cran: plink | Projects | Ecosyste.ms: Papers

10.1093/gigascience/giz028

Rice Galaxy: an open resource for plant science
Cited by: 13
Author(s): Venice Margarette Juanillas, Alexis Dereeper, Nicolas Beaume, Gaëtan Droc, Joshua Gregor A. Dizon, J. Mendoza, Jon Peter Perdon, Locedie Mansueto, Lindsay R. Triplett, Jillian M. Lang, Gabriel Zhou, Kunalan Ratharanjan, Beth Plale, Jason Haga, Jan E. Leach, Manuel Ruiz, Michael J. Thomson, Nickolai Alexandrov, Pierre Larmande, Tobias Kretzschmar, Ramil Mauleon
Software Mentions: 18
Published: over 5 years ago

10.1002/ece3.5763

Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)
Cited by: 18
Author(s): Felix Vaux, Leif K. Rasmuson, Lisa A. Kautzi, Polly S. Rankin, Matthew T. O. Blume, Kelly Lawrence, Sandra Bohn, Kathleen G. O’Malley
Software Mentions: 17
Published: about 5 years ago

10.1111/eva.13202

Adaptive markers distinguish North and South Pacific Albacore amid low population differentiation
Cited by: 15
Author(s): Felix Vaux, Sandra Bohn, John R. Hyde, Kathleen G. O’Malley
Software Mentions: 15
Published: over 3 years ago

10.1111/eva.12965

Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oyster Crassostrea gigas throughout the Northern Hemisphere
Cited by: 11
Author(s): Ben J. G. Sutherland, Claire Rycroft, Anne‐Laure Ferchaud, Rob Saunders, Li Li, Sheng Liu, Amy M. Chan, Sarah P. Otto, Curtis A. Suttle, Kristina M. Miller
Software Mentions: 13
Published: over 4 years ago

10.3390/genes12091443

Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids
Cited by: 8
Author(s): Estelle Bineau, José L. Rambla, Santiago Priego-Cubero, Alexandre Hereil, Frédérique Bitton, Clémence Plissonneau, Antonio Granell, Mathilde Causse
Software Mentions: 11
Published: about 3 years ago

10.1371/journal.pgen.1008748

Polygenic adaptation of rosette growth in Arabidopsis thaliana
Cited by: 19
Author(s): Benedict Wieters, Kim A. Steige, Fei He, Evan Koch, Sebastián E. Ramos-Onsins, Hongya Gu, Ya‐Long Guo, Shamil Sunyaev, Juliette de Meaux
Software Mentions: 11
Published: almost 4 years ago

10.3389/fgene.2021.682638

Scalable and Robust Regression Methods for Phenome-Wide Association Analysis on Large-Scale Biobank Data
Cited by: 2
Author(s): Wenjian Bi, Seunggeun Lee
Software Mentions: 10
Published: over 3 years ago

10.1002/ece3.5064

North‐facing slopes and elevation shape asymmetric genetic structure in the range‐restricted salamander Plethodon shenandoah
Cited by: 10
Author(s): Kevin P. Mulder, Nandadevi Cortés-Rodríguez, Evan H. Campbell Grant, Adrianne B. Brand, Robert C. Fleischer
Software Mentions: 10
Published: over 5 years ago

10.3390/genes12040503

Genomic and Phenotypic Diversity of Cultivated and Wild Tomatoes with Varying Levels of Heat Tolerance
Cited by: 10
Author(s): Mathieu Anatole Tele Ayenan, Agyemang Danquah, Paterne A. Agre, Peter Hanson, Isaac Asante, Eric Danquah
Software Mentions: 10
Published: over 3 years ago

10.3389/fgene.2020.00260

IntAssoPlot: An R Package for Integrated Visualization of Genome-Wide Association Study Results With Gene Structure and Linkage Disequilibrium Matrix
Cited by: 20
Author(s): Fengyu He, Shuangcheng Ding, Hongwei Wang, Feng Qin
Software Mentions: 10
Published: over 4 years ago

10.1186/s13040-019-0201-4

Exploration of a diversity of computational and statistical measures of association for genome-wide genetic studies
Cited by: 3
Author(s): Elisabetta Manduchi, Patryk Orzechowski, Marylyn D. Ritchie, Jason H. Moore
Software Mentions: 9
Published: over 5 years ago

