cran: MatrixEQTL | Projects | Ecosyste.ms: Papers

10.1186/s13059-019-1805-1

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Cited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: about 5 years ago

10.3934/mbe.2020007

Development of a tissue augmented Bayesian model for expression quantitative trait loci analysis
Cited by: 1
Author(s): Yonghua Zhuang, Kristen J. Wade, Laura Saba, Katerina Kechris
Software Mentions: 13
Published: almost 5 years ago

10.1016/j.ebiom.2018.04.010

Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial
Cited by: 28
Author(s): Antonio J. Berlanga‐Taylor, Katharine Plant, Andrew Dahl, Evelyn Lau, Michael Hill, David Sims, Andreas Heger, Jonathan Emberson, Jane Armitage, Robert Clarke, Julian C. Knight
Software Mentions: 11
Published: over 6 years ago

10.7554/eLife.58705

Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants
Cited by: 23
Author(s): Liis Kolberg, Nurlan Kerimov, Hedi Peterson, Kaur Alasoo
Software Mentions: 11
Published: about 4 years ago

10.1371/journal.pcbi.1008223

Causal network inference from gene transcriptional time-series response to glucocorticoids
Cited by: 15
Author(s): Jonathan Lu, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt
Software Mentions: 9
Published: almost 4 years ago

10.1186/1471-2164-14-892

RNA-Seq optimization with eQTL gold standards
Cited by: 24
Author(s): Shannon Ellis, Saloni Gupta, Foram N. Ashar, Joel S. Bader, Andrew B. West, Dan E. Arking
Software Mentions: 9
Published: almost 11 years ago

10.1371/journal.pgen.1008658

Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish
Cited by: 63
Author(s): Arne Jacobs, Madeleine Carruthers, Andrey A. Yurchenko, Н. В. Гордеева, S. S. Alekseyev, Oliver E. Hooker, Jong S. Leong, David R. Minkley, Eric B. Rondeau, Ben F. Koop, Colin E. Adams, Kathryn R. Elmer
Software Mentions: 8
Published: over 4 years ago

10.1186/s13059-015-0675-4

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer
Cited by: 42
Author(s): Eunsun Oh, Stephen M Christensen, Sindhu Ghanta, Jong Cheol Jeong, Octavian Bucur, Benjamin Glass, Laleh Montaser‐Kouhsari, Nicholas W. Knoblauch, Nicholas Bertos, Sadiq M.I. Saleh, Benjamin Haibe‐Kains, Morag Park, Andrew H. Beck
Software Mentions: 7
Published: over 9 years ago

10.1371/journal.pgen.1008662

Discovery of novel hepatocyte eQTLs in African Americans
Cited by: 19
Author(s): Yi Zhong, Tanima De, Cristina Alárcon, C. Sehwan Park, Bianca Lec, Minoli Perera
Software Mentions: 7
Published: over 4 years ago

10.1186/s13059-020-02098-w

Population variation in miRNAs and isomiRs and their impact on human immunity to infection
Cited by: 11
Author(s): Maxime Rotival, Katherine J. Siddle, Martin Silvert, Julien Pothlichet, Hélène Quach, Lluı́s Quintana-Murci
Software Mentions: 7
Published: over 4 years ago

10.1186/s13229-017-0119-y

Exaggerated CpH methylation in the autism-affected brain
Cited by: 30
Author(s): Shannon Ellis, Saloni Gupta, Anna Moes, Andrew B. West, Dan E. Arking
Software Mentions: 7
Published: almost 8 years ago

10.1186/s13059-017-1286-z

Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy
Cited by: 68
Author(s): Matthias Heinig, Michiel E. Adriaens, Sebastian Schäfer, Hanneke W. M. van Deutekom, Elisabeth M. Lodder, James S. Ware, Valentin Schneider, Leanne E. Felkin, Esther E. Creemers, Benjamin Meder, Hugo A. Katus, Frank Rühle, Monika Stoll, François Cambien, Eric Villard, Philippe Charron, András Varró, Nanette H. Bishopric, Alfred L. George, Cristobal dos Remedios, Aida Moreno‐Moral, Francesco Pesce, Anja Bauerfeind, Franz Rüschendorf, Carola Rintisch, Enrico Petretto, Paul J.R. Barton, Stuart A. Cook, Yigal M. Pinto, Connie R. Bezzina, Norbert Hübner
Software Mentions: 7
Published: about 7 years ago

10.1186/s13059-021-02450-8

INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants
Cited by: 3
Author(s): Chenyang Dong, Shane P. Simonett, Sun‐Young Shin, Donnie S. Stapleton, Kathryn L. Schueler, Gary A. Churchill, Leina Lu, Huan Liu, Fulai Jin, Yan Li, Alan D. Attie, Mark P. Keller, Sündüz Keleş
Software Mentions: 7
Published: over 3 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

10.1371/journal.pcbi.1008491

Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness
Cited by: 14
Author(s): Iván Cárcamo-Orive, Marc Henrion, Kuixi Zhu, Noam D. Beckmann, Paige Cundiff, Sara Moein, Zenan Zhang, Melissa Alamprese, Sunita L. D’Souza, Martin Wabitsch, Eric E. Schadt, Thomas Quertermous, Joshua W. Knowles, Rui Chang
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pgen.1009398

