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: ShortRead
https://packages.ecosyste.ms/registries/bioconductor.org/packages/ShortRead
FASTQ input and manipulation
2 versions
Latest release: 11 months ago
35 dependent packages
1,533,617 downloads total
Papers Mentioning ShortRead 119
10.1371/journal.pone.0134481
High Throughput Sequencing of Entamoeba 27nt Small RNA Population Reveals Role in Permanent Gene Silencing But No Effect on Regulating Gene Expression Changes during Stage Conversion, Oxidative, or Heat Shock StressCited by: 12
Author(s): Hanbang Zhang, Gretchen Ehrenkaufer, Dipak Manna, Neil Hall, Upinder Singh
Software Mentions: 1
Published: about 9 years ago
10.4049/jimmunol.2000647
MicroRNA-142 Critically Regulates Group 2 Innate Lymphoid Cell Homeostasis and FunctionCited by: 13
Author(s): Luke B. Roberts, Geraldine M. Jowett, Emily Read, Tomasz Zabinski, Rita Berkachy, Murray E. Selkirk, Ian Jackson, Umar Niazi, Nelomi Anandagoda, Masatake Araki, Kimi Araki, Jagath Kasturiarachchi, Chela James, Tariq Enver, Rachael Nimmo, Rita Antunes Dos Reis, Jane K. Howard, Joana F. Neves, Graham Lord
Software Mentions: 1
Published: over 3 years ago
10.7717/peerj.2693
Mining SNPs in extracellular vesicular transcriptome of<i>Trypanosoma cruzi</i>: a step closer to early diagnosis of neglected Chagas diseaseCited by: 5
Author(s): Pallavi Gaur, Anoop Chaturvedi
Software Mentions: 1
Published: almost 8 years ago
10.1186/s12864-015-2048-5
Weevil endosymbiont dynamics is associated with a clamping of immunityCited by: 27
Author(s): Florent Masson, Yves Moné, Aurélien Vigneron, Agnès Vallier, Nicolas Parisot, Carole Vincent-Monégat, Séverine Balmand, Marie-Christine Carpentier, Anna Zaidman-Rémy, Abdelaziz Heddi
Software Mentions: 1
Published: almost 9 years ago
10.1186/s12885-020-06817-1
Chromosomal instability in untreated primary prostate cancer as an indicator of metastatic potentialCited by: 9
Author(s): Eric T. Miller, Sungyong You, Radu M. Cadaneanu, Minhyung Kim, Jennifer R. Yoon, Sandy T. Liu, Xinmin Li, Lorna Kwan, Jennelle C. Hodge, Michael J. Quist, Catherine S. Grasso, Michael Lewis, Beatrice S. Knudsen, Michael R. Freeman, Isla P. Garraway
Software Mentions: 1
Published: over 4 years ago
10.1186/1756-3305-7-430
The sialotranscriptome of Amblyomma triste, Amblyomma parvum and Amblyomma cajennense ticks, uncovered by 454-based RNA-seqCited by: 62
Author(s): Gustavo García, Luiz Gustavo Gardinassi, José M. C. Ribeiro, Elen Anatriello, Beatriz Rossetti Ferreira, Higo Nasser Santanna Moreira, Cláudio Mafra, Maria Marlene Martins, Matías Pablo Juan Szabó, Isabel Kinney Ferreira de Miranda Santos, Sandra Regina Maruyama
Software Mentions: 1
Published: about 10 years ago
10.1093/aobpla/pls047
SEPALLATA1/2-suppressed mature apples have low ethylene, high auxin and reduced transcription of ripening-related genesCited by: 52
Author(s): Robert J. Schaffer, Hilary S. Ireland, John J. Ross, Toby John Ling, Karine David
Software Mentions: 1
Published: over 11 years ago
10.3390/genes10110872
Genome Maintenance Proteins Modulate Autoimmunity Mediated Primed Adaptation by the Escherichia coli Type I-E CRISPR-Cas SystemCited by: 8
Author(s): Elena Kurilovich, Anna Shiriaeva, Anastasia Metlitskaya, Natalia Morozova, Ivana Ivančić-Baće, Konstantin Severinov, Ekaterina Savitskaya
