cran: SKAT | Projects | Ecosyste.ms: Papers

10.1186/s13073-021-00907-w

Impact of rare and common genetic variation in the interleukin-1 pathway on human cytokine responses
Cited by: 5
Author(s): Rosanne C. van Deuren, Peer Arts, Giulio Cavalli, Martin Jaeger, Marloes Steehouwer, Maartje van de Vorst, Christian Gilissen, Leo A. B. Joosten, Charles A. Dinarello, Musa M. Mhlanga, Vinod Kumar, Mihai G. Netea, Frank L. van de Veerdonk, Alexander Hoischen
Software Mentions: 14
Published: over 3 years ago

10.12688/f1000research.15949.2

The Mega2R package: R tools for accessing and processing genetic data in common formats
Cited by: 0
Author(s): R. Baron, Justin R. Stickel, Daniel E. Weeks
Software Mentions: 12
Published: almost 6 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

10.1038/s41598-021-86871-2

Family-based gene-environment interaction using sequence kernel association test (FGE-SKAT) for complex quantitative traits
Cited by: 0
Author(s): Chao-Yu Guo, Reng-Hong Wang, Hsin-Chou Yang
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pgen.1009772

Rare variants in the endocytic pathway are associated with Alzheimer’s disease, its related phenotypes, and functional consequences
Cited by: 0
Author(s): Lingyu Zhan, Jiajin Li, Brandon Jew, Jae Hoon Sul
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pgen.1008855

Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits
Cited by: 8
Author(s): Wei Cheng, Sohini Ramachandran, Lorin Crawford
Software Mentions: 7
Published: over 4 years ago

10.1186/s12859-021-04126-3

Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources
Cited by: 6
Author(s): Neel Patel, William S. Bush
Software Mentions: 7
Published: over 3 years ago

