bioconductor: SNPRelate | Projects

10.1371/journal.pgen.1009110

Unique genetic signatures of local adaptation over space and time for diapause, an ecologically relevant complex trait, in Drosophila melanogaster
Cited by: 45
Author(s): Priscilla A. Erickson, Cory A. Weller, Daniel Song, Alyssa Bangerter, Paul S. Schmidt, Alan O. Bergland
Software Mentions: 15
Published: about 4 years ago

10.1093/bioinformatics/bty713

Bigmelon: tools for analysing large DNA methylation datasets
Cited by: 47
Author(s): T.J. Gorrie-Stone, Melissa Smart, Ayden Saffari, Karim Malki, Eilís Hannon, Joe Burrage, Jonathan Mill, Meena Kumari, Leonard C Schalkwyk
Software Mentions: 13
Published: about 6 years ago

10.12688/f1000research.15949.2

The Mega2R package: R tools for accessing and processing genetic data in common formats
Cited by: 0
Author(s): R. Baron, Justin R. Stickel, Daniel E. Weeks
Software Mentions: 12
Published: over 5 years ago

10.3389/fmicb.2020.00926

Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus
Cited by: 3
Author(s): Semiramis Castro-Jaimes, Elena Bello-López, Consuelo Velázquez-Acosta, Patricia Volkow-Fernández, Patricia Lozano-Zaraín, Santiago Castillo-Ramírez, Miguel A. Cevallos
Software Mentions: 11
Published: over 4 years ago

10.3389/fgene.2020.00817

Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure
Cited by: 17
Author(s): Júber Herrera-Uribe, Haibo Li, Kristen A Byrne, Zahra F Bond, Crystal L. Loving, Christopher K. Tuggle
Software Mentions: 9
Published: over 4 years ago

10.1038/s41437-021-00418-9

Population genomics and conservation management of a declining tropical rodent
Cited by: 9
Author(s): Brenton von Takach, Cara E. Penton, Brett P. Murphy, Ian J. Radford, Hugh F. Davies, Brydie M. Hill, Sam C. Banks
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.69249

A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
Cited by: 38
Author(s): Ursula Oggenfuss, Thomas Badet, Thomas Wicker, Fanny E. Hartmann, Navreet Singh, Leen Nanchira Abraham, Petteri Karisto, Tiziana Vonlanthen, Christopher C. Mundt, Bruce A. McDonald, Daniel Croll
Software Mentions: 9
Published: about 3 years ago

10.1371/journal.pone.0236084

Mating system is correlated with immunogenetic diversity in sympatric species of Peromyscine mice
Cited by: 0
Author(s): Jesyka Meléndez‐Rosa, Ke Bi, Eileen A. Lacey
Software Mentions: 9
Published: over 4 years ago

10.1002/ece3.4894

Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations
Cited by: 8
Author(s): Suda Parimala Ravindran, Maike Herrmann, Mathilde Cordellier
Software Mentions: 8
Published: almost 6 years ago

10.1111/eva.12761

Pervasive admixture between eucalypt species has consequences for conservation and assisted migration
Cited by: 15
Author(s): Brenton von Takach, Cameron Jack, Justin O. Borevitz, David B. Lindenmayer, Sam C. Banks
Software Mentions: 8
Published: almost 6 years ago

10.3389/fpls.2021.693285

SNP Alleles Associated With Low Bolting Tendency in Sugar Beet
Cited by: 5
Author(s): Samathmika Ravi, G. Campagna, Maria Cristina Della Lucia, Chiara Broccanello, Giovanni Bertoldo, Claudia Chiodi, Laura Maretto, Matteo Moro, Azam Sadat Eslami, Subhashini Srinivasan, Andrea Squartini, Giuseppe Concheri, Piergiorgio Stevanato
Software Mentions: 8
Published: over 3 years ago

10.1007/s00122-021-03882-3

Genomic signatures of selection for resistance to stripe rust in Austrian winter wheat
Cited by: 2
Author(s): Laura Morales, Sebastian Michel, Christian Ametz, Hermann Gregor Dallinger, Franziska Löschenberger, Anton Neumayer, Simone Zimmerl, Hermann Buerstmayr
Software Mentions: 8
Published: over 3 years ago

10.1371/journal.pcbi.1005727

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
Cited by: 40
Author(s): Kevin Murray, Christfried Webers, Cheng Soon Ong, Justin O. Borevitz, Norman Warthmann
Software Mentions: 8
Published: about 7 years ago

10.1093/gbe/evaa191

Coexpression Clusters and Allele-Specific Expression in Metabolism-Based Herbicide Resistance
Cited by: 17
Author(s): Darci A. Giacomini, Eric Patterson, Anita Küpper, Roland Beffa, Todd A. Gaines, Patrick J. Tranel
Software Mentions: 8
Published: about 4 years ago

