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: Rsubread
https://packages.ecosyste.ms/registries/bioconductor.org/packages/Rsubread
Mapping, quantification and variant analysis of sequencing data
2 versions
Latest release: about 1 year ago
14 dependent packages
287,298 downloads total
Papers Mentioning Rsubread 331
10.3390/ijms20143457
Unravelling the Role of Trophoblastic-Derived Extracellular Vesicles in Regulatory T Cell DifferentiationCited by: 25
Author(s): Árpád Ferenc Kovács, Nóra Fekete, Lilla Turiák, András Ács, László Kőhidai, Edit I. Buzás, Éva Pállinger
Software Mentions: 2
Published: over 5 years ago
10.1016/j.stemcr.2018.03.011
HDAC1 and HDAC2 Modulate TGF-β Signaling during Endothelial-to-Hematopoietic TransitionCited by: 25
Author(s): Roshana Thambyrajah, Muhammad Zaki Hidayatullah Fadlullah, Martin Proffitt, Rahima Patel, Shaun M. Cowley, Valérie Kouskoff, Georges Lacaud
Software Mentions: 2
Published: over 6 years ago
10.3390/biology7020031
A Rare De Novo RAI1 Gene Mutation Affecting BDNF-Enhancer-Driven Transcription Activity Associated with Autism and Atypical Smith-Magenis Syndrome PresentationCited by: 12
Author(s): Clemer Abad, Melissa M. Cook, Lei Cao, Julie R. Jones, Nalini R. Rao, Lynn Dukes-Rimsky, Rini Pauly, Cindy Skinner, Yunsheng Wang, Feng Luo, Roger E. Stevenson, Katherina Walz, Anand Srivastava
Software Mentions: 2
Published: over 6 years ago
10.1186/s12977-019-0505-y
HIV-1 Rev interacts with HERV-K RcREs present in the human genome and promotes export of unspliced HERV-K proviral RNACited by: 7
Author(s): Laurie R. Gray, Rachel E. Jackson, Patrick E. H. Jackson, Stefan Bekiranov, David Rekosh, Marie‐Louise Hammarskjöld
Software Mentions: 2
Published: almost 5 years ago
10.1038/s41598-020-66866-1
Diversity and function of terpene synthases in the production of carrot aroma and flavor compoundsCited by: 16
Author(s): Andrew Muchlinski, Mwafaq Ibdah, Shelby Ellison, Mossab Yahyaa, Bhagwat Nawade, Suzanne Laliberte, Douglas Senalik, Petr Šimon, Susan R. Whitehead, Dorothea Tholl
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-020-78560-3
Pan-cancer analysis of genomic properties and clinical outcome associated with tumor tertiary lymphoid structureCited by: 43
Author(s): Ziying Lin, Lixia Huang, Shaoli Li, Jincui Gu, Xiaoxian Cui, Yunyun Zhou
Software Mentions: 1
Published: almost 4 years ago
10.3389/fphys.2020.00052
Phenotypic and Transcriptomic Response of the Grasshopper Oedaleus asiaticus (Orthoptera: Acrididae) to Toxic RutinCited by: 8
Author(s): Xunbing Huang, Shenjin Lv, Zehua Zhang, Babar Hussain Chang
Software Mentions: 1
Published: over 4 years ago
10.3390/v13091768
Nafamostat–Interferon-α Combination Suppresses SARS-CoV-2 Infection In Vitro and In Vivo by Cooperatively Targeting Host TMPRSS2Cited by: 16
Author(s): Aleksandr Ianevski, Rouan Yao, Hilde Lysvand, Gunnveig Grødeland, Nicolas Legrand, Valentyn Oksenych, Eva Žusinaite, Tanel Tenson, Magnar Bjørås, Denis E. Kainov
Software Mentions: 1
Published: about 3 years ago
10.1093/annonc/mdw122
Tumourigenic non-small-cell lung cancer mesenchymal circulating tumour cells: a clinical case studyCited by: 75
