cran: SKAT | Projects | Ecosyste.ms: Papers

10.1080/21678421.2016.1213852

Rare genetic variation in UNC13A may modify survival in amyotrophic lateral sclerosis
Cited by: 22
Author(s): Ben Gaastra, Aleksey Shatunov, Sara L. Pulit, Ashley Jones, William Sproviero, Alexandra Gillett, Zhongbo Chen, Janine Kirby, Isabella Fogh, John Powell, P. Nigel Leigh, Karen Morrison, Pamela J. Shaw, Christopher E. Shaw, Leonard H van den Berg, Jan H. Veldink, Cathryn M. Lewis, Ammar Al‐Chalabi
Software Mentions: 2
Published: about 8 years ago

10.1038/s41398-020-00987-z

Retracted: Identification of de novo mutations in prenatal neurodevelopment-associated genes in schizophrenia in two Han Chinese patient-sibling family-based cohorts
Cited by: 4
Author(s): Shan Jiang, Dan Zhou, Yin-Ying Wang, Peilin Jia, Chunling Wan, Xingwang Li, Guang He, Dongmei Cao, Xiaoqian Jiang, Kenneth S. Kendler, Ming T. Tsuang, Travis Mize, Jain-Shing Wu, Yujie Lu, Lin He, Jingchun Chen, Zhongming Zhao, Xiangning Chen
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-017-13177-7

Adaptive combination of Bayes factors as a powerful method for the joint analysis of rare and common variants
Cited by: 4
Author(s): Wan-Yu Lin, Wei-Jen Chen, Chih-Min Liu, Hai-Gwo Hwu, Steven A. McCarroll, Stephen J. Glatt, Ming T. Tsuang
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0093355

Rare Variants Detection with Kernel Machine Learning Based on Likelihood Ratio Test
Cited by: 7
Author(s): Ping Zeng, Yang Zhao, Liwei Zhang, Shuiping Huang, Feng Chen
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-017-02281-3

Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster
Cited by: 25
Author(s): Izel Fourie Sørensen, Stefan McKinnon Edwards, Palle Duun Rohde, Peter Sørensen
Software Mentions: 2
Published: over 7 years ago

10.1093/bioinformatics/btt409

Assessing association between protein truncating variants and quantitative traits
Cited by: 13
Author(s): Manuel A. Rivas, Matti Pirinen, Matthew J. Neville, Kyle J. Gaulton, Loukas Moutsianas, Cecilia M. Lindgren, Fredrik Karpe, Mark I. McCarthy, Peter Donnelly
Software Mentions: 2
Published: over 11 years ago

10.1016/j.biopsych.2019.04.034

Novel Insight Into the Etiology of Autism Spectrum Disorder Gained by Integrating Expression Data With Genome-wide Association Statistics
Cited by: 59
Author(s): Oliver Pain, Andrew Pocklington, Peter Holmans, Nicholas John Bray, Heath O’Brien, Lynsey S. Hall, Antonio F. Pardiñas, Michael O’Donovan, Richard Anney
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-018-23307-4

Haplotype Heritability Mapping Method Uncovers Missing Heritability of Complex Traits
Cited by: 12
Author(s): Masoud Shirali, Sara Knott, Ricardo Pong‐Wong, Pau Navarro, C.S. Haley
Software Mentions: 2
Published: over 6 years ago

10.21542/gcsp.2020.13

The role of genomics and genetics in pulmonary arterial hypertension
Cited by: 3
Author(s): Emilia M. Swietlik, Stefan Gräf, Nicholas W. Morrell
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2105-14-199

SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies
Cited by: 19
Author(s): Ren‐Hua Chung, Chung-Chin Shih
Software Mentions: 2
Published: over 11 years ago

10.1186/s13073-020-00744-3

Ancestry-specific predisposing germline variants in cancer
Cited by: 27
Author(s): Ninad Oak, Andrew D. Cherniack, R. Jay Mashl, Fred R. Hirsch, Ding Li, Rameen Beroukhim, Zeynep H. Gümüş, Sharon E. Plon, Kuan‐lin Huang
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-017-3573-1

PreMeta: a tool to facilitate meta-analysis of rare-variant associations
Cited by: 2
Author(s): Zheng Zheng Tang, Paul A. Bunn, Ran Tao, Zhouwen Liu, Dan Lin
Software Mentions: 2
Published: almost 8 years ago

10.1186/s13059-021-02361-8

Tejaas: reverse regression increases power for detecting trans-eQTLs
Cited by: 3
Author(s): Saikat Banerjee, Franco L. Simonetti, Kira E. Detrois, Anubhav Kaphle, Raktim Mitra, Rahul Nagial, Johannes Söding
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-020-02121-0

PSCAN: Spatial scan tests guided by protein structures improve complex disease gene discovery and signal variant detection
Cited by: 9
Author(s): Zheng-Zheng Tang, Gregory Sliwoski, Guanhua Chen, Bowen Jin, William S. Bush, Bingshan Li, John A. Capra
Software Mentions: 2
Published: about 4 years ago

10.1186/s13073-017-0486-1

Linkage, whole genome sequence, and biological data implicate variants in RAB10 in Alzheimer’s disease resilience
Cited by: 63
Author(s): Perry G. Ridge, Celeste M. Karch, Simon Hsu, Ivan Arano, Craig C. Teerlink, Mark T.W. Ebbert, Josue D. Gonzalez Murcia, James M. Farnham, Anna R. Damato, Mariet Allen, Xue Wang, Oscar Harari, Victoria Fernández, Rita Guerreiro, José Brás, John Hardy, Ronald G. Munger, Maria C. Norton, Celeste Sassi, Andrew B. Singleton, Steven G. Younkin, Dennis W. Dickson, Todd E. Golde, Nathan D. Price, Nilüfer Ertekin-Taner, Carlos Cruchaga, Alison Goate, Christopher Corcoran, JoAnn T. Tschanz, Lisa Cannon-Albright, John Kauwe
Software Mentions: 2
Published: almost 7 years ago