10.1111/1755-0998.13362

Chromosome‐scale assembly of the genome of Salixdunnii reveals a male‐heterogametic sex determination system on chromosome 7
Cited by: 24
Author(s): Li He, Kai‐Hua Jia, Rengang Zhang, Yuan Wang, Tian-Le Shi, Zhichao Li, Si-Wen Zeng, Xin-Jie Cai, Natascha D. Wagner, Elvira Hörandl, Aline Muyle, Ke Yang, Deborah Charlesworth, Jian‐Feng Mao
Software Mentions: 9
Published: over 3 years ago

10.1093/molbev/msaa266

Genomic Adaptations to Salinity Resist Gene Flow in the Evolution of Floridian Watersnakes
Cited by: 10
Author(s): Rhett M. Rautsaw, Tristan D. Schramer, Rachel Acuña, Lindsay N Arick, Mark DiMeo, Kathryn P. Mercier, Michael Schrum, Andrew J. Mason, Mark J. Margres, Jason L. Strickland, Christopher L. Parkinson
Software Mentions: 9
Published: about 4 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

10.1093/g3journal/jkab238

Whole-genome variation of transposable element insertions in a maize diversity panel
Cited by: 13
Author(s): Yinjie Qiu, Christine H. O’Connor, Rafael Della Coletta, Jonathan S. Renk, Patrick J. Monnahan, Jaclyn M. Noshay, Zhikai Liang, Amanda M. Gilbert, Sarah N. Anderson, Suzanne E. McGaugh, Nathan M. Springer, Candice N. Hirsch
Software Mentions: 9
Published: over 3 years ago

10.1186/s13059-018-1616-9

Population structure of human gut bacteria in a diverse cohort from rural Tanzania and Botswana
Cited by: 61
Author(s): Matthew E.B. Hansen, Meagan A Rubel, Aubrey Bailey, Alessia Ranciaro, S. R. Thompson, Michael C. Campbell, William Beggs, Jaanki R. Dave, Gaonyadiwe George Mokone, Sununguko Wata Mpoloka, Thomas Nyambo, Christian C. Abnet, Stephen J. Chanock, Frederic D. Bushman, Sarah A. Tishkoff
Software Mentions: 8
Published: almost 6 years ago

10.1099/mgen.0.000337

Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes
Cited by: 39
Author(s): Morteza M. Saber, B. Jesse Shapiro
Software Mentions: 8
Published: over 4 years ago

10.1371/journal.pbio.1001555

The Geography of Recent Genetic Ancestry across Europe
Cited by: 318
Author(s): Peter L. Ralph, Graham Coop
Software Mentions: 7
Published: over 11 years ago

10.7554/eLife.58615

GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background
Cited by: 67
Author(s): Nasa Sinnott-Armstrong, Sahin Naqvi, Manuel A. Rivas, Jonathan K. Pritchard
Software Mentions: 7
Published: almost 4 years ago

10.1099/mgen.0.000303

Comparative genomic analysis identifies X-factor (haemin)-independent Haemophilus haemolyticus: a formal re-classification of 'Haemophilus intermedius'
Cited by: 5
Author(s): Tegan M. Harris, Erin P. Price, Derek S. Sarovich, Niels Nørskov‐Lauritsen, Jemima Beissbarth, Anne B. Chang, Heidi Smith‐Vaughan
Software Mentions: 7
Published: almost 5 years ago

10.1002/ece3.4994

Sampling related individuals within ponds biases estimates of population structure in a pond‐breeding amphibian
Cited by: 23
Author(s): Kyle A. O’Connell, Kevin P. Mulder, Jose A. Maldonado, Kathleen L. Currie, Dennis M. Ferraro
Software Mentions: 7
Published: over 5 years ago

10.1186/s12859-020-03945-0

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

10.3389/fpsyt.2021.668297

Estimating the Prevalence and Genetic Risk Mechanisms of ARFID in a Large Autism Cohort
Cited by: 26
Author(s): Tanner Koomar, Taylor Thomas, Natalie R. Pottschmidt, Michael Lutter, Jacob J. Michaelson
Software Mentions: 7
Published: over 3 years ago

10.1534/g3.120.401325

Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
Cited by: 17
Author(s): Alexander F. Gileta, Jianjun Gao, Apurva S. Chitre, Hannah Bimschleger, Celine L. St. Pierre, Shyam Gopalakrishnan, Abraham A. Palmer
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pgen.1009566

Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
Cited by: 19
Author(s): James R. Whiting, Josephine R. Paris, Mijke J. van der Zee, Paul J. Parsons, Detlef Weigel, Bonnie A. Fraser
Software Mentions: 7
Published: over 3 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

