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: DiffBind

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

Differential Binding Analysis of ChIP-Seq Peak Data
1 version
Latest release: about 1 year ago
2 dependent packages
213,043 downloads total

Papers Mentioning DiffBind 217

10.7150/ijbs.45112

Osblr8 orchestrates intrachromosomal loop structure required for maintaining stem cell pluripotency
Cited by: 6
Author(s): Yanbo Zhu, Zi Yan, Zhonghua Du, Shilin Zhang, Changhao Fu, Ying Meng, Wei Xue, Yizhuo Wang, Andrew R. Hoffman, Ji-Fan Hu, Jiuwei Cui, Wei Li
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41388-020-1376-3

The GATA3 X308_Splice breast cancer mutation is a hormone context-dependent oncogenic driver
Cited by: 11
Author(s): Natascha Hruschka, Jorge Ferrer, Maria Subijana, Osvaldo Graña‐Castro, Francisco Del Caño-Ochoa, Laia Paré Brunet, Igor Chernukhin, Ana María Alfaro de Prado Sagrera, Aurélien de Reyniès, Bernhard Kloesch, Suet-Feung Chin, Octavio Burgués, David Andreu, Begoña Bermejo, Juan Miguel Cejalvo, Joe Sutton, Carlos Caldas, Santiago Ramón‐Maiques, Jason S. Carroll, Aleix Prat, Francisco X. Real, Paola Martinelli
Software Mentions: 2
Published: over 4 years ago

10.7554/eLife.35621

A stable mode of bookmarking by TBP recruits RNA polymerase II to mitotic chromosomes
Cited by: 89
Author(s): Sheila S Teves, Luye An, Aarohi Bhargava-Shah, Liangqi Xie, Xavier Darzacq, Robert Tjian
Software Mentions: 2
Published: over 6 years ago

10.1242/bio.043638

Unique trophoblast chromatin environment mediated by the PcG protein SFMBT2
Cited by: 3
Author(s): Priscilla Tang, Kamelia Miri, Susannah Varmuza
Software Mentions: 2
Published: almost 6 years ago

10.1074/jbc.RA120.015152

Genome editing demonstrates that the −5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment
Cited by: 12
Author(s): Puja Agrawal, Steven Blinka, Kirthi Pulakanti, Michael Reimer, Cary Stelloh, Alison E. Meyer, Sridhar Rao
Software Mentions: 2
Published: almost 4 years ago

10.1186/s13059-019-1698-z

VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer
Cited by: 22
Author(s): Andrew N Holding, Federico M. Giorgi, Amanda Donnelly, Amy E Cullen, Sankari Nagarajan, Luke A. Selth, Florian Markowetz
Software Mentions: 2
Published: over 5 years ago

10.14440/jbm.2016.109

ChIP and Chips: Introducing the WormPharm for correlative studies employing pharmacology and genome-wide analyses in C. elegans
Cited by: 8
Author(s): Jung H. Doh, Andrew Moore, İrem Çelen, Michael Moore, Chandran R. Sabanayagam
Software Mentions: 1
Published: over 8 years ago

10.1128/mBio.02128-20

Network Rewiring: Physiological Consequences of Reciprocally Exchanging the Physical Locations and Growth-Phase-Dependent Expression Patterns of the Salmonella fis and dps Genes
Cited by: 10
Author(s): Marina M Bogue, Aalap Mogre, Michael C Beckett, Nicholas R. Thomson, Charles J. Dorman
Software Mentions: 1
Published: about 4 years ago

10.3390/cancers11081142

Epigenome Mapping Identifies Tumor-Specific Gene Expression in Primary Rectal Cancer
Cited by: 9
Author(s): Hannah Flebbe, Feda H. Hamdan, Vijayalakshmi Kari, Julia Kitz, Jochen Gaedcke, B. Michael Ghadimi, Steven A. Johnsen, Marian Grade
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-015-1656-4

Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo
Cited by: 50
Author(s): Yi‐Zhou Jiang, Elisabetta Manduchi, Christian J. Stoeckert, Peter F. Davies
Software Mentions: 1
Published: over 9 years ago

