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: seqLogo

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

Sequence logos for DNA sequence alignments
2 versions
Latest release: about 1 year ago
12 dependent packages
300,976 downloads total

Papers Mentioning seqLogo 24

10.3390/genes10110937

NF-YA Overexpression in Lung Cancer: LUSC
Cited by: 28
Author(s): Eugenia Bezzecchi, Mirko Ronzio, Diletta Dolfini, Roberto Mantovani
Software Mentions: 8
Published: about 5 years ago

Analysis of 5’ gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals
Cited by: 7
Author(s): Nathaniel J. Davies, Peter Krusche, Eran Tauber, Sascha Ott
Software Mentions: 7
Published: about 9 years ago

10.1186/s12864-017-4304-3

Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence
Cited by: 71
Author(s): Hana Hall, Patrick S Medina, Daphne A. Cooper, Spencer E. Escobedo, Jeremiah Rounds, Kaelan J. Brennan, Christopher Vincent, Pedro Miura, R. W. Doerge, Vikki M. Weake
Software Mentions: 7
Published: about 7 years ago

10.7554/eLife.15716

The Arabidopsis thaliana mobilome and its impact at the species level
Cited by: 242
Author(s): Leandro Quadrana, Amanda Bortolini Silveira, George F. Mayhew, Chantal LeBlanc, Robert A. Martienssen, Jeffrey A. Jeddeloh, Vincent Colot
Software Mentions: 5
Published: over 8 years ago

10.1186/1471-2164-15-925

SeAMotE: a method for high-throughput motif discovery in nucleic acid sequences
Cited by: 23
Author(s): Antonella Federico, Davide Cirillo, Riccardo Delli Ponti, Gian Gaetano Tartaglia
Software Mentions: 5
Published: about 10 years ago

10.1371/journal.pone.0107259

Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
Cited by: 48
Author(s): Melanie Spornraft, Benedikt Kirchner, Bettina Haase, Vladimı́r Beneš, Michael W. Pfaffl, Irmgard Riedmaier
Software Mentions: 4
Published: over 10 years ago

10.1186/s12859-018-2489-3

A new sequence logo plot to highlight enrichment and depletion
Cited by: 43
Author(s): Kushal Kumar Dey, Dongyue Xie, Matthew Stephens
Software Mentions: 4
Published: about 6 years ago

10.1186/s13029-015-0040-8

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence
Cited by: 3
Author(s): Connor H. Fortin, Katharina Schulze, Gregory A. Babbitt
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pbio.1002307

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets
Cited by: 51
Author(s): Gregory J. Hogan, Patrick O. Brown, Daniel Herschlag
Software Mentions: 4
Published: about 9 years ago

10.1186/s12859-015-0767-x

DiffLogo: a comparative visualization of sequence motifs
Cited by: 56
Author(s): Martin Nettling, Hendrik Treutler, Jan Grau, Jens Keilwagen, Stefan Posch, Ivo Große
Software Mentions: 3
Published: about 9 years ago

10.3389/fnagi.2020.603793

Sporadic Parkinson’s Disease Potential Risk Loci Identified in Han Ancestry of Chinese Mainland
Cited by: 2
Author(s): Bo Wang, Xin Liu, Shengyuan Xu, Zheng Liu, Yong Zhu, Xiong Zhang, Renshi Xu
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12977-017-0378-x

Modulation of the functional association between the HIV-1 intasome and the nucleosome by histone amino-terminal tails
Cited by: 14
Author(s): Mohamed Salah Benleulmi, Julien Matysiak, Xavier Robert, Csaba Miskey, Eric Mauro, Delphine Lapaillerie, Paul Lesbats, Stéphane Chaignepain, Daniel R. Henríquez, Christina Calmels, Oyindamola Oladosu, Eloïse Thierry, Óscar León, Marc Lavigne, Marie‐Line Andréola, Olivier Delelis, Zoltán Ivics, Marc Ruff, Patrice Gouet, Vincent Parissi
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1004813