10.1186/s13059-020-1930-x

CUBIC: an atlas of genetic architecture promises directed maize improvement
Cited by: 49
Author(s): Haijun Liu, Xiaqing Wang, Yingjie Xiao, Jingyun Luo, Feng Qiao, Wenyu Yang, Ruyang Zhang, Yijiang Meng, Jiamin Sun, Shijuan Yan, Yong Peng, Luyao Niu, Liumei Jian, Wei Song, Jiali Yan, Chunhui Li, Yanxin Zhao, Liu Ya, Marilyn L. Warburton, Jiuran Zhao
Software Mentions: 7
Published: almost 5 years ago

10.3390/genes12060799

ALDH2 p.E504K Variation and Sex Are Major Factors Associated with Current and Quitting Alcohol Drinking in Japanese Oldest Old
Cited by: 4
Author(s): Takashi Sasaki, Yoshinori Nishimoto, Takumi Hirata, Yukiko Abe, Toru Takebayashi, Yasumichi Arai
Software Mentions: 7
Published: over 3 years ago

10.1111/mec.15010

Disentangling structural genomic and behavioural barriers in a sea of connectivity
Cited by: 60
Author(s): Julia Maria Isis Barth, David Villegas‐Ríos, Carla Freitas, Even Moland, Bastiaan Star, Carl André, Halvor Knutsen, Ian Bradbury, Jan Dierking, Christoph Petereit, David Righton, Julian D. Metcalfe, Kjetill S. Jakobsen, Esben Moland Olsen, Sissel Jentoft
Software Mentions: 7
Published: over 5 years ago

10.1016/j.cell.2016.10.026

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
Cited by: 527
Author(s): Lu Chen, Bing Ge, Francesco Paolo Casale, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Yan Yan, Kousik Kundu, Simone Ecker, Avik Datta, David Richardson, Frances Burden, Daniel Mead, Alice Mann, José Marı́a Fernández, Sophia Rowlston, Steven P. Wilder, Samantha Farrow, Xiaojian Shao, John Lambourne, Adriana Redensek, Cornelis A. Albers, Vyacheslav Amstislavskiy, Sofie Ashford, Kim Berentsen, Lorenzo Bomba, Guillaume Bourque, David Bujold, Stephan Busche, Maxime Caron, Shu-Huang Chen, Warren A. Cheung, Olivier Delaneau, Emmanouil T. Dermitzakis, Heather Elding, Irina Colgiu, Frederik Otzen Bagger, Paul Flicek, Ehsan Habibi, Valentina Iotchkova, Eva M. Janssen-Megens, Bowon Kim, Hans Lehrach, Ernesto Lowy, Amit Mandoli, Filomena Matarese, Matthew T. Maurano, John A. Morris, Véra Pancaldi, Farzin Pourfarzad, Karola Rehnström, Augusto Rendon, Thomas S. Risch, Nilofar Sharifi, Simon Maguire, Marc Sultan, Alfonso Valencia, Klaudia Walter, Shuang-Yin Wang, Mattia Frontini, Stylianos E. Antonarakis, Laura Clarke, Marie–Laure Yaspo, Stephan Beck, Roderic Guigó, Daniel Rico, Joost H.A. Martens, Willem H. Ouwehand, Taco W. Kuijpers, Dirk S. Paul, Hendrik G. Stunnenberg, Oliver Stegle, Kate Downes, Tomi Pastinen, Nicole Soranzo
Software Mentions: 7
Published: about 8 years ago

10.3389/fpls.2020.00685

Hybridization Between Yuccas From Baja California: Genomic and Environmental Patterns
Cited by: 9
Author(s): María Clara Arteaga, Rafael Bello-Bedoy, Jaime Gasca-Pineda
Software Mentions: 7
Published: over 4 years ago

10.1111/mec.15287

Landscape drivers of genomic diversity and divergence in woodland Eucalyptus
Cited by: 29
Author(s): Kevin Murray, Jasmine K. Janes, Ashley Jones, Helen M. Bothwell, Rose L. Andrew, Justin O. Borevitz
Software Mentions: 7
Published: about 5 years ago

10.3389/fgene.2021.664379

Putative Causal Variants Are Enriched in Annotated Functional Regions From Six Bovine Tissues
Cited by: 19
Author(s): Claire P. Prowse-Wilkins, Jianghui Wang, Ruidong Xiang, Josie B. Garner, Michael E. Goddard, Amanda J. Chamberlain
Software Mentions: 6
Published: over 3 years ago