MOSTWAS: Multi-Omic Strategies for Transcriptome-Wide Association Studies
Cited by: 37
Author(s): Arjun Bhattacharya, Yun Li, Michael I. Love
Software Mentions: 6
Published: over 3 years ago

10.1186/s12872-021-02166-4

Identification of biomarkers associated with metabolic cardiovascular disease using mRNA-SNP-miRNA regulatory network analysis
Cited by: 4
Author(s): Zhiyuan Fan, Wei Peng, Zhiwen Wang, Ling Zhang, Kuo Li
Software Mentions: 6
Published: over 3 years ago

10.1172/jci.insight.143654

A longitudinal and transancestral analysis of DNA methylation patterns and disease activity in lupus patients
Cited by: 34
Author(s): Patrick Coit, Lourdes Ortíz-Fernández, Edith A. Lewis, W. Joseph McCune, Kathleen Maksimowicz-McKinnon, Amr H. Sawalha
Software Mentions: 6
Published: about 4 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

10.1186/s12864-017-4091-x

5-hydroxymethylcytosine is highly dynamic across human fetal brain development
Cited by: 56
Author(s): Helen Spiers, Eilís Hannon, Leonard C Schalkwyk, Nicholas John Bray, Jonathan Mill
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pgen.1005819

Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age
Cited by: 21
Author(s): Н. А. Иванов, Ran Tao, Joshua G. Chenoweth, Anna C. Brandtjen, Michelle I. Mighdoll, John D. Genova, Ronald D.G. McKay, Yankai Jia, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde, Andrew E. Jaffe
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.37110

Genetic predisposition to uterine leiomyoma is determined by loci for genitourinary development and genome stability
Cited by: 50
Author(s): Niko Välimäki, Heli Kuisma, Annukka Pasanen, Oskari Heikinheimo, Jari Sjöberg, Ralf Bützow, Nanna Sarvilinna, Hanna-Riikka Heinonen, Jaana Tolvanen, Simona Bramante, Tomas Tanskanen, Juha Auvinen, Outi Uimari, Amjad Alkodsi, Rainer Lehtonen, Eevi Kaasinen, Kimmo Palin, Lauri A. Aaltonen
Software Mentions: 5
Published: about 6 years ago

10.1038/srep46203

Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection
Cited by: 25
Author(s): Arun Kommadath, Hua Bao, Igseo Choi, James M. Reecy, James E. Koltes, Eric R. Fritz-Waters, Christopher J. Eisley, Jason R. Grant, R. Rowland, Christopher K. Tuggle, Jack C. M. Dekkers, Joan K. Lunney, Le Luo Guan, Paul Stothard, Graham Plastow
Software Mentions: 5
Published: over 7 years ago

10.1038/s41438-021-00606-y

Integrative genomics reveals paths to sex dimorphism in <i>Salix purpurea</i> L
Cited by: 8
Author(s): Brennan Hyden, Craig H. Carlson, Fred E. Gouker, Jeremy Schmutz, Kerrie Barry, Anna Lipzen, Aarti Sharma, Laura Sandor, Gerald A. Tuskan, Guanying Feng, Matthew S. Olson, Stephen P. DiFazio, Lawrence B. Smart
Software Mentions: 5
Published: over 3 years ago

10.1186/s13073-020-00779-6

Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci
Cited by: 24
Author(s): Tianlu Li, Lourdes Ortiz-Fernández, Eduardo Andrés-León, Laura Ciudad, Biola M. Javierre, Elena López‐Isac, Alfredo Guillén‐Del‐Castillo, Carmen Pilar Simeón-Aznar, Esteban Ballestar, Javier Martín
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0243857

Network preservation reveals shared and unique biological processes associated with chronic alcohol abuse in NAc and PFC
Cited by: 7
Author(s): Eric Vornholt, John W. Drake, Mohammed Mamdani, Gowon O. McMichael, Zachary N. Taylor, Silviu‐Alin Bacanu, Michael F. Miles, Vladimir I. Vladimirov
Software Mentions: 5
Published: almost 4 years ago

10.1186/s13059-019-1840-y

Genetic regulation of gene expression and splicing during a 10-year period of human aging
Cited by: 38
Author(s): Brunilda Balliu, Matthew G. Durrant, Olivia de Goede, Nathan S. Abell, Li X, Boxiang Liu, Michael J. Gloudemans, Naomi L. Cook, Kevin S. Smith, David A. Knowles, Mauro Pala, Francesco Cucca, David Schlessinger, Siddhartha Jaiswal, Chiara Sabatti, Lars Lind, Erik Ingelsson, Stephen B. Montgomery
Software Mentions: 5
Published: about 5 years ago

10.3389/fgene.2021.640266

DNA Methylation and Expression Profiles of Whole Blood in Parkinson’s Disease
Cited by: 28
Author(s): Adrienne Henderson, Qi Wang, Bessie Meechoovet, Ashley L. Siniard, Marcus Naymik, Matthew De Both, Matthew J. Huentelman, Richard J. Caselli, Erika Driver‐Dunckley, Travis Dunckley
Software Mentions: 4
Published: over 3 years ago