10.3389/fgene.2020.00936

NRG1, PIP4K2A, and HTR2C as Potential Candidate Biomarker Genes for Several Clinical Subphenotypes of Depression and Bipolar Disorder
Cited by: 13
Author(s): Аnastasia Levchenko, N. Vyalova, Timur Nurgaliev, Ivan V Pozhidaev, German G. Simutkin, Н. А. Бохан, Светлана Иванова
Software Mentions: 7
Published: about 4 years ago

10.1002/ece3.7654

Looking for the needle in a downsized haystack: Whole‐exome sequencing unravels genomic signals of climatic adaptation in Douglas‐fir (Pseudotsuga menziesii)
Cited by: 1
Author(s): Jan-Peter George, Silvio Schueler, Michael Grabner, Sandra Karanitsch-Ackerl, Konrad Mayer, Michael Stierschneider, Lambert Weißenbacher, Marcela van Loo
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1009422

High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest
Cited by: 25
Author(s): Seyedeh Masoumeh Fotoukkiaii, Nicky Wybouw, Andre H. Kurlovs, Dimitra Tsakireli, Spiros A. Pergantis, Richard M. Clark, John Vontas, Thomas Van Leeuwen
Software Mentions: 7
Published: over 3 years ago

10.1111/eva.12852

Temporal variation in spatial genetic structure during population outbreaks: Distinguishing among different potential drivers of spatial synchrony
Cited by: 27
Author(s): Jérémy Larroque, Simon Legault, Rob C. Johns, Lisa M. Lumley, Michel Cusson, Sébastien Renaut, Roger C. Levesque, Patrick M. A. James
Software Mentions: 7
Published: about 5 years ago

10.1111/eva.13035

Demographic history and genomics of local adaptation in blue tit populations
Cited by: 8
Author(s): Charles Perrier, Quentin Rougemont, Anne Charmantier
Software Mentions: 7
Published: over 4 years ago

10.3389/fpls.2018.00029

Population Genetic Structure in Glyphosate-Resistant and -Susceptible Palmer Amaranth (Amaranthus palmeri) Populations Using Genotyping-by-sequencing (GBS)
Cited by: 26
Author(s): Anita Küpper, Harish Manmathan, Darci A. Giacomini, Eric Patterson, William B. McCloskey, Todd A. Gaines
Software Mentions: 7
Published: almost 7 years ago

10.1534/g3.117.300152

Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (Phylloscopus collybita abietinus/P. tristis)
Cited by: 4
Author(s): Venkat Talla, Faheema Kalsoom, Daria Shipilina, И. М. Марова, Niclas Backström
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41598-021-87829-0

GWAS analysis reveals distinct pathogenicity profiles of Australian Parastagonospora nodorum isolates and identification of marker-trait-associations to septoria nodorum blotch
Cited by: 7
Author(s): H. Phan, Eiko Furuki, Lukas Hunziker, Kasia Rybak, Kar‐Chun Tan
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-020-69101-z

STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts
Cited by: 21
Author(s): Sheila A. Kitchen, Gregory Von Kuster, Kate L. Vasquez Kuntz, Hannah Reich, Webb Miller, Sean Griffin, Nicole D. Fogarty, Iliana B. Baums
Software Mentions: 6
Published: over 4 years ago

10.1073/pnas.2104315118

Global range expansion history of pepper (Capsicumspp.) revealed by over 10,000 genebank accessions
Cited by: 39
Author(s): Pasquale Tripodi, M. Timothy Rabanus‐Wallace, Lorenzo Barchi, Sandip M. Kale, Salvatore Esposito, Alberto Acquadro, Roland Schafleitner, Maarten van Zonneveld, Jaime Prohens, María José Díez, Andreas Börner, Jérémy Salinier, Bernard Caromel, Arnaud Bovy, Filiz Boyaci, Gancho Pasev, Ronny Brandt, Axel Himmelbach, Ezio Portis, Richard Finkers, Sergio Lanteri, Ilan Paran, Véronique Lefebvre, Giovanni Giuliano, Nils Stein
Software Mentions: 6
Published: over 3 years ago

10.1038/s42003-021-01908-6

Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color
Cited by: 8
Author(s): Michaël Abrouk, Naveenkumar Athiyannan, Thomas Müller, Yveline Pailles, Christoph Stritt, Anne Roulin, Chenggen Chu, Shuyu Liu, Takumi Morita, Hirokazu Handa, Jesse Poland, Beat Keller, Simon G. Krattinger
Software Mentions: 6
Published: over 3 years ago

10.3389/fvets.2021.733357

Chytridiomycosis Outbreak in a Chilean Giant Frog (Calyptocephalella gayi) Captive Breeding Program: Genomic Characterization and Pathological Findings
Cited by: 5
Author(s): Mario Alvarado‐Rybak, Paz Acuña, Alexandra Peñafiel‐Ricaurte, Thomas R. Sewell, Simon J. O’Hanlon, Matthew C. Fisher, Andrés Valenzuela‐Sánchez, Andrew A. Cunningham, Claudio Soto‐Azat
Software Mentions: 6
Published: about 3 years ago

