cran: coloc | Projects | Ecosyste.ms: Papers

10.1016/j.xpro.2021.100768

A computational approach for identification of core modules from a co-expression network and GWAS data
Cited by: 0
Author(s): Olivia L. Sabik, Cheryl Ackert‐Bicknell, Charles R. Farber
Software Mentions: 16
Published: about 3 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.pgen.1008530

Genetic variation in GC and CYP2R1 affects 25-hydroxyvitamin D concentration and skeletal parameters: A genome-wide association study in 24-month-old Finnish children
Cited by: 12
Author(s): Anders Kämpe, Maria Enlund-Cerullo, Saara Valkama, Elisa Holmlund-Suila, Jenni Rosendahl, Helena Hauta-alus, Minna Pekkinen, Sture Andersson, Outi Mäkitie
Software Mentions: 10
Published: almost 5 years ago

10.7554/eLife.41673

Genetic effects on promoter usage are highly context-specific and contribute to complex traits
Cited by: 48
Author(s): Kaur Alasoo, Julia Rodrigues, John Danesh, Daniel F. Freitag, Dirk S. Paul, Daniel J Gaffney
Software Mentions: 8
Published: over 5 years ago

10.1186/s13073-020-00806-6

Whole blood co-expression modules associate with metabolic traits and type 2 diabetes: an IMI-DIRECT study
Cited by: 8
Author(s): Valborg Guðmundsdóttir, Helle Pedersen, Gianluca Mazzoni, Kristine H. Allin, Anna Artati, Joline W.J. Beulens, Karina Banasik, Caroline Brorsson, Henna Cederberg, Elizaveta Chabanova, Federico De Masi, Petra Elders, Ian Forgie, G Giordano, Harald Grallert, Ramneek Gupta, Mark Haid, Torben Hansen, Tue H. Hansen, Andrew T. Hattersley, Alison Heggie, Mun‐Gwan Hong, Angus G. Jones, Robert W. Koivula, Tarja Kokkola, Markku Laakso, Peter Løngreen, Anubha Mahajan, Andrea Mari, Colin N.A. Palmer, Donna McEvoy, Petra B. Musholt, Imre Pávó, Cornelia Prehn, Hartmut Ruetten, Martin Ridderstråle, Femke Rutters, Sapna Sharma, Roderick C. Slieker, Ali Syed, Juan Fernández Tajes, Cecilia Engel Thomas, Henrik S. Thomsen, Jagadish Vangipurapu, Henrik Vestergaard, Ana Viñuela, Agata Wesolowska-Andersen, Mark Walker, Jerzy Adamski, Jochen M. Schwenk, Mark McCarthy, Ewan R. Pearson, Emmanouil T. Dermitzakis, Paul W. Franks, Oluf Pedersen, Søren Brunak
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41398-020-0710-4

Large epigenome-wide association study of childhood ADHD identifies peripheral DNA methylation associated with disease and polygenic risk burden
Cited by: 49
Author(s): Michael A. Mooney, Peter Ryabinin, Beth Wilmot, Priya Bhatt, Jonathan Mill, Joel T. Nigg
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pgen.1005908

Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease
Cited by: 83
Author(s): James E. Peters, Paul Lyons, James C. Lee, Alison F. Richard, Mary D Fortune, Paul Newcombe, Sylvia Richardson, Kenneth G. C. Smith
Software Mentions: 6
Published: over 8 years ago

10.1016/j.ajhg.2019.05.010

Genetic and Epigenetic Fine Mapping of Complex Trait Associated Loci in the Human Liver
Cited by: 33
Author(s): Minal Çalışkan, Elisabetta Manduchi, Harish Rao, Julian A. Segert, Márcia Holsbach Beltrame, Marco Trizzino, YoSon Park, Samuel White Baker, Alessandra Chesi, Matthew E. Johnson, Kenyaita M. Hodge, Michelle E. Leonard, Bao‐Li Loza, Xin Dong, Andrea M. Berrido, Nicholas J. Hand, Robert C. Bauer, Andrew D. Wells, Kim M. Olthoff, Abraham Shaked, Daniel J. Rader, Struan F.A. Grant, Christopher D. Brown
Software Mentions: 6
Published: about 5 years ago

10.7554/eLife.57492

Alternative polyadenylation mediates genetic regulation of gene expression
Cited by: 33
Author(s): Briana E Mittleman, Sebastian Pott, Shane Warland, Teng Zeng, Zepeng Mu, Mayher Kaur, Yoav Gilad, Yang Li
Software Mentions: 5
Published: about 4 years ago