10.1186/s40246-016-0063-5

Human genome meeting 2016
Cited by: 10
Author(s): Arpita Srivastava, Y. Wang, Raymond Y. Huang, Chris J. Skinner, Tommy G. Thompson, Lucille Addison Pollard, Teresa L. Wood, Feng Luo, Robert B. Stevenson, Renato Polimanti, Joel Gelernter, Xin-Ying Lin, I. Y. Lim, Yi-Chieh Wu, Ai Ling Teh, L. Chen, I. M. Aris, Soo-Youn Soh, Mya Thway Tint, Julia L. MacIsaac, Fui W Yap, Kenneth Kwek, S. M. Saw, Michael S. Kobor, Michael J. Meaney, Keith M. Godfrey, Yap Seng Chong, Joanna D. Holbrook, Y. S. Lee, P. D. Gluckman, Neerja Karnani, Ashish Kapoor, D. Lee, Aravinda Chakravarti, Christian Maercker, Fritz Graf, Michael Boutros, Georgios Stamoulis, Fabio Santoni, Periklis Makrythanasis, Audrey Letourneau, Michel Guipponi, Nikolaos Panousis, Marco Garieri, Pascale Ribaux, Emilie Falconnet, Christelle Borel, Stylianos E. Antonarakis, Sonia Kumar, Joanne E. Curran, John Blangero, Samit Chatterjee, Jennifer A. Akiyama, Dallas R. Auer, Courtney Berrios, L Pennacchio, Tarak Donti, Gerarda Cappuccio, Marcus J. Miller, Paldeep S. Atwal, A. L. Kennedy, Aaron L. Cardon, Carlos A. Bacino, Lisa Emrick, Jozef Hertecant, F Bäumer, Brenda E. Porter, Matthew N. Bainbridge, Penelope E. Bonnen, Brett H. Graham, Reid Sutton, Qin Sun, Sarah H. Elsea, Zhi-Liang Hu, P. Wang, Yun Zhu, Jinying Zhao, Momiao Xiong, David A. Bennett, Alfredo Hidalgo‐Miranda, Sandra Romero-Córdoba, Sergio Rodrı́guez-Cuevas, Rosa Rebollar-Vega, Elena Tagliabue, Maria Iorio, Elvira D’Ippolito, Stefano Baroni, Bogumił Kaczkowski, Yoïchi Tanaka, Hideya Kawaji, Albin Sandelin, Robin Andersson, Masumi Itoh, Timo Lassmann, Yoshihide Hayashizaki, Piero Carninci, Alistair R.R. Forrest, Colin A. Semple, Elisabeth Rosenthal, Brian H. Shirts, Laura M. Amendola, Cecilia Gracia Gallego, Martha Horike‐Pyne, Amber Burt, Peggy D. Robertson, P. Beyers, Chris Nefcy, DL Veenstra, Fuki M. Hisama, Robin L. Bennett, Michael O. Dorschner, Deborah A. Nickerson, Joseph D. Smith, Karynne Patterson, David R. Crosslin, Rami Nassir, N. Zubair, Tom Harrison, Ulrike Peters, Gail P. Jarvik, Francesca Menghi, Koichiro Inaki, Xingyi Woo, Prerna Kumar, Krzysztof R. Grzęda, Ankit Malhotra, H. Kim, Duygu Ucar, Phung Trang Shreckengast, Krishna Karuturi, James Keck, James Chuang, E. T. Liu, Boyang Ji, Alioto Tyler, Guruprasad Ananda, G. Carter, Hamid Nikbakht, Martin Montagne, Michele Zeinieh, A. Harutyunyan, Melissa K. McConechy, Nada Jabado, Pierre Lavigne, Jacek Majewski, Jennifer B. Goldstein, Michael J. Overman, Gauri Varadhachary, Rachna T. Shroff, Robert A. Wolff, M. M. Javle, Andy Futreal, D. Fogelman, Leny Bravo, Williams Fajardo, Humberto Serna Gómez, Carlos Castañeda, Christian Rolfo, Joseph A. Pinto, Kadir C. Akdemir, Lynda Chin, Shanna Patterson, Cara Statz, Susan M. Mockus, S. N. Nikolaev, Ximena Bonilla, Laurent Parmentier, Bryan King, Fedor Bezrukov, Gulhan Kaya, Vincent Zoete, Vladimir B. Seplyarskiy, Heather Sharpe, Thomas W. McKee, Konstantin Popadin, Nicole Basset-Séguin, Rouaa Ben Chaabene, M. E. Andrianova, C Verdan, K. Grosdemange, Olga Sumara, Martin Eilers, Iannis Aifantis, Olivier Michielin, FJ de Sauvage, Stylianos E. Antonarakis, Somsak Likhitrattanapisal, Stephen E. Lincoln, Allison W. Kurian, Andrea Desmond, Shihui Yang, Yukio Kobayashi, James M. Ford, Leif W. Ellisen, Ted Peters, Karine Alvarez, Emporia Faith Hollingsworth, Dolores López‐Terrada, Alex Hastie, Željko Džakula, Andy Wing Chun Pang, Elaine T. Lam, Thomas Anantharaman, Michael Saghbini, Hua Cao, BioNano Genomics, Claudia Gonzaga‐Jauregui, Lijia Ma, Alejandra King, Erika B. Rosenzweig, U. B. Krishnan, Jeffrey G. Reid, J. D. Overton, Frederick E. Dewey, Woo-Keun Chung, Kathy M. Small, Adam P. DeLuca, Frans P.M. Cremers, Richard A. Lewis, V. Puech, Benjamin Bakall, R. Silva-Garcia, Klaus Rohrschneider, Marie Leys, Fadi Shaya, Edwin M Stone, Nara Sobreira, François Schiettecatte, Hong‐Qing Ling, Eric Pugh, David R. Witmer, Kyle M. Hetrick, P. Zhang, Kimberly F. Doheny, David Valle, Ada Hamosh, Shalini N. Jhangiani, Zeynep Coban Akdemir, Matthew N. Bainbridge, Wu‐Lin Charng, Wojciech Wiszniewski, Tomasz Gambin, Ender Karaca, Yavuz Bayram, Mohammad K. Eldomery, Jennifer E. Posey, Hv. Doddapaneni, Jingyuan Hu, V. Reid Sutton, Donna M. Muzny, Eric Boerwinkle, James R. Lupski, Richard A. Gibbs, Sandhya Shekar, William Salerno, Adam C. English, Adina Mangubat, Jeremy Bruestle, Adrian Thorogood, Bartha Maria Knoppers, Global Alliance for Genomics, Hazuki Takahashi, Kazuhiro R. Nitta, A. Kozhuharova, Ana Maria Suzuki, Hemant Sharma, Diego Cotella, Claudia Santoro, S. Zucchelli, Stefano Gustincich, J. J. Mulvihill, Gareth Baynam, W. A. Gahl, Stephen C. Groft, Kenjiro Kosaki, Paul Lasko, Béla Melegh, Domenica Taruscio, Rajarshi Ghosh, Sharon E. Plon, Steven E. Scherer, Xiang Qin, Rashesh Sanghvi, Kimberly Walker, Tsoyu Chiang, Donna M. Muzny, L. Wang, John L. Black, Eric Boerwinkle, Richard M. Weinshilboum, R.A. Gibbs, Tatiana V. Karpinets, Tiffany L. Calderone, Khalida Wani, Xiaoxing Yu, Caitlin Creasy, Cara L. Haymaker, Marie-Andrée Forget, Vashisht Gopal Yennu Nanda, Jason Roszik, Jennifer A. Wargo, Lauren E. Haydu, Xiaofei Song, Alexander J. Lazar, Jeffrey E. Gershenwald, M. A. Davies, Chantale Bernatchez, J. Zhang, Simon Woodman, Elissa J. Chesler, Todd B. Reynolds, Jason A Bubier, C M D Wendell Phillips, Michael A. Langston, Erich J. Baker, Nancy U. Lin, Christopher I. Amos, Vince D. Calhoun, Otto Dobretsberger, M. Egger, F. Leimgruber, Simon Sadedin, Alicia Oshlack, Victor Andrew A. Antonio, Noriaki Ono, Clark Kendrick Go, Zaheer Ahmed, Mohan Bolisetty, Saman Zeeshan, Esther Aguirre Anguiano, Abhishek Sarkar, Madhusudan R. Nandineni, Chao Zeng, Jie Shao, Tianzhu Liang, Kevin Pham, Y. Chee-Wei, Dongsheng Li, W. Lai-Ping, Duan Lian, Rick Ong Twee Hee, Yuzaimi Yunus, Farhang Aghakhanian, Siti Shuhada Mokhtar, C. V. Lok-Yung, Jong Bhak, Matthew Phipps, Xu Shuhua, T. Yik-Ying, Vinod Kumar, Hoh BoonPeng, Ian Campbell, Mary‐Anne Young, Pettengill