10.1016/j.ajhg.2018.04.011

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS
Cited by: 118
Author(s): Amanda Dobbyn, Laura Huckins, James Boocock, Laura Sloofman, Benjamin S. Glicksberg, Claudia Giambartolomei, Gabriel E. Hoffman, Thanneer M. Perumal, Kiran Girdhar, Yan Jiang, Towfique Raj, Douglas M. Ruderfer, Robin Kramer, Dalila Pinto, Schahram Akbarian, Panos Roussos, Enrico Domenici, Bernie Devlin, Pamela Sklar, Eli A. Stahl, Solveig K. Sieberts
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-017-1838-y

pulver: an R package for parallel ultra-rapid p-value computation for linear regression interaction terms
Cited by: 1
Author(s): Sophie Molnos, Clemens Baumbach, Simone Wahl, Martina Müller‐Nurasyid, Konstantin Strauch, Rui Wang-Sattler, Mélanie Waldenberger, Thomas Meitinger, Jerzy Adamski, Gabi Kastenmüller, Karsten Suhre, Annette Peters, Harald Grallert, Fabian J. Theis, Christian Gieger
Software Mentions: 4
Published: about 7 years ago

10.1038/s41597-020-00642-8

Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
Cited by: 65
Author(s): Solveig K. Sieberts, Thanneer M. Perumal, Minerva M. Carrasquillo, Mariet Allen, Joseph S. Reddy, Gabriel E. Hoffman, Kristen K. Dang, John N. Calley, Philip J. Ebert, James A. Eddy, X Wang, Anna K. Greenwood, Sara Mostafavi, Schahram Akbarian, Jaroslav Bendl, Michael S. Breen, Kristen J. Brennand, Leanne Brown, Andrew Browne, Joseph D. Buxbaum, Alex Charney, Andrew Chess, Lizette Couto, Greg Crawford, Olivia Devillers, Bernie Devlin, Amanda Dobbyn, Enrico Domenici, Michele Filosi, Elie Flatow, Nancy Francoeur, John F. Fullard, Sergio Espeso-Gil, Kiran Girdhar, Attila Gulyás-Kovács, Ruben C. Gur, Chang Gyu Hahn, Vahram Haroutunian, Mads E. Hauberg, Laura Huckins, Rivka Jacobov, Yonghua Jiang, Jessica Johnson, Bibi Kassim, Y Kim, Lambertus Klei, Robin Kramer, Mario Lauria, Thomas Lehner, David A. Lewis, Barbara K. Lipska, Kelsey S. Montgomery, Royce Park, Chaggai Rosenbluh, Panos Roussos, Douglas M. Ruderfer, Geetha Senthil, Hardik Shah, Laura Sloofman, Song Li, Eli Stahl, Patrick F. Sullivan, Roberto Visintainer, J Wang, Y C Wang, Jennifer Wiseman, Eva Xia, W Zhang, Elizabeth Zharovsky, Laura Addis, Sadiya N. Addo, David Airey, Matthias Arnold, David A. Bennett, Ying Bi, Knut Biber, Colette Blach, E Bradhsaw, Patrick McKinley Brennan, R Canet-Aviles, Shaolong Cao, A Cavalla, Yooree Chae, W W Chen, Joyce Cheng, David A. Collier, Jeffrey L. Dage, Eric B. Dammer, J Davis, J Davis, Derek Drake, Duc Duong, Brian J. Eastwood, Michelle E. Ehrlich, Benjamin M. Ellingson, Brett W. Engelmann, Sahar Esmaeeli-Nieh, Daniel Felsky, Cory C. Funk, Chris Gaiteri
Software Mentions: 4
Published: about 4 years ago

10.1534/g3.119.400821

TM3’seq: A Tagmentation-Mediated 3’ Sequencing Approach for Improving Scalability of RNAseq Experiments
Cited by: 28
Author(s): Luisa F. Pallares, Serge Picard, Julien F. Ayroles
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-018-30583-7

The landscape of the A-to-I RNA editome from 462 human genomes
Cited by: 14
Author(s): Zhangyi Ouyang, Chao Ren, Feng Liu, Gaole An, Xiaochen Bo, Wenjie Shu
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-016-1161-z

Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment
Cited by: 37
Author(s): Hong Pan, Joanna D. Holbrook, Neerja Karnani, Chee Keong Kwoh
Software Mentions: 3
Published: over 8 years ago

10.1186/s13073-020-00778-7

Mitochondrial DNA copy number can influence mortality and cardiovascular disease via methylation of nuclear DNA CpGs
Cited by: 49
Author(s): Christina A Castellani, Ryan J. Longchamps, Jason A. Sumpter, Charles E. Newcomb, John Lane, Megan L. Grove, Jan Bressler, Jennifer A. Brody, James S. Floyd, Traci M. Bartz, Kent D. Taylor, Penglong Wang, Adrienne Tin, Josef Coresh, James S. Pankow, Myriam Fornage, Eliseo Güallar, Brian O’Rourke, Nathan Pankratz, Chunyu Liu, Daniel Levy, Nona Sotoodehnia, Eric Boerwinkle, Dan E. Arking
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1007616