10.7554/eLife.48476

Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease
Cited by: 29
Author(s): Matteo D’Antonio, Joaquin Reyna, David Jakubosky, Maureen D. Donovan, Marc Jan Bonder, Hiroko Matsui, Oliver Stegle, Naoki Nariai, Agnieszka D’Antonio‐Chronowska, Kelly A. Frazer
Software Mentions: 5
Published: almost 5 years ago

10.7554/eLife.33480

Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes
Cited by: 86
Author(s): David A. Knowles, Courtney K Burrows, John Blischak, Kristen Patterson, Daniel J. Serie, Nadine Norton, Carole Ober, Jonathan K. Pritchard, Yoav Gilad
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-021-88827-y

A web-based survey on various symptoms of computer vision syndrome and the genetic understanding based on a multi-trait genome-wide association study
Cited by: 4
Author(s): Keito Yoshimura, Yuji Morita, Kenji Konomi, Sachiko Ishida, Daisuke Fujiwara, Keisuke Kobayashi, Masami Tanaka
Software Mentions: 5
Published: over 3 years ago

10.1186/s13148-021-01041-5

Epigenome-wide association study of whole blood gene expression in Framingham Heart Study participants provides molecular insight into the potential role of CHRNA5 in cigarette smoking-related lung diseases
Cited by: 11
Author(s): Chen Yao, Roby Joehanes, Rory Wilson, Toshiko Tanaka, Luigi Ferrucci, Anja Kretschmer, Holger Prokisch, Katharina Schramm, Christian Gieger, Annette Peters, Mélanie Waldenberger, Carola Marzi, Christian Herder, Daniel Levy
Software Mentions: 4
Published: over 3 years ago

10.1002/gepi.22374

Multi‐tissue transcriptome‐wide association studies
Cited by: 8
Author(s): Nastasiya F. Grinberg, Chris Wallace
Software Mentions: 4
Published: over 3 years ago

10.1186/s13059-020-01997-2

Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts
Cited by: 29
Author(s): Benjamin H. Mullin, Jennifer Tickner, Kun Zhu, Jacob Kenny, Shelby Mullin, Suzanne J. Brown, Frank Dudbridge, Nathan J. Pavlos, Edward S. Mocarski, John P. Walsh, Jiake Xu, Scott G. Wilson
Software Mentions: 4
Published: over 4 years ago

10.1186/s13073-020-00754-1

Multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults
Cited by: 20
Author(s): Robert F. Hillary, Daniel Trejo Baños, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, Sven Erik Ojavee, Qian Zhang, David C. Liewald, Craig W. Ritchie, Kathryn Evans, Elliot M. Tucker‐Drob, Naomi R. Wray, Allan F. McRae, Peter M. Visscher, Ian J. Deary, Matthew R. Robinson, Riccardo E. Marioni
Software Mentions: 4
Published: about 4 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

10.1371/journal.pgen.1008104

A meta-analysis of genome-wide association studies of epigenetic age acceleration
Cited by: 77
Author(s): Jude Gibson, Tom C. Russ, Toni‐Kim Clarke, David M. Howard, Robert F. Hillary, Kathryn Evans, Richard M Martin, Mairead Lesley Bermingham, Stewart W. Morris, Archie Campbell, Caroline Hayward, Alison Murray, David J. Porteous, Steve Horvath, Ake T. Lu, Andrew M. McIntosh, Heather C. Whalley, Riccardo E. Marioni
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pgen.1009440

A more accurate method for colocalisation analysis allowing for multiple causal variants
Cited by: 87
Author(s): Chris Wallace
Software Mentions: 4
Published: almost 3 years ago

10.1186/s12859-021-04170-z

Estimating colocalization probability from limited summary statistics
Cited by: 3
Author(s): Emily King, Fengjiao Dunbar, J. Wade Davis, Jacob F. Degner
Software Mentions: 4
Published: over 3 years ago

10.3390/cells9102257

Pleiotropic Locus 15q24.1 Reveals a Gender-Specific Association with Neovascular but Not Atrophic Age-Related Macular Degeneration (AMD)
Cited by: 5
Author(s): Christina Kiel, Tobias Strunz, Felix Graßmann, Bernhard H. F. Weber
Software Mentions: 4
Published: almost 4 years ago