10.1186/1751-0473-6-4

Parallel biocomputing
Cited by: 0
Author(s): Kenneth S Kompass, Thomas J. Hoffmann, John S. Witte
Software Mentions: 6
Published: over 13 years ago

10.3389/fgene.2021.731355

HandyCNV: Standardized Summary, Annotation, Comparison, and Visualization of Copy Number Variant, Copy Number Variation Region, and Runs of Homozygosity
Cited by: 5
Author(s): Juefei Zhou, Liyuan Liu, Thomas Lopdell, Dorian J. Garrick, Yiting Shi
Software Mentions: 6
Published: about 3 years ago

10.1111/age.12873

Genomic regions influencing intramuscular fat in divergently selected rabbit lines
Cited by: 15
Author(s): Bolívar Samuel Sosa-Madrid, Pilar Hernández, A. Blasco, Chris Haley, Luca Fontanesi, M. A. Santacreu, Ramona N. Pena, Pau Navarro, Noelia Ibáñez‐Escriche
Software Mentions: 6
Published: about 5 years ago

10.1038/s41598-017-12621-y

Reconstructing human population history from dental phenotypes
Cited by: 44
Author(s): Hannes Rathmann, Hugo Reyes-Centeno, Silvia Ghirotto, Nicole Creanza, Tsunehiko Hanihara, Katerina Harvati
Software Mentions: 6
Published: about 7 years ago

10.1111/eva.12765

Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge (Esox masquinongy) from the St. Lawrence River basin
Cited by: 14
Author(s): Quentin Rougemont, Anne Carrier, Jérémy Le Luyer, Anne‐Laure Ferchaud, John M. Farrell, Daniel Hatin, Philippe Brodeur, Louis Bernatchez
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1008804

Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility
Cited by: 24
Author(s): Maya Hiltpold, Guanglin Niu, Naveen Kumar Kadri, Danang Crysnanto, Zih-Hua Fang, Mirjam Spengeler, F. Schmitz‐Hsu, Christian Fuerst, Hermann Schwarzenbacher, Franz R. Seefried, Frauke Seehusen, Ulrich Witschi, Angelika Schnieke, R. Fries, Heinrich Bollwein, Krzysztof Flisikowski, Hubert Pausch
Software Mentions: 6
Published: over 4 years ago

10.3390/biology10080734

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin
Cited by: 4
Author(s): Xiaoyun Zhou, Shaokui Yi, Wenhao Zhao, Qiong Zhou, Jianzhong Shen, Dapeng Li, Bin Huo, Rong Tang
Software Mentions: 6
Published: over 3 years ago

10.1002/ece3.5961

Do different rates of gene flow underlie variation in phenotypic and phenological clines in a montane grasshopper community?
Cited by: 4
Author(s): R. O. Slatyer, Sean D. Schoville, César R. Nufio, Lauren B. Buckley
Software Mentions: 6
Published: almost 5 years ago

10.7554/eLife.59929

Gene expression variability in human and chimpanzee populations share common determinants
Cited by: 27
Author(s): Benjamin Jung Fair, Lauren E. Blake, Abhishek Sarkar, Bryan J. Pavlovic, Claudia Cuevas, Yoav Gilad
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-018-24580-z

Sex-specific glioma genome-wide association study identifies new risk locus at 3p21.31 in females, and finds sex-differences in risk at 8q24.21
Cited by: 50
Author(s): Quinn T. Ostrom, Ben Kinnersley, Margaret Wrensch, Jeanette E. Eckel‐Passow, Georgina Armstrong, Terri Rice, Yanwen Chen, John K. Wiencke, Lucie McCoy, Helen M. Hansen, Christopher I. Amos, Jonine L. Bernstein, Elizabeth B. Claus, Dora Il’yasova, Christoffer Johansen, Daniel H. Lachance, Rose Lai, Ryan Merrell, Sara H. Olson, Siegal Sadetzki, Joellen M. Schildkraut, Sanjay Shete, Joshua B. Rubin, Justin D. Lathia, Michael E. Berens, Ulrika Andersson, Preetha Rajaraman, Stephen J. Chanock, Martha S. Linet, Zhaoming Wang, Meredith Yeager, Richard S. Houlston, Robert B. Jenkins, Beatrice Melin, Melissa L. Bondy, Jill S. Barnholtz‐Sloan
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-021-86287-y

