complexity Regions within Primate ProteinsCited by: 19
Author(s): Carolyn Lenz, Wilfried Haerty, G. Brian Golding
Software Mentions: 1
Published: over 10 years ago
10.1093/gbe/evu102
Deciphering the Genetic Blueprint behind Holstein Milk Proteins and ProductionCited by: 35
Author(s): Hyun-Jeong Lee, Jaemin Kim, Taeheon Lee, Jun-Kyu Son, Hobaek Yoon, Ki Hyun Baek, Jin Young Jeong, Yong-Min Cho, Kyung-Tai Lee, Byoung‐Chul Yang, Hyun-Joo Lim, Kwang-Hyun Cho, Tae-Hun Kim, Eung Gi Kwon, Jungrye Nam, Woori Kwak, Seoae Cho, Heebal Kim
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pgen.0020186
Soft Sweeps III: The Signature of Positive Selection from Recurrent MutationCited by: 266
Author(s): Pleuni S. Pennings, Joachim Hermisson
Software Mentions: 1
Published: almost 19 years ago
10.1186/1471-2105-12-111
MixtureTree: a program for constructing phylogenyCited by: 6
Author(s): Shu‐Chuan Chen, Michael S. Rosenberg, Bruce G. Lindsay
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.pgen.1002326
Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human GenomeCited by: 156
Author(s): Kirk E. Lohmueller, Anders Albrechtsen, Yingrui Li, Su Yeon Kim, Thorfinn Sand Korneliussen, Nicolas Vinckenbosch, Geng Tian, Emilia Huerta‐Sánchez, Alison F. Feder, Niels Grarup, Torben Jørgensen, Tao Jiang, Daniel R. Witte, Annelli Sandbæk, Ines Hellmann, Torsten Lauritzen, Torben Hansen, Oluf Pedersen, Jun Wang, Rasmus Nielsen
Software Mentions: 1
Published: about 13 years ago
10.1371/journal.pgen.1001178
Allele-Specific Down-Regulation of RPTOR Expression Induced by Retinoids Contributes to Climate AdaptationsCited by: 17
Author(s): Chang Sun, Catherine Southard, David B. Witonsky, Ralf Kittler, Anna Di Rienzo
Software Mentions: 1
Published: about 14 years ago
10.1371/journal.pgen.1008027
Genetic signatures of gene flow and malaria-driven natural selection in sub-Saharan populations of the "endemic Burkitt Lymphoma belt"Cited by: 19
Author(s): Mateus H. Gouveia, Andrew W. Bergen, Víctor Borda, Kelly Nunes, Thiago Peixoto Leal, Martin D. Ogwang, Edward D. Yeboah, James E. Mensah, Tobias Kinyera, Isaac Otim, Hadijah Nabalende, Ismail D. Legason, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Patrick Kerchan, Kishor Bhatia, Steven J. Reynolds, Richard B. Birtwum, Andrew A. Adjei, Yao Tettey, Evelyn Tay, Robert N. Hoover, Ruth M. Pfeiffer, Robert J. Biggar, James J. Goedert, Ludmila Prokunina–Olsson, Michael Dean, Meredith Yeager, Maria Fernanda Lima‐Costa, Ann W. Hsing, Sarah A. Tishkoff, Stephen J. Chanock, Eduardo Tarazona‐Santos, Sam M. Mbulaiteye
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pgen.1005851
Demographically-Based Evaluation of Genomic Regions under Selection in Domestic DogsCited by: 72
Author(s): Adam H. Freedman, Rena M. Schweizer, Diego Ortega‐Del Vecchyo, Eunjung Han, Brian W. Davis, Ilan Gronau, Pedro M. Silva, Marco Galaverni, Zhenxin Fan, Peter W. Marx, Belén Lorente-Galdós, Óscar Ramírez, Farhad Hormozdiari, Can Alkan, Carles Vilà, Kevin Squire, Eli Geffen, Josip Kusak, Adam R. Boyko, Heidi G. Parker, Clarence Lee, Vasisht Tadigotla, Adam Siepel, Carlos D. Bustamante, Timothy T. Harkins, Stanley F. Nelson, Tomàs Marquès‐Bonet, Elaine A. Ostrander, Robert K. Wayne, John Novembre
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pgen.1003080
Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African AdmixtureCited by: 322
Author(s): John E. Pool, Russell Corbett-Detig, Ryuichi P. Sugino, Kristian Stevens, Charis Cardeno, Marc W. Crepeau, Pablo Duchen, J. J. Emerson, Perot Saelao, David J. Begun, Charles H. Langley
Software Mentions: 1
Published: almost 12 years ago
10.1186/1471-2156-7-16
Fast "coalescent" simulationCited by: 211
Author(s): Paul Marjoram, Jeff Wall
Software Mentions: 1
Published: over 18 years ago
10.1093/gbe/evu271
A Neutrality Test for Detecting Selection on DNA Methylation Using Single Methylation Polymorphism Frequency SpectrumCited by: 22
Author(s): Jun Wang, Chuanzhu Fan
Software Mentions: 1