James, Lifepool, Manjari Rain, Ghulam Mohammad, Ritushree Kukreti, Qadar Pasha, Ainur Akilzhanova, C. Guelly, Zhannur Abilova, Saule Rakhimova, Ainur Akhmetova, Ulykbek Kairov, Slave Trajanoski, Zhaxybay Zhumadilov, Makhabbat Bekbossynova, Cassie A. Schumacher, Sardul Singh Sandhu, Timothy T. Harkins, Vladimir Makarov, Robert Glenn, Zeineen Momin, B. Dilrukshi, Hsiao Tuan Chao, Qingchang Meng, Brent M. Gudenkauf, R. Kshitij, Joy C. Jayaseelan, Caitlin Nessner, S. Lee, K. Blankenberg, Lora Lewis, Yi Han, Huyen Dinh, S. Jireh, Christian Buhay, X. Liu, Q. Wang, Yao Ding, Narayanan Veeraraghavan, Ya Ping Yang, Arthur L. Beaudet, Christine M. Eng, Kim C. Worley, Y. Liu, Daniel Hughes, Shwetha C. Murali, R. Alan Harris, Adam C. English, Oliver A. Hampton, Peter A. Larsen, Christine R. Beck, M. Wang, Christie Kovar, William Salerno, Anne D. Yoder, Stephen M. Richards, Jeffrey Rogers, M. Raveenedran, Chenghai Xue, Mahmoud Dahdouli, Linda J. Cox, Guangyi Fan, Betsy Ferguson, J. Hovarth, Zachary P. Johnson, Sree Kanthaswamy, M. Kubisch, Martin Ward Platt, Daniel G. Smith, Eric J. Vallender, Roger W. Wiseman, Jennifer E. Below, Fuli Yu, Jaime Lin, Y. Zhang, Zhengqing Ouyang, Andrew Moore, Z. Wang, Johannes Hofmann, Purdue Mp, Rachael Z. Stolzenberg‐Solomon, Shelsey J. Weinstein, Demetrius Albanês, C. S. Liu, Wei‐Yi Cheng, Timothy Lin, Qiong Lan, Nathaniel Rothman, SI Berndt, E. S. Chen, Hoda Bahrami, A. Khoshzaban, S. Heidari Keshal, K. K. R. Alharbi, M. Zhalbinova, Ainur Akilzhanova, Mahabbat Bekbosynova, Ш.К. Мырзахметова, Maher Matar, N. Mili, Robert J. Molinari, Yussanne Ma, Stéphane Guerrier, Nasser A. Elhawary, Mohammed T. Tayeb, Neda M. Bogari, N. Qotb, Sarah A. McClymont, Paul W. Hook, Loyal A. Goff, Andrew S. McCallion, Yong Kong, Jacob Charette, Wanda L. Hicks, Jürgen Κ. Naggert, Lue Ping Zhao, Patsy M. Nishina, Burhan Edrees, Mohammad Athar, Faisal A. Al‐Allaf, Mohiuddin M. Taher, Wahab Khan, Abdellatif Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, Abeer Abdullah Al Anazi, N. Altayeb, Muhammad Ahmed, K. Alansary, Zainularifeen Abduljaleel, Anton Kratz, Pascal Béguin, Stéphane Poulain, Makoto Kaneko, C. Takahiko, Atsuko Matsunaga, Sachi Kato, Nicolas Bertin, Réjan Vigot, Charles Plessy, Thomas Lavstsen, Dan Graur, Jens Friis-Nielsen, Jose M. G. Izarzugaza, Søren Brunak, Anurupa Chakraborty, Jolly Basak, and Rajendrani Mukhopadhyay, Benjamin Soibam, Dhritishree Das, Nupur Biswas, Das S, Sinjini Sarkar, Anirban Maitra, Chandan Kumar Panda, Prasenjit Majumder, Heba Morsy, Ahmed Mohammed Gaballah, M Parikh Samir, M. Shamseya, Hisham Mahrous, Ayesha Ghazal, Waleed Arafat, M. Hashish, Joshua J. Gruber, Natalie Jaeger, Matthew Snyder, Kashyap Patel, Shannon Bowman, Trisha N. Davis, D Kraushaar, Amy B. Emerman, Salvatore Russello, Noa Henig, Cynthia L. Hendrickson, K. Zhang, Mauricio Rodríguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales, Natalie Jäger, J. Chen, Robert W. Haile, Megan P. Hitchins, Julia Brooks, Silvia Jiménez-Morales, Mónica Morales Ramírez, Javier Martín‐Núñez, Valerie Bekker, Yriana Rodrigues Leal, Esteban Jiménez, Aída Carolina Medina, Alfredo Hidalgo, Jorge Mejía, V. Halytskiy, Jürgen Κ. Naggert, Gayle B. Collin, K. DeMauro, R. Hanusek, K. Belhassa, Khadija Belhassan, Laila Bouguenouch, I. Samri, H. Sayel, Fz. moufid, I. El Bouchikhi, S. Trhanint, H. Hamdaoui, I. Elotmani, I. Khtiri, O. Kettani, L. Quibibo, M. Ahagoud, Mohammed Abdou Abbassi, Karim Ouldim, А. В. Марусин, А. Н. Корнетов, M. G. Swarovskaya, K. Vagaiceva, Vadim Stepanov, Eva Maria Cutiongco de la Paz, Rody G. Sy, Julián Nevado, Paul Ferdinand M. Reganit, L. C. S. dos Santos, Jose Donato A. Magno, Felix Eduardo R. Punzalan, Deborah Ignacia D. Ona, Erasmo Gonzalo D.V. Llanes, R. L. Santos-Cortes, Raphael Enrique Tiongco, Jaime Alfonso M. Aherrera, Lauro L. Abrahan, P. Pagauitan-Alan, Kathryn H. Morelli, J. S. Domire, Nibedita Pyne, Shirley F. Harper, Ralph Royal Burgess, Mamdooh Gari, Ashraf Dallol, Haneen Alsehli, Abdullah Gari, Mamdooh Gari, A. A. Abuzenadah, M. G. Thomas, Mahadeo A. Sukhai, Shruti Garg, Maksym Misyura, T. Zhang, Anna Schuh, Tracy Stockley, Suzanne Kamel‐Reid, Stephen T. Sherry, Chunlin Xiao, Douglas J. Slotta, Kurt Rodarmer, Michael Feolo, Michael Kimelman, Georgy Godynskiy, Christopher D. O’Sullivan, Eugene Yaschenko, Claudia Rangel‐Escareño, H. Rueda-Zarate, Iftikhar Aslam Tayubi, Reema R Mohammed, Iqbal Ike K. Ahmed, Tamar Ahmed, Sahil Seth, Samirkumar B. Amin, Xinjie Mao, Hui Sun, Roeland Verhaak, S. J. Whiite, Jesse Farek, Z. Kahn, Takeya Kasukawa, Marina Lizio, Jayson Harshbarger, S. Hisashi, Jessica Severin, A. Imad, Sedef Şahin, Thomas Charles Augustus Freeman, Katherine Unger Baillie, Sandhya Shekar, Abbes Salem, Mecheala Abbas Ali, Ahmed Ibrahim, M. Sofi Ibrahim, H Barrera, Lourdes Garza, Julian Torres, V. Barajas, Alfredo Ulloa‐Aguirre, David Kershenobich, Shahroj Mortaji, Pedro Guizar, Eliezer Loera, Karen Moreno, Adriana De León, Daniela Monsiváis, Jackeline Gómez, Raquel Cardiel, Jesús Carlos Fernández-López, V. Bonifaz-Peña, Andrew Contreras, Linda M. Polfus, X. Wang, Vivek Philip, A. A. Abuzenadah, Rola Turki, Asli Uyar, A. Kaygun, Sayed Zaman, E. García de Castro Márquez, Josna George, Cynthia L. Hendrickson, Dakota Starr, Mark E. Baird, Brian Kirkpatrick, Kent J. Sheets, Rainer Nitsche, L. Prieto-Lafuente, Melissa Landrum, J. Lee, Wendy S. Rubinstein, Donna Maglott, P. K. R. Thavanati, A. Escoto de Dios, Rolando Hernandez, M. E. Aguilar Aldrate, Mirna Mejia, K. R. R. Kanala, Neelum Shahzad, Elisabeth Huber, Alice J. Dan, Wolfgang Herr, G. Sprotte, Josef Köstler, Andreas Hiergeist, AE Gessner, Reinhard Andreesen, Elmar Holler, Faisal A. Al‐Allaf, Abdullah A. Al-Ashwal, Mohiuddin M. Taher, Halah Abalkhail, Ahmad F. Al-Allaf, R. Bamardadh, Olga Filiptsova, M. M. Kobets, Yu. M. Kobets, Ievgeniia Burlaka, I. Timoshyna, M. M. Kobets, Muhammad Mohiuddin, A. Zainularifeen, Alfaqih Samar Mohammed, Tarek Owaidah
Software Mentions: 7
Published: over 8 years ago