Population genomic analyses of schistosome parasites highlight critical challenges facing endgame elimination efforts
Cited by: 9
Author(s): Jonathan A. Shortt, Laura E. Timm, Nicole R. Hales, Zachary L. Nikolakis, Drew R. Schield, Blair W. Perry, Yang Liu, Bo Zhong, Elizabeth J. Carlton, David D. Pollock
Software Mentions: 6
Published: over 3 years ago

10.1186/s13073-014-0107-1

Complex host genetics influence the microbiome in inflammatory bowel disease
Cited by: 316
Author(s): Dan Knights, Mark S. Silverberg, Rinse K. Weersma, Dirk Gevers, Gerard Dijkstra, Hailiang Huang, Andrea D. Tyler, Suzanne van Sommeren, Floris Imhann, Joanne M. Stempak, Hu Huang, Pajau Vangay, Gabriel A. Al‐Ghalith, Caitlin Russell, Jenny Sauk, Jo Knight, Mark J. Daly, Curtis Huttenhower, Ramnik J. Xavier
Software Mentions: 6
Published: almost 10 years ago

10.1093/gbe/evx067

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations
Cited by: 37
Author(s): Julia Maria Isis Barth, Malte Damerau, Michael Matschiner, Sissel Jentoft, Reinhold Hanel
Software Mentions: 6
Published: over 7 years ago

10.1038/sdata.2018.185

The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease
Cited by: 284
Author(s): Minghui Wang, Noam D. Beckmann, Panos Roussos, Erming Wang, Xianxiao Zhou, Qian Wang, Chi Ming, Ryan Neff, Wanli Ma, John F. Fullard, Mads E. Hauberg, Jaroslav Bendl, Mette A. Peters, Ben Logsdon, Pei Wang, Milind Mahajan, Lara M. Mangravite, Eric B. Dammer, Duc M. Duong, James J. Lah, Nicholas T. Seyfried, Aĺlan I. Levey, Joseph D. Buxbaum, Michelle E. Ehrlich, Sam Gandy, Pavel Katsel, Vahram Haroutunian, Eric E. Schadt, Bin Zhang
Software Mentions: 6
Published: about 6 years ago

10.1534/g3.114.016196

A Multipurpose, High-Throughput Single-Nucleotide Polymorphism Chip for the Dengue and Yellow Fever Mosquito, Aedes aegypti
Cited by: 53
Author(s): Benjamin R. Evans, Andrea Gloria‐Soria, Lin Hou, Carolyn S. McBride, Mariangela Bonizzoni, Hongyu Zhao, Jeffrey R. Powell
Software Mentions: 6
Published: over 9 years ago

10.1186/s13072-017-0144-2

Regions of common inter-individual DNA methylation differences in human monocytes: genetic basis and potential function
Cited by: 19
Author(s): Christopher Schröder, Elsa Leitão, Stefan Wallner, Gerd Schmitz, Ludger Klein‐Hitpass, Anupam Sinha, Karl‐Heinz Jöckel, Markus M. Nöthen, Per Hoffmann, Markus M. Nöthen, Michael Steffens, Peter Ebert, Sven Rahmann, Bernhard Horsthemke
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pcbi.1008044

Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits
Cited by: 15
Author(s): Craig A. Glastonbury, Sara L. Pulit, Julius Honecker, Jenny C Censin, Samantha Laber, Hanieh Yaghootkar, Nilüfer Rahmioğlu, Emilie Pastel, Katarina Kos, Andrew M. Pitt, Michelle Hudson, Christoffer Nellåker, Nicola L. Beer, Hans Hauner, Christian M. Becker, Krina T. Zondervan, Timothy M. Frayling, Melina Claussnitzer, Cecilia M. Lindgren
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

10.1093/molbev/msab084

Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation
Cited by: 8
Author(s): Haruna Nakamura, Mitsuto Aibara, Rei Kajitani, Hillary D. J. Mrosso, Semvua Isa Mzighani, Atsushi Toyoda, Takehiko Itoh, Norihiro Okada, Masato Nikaido
Software Mentions: 6
Published: over 3 years ago

10.1093/g3journal/jkab274

Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland
Cited by: 1
Author(s): S. Eryn McFarlane, Josephine M. Pemberton
Software Mentions: 6
Published: over 3 years ago

10.3390/ijms22126319

Expression Quantitative Trait Loci (eQTLs) Associated with Retrotransposons Demonstrate their Modulatory Effect on the Transcriptome
Cited by: 6
Author(s): Sulev Kõks, Abigail L Pfaff, Vivien J. Bubb, John P. Quinn
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0150495