Published: almost 10 years ago
10.1093/gbe/evaa022
Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population StructureCited by: 4
Author(s): Hillary Koch, Michael DeGiorgio
Software Mentions: 1
Published: almost 5 years ago
10.1186/1471-2148-9-123
A complex selection signature at the human AVPR1B geneCited by: 11
Author(s): Rachele Cagliani, Matteo Fumagalli, Diego Forni, Stefania Riva, Matteo Cereda, Giacomo P. Comi, Linda Pattini, Nereo Bresolin, Manuela Sironi
Software Mentions: 1
Published: over 15 years ago
10.1093/gbe/evaa087
mstree: A Multispecies Coalescent Approach for Estimating Ancestral Population Size and Divergence Time during Speciation with Gene FlowCited by: 0
Author(s): Junfeng Liu, Qiao Li, Qingzhu Yang
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0055469
Signature of Balancing Selection at the MC1R Gene in Kunming Dog PopulationsCited by: 14
Author(s): Guodong Wang, Lu-Guang Cheng, Ruoxi Fan, David M. Irwin, Shusheng Tang, Jian‐Guo Peng, Yaping Zhang
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0060123
The Effect of Single Recombination Events on Coalescent Tree Height and ShapeCited by: 14
Author(s): Luca Ferretti, Filippo Disanto, Thomas Wiehe
Software Mentions: 1
Published: over 11 years ago
10.1186/s13073-016-0274-3
Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureusCited by: 20
Author(s): Hsie-Chia Chang, Janina Dordel, Tjibbe Donker, Colin J. Worby, Edward J. Feil, William P. Hanage, Stephen D. Bentley, Susan S. Huang, Marc Lipsitch
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.pone.0009827
Diversity in the Glucose Transporter-4 Gene (SLC2A4) in Humans Reflects the Action of Natural Selection along the Old-World Primates EvolutionCited by: 10
Author(s): Eduardo Tarazona‐Santos, Cristina Fabbri, Meredith Yeager, Wagner C. S. Magalhães, Laurie Burdett, Andrew Crenshaw, Davide Pettener, Stephen J. Chanock
Software Mentions: 1
Published: over 14 years ago
10.1186/s12859-018-2061-1
Simulating variance heterogeneity in quantitative genome wide association studiesCited by: 6
Author(s): Ahmad Al Kawam, Mustafa Alshawaqfeh, James J. Cai, Erchin Serpedin, Aniruddha Datta
Software Mentions: 1
Published: over 6 years ago
10.1038/s41437-018-0148-0
The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structureCited by: 25
Author(s): Willy Rodríguez, Olivier Mazet, Simona Grusea, Armando Arredondo, Josué Corujo, Simon Boitard, Lounès Chikhi
Software Mentions: 1
Published: about 6 years ago
10.1371/journal.pone.0001367
Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and RelatednessCited by: 213
Author(s): Martha T. Hamblin, Marilyn L. Warburton, Edward S. Buckler
Software Mentions: 1
Published: almost 17 years ago
10.1371/journal.pone.0070801
Functional Gene Polymorphism to Reveal Species History: The Case of the CRTISO Gene in Cultivated CarrotsCited by: 14
Author(s): Vanessa Soufflet-Freslon, Matthieu Jourdan, Jérémy Clotault, Sébastien Huet, Mathilde Briard, Didier Peltier, Emmanuel Geoffriau
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0099081
Detecting Selection in the Blue Crab, Callinectes sapidus, Using DNA Sequence Data from Multiple Nuclear Protein-Coding GenesCited by: 12
Author(s): Bree K. Yednock, Joseph E. Neigel
Software Mentions: 1
Published: over 10 years ago
10.1038/s41437-017-0005-6
The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choiceCited by: 68
Author(s): Lounès Chikhi, Willy Rodríguez, Simona Grusea, Patrícia Santos, Simon Boitard, Olivier Mazet
Software Mentions: 1
Published: almost 7 years ago
10.1186/1471-2156-14-11
Reconstructing past changes in locus-specific recombination ratesCited by: 4
Author(s): Murray P. Cox, Barbara R. Holland, Matthew C Wilkins, Jan Schmid
Software Mentions: 1
Published: almost 12 years ago
10.1038/s41437-021-00426-9
Inferring number of populations and changes in connectivity under the n-island modelCited by: 18
Author(s): Armando Arredondo, Beatriz Mourato, Khoa Nguyen, Simon Boitard, Willy Rodríguez, Camille Noûs, Olivier Mazet, Lounès Chikhi
