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: NuPoP

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

An R package for nucleosome positioning prediction
1 version
Latest release: about 1 year ago
1 dependent package
22,714 downloads total

Papers Mentioning NuPoP 18

Concentration dependent chromatin states induced by the bicoid morphogen gradient
Cited by: 76
Author(s): Colleen E Hannon, Shelby A. Blythe, Eric Wieschaus
Software Mentions: 7
Published: about 7 years ago

10.1186/s12859-021-04240-2

Chemical map-based prediction of nucleosome positioning using the Bioconductor package nuCpos
Cited by: 4
Author(s): Hiroaki Kato, Mitsuhiro Shimizu, Takeshi Urano
Software Mentions: 5
Published: over 3 years ago

10.1186/s13059-015-0671-8

An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum
Cited by: 76
Author(s): Alaguraj Veluchamy, Achal Rastogi, Xin Lin, Bérangère Lombard, Omer Murik, Y. Thomas, Florent Dingli, Máximo Rivarola, Sandra Ott, Xinyue Liu, Yan Sun, Pablo D. Rabinowicz, James S. McCarthy, Andrew E. Allen, Damarys Loew, Chris Bowler, Leïla Tirichine
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pcbi.1004894

Nucleosome Presence at AML-1 Binding Sites Inversely Correlates with Ly49 Expression: Revelations from an Informatics Analysis of Nucleosomes and Immune Cell Transcription Factors
Cited by: 4
Author(s): Andrew Wight, Doo Yang, Ilya Ioshikhes, Andrew P. Makrigiannis
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2017.00123

Drosophila Model for the Analysis of Genesis of LIM-kinase 1-Dependent Williams-Beuren Syndrome Cognitive Phenotypes: INDELs, Transposable Elements of the Tc1/Mariner Superfamily and MicroRNAs
Cited by: 8
Author(s): Е. В. Савватеева-Попова, Aleksandr V. Zhuravlev, Václav Brázda, Г. А. Захаров, A. N. Kaminskaya, А. В. Медведева, Е. А. Никитина, Elena V. Tokmatcheva, Julia F. Dolgaya, Д. А. Куликова, Olga G. Zatsepina, S. Yu. Funikov, Sergei Ryazansky, М. Б. Евгеньев
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0075911

NSD1 Mitigates Caspase-1 Activation by Listeriolysin O in Macrophages
Cited by: 12
Author(s): Olivia S. Sakhon, Kaitlin A. Victor, Anthony Choy, Tokuji Tsuchiya, Thomas Eulgem, Joao H. F. Pedra
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0030006

Histone H2A (H2A.X and H2A.Z) Variants in Molluscs: Molecular Characterization and Potential Implications For Chromatin Dynamics
Cited by: 29
Author(s): Rodrigo González-Romero, Ciro Rivera-Casas, Lindsay J. Frehlick, Josefina Méndez, Juan Ausió, José M. Eirín‐López
Software Mentions: 1
Published: almost 13 years ago

10.1007/s00125-017-4471-4

Epigenetic modifications of the Zfp/ZNF423 gene control murine adipogenic commitment and are dysregulated in human hypertrophic obesity
Cited by: 39
Author(s): Michele Longo, Gregory Alexander Raciti, Federica Zatterale, Luca Parrillo, Antonella Desiderio, Rosa Spinelli, Ann Hammarstedt, Shahram Hedjazifar, Jenny Hoffmann, Cecilia Nigro, Paola Mirra, Francesca Fiory, Pietro Formisano, Claudia Miele, Ulf Smith, Francesco Béguinot
Software Mentions: 1
Published: about 7 years ago

10.1038/srep24133

A deformation energy-based model for predicting nucleosome dyads and occupancy
Cited by: 10
Author(s): Guoqing Liu, Yongzhong Xing, Hongyu Zhao, Jianying Wang, Sirong Yu, Liang Cai
Software Mentions: 1
Published: over 8 years ago

10.1038/srep43526

Specific CpG hyper-methylation leads to Ankrd26 gene down-regulation in white adipose tissue of a mouse model of diet-induced obesity
Cited by: 33
Author(s): Gregory Alexander Raciti, Rosa Spinelli, Antonella Desiderio, Michele Longo, Luca Parrillo, Cecilia Nigro, Vittoria D’Esposito, Paola Mirra, Francesca Fiory, Vincenzo Pilone, Pietro Forestieri, Pietro Formisano, Ira Pastan, Claudia Miele, Francesco Béguinot
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-018-19831-y

Controlling AOX1 promoter strength in Pichia pastoris by manipulating poly (dA:dT) tracts
Cited by: 13
Author(s): Jun Yang, Hao Cai, Jie Liu, Min Zeng, Jiawei Chen, Qing Cheng, Linghua Zhang
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-019-45411-9

ZNF518B gene up-regulation promotes dissemination of tumour cells and is governed by epigenetic mechanisms in colorectal cancer
Cited by: 11
Author(s): Francisco Gimeno-Valiente, Ángela L. Riffo‐Campos, Azahara Vallet-Sánchez, Sofía Siscar-Lewin, Valentina Gambardella, Luís Franco, Josefa Castillo, Gerardo López-Rodas
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-13-49

Structural features based genome-wide characterization and prediction of nucleosome organization
Cited by: 12
Author(s): Yanglan Gan, Jihong Guan, Shuigeng Zhou, Weixiong Zhang
Software Mentions: 1
Published: over 12 years ago

10.18632/oncotarget.25016

Role of epigenetic factors in the selection of the alternative splicing isoforms of human <i>KRAS</i> in colorectal cancer cell lines
Cited by: 15
Author(s): Ángela L. Riffo‐Campos, Francisco Gimeno-Valiente, Fernanda Mariel Rodríguez, Andrés Cervantes, Gerardo López-Rodas, Luís Franco, Josefa Castillo
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-11-346

Predicting nucleosome positioning using a duration Hidden Markov Model
Cited by: 126
Author(s): Xi Li, Yvonne Fondufe‐Mittendorf, Lei Xia, Jared Flatow, Jonathan Widom, Ji-Ping Z Wang
Software Mentions: 1
Published: over 14 years ago

10.1186/s12896-016-0238-0

Mechanisms underlying epigenetic and transcriptional heterogeneity in Chinese hamster ovary (CHO) cell lines
Cited by: 44
Author(s): Nathalie Veith, Holger Ziehr, Roderick A.F. MacLeod, Stella Marie Reamon-Buettner
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pbio.1001206

Repressive LTR Nucleosome Positioning by the BAF Complex Is Required for HIV Latency
Cited by: 150
Author(s): Hasan Rafati, Maribel Parra, Shweta Hakre, Yuri M. Moshkin, Eric Verdin, Tokameh Mahmoudi
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0038531

Dissecting Epigenetic Silencing Complexity in the Mouse Lung Cancer Suppressor Gene Cadm1
Cited by: 5
Author(s): Stella Marie Reamon-Buettner, Jürgen Borlak
Software Mentions: 1
Published: over 12 years ago