Network Analysis of Metabolite GWAS Hits: Implication of CPS1 and the Urea Cycle in Weight Maintenance
Cited by: 11
Author(s): Alice Matone, Marie Pier Scott-Boyer, Jérôme Carayol, Parastoo Fazelzadeh, Grégory Lefebvre, Armand Valsesia, Céline Charon, Jacques Vervoort, Arne Astrup, Wim H. M. Saris, Melissa J. Morine, Jörg Hager
Software Mentions: 6
Published: over 8 years ago

10.3389/fgene.2021.698033

ACE2 Netlas: In silico Functional Characterization and Drug-Gene Interactions of ACE2 Gene Network to Understand Its Potential Involvement in COVID-19 Susceptibility
Cited by: 4
Author(s): Gita A. Pathak, Frank R. Wendt, Aranyak Goswami, Dóra Koller, Flavio De Angelis, Covid Host Genetics Initiative, Renato Polimanti
Software Mentions: 5
Published: about 3 years ago

10.3389/fpls.2021.675859

Pre-emptive Breeding Against Karnal Bunt Infection in Common Wheat: Combining Genomic and Agronomic Information to Identify Suitable Parents
Cited by: 3
Author(s): Livinus Emebiri, Shane Hildebrand, Mui-Keng Tan, Philomin Juliana, Pawan Kumar Singh, Guillermo Fuentes-Dávila, Ravi P. Singh
Software Mentions: 5
Published: over 3 years ago

10.1186/s42523-020-00038-4

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution
Cited by: 23
Author(s): Yuliaxis Ramayo-Caldas, Francesc X. Prenafeta-Boldú, Laura M. Zingaretti, Olga González‐Rodríguez, Antoni Dalmau, Raquel Quintanilla, María Ballester
Software Mentions: 5
Published: over 4 years ago

10.1186/s12915-021-01139-5

The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host switching
Cited by: 21
Author(s): Tobias Mourier, Denise Anete Madureira de Alvarenga, Abhinav Kaushik, Anielle de Pina-Costa, Olga Douvropoulou, Qingtian Guan, Francisco J. Guzmán‐Vega, Sarah Forrester, Filipe Vieira Santos de Abreu, Cesare Bianco Júnior, Júlio César de Souza, Sílvia Bahadian Moreira, Zelinda Maria Braga Hirano, Alcides Pissinatti, Maria de Fátima Ferreira-da-Cruz, Ricardo Lourenço de Oliveira, Stefan T. Arold, Daniel C. Jeffares, Patrícia Brasil, Cristiana Ferreira Alves de Brito, Richard Culleton, Cláudio Tadeu Daniel-Ribeiro, Arnab Pain
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pgen.1009705

A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis
Cited by: 22
Author(s): Masatoshi Nakamoto, Toshitaka Uchino, Eriko Koshimizu, Yudai Kuchiishi, Ryota Sekiguchi, Liu Wang, Ryusuke Sudo, Masato Endo, Yann Guiguen, Manfred Schartl, John H. Postlethwait, Takashi Sakamoto
Software Mentions: 5
Published: about 3 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

10.1111/eva.12684

Landscape genomics provides evidence of climate‐associated genetic variation in Mexican populations of Quercus rugosa
Cited by: 50
Author(s): Karina Martins, Paul F. Gugger, Jesús Llanderal‐Mendoza, Antonio González‐Rodríguez, Sorel Fitz‐Gibbon, Jianli Zhao, Hernando Rodríguez‐Correa, Ken Oyama, Victoria L. Sork
Software Mentions: 5
Published: about 6 years ago

10.1002/ece3.4981

Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America
Cited by: 37
Author(s): Philip Lavretsky, Thijs Janzen, Kevin G. McCracken
Software Mentions: 5
Published: over 5 years ago

10.1002/ece3.3583

Development of a genotype‐by‐sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure
Cited by: 5
Author(s): Michael E. Donaldson, Yessica Rico, Karsten Hueffer, Halie M. Rando, Anna V. Kukekova, Christopher J. Kyle
Software Mentions: 5
Published: almost 7 years ago

