cran: plink | Projects | Ecosyste.ms: Papers

10.1111/1755-0998.13044

Rapid identification and interpretation of gene–environment associations using the new R.SamBada landscape genomics pipeline
Cited by: 15
Author(s): Solange Duruz, Natalia Sevane, Oliver Selmoni, Elia Vajana, Kevin Leempoel, Sylvie Stucki, Pablo Orozco‐terWengel, Estelle Rochat, S. Dunner, Michael William Bruford, Stéphane Joost
Software Mentions: 4
Published: over 5 years ago

10.1111/pbi.13339

Balancing the double‐edged sword effect of increased resistant starch content and its impact on rice texture: its genetics and molecular physiological mechanisms
Cited by: 33
Author(s): Sabiha Parween, Joanne Jerenice Añonuevo, Vito M. Butardo, Gopal Misra, Roslen Anacleto, Cindy Llorente, Ondřej Kosík, Marissa V. Romero, E.H. Bandonill, Merlyn S. Mendioro, Alison Lovegrove, Alisdair R. Fernie, Yariv Brotman, Nese Sreenivasulu
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13007-021-00797-4

AprGPD: the apricot genomic and phenotypic database
Cited by: 2
Author(s): Chen Chen, Huimin Liu, Ningning Gou, Mengzhen Huang, Wei Xu, Xuchun Zhu, Mingyu Yin, Haikun Bai, Lin Wang, Tana Wuyun
Software Mentions: 4
Published: about 3 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: almost 11 years ago

10.1371/journal.pgen.1008780

Using prior information from humans to prioritize genes and gene-associated variants for complex traits in livestock
Cited by: 10
Author(s): Biaty Raymond, Loïc Yengo, Roy Costilla, C. Schrooten, A.C. Bouwman, Ben J. Hayes, R.F. Veerkamp, Peter M. Visscher
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1009036

Polygenic risk for autism spectrum disorder associates with anger recognition in a neurodevelopment-focused phenome-wide scan of unaffected youths from a population-based cohort
Cited by: 5
Author(s): Frank R. Wendt, Carolina Muniz Carvalho, Gita A Pathak, Joel Gelernter, Renato Polimanti
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1006314

Pleiotropic Associations of Allelic Variants in a 2q22 Region with Risks of Major Human Diseases and Mortality
Cited by: 26
Author(s): Alexander M. Kulminski, Liyun He, Irina Culminskaya, Yury Loika, Yelena Kernogitski, Konstantin G. Arbeev, Elena Loiko, Liubov Arbeeva, Olivia Bagley, Matt Duan, Arseniy Yashkin, Fang Fang, Mikhail Kovtun, Svetlana V. Ukraintseva, Deqing Wu, Anatoliy I. Yashin
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pgen.1007087

Comprehensive molecular profiling of 718 Multiple Myelomas reveals significant differences in mutation frequencies between African and European descent cases
Cited by: 64
Author(s): Zarko Manojlovic, Austin Christofferson, Winnie S. Liang, Jessica Aldrich, Megan Washington, Shukmei Wong, Daniel C. Rohrer, Scott D. Jewell, Rick A. Kittles, Mary DeRome, Daniel Auclair, David W. Craig, Jonathan J. Keats, John D. Carpten
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pgen.1008348

Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon
Cited by: 35
Author(s): Quentin Rougemont, Jean‐Sébastien Moore, Thibault Leroy, Éric Normandeau, Eric B. Rondeau, Ruth E. Withler, Donald M. Van Doornik, Penelope A. Crane, Kerry A. Naish, John Carlos Garza, Terry D. Beacham, Ben F. Koop, Louis Bernatchez
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1003959

Low Frequency Variants, Collapsed Based on Biological Knowledge, Uncover Complexity of Population Stratification in 1000 Genomes Project Data
Cited by: 31
Author(s): Carrie Moore, John R. Wallace, Daniel Wolfe, Alex T. Frase, Sarah A. Pendergrass, Kenneth M. Weiss, Marylyn D. Ritchie
Software Mentions: 4
Published: almost 11 years ago

10.1371/journal.pone.0233254

Genetic variation associated with PPO-inhibiting herbicide tolerance in sorghum
Cited by: 4
Author(s): Pragya Adhikari, Emma Goodrich, Samuel B. Fernandes, Alexander E. Lipka, Patrick J. Tranel, Patrick J. Brown, Tiffany M. Jamann
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pone.0101488

A Genome Wide Meta-Analysis Study for Identification of Common Variation Associated with Breast Cancer Prognosis
Cited by: 28
Author(s): Sajjad Rafiq, Sofia Khan, William Tapper, Andrew Collins, Rosanna Upstill-Goddard, Susan M. Gerty, Carl Blomqvist, Kristiina Aittomäki, Fergus J. Couch, Jing Liu, Heli Nevanlinna, Diana Eccles
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0216366