10.1534/g3.118.200129

Genome-Wide Association Mapping Uncovers Fw1, a Dominant Gene Conferring Resistance to Fusarium Wilt in Strawberry
Cited by: 40
Author(s): Dominique D A Pincot, Thomas J. Poorten, Michael A. Hardigan, Julia M. Harshman, Charlotte B. Acharya, Glenn Cole, Thomas R. Gordon, Michelle Stueven, Patrick P. Edger, Steven J. Knapp
Software Mentions: 6
Published: over 6 years ago

10.1186/s13045-018-0679-0

Whole-exon sequencing of human myeloma cell lines shows mutations related to myeloma patients at relapse with major hits in the DNA regulation and repair pathways
Cited by: 31
Author(s): Benoît Tessoulin, Agnès Moreau-Aubry, Géraldine Descamps, Patricia Gomez‐Bougie, Sophie Maïga, Alban Gaignard, David Chiron, Emmanuelle Ménoret, Steven Le Gouill, Philippe Moreau, Martine Amiot, Catherine Pellat‐Deceunynck
Software Mentions: 6
Published: almost 6 years ago

10.1002/ece3.8040

Genome‐wide analysis reveals demographic and life‐history patterns associated with habitat modification in landlocked, deep‐spawning sockeye salmon ( Oncorhynchus nerka )
Cited by: 0
Author(s): Farida Samad-zada, Brett T. van Poorten, Shannon L. Harris, Lyse Godbout, Michael A. Russello
Software Mentions: 6
Published: about 3 years ago

10.1038/s41438-018-0090-6

Genetic characterization of worldwide Prunus domestica (plum) germplasm using sequence-based genotyping
Cited by: 50
Author(s): Tetyana Zhebentyayeva, Vijay Shankar, R. Scorza, Ann M. Callahan, Michel Ravelonandro, Sarah Castro, Theodore M. DeJong, Christopher Saski, Chris Dardick
Software Mentions: 6
Published: almost 6 years ago

10.1002/ece3.6418

Genomic signals found using RNA sequencing show signatures of selection and subtle population differentiation in walleye (Sander vitreus) in a large freshwater ecosystem
Cited by: 12
Author(s): Matt J. Thorstensen, Jennifer D. Jeffrey, Jason R. Treberg, Douglas A. Watkinson, Eva C. Enders, Ken M. Jeffries
Software Mentions: 6
Published: over 4 years ago

10.3389/fmicb.2018.02137

Traditional Norwegian Kveik Are a Genetically Distinct Group of Domesticated Saccharomyces cerevisiae Brewing Yeasts
Cited by: 36
Author(s): Richard Preiss, Caroline Tyrawa, Kristoffer Krogerus, Lars Marius Garshol, George van der Merwe
Software Mentions: 6
Published: about 6 years ago

10.1038/s41438-020-0316-2

Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. ‘Manitoba 37’
Cited by: 16
Author(s): Sagar Patel, Michael Robben, Anne Fennell, Jason P. Londo, Dilmini Alahakoon, Roberto Villegas-Diaz, Padmapriya Swaminathan
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0252207

Genomic diversity of 39 samples of Pyropia species grown in Japan
Cited by: 4
Author(s): Yukio Nagano, Kei Kimura, Genta Kobayashi, Yoshio Kawamura
Software Mentions: 6
Published: over 3 years ago

10.1111/mpp.12964

A complex network of additive and epistatic quantitative trait loci underlies natural variation of Arabidopsis thaliana quantitative disease resistance to Ralstonia solanacearum under heat stress
Cited by: 22
Author(s): Nathalie Aoun, Henri Desaint, Léa Boyrie, Maxime Bonhomme, Laurent Deslandes, Richard Berthomé, Fabrice Roux
Software Mentions: 6
Published: about 4 years ago

10.1186/s12864-020-6616-y

Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.)
Cited by: 29
Author(s): Anthony Bernard, Annarita Marrano, Armel Donkpegan, Patrick J. Brown, Charles A. Leslie, David B. Neale, Fabrice Lheureux, Elisabeth Dirlewanger
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-019-42988-z

Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms
Cited by: 6
Author(s): Bo‐Hye Nam, DongAhn Yoo, Young‐Ok Kim, Jung Youn Park, Younhee Shin, Ga-Hee Shin, Chan-Il Park, Heebal Kim, Woori Kwak
Software Mentions: 6
Published: over 5 years ago

10.1038/s41416-018-0141-7

Rare germline variants in DNA repair genes and the angiogenesis pathway predispose prostate cancer patients to develop metastatic disease
Cited by: 36
Author(s): Martina Mijušković, Ed Saunders, Daniel Leongamornlert, Sarah Wakerell, Ian Whitmore, Tokhir Dadaev, Clara Cieza-Borrella, Koveela Govindasami, Mark N. Brook, Christopher A. Haiman, David V. Conti, Rosalind Eeles, Zsofia Kote‐Jarai
Software Mentions: 5
Published: over 6 years ago