10.1186/s12859-019-2611-1

sim1000G: a user-friendly genetic variant simulator in R for unrelated individuals and family-based designs
Cited by: 18
Author(s): Apostolos Dimitromanolakis, Jingxiong Xu, Agnieszka Król, Laurent Briollais
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pgen.1008984

Natural variation in a glucuronosyltransferase modulates propionate sensitivity in a C. elegans propionic acidemia model
Cited by: 16
Author(s): Huimin Na, Stefan Zdraljevic, Robyn E. Tanny, Albertha J.M. Walhout, Erik C. Andersen
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0156895

A Comparative Study of Five Association Tests Based on CpG Set for Epigenome-Wide Association Studies
Cited by: 14
Author(s): Qiuyi Zhang, Yang Zhao, Ruyang Zhang, Yongyue Wei, Honggang Yi, Fang Shao, Feng Chen
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pcbi.1007663

RAINBOW: Haplotype-based genome-wide association study using a novel SNP-set method
Cited by: 36
Author(s): Kosuke Hamazaki, Hiroyoshi Iwata
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pgen.1009010

Candidate variants in TUB are associated with familial tremor
Cited by: 2
Author(s): M. Reza Sailani, Fereshteh Jahanbani, Charles W. Abbott, Hayan Lee, Amin Zia, Shannon Rego, Juliane Winkelmann, Franziska Hopfner, Tahir Naeem Khan, Nicholas Katsanis, Stefanie H. Müller, Daniela Berg, Katherine M. Lyman, Christian Mychajliw, G. Deuschl, Jonathan A. Bernstein, Gregor Kuhlenbäumer, M Snyder
Software Mentions: 5
Published: over 4 years ago

10.1038/s41416-018-0141-7

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

10.1098/rsob.170125

Statistical methods to detect pleiotropy in human complex traits
Cited by: 98
Author(s): Sophie Hackinger, Eleftheria Zeggini
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pcbi.1008517

Network propagation of rare variants in Alzheimer’s disease reveals tissue-specific hub genes and communities
Cited by: 1
Author(s): Marzia Antonella Scelsi, Valerio Napolioni, Michael D. Greicius, André Altmann
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12863-015-0313-x

Filtering genetic variants and placing informative priors based on putative biological function
Cited by: 4
Author(s): Stefanie Friedrichs, Dörthe Malzahn, Elizabeth Pugh, Marcio Almeida, Xiao Qing Liu, Julia N. Bailey
Software Mentions: 5
Published: almost 9 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: over 8 years ago

10.1371/journal.pcbi.1008819

Boosting GWAS using biological networks: A study on susceptibility to familial breast cancer
Cited by: 3
Author(s): Héctor Climente-González, Christine Lonjou, Fabienne Lesueur, Dominique Stoppa‐Lyonnet, Nadine Andrieu, Chloé-Agathe Azencott
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0041694

Multiple Regression Methods Show Great Potential for Rare Variant Association Tests
Cited by: 20
Author(s): Changjiang Xu, Martin Ladouceur, Zari Dastani, J. Brent Richards, Antonio Ciampi, Celia M.T. Greenwood
Software Mentions: 5
Published: over 12 years ago

10.1038/s42003-020-0885-5

Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes
Cited by: 5
Author(s): Peter A. Perrino, Lidiya Talbot, Rose Kirkland, Amanda Hill, Amanda R. Rendall, Hayley S. Mountford, Jenny C. Taylor, Alexzandrea N Buscarello, Nayana Lahiri, Anand Saggar, R. Holly Fitch, Dianne F. Newbury
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pone.0179364

DoEstRare: A statistical test to identify local enrichments in rare genomic variants associated with disease
Cited by: 6
Author(s): Elodie Persyn, Matilde Karakachoff, Solena Le Scouarnec, Camille Le Clézio, Dominique Campion, Emmanuelle Génin, Jean‐Jacques Schott, Richard Redon, Lise Bellanger, Christian Dina
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0139642

Assessing the Power of Exome Chips
Cited by: 6
Author(s): Christian M. Page, Sergio E. Baranzini, Bjørn-Helge Mevik, Steffan Daniël Bos, Hanne F. Harbo, Bettina Kulle Andreassen
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pgen.1003443

Analysis of Rare, Exonic Variation amongst Subjects with Autism Spectrum Disorders and Population Controls
Cited by: 128
Author(s): Li Liu, Aniko Sabo, Benjamin M. Neale, Uma Nagaswamy, Christine Stevens, Elaine T. Lim, Corneliu Bodea, Donna M. Muzny, Jeffrey G. Reid, Eric Banks, Hilary Coon, Mark A. DePristo, Huyen Dinh, Tim Fennel, Jason Flannick, Stacey Gabriel, Kiran Garimella, Shannon Gross, Alicia Hawes, Lora Lewis, Vladimir Makarov, Jared Maguire, Irene Newsham, Ryan Poplin, Stephan Ripke, Khalid Shakir, Kaitlin E. Samocha, Yuanqing Wu, Eric Boerwinkle, Joseph D. Buxbaum, Edwin H. Cook, Bernie Devlin, Gerard D. Schellenberg, James S. Sutcliffe, Mark J. Daly, Richard A. Gibbs, Kathryn Roeder
Software Mentions: 4
Published: over 11 years ago

10.1038/s41598-021-82547-z

An evaluation of approaches for rare variant association analyses of binary traits in related samples
Cited by: 4
Author(s): Ming-Huei Chen, Achilleas Pitsillides, Qiong Yang
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pgen.1003075