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning
Cited by: 46
Author(s): Janine Arloth, Gökçen Eraslan, Till F. M. Andlauer, Jade Martins, Stella Iurato, Brigitte Kühnel, Mélanie Waldenberger, Josef Frank, Ralf Gold, Bernhard Hemmer, Felix Luessi, Sandra Nischwitz, Friedemann Paul, Heinz Wiendl, Christian Gieger, Stefanie Heilmann‐Heimbach, Tim Kacprowski, Matthias Laudes, Thomas Meitinger, Annette Peters, Rajesh Rawal, Konstantin Strauch, Susanne Lucae, Bertram Müller‐Myhsok, Marcella Rietschel, Fabian J. Theis, Elisabeth B. Binder, Nikola S. Mueller
Software Mentions: 3
Published: almost 5 years ago

10.3389/fgene.2018.00294

Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline
Cited by: 23
Author(s): Shinya Tasaki, Chris Gaiteri, Sara Mostafavi, Lei Yu, Yanling Wang, Philip L. De Jager, David A. Bennett
Software Mentions: 3
Published: over 6 years ago

10.1186/s13148-019-0699-9

Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing
Cited by: 14
Author(s): Xiaojian Shao, Marie Hudson, Inés Colmegna, Celia Greenwood, Marvin J. Fritzler, Philip Awadalla, Tomi Pastinen, Sasha Bernatsky
Software Mentions: 3
Published: over 5 years ago

10.1186/s13148-021-01148-9

Identifying causal models between genetically regulated methylation patterns and gene expression in healthy colon tissue
Cited by: 6
Author(s): Anna Díez-Villanueva, Mireia Jordà, Robert Carreras‐Torres, Henar Alonso, David Cordero, Elisabet Guinó, Xavier Sanjuán, Cristina Santos, Ramón Salazar, Rebeca Sanz‐Pamplona, Vı́ctor Moreno
Software Mentions: 3
Published: over 3 years ago

10.3390/biology7010016

Integrated Systems Approach Reveals Sphingolipid Metabolism Pathway Dysregulation in Association with Late-Onset Alzheimer’s Disease
Cited by: 2
Author(s): John Malamon, Andres Kriete
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.4466

Global analysis of A-to-I RNA editing reveals association with common disease variants
Cited by: 20
Author(s): Oscar Franzén, Raili Ermel, Katyayani Sukhavasi, Rajeev Jain, Anamika Jain, Christer Betsholtz, Chiara Giannarelli, Jason C. Kovacic, Arno Ruusalepp, Josefin Skogsberg, Ke Hao, Eric E. Schadt, Johan Björkegren
Software Mentions: 3
Published: over 6 years ago

10.1186/s13059-019-1876-z

Non-coding RNAs underlie genetic predisposition to breast cancer
Cited by: 18
Author(s): Mahdi Moradi Marjaneh, Jonathan Beesley, Tracy A. O’Mara, Pamela Mukhopadhyay, Lambros T. Koufariotis, Stephen H. Kazakoff, Nehal Hussein, Laura Fachal, Nenad Bartoniček, Kristine M. Hillman, Susanne Kaufmann, Haran Sivakumaran, Chanel E. Smart, Amy E. McCart Reed, Kaltin Ferguson, Jodi M. Saunus, Sunil R. Lakhani, Daniel R. Barnes, Antonis C. Antoniou, Marcel E. Dinger, Nicola Waddell, Douglas F. Easton, Alison M. Dunning, Georgia Chenevix-Trench, Stacey L. Edwards, Juliet D. French
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41598-021-85544-4

Versatile knowledge guided network inference method for prioritizing key regulatory factors in multi-omics data
Cited by: 15
Author(s): Christoph Ogris, Yue Hu, Janine Arloth, Nikola S. Müller
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pgen.1007755

Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus
Cited by: 30
Author(s): Vivek Nanda, Ting Wang, Milos Pjanic, Boxiang Liu, Trieu Nguyen, Ljubica Matic, Ulf Hedin, Simon Koplev, Lijiang Ma, Oscar Franzén, Arno Ruusalepp, Eric E. Schadt, Johan Björkegren, Stephen B. Montgomery, M Snyder, Thomas Quertermous, Nicholas J. Leeper, Clint L. Miller
Software Mentions: 3
Published: about 6 years ago

10.1534/g3.114.013748

Quantitative Trait Locus Mapping Methods for Diversity Outbred Mice
Cited by: 183
Author(s): Daniel M. Gatti, Karen L. Svenson, Andrey A. Shabalin, Long Yang Wu, William Valdar, Petr Šimeček, Neal Goodwin, Riyan Cheng, Daniel Pomp, Abraham A. Palmer, Elissa J. Chesler, Karl W. Broman, Gary A. Churchill
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0137671

Integrating mRNA and miRNA Weighted Gene Co-Expression Networks with eQTLs in the Nucleus Accumbens of Subjects with Alcohol Dependence
Cited by: 70
Author(s): Mohammed Mamdani, Vernell Williamson, Gowon O. McMichael, Tana Blevins, Fazil Alıev, Amy Adkins, Laura M. Hack, Tim B. Bigdeli, Andrew D. van der Vaart, Bradley Todd Web, Silviu‐Alin Bacanu, Gursharan Kalsi, Kenneth S. Kendler, Michael F. Miles, Danielle M. Dick, Brien P. Riley, Catherine I. Dumur, Vladimir I. Vladimirov
Software Mentions: 3
Published: about 9 years ago