10.1126/sciadv.aaw3095

GWAS on longitudinal growth traits reveals different genetic factors influencing infant, child, and adult BMI
Cited by: 76
Author(s): Alexessander Couto Alves, N. Maneka G. De Silva, Ville Karhunen, Ulla Sovio, Shikta Das, H. Rob Taal, Nicole M. Warrington, Arie Y. Lewin, Marika Kaakinen, Diana L. Cousminer, Elisabeth Thiering, Nicholas J. Timpson, Tom A Bond, Estelle Lowry, Christopher D. Brown, Xavier Estivill, Virpi Lindi, Jonathan P. Bradfield, Frank Geller, Doug Speed, Lachlan Coin, Marie Loh, Sheila J. Barton, Lawrence J. Beilin, Hans Bisgaard, Klaus Bønnelykke, Rohia Alili, Ida J. Hatoum, Katharina Schramm, Rufus Cartwright, Charles Munier, Vincenzo Salerno, Karine Clément, Annique Claringbould, Cornelia M. van Duijn, Elena Moltchanova, Johan G. Eriksson, Cathy E. Elks, Bjarke Feenstra, Claudia Flexeder, Stephen Franks, Timothy M. Frayling, Rachel M. Freathy, Paul Elliott, Elisabeth Widén, Hákon Hákonarson, Andrew T. Hattersley, Alina Rodriguez, Marco Banterle, Joachim Heinrich, Barbara Heude, John W. Holloway, Albert Hofman, Elina Hyppönen, Hazel Inskip, Lee M. Kaplan, Åsa K. Hedman, Esa Läärä, Holger Prokisch, Harald Grallert, Timo A. Lakka, Debbie A. Lawlor, Mads Melbye, Tarunveer S. Ahluwalia, M. Marinelli, Iona Y. Millwood, Lyle J. Palmer, Craig E. Pennell, John Perry, Susan M. Ring, Markku J. Savolainen, Fernando Rivadeneira, Marie Standl, Jordi Sunyer, Carla M. T. Tiesler, André G. Uitterlinden, William Schierding, Justin M. O’Sullivan, Inga Prokopenko, Karl‐Heinz Herzig, George Davey Smith, Paul O’Reilly, Janine F. Felix, Jessica L. Buxton, Alexandra I. F. Blakemore, Ken K. Ong, Vincent W. V. Jaddoe, Struan F.A. Grant, Sylvain Sebért, Mark McCarthy, Marjo‐Riitta Järvelin
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1008934

A mega-analysis of expression quantitative trait loci in retinal tissue
Cited by: 20
Author(s): Tobias Strunz, Christina Kiel, Felix Graßmann, Rinki Ratnapriya, Madeline Kwicklis, Marcus Karlstetter, Sascha Fauser, Nicole Arend, Anand Swaroop, Thomas Langmann, Armin Wolf, Bernhard H. F. Weber
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pcbi.1007778

A powerful and versatile colocalization test
Cited by: 10
Author(s): Yangqing Deng, Wei Pan
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pcbi.1008336

LocusFocus: Web-based colocalization for the annotation and functional follow-up of GWAS
Cited by: 25
Author(s): Naim Panjwani, Fan Wang, Scott Mastromatteo, Allen Bao, Cheng Wang, Gengming He, Jiafen Gong, Johanna M. Rommens, Lei Sun, Lisa J. Strug
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.1008720

Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses
Cited by: 144
Author(s): Chris Wallace
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1004383

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics
Cited by: 1,738
Author(s): Claudia Giambartolomei, Damjan Vukcevic, Eric E. Schadt, Lude Franke, Aroon D. Hingorani, Chris Wallace, Vincent Plagnol
Software Mentions: 3
Published: over 10 years ago

10.3390/cells10092395

Assigning Co-Regulated Human Genes and Regulatory Gene Clusters
Cited by: 4
Author(s): Tobias Strunz, Martin Kellner, Christina Kiel, Bernhard H. F. Weber
Software Mentions: 3
Published: about 3 years ago

10.1186/s13059-021-02287-1

Genetic variation and microRNA targeting of A-to-I RNA editing fine tune human tissue transcriptomes
Cited by: 19
Author(s): Eddie Park, Yan Jiang, Lili Hao, Jingyi Hui, Yi Xing
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-82169-5

