Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: motifbreakR
https://packages.ecosyste.ms/registries/bioconductor.org/packages/motifbreakR
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
1 version
Latest release: about 1 year ago
16,647 downloads total
Papers Mentioning motifbreakR 13
10.1186/s13059-021-02484-y
Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implicationsCited by: 5
Author(s): Benjamin Planterose Jiménez, Manfred Kayser, Athina Vidaki
Software Mentions: 10
Published: over 3 years ago
10.1186/s13073-021-00908-9
scGRNom: a computational pipeline of integrative multi-omics analyses for predicting cell-type disease genes and regulatory networksCited by: 16
Author(s): Ting Jin, Peter Rehani, Mufang Ying, Jiawei Huang, Shuang Liu, Panagiotis Roussos, Daifeng Wang
Software Mentions: 7
Published: over 3 years ago
10.3389/fgene.2020.00730
ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic VariantsCited by: 3
Author(s): Mohith Manjunath, Yi Zhang, Shilu Zhang, Sushmita Roy, Pablo Pérez-Piñera, Jun S. Song
Software Mentions: 6
Published: over 4 years ago
10.3389/fgene.2016.00002
Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the ChallengesCited by: 16
Author(s): Louise B. Thingholm, Lars van Brakel Andersen, Enes Makalic, Melissa C. Southey, Mads Thomassen, Lise Lotte Hansen
Software Mentions: 6
Published: almost 9 years ago
10.1093/bioinformatics/btv470
<i>motifbreakR</i>: an R/Bioconductor package for predicting variant effects at transcription factor binding sitesCited by: 179
Author(s): Simon Coetzee, Gerhard A. Coetzee, Dennis J. Hazelett
Software Mentions: 4
Published: over 9 years ago
10.1186/s40164-018-0123-8
Methylome of human senescent hematopoietic progenitorsCited by: 5
Author(s): Stephen Capone, Anthony Colombo, Benjamin K. Johnson, Tim Triche, Giridharan Ramsingh
Software Mentions: 4
Published: about 6 years ago
10.7554/eLife.29329
Epigenetic profiling of growth plate chondrocytes sheds insight into regulatory genetic variation influencing heightCited by: 34
Author(s): Michael H. Guo, Zun Liu, Jessie Willen, Cameron Shaw, Daniel Richard, Evelyn Jagoda, Andrew C. Doxey, Joel N. Hirschhorn, Terence D. Capellini
Software Mentions: 3
Published: about 7 years ago
10.1016/j.cell.2020.08.008
The Polygenic and Monogenic Basis of Blood Traits and DiseasesCited by: 325
Author(s): Dragana Vuckovic, Erik L. Bao, Parsa Akbari, Caleb A. Lareau, Abdou Mousas, Tao Jiang, Ming-Huei Chen, Laura M. Raffield, Manuel Tardáguila, Jennifer E. Huffman, Scott C. Ritchie, Karyn Mégy, Hannes Ponstingl, Christopher J. Penkett, Patrick K. Albers, Emilie M. Wigdor, Saori Sakaue, Arden Moscati, Regina Manansala, Ken Sin Lo, Huijun Qian, Masato Akiyama, Traci M. Bartz, Yoav Ben‐Shlomo, Andrew D Beswick, Jette Bork-Jensen, Erwin P. Böttinger, Jennifer A. Brody, Frank J.A. van Rooij, Kumaraswamy Naidu Chitrala, Peter W.F. Wilson, Hélène Choquet, John Danesh, Emanuele Di Angelantonio, Niki Dimou, Jingzhong Ding, Paul Elliott, Tõnu Esko, Michele K. Evans, Stephan B. Felix, James S. Floyd, Linda Broer, Niels Grarup, Michael H. Guo, Qi Guo, Andreas Greinacher, Jeff Haessler, Torben Hansen, Joanna M. M. Howson, Wei Huang, Eric Jorgenson, Tim Kacprowski, Mika Kähönen, Yoichiro Kamatani, Masahiro Kanai, Savita Karthikeyan, Fotios Koskeridis, Leslie A. Lange, Terho Lehtimäki, Allan Linneberg, Yongmei Liu, Leo-Pekka Lyytikäinen, Ani Manichaikul, Koichi Matsuda, Karen L. Mohlke, Nina Mononen, Yoshinori Murakami, Girish N. Nadkarni, Kjell Nikus, Nathan Pankratz, Oluf Pedersen, Michael Preuss, Bruce M. Psaty, Olli T. Raitakari, Stephen S. Rich, Blanca Rodriguez, Jonathan D. Rosen, Jerome I. Rotter, Petra Schubert, Cassandra N. Spracklen, Praveen Surendran, Hua Tang, Jean‐Claude Tardif, Mohsen Ghanbari, Uwe Völker, Henry Völzke, Nicholas A. Watkins, Stefan Weiß, VA Million Veteran Program, Na Cai, Kousik Kundu, Stephen Watt, Klaudia Walter, Alan B. Zonderman, Kelly Cho, Yun Li, Ruth J.F. Loos, Julian C. Knight, Michel Georges, Oliver Stegle, Εvangelos Εvangelou, Yukinori Okada, David Roberts, Michael Inouye, Andrew D. Johnson, Paul L. Auer, William Astle, Alexander P. Reiner, Adam S. Butterworth, Willem H. Ouwehand, Guillaume Lettre, Vijay G. Sankaran, Nicole Soranzo
Software Mentions: 2
Published: over 4 years ago
10.3390/ijms22147240
A Panel of rSNPs Demonstrating Allelic Asymmetry in Both ChIP-seq and RNA-seq Data and the Search for Their Phenotypic Outcomes through Analysis of DEGsCited by: 5
Author(s): Elena E. Korbolina, L. O. Bryzgalov, Diana Z. Ustrokhanova, Sergey Postovalov, Dmitry V. Poverin, Igor S. Damarov, T. I. Merkulova
Software Mentions: 2
Published: over 3 years ago
10.1038/s41398-021-01493-6
Transcriptional-regulatory convergence across functional MDD risk variants identified by massively parallel reporter assaysCited by: 9
Author(s): Bernard Mulvey, Joseph D. Dougherty
Software Mentions: 1
Published: over 3 years ago
10.1038/srep43709
Functional annotation of sixty-five type-2 diabetes risk SNPs and its application in risk predictionCited by: 4
Author(s): Yiming Wu, Runyu Jing, Yongcheng Dong, Qifan Kuang, Yan Li, Ziyan Huang, Wei Gan, Yue Xue, Yizhou Li, Menglong Li
Software Mentions: 1
Published: almost 8 years ago
10.1038/srep30509
Enrichment of risk SNPs in regulatory regions implicate diverse tissues in Parkinson’s disease etiologyCited by: 49
Author(s): Simon Coetzee, Steven Pierce, Patrik Brundin, Lena Brundin, Dennis J. Hazelett, Gerhard A. Coetzee
Software Mentions: 1
Published: over 8 years ago
10.1186/s13072-015-0050-4
Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genomeCited by: 255
Author(s): Yu Gyoung Tak, Peggy J. Farnham
Software Mentions: 1
Published: about 9 years ago