10.21203/rs.3.rs-673011/v1

Impact of natural selection on global patterns of genetic variation, and association with clinical phenotypes, at genes involved in SARS-CoV-2 infection.
Cited by: 2
Author(s): Chao Zhang, Anurag Verma, Yuanqing Feng, Marcelo C.R. Melo, Michael A. McQuillan, Matthew E.B. Hansen, Anastasia Lucas, Joseph Park, Alessia Ranciaro, S. R. Thompson, Meghan A. Rubel, Michael C. Campbell, William Beggs, Jibril Hirbo, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Marcus B. Jones, Thomas Nyambo, Dawit Wolde Meskel, Gurja Belay, Charles Fokunang, Alfred K. Njamnshi, Sabah A. Omar, Scott M. Williams, Daniel J. Rader, Marylyn D. Ritchie, César de la Fuente-Núñez, Giorgio Sirugo, Sarah A. Tishkoff
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0087645

Integration of Sequence Data from a Consanguineous Family with Genetic Data from an Outbred Population Identifies PLB1 as a Candidate Rheumatoid Arthritis Risk Gene
Cited by: 30
Author(s): Yukinori Okada, Dorothée Diogo, Jeffrey D. Greenberg, Faten Mouassess, Walid Al Achkar, Robert S. Fulton, Joshua C. Denny, Namrata Gupta, Daniel B. Mirel, Stacy Gabriel, Gang Li, Joel M. Kremer, Dimitrios A. Pappas, Robert J. Carroll, Anne E. Eyler, Gosia Trynka, Eli A. Stahl, Jing Cui, Richa Saxena, Marieke J. H. Coenen, Henk‐Jan Guchelaar, Tom W J Huizinga, Philippe Dieudé, Xavier Mariette, Anne Barton, Helena Canhão, João Eurico Fonseca, Niek de Vries, Paul P. Tak, Larry W. Moreland, S. Louis Bridges, Corinne Miceli‐Richard, Hyon K. Choi, Yoichiro Kamatani, Pilar Galán, Mark Lathrop, Towfique Raj, Philip L. De Jager, Soumya Raychaudhuri, Jane Worthington, Leonid Padyukov, Lars Klareskog, Katherine A. Siminovitch, Peter K. Gregersen, Elaine R. Mardis, Thurayya Arayssi, L. Kazkaz, Robert M. Plenge
Software Mentions: 2
Published: almost 11 years ago

10.1002/mgg3.576

Exome sequencing in families with chronic central serous chorioretinopathy
Cited by: 13
Author(s): Rosa L. Schellevis, Elon H. C. van Dijk, Myrte B. Breukink, Jan E.E. Keunen, Gijs Santen, Carel B. Hoyng, Eiko K. de Jong, Camiel J F Boon, Anneke I. den Hollander
Software Mentions: 2
Published: almost 6 years ago

10.1186/1471-2164-15-632

The power comparison of the haplotype-based collapsing tests and the variant-based collapsing tests for detecting rare variants in pedigrees
Cited by: 4
Author(s): Wei Guo, Yin Yao Shugart
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-016-3310-1

Maternal smoking impacts key biological pathways in newborns through epigenetic modification in Utero
Cited by: 40
Author(s): Daniel M. Rotroff, Bonnie R. Joubert, Skylar W. Marvel, Siri Eldevik Håberg, Michael C. Wu, Roy Miodini Nilsen, Per Magne Ueland, Wenche Nystad, Stephanie J. London, Alison A. Motsinger‐Reif
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0173784

Common and rare exonic MUC5B variants associated with type 2 diabetes in Han Chinese
Cited by: 10
Author(s): Guanjie Chen, Zhenjian Zhang, Sally N. Adebamowo, Guozheng Liu, Adebowale Adeyemo, Yanxun Zhou, Ayo P. Doumatey, Chuntao Wang, Jie Zhou, Wenqiang Yan, Daniel Shriner, Fasil Tekola‐Ayele, Amy R. Bentley, Congqing Jiang, Charles N. Rotimi
Software Mentions: 2
Published: over 7 years ago

10.1111/acel.12964

CpG‐related SNPs in the MS4A region have a dose‐dependent effect on risk of late–onset Alzheimer disease
Cited by: 7
Author(s): Yiyi Ma, Gyungah Jun, Jaeyoon Chung, Xiaoling Zhang, Brian W. Kunkle, Adam C. Naj, Charles C. White, David A. Bennett, Philip L. De Jager, Richard Mayeux, Jonathan L. Haines, Margaret A. Pericak‐Vance, Gerard D. Schellenberg, Lindsay A. Farrer, Kathryn L. Lunetta
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12030419

Set-Based Rare Variant Expression Quantitative Trait Loci in Blood and Brain from Alzheimer Disease Study Participants
Cited by: 5
Author(s): Devanshi Patel, Xiaoling Zhang, John Farrell, Kathryn L. Lunetta, Lindsay A. Farrer
Software Mentions: 2
Published: over 3 years ago

10.12688/wellcomeopenres.14677.4

Stage 2 Registered Report: Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: testing the double hit hypothesis
Cited by: 0
Author(s): Dianne F. Newbury, Nuala H. Simpson, Paul A. Thompson, Dorothy V. M. Bishop
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-017-1212-4