10.7705/biomedica.4753

Análisis de la variabilidad genética de una muestra de la población de Bogotá: hacia la constitución de un mapa de haplotipos
Cited by: 2
Author(s): Juan David Caicedo, Alejandro Cáceres, Carlos E. Arboleda-Bustos, María Fernanda Mahecha, Jenny Ortega, Gonzalo Arboleda, Humberto Arboleda
Software Mentions: 5
Published: about 5 years ago

10.7717/peerj.11580

Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach
Cited by: 0
Author(s): Siroj Bakoev, Aleksei Traspov, Lyubov Getmantseva, А. А. Белоус, Т. В. Карпушкина, Olga Kostyunina, А. В. Усатов, Tatiana V. Tatarinova
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-021-07722-y

Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae
Cited by: 1
Author(s): Melina Campos, Luísa D P Rona, Katie Willis, George K. Christophides, Robert M. MacCallum
Software Mentions: 5
Published: over 3 years ago

10.1534/g3.119.400986

Adaptation to Industrial Stressors Through Genomic and Transcriptional Plasticity in a Bioethanol Producing Fission Yeast Isolate
Cited by: 1
Author(s): Dane Vassiliadis, Koon Ho Wong, Jo Anne Blinco, Geoff Dumsday, Alex Andrianopoulos, Brendon J. Monahan
Software Mentions: 5
Published: over 4 years ago

10.1111/eva.12659

Recent advances in conservation and population genomics data analysis
Cited by: 77
Author(s): Sarah A. Hendricks, Eric C. Anderson, Tiago Antão, Louis Bernatchez, Brenna R. Forester, Brittany A. Garner, Brian K. Hand, Paul A. Hohenlohe, Marty Kardos, Ben F. Koop, Arun Sethuraman, Robin S. Waples, Gordon Luikart
Software Mentions: 5
Published: over 6 years ago

10.1111/pbi.13115

Genome‐wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed
Cited by: 48
Author(s): Jun Zou, Limin Mao, Jie Qiu, Meng Wang, Jia Lu, Dongya Wu, Zhesi He, Meihong Chen, Yifei Shen, Enhui Shen, Yongji Huang, Ruiyuan Li, Dandan Hu, Lei Shi, Kai Wang, Qian Zhu, Chu-Yu Ye, Ian Bancroft, Graham J. King, Jinling Meng
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-017-1589-9

Subgroup detection in genotype data using invariant coordinate selection
Cited by: 6
Author(s): Daniel Fischer, Mervi Honkatukia, Maria Tuiskula-Haavisto, Klaus Nordhausen, D. Cavero, Rudolf Preisinger, Johanna Vilkki
Software Mentions: 5
Published: over 7 years ago

10.1093/gigascience/giaa088

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning
Cited by: 16
Author(s): Eugenie C Yen, Shane McCarthy, Juan A. Galarza, Tomas N Generalovic, Sarah Pelan, Petr Nguyen, Joana I. Meier, Ian A. Warren, Johanna Mappes, Richard Durbin, Chris D. Jiggins
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-018-5271-z

Genomic insights into virulence mechanisms of Leishmania donovani: evidence from an atypical strain
Cited by: 23
Author(s): Sumudu R. Samarasinghe, Nilakshi Samaranayake, Udeshika Kariyawasam, Yamuna Deepani Siriwardana, Hideo Imamura, Nadira D. Karunaweera
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.gpb.2018.07.006

SeqSQC: A Bioconductor Package for Evaluating the Sample Quality of Next-generation Sequencing Data
Cited by: 6
Author(s): Qian Liu, Qiang Hu, Song Yao, Marilyn L. Kwan, Janise M. Roh, Hua Zhao, Christine B. Ambrosone, Lawrence H. Kushi, Song Liu, Qianqian Zhu
Software Mentions: 5
Published: over 5 years ago

10.1186/1471-2164-15-S7-S4

SNPs selection using support vector regression and genetic algorithms in GWAS
Cited by: 11
Author(s): Fabrízzio Condé de Oliveira, Carlos Cristiano Hasenclever Borges, Fernanda Nascimento Almeida, Fabyano Fonseca e Silva, Rui da Silva Verneque, Marcos Vinícius Gualberto Barbosa da Silva, Wagner Arbex
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pgen.1006335

Family Based Whole Exome Sequencing Reveals the Multifaceted Role of Notch Signaling in Congenital Heart Disease
Cited by: 54
Author(s): Christoph Preuß, M. Capredon, Florian Wünnemann, Philippe Chétaille, Andrea Prince, Béatrice Godard, Séverine Leclerc, Nara Sobreira, Hua Ling, Philip Awadalla, Maryse Thibeault, Paul Khairy, Mark E. Samuels, Grégor Andelfinger
Software Mentions: 5
Published: about 8 years ago