A Unified Method for Detecting Secondary Trait Associations with Rare Variants: Application to Sequence Data
Cited by: 6
Author(s): Dajiang Liu, Suzanne M. Leal
Software Mentions: 4
Published: about 12 years ago

10.1186/s12919-016-0057-2

Association of rare haplotypes on ULK4 and MAP4 genes with hypertension
Cited by: 11
Author(s): Ananda S. Datta, Yuan Zhang, Lei Zhang, Swati Biswas
Software Mentions: 4
Published: about 8 years ago

10.1186/s12920-020-0684-3

Adaptive Fisher method detects dense and sparse signals in association analysis of SNV sets
Cited by: 2
Author(s): Xiaoyu Cai, Lo‐Bin Chang, Jordan Potter, Chi Song
Software Mentions: 4
Published: over 4 years ago

10.3389/fpls.2019.01249

Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence
Cited by: 9
Author(s): Anna Furches, David Kainer, Deborah Weighill, Annabel Large, Piet Jones, Angelica M. Walker, Jonathon Romero, João Gabriel Felipe Machado Gazolla, Wayne Joubert, Manesh Shah, Jared Streich, Priya Ranjan, Jeremy Schmutz, Avinash Sreedasyam, David Macaya‐Sanz, Nan Zhao, Madhavi Z. Martin, Xiaolan Rao, Richard A. Dixon, Stephen P. DiFazio, Timothy J. Tschaplinski, Jay Chen, Gerald A. Tuskan, Daniel Jacobson
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-018-2591-6

Real world scenarios in rare variant association analysis: the impact of imbalance and sample size on the power in silico
Cited by: 18
Author(s): Mengjie Zhang, Anna O. Basile, Sarah A. Pendergrass, Marylyn D. Ritchie
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1007530

Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic
Cited by: 31
Author(s): Ryan Sun, Shirley Hui, Gary D. Bader, Xihong Lin, Peter Kraft
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pcbi.1009250

IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA
Cited by: 7
Author(s): Zhonghe Shao, Ting Wang, Meng Zhang, Zhou Jiang, Shuiping Huang, Ping Zeng
Software Mentions: 4
Published: over 3 years ago

10.3390/genes11121408

‘There and Back Again’—Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension
Cited by: 8
Author(s): Emilia M. Swietlik, Matina Prapa, Jennifer Martin, Divya Pandya, Kathryn Auckland, Nicholas W. Morrell, Stefan Gräf
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0105074

Functional Analysis of Variance for Association Studies
Cited by: 26
Author(s): Olga A. Vsevolozhskaya, Dmitri V. Zaykin, Mark C. Greenwood, Colin Wei, Qing Lu
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0080540

Association Testing Strategy for Data from Dense Marker Panels
Cited by: 1
Author(s): Donghyung Lee, Silviu‐Alin Bacanu
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pgen.1005963

De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects
Cited by: 87
Author(s): James R. Priest, Kazutoyo Osoegawa, Nebil Mohammed, Vivek Nanda, Ramendra K. Kundu, Kathleen Schultz, Edward J. Lammer, Santhosh Girirajan, Todd E. Scheetz, Daryl Waggott, François Haddad, Sushma Reddy, Daniel Bernstein, Trudy L. Burns, Jeffrey D. Steimle, Xinan Yang, Ivan P. Moskowitz, Matthew E. Hurles, Richard P. Lifton, Debbie Nickerson, Michael J. Bamshad, Evan E. Eichler, Seema Mital, Val C. Sheffield, Thomas Quertermous, Bruce D. Gelb, Michael A. Portman, Euan A. Ashley
Software Mentions: 3
Published: over 8 years ago

10.1186/1753-6561-8-S1-S41

Kernel score statistic for dependent data
Cited by: 7
Author(s): Dörthe Malzahn, Stefanie Friedrichs, Albert Rosenberger, Heike Bickeböller
Software Mentions: 3
Published: over 10 years ago

10.1038/srep28389

Conditioning adaptive combination of P-values method to analyze case-parent trios with or without population controls
Cited by: 1
Author(s): Wan-Yu Lin, Yun-Chieh Liang
Software Mentions: 3
Published: over 8 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

10.1186/s12929-014-0088-9

Identifying rare and common disease associated variants in genomic data using Parkinson's disease as a model
Cited by: 6
Author(s): Ying Lin, Ai-Ru Hsieh, Ching Lin Hsiao, Shang Jung Wu, Hui‐Min David Wang, Ie Bin Lian, Cathy S.J. Fann
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0154181

Incorporating Non-Coding Annotations into Rare Variant Analysis
Cited by: 9
Author(s): Tom G Richardson, Colin Campbell, Nicholas J. Timpson, Tom R. Gaunt
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0130329

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

10.1186/s12859-020-3511-0

TS: a powerful truncated test to detect novel disease associated genes using publicly available gWAS summary data
Cited by: 1
Author(s): Jianjun Zhang, Xuan Guo, Samantha Gonzales, Jingjing Yang, Xuexia Wang
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0207677

The impact of a fine-scale population stratification on rare variant association test results
Cited by: 27
Author(s): Elodie Persyn, Richard Redon, Lise Bellanger, Christian Dina
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pgen.1006260

Novel Genetic Variants for Cartilage Thickness and Hip Osteoarthritis
Cited by: 73
Author(s): Martha C. Castaño-Betancourt, Dan S. Evans, Yolande F M Ramos, Cindy G. Boer, Sarah Metrustry, Youfang Liu, Wouter den Hollander, Jeroen van Rooij, Virginia B. Kraus, Michelle S. Yau, Braxton D. Mitchell, Kenneth Muir, Albert Hofman, Michael Doherty, Sally Doherty, Weiya Zhang, Robert Kraaij, Fernando Rivadeneira, Elizabeth Barrett‐Connor, Rose A. Maciewicz, N K Arden, Rob G H H Nelissen, Margreet Kloppenburg, Joanne M. Jordan, Michael C. Nevitt, P. Eline Slagboom, Deborah Hart, Floris P. J. G. Lafeber, Unnur Styrkársdóttir, Eleftheria Zeggini, Εvangelos Εvangelou, Tim D. Spector, André G. Uitterlinden, Nancy E Lane, Ingrid Meulenbelt, Ana M. Valdes, Joyce B. J. van Meurs
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-019-39113-5

