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: MotifDb

https://packages.ecosyste.ms/registries/bioconductor.org/packages/MotifDb

An Annotated Collection of Protein-DNA Binding Sequence Motifs
1 version
Latest release: 10 months ago
17 dependent packages
94,564 downloads total

Papers Mentioning MotifDb 17

10.1186/s12864-018-4559-3

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
Cited by: 133
Author(s): Jianhong Ou, Haibo Li, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu
Software Mentions: 14
Published: over 6 years ago

10.7554/eLife.07836

Lipid-mediated regulation of SKN-1/Nrf in response to germ cell absence
Cited by: 158
Author(s): Michael J. Steinbaugh, Sri Devi Narasimhan, Stacey Robida-Stubbs, Lorenza E Moronetti Mazzeo, Jonathan M. Dreyfuss, John M. Hourihan, Prashant Raghavan, Theresa N. Operaña, Reza Esmaillie, T. Keith Blackwell
Software Mentions: 13
Published: almost 9 years ago

10.12688/f1000research.17976.2

TFutils: Data structures for transcription factor bioinformatics
Cited by: 2
Author(s): Benjamin J. Stubbs, Shweta Gopaulakrishnan, Kimberly Glass, Nathalie Pochet, Celine Everaert, Benjamin A. Raby, Vincent J. Carey
Software Mentions: 10
Published: about 5 years ago

10.1007/s00401-020-02224-9

Altered DNA methylation profiles in blood from patients with sporadic Creutzfeldt–Jakob disease
Cited by: 14
Author(s): Luke C. Dabin, Fernando Guntoro, Tracy Campbell, Tony Bélicard, Adam R. Smith, Rebecca G. Smith, Rachel Raybould, Jonathan M. Schott, Katie Lunnon, Peter Sarkies, John Collinge, Simon Mead, Emmanuelle Viré
Software Mentions: 10
Published: almost 4 years ago

10.1038/s41388-018-0450-6

The miR-96 and RARγ signaling axis governs androgen signaling and prostate cancer progression
Cited by: 40
Author(s): Mark D. Long, Prashant Singh, James R. Russell, Gerard Llimos, Spencer R. Rosario, Abbas Rizvi, Patrick R. van den Berg, Jason Kirk, Lara E. Sucheston‐Campbell, Dominic J. Smiraglia, Moray J. Campbell
Software Mentions: 9
Published: almost 6 years ago

10.3389/fgene.2020.00730

ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants
Cited by: 3
Author(s): Mohith Manjunath, Yi Zhang, Shilu Zhang, Sushmita Roy, Pablo Pérez-Piñera, Jun S. Song
Software Mentions: 6
Published: about 4 years ago

10.7554/eLife.31683

Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm
Cited by: 36
Author(s): Xinan Yang, Rangarajan D. Nadadur, Catharina R.E. Hilvering, Valerio Bianchi, Michael S. Werner, Stefan R. Mazurek, Margaret Gadek, Karen Shen, Joseph D. Goldman, Leonid Tyan, Jenna C. Bekeny, Johnathon M Hall, Nutishia Lee, Carlos Perez-Cervantes, Ozanna Burnicka-Turek, Kenneth D. Poss, Christopher R. Weber, Wouter de Laat, Alexander J. Ruthenburg, Ivan P. Moskowitz
Software Mentions: 5
Published: over 6 years ago

10.1093/bioinformatics/btv470

<i>motifbreakR</i>: an R/Bioconductor package for predicting variant effects at transcription factor binding sites
Cited by: 179
Author(s): Simon Coetzee, Gerhard A. Coetzee, Dennis J. Hazelett
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12864-016-2729-8

A systematic, large-scale comparison of transcription factor binding site models
Cited by: 13
Author(s): Daniela Hombach, Jana Marie Schwarz, Peter N. Robinson, Markus Schuelke, Dominik Seelow
Software Mentions: 4
Published: about 8 years ago

10.1186/s12864-015-2164-2

The direction of cross affects obesity after puberty in male but not female offspring
Cited by: 5
Author(s): Stefan Kärst, Danny Arends, Sebastian Heise, Jan Trost, Marie–Laure Yaspo, Vyacheslav Amstislavskiy, Thomas S. Risch, Hans Lehrach, Gudrun A. Brockmann
Software Mentions: 4
Published: over 8 years ago

10.3390/ijms19082285

Effect of ACTH and hCG on the Expression of Gonadotropin-Inducible Ovarian Transcription Factor 1 (Giot1) Gene in the Rat Adrenal Gland
Cited by: 6
Author(s): Karol Jopek, Marianna Tyczewska, Manjunath Ramanjaneya, Marta Szyszka, Piotr Celichowski, Paulina Milecka, Ludwik K. Malendowicz, Marcin Ruciński
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13072-015-0049-x

Roles of cofactors and chromatin accessibility in Hox protein target specificity
Cited by: 46
Author(s): Ching Yew Beh, Sherif El‐Sharnouby, Aikaterini Chatzipli, Steven Russell, Siew Woh Choo, Robert A. White
Software Mentions: 3
Published: over 8 years ago

10.1186/s13072-018-0174-4

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding
Cited by: 51
Author(s): Satyanarayan Rao, Tsu-Pei Chiu, Judith F. Kribelbauer, Richard S. Mann, Harmen J. Bussemaker, Remo Rohs
Software Mentions: 2
Published: over 6 years ago

10.1186/s13072-017-0169-6

A screening system to identify transcription factors that induce binding site-directed DNA demethylation
Cited by: 40
Author(s): Tsuyoshi Suzuki, Shiori Maeda, Erina Furuhata, Yuri Shimizu, Hajime Nishimura, Mami Kishima, Harukazu Suzuki
Software Mentions: 2
Published: over 6 years ago

10.1186/1472-6882-14-14

Sho-saiko-to, a traditional herbal medicine, regulates gene expression and biological function by way of microRNAs in primary mouse hepatocytes
Cited by: 11
Author(s): Kwang Hoon Song, Yun Hee Kim, Bu-Yeo Kim
Software Mentions: 2
Published: over 10 years ago

10.3390/nu13010038

Mexican Ganoderma Lucidum Extracts Decrease Lipogenesis Modulating Transcriptional Metabolic Networks and Gut Microbiota in C57BL/6 Mice Fed with a High-Cholesterol Diet
Cited by: 15
Author(s): Sandra Romero-Córdoba, Iván Salido-Guadarrama, María E Meneses, Giulia Cosentino, Marilena V. Iorio, Elda Tagliabue, Nimbe Torres, Mónica Sánchez‐Tapia, M. Bonilla, Iván Castillo, Beatriz Petlacalco, Armando R. Tovar, D. Martínez-Carrera
Software Mentions: 2
Published: over 3 years ago

10.1186/s12958-016-0156-y

Experimental and bioinformatic analysis of cultured Bovine Endometrial Cells (BEND) responding to interferon tau (IFNT)
Cited by: 6
Author(s): Sergio Palma-Vera, Ralf Einspanier
Software Mentions: 1
Published: over 8 years ago