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: IsoformSwitchAnalyzeR

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

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
1 version
Latest release: about 1 year ago
24,290 downloads total

Papers Mentioning IsoformSwitchAnalyzeR 16

10.12688/f1000research.15398.3

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Cited by: 53
Author(s): Michael I. Love, Charlotte Soneson, Rob Patro
Software Mentions: 16
Published: about 6 years ago

10.1371/journal.pone.0232646

Two-step mixed model approach to analyzing differential alternative RNA splicing
Cited by: 0
Author(s): Li Luo, Huining Kang, Xichen Li, Scott A. Ness, Christine A. Stidley
Software Mentions: 7
Published: about 4 years ago

10.3390/cancers12061453

DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3′-End Usage
Cited by: 16
Author(s): Jamal Elhasnaoui, Valentina Miano, Giulio Ferrero, Elena Doria, Antonette E. Leon, Aline S C Fabrício, Laura Annaratone, Isabella Castellano, Anna Sapino, Michele De Bortoli
Software Mentions: 7
Published: over 4 years ago

10.1038/s42003-021-02095-0

Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis
Cited by: 28
Author(s): Mariana Galvão Ferrarini, Avantika Lal, Rita Rebollo, Andreas J. Gruber, Andrea Guarracino, Itziar Martinez Gonzalez, Taylor Floyd, Daniel Siqueira de Oliveira, Justin Shanklin, Ethan Beausoleil, Taneli Pusa, Brett E. Pickett, Vanessa Aguiar‐Pulido
Software Mentions: 7
Published: over 3 years ago

10.3390/plants9121700

Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots
Cited by: 8
Author(s): Evgeny A. Zorin, Alexey М. Afonin, Olga A. Kulaeva, Emma S. Gribchenko, O. Y. Shtark, Vladimir A. Zhukov
Software Mentions: 7
Published: almost 4 years ago

10.3389/fdata.2021.725095

NPARS—A Novel Approach to Address Accuracy and Reproducibility in Genomic Data Science
Cited by: 2
Author(s): Li Ma, Erich A. Peterson, Ik Jae Shin, Jason Muesse, Katy Marino, Matthew A. Steliga, Donald J. Johann
Software Mentions: 6
Published: about 3 years ago

10.1038/s41398-021-01561-x

Comparison of mouse models reveals a molecular distinction between psychotic illness in PWS and schizophrenia
Cited by: 5
Author(s): Simona Zahova, Trevor Humby, Jennifer R. Davies, Joanne Morgan, Anthony R Isles
Software Mentions: 6
Published: over 3 years ago

10.1186/s13059-020-02028-w

tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
Cited by: 34
Author(s): Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Alberto Lerma, Ana Alastrue‐Agudo, Pablo Bonilla, Jeremy R.B. Newman, Shunichi Kosugi, Lauren McIntyre, Victoria Moreno‐Manzano, Ana Conesa
Software Mentions: 5
Published: over 4 years ago

10.3389/fpls.2021.653183

Transcriptome Analysis of Tetraploid and Octoploid Common Reed (Phragmites australis)
Cited by: 5
Author(s): Cui Wang, Tong Wang, Meiqi Yin, Franziska Eller, Lele Liu, Hans Brix, Weihua Guo
Software Mentions: 4
Published: over 3 years ago

10.3389/fgene.2020.566320

Transcriptomic and Epigenomic Dynamics of Honey Bees in Response to Lethal Viral Infection
Cited by: 11
Author(s): Hongmei Li-Byarlay, Humberto Boncristiani, Gary W. Howell, Jacob Herman, Lindsay V. Clark, Micheline K. Strand, David R. Tarpy, Olav Rueppell
Software Mentions: 4
Published: about 4 years ago

10.3389/fpls.2018.01209

Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses
Cited by: 39
Author(s): Jérémie Bazin, Natali Romero, Richard Rigo, Céline Charon, Thomas Blein, Federico Ariel, Martín Crespi
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.ppat.1008401

Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis
Cited by: 35
Author(s): Jérémie Bazin, Kadarkaraisamy Mariappan, Yunhe Jiang, Thomas Blein, Ronny Völz, Martín Crespi, Heribert Hirt
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.33178

ICE1 promotes the link between splicing and nonsense-mediated mRNA decay
Cited by: 48
Author(s): T. Baird, Ken Chih-Chien Cheng, Yu‐Chi Chen, Eugen Buehler, Scott E. Martin, James Inglese, J. Robert Hogg
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms22168951

OTX2 Homeoprotein Functions in Adult Choroid Plexus
Cited by: 4
Author(s): Anabelle Planques, Vanessa Oliveira Moreira, David Benacom, C. Bernard, Laurent Jourdren, Corinne Blugeon, Florent Dingli, Vanessa Masson, Damarys Loew, Alain Prochiantz, Ariel A. Di Nardo
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms22137165

A Transcriptome-Wide Isoform Landscape of Melanocytic Nevi and Primary Melanomas Identifies Gene Isoforms Associated with Malignancy
Cited by: 7
Author(s): Siras Hakobyan, Henry Loeffler‐Wirth, Arsen Arakelyan, Hans Binder, Manfred Kunz
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1007095

Aberrant DNA methylation defines isoform usage in cancer, with functional implications
Cited by: 14
Author(s): Yunching Chen, Laura Elnitski
Software Mentions: 1
Published: over 5 years ago