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: CAGEr
https://packages.ecosyste.ms/registries/bioconductor.org/packages/CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
1 version
Latest release: about 1 year ago
2 dependent packages
29,417 downloads total
Papers Mentioning CAGEr 27
10.15252/msb.20209539
Predictive features of gene expression variation reveal mechanistic link with differential expressionCited by: 36
Author(s): Olga M. Sigalova, Amirreza Shaeiri, Mattia Forneris, Eileen E. M. Furlong, Judith B. Zaugg
Software Mentions: 30
Published: over 4 years ago
10.12688/f1000research.18456.1
A step-by-step guide to analyzing CAGE data using R/BioconductorCited by: 10
Author(s): Malte Thodberg, Albin Sandelin
Software Mentions: 20
Published: over 5 years ago
10.1186/s12859-019-3029-5
CAGEfightR: analysis of 5′-end data using R/BioconductorCited by: 35
Author(s): Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin
Software Mentions: 13
Published: about 5 years ago
10.1186/s13059-020-02245-3
High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative startsCited by: 28
Author(s): Minghao Chia, Li Cai, Sueli Marques, Vicent Pelechano, Nicholas M. Luscombe, Folkert J. van Werven
Software Mentions: 10
Published: almost 4 years ago
10.7717/peerj.11983
Identifying transcript 5′ capped ends in <i>Plasmodium falciparum</i>Cited by: 2
Author(s): Philip Shaw, Jittima Piriyapongsa, Pavita Kaewprommal, Chayaphat Wongsombat, Chadapohn Chaosrikul, Krirkwit Teeravajanadet, Manon Boonbangyang, Chairat Uthaipibull, Sumalee Kamchonwongpaisan, Sissades Tongsima
Software Mentions: 8
Published: about 3 years ago
10.26508/lsa.202000897
Tissue-selective alternate promoters guide NLRP6 expressionCited 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
10.1016/j.molcel.2021.03.013
Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repressionCited by: 17
Author(s): Amy Tresenrider, Kaitlin Morse, Victoria Jorgensen, Minghao Chia, Hanna Liao, Folkert J. van Werven, Elçin Ünal
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pbio.2003903
Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila developmentCited by: 62
Author(s): Hong Zhang, Shengqian Dou, Feng He, Junjie Luo, Liping Wei, Jian Lü
Software Mentions: 6
Published: over 6 years ago
10.1371/journal.pgen.1008864
Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropodsCited by: 52
Author(s): Samuel H. Lewis, Laura Ross, Stevie A. Bain, Eleni Pahita, Stephen A. Smith, Richard Cordaux, Eric A. Miska, Boris Lenhard, Francis M. Jiggins, Peter Sarkies
Software Mentions: 6
Published: over 4 years ago
10.1371/journal.pgen.1006231
Linking Core Promoter Classes to Circadian TranscriptionCited by: 7
Author(s): Pål O. Westermark
Software Mentions: 5
Published: over 8 years ago
10.1186/s13059-021-02460-6
Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritabilityCited by: 23
Author(s): Xin Ge, Mojca Frank-Bertoncelj, Kerstin Klein, Amanda McGovern, Tadeja Kuret, Miranda Houtman, Blaž Burja, Raphael Micheroli, Chenfu Shi, Miriam Marks, Andrew Filer, Christopher D. Buckley, Gisela Orozco, Oliver Distler, Andrew P. Morris, Paul Martin, Stephen Eyre, Caroline Ospelt
Software Mentions: 5
Published: about 3 years ago
10.1038/s41598-018-25748-3
Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR/Cas9Cited by: 15
Author(s): Yoshiyuki Sakaguchi, Keizo Nishikawa, Shigeto Seno, Hideo Matsuda, Hiroshi Takayanagi, Masaru Ishii
Software Mentions: 5
Published: over 6 years ago
10.15252/embj.2020105564
Integrator is recruited to promoter‐proximally paused RNA Pol II to generate <i>Caenorhabditis elegans</i> piRNA precursorsCited by: 21
Author(s): Toni Beltran, Eleni Pahita, Subhanita Ghosh, Boris Lenhard, Peter Sarkies
Software Mentions: 4
Published: almost 4 years ago
10.1186/s12864-017-3863-7
A high-quality annotated transcriptome of swine peripheral bloodCited by: 7
Author(s): Haibo Li, Timothy P. L. Smith, Dan Nonneman, Jack C. M. Dekkers, Christopher K. Tuggle
Software Mentions: 3
Published: over 7 years ago
10.3389/fcell.2021.679544
CRISPR-Cas9 Editing of Human Histone Deubiquitinase Gene USP16 in Human Monocytic Leukemia Cell Line THP-1Cited by: 2