Cranial deformation and genetic diversity in three adolescent male individuals from the Great Migration Period from Osijek, eastern Croatia
Cited by: 11
Author(s): Daniel Fernandes, Kendra Sirak, Olivia Cheronet, Rachel Howcroft, Mislav Čavka, Dženi Los, Josip Burmaz, Ron Pinhasi, Mario Novak
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0008830

Application of Gene Network Analysis Techniques Identifies AXIN1/PDIA2 and Endoglin Haplotypes Associated with Bicuspid Aortic Valve
Cited by: 51
Author(s): Eric C. Wooten, Lakshmanan K. Iyer, Maria Claudia Montefusco, Alyson Kelley Hedgepeth, David A. Payne, Navin K. Kapur, David E. Housman, Michael E. Mendelsohn, Gordon S. Huggins
Software Mentions: 4
Published: almost 15 years ago

10.1371/journal.pone.0233808

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina
Cited by: 20
Author(s): Pierre Luisi, Angelina García, Juan Manuel Berros, Josefina María Brenda Motti, Darío Alfredo Demarchi, Emma Alfaro, Eliana Aquilano, Carina F. Argüelles, Sergio Alejandro Avena, Graciela Bailliet, Julieta Beltramo, Cláudio M. Bravi, Mariela Cuello, Cristina Beatriz Dejean, José Edgardo Dipierri, Laura Smeldy Jurado Medina, José Luis Lanata, Marina Muzzio, María Laura Parolin, Maia Pauro, Paula B. Paz Sepúlveda, Daniela Rodríguez Golpe, Maria Rita de Morais Chaves Santos, Marisol Schwab, Natalia Silvero, Jeremías Enrique Zubrzycki, Virgínia Ramallo, Hernán Dopazo
Software Mentions: 4
Published: over 4 years ago

10.1016/j.cels.2015.01.001

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics
Cited by: 239
Author(s): Ebrahim Afshinnekoo, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, Darryl Reeves, Jorge Gandara, Sagar Chhangawala, Sofia Ahsanuddin, Amber Simmons, Timothy Nessel, Bharathi Sundaresh, Elizabeth Pereira, Ellen Jorgensen, Sergios‐Orestis Kolokotronis, Nell Kirchberger, Isaac Garcia, David R. Gandara, Sean Dhanraj, Tanzina Nawrin, Yogesh Saletore, Noah Alexander, Priyanka Vijay, Elizabeth Hénaff, Paul Zumbo, Michael Walsh, Gregory D. O’Mullan, Scott Tighe, Joel T. Dudley, Anya Dunaif, Sean Ennis, Eoghan O'Halloran, Tiago R. Magalhães, Braden Boone, Angela L. Jones, Theodore R. Muth, Katie Schneider Paolantonio, Elizabeth Alter, Eric E. Schadt, Jeanne Garbarino, Robert J. Prill, Jane M. Carlton, Shawn Levy, Christopher E. Mason
Software Mentions: 4
Published: over 9 years ago

10.1038/s42003-021-01823-w

Shared associations identify causal relationships between gene expression and immune cell phenotypes
Cited by: 2
Author(s): Christiane Gasperi, Sung Chun, Shamil Sunyaev, Chris Cotsapas
Software Mentions: 4
Published: over 3 years ago

10.1038/s42003-021-02550-y

Composite trait Mendelian randomization reveals distinct metabolic and lifestyle consequences of differences in body shape
Cited by: 10
Author(s): Jonathan Sulc, Anthony Sonrel, Ninon Mounier, Chiara Auwerx, Eirini Marouli, Liza Darrous, Bogdan Draganski, Tuomas O. Kilpeläinen, Peter K. Joshi, Ruth J.F. Loos, Zoltán Kutalik
Software Mentions: 4
Published: about 3 years ago

10.1002/ece3.4304

Genomic divergence between SpanishLittorina saxatilisecotypes unravels limited admixture and extensive parallelism associated with population history
Cited by: 25
Author(s): Tony Kess, Juan Galindo, Elizabeth G. Boulding
Software Mentions: 4
Published: over 6 years ago

10.1002/edm2.74

Gene‐diet quality interactions on haemoglobin A1c and type 2 diabetes risk: The Airwave Health Monitoring Study
Cited by: 5
Author(s): Rebeca Eriksen, Rachel Gibson, Maria Aresu, Andy Heard, Queenie Chan, Εvangelos Εvangelou, He Gao, Paul Elliott, Gary Frost
Software Mentions: 4
Published: over 5 years ago