The impact of rare and low-frequency genetic variants in common disease
Cited by: 256
Author(s): Lorenzo Bomba, Klaudia Walter, Nicole Soranzo
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0069226

A Linkage Disequilibrium–Based Approach to Selecting Disease-Associated Rare Variants
Cited by: 10
Author(s): Rajesh Talluri, Sanjay Shete
Software Mentions: 2
Published: over 11 years ago

10.1186/s12859-019-2877-3

GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data
Cited by: 19
Author(s): Enrico Mossotto, James J. Ashton, Luke O’Gorman, Reuben J. Pengelly, R Mark Beattie, Ben D. MacArthur, Sarah Ennis
Software Mentions: 2
Published: over 5 years ago

10.3389/fpsyt.2021.645746

Endocannabinoid Gene × Gene Interaction Association to Alcohol Use Disorder in Two Adolescent Cohorts
Cited by: 4
Author(s): Laurent Elkrief, Sean Spinney, Daniel E. Vosberg, Tobias Banaschewski, Arun L.W. Bokde, Erin Burke Quinlan, Sylvane Desrivières, Herta Flor, Hugh Garavan, Penny Gowland, Andreas Heinz, Rüdiger Brühl, Jean‐Luc Martinot, Marie‐Laure Paillère Martinot, Frauke Nees, Dimitri Papadopoulos Orfanos, Luise Poustka, Sarah Hohmann, Sabina Millenet, Juliane H. Fröhner, Michael N. Smolka, Henrik Walter, Robert Whelan, Gunter Schümann, Zdenka Pausová, Tomáš Paus, Guillaume Huguet, Patricia Conrod
Software Mentions: 2
Published: over 3 years ago

10.3389/fgene.2020.00679

Integration of GWAS and eQTL Analysis to Identify Risk Loci and Susceptibility Genes for Gastric Cancer
Cited by: 9
Author(s): Jiazuan Ni, Bin Deng, Meng Zhu, Yuzhuo Wang, Caiwang Yan, Tianpei Wang, Yaqian Liu, Gang Li, Yanbing Ding, Guangfu Jin
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2015.00149

A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing
Cited by: 41
Author(s): Qian Wang, Qiongshi Lu, Hongyu Zhao
Software Mentions: 2
Published: over 9 years ago

10.1534/g3.116.035485

On Robust Association Testing for Quantitative Traits and Rare Variants
Cited by: 10
Author(s): Peng Wei, Ying Cao, Yiwei Zhang, Zhiyuan Xu, Il-Youp Kwak, Eric Boerwinkle, Wei Pan
Software Mentions: 2
Published: almost 8 years ago

10.3389/fgene.2019.00572

metaFARVAT: An Efficient Tool for Meta-Analysis of Family-Based, Case-Control, and Population-Based Rare Variant Association Studies
Cited by: 0
Author(s): Longfei Wang, Sung Young Lee, Dandi Qiao, Michael H. Cho, Edwin K. Silverman, Christoph Lange, Sungho Won
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2012.00173

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

10.3389/fgene.2014.00011

Exploring the potential benefits of stratified false discovery rates for region-based testing of association with rare genetic variation
Cited by: 4
Author(s): Changjiang Xu, Antonio Ciampi, Celia M.T. Greenwood
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1009754

Multi-scale inference of genetic trait architecture using biologically annotated neural networks
Cited by: 9
Author(s): Pınar Demetçi, Wei Cheng, Gregory Darnell, Xiang Zhou, Sohini Ramachandran, Lorin Crawford
Software Mentions: 2
Published: over 3 years ago

10.1186/s12919-016-0061-6

Identification of low frequency and rare variants for hypertension using sparse-data methods
Cited by: 1
Author(s): Ji-Hyung Shin, Ruiyang Yi, Shelley B. Bull
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2013.00232

The power of regional heritability analysis for rare and common variant detection: simulations and application to eye biometrical traits
Cited by: 29
Author(s): Yoshinobu Uemoto, Ricardo Pong‐Wong, Pau Navarro, Véronique Vitart, Caroline Hayward, James F. Wilson, Igor Rudan, Harry Campbell, Nicholas D. Hastie, Alan F. Wright, Chris Haley
Software Mentions: 2
Published: almost 12 years ago

10.3389/fgene.2020.562855

Whole Transcriptome Analysis Identifies the Taxonomic Status of a New Chinese Native Cattle Breed and Reveals Genes Related to Body Size
Cited by: 2
Author(s): Xiaodong Zheng, Jin Cheng, Wenjuan Qin, Nyamsuren Balsai, Xuan-Jian Shang, Mengting Zhang, Hongquan Chen
Software Mentions: 2
Published: about 4 years ago

10.1038/srep37444

A Nonparametric Regression Approach to Control for Population Stratification in Rare Variant Association Studies
Cited by: 11
Author(s): Qiuying Sha, Kui Zhang, Shuanglin Zhang
Software Mentions: 2
Published: about 8 years ago

10.1002/fes3.292

Gene‐based mapping of trehalose biosynthetic pathway genes reveals association with source‐ and sink‐related yield traits in a spring wheat panel
Cited by: 12
Author(s): Danilo Hottis Lyra, Cara A. Griffiths, Amy Watson, Ryan Joynson, Gemma Molero, Alina-Andrada Igna, Keywan Hassani‐Pak, Matthew Reynolds, Anthony Hall, M. J. Paul
Software Mentions: 2
Published: over 3 years ago

10.1038/s41431-020-0639-3

The exhaustive genomic scan approach, with an application to rare-variant association analysis
Cited by: 2
Author(s): George Kanoungi, Michael Nothnagel, Tim Becker, Dmitriy Drichel
Software Mentions: 2
Published: over 4 years ago