Behçet’s disease and genetic interactions between HLA-B*51 and variants in genes of autoinflammatory syndromes
Cited by: 17
Author(s): Sergio Burillo‐Sanz, Marco-Antonio Montes-Cano, José‐Raúl García‐Lozano, Israel Olivas-Martínez, Norbérto Ortego-Centeno, Francisco-José García-Hernández, Gerard Espinosa, Jenaro Graña Gil, Juan Sánchez‐Bursón, M. R. Julià, Roser Solans, Ricardo Blanco, Ana-Celia Barnosi-Marín, Ricardo Gómez de la Torre, P. Fanlo, Mónica Rodríguez-Carballeira, Luis Rodríguez‐Rodríguez, Teresa Camps, Santos Castañeda, Juan-José Alegre-Sancho, Javier Martı́n, María Francisca González‐Escribano
Software Mentions: 3
Published: almost 6 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

10.1038/s41598-017-00712-9

Longitudinal data analysis for rare variants detection with penalized quadratic inference function
Cited by: 1
Author(s): Hongyan Cao, Li Zhi, Yang Huang, Yuehua Cui, Yanbo Zhang
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-021-03968-1

Penalized partial least squares for pleiotropy
Cited by: 2
Author(s): Camilo Broc, Thérèse Truong, Benoît Liquet
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pntd.0009507

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

10.1038/s41598-018-26453-x

Blood lipid-related low-frequency variants in LDLR and PCSK9 are associated with onset age and risk of myocardial infarction in Japanese
Cited by: 14
Author(s): Tomoyuki Tajima, Hiroyuki Morita, Kei Ito, Tsutomu Yamazaki, Michiaki Kubo, Issei Komuro, Yukihide Momozawa
Software Mentions: 3
Published: over 6 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

10.1371/journal.pgen.1006573

A Model of Compound Heterozygous, Loss-of-Function Alleles Is Broadly Consistent with Observations from Complex-Disease GWAS Datasets
Cited by: 33
Author(s): Jaleal Sanjak, Anthony D. Long, Kevin R. Thornton
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13059-017-1147-9

Discovery and functional prioritization of Parkinson’s disease candidate genes from large-scale whole exome sequencing
Cited by: 92
Author(s): Iris E. Jansen, Hui Ye, Sasja Heetveld, Marie C. Lechler, Helen Michels, Renée I. Seinstra, Steven Lubbe, Valérie Drouet, Suzanne Lesage, Elisa Majounie, J. Raphael Gibbs, Mike A. Nalls, Mina Ryten, Juan A. Botía, Jana Vandrovcová, Javier Simón‐Sánchez, Melissa Castillo-Lizardo, Patrizia Rizzu, Cornelis Blauwendraat, Amit K. Chouhan, Yarong Li, Puja Yogi, Najaf Amin, Cornelia M. van Duijn, Huw R. Morris, Alexis Brice, Andrew B. Singleton, Della David, Ellen A. A. Nollen, Sandeep Jain, Zhandong Liu, Peter Heutink
Software Mentions: 3
Published: almost 8 years ago

10.1002/gepi.21743

VAAST 2.0: Improved Variant Classification and Disease‐Gene Identification Using a Conservation‐Controlled Amino Acid Substitution Matrix
Cited by: 128
Author(s): Hao Hu, Chad Huff, Barry Moore, Steven Flygare, Martin G. Reese, Mark Yandell
Software Mentions: 3
Published: over 11 years ago

10.1016/j.ajhg.2017.05.015

A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases
Cited by: 33
Author(s): Daniel Greene, Nihr BioResource, Sylvia Richardson, Ernest Turro
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pgen.1008802

A phenome-wide association study of 26 mendelian genes reveals phenotypic expressivity of common and rare variants within the general population
Cited by: 12
Author(s): Catherine Tcheandjieu, Matthew Aguirre, Stefan Gustafsson, Priyanka Saha, Praneetha Potiny, Melissa Haendel, Erik Ingelsson, Manuel A. Rivas, James R. Priest
Software Mentions: 3
Published: about 4 years ago

10.1002/gepi.22264

Population genetic simulation study of power in association testing across genetic architectures and study designs
Cited by: 6
Author(s): Dominic M. H. Tong, Ryan D. Hernández
Software Mentions: 3
Published: about 5 years ago

10.1093/hmg/ddx328

Exome-wide association study reveals novel psoriasis susceptibility locus at TNFSF15 and rare protective alleles in genes contributing to type I IFN signalling
Cited by: 34
Author(s): Nick Dand, Sören Mucha, Lam C. Tsoi, Satveer K. Mahil, Philip E. Stuart, Andreas Arnold, Hansjörg Baurecht, A. D. Burden, Kristina Callis Duffin, Vinod Chandran, Charles Curtis, Das S, David Ellinghaus, Eva Ellinghaus, Charlotta Enerbäck, Tõnu Esko, Dafna D. Gladman, Christopher E.M. Griffiths, Jóhann E. Guðjónsson, Per Hoffman, Georg Homuth, Ulrike Hüffmeier, Gerald G. Krueger, Matthias Laudes, Sang Hyuck Lee, Wolfgang Lieb, Henry W. Lim, Sabine Löhr, Ulrich Mrowietz, Martina Müller-Nurayid, Markus M. Nöthen, Annette Peters, Proton Rahman, André Reis, Nick J. Reynolds, Elke Rodríguez, Carsten Oliver Schmidt, Sarah Spain, Konstantin Strauch, Trilokraj Tejasvi, John J. Voorhees, Richard B Warren, Michael Weichenthal, Stephan Weidinger, Matthew Zawistowski, Rajan P. Nair, Francesca Capon, Catherine Smith, Richard Trembath, Gonçalo R. Abecasis, James T. Elder, André Franke, Michael A. Simpson, Jonathan Barker
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1007784

Efficient and flexible Integration of variant characteristics in rare variant association studies using integrated nested Laplace approximation
Cited by: 4
Author(s): Hana Sušak, Laura Serra, German Demidov, Raquel Rabionet, Laura Domènech, Mattia Bosio, Francesc Muyas, Xavier Estivill, Geòrgia Escaramís, Stephan Ossowski
Software Mentions: 3
Published: almost 4 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: over 3 years ago

