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: DNAshapeR
https://packages.ecosyste.ms/registries/bioconductor.org/packages/DNAshapeR
High-throughput prediction of DNA shape features
1 version
Latest release: about 1 year ago
13,981 downloads total
Papers Mentioning DNAshapeR 10
10.1371/journal.pgen.1007102
Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-contentCited by: 16
Author(s): Daniele Colombo, Lukas Burger, Tuncay Baubec, Dirk Schübeler
Software Mentions: 10
Published: almost 7 years ago
10.1371/journal.pcbi.1007814
Genome-wide prediction of topoisomerase IIβ binding by architectural factors and chromatin accessibilityCited by: 4
Author(s): Pedro Manuel Martínez-García, Miguel García-Torres, Federico Divina, José Terrón-Bautista, Irene Delgado‐Sainz, Felipe Cortés‐Ledesma
Software Mentions: 8
Published: almost 4 years ago
10.15252/msb.20209885
Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor functionCited by: 12
Author(s): Wim J. de Jonge, Mariël Brok, Philip Lijnzaad, Patrick Kemmeren, Frank C. P. Holstege
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pgen.1007793
Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noiseCited by: 26
Author(s): Stefanie Schöne, Melissa Bothe, Edda Einfeldt, Marina Borschiwer, Philipp Benner, Martin Vingron, Morgane Thomas‐Chollier, Sebastiaan H. Meijsing
Software Mentions: 5
Published: about 6 years ago
10.1371/journal.pcbi.1005921
Probing instructions for expression regulation in gene nucleotide compositionsCited by: 11
Author(s): Chloé Bessière, May Taha, Florent Petitprez, Jimmy Vandel, Jean‐Michel Marin, Laurent Bréhélin, Sophie Lèbre, Charles-Henri Lecellier
Software Mentions: 3
Published: almost 7 years ago
10.7554/eLife.39595
Fine-mapping cis-regulatory variants in diverse human populationsCited by: 47
Author(s): Ashley K. Tehranchi, Brian Hie, Michael Dacre, Irene M. Kaplow, Kade P Pettie, Peter A. Combs, Hunter B. Fraser
Software Mentions: 2
Published: almost 6 years ago
10.1186/s13072-018-0174-4
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA bindingCited by: 51
Author(s): Satyanarayan Rao, Tsu-Pei Chiu, Judith F. Kribelbauer, Richard S. Mann, Harmen J. Bussemaker, Remo Rohs
Software Mentions: 2
Published: almost 7 years ago
10.1186/s12864-017-3785-4
Transversions have larger regulatory effects than transitionsCited by: 65
Author(s): Cong Guo, Ian C. McDowell, Michael Nodzenski, Denise M. Scholtens, Andrew S. Allen, William L. Lowe, Timothy E. Reddy
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0216515
HIV chromatin is a preferred target for drugs that bind in the DNA minor grooveCited by: 2
Author(s): Clayton K. Collings, Donald W. Little, Samuel Schäfer, J.C. Anderson
Software Mentions: 1
Published: almost 5 years ago
10.3389/fgene.2021.705038
Epigenetic Marks and Variation of Sequence-Based Information Along Genomic Regions Are Predictive of Recombination Hot/Cold Spots in Saccharomyces cerevisiaeCited by: 0
Author(s): Guoqing Liu, Shuangjian Song, Qiguo Zhang, Biyu Dong, Yu Sun, Guojun Liu, Xingbo Zhao
Software Mentions: 1
Published: over 3 years ago