10.1186/s12864-020-07111-x

Genome-wide patterns of differentiation within and among U.S. commercial honey bee stocks
Cited by: 19
Author(s): Perot Saelao, Michael Simone-Finstrom, Arián Avalos, Lelania Bilodeau, Robert G. Danka, Lilia de Guzman, Frank D. L. Rinkevich, Philip Tokarz
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-021-07592-4

RNA sequencing describes both population structure and plasticity-selection dynamics in a non-model fish
Cited by: 8
Author(s): Matt J. Thorstensen, Melinda R. Baerwald, Ken M. Jeffries
Software Mentions: 4
Published: over 3 years ago

10.1038/s41598-021-85909-9

Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using RAD-Seq
Cited by: 7
Author(s): Maddumage Dona Ginushika Priyadarshani Premarathne, Nami Fukutome, Kazuaki Yamasaki, Fumiyo Hayakawa, Atsushi J. Nagano, Hisataka Mizuno, Nobuo Ibaragi, Yukio Nagano
Software Mentions: 4
Published: over 3 years ago

10.1534/g3.117.300495

Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies
Cited by: 31
Author(s): Thomas D. Brekke, Katherine A. Steele, John F. Mulley
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-021-85203-8

GWAS findings improved genomic prediction accuracy of lipid profile traits: Tehran Cardiometabolic Genetic Study
Cited by: 8
Author(s): Mahdi Akbarzadeh, Saeid Rasekhi Dehkordi, Mahmoud Amiri Roudbar, Mehdi Sargolzaei, Kamran Guity, Bahareh Sedaghati-Khayat, Parisa Riahi, Fereidoun Azizi, Maryam Sadat Daneshpour
Software Mentions: 4
Published: over 3 years ago

10.1111/eva.12650

Human activities and landscape features interact to closely define the distribution and dispersal of an urban commensal
Cited by: 23
Author(s): Qian Tang, Grace Kah Mun Low, John Lim, Chyi Yin Gwee, Frank E. Rheindt
Software Mentions: 4
Published: over 6 years ago

10.1534/g3.116.026914

Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance inGlycine soja, the Wild Progenitor of Cultivated Soybeans
Cited by: 39
Author(s): Justin Anderson, Thomas J. Y. Kono, Robert M. Stupar, Michael B. Kantar, Peter L. Morrell
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pbio.2003583

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species
Cited by: 146
Author(s): Abigail Lind, Jennifer H. Wisecaver, Catarina Lameiras, Philipp Wiemann, Jonathan M. Palmer, Nancy P. Keller, Fernando Rodrigues, Gustavo H. Goldman, Antonis Rokas
Software Mentions: 4
Published: about 7 years ago

10.1111/pbi.13516

Genome‐wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness
Cited by: 23
Author(s): Gopal Misra, Saurabh Badoni, Sabiha Parween, Rakesh Kumar Singh, Hei Leung, Olufunmilayo Ladejobi, Richard Mott, Nese Sreenivasulu
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41598-018-29433-3

Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer’s Disease and Reconstruction of Relevant Biological Mechanisms
Cited by: 46
Author(s): Shashank Khanna, Daniel Domingo‐Fernándéz, Anandhi Iyappan, Mohammad Asif Emon, Martin Hofmann-Apitius, Holger Fröhlich
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0225834

Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken
Cited by: 5
Author(s): Rooksana E. Noorai, Vijay Shankar, Nowlan H. Freese, Christopher M. Gregorski, Steve Chapman
Software Mentions: 4
Published: almost 5 years ago

10.1534/genetics.118.301589

Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate
Cited by: 17
Author(s): Pip Wilson, Jared Streich, Kevin Murray, Steven R. Eichten, Riyan Cheng, Nicola Aitken, Kurt A. Spokas, Norman Warthmann, Sean P. Gordon, Accession Contributors, John P. Vogel, Justin O. Borevitz
Software Mentions: 4
Published: about 6 years ago

10.1186/s13059-019-1686-3

Whole genomes and transcriptomes reveal adaptation and domestication of pistachio
Cited by: 71
Author(s): Lin Zeng, Xiaolong Tu, He Dai, Fengming Han, LU Bing-she, Ming-Shan Wang, Hojjat Asadollahpour Nanaei, Ali Tajabadipour, Mehdi Mansouri, Xiaolong Li, Lili Ji, David M. Irwin, Zhou Hong, Min Liu, Hongkun Zheng, Ali Esmailizadeh, Dong‐Dong Wu
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0249176

The role of a mechanistic host in maintaining arctic rabies variant distributions: Assessment of functional genetic diversity in Alaskan red fox (Vulpes vulpes)
Cited by: 0
Author(s): Tristan M. Baecklund, Jaycee Morrison, Michael E. Donaldson, Karsten Hueffer, Christopher J. Kyle
Software Mentions: 4
Published: over 3 years ago