10.1111/eva.12514

Profiling the immunome of little brown myotis provides a yardstick for measuring the genetic response to white-nose syndrome
Cited by: 24
Author(s): Michael E. Donaldson, Christina M. Davy, Craig K. R. Willis, Scott McBurney, Allysia Park, Christopher J. Kyle
Software Mentions: 4
Published: about 7 years ago

10.1111/eva.12914

Spatial genetic structure in a crustacean herbivore highlights the need for local considerations in Baltic Sea biodiversity management
Cited by: 14
Author(s): Pierre De Wit, Per R. Jonsson, Ricardo T. Pereyra, Marina Panova, Carl André, Kerstin Johannesson
Software Mentions: 4
Published: almost 5 years ago

10.1111/eva.12990

Genomic population structure of Striped Bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River
Cited by: 12
Author(s): Nathalie M. LeBlanc, Benjamin I. Gahagan, Samuel N. Andrews, Trevor S. Avery, Gregory Neils Puncher, Benjamin J. Reading, Colin F. Buhariwalla, R. Allen Curry, Andrew R. Whiteley, Scott A. Pavey
Software Mentions: 4
Published: over 4 years ago

10.1111/eva.12987

Size reductions and genomic changes within two generations in wild walleye populations: associated with harvest?
Cited by: 24
Author(s): Ella Bowles, Kia Marin, Stephanie Mogensen, Pamela MacLeod, Dylan J. Fraser
Software Mentions: 4
Published: over 4 years ago

10.1111/eva.12407

Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees
Cited by: 27
Author(s): Victoria L. Pritchard, Jaakko Erkinaro, Matthew Kent, Eero Niemelä, Panu Orell, Sigbjørn Lien, Craig R. Primmer
Software Mentions: 4
Published: over 8 years ago

10.3389/fbioe.2020.00886

regSNPs-ASB: A Computational Framework for Identifying Allele-Specific Transcription Factor Binding From ATAC-seq Data
Cited by: 2
Author(s): Siwen Xu, Weixing Feng, Zixiao Lu, Christina Y. Yu, Wei Shao, Harikrishna Nakshatri, Jill L. Reiter, Hongyu Gao, Xun Chu, Yue Wang, Yunlong Liu
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2020.00891

Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats
Cited by: 13
Author(s): Romain De Oliveira, Hélène Rimbert, François Balfourier, Jonathan Kitt, Emeric Dynomant, Jan Vrána, Jaroslav Doležel, Federica Cattonaro, Etienne Paux, Frédéric Choulet
Software Mentions: 4
Published: over 4 years ago

10.3389/fgene.2019.01384

Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies
Cited by: 10
Author(s): Anthony Piot, Julien Prunier, Nathalie Isabel, Jaroslav Klápště, Yousry A. El‐Kassaby, Juan Carlos Villarreal Aguilar, Ilga Porth
Software Mentions: 4
Published: almost 5 years ago

10.3389/fpls.2017.01279

Sequence Polymorphisms and Structural Variations among Four Grapevine (Vitis vinifera L.) Cultivars Representing Sardinian Agriculture
Cited by: 23
Author(s): Luca Mercenaro, G. Nieddu, Andrea Porceddu, Mario Pezzotti, Salvatore Camiolo
Software Mentions: 4
Published: over 7 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

10.3390/genes11010082

Genome-Wide Association Study and Subsequent Exclusion of ATCAY as a Candidate Gene Involved in Equine Neuroaxonal Dystrophy Using Two Animal Models
Cited by: 3
Author(s): Erin N. Hales, Christina Esparza, Sichong Peng, Anna R. Dahlgren, Janel Peterson, Andrew D. Miller, Carrie J. Finno
Software Mentions: 4
Published: almost 5 years ago

10.1534/genetics.118.300712

Assessing the Genetic Landscape of Animal Behavior
Cited by: 24
Author(s): Ryan A. York
Software Mentions: 4
Published: over 6 years ago

10.1186/s13059-020-02248-0

The variant call format provides efficient and robust storage of GWAS summary statistics
Cited by: 55
Author(s): M. Lyon, Shea J. Andrews, Benjamin Elsworth, Tom R. Gaunt, Gibran Hemani, Edoardo Marcora
Software Mentions: 4
Published: almost 4 years ago

10.1093/gbe/evab073

Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation
Cited by: 8
Author(s): Gabriel Schweizer, Muhammad Bilal Haider, Gustavo Barroso, Nicole Rössel, Karin Münch, Regine Kahmann, Julien Dutheil
Software Mentions: 4
Published: over 3 years ago

10.1186/s13073-015-0196-5

Genomic prediction of celiac disease targeting HLA-positive individuals
Cited by: 24
Author(s): Gad Abraham, Alexia Rohmer, Jason A. Tye‐Din, Michael Inouye
Software Mentions: 4
Published: over 9 years ago