10.1074/jbc.RA118.002894

Up-regulation of the kinase gene SGK1 by progesterone activates the AP-1–NDRG1 axis in both PR-positive and -negative breast cancer cells
Cited by: 23
Author(s): Mukul Godbole, Trupti Togar, Kuldeep Patel, Bhasker Dharavath, Neelima Yadav, Sharan Janjuha, Nilesh Gardi, Kanishka Tiwary, Prachi Terwadkar, Sanket Desai, Ratnam Prasad, Hemant Dhamne, Kunal Karve, Sameer Salunkhe, Dhananjay Kawle, Pratik Chandrani, Shilpee Dutt, Sudeep Gupta, Rajendra Badwe, Amit Dutt
Software Mentions: 1
Published: almost 6 years ago

10.1186/s40425-019-0517-0

HDAC6 selective inhibition of melanoma patient T-cells augments anti-tumor characteristics
Cited by: 54
Author(s): Andressa S. Laino, Brian C. Betts, Anandharaman Veerapathran, Igor Dolgalev, Amod A. Sarnaik, Steven N. Quayle, Simon Jones, Jeffrey S. Weber, David Woods
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.molcel.2012.11.013

Latent Regulatory Potential of Human-Specific Repetitive Elements
Cited by: 58
Author(s): Michelle C. Ward, Michael D. Wilson, Nuno L. Barbosa‐Morais, Dominic Schmidt, Rory Stark, Qun Pan, Petra Schwalie, Suraj Menon, Margus Lukk, Stephen Watt, David Thybert, Claudia Kutter, Kristina Kirschner, Paul Flicek, Benjamin J. Blencowe, Duncan T. Odom
Software Mentions: 1
Published: almost 12 years ago

10.1186/s13059-018-1428-y

Histone H4 acetylation regulates behavioral inter-individual variability in zebrafish
Cited by: 21
Author(s): Ángel‐Carlos Román, Julián Vicente-Page, Alfonso Pérez‐Escudero, José María Carvajal-González, Pedro M. Fernández-Salguero, Gonzalo G. de Polavieja
Software Mentions: 1
Published: over 6 years ago

10.1186/s13059-016-1017-x

Mapping H4K20me3 onto the chromatin landscape of senescent cells indicates a function in control of cell senescence and tumor suppression through preservation of genetic and epigenetic stability
Cited by: 63
Author(s): David M. Nelson, Farah Jaber-Hijazi, John Cole, Neil Robertson, Jeffrey S. Pawlikowski, Kevin Norris, Steven W. Criscione, Nikolay A. Pchelintsev, D Piscitello, Nicholas Stong, Taranjit Singh, Tony McBryan, Gabriel Otte, Colin Nixon, William Clark, Harold Riethman, Hong Gyun Wu, Gunnar Schotta, Benjamin A. Garcia, Nicola Neretti, Duncan Martin Baird, Shelley L. Berger, Peter D. Adams
Software Mentions: 1
Published: over 8 years ago

10.1038/s42003-020-0798-3

Deletion of a conserved Gata2 enhancer impairs haemogenic endothelium programming and adult Zebrafish haematopoiesis
Cited by: 23
Author(s): Tomasz Dobrzycki, Christopher B. Mahony, Mónika Krecsmarik, Cansu Koyunlar, Rossella Rispoli, Joke Peulen-Zink, Kirsten J. Gussinklo, Bakhta Fedlaoui, Emma de Pater, Roger Patient, Rui Monteiro
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13148-020-00953-y

DNA hydroxymethylation is associated with disease severity and persists at enhancers of oncogenic regions in multiple myeloma
Cited by: 8
Author(s): Jean-Baptiste Alberge, Florence Magrangeas, Mirko Wagner, Soline Denié, Catherine Guérin‐Charbonnel, Loı̈c Campion, Michel Attal, Hervé Avet‐Loiseau, Thomas Carell, Philippe Moreau, Stéphane Minvielle, Aurélien A. Sérandour
Software Mentions: 1
Published: about 4 years ago