10.3389/fnagi.2016.00115

AMD Genetics in India: The Missing Links
Cited by: 5
Author(s): Akshay Anand, Kaushal Sharma, Suresh Sharma, Ramandeep Singh, Neel Sharma, T. S. Keshava Prasad
Software Mentions: 2
Published: over 8 years ago

10.1186/1753-6561-8-S1-S58

Identifying rare variant associations in population-based and family-based designs
Cited by: 2
Author(s): Asuman Türkmen, Shili Lin
Software Mentions: 2
Published: over 10 years ago

10.1038/s41431-018-0266-4

Exploring rare and low-frequency variants in the Saguenay–Lac-Saint-Jean population identified genes associated with asthma and allergy traits
Cited by: 9
Author(s): Andréanne Morin, Anne-Marie Madore, Tony Kwan, Masashi Ban, Jukka Partanen, Lars Rönnblom, Ann‐Christine Syvänen, Stephen Sawcer, Hendrik G. Stunnenberg, Mark Lathrop, Tomi Pastinen, Catherine Laprise
Software Mentions: 2
Published: about 6 years ago

10.3389/fgene.2014.00323

A comprehensive evaluation of collapsing methods using simulated and real data: excellent annotation of functionality and large sample sizes required
Cited by: 13
Author(s): Carmen Dering, Inke R. König, Laura B. Ramsey, Mary V. Relling, Wenjian Yang, Andreas Ziegler
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0217620

Multiple rare and common variants in APOB gene locus associated with oxidatively modified low-density lipoprotein levels
Cited by: 8
Author(s): Eleonora Khlebus, В. А. Куценко, А. Н. Мешков, А. И. Ершова, А. В. Киселева, Anton Shevtsov, Natalia Shcherbakova, Anastasia A. Zharikova, В. З. Ланкин, А. К. Тихазе, И Е Чазова, E. B. Yarovaya, О. М. Drapkina, S. А. Boytsov
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0230035

Genetic loci associated with prevalent and incident myocardial infarction and coronary heart disease in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium
Cited by: 5
Author(s): Julie Hahn, Yi Fu, M. R. W. Brown, Joshua C. Bis, Paul S. de Vries, Mary F. Feitosa, Lisa R. Yanek, Stefan Weiß, Franco Giulianini, Albert V. Smith, Xiuqing Guo, Traci M. Bartz, Diane M. Becker, Lewis C. Becker, Eric Boerwinkle, Jennifer A. Brody, Yii Der Ida Chen, Oscar H. Franco, Megan L. Grove, Tamara B. Harris, Albert Hofman, Shih Jen Hwang, B Král, Lenore J. Launer, Marcello Ricardo Paulista Markus, Kenneth Rice, Stephen S. Rich, Paul M. Ridker, Fernando Rivadeneira, Jerome I. Rotter, Nona Sotoodehnia, Kent D. Taylor, André G. Uitterlinden, Uwe Völker, Henry Völzke, Jie Yao, Daniel I. Chasman, Marcus Dörr, Vilmundur Gudnason, Rasika A. Mathias, Wendy S. Post, Bruce M. Psaty, Abbas Dehghan, Christopher J. O’Donnell, Alanna C. Morrison
Software Mentions: 2
Published: about 4 years ago

10.1038/s42003-020-01487-y

Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci
Cited by: 13
Author(s): Lvwen Ning, Josephine Mun‐Yee Ko, V. Y. H. Yu, Hoi Yan Ng, Candy King-Chi Chan, Lihua Tao, Shiu-Yeung Lam, Merrin Man-Long Leong, Roger K.C. Ngan, Dora Lai-Wan Kwong, Anne W.M. Lee, Wai‐Tong Ng, Ashley Cheng, Stewart Y. Tung, Victor Lee, Ka-On Lam, Chung-Kong Kwan, Wing-Sum Li, Stephen S.-T. Yau, Jin‐Xin Bei, Maria Li Lung
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0069633

Bayesian Detection of Causal Rare Variants under Posterior Consistency
Cited by: 10
Author(s): Faming Liang, Momiao Xiong
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0136796

Association of Genes, Pathways, and Haplogroups of the Mitochondrial Genome with the Risk of Colorectal Cancer: The Multiethnic Cohort
Cited by: 26
Author(s): Yuqing Li, Kenneth B. Beckman, Christian Caberto, Rémi Kazma, Annette Lum-Jones, Christopher A. Haiman, Loı̈c Le Marchand, Daniel O. Stram, Richa Saxena, Iona Cheng
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0210870

Family-based association tests for rare variants with censored traits
Cited by: 2
Author(s): Wenjing Qi, Andrew S. Allen, Yi-Ju Li
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1005165

The Power of Gene-Based Rare Variant Methods to Detect Disease-Associated Variation and Test Hypotheses About Complex Disease
Cited by: 123
Author(s): Loukas Moutsianas, Vineeta Agarwala, Christian Fuchsberger, Jason Flannick, Manuel A. Rivas, Kyle J. Gaulton, Patrick K. Albers, Gil McVean, Michael Boehnke, David Altshuler, Mark I. McCarthy
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0142649

Pooled Sequencing of Candidate Genes Implicates Rare Variants in the Development of Asthma Following Severe RSV Bronchiolitis in Infancy
Cited by: 9
Author(s): Dara G. Torgerson, Tusar Giri, Todd E. Druley, Jie Zheng, Scott Huntsman, Max A. Seibold, Andrew L. Young, Toni Schweiger, Huiqing Yin‐Declue, Geneline Sajol, Kenneth B. Schechtman, Ryan D. Hernández, Adrienne G. Randolph, Leonard B. Bacharier, Mario Castro
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0152667