10.1186/s40104-016-0089-5

Selection signatures in Canchim beef cattle
Cited by: 23
Author(s): Ismael Urbinati, Nedenia Bonvino Stafuzza, Marcos T. Oliveira, T.C.S. Chud, R. H. Higa, Luciana Correia de Almeida Regitano, M. M. de Alencar, Marcos Eli Buzanskas, Danísio Prado Munari
Software Mentions: 4
Published: over 8 years ago

10.1080/15476286.2020.1777768

Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples
Cited by: 10
Author(s): Fabiola Curion, Adam E. Handel, Moustafa Attar, Giuseppe Gallone, Rory Bowden, M Z Cader, Michael B. Clark
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-017-06214-y

Genotype-environment interaction on human cognitive function conditioned on the status of breastfeeding and maternal smoking around birth
Cited by: 9
Author(s): Sang Lee, W. M. Shalanee P. Weerasinghe, J. H. J. van der Werf
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-017-13901-3

Population genomics of Wolbachia and mtDNA in Drosophila simulans from California
Cited by: 15
Author(s): Sarah Signor
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-28017-5

Consistent signatures of selection from genomic analysis of pairs of temporal and spatial Plasmodium falciparum populations from The Gambia
Cited by: 29
Author(s): Alfred Amambua-Ngwa, David Jeffries, Roberto Amato, Archibald Worwui, Karim Mane, Sukai Ceesay, Haddy Nyang, Davis Nwakanma, Joseph Okebe, Dominic P. Kwiatkowski, David J. Conway, Umberto D’Alessandro
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-69925-9

Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers
Cited by: 27
Author(s): Kwabena Darkwa, Paterne A. Agre, Bunmi Olasanmi, Kazuo Iseki, Ryo Matsumoto, Adrian F. Powell, Guillaume Bauchet, David De Koeyer, Satoru Muranaka, Patrick Adebola, Robert Asiedu, Ryohei Terauchi, Asrat Asfaw
Software Mentions: 4
Published: over 4 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

10.1038/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

10.1093/hmg/ddy206

Genome-wide survey of parent-of-origin effects on DNA methylation identifies candidate imprinted loci in humans
Cited by: 20
Author(s): Gabriel Cuéllar-Partida, Charles Laurin, Susan M. Ring, Tom R. Gaunt, Allan F. McRae, Peter M. Visscher, Grant W. Montgomery, Nicholas G. Martin, Gibran Hemani, Matthew Suderman, Caroline L Relton, George Davey Smith, David M. Evans
Software Mentions: 4
Published: over 6 years ago

10.1002/humu.23765

Heterozygosity mapping for human dominant trait variants
Cited by: 2
Author(s): Atsuko Imai‐Okazaki, Yang Li, Sukanya Horpaopan, Yasser Riazalhosseini, Masoud Garshasbi, Yaël P. Mossé, Di Zhang, Isabelle Schrauwen, Aarushi Sharma, Cathy S.J. Fann, Suzanne M. Leal, Mark Lathrop, Jürg Ott
Software Mentions: 4
Published: over 5 years ago

10.3390/ijerph17145217

Association of Genetic and Environmental Factors with Non-Alcoholic Fatty Liver Disease in a Chinese Han Population
Cited by: 5
Author(s): Zheng Li, Cheng-Yin Ye, Li Wang, Jinmei Li, Lei Yang
Software Mentions: 4
Published: over 4 years ago

10.1186/1471-2164-15-85

Variant calling in low-coverage whole genome sequencing of a Native American population sample
Cited by: 31
Author(s): Chris Bizon, Michael Spiegel, Scott A. Chasse, Ian R. Gizer, Yun Li, Ewa Malc, Piotr A. Mieczkowski, Josh K Sailsbery, Xiaoshu Wang, Cindy L. Ehlers, Kirk C. Wilhelmsen
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-020-6603-3

Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq
Cited by: 9
Author(s): Maria Luisa Martin Cerezo, Marek Kučka, Karol Zub, Yingguang Frank Chan, Jarosław Bryk
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1006976

Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations
Cited by: 43
Author(s): Nina Hollfelder, Carina M. Schlebusch, Torsten Günther, Hiba Babiker, Hisham Y. Hassan, Mattias Jakobsson
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-018-5168-x

Evaluation of whole exome sequencing as an alternative to BeadChip and whole genome sequencing in human population genetic analysis
Cited by: 8
Author(s): Zoltán Maróti, Zsolt Boldogkői, Dóra Tombácz, M Snyder, Tibor Kalmár
Software Mentions: 3
Published: about 6 years ago