10.1186/s10020-020-00266-z

The transcriptome-wide association search for genes and genetic variants which associate with BMI and gestational weight gain in women with type 1 diabetes
Cited by: 2
Author(s): Agnieszka H. Ludwig-Słomczyńska, Michał Seweryn, Przemysław Kapusta, Ewelina Pitera, Urszula Mantaj, Katarzyna Cyganek, Paweł Gutaj, Łucja Dobrucka, Ewa Wender-Ożegowska, Maciej Małecki, Paweł Wołkow
Software Mentions: 4
Published: almost 4 years ago

10.1111/jpy.13079

Foliose Ulva Species Show Considerable Inter‐Specific Genetic Diversity, Low Intra‐Specific Genetic Variation, and the Rare Occurrence of Inter‐Specific Hybrids in the Wild
Cited by: 20
Author(s): Antoine Fort, Marcus McHale, Kévin Cascella, Philippe Potin, Björn Usadel, Michael D. Guiry, Ronan Sulpice
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0204279

Multiple genomic regions influence root morphology and seedling growth in cultivated sunflower (Helianthus annuus L.) under well-watered and water-limited conditions
Cited by: 19
Author(s): Rishi R. Masalia, Andries A. Temme, Nicole de leon Torralba, John M. Burke
Software Mentions: 4
Published: about 6 years ago

10.1534/g3.120.401196

Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces
Cited by: 5
Author(s): Leo Zeitler, Jeffrey Ross‐Ibarra, Markus G Stetter
Software Mentions: 4
Published: over 4 years ago

10.1186/s12859-018-2512-8

A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data
Cited by: 9
Author(s): A. M. C. Chan, Amy L. Williams, Jean‐Luc Jannink
Software Mentions: 4
Published: almost 6 years ago

10.1534/g3.120.401306

Genotypic Characterization of the U.S. Peanut Core Collection
Cited by: 10
Author(s): Paul I. Otyama, R.S. Kulkarni, Kelly D. Chamberlin, Peggy Ozias‐Akins, Ye Chu, Lori M. Lincoln, Gregory E. MacDonald, Noelle L. Anglin, Sudhansu Dash, David J. Bertioli, David Fernández-Baca, Michelle A. Graham, Steven B. Cannon, Ethalinda K. S. Cannon
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-021-90170-1

Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity
Cited by: 0
Author(s): Tanya N. Phung, Timothy H. Webster, Elizabeth Lenkiewicz, Smriti Malasi, Mariacarla Andreozzi, Ann E. McCullough, Karen S. Anderson, Barbara A. Pockaj, Melissa A. Wilson, Michael T. Barrett
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-89399-7

Prostate cancer risk variants of the HOXB genetic locus
Cited by: 5
Author(s): William D. Dupont, Joan P. Breyer, Spenser H Johnson, W. Dale Plummer, Jeffrey R. Smith
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pntd.0009507

Whole-exome sequencing reveals insights into genetic susceptibility to Congenital Zika Syndrome
Cited by: 5
Author(s): Víctor Borda, Ronaldo da Silva Francisco, João Batista Pereira de Carvalho, Guilherme Loss de Morais, Átila Duque Rossi, Paula Pezzuto, Girlene S. Azevedo, Bruno Luiz Fonseca Schamber-Reis, Elyzabeth Avvad Portari, Adriana Melo, Maria Elisabeth Lopes Moreira, Letícia da Cunha Guida, Daniela P. Cunha, Leonardo Henrique Ferreira Gomes, Zilton Farias Meira de Vasconcelos, Fabio R. Faucz, Amílcar Tanuri, Constantine A. Stratakis, Renato Santana Aguiar, Cynthia Chester Cardoso, Ana Tereza Ribeiro de Vasconcelos
Software Mentions: 3
Published: over 3 years ago

10.1534/g3.119.400759

Novel Bayesian Networks for Genomic Prediction of Developmental Traits in Biomass Sorghum
Cited by: 22
Author(s): José Fortunato Ferreira Santos, Samuel B. Fernandes, Scott McCoy, Roberto Lozano, Patrick J. Brown, Andrew D. B. Leakey, Edward S. Buckler, Antônio Augusto Franco Garcia, Michael A. Gore
Software Mentions: 3
Published: almost 5 years ago

10.3390/biology9090277

Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region
Cited by: 5
Author(s): Li Lian Wong, Zulaikha Mat Deris, Yoji Igarashi, Songqian Huang, Shuichi Asakawa, Qasim Ayub, Shu Yong Lim, Mhd Ikhwanuddin, Shumpei Iehata, Ken‐ichi Okamoto, . Mariom, Md. Asaduzzaman
Software Mentions: 3
Published: about 4 years ago

10.1186/s12862-018-1296-9

Phylogenomics of a putatively convergent novelty: did hypertrophied lips evolve once or repeatedly in Lake Malawi cichlid fishes?
Cited by: 14
Author(s): C. Darrin Hulsey, Jimmy Zheng, Roi Holzman, Michael E. Alfaro, Melisa Olave, Axel Meyer
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1006710