Software Mentions: 1
Published: almost 5 years ago
10.1016/j.gdata.2017.07.006
Profiling and characterization of a longissimus dorsi muscle microRNA dataset from an F 2 Duroc × Pietrain pig resource populationCited by: 4
Author(s): Kaitlyn R. Daza, Juan P. Steibel, Deborah Velez‐Irizarry, Nancy E. Raney, R. O. Bates, Catherine W. Ernst
Software Mentions: 1
Published: about 7 years ago
10.1186/1756-0381-5-6
How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?Cited by: 36
Author(s): Xiaoqing Yu, Kishore Guda, Joseph E. Willis, Marty L Veigl, Benlian Wang, Sanford D. Markowitz, Mark D. Adams, Shuying Sun
Software Mentions: 1
Published: about 12 years ago
10.1038/s41438-020-0299-z
The RhHB1/RhLOX4 module affects the dehydration tolerance of rose flowers (Rosa hybrida) by fine-tuning jasmonic acid levelsCited by: 13
Author(s): Youwei Fan, Jitao Liu, Jing Zou, Xiangyu Zhang, Liwei Jiang, Kun Liu, Peitao Lü, Junping Gao, Changqing Zhang
Software Mentions: 1
Published: over 4 years ago
10.1016/j.immuni.2013.08.038
Germinal Center Centroblasts Transition to a Centrocyte Phenotype According to a Timed Program and Depend on the Dark Zone for Effective SelectionCited by: 213
Author(s): Oliver Bannard, Robert M. Horton, Christopher D.C. Allen, Jinping An, Takashi Nagasawa, Jason G. Cyster
Software Mentions: 1
Published: almost 11 years ago
10.1186/s40104-018-0241-5
Imputation from SNP chip to sequence: a case study in a Chinese indigenous chicken populationCited by: 32
Author(s): Shaopan Ye, Xiaolong Yuan, Xueni Lin, Ning Gao, Yuanyu Luo, Zanmou Chen, Jiaqi Li, Xiquan Zhang, Zhe Zhang
Software Mentions: 1
Published: over 6 years ago
10.3390/ijms18102046
Characterization of Growth Hormone Resistance in Experimental and Ulcerative ColitisCited by: 15
Author(s): Christoffer Soendergaard, Peter Helding Kvist, Peter Thygesen, Mats Reslow, Ole Haagen Nielsen, John J. Kopchick, Thomas Lindebo Holm
Software Mentions: 1
Published: almost 7 years ago
10.1186/1756-0500-7-144
Analysis options for high-throughput sequencing in miRNA expression profilingCited by: 67
Author(s): Tomasz Stokowy, Markus Eszlinger, Michał Świerniak, Krzysztof Fujarewicz, Barbara Jarząb, Ralf Paschke, Knut Krohn
Software Mentions: 1
Published: over 10 years ago
10.1186/s13104-016-2137-9
Novel microsatellite markers for Distylium lepidotum (Hamamelidaceae) endemic to the Ogasawara IslandsCited by: 3
Author(s): Kyoko Sugai, Suzuki Setsuko
Software Mentions: 1
Published: about 8 years ago
10.1371/journal.pone.0042882
Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed TissueCited by: 162
Author(s): John Morlan, Kunbin Qu, Dominick Sinicropi
Software Mentions: 1
Published: about 12 years ago
10.1186/s12864-015-1948-8
Generation of a de novo transcriptome from equine lamellar tissueCited by: 13
Author(s): Heather M. Holl, Shan Gao, Zhangjun Fei, Caroline Andrews, Samantha A. Brooks
Software Mentions: 1
Published: almost 9 years ago
10.1128/mBio.02169-18
Avoidance of Trinucleotide Corresponding to Consensus Protospacer Adjacent Motif Controls the Efficiency of Prespacer Selection during Primed AdaptationCited by: 11
Author(s): Olga Musharova, Danylo Vyhovskyi, Sofia Medvedeva, Jelena Guzina, Yulia Zhitnyuk, M. Djordjevic, Konstantin Severinov, Ekaterina Savitskaya
Software Mentions: 1
Published: over 5 years ago