10.12688/f1000research.9271.1

Automated quality control for genome wide association studies
Cited by: 10
Author(s): Sally R. Ellingson, David W. Fardo
Software Mentions: 3
Published: over 8 years ago

10.1111/age.12853

Accuracies of genomic prediction for twenty economically important traits in Chinese Simmental beef cattle
Cited by: 19
Author(s): Bo Zhu, Ping Guo, Z. Wang, W. Zhang, Y. Chen, Long Zhang, Huijiang Gao, Xue Gao, Lingyang Xu, J. Li
Software Mentions: 3
Published: about 5 years ago

10.1186/s13148-020-00934-1

DNA methylation mediates the effect of cocaine use on HIV severity
Cited by: 12
Author(s): Chang Shu, Amy C. Justice, Xinyu Zhang, Zuoheng Wang, Dana B. Hancock, Eric O. Johnson, Ke Xu
Software Mentions: 3
Published: about 4 years ago

10.1186/s12711-017-0301-x

Evaluation of the accuracy of imputed sequence variant genotypes and their utility for causal variant detection in cattle
Cited by: 86
Author(s): Hubert Pausch, Iona M. MacLeod, R. Fries, Reiner Emmerling, P.J. Bowman, Hans D. Daetwyler, Michael E. Goddard
Software Mentions: 3
Published: over 7 years ago

10.1111/age.13075

Association of inbreeding and regional equine leucocyte antigen homozygosity with the prevalence of insect bite hypersensitivity in Old Kladruber horse
Cited by: 4
Author(s): L. Vostrý, Hana Vostrá-Vydrová, J. Čítek, Gregor Gorjanc, Ino Čurik
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0140749

A Non-Synonymous HMGA2 Variant Decreases Height in Shetland Ponies and Other Small Horses
Cited by: 47
Author(s): Mirjam Frischknecht, Vidhya Jagannathan, Philippe Plattet, Markus Neuditschko, Heidi Signer-Hasler, Iris Bachmann, Alicja Pacholewska, Cord Drögemüller, Elisabeth Dietschi, Christine Flury, Stefan Rieder, Tosso Leeb
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-021-86389-7

Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential
Cited by: 7
Author(s): Jing Su, Kai Xu, Zirong Li, Yumei Hu, Zhongli Hu, Xianwei Zheng, Shufeng Song, Zhonghai Tang, Lanzhi Li
Software Mentions: 3
Published: over 3 years ago

10.1186/s12711-021-00650-1

A major QTL at the LHCGR/FSHR locus for multiple birth in Holstein cattle
Cited by: 11
Author(s): Sarah Widmer, Franz R. Seefried, Peter von Rohr, Irene M. Häfliger, Mirjam Spengeler, Cord Drögemüller
Software Mentions: 3
Published: over 3 years ago

10.1111/age.12638

Genome-wide association study for reproductive traits in a Large White pig population
Cited by: 49
Author(s): Y. Wang, Xiangdong Ding, Zhen Tan, Kai Xing, Tao Yang, Yuchun Pan, Shuangli Mi, Dongxiao Sun, C. Wang
Software Mentions: 3
Published: almost 7 years ago

10.1534/genetics.120.303096

Detecting Shared Genetic Architecture Among Multiple Phenotypes by Hierarchical Clustering of Gene-Level Association Statistics
Cited by: 8
Author(s): Melissa R. McGuirl, Samuel Pattillo Smith, Björn Sandstede, Sohini Ramachandran
Software Mentions: 3
Published: over 4 years ago

10.1186/s12864-020-06925-z

Population structure, genetic diversity, and selective signature of Chaka sheep revealed by whole genome sequencing
Cited by: 9
Author(s): Jie Cheng, Huangqing Zhao, Ningbo Chen, Xiukai Cao, Quratulain Hanif, Li Pi, Linyong Hu, Buren Chaogetu, Yongzhen Huang, Xianyong Lan, Chuzhao Lei, Hong Chen
Software Mentions: 3
Published: over 4 years ago

10.1186/gb-2010-11-1-r10

Characterization of X-Linked SNP genotypic variation in globally distributed human populations
Cited by: 31
Author(s): Amanda M. Casto, Jun Z. Li, Devin Absher, R Myers, Sohini Ramachandran, Marcus W. Feldman
Software Mentions: 3
Published: almost 15 years ago

10.1038/s42003-020-0937-x

Single-cell expression and Mendelian randomization analyses identify blood genes associated with lifespan and chronic diseases
Cited by: 6
Author(s): Arnaud Chignon, Valentin Bon-Baret, Marie-Chloé Boulanger, Zhonglin Li, Déborah Argaud, Yohan Bossé, Sébastien Thériault, Benoît J. Arsenault, Patrick Mathieu
Software Mentions: 3
Published: over 4 years ago