10.1186/s12920-019-0516-5

Meta-Qtest: meta-analysis of quadratic test for rare variants
Cited by: 2
Author(s): Jieun Ka, Jae‐Hoon Lee, Yongkang Kim, Bermseok Oh, Taesung Park
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pcbi.1004993

Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level
Cited by: 10
Author(s): X. Jessie Jeng, Z. John Daye, Wenbin Lu, Jung Ying Tzeng
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-018-2066-9

Pathway-based approach using hierarchical components of rare variants to analyze multiple phenotypes
Cited by: 5
Author(s): Sung Young Lee, Yongkang Kim, Sungkyoung Choi, Heungsun Hwang, Taesung Park
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2020.568052

Whole-Exome Sequencing of Discordant Monozygotic Twin Families for Identification of Candidate Genes for Microtia-Atresia
Cited by: 7
Author(s): Xinmiao Fan, Ping Lu, Hao Sun, Yu‐Shan Chen, Pu Wang, Tao Liu, Rui Jiang, Xuegong Zhang, Xiaowei Chen
Software Mentions: 3
Published: about 4 years ago

10.3389/fpls.2020.545748

Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa
Cited by: 20
Author(s): Hari B. Chhetri, Anna Furches, David Macaya‐Sanz, Alejandro R. Walker, David Kainer, Piet Jones, Anne E. Harman‐Ware, Timothy J. Tschaplinski, Daniel Jacobson, Gerald A. Tuskan, Stephen P. DiFazio
Software Mentions: 3
Published: over 4 years ago

10.1093/database/bax049

Benchmarking distributed data warehouse solutions for storing genomic variant information
Cited by: 9
Author(s): Marek Wiewiórka, Dawid P Wysakowicz, Michał Okoniewski, Tomasz Gambin
Software Mentions: 3
Published: almost 8 years ago

10.1093/bfgp/elu012

Methodology for the analysis of rare genetic variation in genome-wide association and re-sequencing studies of complex human traits
Cited by: 17
Author(s): Loukas Moutsianas, Andrew P. Morris
Software Mentions: 3
Published: over 10 years ago

10.1016/j.ebiom.2020.103157

Whole genome sequence analyses of eGFR in 23,732 people representing multiple ancestries in the NHLBI trans-omics for precision medicine (TOPMed) consortium
Cited by: 13
Author(s): Bridget M. Lin, Kelsey Grinde, Jennifer A. Brody, Charles E. Breeze, Laura M. Raffield, Josyf C. Mychaleckyj, Timothy A. Thornton, James A. Perry, Leslie J. Baier, Lisa de las Fuentes, Xiuqing Guo, Benjamin D. Heavner, Robert L. Hanson, Yi‐Jen Hung, Huijun Qian, Chao A. Hsiung, Shih‐Jen Hwang, Margaret R Irvin, Deepti Jain, Tanika N. Kelly, Sayuko Kobes, Leslie A. Lange, James P. Lash, Yun Li, Xiaoming Liu, Xuenan Mi, Solomon K. Musani, George Papanicolaou, Afshin Parsa, Alex P. Reiner, Saeedeh Salimi, Wayne H‐H Sheu, Alan R. Shuldiner, Kent D. Taylor, Albert V. Smith, Jennifer A. Smith, Adrienne Tin, Dhananjay Vaidya, Robert B. Wallace, Kenichi Yamamoto, Saori Sakaue, Koichi Matsuda, Yoichiro Kamatani, Yukihide Momozawa, Lisa R. Yanek, Betsi A Young, Wei Zhao, Yukinori Okada, Gonzalo Abecasis, Bruce M. Psaty, Donna K. Arnett, Eric Boerwinkle, Jianwen Cai, Ida Yii-Der Chen, Adolfo Correa, L. Adrienne Cupples, Jiang He, Sharon L.R. Kardia, Charles Kooperberg, Rasika A. Mathias, Braxton D. Mitchell, Deborah A. Nickerson, Steve T Turner, Ramachandran S. Vasan, Jerome I. Rotter, Daniel Levy, Holly Kramer, Anna Köttgen, NHLBI Trans-Omics for Precision Medicine Consortium, TOPMed Kidney Working Group, Stephen S. Rich, Danyu Lin, Sharon R. Browning, Nora Franceschini
Software Mentions: 3
Published: almost 4 years ago

10.1155/2015/852341

Clique-Based Clustering of Correlated SNPs in a Gene Can Improve Performance of Gene-Based Multi-Bin Linear Combination Test
Cited by: 8
Author(s): Yung Joon Yoo, Sun Ah Kim, Shelley B. Bull
Software Mentions: 3
Published: almost 10 years ago

10.1093/molbev/msu397

Pooled Sequencing and Rare Variant Association Tests for Identifying the Determinants of Emerging Drug Resistance in Malaria Parasites
Cited by: 37
Author(s): Ian H. Cheeseman, Marina McDew-White, Aung Pyae Phyo, Kanlaya Sriprawat, François Nosten, Timothy J. Anderson
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0229217

Testing gene-environment interactions for rare and/or common variants in sequencing association studies
Cited by: 4
Author(s): Zihan Zhao, Jianjun Zhang, Qiuying Sha, Hao Han
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12863-018-0647-2

Application of novel and existing methods to identify genes with evidence of epigenetic association: results from GAW20
Cited by: 1
Author(s): Angga M Fuady, Samantha Lent, Chloé Sarnowski, Nathan L. Tintle
Software Mentions: 3
Published: over 6 years ago

10.1038/s41421-020-00231-4

Initial whole-genome sequencing and analysis of the host genetic contribution to COVID-19 severity and susceptibility
Cited by: 150
Author(s): Fang Wang, Shujia Huang, Rongsui Gao, Yuwen Zhou, Changxiang Lai, Zhichao Li, Wenjie Xian, Xiaobo Qian, Zhiyu Li, Yushan Huang, Qiyuan Tang, Panhong Liu, Ruikun Chen, Rong Liu, Xuan Li, Xin Tong, Xuan Zhou, Yong Bai, Gang Dong, Tao Zhang, Xun Xu, Jian Wang, Huanming Yang, Siyang Liu, Qin He, Xin Jin, Lei Liu
Software Mentions: 3
Published: about 4 years ago