10.1038/s41598-019-55590-0

Genome-wide human brain eQTLs: In-depth analysis and insights using the UKBEC dataset
Cited by: 16
Author(s): Letitia M. F. Sng, Peter Thomson, Daniah Trabzuni
Software Mentions: 2
Published: almost 5 years ago

10.15252/emmm.201707838

Genomic structural variations lead to dysregulation of important coding and non‐coding <scp>RNA</scp> species in dilated cardiomyopathy
Cited by: 38
Author(s): Jan Haas, Stefan Mester, Alan Lai, Karen Frese, Farbod Sedaghat‐Hamedani, Elham Kayvanpour, Tobias Rausch, Rouven Nietsch, Jes‐Niels Boeckel, Avisha Carstensen, Mirko Völkers, Carsten Dietrich, Dietmar Pils, Ali Amr, Daniel Benjamin Holzer, Diana Bordalo, Daniel Oehler, Tanja Weis, Derliz Mereles, Sebastian Buss, Eva Riechert, Emil Wirsz, Maximilian Wuerstle, Jan O. Korbel, Andreas Keller, Hugo A. Katus, Andreas E. Posch, Benjamin Meder
Software Mentions: 2
Published: about 7 years ago

10.3389/fcell.2020.00492

Identification of Prognostic Biomarkers for Multiple Solid Tumors Using a Human Villi Development Model
Cited by: 9
Author(s): Botao Zhang, Zhengliang Wang, Hongxia Li, Feng Li, Wenbin Li, Shujun Cheng
Software Mentions: 2
Published: over 4 years ago

10.1186/s40478-021-01140-7

Expression of an alternatively spliced variant of SORL1 in neuronal dendrites is decreased in patients with Alzheimer’s disease
Cited by: 7
Author(s): Giulia Monti, Mads Kjølby, Anne Mette Jensen, Mariet Allen, Juliane Reiche, Peter L. Møller, Raquel Comaposada-Baró, Bartlomiej E. Zolkowski, Carmen Silvia de Campos Almeida Vieira, Margarita Melnikova Jørgensen, Ida E. Holm, Paul N. Valdmanis, Niels Wellner, Christian Bjerggaard Vægter, Sarah Lincoln, Anders Nykjær, Nilüfer Ertekin-Taner, Jessica E. Young, Mette Nyegaard, Olav M. Andersen
Software Mentions: 2
Published: over 3 years ago

10.3389/fnins.2018.00699

The Molecular and Neuropathological Consequences of Genetic Risk for Alzheimer's Dementia
Cited by: 43
Author(s): Shinya Tasaki, Chris Gaiteri, Sara Mostafavi, Philip L. De Jager, David A. Bennett
Software Mentions: 2
Published: about 6 years ago

10.3389/fonc.2020.602104

Cis- and Trans-Acting Expression Quantitative Trait Loci of Long Non-Coding RNA in 2,549 Cancers With Potential Clinical and Therapeutic Implications
Cited by: 11
Author(s): Wenzhi Li, Chaoqun Xu, Jin-Tao Guo, Ke Liu, Yudi Hu, Dan Wu, Hongqing Fang, Yun Zou, Ziwei Wei, Zhong Wang, Ying Zhou, Qiyuan Li
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2021.661635

Genetic Effects and Expression Patterns of the Nitrate Transporter (NRT) Gene Family in Populus tomentosa
Cited by: 14
Author(s): Леи Жао, Panfei Chen, Peng Liu, Yuepeng Song, Deqiang Zhang
Software Mentions: 2
Published: over 3 years ago

10.1534/g3.119.400549

Transcriptome-Wide Association Supplements Genome-Wide Association in <i>Zea mays</i>
Cited by: 54
Author(s): Karl A. Kremling, Christine H. Diepenbrock, Michael A. Gore, Edward S. Buckler, Nonoy Bandillo
Software Mentions: 2
Published: about 5 years ago

10.1186/s13059-016-1041-x

An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation
Cited by: 270
Author(s): Eilís Hannon, Emma Dempster, Joana Viana, Joe Burrage, Adam R. Smith, Robert C. MacDonald, David St Clair, Colette J Mustard, Gerome Breen, Sebastian Therman, Jaakko Kaprio, Timothea Toulopoulou, Hilleke E. Hulshoff Pol, Marc M. Bohlken, René S. Kahn, Igor Nenadić, Christina M. Hultman, Robin M. Murray, David A. Collier, Nick Bass, Hugh Gurling, Andrew McQuillin, Leonard C. Schalkwyk, Jonathan Mill
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pcbi.1005033

Bipartite Community Structure of eQTLs
Cited by: 50
Author(s): John Platig, Peter J. Castaldi, Dawn L. DeMeo, John Quackenbush
Software Mentions: 2
Published: about 8 years ago

