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: pypi: iCount

https://packages.ecosyste.ms/registries/pypi.org/packages/iCount

Computational pipeline for analysis of iCLIP data
1 version
Latest release: about 7 years ago
8 downloads last month

Papers Mentioning iCount 18

Imp/IGF2BP levels modulate individual neural stem cell growth and division through myc mRNA stability
Cited by: 48
Author(s): Tamsin J Samuels, Aino I Järvelin, David Ish‐Horowicz, Ilan Davis
Software Mentions: 7
Published: over 4 years ago

10.1016/j.molcel.2019.01.017

System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection
Cited by: 122
Author(s): Manuel García-Moreno, Marko Noerenberg, Shuai Ni, Aino I Järvelin, Esther González-Almela, Caroline E. Lenz, Marcel Bach-Pagés, Victoria Cox, Rosario Avolio, Thomas W. Davis, Svenja Hester, Thibault J.M. Sohier, Bingnan Li, Gregory Heikel, Gracjan Michlewski, Miguel Á. Sanz, Luís Carrasco, Emiliano P. Ricci, Vicent Pelechano, Ilan Davis, Bernd Fischer, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 7
Published: over 5 years ago

10.12688/wellcomeopenres.16791.1

Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer
Cited by: 9
Author(s): Oscar G. Wilkins, Charlotte Capitanchik, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-021-02298-y

SRSF3 and SRSF7 modulate 3′UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels
Cited by: 26
Author(s): Oliver D. Schwich, Nicole Blümel, Mario Keller, Marius Wegener, Samarth Thonta Setty, Melinda Elaine Brunstein, Ina Poser, Igor Ruiz de los Mozos, Beatrix Suess, Christian Münch, François McNicoll, Kathi Zarnack, Michaela Müller-McNicoll
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.52896

Recruitment of mRNAs to P granules by condensation with intrinsically-disordered proteins
Cited by: 88
Author(s): Chih Yung S. Lee, Andrea Putnam, Tu Lu, Shuai Xin He, John Paul T. Ouyang, Géraldine Seydoux
Software Mentions: 4
Published: over 4 years ago

10.1016/j.cell.2018.07.001

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing
Cited by: 110
Author(s): Jan Attig, Antonella Federico, Clare Gooding, Anob M. Chakrabarti, Aarti Singh, Nejc Haberman, Julian A. Zagalak, Warren Emmett, Christopher W. Smith, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 4
Published: about 6 years ago

10.1016/j.celrep.2016.06.096

Exon Junction Complexes Show a Distributional Bias toward Alternatively Spliced mRNAs and against mRNAs Coding for Ribosomal Proteins
Cited by: 60
Author(s): Christian Hauer, Jana Sieber, Thomas Schwarzl, Ina Hollerer, Tomaž Curk, Anne-Marie Alleaume, Matthias W. Hentze, Andreas E. Kulozik
Software Mentions: 4
Published: about 8 years ago

10.1093/gigascience/giaa108

Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis
Cited by: 5
Author(s): Florian Heyl, Daniel Maticzka, Michaël Uhl, Rolf Backofen
Software Mentions: 4
Published: almost 4 years ago

10.7554/eLife.37419

SRSF3 promotes pluripotency through Nanog mRNA export and coordination of the pluripotency gene expression program
Cited by: 44
Author(s): Madara Ratnadiwakara, Stuart K. Archer, Craig Dent, Igor Ruiz de los Mozos, Traude H. Beilharz, Anja S Knaupp, Christian M. Nefzger, José M. Polo, Minna‐Liisa Änkö
Software Mentions: 3
Published: over 6 years ago

10.1016/j.molcel.2019.01.033

P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress
Cited by: 63
Author(s): А. Н. Бугай, Alexandre J.C. Quaresma, Caroline C. Friedel, Tina Lenasi, Robert Düster, Christopher R. Sibley, Koh Fujinaga, Petra Kukanja, Thomas Hennig, Melanie Blasius, Matthias Geyer, Jernej Ule, Lars Dölken, Matjaž Barborič
Software Mentions: 3
Published: over 5 years ago

10.1186/gb-2012-13-8-r67

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
Cited by: 197
Author(s): Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule
Software Mentions: 2
Published: over 12 years ago

10.1186/s13059-016-1130-x

Insights into the design and interpretation of iCLIP experiments
Cited by: 70
Author(s): Nejc Haberman, Ina Huppertz, Jan Attig, Julian König, Zhen Wang, Christian Hauer, Matthias W. Hentze, Andreas E. Kulozik, Hervé Le Hir, Tomaž Curk, Christopher R. Sibley, Kathi Zarnack, Jernej Ule
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0116899

Deletion of AU-Rich Elements within the Bcl2 3′UTR Reduces Protein Expression and B Cell Survival In Vivo
Cited by: 11
Author(s): Manuel D. Díaz-Muñoz, Sarah E. Bell, Martin Turner
Software Mentions: 1
Published: over 9 years ago

10.1155/2015/395816

Unravelling the RNA-Binding Properties of SAFB Proteins in Breast Cancer Cells
Cited by: 7
Author(s): Elaine Hong, Andrew Best, Hannah Gautrey, Jas Min Chin, Anshuli Razdan, Tomaž Curk, David J. Elliott, Alison Tyson-Capper
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0048084

Perturbation of Chromatin Structure Globally Affects Localization and Recruitment of Splicing Factors
Cited by: 50
Author(s): Ignacio E. Schor, David Llères, Guillermo Risso, Andrea Pawellek, Jernej Ule, Angus I. Lamond, Alberto R. Kornblihtt
Software Mentions: 1
Published: almost 12 years ago

10.1016/j.devcel.2020.10.006

Subcellular mRNA Localization Regulates Ribosome Biogenesis in Migrating Cells
Cited by: 41
Author(s): Maria Dermit, Martin Dodel, Flora Lee, Muhammad S. Azman, Hagen Schwenzer, J. Louise Jones, Sarah P. Blagden, Jernej Ule, Faraz K. Mardakheh
Software Mentions: 1
Published: almost 4 years ago

10.1042/BST20191059

Zooming in on protein–RNA interactions: a multi-level workflow to identify interaction partners
Cited by: 10
Author(s): Alessio Colantoni, Jakob Rupert, Andrea Vandelli, Gian Gaetano Tartaglia, Elsa Zacco
Software Mentions: 1
Published: about 4 years ago

10.1016/j.omtn.2020.10.009

Identifying Cleaved and Noncleaved Targets of Small Interfering RNAs and MicroRNAs in Mammalian Cells by SpyCLIP
Cited by: 4
Author(s): Yao Zhang, Yilan Teng, Wangwen Xiao, Beiying Xu, Ya Zhao, Weihua Li, Ligang Wu
Software Mentions: 1
Published: almost 4 years ago