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: ensembldb

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

Utilities to create and use Ensembl-based annotation databases
2 versions
Latest release: about 1 year ago
36 dependent packages
925,088 downloads total

Papers Mentioning ensembldb 12

10.1371/journal.pcbi.1007664

Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Cited by: 122
Author(s): Michael I. Love, Charlotte Soneson, Peter Hickey, Lisa K. Johnson, Nicholas Pierce, Lori Shepherd, Martin Morgan, Rob Patro
Software Mentions: 19
Published: almost 5 years ago

10.12688/f1000research.10742.2

haploR: an R package for querying web-based annotation tools
Cited by: 20
Author(s): Ilya Y. Zhbannikov, Konstantin G. Arbeev, Svetlana V. Ukraintseva, Anatoliy I. Yashin
Software Mentions: 13
Published: over 7 years ago

10.1038/s41419-020-2477-1

Deficiency in the autophagy modulator Dram1 exacerbates pyroptotic cell death of Mycobacteria-infected macrophages
Cited by: 22
Author(s): Rui Zhang, Mónica Varela, Gabriel Forn-Cuní, Vincenzo Torraca, Michiel van der Vaart, Annemarie H. Meijer
Software Mentions: 7
Published: over 4 years ago

10.26508/lsa.202000897

Tissue-selective alternate promoters guide NLRP6 expression
Cited by: 1
Author(s): Nathan A. Bracey, Jaye M. Platnich, Arthur Lau, Hyunsoo Chung, M. Eric Hyndman, Justin A. MacDonald, Justin Chun, Paul L. Beck, Stephen E. Girardin, Paul M. Gordon, Daniel A. Muruve
Software Mentions: 7
Published: almost 4 years ago

10.1093/bioinformatics/btz031

ensembldb: an R package to create and use Ensembl-based annotation resources
Cited by: 76
Author(s): Johannes Michael Rainer, Laurent Gatto, Christian X. Weichenberger
Software Mentions: 7
Published: almost 6 years ago

10.7554/eLife.66904

Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology
Cited by: 14
Author(s): Markus Terrey, Scott I. Adamson, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 5
Published: over 3 years ago

10.3389/fcell.2021.667852

Metabolic and Immunological Subtypes of Esophageal Cancer Reveal Potential Therapeutic Opportunities
Cited by: 8
Author(s): Ryan J. King, Fang Qiu, Fang Yu, Pankaj K. Singh
Software Mentions: 5
Published: over 3 years ago

10.3390/cancers12082046

Pan-Cancer Analysis of the Genomic Alterations and Mutations of the Matrisome
Cited by: 45
Author(s): Valerio Izzi, Martin N. Davis, Alexandra Naba
Software Mentions: 4
Published: over 4 years ago

10.7554/eLife.62731

GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis
Cited by: 22
Author(s): Markus Terrey, Scott I. Adamson, Alana L. Gibson, Tianda Deng, Ryuta Ishimura, Jeffrey H. Chuang, Susan L. Ackerman
Software Mentions: 4
Published: about 4 years ago

10.1515/jib-2018-0090

Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions
Cited by: 0
Author(s): Yaoyong Li, Elisa Aguilar‐Martínez, Andrew D. Sharrocks
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0236338

Relative quantification of BCL2 mRNA for diagnostic usage needs stable uncontrolled genes as reference
Cited by: 1
Author(s): Nehanjali Dwivedi, Sreejeta Mondal, P K Smitha, T Sowmya, Kartik Sachdeva, Christopher Bathula, K Vishnupriyan, K.S. Nataraj, Sharat Damodar, Sujan Dhar, Manjula Das
Software Mentions: 2
Published: over 4 years ago

10.15252/embj.2020104763

Translation of small downstream ORFs enhances translation of canonical main open reading frames
Cited by: 64
Author(s): Qiushuang Wu, Matthew Wright, Madelaine Gogol, W. David Bradford, Ning Zhang, Ariel Bazzini
Software Mentions: 2
Published: over 4 years ago