10.1186/s13059-018-1601-3

Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation
Cited by: 86
Author(s): Lucas T. Husquin, Maxime Rotival, Maud Fagny, Hélène Quach, Nora Zidane, Lisa M. McEwen, Julia L. MacIsaac, Michæl S. Kobor, Hugues Aschard, Étienne Patin, Lluís Quintana‐Murci
Software Mentions: 2
Published: almost 6 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/s13073-018-0527-4

Elevated polygenic burden for autism is associated with differential DNA methylation at birth
Cited by: 79
Author(s): Eilís Hannon, Diana Schendel, Christine Ladd‐Acosta, Jakob Grove, Christine Søholm Hansen, Shan V. Andrews, David M. Hougaard, Michaeline Bresnahan, Ole Mors, Mads V. Hollegaard, Marie Bækvad‐Hansen, Mady Hornig, Preben Bo Mortensen, Anders D. Børglum, Thomas Werge, Marianne Giørtz Pedersen, Merete Nordentoft, Joseph D. Buxbaum, M. Daniele Fallin, Jonas Bybjerg‐Grauholm, Abraham Reichenberg, Jonathan Mill
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-6228-6

Analyses of inter-individual variations of sperm DNA methylation and their potential implications in cattle
Cited by: 17
Author(s): Shuli Liu, Lingzhao Fang, Yang Zhou, D. R. dos Santos, Ruidong Xiang, Hans D. Daetwyler, Amanda J. Chamberlain, John B. Cole, Congjun Li, Ying Yu, Li Ma, Shengli Zhang, George E. Liu
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-018-4997-y

Fasting and time of day independently modulate circadian rhythm relevant gene expression in adipose and skin tissue
Cited by: 6
Author(s): Alexessander Couto Alves, Craig A. Glastonbury, Julia S. El-Sayed Moustafa, Kerrin S. Small
Software Mentions: 2
Published: about 6 years ago

10.1016/j.jaci.2019.12.910

Lymphocyte DNA methylation mediates genetic risk at shared immune-mediated disease loci
Cited by: 18
Author(s): Alexander D. Clark, Nisha Nair, Amy E. Anderson, Nishanthi Thalayasingam, Najib Naamane, Andrew Skelton, Julie Diboll, Anne Barton, Stephen Eyre, John D. Isaacs, Arthur G. Pratt, Louise N. Reynard
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-019-51592-0

Resistin expression in human monocytes is controlled by two linked promoter SNPs mediating NFKB p50/p50 binding and C-methylation
Cited by: 8
Author(s): Dilip Kumar, Bernett Lee, Kia Joo Puan, Wendy Lee, Boris San Luis, Nurhashikin Yusof, Anand Kumar Andiappan, Ricardo del Rosario, Jérémie Poschmann, Pavanish Kumar, Gennaro DeLibero, Amit Singhal, Shyam Prabhakar, Yun Wang, Michael Poidinger, Olaf Rötzschke
Software Mentions: 2
Published: about 5 years ago

10.1038/s41598-020-74121-w

Genetic regulation of gene expression of MIF family members in lung tissue
Cited by: 8
Author(s): Laura Flórez-Sampedro, Corry‐Anke Brandsma, Maaike de Vries, Wim Timens, Rene Bults, Cornelis J Vermeulen, Maarten van den Berge, Ma’en Obeidat, Philippe Joubert, David C. Nickle, Gerrit J. Poelarends, Alen Faiz, Barbro N. Melgert
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-021-86690-5

Variable expression quantitative trait loci analysis of breast cancer risk variants
Cited by: 4
Author(s): George A. R. Wiggins, Michael A. Black, Anita K. Dunbier, Tony R. Merriman, John F. Pearson, Logan C. Walker
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0067899

An Information-Theoretic Machine Learning Approach to Expression QTL Analysis
Cited by: 26
Author(s): Tao Huang, Yu-Dong Cai
Software Mentions: 1
Published: over 11 years ago

10.1111/jcmm.14315

Multi‐omics integrative analysis identified SNP‐methylation‐mRNA: Interaction in peripheral blood mononuclear cells
Cited by: 9
Author(s): Yihua Lu, Binghua Wang, Fei Jiang, Xing‐Bo Mo, Long‐Fei Wu, Pei He, Xin Lu, Fei‐Yan Deng, Shu‐Feng Lei
Software Mentions: 1
Published: over 5 years ago

10.1186/s12859-021-04307-0

A pipeline for RNA-seq based eQTL analysis with automated quality control procedures
Cited by: 13
Author(s): Tao Wang, Yongzhuang Liu, Junpeng Ruan, Xianjun Dong, Yadong Wang, Jiajie Peng
Software Mentions: 1
Published: over 3 years ago