10.3389/fgene.2014.00105

Assessing the functional consequence of loss of function variants using electronic medical record and large-scale genomics consortium efforts
Cited by: 3
Author(s): Patrick Sleiman, Jonathan P. Bradfield, Frank Mentch, Berta Almoguera, John J. Connolly, Hákon Hákonarson
Software Mentions: 3
Published: over 10 years ago

10.3389/fgene.2019.01045

Population Genetic Analysis of Modern and Ancient DNA Variations Yields New Insights Into the Formation, Genetic Structure, and Phylogenetic Relationship of Northern Han Chinese
Cited by: 25
Author(s): Pengyu Chen, Jian Wu, Li Luo, Hongyan Gao, Mengge Wang, Xing Zou, Yingxiang Li, Chen Gang, Haibo Luo, Limei Yu, Yanyan Han, Jia Fu, Guanglin He
Software Mentions: 3
Published: about 5 years ago

10.1186/s13059-019-1852-7

Genotype-free demultiplexing of pooled single-cell RNA-seq
Cited by: 51
Author(s): Jun Xu, Caitlin Falconer, Quan Nguyen, Joanna Crawford, Brett McKinnon, Sally Mortlock, Anne Senabouth, Stacey Andersen, Han Sheng Chiu, Longda Jiang, Nathan J. Palpant, Jian Yang, Martin Mueller, Alex W. Hewitt, Alice Pébay, Grant W. Montgomery, Joseph E. Powell, Lachlan Coin
Software Mentions: 3
Published: almost 5 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/s13059-020-1938-2

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice
Cited by: 69
Author(s): Jae Young Choi, Zoe N. Lye, Simon C. Groen, Xiaofeng Dai, Priyesh Rughani, Sophie Zaaijer, Eoghan Harrington, Sissel Juul, Michael D. Purugganan
Software Mentions: 3
Published: almost 5 years ago

10.1111/age.13068

A natural knockout of the MYO7A gene leads to pre‐weaning mortality in pigs
Cited by: 4
Author(s): Martijn F.L. Derks, Hendrik Jan Megens, W. L. Giacomini, M.A.M. Groenen, Marcos S. Lopes
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-89509-5

Kernel machine SNP set analysis finds the association of BUD13, ZPR1, and APOA5 variants with metabolic syndrome in Tehran Cardio-metabolic Genetics Study
Cited by: 4
Author(s): Mahdi Akbarzadeh, Bahareh Sedaghati-Khayat, Niloufar Javanrouh Givi, Leila Najd Hassan Bonab, Fereidoun Azizi, Maryam Sadat Daneshpour
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-019-5529-0

Genome-wide data from the Bubi of Bioko Island clarifies the Atlantic fringe of the Bantu dispersal
Cited by: 5
Author(s): Pere Gelabert, Manuel Ferrando-Bernal, Toni de-Dios, Benedetta Mattorre, Elena Campoy, Amaya Gorostiza, Étienne Patin, Antonio González-Martı́n, Carles Lalueza-Fox
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.101461

The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese
Cited by: 20
Author(s): Xin Zhao, Xiaomin Liu, Aiping Zhang, Huashuai Chen, Qing Huo, Weiyang Li, Rui Ye, Zhihua Chen, Liping Liang, Alison Liu, Juan Shen, Xin Jin, Wenwen Li, Marianne Nygaard, Xiao Liu, Yong Hou, Ting Ni, Lars Bolund, William K. Gottschalk, Wei Tao, Jun Gu, Xiao-Li Tian, Huanming Yang, Jian Wang, Xun Xu, Michael W. Lutz, Junxia Min, Yi Zeng, Chao Nie
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-37086-5

Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production
Cited by: 11
Author(s): Rafał M. Gutaker, Maricris Zaidem, Yong‐Bi Fu, Axel Diederichsen, Oliver Smith, Roselyn Ware, Robin G. Allaby
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-5142-7

Genetic variants in nuclear DNA along with environmental factors modify mitochondrial DNA copy number: a population-based exome-wide association study
Cited by: 11
Author(s): Zhihua Li, Meng Zhu, Jiangbo Du, Hongxia Ma, Guangfu Jin, Juncheng Dai
Software Mentions: 3
Published: about 6 years ago

10.3389/fgene.2019.00675

Scanning of Genetic Variants and Genetic Mapping of Phenotypic Traits in Gilthead Sea Bream Through ddRAD Sequencing
Cited by: 12
Author(s): Dimitrios Kyriakis, Alexandros Kanterakis, Tereza Manousaki, Alexandros Tsakogiannis, Michalis Tsagris, Ioannis Tsamardinos, Leonidas Papaharisis, Dimitrios Chatziplis, George Potamias, Costas S. Tsigenopoulos
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2948-z

Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy
Cited by: 8
Author(s): Candice Brinkmeyer-Langford, Cynthia Balog-Alvarez, James J. Cai, Brian W. Davis, Joe N. Kornegay
Software Mentions: 3
Published: over 8 years ago

10.1186/s12862-021-01894-7

Positive selection of skeleton-related genes during duck domestication revealed by whole genome sequencing
Cited by: 4
Author(s): Tao Zhu, Xin Qi, Yu Chen, Liang Wang, Xueze Lv, Weijia Yang, Jianwei Zhang, Kaiyang Li, Zhonghua Ning, Zhihua Jiang, Lujiang Qu
Software Mentions: 3
Published: about 3 years ago

10.7554/eLife.36011

Oscillatory hyperactivity and hyperconnectivity in young APOE-ɛ4 carriers and hypoconnectivity in Alzheimer’s disease
Cited by: 68
Author(s): Loes Koelewijn, Thomas Lancaster, David Edmund Johannes Linden, Diana C. Dima, Bethany Routley, Lorenzo Magazzini, Kali Barawi, Lisa Brindley, Rachael Adams, Katherine E. Tansey, Aline Bompas, Andrea Tales, Antony James Bayer, Krish Devi Singh
Software Mentions: 3
Published: over 5 years ago

10.1186/s13073-017-0426-0

Integrated genomic analysis of mitochondrial RNA processing in human cancers
Cited by: 25
Author(s): Youssef Idaghdour, Alan Hodgkinson
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2021.714852

iSheep: an Integrated Resource for Sheep Genome, Variant and Phenotype
Cited by: 9
Author(s): Zhonghuang Wang, Qianghui Zhu, Xin Li, Junwei Zhu, Dongmei Tian, Si-Si Zhang, Hailong Kang, Cuiping Li, Lili Dong, Wenming Zhao, Menghua Li
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2020.00286

Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat
Cited by: 16
Author(s): Jun-Jie Wang, Teng Zhang, Qiu-Ming Chen, Ruiqian Zhang, Lan Li, Shun‐Feng Cheng, Wei Shen, Chuzhao Lei
Software Mentions: 3
Published: over 4 years ago

10.1186/s12859-014-0418-7

Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations
Cited by: 41
Author(s): Vikas Bansal, Ondrej Libiger
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-015-1991-5

Copy number variations in the genome of the Qatari population
Cited by: 8
Author(s): Khalid Fakhro, Noha A. Yousri, Juan L. Rodríguez-Flores, Amal Robay, Michelle R. Staudt, Francisco Agosto-Perez, Jacqueline Salit, Joel A. Malek, Karsten Suhre, Amin Jayyousi, Mahmoud Zirie, Dora J. Stadler, Jason G. Mezey, Ronald G. Crystal
Software Mentions: 3
Published: about 9 years ago

10.1186/s12859-018-2229-8

Performance of epistasis detection methods in semi-simulated GWAS
Cited by: 16
Author(s): Clément Chatelain, Guillermo Durand, Vincent Thuillier, Franck Augé
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2021.704538

CoMM-S4: A Collaborative Mixed Model Using Summary-Level eQTL and GWAS Datasets in Transcriptome-Wide Association Studies
Cited by: 3
Author(s): Yi Yang, Kar-Fu Yeung, Jin Liu
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0238255

Most frequent South Asian haplotypes of ACE2 share identity by descent with East Eurasian populations
Cited by: 24
Author(s): Anshika Srivastava, Rudra Kumar Pandey, Prajjval Pratap Singh, Pramod Kumar, Avinash Arvind Rasalkar, Rakesh Tamang, George van Driem, Pankaj Shrivastava, Gyaneshwer Chaubey
Software Mentions: 3
Published: about 4 years ago

10.1002/ece3.5828

Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish
Cited by: 38
Author(s): Tony Kess, Paul Bentzen, Sarah J. Lehnert, Emma V. A. Sylvester, Sigbjørn Lien, Matthew Kent, Marion Sinclair-Waters, Corey J. Morris, Brendan F. Wringe, Robert Fairweather, Ian Bradbury
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0020042

A Locus on Chromosome 5 Is Associated with Dilated Cardiomyopathy in Doberman Pinschers
Cited by: 44
Author(s): Theresa-Bernadette Mausberg, Gerhard Wess, Julia Simak, Lena Keller, Michaela Drögemüller, Cord Drögemüller, Matthew T. Webster, Hannah Stephenson, J. Dukes‐McEwan, Tosso Leeb
Software Mentions: 3
Published: over 13 years ago