Transcriptome-wide Mendelian randomization study prioritising novel tissue-dependent genes for glioma susceptibility
Cited by: 6
Author(s): Jamie Robinson, Richard M. Martin, Spiridon Tsavachidis, Amy Howell, Caroline L Relton, Georgina Armstrong, Melissa L. Bondy, Jie Zheng, Kathreena M. Kurian
Software Mentions: 3
Published: over 3 years ago

10.1101/2021.08.13.21261910

Gene-environment interaction analysis incorporating sex, cardiometabolic diseases, and multiple deprivation index reveals novel genetic associations with COVID-19 severity
Cited by: 0
Author(s): Kenneth Westerman, Joanna Lin, Magda Sevilla-Gonzalez, Beza Tadess, Alisa K. Manning, Casey Marchek
Software Mentions: 3
Published: about 3 years ago

10.1186/s13073-021-00971-2

Genome-wide analyses of multiple obesity-related cytokines and hormones informs biology of cardiometabolic traits
Cited by: 5
Author(s): Karlijn Meeks, Amy R. Bentley, Mateus H. Gouveia, Guanjie Chen, Jie Zhou, Lijing Lin, Adebowale Adeyemo, Ayo P. Doumatey, Charles Rotimi
Software Mentions: 2
Published: almost 3 years ago

10.1172/jci.insight.144392

Proteomic profiling reveals biomarkers and pathways in type 2 diabetes risk
Cited by: 23
Author(s): Debby Ngo, Mark D. Benson, Jonathan Z. Long, Zsu-Zsu Chen, Ruiqi Wang, Anjali K. Nath, Michelle J. Keyes, Dongxiao Shen, Sumita Sinha, Eric Kuhn, Jordan Morningstar, Xu Shi, Bennet Peterson, Christopher T. Chan, Daniel H. Katz, Usman A. Tahir, Laurie Farrell, Olle Melander, Jonathan D. Mosley, Steven A. Carr, Ramachandran S. Vasan, Martin G. Larson, J. Gustav Smith, Thomas J. Wang, Qiong Yang, Robert E. Gerszten
Software Mentions: 2
Published: over 3 years ago

10.1002/jbmr.3605

Identification of Novel Loci Associated With Hip Shape: A Meta‐Analysis of Genomewide Association Studies
Cited by: 44
Author(s): Denis Baird, Daniel S. Evans, Frederick Kamanu, Jennifer S. Gregory, Fiona Saunders, Claudiu V. Giuraniuc, Rebecca Barr, Richard M. Aspden, Deborah A. Jenkins, Douglas P. Kiel, Eric S. Orwoll, Steven R. Cummings, Nancy E Lane, Benjamin H. Mullin, Frances Williams, J. Brent Richards, Scott G. Wilson, Tim D. Spector, Benjamin G Faber, Debbie A. Lawlor, Elin Grundberg, Claes Ohlsson, Ulrika Pettersson-Kymmer, Terence D. Capellini, Daniel Richard, Thomas Beck, David M. Evans, Lavinia Paternoster, David Karasik, Jonathan H Tobias
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.ppat.1007372

Apolipoprotein E is an HIV-1-inducible inhibitor of viral production and infectivity in macrophages
Cited by: 16
Author(s): Rokeya Siddiqui, Shinya Suzu, Munetaka Ueno, Hesham Nasser, Ryota Koba, Farzana Bhuyan, Osamu Noyori, Sofiane Hamidi, Guojun Sheng, Mariko Yasuda-Inoue, Takayuki Hishiki, Sayaka Sukegawa, Eri Miyagi, Klaus Strebel, Shuzo Matsushita, Kunitada Shimotohno, Yasuo Ariumi
Software Mentions: 2
Published: almost 6 years ago

10.1039/c8ra00265g

Pyridazine-bridged cationic diiridium complexes as potential dual-mode bioimaging probes
Cited by: 13
Author(s): Ruth Daniels, Luke K. McKenzie, Jonathan R. Shewring, Julia A. Weinstein, Valery N. Kozhevnikov, Helen E. Bryant
Software Mentions: 2
Published: over 6 years ago

10.3389/fpls.2013.00238

ARP2/3 localization in Arabidopsis leaf pavement cells: a diversity of intracellular pools and cytoskeletal interactions
Cited by: 33
Author(s): Chunhua Zhang, Eileen L. Mallery, Daniel B. Szymanski
Software Mentions: 2
Published: over 11 years ago