A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa
Cited by: 27
Author(s): Rafal S. Sobota, Catherine M. Stein, Nuri Kodaman, Isaac Maro, Wendy Wieland-Alter, Robert P. Igo, Albert Magohe, La Shaunda L. Malone, Keith Chervenak, Noémi B. Hall, Mecky Matee, Harriet Mayanja‐Kizza, Moses Joloba, Jason H. Moore, William K. Scott, Timothy Lahey, W. Henry Boom, C. Fordham von Reyn, Scott M. Williams, Giorgio Sirugo
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-021-82437-4

Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm
Cited by: 38
Author(s): Jéssica Delfini, Vânia Moda-Cirino, José dos Santos Neto, Paulo Maurício Ruas, Gustavo César Sant’Ana, Paul Gepts, Leandro Simões Azeredo Gonçalves
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12983-019-0335-8

Persistence of multiple patterns and intraspecific polymorphism in multi-species Müllerian communities of net-winged beetles
Cited by: 14
Author(s): Matěj Boček, Dominik Kusy, Michal Motyka, Ladislav Bocák
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-019-49467-5

The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone
Cited by: 18
Author(s): Swaine L. Chen, Ying Ding, Anucha Apisarnthanarak, Shirin Kalimuddin, Sophia Archuleta, Sharifah Faridah Syed Omar, Partha Pratim De, Tse Hsien Koh, Kean Lee Chew, Nadia Atiya, Nuntra Suwantarat, Rukumani Devi Velayuthan, Joshua Wong, David C. Lye
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-017-05087-5

Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits
Cited by: 21
Author(s): Elena Plekhanova, M. A. Vishnyakova, С. В. Булынцев, Peter L. Chang, Noelia Carrasquilla‐Garcia, Kassaye Negash, Eric J. B. von Wettberg, Nina Noujdina, Douglas R. Cook, Maria Samsonova, Sergey V. Nuzhdin
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2021.631250

Adaptive Gene Content and Allele Distribution Variations in the Wild and Domesticated Populations of Saccharomyces cerevisiae
Cited by: 12
Author(s): Dayong Han, Pei‐Jie Han, Karl Rumbold, Anbessa Dabassa Koricha, Shoufu Duan, Liang Song, Junyan Shi, Kuan Li, Qiming Wang, Feng‐Yan Bai
Software Mentions: 3
Published: almost 4 years ago

10.1038/srep36789

Population genomic analysis uncovers environmental stress-driven selection and adaptation of Lentinula edodes population in China
Cited by: 18
Author(s): Yang Xiao, Xuanjin Cheng, Jun Liu, Chuang Li, Wenyan Nong, Yinbing Bian, Man Kit Cheung, Hoi Shan Kwan
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-018-24219-z

A mega-analysis of expression quantitative trait loci (eQTL) provides insight into the regulatory architecture of gene expression variation in liver
Cited by: 51
Author(s): Tobias Strunz, Felix Graßmann, Javier Gayán, Satu Nahkuri, Débora C. Souza-Costa, Cyrille Maugeais, Sascha Fauser, Everson Nogoceke, Bernhard H. F. Weber
Software Mentions: 3
Published: over 6 years ago

10.1038/s41438-019-0132-8

Genetic diversity, population structure, and relationships in a collection of pepper (Capsicum spp.) landraces from the Spanish centre of diversity revealed by genotyping-by-sequencing (GBS)
Cited by: 57
Author(s): Leandro Pereira-Dias, Santiago Vilanova, Ana Fita, Jaime Prohens, Adrián Rodríguez‐Burruezo
Software Mentions: 3
Published: over 5 years ago

10.1093/jxb/erz256

Dissecting the genome-wide genetic variants of milling and appearance quality traits in rice
Cited by: 24
Author(s): Gopal Misra, Roslen Anacleto, Saurabh Badoni, Vito M. Butardo, Lilia Molina, Andreas Graner, Matty Demont, Matthew K. Morell, Nese Sreenivasulu
Software Mentions: 3
Published: over 5 years ago

10.1038/s42003-021-02380-y

Adaptive divergence and post-zygotic barriers to gene flow between sympatric populations of a herbivorous mite
Cited by: 10
Author(s): Ernesto Villacis‐Perez, Simon Snoeck, Andre H. Kurlovs, Richard M. Clark, Johannes A. J. Breeuwer, Thomas Van Leeuwen
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2156-14-43

Reintroductions and genetic introgression from domestic pigs have shaped the genetic population structure of Northwest European wild boar
Cited by: 47
Author(s): Daniel J. Goedbloed, Pim van Hooft, Hendrik‐Jan Megens, Katharina Langenbeck, Walburga Lutz, R.P.M.A. Crooijmans, S.E. van Wieren, Ron Ydenberg, Herbert H. T. Prins
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12864-018-4841-4