An Optimal Bahadur-Efficient Method in Detection of Sparse Signals with Applications to Pathway Analysis in Sequencing Association Studies
Cited by: 2
Author(s): Hongying Dai, Guodong Wu, Michael C. Wu, Degui Zhi
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1005403

A New Method for Detecting Associations with Rare Copy-Number Variants
Cited by: 14
Author(s): Jung-Ying Tzeng, Patrik K. E. Magnusson, Patrick F. Sullivan, Jin P. Szatkiewicz
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pgen.1003258

Properties and Modeling of GWAS when Complex Disease Risk Is Due to Non-Complementing, Deleterious Mutations in Genes of Large Effect
Cited by: 81
Author(s): Kevin R. Thornton, Andrew J. Foran, Anthony D. Long
Software Mentions: 2
Published: over 11 years ago

10.12688/f1000research.19444.1

Exome sequencing in genetic disease: recent advances and considerations
Cited by: 21
Author(s): Jay P. Ross, Patrick A. Dion, Guy A. Rouleau
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0042530

Comparison of Statistical Tests for Association between Rare Variants and Binary Traits
Cited by: 9
Author(s): Silviu‐Alin Bacanu, Matthew R. Nelson, John C. Whittaker
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1007186

Identifying and exploiting trait-relevant tissues with multiple functional annotations in genome-wide association studies
Cited by: 27
Author(s): Xingjie Hao, Ping Zeng, Shujun Zhang, Xiang Zhou
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1009482

Novel Variance-Component TWAS method for studying complex human diseases with applications to Alzheimer’s dementia
Cited by: 30
Author(s): Shizhen Tang, Aron S. Buchman, Philip L. De Jager, David A. Bennett, Michael P. Epstein, Jingjing Yang
Software Mentions: 2
Published: over 3 years ago

10.1186/s12883-021-02215-7

Study of the collagen type VI alpha 3 (COL6A3) gene in Parkinson’s disease
Cited by: 5
Author(s): Chong‐Yao Jin, Ran Zheng, Zhi‐Hao Lin, Nai‐Jia Xue, Ying Chen, Ting Gao, Yiqun Yan, Yi Fang, Yaping Yan, Xinzhen Yin, Jun Tian, Jiali Pu, Baorong Zhang
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0169158

Targeted Sequencing of FKBP5 in Suicide Attempters with Bipolar Disorder
Cited by: 8
Author(s): Marie E. Breen, Sophia C. Gaynor, Eric Monson, Kelly de Klerk, Meredith G. Parsons, Terry A. Braun, Adam P. DeLuca, Peter P. Zandi, James B. Potash, Virginia L. Willour
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-15-24

A method to incorporate prior information into score test for genetic association studies
Cited by: 1
Author(s): Sergii Zakharov, Garrett H. K. Teoh, Agus Salim, Anbupalam Thalamuthu
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12919-016-0026-9

On combining family- and population-based sequencing data
Cited by: 1
Author(s): Yuriko Katsumata, David W. Fardo
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pgen.1009596

Rare variants regulate expression of nearby individual genes in multiple tissues
Cited by: 3
Author(s): Jiajin Li, Nahyun Kong, Buhm Han, Jae Hoon Sul
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-018-2475-9

Learning the optimal scale for GWAS through hierarchical SNP aggregation
Cited by: 11
Author(s): Florent Guinot, Marie Szafranski, Christophe Ambroise, Franck Samson
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0166628

Meta-GWAS and Meta-Analysis of Exome Array Studies Do Not Reveal Genetic Determinants of Serum Hepcidin
Cited by: 2
Author(s): Tessel E. Galesloot, Niek Verweij, Michela Traglia, Caterina Barbieri, Freerk van Dijk, Anneke Geurts-Moespot, Domenico Girelli, Lambertus A. Kiemeney, Fred C.G.J. Sweep, Morris A. Swertz, Peter Der Van Meer, Clara Camaschella, Daniela Toniolo, Sita H. Vermeulen, Pim Der Van Harst, Dorine W. Swinkels
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0139355

Weighted Score Tests Implementing Model-Averaging Schemes in Detection of Rare Variants in Case-Control Studies
Cited by: 4
Author(s): Brandon J. Coombes, Saonli Basu, Sharmistha Guha, Nicholas J. Schork
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pgen.1008081

FunSPU: A versatile and adaptive multiple functional annotation-based association test of whole-genome sequencing data
Cited by: 16
Author(s): Yiding Ma, Peng Wei
Software Mentions: 2
Published: over 5 years ago

10.1186/s12920-018-0344-z

Exact association test for small size sequencing data
Cited by: 1
Author(s): Joowon Lee, Seungyeoun Lee, Jin‐Young Jang, Taesung Park
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-019-0475-x

Identification of sequence variants associated with severe microtia-astresia by targeted sequencing
Cited by: 10
Author(s): Pu Wang, Yibei Wang, Xinmiao Fan, Yaping Liu, Yue Fan, Tao Liu, Chongjian Chen, Shuyang Zhang, Xiaowei Chen
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0239824

Meta-analysis of whole-exome sequencing data from two independent cohorts finds no evidence for rare variant enrichment in Parkinson disease associated loci
Cited by: 10
Author(s): Johannes Jernqvist Gaare, Gonzalo S. Nido, Christian Dölle, Paweł Sztromwasser, Guido Alves, Ole‐Bjørn Tysnes, Kristoffer Haugarvoll, Charalampos Tzoulis
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0135918