10.1007/s00125-021-05428-0

Analysis of overlapping genetic association in type 1 and type 2 diabetes
Cited by: 19
Author(s): Jamie Inshaw, Carlo Sidore, Francesco Cucca, M. Irina Stefana, Crouch Djm., Mark McCarthy, Anubha Mahajan, John A. Todd
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-019-45747-2

Interleukin-18 as a drug repositioning opportunity for inflammatory bowel disease: A Mendelian randomization study
Cited by: 22
Author(s): Lauren Mokry, Sirui Zhou, Cong Guo, Robert A. Scott, Luke Devey, Claudia Langenberg, Nick Wareham, Dawn Waterworth, Lon R. Cardon, Philippe Sanséau, George Davey Smith, J. Brent Richards
Software Mentions: 2
Published: about 5 years ago

10.1016/j.ajhg.2021.03.009

A catalog of GWAS fine-mapping efforts in autoimmune disease
Cited by: 20
Author(s): Minal Çalışkan, Christopher D. Brown, Joseph C. Maranville
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0074687

The Rab11 Effector Protein FIP1 Regulates Adiponectin Trafficking and Secretion
Cited by: 22
Author(s): Brian P. Carson, Josep Maria del Bas, José María Moreno-Navarrete, José Manuel Fernández‐Real, Sílvia Mora
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pgen.1006646

Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization
Cited by: 186
Author(s): Xiaoquan Wen, Roger Piqué-Regi, Francesca Luca
Software Mentions: 2
Published: over 7 years ago

10.1016/j.ajhg.2020.04.007

Characterizing the Causal Pathway for Genetic Variants Associated with Neurological Phenotypes Using Human Brain-Derived Proteome Data
Cited by: 50
Author(s): Nelson Kibinge, Caroline L Relton, Tom R. Gaunt, Tom G Richardson
Software Mentions: 2
Published: over 4 years ago

10.1002/ijc.32947

Mendelian randomisation analysis of circulating adipokines and C‐reactive protein on breast cancer risk
Cited by: 19
Author(s): Tim Robinson, Richard M. Martin, James Yarmolinsky
Software Mentions: 2
Published: over 4 years ago

10.1186/s13024-021-00449-0

Beyond association: successes and challenges in linking non-coding genetic variation to functional consequences that modulate Alzheimer’s disease risk
Cited by: 18
Author(s): Gloriia Novikova, Shea J. Andrews, Alan E. Renton, Edoardo Marcora
Software Mentions: 2
Published: over 3 years ago

10.3390/molecules21101382

Towards Water Soluble Mitochondria-Targeting Theranostic Osmium(II) Triazole-Based Complexes
Cited by: 16
Author(s): Salem A. E. Omar, Paul A. Scattergood, Luke K. McKenzie, Helen E. Bryant, Julia A. Weinstein, Paul I. P. Elliott
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12863-021-00975-2

Mapping methylation quantitative trait loci in cardiac tissues nominates risk loci and biological pathways in congenital heart disease
Cited by: 6
Author(s): Ming Li, Chao Lyu, Manyan Huang, Catherine Do, Benjamin Tycko, Philip J. Lupo, Stewart L. MacLeod, Christopher E. Randolph, Nianjun Liu, John S. Witte, Charlotte A. Hobbs
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-020-02252-4

Exploiting the GTEx resources to decipher the mechanisms at GWAS loci
Cited by: 117
Author(s): Alvaro N. Barbeira, Rodrigo Bonazzola, Eric R. Gamazon, Yanyu Liang, YoSon Park, Sarah Kim-Hellmuth, Gao Wang, Zhuoxun Jiang, Dan Zhou, Farhad Hormozdiari, Boxiang Liu, Abhiram Rao, Andrew R Hamel, Milton Pividori, François Aguet, Lisa Bastarache, Daniel M. Jordan, Marie Verbanck, Ron Do, Matthew Stephens, Kristin Ardlie, Mark McCarthy, S Montgomery, Ayellet V. Segrè, Christopher D. Brown, Tuuli Lappalainen, Xiaoquan Wen, Hae Kyung Im
Software Mentions: 2
Published: over 3 years ago

10.1534/g3.118.200469

Evidence of<i>Zip1</i>Promoting Sister Kinetochore Mono-orientation During Meiosis in Budding Yeast
Cited by: 10
Author(s): Hemant Kumar Prajapati, Meenakshi Agarwal, Santanu Ghosh
Software Mentions: 2
Published: almost 6 years ago

Projects: cran: coloc

Papers Mentioning coloc 49