10.1002/ece3.4278

Population structure of a vector of human diseases: Aedes aegypti in its ancestral range, Africa
Cited by: 53
Author(s): Panayiota Kotsakiozi, Benjamin R. Evans, Andrea Gloria‐Soria, Basile Kamgang, Martin N. Mayanja, Julius J. Lutwama, Gilbert Le Goff, Diégo Ayala, Christophe Paupy, Athanase Badolo, João Pinto, Carla A. Sousa, Arlete D. Troco, Jeffrey R. Powell
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.39725

Reduced signal for polygenic adaptation of height in UK Biobank
Cited by: 279
Author(s): Jeremy J Berg, Arbel Harpak, Nasa Sinnott-Armstrong, Anja Moltke Joergensen, Hakhamanesh Mostafavi, Yair Field, Evan A. Boyle, Xinjun Zhang, Fernando Racimo, Jonathan K. Pritchard, Graham Coop
Software Mentions: 3
Published: over 5 years ago

10.1002/ece3.4891

Characterizing neutral and adaptive genomic differentiation in a changing climate: The most northerly freshwater fish as a model
Cited by: 9
Author(s): Kathleen G. O’Malley, Felix Vaux, Andrew N. Black
Software Mentions: 3
Published: almost 6 years ago

10.3389/fgene.2018.00266

Correcting for Population Stratification Reduces False Positive and False Negative Results in Joint Analyses of Host and Pathogen Genomes
Cited by: 15
Author(s): Olivier Naret, Nimisha Chaturvedi, István Bartha, Christian Hammer, Jacques Fellay
Software Mentions: 3
Published: over 6 years ago

10.3389/fimmu.2021.662171

Inflammatory Protein Profiles in Plasma of Candidaemia Patients and the Contribution of Host Genetics to Their Variability
Cited by: 6
Author(s): Vasiliki Matzaraki, Kieu Le, Martin Jaeger, Raúl Aguirre-Gamboa, Melissa D. Johnson, Serena Sanna, Diletta Rosati, Lude Franke, Alexandra Zhernakova, Jingyuan Fu, Sebo Withoff, Iris Jonkers, Yang Li, Leo A. B. Joosten, Mihai G. Netea, Cisca Wijmenga, Vinod Kumar
Software Mentions: 3
Published: about 3 years ago

10.1186/s12864-018-5364-8

Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables
Cited by: 8
Author(s): Edoardo Giacopuzzi, Massimo Gennarelli, Chiara Sacco, Alice Filippini, Jessica Mingardi, Chiara Magri, Alessandro Barbon
Software Mentions: 3
Published: almost 6 years ago

10.3389/fninf.2014.00029

A review of multivariate analyses in imaging genetics
Cited by: 91
Author(s): Jingyu Liu, Vince D. Calhoun
Software Mentions: 3
Published: over 10 years ago

10.1111/age.12752

Genetic diversity analysis of French goat populations reveals selective sweeps involved in their differentiation
Cited by: 21
Author(s): Claire Oget, Bertrand Servin, Isabelle Palhière
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pmed.1003498

Polygenic risk scores in cardiovascular risk prediction: A cohort study and modelling analyses
Cited by: 83
Author(s): Luanluan Sun, Lisa Pennells, Stephen Kaptoge, Christopher P. Nelson, Scott C. Ritchie, Gad Abraham, Matthew Arnold, Steven Bell, Thomas Bolton, Stephen Burgess, Frank Dudbridge, Qi Guo, Eleni Sofianopoulou, David P. Stevens, John R. Thompson, Adam S. Butterworth, Angela Wood, John Danesh, Nilesh J. Samani, Michael Inouye, Emanuele Di Angelantonio
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-018-4749-z

Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs
Cited by: 11
Author(s): Matthew T. Oetjens, Axel Martin, Krishna R. Veeramah, Jeffrey M. Kidd
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-021-97350-z

Genetic predisposition to tinnitus in the UK Biobank population
Cited by: 1
Author(s): Madeleine E Urbanek, Jian Zuo
Software Mentions: 3
Published: about 3 years ago

10.1038/srep15786

Genome-wide analysis correlates Ayurveda Prakriti
Cited by: 73
Author(s): Periyasamy Govindaraj, Sheikh Nizamuddin, Sharath Anugula, Vuskamalla Jyothi, Harish Rotti, Ritu Raval, Jayakrishna Nayak, Balakrishna K Bhat, B V Prasanna, Pooja Shintre, Mayura Sule, Kalpana Joshi, Amrish P Dedge, Ramachandra Bharadwaj, G G Gangadharan, Sreekumaran Nair, P. M. Gopinath, Bhushan Patwardhan, Paturu Kondaiah, Kapaettu Satyamoorthy, Marthanda Varma Sankaran Valiathan, Kumarasamy Thangaraj
Software Mentions: 3
Published: about 9 years ago

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