Using Hamming Distance as Information for SNP-Sets Clustering and Testing in Disease Association Studies
Cited by: 24
Author(s): Charlotte Wang, Wen-Hsin Kao, Chuhsing Kate Hsiao
Software Mentions: 2
Published: about 9 years ago

10.1186/1753-6561-8-S1-S43

Analysis of Genetic Analysis Workshop 18 data with gene-based penalized regression
Cited by: 1
Author(s): Kristin L. Ayers, Heather J. Cordell
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.3187

Common and rare genetic markers of lipid variation in subjects with type 2 diabetes from the ACCORD clinical trial
Cited by: 11
Author(s): Skylar W. Marvel, Daniel M. Rotroff, Michael J. Wagner, John B. Buse, Tammy M. Havener, Howard L. McLeod, Alison A. Motsinger‐Reif
Software Mentions: 1
Published: over 7 years ago

10.12688/wellcomeopenres.12583.3

Meta-analysis of exome array data identifies six novel genetic loci for lung function
Cited by: 18
Author(s): Victoria E. Jackson, Jeanne C. Latourelle, Louise V. Wain, Albert V. Smith, Megan L. Grove, Traci M. Bartz, Ma’en Obeidat, Michael A. Province, Wei Gao, Beenish Qaiser, David J. Porteous, Patricia A. Cassano, Tarunveer S. Ahluwalia, Niels Grarup, Li Jin, Elisabeth Altmaier, Jonathan Marten, Sarah E. Harris, Ani Manichaikul, Tess D. Pottinger, Ruifang Li‐Gao, Allan Lind-Thomsen, Anubha Mahajan, Lies Lahousse, Medea Imboden, Alexander Teumer, Bram P. Prins, Leo-Pekka Lyytikäinen, Guðný Eiríksdóttir, Nora Franceschini, Colleen M. Sitlani, Jennifer A. Brody, Yohan Bossé, Wim Timens, Aldi T. Kraja, Anu Loukola, Wenbo Tang, Yongmei Liu, Jette Bork-Jensen, Johanne Marie Justesen, Allan Linneberg, Leslie A. Lange, Rajesh Rawal, Stefan Karrasch, Jennifer E. Huffman, Blair H. Smith, Gail Davies, Kristin M. Burkart, Josyf C. Mychaleckyj, Tobias N Bonten, Stefan Enroth, Lars Lind, Guy Brusselle, Ashish Kumar, Beate Stubbe, Mika Kähönen, Annah B. Wyss, Bruce M. Psaty, Susan R. Heckbert, Ke Hao, Taina Rantanen, Stephen B. Kritchevsky, Kurt Lohman, Tea Skaaby, Charlotta Pisinger, Torben Hansen, Holger Schulz, Ozren Polašek, Archie Campbell, John M. Starr, Stephen S. Rich, Dennis O. Mook‐Kanamori, Åsa Johansson, Erik Ingelsson, André G. Uitterlinden, Stefan Weiß, Olli T. Raitakari, Vilmundur Gudnason, Kari E. North, Sina A. Gharib, Don D. Sin, Kent D. Taylor, George T. O’Connor, Jaakko Kaprio, Tamara B. Harris, Oluf Pederson, Henrik Vestergaard, James G. Wilson, Konstantin Strauch, Caroline Hayward, Shona M. Kerr, Ian J. Deary, R. Graham Barr, Renée de Mutsert, Ulf Gyllensten, Andrew P. Morris, M. Arfan Ikram, Nicole Probst‐Hensch, Sven Gläser, Eleftheria Zeggini, Terho Lehtimäki, David P. Strachan, Josée Dupuis, Alanna C. Morrison, Ian P. Hall, Martin D. Tobin, Stephanie J. London
Software Mentions: 1
Published: over 6 years ago

10.1186/s12862-017-0897-z

Susceptibility to type 2 diabetes may be modulated by haplotypes in G6PC2, a target of positive selection
Cited by: 14
Author(s): Nasser M. Al-Daghri, Chiara Pontremoli, Rachele Cagliani, Diego Forni, Majed S. Alokail, Omar S. Al‐Attas, Shaun Sabico, Stefania Riva, Mario Clerici, Manuela Sironi
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41380-018-0263-6

Uncovering the complex genetics of human character
Cited by: 72
Author(s): Igor Zwir, Javier Arnedo, Coral del Val, Laura Pulkki‐Råback, Bettina Konte, Sarah Yang, Rocío Romero-Záliz, Mirka Hintsanen, Kevin M. Cloninger, Danilo Garcia, Dragan M. Švrakić, Sándor Rózsa, Maribel Martínez, Leo-Pekka Lyytikäinen, Ina Giegling, Mika Kähönen, Helena Hernández‐Cuervo, Ilkka Seppälä, Emma Raitoharju, Gabriel A. de Erausquin, Olli T. Raitakari, Dan Rujescu, Teodor T. Postolache, Joohon Sung, Liisa Keltikangas‐Järvinen, Terho Lehtimäki, C. Robert Cloninger
Software Mentions: 1
Published: about 6 years ago