10.1002/ana.24840

Genetic variation at 16q24.2 is associated with small vessel stroke
Cited by: 68
Author(s): Matthew Traylor, Rainer Malik, Mike A. Nalls, Ioana Cotlarciuc, Farid Radmanesh, Guðmar Þorleifsson, Ken B. Hanscombe, Carl D. Langefeld, Danish Saleheen, Natalia S. Rost, İdil Yet, Tim D. Spector, Jordana T. Bell, Eilís Hannon, Jonathan Mill, Ganesh Chauhan, Stéphanie Debette, Joshua C. Bis, W. T. Longstreth, M. Arfan Ikram, Lenore J. Launer, Sudha Seshadri, Monica Anne Hamilton‐Bruce, Jordi Jiménez‐Conde, John W. Cole, Reinhold Schmidt, Agnieszka Słowik, Robin Lemmens, Arne Lindgren, Olle Melander, Raji P. Grewal, Ralph L. Sacco, Tatjana Rundek, Kathryn M. Rexrode, Donna K. Arnett, Julie A. Johnson, Oscar Benavente, Sylvia Wasssertheil-Smoller, Lee J, Sara L. Pulit, Quenna Wong, Stephen S. Rich, Paul I. W. de Bakker, Patrick F. McArdle, Daniel Woo, Chris Anderson, Huichun Xu, Laura Heitsch, Myriam Fornage, Christina Jern, Kári Stefánsson, Unnur Þorsteinsdóttir, Sólveig Grétarsdóttir, Cathryn M. Lewis, Pankaj Sharma, Cathie Sudlow, Peter M. Rothwell, Giorgio B. Boncoraglio, Vincent Thijs, Christopher Levi, James F. Meschia, Jonathan Rosand, Steven J. Kittner, Braxton D. Mitchell, Martin Dichgans, Bradford B. Worrall, Hugh S. Markus
Software Mentions: 1
Published: over 7 years ago

10.3390/genes12081174

Search for a Functional Genetic Variant Mimicking the Effect of SGLT2 Inhibitor Treatment
Cited by: 2
Author(s): Siqi Wang, M. Abdullah Said, Hilde E. Groot, Peter J. van der Most, Chris H. L. Thio, Yordi J. van de Vegte, Niek Verweij, Harold Snieder, Pim van der Harst
Software Mentions: 1
Published: over 3 years ago

10.3390/genes8060167

Effects of Type 1 Diabetes Risk Alleles on Immune Cell Gene Expression
Cited by: 15
Author(s): Ram Ramesh, Grant Morahan
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-49617-9

Peripheral Blood Mononuclear Cell Oxytocin and Vasopressin Receptor Expression Positively Correlates with Social and Behavioral Function in Children with Autism
Cited by: 13
Author(s): Irena Voinsky, Sirish C. Bennuri, Julie Svigals, Richard E. Frye, Shannon Rose, David Genevieve
Software Mentions: 1
Published: about 5 years ago

10.12688/wellcomeopenres.15846.2

Variants associated with HHIP expression have sex-differential effects on lung function
Cited by: 3
Author(s): Katherine A. Fawcett, Ma’en Obeidat, Carl Melbourne, Nick Shrine, Anna L Guyatt, Catherine John, Jian’an Luan, Anne Richmond, Marta R Moksnes, Raquel Granell, Stefan Weiß, Medea Imboden, Sebastian May-Wilson, Pirro G. Hysi, Thibaud Boutin, Laura Portas, Claudia Flexeder, Sarah E. Harris, Carol A. Wang, Leo Pekka Lyytikäinen, Teemu Palviainen, Rachel E. Foong, Dirk Keidel, Cosetta Minelli, Claudia Langenberg, Yohan Bossé, Maarten van den Berge, Don D. Sin, Ke Hao, Archie Campbell, David J. Porteous, Sandosh Padmanabhan, Blair H. Smith, David M. Evans, Sue Ring, Arnulf Langhammer, Kristian Hveem, Cristen J. Willer, Ralf Ewert, Beate Stubbe, Nicola Pirastu, Lucija Klarić, Peter K. Joshi, Karina Patasova, Massimo Mangino, Ozren Polašek, John M. Starr, Stefan Karrasch, Konstantin Strauch, Thomas Meitinger, Igor Rudan, Taina Rantanen, Kirsi H. Pietiläinen, Mika Kähönen, Olli T. Raitakari, Graham Hall, Peter D. Sly, Craig E. Pennell, Jaakko Kaprio, Terho Lehtimäki, Véronique Vitart, Ian J. Deary, Debbie Jarvis, James F. Wilson, Tim D. Spector, Nicole Probst‐Hensch, Nicholas J. Wareham, Henry Völzke, John Henderson, David P. Strachan, Ben Brumpton, Caroline Hayward, Ian P. Hall, Martin D. Tobin, Louise V. Wain
Software Mentions: 1
Published: over 3 years ago

10.1186/s12859-019-3314-3

Bayesian differential analysis of gene regulatory networks exploiting genetic perturbations
Cited by: 2
Author(s): Yan Li, Dayou Liu, Tengfei Li, Yi-hua Zhu
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pcbi.1003790

MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis
Cited by: 33
Author(s): Seungyeul Yoo, Tao Huang, Joshua D. Campbell, Eunjee Lee, Zhidong Tu, Mark W. Geraci, Charles A. Powell, Eric E. Schadt, Avrum Spira, Jun Zhu
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pgen.1005694

Transcript Expression Data from Human Islets Links Regulatory Signals from Genome-Wide Association Studies for Type 2 Diabetes and Glycemic Traits to Their Downstream Effectors
Cited by: 171
Author(s): Martijn van de Bunt, Jocelyn E. Manning Fox, Xiao-Qing Dai, Amy Barrett, Caleb L. Grey, Lei Li, Amanda J. Bennett, Paul Johnson, R. V. Rajotte, Kyle J. Gaulton, Emmanouil T. Dermitzakis, Patrick E. MacDonald, Mark I. McCarthy, Anna L. Gloyn
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12859-014-0392-0