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0038667
Genotype-Based Test in Mapping Cis-Regulatory Variants from Allele-Specific Expression DataCited by: 8
Author(s): J Lefebvre, Emilio Vello, Bing Ge, Stephen B. Montgomery, Emmanouil T. Dermitzakis, Tomi Pastinen, Damian Labuda
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0021605
Bonobos Fall within the Genomic Variation of ChimpanzeesCited by: 51
Author(s): Anne Fischer, Kay Prüfer, Jeffrey M. Good, Michel Halbwax, Victor Wiebe, Claudine André, Rebeca Atencia, Lawrence Mugisha, Susan E. Ptak, Svante Pääbo
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.pone.0110579
On the Prospect of Identifying Adaptive Loci in Recently Bottlenecked PopulationsCited by: 45
Author(s): Yu Ping Poh, Vera Domingues, Hopi E. Hoekstra, Jeffrey D. Jensen
Software Mentions: 1
Published: almost 10 years ago
10.1186/s40709-017-0064-0
A survey of methods and tools to detect recent and strong positive selectionCited by: 82
Author(s): Pavlos Pavlidis, Nikolaos Alachiotis
Software Mentions: 1
Published: over 7 years ago
10.1371/journal.pone.0105410
Adaptive Human CDKAL1 Variants Underlie Hormonal Response Variations at the Enteroinsular AxisCited by: 6
Author(s): Chia‐Lin Chang, James J. Cai, Shang Yu Huang, Po Jen Cheng, Ho Yen Chueh, Sze-Bi Hsu
Software Mentions: 1
Published: about 10 years ago
10.1007/s10858-017-0096-7
Site-selective 13C labeling of proteins using erythroseCited by: 16
Author(s): Ulrich Weininger
Software Mentions: 1
Published: over 7 years ago
10.1186/1471-2156-8-65
A multi-marker test based on family data in genome-wide association studyCited by: 7
Author(s): Zhaogong Zhang, Shuanglin Zhang, Qiuying Sha
Software Mentions: 1
Published: about 17 years ago
10.1186/2041-2223-2-24
Contrasting signals of positive selection in genes involved in human skin-color variation from tests based on SNP scans and resequencingCited by: 17
Author(s): Johanna M. de Gruijter, Oscar Lao, Mark Vermeulen, Yali Xue, Cara Woodwark, Christopher Gillson, Alison J. Coffey, Qasim Ayub, S. Qasim Mehdi, Manfred Kayser, Chris Tyler‐Smith
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.pone.0038862
Evolutionary Responses to a Constructed Niche: Ancient Mesoamericans as a Model of Gene-Culture CoevolutionCited by: 35
Author(s): Tábita Hünemeier, Carlos Eduardo G. Amorim, Soledad de Azevedo, Verônica Contini, Víctor Acuña-Alonzo, Francisco Rothhammer, Jean‐Michel Dugoujon, Stéphane Mazières, Ramiro Barrantes, Teresa Villarreal-Molina, Vanessa Rodrigues Paixão‐Côrtes, Francisco M. Salzano, Samuel Cañizales-Quinteros, Andrés Ruiz-Linares, María Cátira Bortolini
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0021014
On Identifying the Optimal Number of Population Clusters via the Deviance Information CriterionCited by: 47
Author(s): Hong Gao, Katarzyna Bryc, Carlos D. Bustamante
Software Mentions: 1
Published: over 13 years ago
10.1186/1471-2156-13-22
Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian ComputationCited by: 46
Author(s): Sen Li, Mattias Jakobsson
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.pone.0004269
Accurate Inference of Subtle Population Structure (and Other Genetic Discontinuities) Using Principal CoordinatesCited by: 60
Author(s): Patrick A. Reeves, Christopher M. Richards
Software Mentions: 1
Published: almost 16 years ago
10.1371/journal.ppat.1001344
Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected InfantsCited by: 184
Author(s): Nicholas Renzette, Bornali Bhattacharjee, Jeffrey D. Jensen, Laura Gibson, Timothy F. Kowalik
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.pone.0009695
FaaPred: A SVM-Based Prediction Method for Fungal Adhesins and Adhesin-Like ProteinsCited by: 34
Author(s): Jayashree Ramana, Dinesh Gupta
Software Mentions: 1
Published: over 14 years ago
10.1098/rspb.2014.1448
Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoplesCited by: 79
Author(s): Sen Li, Carina M. Schlebusch, Mattias Jakobsson