10.1038/s41380-018-0112-7

Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation
Cited by: 165
Author(s): Joshua C. Bis, Xueqiu Jian, Brian W. Kunkle, Yuning Chen, Kara L. Hamilton‐Nelson, William S. Bush, William Salerno, Daniel Lancour, Yiyi Ma, Alan E. Renton, Edoardo Marcora, John Farrell, Yi Zhao, Liming Qu, Shahzad Ahmad, Najaf Amin, Philippe Amouyel, Gary W. Beecham, Jennifer E. Below, Dominique Campion, Laura B. Cantwell, Camille Charbonnier, Jaeyoon Chung, Paul K. Crane, Carlos Cruchaga, L. Adrienne Cupples, Jean‐François Dartigues, Stéphanie Debette, Jean‐François Deleuze, Lucinda A. Fulton, Stacey Gabriel, Emmanuelle Génin, Richard A. Gibbs, Alison Goate, Benjamin Grenier‐Boley, Namrata Gupta, Jonathan L. Haines, Aki S. Havulinna, Seppo Helisalmi, Mikko Hiltunen, Daniel P. Howrigan, M. Arfan Ikram, Jaakko Kaprio, Jan Konrad, Amanda B. Kuzma, Eric S. Lander, Mark Lathrop, Terho Lehtimäki, Honghuang Lin, Kari M. Mattila, Richard Mayeux, Donna M. Muzny, Waleed Nasser, Benjamin M. Neale, Kwangsik Nho, Gaël Nicolas, Devanshi Patel, Margaret A. Pericak‐Vance, Markus Perola, Bruce M. Psaty, Olivier Quenez, Farid Rajabli, Richard Redon, Christiane Reitz, Anne M. Remes, Veikko Salomaa, Chloé Sarnowski, Helena Schmidt, Michael A. Schmidt, Reinhold Schmidt, Hilkka Soininen, Timothy A. Thornton, Giuseppe Tosto, Christophe Tzourio, Sven J. van der Lee, Cornelia M. van Duijn, Otto Valladares, Badri N. Vardarajan, Li-San Wang, Weixin Wang, Ellen M. Wijsman, Richard K. Wilson, Daniela Witten, Kim C. Worley, Xiaoling Zhang, Alzheimer’s Disease Sequencing, Céline Bellenguez, Jean‐Charles Lambert, Mitja Kurki, Aarno Palotie, Mark J. Daly, Eric Boerwinkle, Kathryn L. Lunetta, Anita L. DeStefano, Josée Dupuis, Eden R. Martin, Gerard D. Schellenberg, Sudha Seshadri, Adam C. Naj, Myriam Fornage, Lindsay A. Farrer
Software Mentions: 1
Published: over 6 years ago

10.1186/s12920-018-0323-4

Deleterious genetic variants in ciliopathy genes increase risk of ritodrine-induced cardiac and pulmonary side effects
Cited by: 14
Author(s): Hiromi Seo, Eun Jin Kwon, Young Ah You, Yoomi Park, Byung Joo Min, Kyunghun Yoo, Han Sung Hwang, Ju Han Kim, Young Ju Kim
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41380-018-0264-5

Uncovering the complex genetics of human temperament
Cited by: 62
Author(s): Igor Zwir, Javier Arnedo, Coral del Val, Laura Pulkki‐Råback, Bettina Konte, Sarah Yang, Rocío Romero-Záliz, Mirka Hintsanen, Kevin M. Cloninger, Danilo Garcia, Dragan M. Švrakić, Sándor Rózsa, Maribel Martínez, Leo Pekka Lyytikäinen, Ina Giegling, Mika Kähönen, Helena Hernández‐Cuervo, Ilkka Seppälä, Emma Raitoharju, Gabriel A. de Erausquin, Olli T. Raitakari, Dan Rujescu, Teodor T. Postolache, Joohon Sung, Liisa Keltikangas‐Järvinen, Terho Lehtimäki, C. Robert Cloninger
Software Mentions: 1
Published: about 6 years ago

10.1002/mgg3.1218

Panel‐based targeted exome sequencing reveals novel candidate susceptibility loci for age‐related cataracts in Chinese Cohort
Cited by: 1
Author(s): Jiankang Li, Lili Li, Wei Li, Ziwei Wang, Feng‐Juan Gao, Fangyuan Hu, Shenghai Zhang, Su Qu, Jie Huang, Lu-Sheng Wang, Jihong Wu, Fang Chen
Software Mentions: 1
Published: over 4 years ago

10.1186/s12920-018-0345-y

WISARD: workbench for integrated superfast association studies for related datasets
Cited by: 10
Author(s): Sung Young Lee, Sungkyoung Choi, Dandi Qiao, Michael Cho, Edwin K. Silverman, Taesung Park, Sungho Won
Software Mentions: 1
Published: over 6 years ago

10.1186/s12885-017-3722-6

Genomic determinants of long-term cardiometabolic complications in childhood acute lymphoblastic leukemia survivors
Cited by: 14
Author(s): Jade England, Simon Drouin, Patrick Beaulieu, Pascal St-Onge, Maja Krajinović, Caroline Laverdière, Émile Lévy, Valérie Marcil, Daniel Sinnett
Software Mentions: 1
Published: about 7 years ago

10.1186/s13075-018-1637-5

Next-generation sequencing profiling of mitochondrial genomes in gout
Cited by: 13
Author(s): Chia‐Chun Tseng, Chung‐Jen Chen, Jeng‐Hsien Yen, Hsi‐Yuan Huang, Jan‐Gowth Chang, Shun‐Jen Chang, Wei‐Ting Liao
Software Mentions: 1
Published: over 6 years ago

10.1186/s12920-021-01073-z

Sequencing of neurofilament genes identified NEFH Ser787Arg as a novel risk variant of sporadic amyotrophic lateral sclerosis in Chinese subjects
Cited by: 5
Author(s): Feng Lin, Wanhui Lin, Chaofeng Zhu, Ji-lan Lin, Jingxian Zhu, Xuying Li, Zhanjun Wang, Chaodong Wang, Huapin Huang
Software Mentions: 1
Published: about 3 years ago