Meta-eQTL: a tool set for flexible eQTL meta-analysis
Cited by: 7
Author(s): Antonio Fabio Di Narzo, Haoxiang Cheng, Jianwei Lu, Ke Hao
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12711-020-00579-x

Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits
Cited by: 16
Author(s): Yan Liu, Xiaolei Liu, Zhiwei Zheng, Tingting Ma, Ying Liu, Huan Long, Hui‐Ling Cheng, Ming Fang, Jing Gong, Xinyun Li, Shuhong Zhao, Xuewen Xu
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.pgen.1008718

Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits
Cited by: 78
Author(s): Suzanne Vogelezang, Jonathan P. Bradfield, Tarunveer S. Ahluwalia, John A. Curtin, Timo A. Lakka, Niels Grarup, Markus Scholz, Peter J. van der Most, Claire Monnereau, Evie Stergiakouli, Anni Heiskala, Momoko Horikoshi, Iryna O. Fedko, Natàlia Vilor‐Tejedor, Diana L. Cousminer, Marie Standl, Carol A. Wang, Jorma Viikari, Frank Geller, Carmen Íñiguez, Niina Pitkänen, Alessandra Chesi, Jonas Bacelis, Loïc Yengo, Maties Torrent, Ιωάννα Ντάλλα, Øyvind Helgeland, Saskia Selzam, Judith M. Vonk, Mohammed H. Zafarmand, Barbara Heude, I. Sadaf Farooqi, Akram Alyass, Robin N Beaumont, Christian Theil Have, Peter Rzehak, José Ramón Bilbao, Theresia M. Schnurr, Inês Barroso, Klaus Bønnelykke, Lawrence J. Beilin, Lisbeth Carstensen, Charles Munier, Bo Chawes, Karine Clément, Ricardo Closa‐Monasterolo, Adnan Čustović, Johan G. Eriksson, Joaquín Escribano, Maria M. Groen-Blokhuis, Veit Grote, Dariusz Gruszfeld, Hákon Hákonarson, Torben Hansen, Andrew T. Hattersley, Mette Hollensted, Jouke‐Jan Hottenga, Elina Hyppönen, Stefan Johansson, Raimo Joro, Mika Kähönen, Ville Karhunen, Wieland Kieß, Bridget Knight, Berthold Koletzko, Andreas Kühnapfel, Kathrin Landgraf, Jean‐Paul Langhendries, Terho Lehtimäki, Jaakko T. Leinonen, Aihuali Li, Virpi Lindi, Estelle Lowry, Mariona Bustamante, Carolina Medina‐Gomez, Mads Melbye, Kim F. Michaelsen, Camilla Schmidt Morgen, Trevor A. Mori, Tenna Ruest Haarmark Nielsen, Harri Niinikoski, Albertine J. Oldehinkel, Katja Pahkala, Kalliope Panoutsopoulou, Oluf Pedersen, Craig E. Pennell, Christine Power, Sijmen A. Reijneveld, Fernando Rivadeneira, Angela Simpson, Peter D. Sly, Jakob Stokholm, Kook K Teo, Elisabeth Thiering, Nicholas J. Timpson, André G. Uitterlinden, Catharina E. M. van Beijsterveldt, Barbera D. C. van Schaik, Marc Vaudel, Elvira Verduci, Rebecca K. Vinding, Mandy Vogel, Eleftheria Zeggini, Sylvain Sebért, Mads Vendelbo Lind, Christopher D. Brown, Loreto Santa‐Marina, Eva Reischl, Christine Frithioff-Bøjsøe, David Meyre, Eleanor Wheeler, Ken K. Ong, Ellen Aagaard Nøhr, Tanja G. M. Vrijkotte, Gerard H. Koppelman, Robert Plomin, Pål Rasmus Njølstad, George Dedoussis, Philippe Froguel, Thorkild I A Sørensen, Bo Jacobsson, Rachel M. Freathy, Babette S. Zemel, Olli T. Raitakari, Martine Vrijheid, Bjarke Feenstra, Leo-Pekka Lyytikäinen, Harold Snieder, Holger Kirsten, Patrick G. Holt, Joachim Heinrich, Elisabeth Widén, Jordi Sunyer, Dorret I. Boomsma, Marjo‐Riitta Järvelin, Antje Körner, George Davey Smith, Jens-Christian Holm, Mustafa Atalay, Clare Murray, Hans Bisgaard, Mark McCarthy, Vincent W.V. Jaddoe, Struan F.A. Grant, Janine F. Felix
Software Mentions: 1
Published: about 4 years ago

10.1186/s12864-016-3258-1

ulfasQTL: an ultra-fast method of composite splicing QTL analysis
Cited by: 12
Author(s): Qian Yang, Yue Hu, Jun Li, Xuegong Zhang
Software Mentions: 1
Published: almost 8 years ago

Projects: cran: MatrixEQTL

Papers Mentioning MatrixEQTL 81