10.1093/hmg/ddw283

Collapsed methylation quantitative trait loci analysis for low frequency and rare variants
Cited by: 11
Author(s): Tom G Richardson, Hashem A. Shihab, Gibran Hemani, Jie Zheng, Eilís Hannon, Jonathan Mill, Elena Carnero‐Montoro, Jordana T. Bell, Oliver Lyttleton, Wendy L. McArdle, Susan M. Ring, Santiago Rodriguez, Colin Campbell, George Davey Smith, Caroline L Relton, Nicholas J. Timpson, Tom R. Gaunt
Software Mentions: 5
Published: about 8 years ago

10.1111/pbi.13051

Integrating a genome‐wide association study with a large‐scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice
Cited by: 50
Author(s): Roslen Anacleto, Saurabh Badoni, Sabiha Parween, Vito M. Butardo, Gopal Misra, Rosa Paula Cuevas, Markus Kuhlmann, Trinidad P. Trinidad, Aida C. Mallillin, Cecilia Acuin, Anthony R. Bird, Matthew K. Morell, Nese Sreenivasulu
Software Mentions: 5
Published: almost 6 years ago

10.1371/journal.pcbi.1004842

Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
Cited by: 522
Author(s): Jerome Kelleher, Alison Etheridge, Gil McVean
Software Mentions: 5
Published: over 8 years ago

10.3390/biology10090907

Dissecting Bread Wheat Heterosis through the Integration of Agronomic and Physiological Traits
Cited by: 6
Author(s): Kevin Gimenez, Pierre Blanc, O. Argillier, Jean-Baptiste Pierre, Jacques Le Gouis, Etienne Paux
Software Mentions: 5
Published: about 3 years ago

10.1186/s12864-017-3920-2

Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus
Cited by: 59
Author(s): Bárbara S. F. Müller, Leandro G. Neves, Janeo Eustáquio de Almeida Filho, M. D. V. de Resende, Patricio Muñoz, P. E. T. dos Santos, E. Paludzyszyn Filho, Matias Kirst, Dário Grattapaglia
Software Mentions: 5
Published: over 7 years ago

10.1038/s41438-021-00544-9

The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative
Cited by: 18
Author(s): Josué Barrera‐Redondo, Guillermo Sánchez‐de la Vega, Jonás A. Aguirre‐Liguori, Gabriela Castellanos‐Morales, Yocelyn T. Gutiérrez-Guerrero, Xitlali Aguirre-Dugua, Erika Aguirre‐Planter, Maud I. Tenaillon, Rafael Lira‐Saade, Luis E. Eguiarte
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0154722

Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection
Cited by: 14
Author(s): Polina Drozdova, О. В. Тарасов, Andrew G. Matveenko, Elina A. Radchenko, Julia V. Sopova, Dmitrii E. Polev, Sergey G. Inge-Vechtomov, Pavel Dobrynin
Software Mentions: 5
Published: over 8 years ago

10.1038/s41438-021-00648-2

Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach
Cited by: 22
Author(s): Qiuping Tan, Sen Li, Yuzheng Zhang, Min Chen, Binbin Wen, Shan Jiang, Xiude Chen, Xiling Fu, Dongmei Li, Wu H, Yong Wang, Wei Xiao, Ling Li
Software Mentions: 5
Published: about 3 years ago

10.3390/ijms22073436

Genotyping by Sequencing Reveals Genetic Relatedness of Southwestern U.S. Blue Maize Landraces
Cited by: 4
Author(s): Amol N. Nankar, Richard C. Pratt
Software Mentions: 5
Published: over 3 years ago

10.1111/1755-0998.12694

An integrated framework to identify wildlife populations under threat from climate change
Cited by: 64
Author(s): Orly Razgour, John B. Taggart, Stéphanie Manel, Javier Juste, Carlos Ibáñez, Hugo Rebelo, Antton Alberdi, Gareth Jones, Kirsty Park
Software Mentions: 5
Published: over 7 years ago

10.1093/gbe/evaa062

The Origin and Composition of Korean Ethnicity Analyzed by Ancient and Present-Day Genome Sequences
Cited by: 16
Author(s): Jung-Eun Kim, Sungwon Jeon, Jae-Pil Choi, Asta Blažytė, Yeonsu Jeon, Jong‐Il Kim, Jun Ohashi, Katsushi Tokunaga, Sumio Sugano, Suthat Fucharoen, Fahd Al-Mulla, Jong Bhak
Software Mentions: 5
Published: over 4 years ago

10.15252/msb.20199270

Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance
Cited by: 22
Author(s): Stephan Kamrad, Jan Großbach, María Rodríguez-López, Michael Mülleder, StJohn Townsend, Valentina Cappelletti, Gorjan Stojanovski, Clara Correia‐Melo, Paola Picotti, Andreas Beyer, Markus Ralser, Jürg Bähler
Software Mentions: 5
Published: over 4 years ago