10.1002/cam4.2215

Genetic variants in p53 signaling pathway genes predict chemotherapy efficacy in colorectal cancer
Cited by: 5
Author(s): Ke Zhang, Yujie Meng, Xin Cao, Ye Xu, Mulong Du, Yuan Wu, Lingxiang Liu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12881-015-0250-6

Genetic contribution of SCARB1 variants to lipid traits in African Blacks: a candidate gene association study
Cited by: 12
Author(s): Vipavee Niemsiri, Xingbin Wang, Dilek Pirim, Zaheda H. Radwan, Clareann H. Bunker, M. Michael Barmada, M. Ilyas Kamboh, F. Yesim Demirci
Software Mentions: 1
Published: about 9 years ago

10.1002/brb3.651

Targeted sequencing identifies genetic polymorphisms of flavin-containing monooxygenase genes contributing to susceptibility of nicotine dependence in European American and African American
Cited by: 11
Author(s): Tian-Xiao Zhang, Nancy L. Saccone, Laura J. Bierut, John P. Rice
Software Mentions: 1
Published: over 7 years ago

10.1093/brain/awx082

A comprehensive analysis of rare genetic variation in amyotrophic lateral sclerosis in the UK
Cited by: 65
Author(s): Sarah Morgan, Aleksey Shatunov, William Sproviero, Ashley Jones, Maryam Shoai, Deborah Hughes, Ahmad Al Khleifat, Andrea Malaspina, Karen Morrison, Pamela J. Shaw, Christopher E. Shaw, Katie Sidle, Richard W. Orrell, Pietro Fratta, John Hardy, Alan Pittman, Ammar Al‐Chalabi
Software Mentions: 1
Published: over 7 years ago

10.1186/s12881-020-01046-6

Quantitative phenotype scan statistic (QPSS) reveals rare variant associations with Alzheimer’s disease endophenotypes
Cited by: 2
Author(s): Yuriko Katsumata, David W. Fardo
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2350-13-52

SNP-set analysis replicates acute lung injury genetic risk factors
Cited by: 17
Author(s): Nuala J. Meyer, Z. John Daye, Melanie Rushefski, Richard Aplenc, Paul N. Lanken, Michael G. S. Shashaty, Jason D. Christie, Rui Feng
Software Mentions: 1
Published: over 12 years ago

10.1136/annrheumdis-2016-210592

A rare coding allele in<i>IFIH1</i>is protective for psoriatic arthritis
Cited by: 21
Author(s): Ashley Budu-Aggrey, John Bowes, Philip E. Stuart, Matthew Zawistowski, Lam C. Tsoi, Rajan P. Nair, Deepak R. Jadon, Neil McHugh, Eleanor Korendowych, James T. Elder, Anne Barton, Soumya Raychaudhuri
Software Mentions: 1
Published: over 7 years ago

10.1038/bjc.2016.50

Gene and pathway level analyses of germline DNA-repair gene variants and prostate cancer susceptibility using the iCOGS-genotyping array
Cited by: 16
Author(s): Edward J. Saunders, Tokhir Dadaev, Daniel Leongamornlert, Ali Amin Al Olama, Sara Benlloch, Graham G. Giles, Fredrik Wiklund, Henrik Grönberg, Christopher A. Haiman, Johanna Schleutker, Børge G. Nordestgaard, Ruth C. Travis, David E. Neal, Nora Pasayan, Kay–Tee Khaw, Janet L. Stanford, William J. Blot, Stephen N. Thibodeau, Christiane Maier, Adam S. Kibel, Cezary Cybulski, Lisa A. Cannon‐Albright, Hermann Brenner, Jong Y. Park, Radka Kaneva, Jyotsna Batra, Manuel R. Teixeira, Hardev Pandha, Koveela Govindasami, Ken Muir, Douglas F. Easton, Rosalind Eeles, Zsofia Kóte-Jarai
Software Mentions: 1
Published: over 8 years ago

10.1186/s12909-020-02482-x

Evaluating the impact of a medical school cohort sexual health course on knowledge, counseling skills and sexual attitude change
Cited by: 9
Author(s): Michael W. Ross, Carey Roth Bayer, A.W. Shindel, Eli Coleman
Software Mentions: 1
Published: almost 4 years ago

10.1093/bioinformatics/btt177

A powerful and efficient set test for genetic markers that handles confounders
Cited by: 71
Author(s): Jennifer Listgarten, Christoph Lippert, Eun Yong Kang, Jing Xiang, Carl Kadie, David Heckerman
Software Mentions: 1
Published: over 11 years ago

10.1093/bioinformatics/btu504

Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
Cited by: 34
Author(s): Christoph Lippert, Jing Xiang, Danilo Horta, Christian Widmer, Carl Kadie, David Heckerman, Jennifer Listgarten
Software Mentions: 1
Published: over 10 years ago

10.1093/bioinformatics/bts568

‘Location, Location, Location’: a spatial approach for rare variant analysis and an application to a study on non-syndromic cleft lip with or without cleft palate
Cited by: 21
Author(s): Heide Fier, Sungho Won, Dmitry Prokopenko, Taofik AlChawa, Kerstin U. Ludwig, Rolf Fimmers, Edwin K. Silverman, Marcello Pagano, Elisabeth Mangold, Christoph Lange
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-14-50

Comparison of similarity-based tests and pooling strategies for rare variants
Cited by: 2
Author(s): Sergii Zakharov, Agus Salim, Anbupalam Thalamuthu
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2105-14-210

Gene set analysis using variance component tests
Cited by: 28
Author(s): Yen‐Tsung Huang, Xihong Lin
Software Mentions: 1
Published: over 11 years ago

Projects: cran: SKAT

Papers Mentioning SKAT 407