Genetic Analysis of the Cardiac Methylome at Single Nucleotide Resolution in a Model of Human Cardiovascular Disease
Cited by: 18
Author(s): Michelle D. Johnson, Michael Mueller, Martyna Adamowicz-Brice, Melissa J. Collins, Pascal Gellert, Klio Maratou, Prashant K. Srivastava, Maxime Rotival, Shahena Butt, Laurence Gamé, Santosh S. Atanur, Nicholas Silver, Penny J. Norsworthy, Sarah R. Langley, Enrico Petretto, Michal Pravenec, Timothy J. Aitman
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0004495

Query Large Scale Microarray Compendium Datasets Using a Model-Based Bayesian Approach with Variable Selection
Cited by: 9
Author(s): Ming Hu, Zhaohui S. Qin
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0047314

Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli
Cited by: 42
Author(s): Chi Yang, Tzu Wen Huang, Shiau Yi Wen, Ching-Yun Chang, Shih Feng Tsai, Whei-Fen Wu, Chia Hui Chang
Software Mentions: 2
Published: about 12 years ago

10.1093/bioinformatics/btw024

TFBSTools: an R/bioconductor package for transcription factor binding site analysis
Cited by: 239
Author(s): Ge Tan, Boris Lenhard
Software Mentions: 2
Published: almost 9 years ago

10.1093/bioinformatics/btt297

viRome: an R package for the visualization and analysis of viral small RNA sequence datasets
Cited by: 40
Author(s): Michael Watson, Esther Schnettler, Alain Kohl
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-15-750

Characteristics of replication-independent endogenous double-strand breaks in Saccharomyces cerevisiae
Cited by: 8
Author(s): Monnat Pongpanich, Maturada Patchsung, Jirapan Thongsroy, Apiwat Mutirangura
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1002339

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo
Cited by: 222
Author(s): Chung Yi Nien, Hsiao Lan Liang, Stephen Butcher, Yujia Sun, Shengbo Fu, Tenzin Gocha, Nikolai Kirov, J. Robert Manak, Christine Rushlow
Software Mentions: 2
Published: about 13 years ago

10.1186/s13059-020-01982-9

Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins
Cited by: 124
Author(s): Eric L. Van Nostrand, Gabriel A. Pratt, Brian A. Yee, Emily C. Wheeler, Steven M. Blue, Jasmine R. Mueller, Samuel S. Park, Keri E. Garcia, Chelsea Gelboin-Burkhart, Thai B. Nguyen, Ines Rabano, Rebecca Stanton, Balaji Sundararaman, Ruth Wang, Xiang‐Dong Fu, Brenton R. Graveley, G Yeo
Software Mentions: 1
Published: over 4 years ago

10.15252/msb.20145524

Causal signals between codon bias, <scp>mRNA</scp> structure, and the efficiency of translation and elongation
Cited by: 231
Author(s): Cristina Bianca Pop, Silvi Rouskin, Nicholas T. Ingolia, Lianshu Han, Eric M. Phizicky, Jonathan S. Weissman, Daphne Koller
Software Mentions: 1
Published: about 10 years ago

10.1093/database/bav072

Database of RNA binding protein expression and disease dynamics (READ DB)
Cited by: 10
Author(s): Seyedsasan Hashemikhabir, Yaseswini Neelamraju, Sarath Chandra Janga
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pgen.1006761

Identification of breast cancer associated variants that modulate transcription factor binding
Cited by: 37
Author(s): Yunxian Liu, Ninad M. Walavalkar, Mikhail G. Dozmorov, Stephen S. Rich, Mete Civelek, Kristin A. Guertin
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-021-86225-y

Identification of deleterious recessive haplotypes and candidate deleterious recessive mutations in Japanese Black cattle
Cited by: 5
Author(s): Shinji Sasaki, Toshio Watanabe, Takayuki Ibi, Kiyotoshi Hasegawa, Yoichi Sakamoto, Shunsuke Moriwaki, Kazuhito Kurogi, Akifumi Ogino, Takanori Yasumori, Hiroyuki Wakaguri, Eiji Muraki, Youko Miki, Yuichi Yoshida, Yoshinobu Inoue, Ichiro Tabuchi, Ken Iwao, Taichi Arishima, Keisuke Kawashima, Masao Watanabe, Sumio Sugano, Yoshikazu Sugimoto, Yutaka Suzuki
Software Mentions: 1
Published: almost 4 years ago