10.1186/s12711-020-00592-0

A systems biology framework integrating GWAS and RNA-seq to shed light on the molecular basis of sperm quality in swine
Cited by: 22
Author(s): Marta Gòdia, Antônio Reverter, Rayner González-Prendes, Yuliaxis Ramayo-Caldas, Anna Castelló, Joan E. Rodríguez-Gil, Armand Sánchez, Alex Clop
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pgen.1009389

Gene disruption by structural mutations drives selection in US rice breeding over the last century
Cited by: 6
Author(s): Justin N. Vaughn, Walid Korani, Joshua C. Stein, Jeremy D. Edwards, Daniel G. Peterson, Sheron Simpson, Ramey C Youngblood, Jane Grimwood, Kapeel Chougule, Doreen Ware, Anna M. McClung, Brian E. Scheffler
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-021-07755-3

Identification of candidate genomic regions for chicken egg number traits based on genome-wide association study
Cited by: 10
Author(s): Xiurong Zhao, Changsheng Nie, Jinxin Zhang, Xinghua Li, Tao Zhu, Zi Guan, Yu Chen, Liang Wang, Xue Ze Lv, Weijia Yang, Yaxiong Jia, Zhonghua Ning, Haiying Li, Changqing Qu, Huie Wang, Lujiang Qu
Software Mentions: 5
Published: over 3 years ago

10.1093/molbev/msab078

Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia
Cited by: 21
Author(s): Laura Buggiotti, Andrey A. Yurchenko, N. A. Yudin, Christy J. Vander Jagt, Nadezhda V. Vorobieva, Mariya A. Kusliy, S. Vasiliev, Andrey N. Rodionov, O. I. Boronetskaya, N. A. Zinovieva, Alexander S. Graphodatsky, Hans D. Daetwyler, Denis M. Larkin
Software Mentions: 5
Published: over 3 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

10.1371/journal.pntd.0007910

Dispersal patterns of Trypanosoma cruzi in Arequipa, Peru
Cited by: 4
Author(s): Alexander S. F. Berry, Renzo Salazar-Sánchez, Ricardo Castillo-Neyra, Katty Borrini-Mayorí, Claudia Arevalo-Nieto, Claudia Chipana-Ramos, Melina Vargas-Maquera, Jenny Ancca-Juárez, César Náquira-Velarde, Michael Z. Levy, Dustin Brisson
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0006034

Targeting 160 Candidate Genes for Blood Pressure Regulation with a Genome-Wide Genotyping Array
Cited by: 101
Author(s): Siim Sõber, Elin Org, Katrin Kepp, Peeter Juhanson, S. Eyheramendy, Christian Gieger, Peter Lichtner, Norman Klopp, Gudrun Veldre, Margus Viigimaa, Angela Döring, Margus Putku, Piret Kelgo, Sue Shaw‐Hawkins, Philip J. Howard, Abiodun Onipinla, Richard Dobson, Stephen Newhouse, Brown Mj, Anna F. Dominiczak, John Connell, Nilesh J. Samani, Martin Farrall, Mark Caulfield, Patricia B. Munroe, Thomas Illig, Heinz‐Erich Wichmann, Thomas Meitinger, Maris Laan
Software Mentions: 5
Published: over 15 years ago

10.1186/s13099-019-0312-y

Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach
Cited by: 11
Author(s): Maria Gazouli, Nikolas Dovrolis, André Franke, George M. Spyrou, Leonardo Antonio Sechi, George Kolios
Software Mentions: 5
Published: over 5 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

10.1371/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.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

10.3389/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

10.3389/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

10.1186/s12863-016-0372-7

Rare intronic variants of TCF7L2 arising by selective sweeps in an indigenous population from Mexico
Cited by: 3
Author(s): José Luís Acosta, Alma Cristal Hernández-Mondragón, Laura Carolina Correa-Acosta, Sandra Nathaly Cazañas-Padilla, Berenice Chávez-Florencio, Elvia Yamilet Ramírez-Vega, Tulia Monge-Cázares, Carlos A. Aguilar-Salinas, Teresa Tusié-Luna, Laura del Bosque-Plata
Software Mentions: 4
Published: over 8 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.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

10.1111/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

10.1111/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.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.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

10.1371/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

10.3389/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

10.1016/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

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