Genome sequence and population declines in the critically endangered greater bamboo lemur (Prolemur simus) and implications for conservation
Cited by: 16
Author(s): Melissa T. R. Hawkins, Ryan R. Culligan, Cynthia L. Frasier, Rebecca B. Dikow, Ryan A. Hagenson, Runhua Lei, Edward E. Louis
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0130329

Exome Analyses of Long QT Syndrome Reveal Candidate Pathogenic Mutations in Calmodulin-Interacting Genes
Cited by: 26
Author(s): Daichi Shigemizu, Takeshi Aiba, Hidewaki Nakagawa, Kouichi Ozaki, Fuyuki Miya, Wataru Satake, Tatsushi Toda, Yoshihiro Miyamoto, Akihiro Fujimoto, Yutaka Suzuki, Michiaki Kubo, Tatsuhiko Tsunoda, Wataru Shimizu, Toshihiro Tanaka
Software Mentions: 3
Published: over 9 years ago

10.1186/s12711-021-00664-9

A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes
Cited by: 14
Author(s): Elaheh Rostamzadeh Mahdabi, Ali Esmailizadeh, Ahmad Ayatollahi Mehrgardi, Masood Asadi Fozi
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0208217

Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia
Cited by: 61
Author(s): Brian P. Ward, Gina Brown-Guedira, F. L. Kolb, David A. Van Sanford, Priyanka Tyagi, Clay Sneller, Carl A. Griffey
Software Mentions: 3
Published: over 5 years ago

10.1002/mgg3.459

Identification of paternal uniparental disomy on chromosome 22 and ade novodeletion on chromosome 18 in individuals with orofacial clefts
Cited by: 3
Author(s): Ganiyu Oyediran Oseni, Deepti Jain, Peter Mossey, Tamara Busch, Lord Jephthah Joojo Gowans, Mekonen Eshete, Wasiu Lanre Adeyemo, Cecelia Laurie, Cathy C. Laurie, Arwa I. Owais, Peter B Olaitan, Babatunde S. Aregbesola, Fadekemi Olufunmilayo Oginni, S.A. Bello, Peter Donkor, Rosemary Audu, Chika Onwuamah, Solomon Obiri‐Yeboah, Gyikua Plange‐Rhule, Olugbenga M. Ogunlewe, Olutayo James, Taiye Halilu, Firke Abate, Lukman O. Abdur-Rahman, Abimbola V. Oladugba, Mary L. Marazita, Jeffrey C. Murray, Adebowale Adeyemo, Azeez Butali
Software Mentions: 3
Published: about 6 years ago

10.1111/eva.12580

Great tits and the city: Distribution of genomic diversity and gene–environment associations along an urbanization gradient
Cited by: 40
Author(s): Charles Perrier, Ana Lozano del Campo, Marta Szulkin, Virginie Demeyrier, Arnaud Grégoire, Anne Charmantier
Software Mentions: 3
Published: almost 7 years ago

10.1186/s13100-018-0143-2

Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
Cited by: 17
Author(s): Fritjof Lammers, Moritz Blumer, Cornelia Rücklé, Maria A. Nilsson
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-019-5485-8

The genome of the soybean cyst nematode (Heterodera glycines) reveals complex patterns of duplications involved in the evolution of parasitism genes
Cited by: 51
Author(s): Rick E. Masonbrink, Tom Maier, Usha Muppirala, Arun S. Seetharam, Étienne Lord, Parijat S. Juvale, Jeremy Schmutz, Nia Johnson, Dmitry Korkin, Melissa G. Mitchum, Benjamin Mimee, Sebastian Eves‐van den Akker, Matthew E. Hudson, Andrew J. Severin, Thomas J. Baum
Software Mentions: 3
Published: almost 6 years ago

10.1093/g3journal/jkaa027

Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion
Cited by: 2
Author(s): Peter J. Higgins, Cooper Alastair Grace, Soon Lee, Matthew R. Goddard
Software Mentions: 3
Published: almost 4 years ago

10.1111/eva.13023

Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population
Cited by: 17
Author(s): Meng Yue Wu, Grace Kah Mun Low, Antonio Forcina, Hein van Grouw, Benjamin P. Y‐H. Lee, Rachel Rui Ying Oh, Frank E. Rheindt
Software Mentions: 3
Published: over 4 years ago

10.1093/g3journal/jkab002

De novowhole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope
Cited by: 4
Author(s): Margarida Gonçalves, Hans R. Siegismund, Bettine Jansen van Vuuren, Klaus‐Peter Koepfli, Nathalie Ferrand, Raquel Godinho
Software Mentions: 3
Published: almost 4 years ago

10.1038/s41598-019-40144-1

Genomics-based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and Genotyping-By-Sequencing
Cited by: 34
Author(s): Ying Hu, M. D. V. de Resende, Aureliano Bombarely, Maria Brym, Elias Bassil, Alan H. Chambers
Software Mentions: 3
Published: over 5 years ago

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