Author(s): Iveta Gažová, Lucas Lefèvre, Stephen J. Bush, Rocío Rojo, David Hume, Andreas Lengeling, Kim M. Summers
Software Mentions: 3
Published: over 3 years ago
10.3389/fncel.2019.00391
The WWOX Gene Influences Cellular Pathways in the Neuronal Differentiation of Human Neural Progenitor CellsCited by: 11
Author(s): Katarzyna Kośla, Elżbieta Płuciennik, Ewa Styczeń-Binkowska, Magdalena Nowakowska, Magdalena Orzechowska, Andrzej K. Bednarek
Software Mentions: 3
Published: about 5 years ago
10.1186/s12915-021-01004-5
Transcription initiation of distant core promoters in a large-sized genome of an insectCited by: 2
Author(s): Qing Liu, Feng Jiang, Jie Zhang, Li Xiao, Le Kang
Software Mentions: 3
Published: over 3 years ago
10.1016/j.isci.2020.101741
The PWWP2A Histone Deacetylase Complex Represses Intragenic Spurious Transcription Initiation in mESCsCited by: 8
Author(s): Guifeng Wei, Neil Brockdorff, Tianyi Zhang
Software Mentions: 2
Published: about 4 years ago
10.1186/s12864-020-07353-9
Alternative Polyadenylation in response to temperature stress contributes to gene regulation in Populus trichocarpaCited by: 6
Author(s): Chao Yan, Yupeng Wang, Tao Lyu, Zhikang Hu, Ning Ye, Weixin Liu, Jiyuan Li, Xiaohua Yao, Hengfu Yin
Software Mentions: 2
Published: almost 4 years ago
10.3390/dj9040044
Effect of Butyric Acid in the Proliferation and Migration of Junctional Epithelium in the Progression of Periodontitis: An In Vitro StudyCited by: 2
Author(s): Taichi Ishikawa, Daisuke Sasaki, Ryo Aizawa, Yu Shimoyama, Masahide Yamamoto, Tarou Irié, Masahiro Sasaki
Software Mentions: 2
Published: over 3 years ago
10.3389/fcell.2020.00498
The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1Cited by: 22
Author(s): Iveta Gažová, Lucas Lefèvre, Stephen J. Bush, Sara Clohisey, Peter Arner, Michiel de Hoon, Jessica Severin, Lucas van Duin, Robin Andersson, Andreas Lengeling, David Hume, Kim M. Summers
Software Mentions: 2
Published: over 4 years ago
10.1038/srep28594
The rubber tree genome shows expansion of gene family associated with rubber biosynthesisCited by: 91
Author(s): Nyok-Sean Lau, Yuko Makita, Mika Kawashima, Todd D. Taylor, Shinji Kondo, Ahmad Sofiman Othman, Alexander Chong Shu‐Chien, Minami Matsui
Software Mentions: 2
Published: over 8 years ago
10.1063/5.0041227
Investigation of the hepatic development in the coculture of hiPSCs-derived LSECs and HLCs in a fluidic microenvironmentCited by: 7
Author(s): Mathieu Danoy, Yannick Tauran, Stéphane Poulain, Rachid Jellali, Johanna Bruce, Marjorie Leduc, Morgane Le Gall, Yuta Koui, Hiroshi Arakawa, Françoise Gilard, Bertrand Gakière, Yukio Kato, Charles Plessy, Taketomo Kido, Atsushi Miyajima, Yasuyuki Sakai, Éric Leclerc
Software Mentions: 2
Published: over 3 years ago
10.1186/s12864-020-06787-5
Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seqCited by: 62
Author(s): Lia Chappell, Philipp Ross, Lindsey M. Orchard, Timothy J. Russell, Thomas D. Otto, Matthew Berriman, Julian C. Rayner, Manuel Llinás
Software Mentions: 1
Published: over 4 years ago
10.1186/s12864-018-4504-5
Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordateCited by: 12
Author(s): Gemma B. Danks, Pavla Navrátilová, Boris Lenhard, Eric M. Thompson
Software Mentions: 1
Published: over 6 years ago
10.1038/s42003-021-02340-6
Evolution of tissue and developmental specificity of transcription start sites in Bos taurus indicusCited by: 2
Author(s): Mehrnush Forutan, Elizabeth M. Ross, Amanda J. Chamberlain, Loan Nguyen, Brett Mason, S. S. Moore, Josie B. Garner, Ruidong Xiang, Ben J. Hayes
Software Mentions: 1
Published: over 3 years ago
10.1038/s41416-020-0971-y
Mac-2-binding protein glycan isomer enhances the aggressiveness of hepatocellular carcinoma by activating mTOR signalingCited by: 19
Author(s): Dolgormaa Gantumur, Norifumi Harimoto, Norihiro Ishii, Takahiro Yamanaka, Kaoru Hagiwara, Mariko Tsukagoshi, Takamichi Igarashi, Akira Watanabe, Norio Kubo, Kenichiro Araki, Tadashi Handa, Takehiko Yokobori, Tetsunari Oyama, Hiroyuki Kuwano, Ken Shirabe
Software Mentions: 1
Published: over 4 years ago