Software Mentions: 1
Published: about 10 years ago
10.1098/rspb.2020.1206
Genomic evidence for the Old divergence of Southern European wolf populationsCited by: 6
Author(s): Pedro M. Silva, Marco Galaverni, Diego Ortega‐Del Vecchyo, Zhenxin Fan, Romolo Caniglia, Elena Fabbri, Ettore Randi, Robert K. Wayne, Raquel Godinho
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0080710
X-Linked MTMR8 Diversity and Evolutionary History of Sub-Saharan PopulationsCited by: 1
Author(s): Damian Labuda, Vania Yotova, Jean‐François Lefebvre, Claudia Moreau, Gerd Utermann, Scott M. Williams
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0046947
Genealogy-Based Methods for Inference of Historical Recombination and Gene Flow and Their Application in Saccharomyces cerevisiaeCited by: 9
Author(s): Paul A. Jenkins, Yun S. Song, Rachel B. Brem
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pone.0121543
Pleistocene Niche Stability and Lineage Diversification in the Subtropical Spider Araneus omnicolor (Araneidae)Cited by: 38
Author(s): Elen Arroyo Peres, Thadeu Sobral‐Souza, Manolo F. Perez, Isabel A. S. Bonatelli, Daniel P. Silva, Márcio J. Silva, Vera Nisaka Solferini
Software Mentions: 1
Published: over 9 years ago
10.1186/1471-2148-8-274
The evolution of TEP1, an exceptionally polymorphic immunity gene in Anopheles gambiaeCited by: 49
Author(s): Darren J. Obbard, Deborah M. Callister, Francis M. Jiggins, Dinesh C. Soares, Guiyun Yan, Tom J. Little
Software Mentions: 1
Published: about 16 years ago
10.1186/1471-2105-14-216
Rapid forward-in-time simulation at the chromosome and genome levelCited by: 16
Author(s): Andre J. Aberer, Alexandros Stamatakis
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0001686
Parallel Selection on TRPV6 in Human PopulationsCited by: 45
Author(s): David A. Hughes, Kun Tang, Rainer Strotmann, Torsten Schöneberg, Jean Prenen, Bernd Nilius, Mark Stoneking
Software Mentions: 1
Published: over 16 years ago
10.1371/journal.pone.0036642
Evolution of Neutral and Flowering Genes along Pearl Millet (Pennisetum glaucum) DomesticationCited by: 10
Author(s): Ghayas Lakis, Miguel Navascués, Samah Rekima, Mathieu Simon, Marie‐Stanislas Remigereau, Magalie Leveugle, Najat Takvorian, Françoise Lamy, Frantz Depaulis, Thierry Robert
Software Mentions: 1
Published: over 12 years ago
10.1186/1471-2148-13-9
A genetic polymorphism evolving in parallel in two cell compartments and in two cladesCited by: 6
Author(s): Ward B. Watt, Richard R. Hudson, Baiqing Wang, Edward Chung Yern Wang
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pone.0110075
Balancing Selection on CDH2 May Be Related to the Behavioral Features of the Belgian MalinoisCited by: 13
Author(s): Xue Cao, David M. Irwin, Liu Yan-hu, Lu-Guang Cheng, Lu Wang, Guodong Wang, Yaping Zhang
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0006942
Genetic Variation in the Proximal Promoter of ABC and SLC Superfamilies: Liver and Kidney Specific Expression and Promoter Activity Predict VariationCited by: 35
Author(s): Stephanie Hesselson, Pär Matsson, James E. Shima, Hisashi Fukushima, Sook Wah Yee, Yuya Kobayashi, Jason M. Gow, Connie Ha, Benjamin Ma, Annie Poon, Susan J. Johns, Doug Stryke, Richard A. Castro, Harunobu Tahara, Ji Ha Choi, Ligong Chen, Nicolas Picard, Elin Sundström Sjödin, Maarke J.E. Roelofs, Thomas E. Ferrin, R Myers, Deanna L. Kroetz, Pui‐Yan Kwok, Kathleen M. Giacomini
Software Mentions: 1
Published: about 15 years ago
10.1371/journal.pone.0128407
The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of DivergenceCited by: 4
Author(s): James B. Pettengill
Software Mentions: 1
Published: about 9 years ago
10.1016/j.celrep.2013.09.042
Hybridization Reveals the Evolving Genomic Architecture of SpeciationCited by: 119
Author(s): Marcus R. Kronforst, Matthew E.B. Hansen, Nicholas G. Crawford, Jason R. Gallant, W. Zhang, Rob J. Kulathinal, Durrell D. Kapan, Sean P. Mullen
Software Mentions: 1
Published: about 11 years ago