10.1007/s00401-019-01976-3

Loss of DPP6 in neurodegenerative dementia: a genetic player in the dysfunction of neuronal excitability
Cited by: 33
Author(s): Rita Cacace, Bavo Heeman, Sara Van Mossevelde, Arne De Roeck, Julie Hoogmartens, Peter De Rijk, Helena Gossye, Kristof De Vos, Wouter De Coster, Mojca Stražišar, Greet De Baets, Joost Schymkowitz, Frédéric Rousseau, Nathalie Geerts, Tim De Pooter, Karin Peeters, Anne Sieben, Jean‐Jacques Martin, Sebastiaan Engelborghs, Eric Salmon, Patrick Santens, Rik Vandenberghe, Patrick Cras, Peter Paul De Deyn, John C. van Swieten, Cornelia M. van Duijn, Julie van der Zee, Kristel Sleegers, Christine Van Broeckhoven
Software Mentions: 3
Published: almost 6 years ago

10.1186/s40364-018-0133-z

Associations of single nucleotide polymorphisms with mucinous colorectal cancer: genome-wide common variant and gene-based rare variant analyses
Cited by: 4
Author(s): Michelle E. Penney, Patrick S. Parfrey, Sevtap Savas, Yildiz E. Yilmaz
Software Mentions: 3
Published: over 6 years ago

10.3389/fgene.2019.00007

A New Panel-Based Next-Generation Sequencing Method for ADME Genes Reveals Novel Associations of Common and Rare Variants With Expression in a Human Liver Cohort
Cited by: 35
Author(s): Kathrin Klein, Roman Tremmel, Stefan Winter, Sarah Fehr, Florian Battke, Tim Scheurenbrand, Elke Schaeffeler, Saskia Biskup, Matthias Schwab, Ulrich M. Zanger
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12920-015-0094-0

The cis and trans effects of the risk variants of coronary artery disease in the Chr9p21 region
Cited by: 18
Author(s): Wei Zhao, Jennifer A. Smith, Guangmei Mao, Myriam Fornage, Patricia A. Peyser, Yan V. Sun, Stephen T. Turner, Sharon L.R. Kardia
Software Mentions: 2
Published: over 9 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.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.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.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

10.1371/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

10.1111/acel.12261

Exome sequencing of three cases of familial exceptional longevity
Cited by: 14
Author(s): Timothy P. Cash, Guillermo Pita, Orlando Domı́nguez, María R. Alonso, Leticia T. Moreno, Consuelo Borrás, Leocadio Rodrı́guez-Mañas, Catalina Santiago, Nuria Garatachea, Alejandro Lucía, Juan A. Avellana, José Viña, Anna González‐Neira, Manuel Serrano
Software Mentions: 2
Published: over 10 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: over 9 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

10.1186/1471-2105-14-199

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/s12864-016-2459-y

GWASeq: targeted re-sequencing follow up to GWAS
Cited by: 7
Author(s): Matthew P. Salomon, Wai Lok Sibon Li, Christopher K. Edlund, John L. Morrison, Barbara K. Fortini, Aung Ko Win, David V. Conti, Duncan C. Thomas, David Duggan, Daniel D. Buchanan, Mark A. Jenkins, John L. Hopper, Steven Gallinger, Loı̈c Le Marchand, Polly A. Newcomb, Graham Casey, Paul Marjoram
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0126637

Association between Stress Response Genes and Features of Diurnal Cortisol Curves in the Multi-Ethnic Study of Atherosclerosis: A New Multi-Phenotype Approach for Gene-Based Association Tests
Cited by: 6
Author(s): Zihuai He, Erin Payne, Bhramar Mukherjee, Seunggeun Lee, Jennifer A. Smith, Erin B. Ware, Brisa N. Sánchez, Teresa E. Seeman, Sharon L.R. Kardia, Ana V. Diez Roux
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0153803

A Protein Domain and Family Based Approach to Rare Variant Association Analysis
Cited by: 5
Author(s): Tom G Richardson, Hashem A. Shihab, Manuel A. Rivas, Mark I. McCarthy, Colin Campbell, Nicholas J. Timpson, Tom R. Gaunt
Software Mentions: 2
Published: over 8 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

10.1371/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

10.1186/s12859-021-04356-5

Wavelet Screening: a novel approach to analyzing GWAS data
Cited by: 2
Author(s): William Robert Paul Denault, Håkon K. Gjessing, Julius Juodakis, Bo Jacobsson, Astanand Jugessur
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0223273

eQTL mapping of rare variant associations using RNA-seq data: An evaluation of approaches
Cited by: 2
Author(s): Sharon M. Lutz, Annie Thwing, Tasha E. Fingerlin
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0110740

Whole Exome Sequencing Identifies Novel Genes for Fetal Hemoglobin Response to Hydroxyurea in Children with Sickle Cell Anemia
Cited by: 28
Author(s): Vivien A. Sheehan, Jacy R. Crosby, Aniko Sabo, Nicole A. Mortier, Thad A. Howard, Donna M. Muzny, Shannon Dugan-Perez, Banu Aygün, Kerri Nottage, Eric Boerwinkle, Richard A. Gibbs, Russell E. Ware, Jonathan M. Flanagan
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-14-569

Combined genotype and haplotype tests for region-based association studies
Cited by: 8
Author(s): Sergii Zakharov, Tien Yin Wong, Tin Aung, Eranga N. Vithana, Chiea‐Chuen Khor, Agus Salim, Anbupalam Thalamuthu
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0219926

Gene-based genome-wide association studies and meta-analyses of conotruncal heart defects
Cited by: 14
Author(s): Anshuman Sewda, A. J. Agopian, Elizabeth Goldmuntz, Hákon Hákonarson, Bernice E. Morrow, Deanne Taylor, Laura E. Mitchell
Software Mentions: 2
Published: over 5 years ago

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: over 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

10.1371/journal.pone.0188566

A non-threshold region-specific method for detecting rare variants in complex diseases
Cited by: 4
Author(s): Ai-Ru Hsieh, Dao-Peng Chen, Amrita Chattopadhyay, Yingju Li, Chien-Ching Chang, Cathy S.J. Fann
Software Mentions: 2
Published: about 7 years ago

Projects: cran: SKAT

Papers Mentioning SKAT 407