Author(s): Christopher J. Morrow, Francesca Trapani, Robert Metcalf, Giulia Bertolini, Cassandra L. Hodgkinson, Garima Khandelwal, Paul A. Kelly, Melanie Galvin, Louise Carter, Kathryn Simpson, Stuart C. Williamson, Christopher Wirth, Nicole Simms, L. Frankliln, Kristopher K. Frese, Dominic G. Rothwell, Daisuke Nonaka, Crispin Miller, Ged Brady, Fiona Blackhall, Caroline Dive
Software Mentions: 1
Published: over 8 years ago
10.1186/s12920-019-0630-4
Identification of lung cancer gene markers through kernel maximum mean discrepancy and information entropyCited by: 4
Author(s): Zhixun Zhao, Hui Peng, Xiaocai Zhang, Yi Zheng, Fang Chen, Liang Fang, Jinyan Li
Software Mentions: 1
Published: almost 5 years ago
10.1186/s12864-017-3857-5
Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reeseiCited by: 48
Author(s): Gustavo Pagotto Borin, Camila Cristina Sanchez, Eliane Silva de Santana, Guilherme Keppe Zanini, Renato Augusto Corrêa dos Santos, Angélica de Oliveira Pontes, Aline Tieppo de Souza, Roberta Maria Menegaldo Tavares Soares Dal’Mas, Diego Mauricio Riaño‐Pachón, Gustavo H. Goldman, Juliana Velasco de Castro Oliveira
Software Mentions: 1
Published: over 7 years ago
10.3389/fcell.2021.693154
Linking Chromosomal Silencing With Xist Expression From Autosomal Integrated TransgenesCited by: 4
Author(s): Ikrame Naciri, Bryan Lin, Chiu-Ho Webb, Shan Jiang, Sarah Carmona, Wenzhu Liu, A Mortazavi, Sha Sun
Software Mentions: 1
Published: over 3 years ago
10.3389/fcell.2020.00237
Site-Dependent Lineage Preference of Adipose Stem CellsCited by: 11
Author(s): Tingliang Wang, Ryan C. Hill, Monika Dzieciątkowska, Lian Zhu, Aniello M. Infante, Gangqing Hu, Kirk C. Hansen, Ming Pei
Software Mentions: 1
Published: over 4 years ago
10.1093/hmg/ddv637
Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomicsCited by: 83
Author(s): Adam E. Handel, Satyan Chintawar, Tatjana Lalic, Emma Whiteley, Jane Vowles, Alice Giustacchini, Karène Argoud, P. Sopp, Mahito Nakanishi, Rory Bowden, Sally A. Cowley, Sarah E. Newey, Colin J. Akerman, Chris P. Ponting, M Z Cader
Software Mentions: 1
Published: almost 9 years ago
10.3390/v13020292
Comparative Transcriptome Profiling of Human and Pig Intestinal Epithelial Cells after Porcine Deltacoronavirus InfectionCited by: 11
Author(s): Diana Cruz-Pulido, Patricia A. Boley, Wilberforce Zachary Ouma, Moyasar A. Alhamo, Linda J. Saif, Scott P. Kenney
Software Mentions: 1
Published: almost 4 years ago
10.3390/v12060642
Potential Antiviral Options against SARS-CoV-2 InfectionCited by: 87
Author(s): Aleksandr Ianevski, Rouan Yao, Mona Høysæter Fenstad, Svetlana Biza, Eva Žusinaite, Tuuli Reisberg, Hilde Lysvand, Kirsti Løseth, Veslemøy Malm Landsem, Janne Fossum Malmring, Valentyn Oksenych, Sten Even Erlandsen, Per Arne, Lars Hagen, Caroline Hild Pettersen, Tanel Tenson, Jan Egil Afset, Svein Arne Nordbø, Magnar Bjørås, Denis E. Kainov
Software Mentions: 1
Published: over 4 years ago
10.3390/cells10061452
Identification of Lung and Blood Microbiota Implicated in COVID-19 PrognosisCited by: 7
Author(s): Kypros Dereschuk, Lauren Apostol, Ishan Ranjan, Jaideep Chakladar, Wei Tse Li, Mahadevan Rajasekaran, Eric Y. Chang, Weg M. Ongkeko
Software Mentions: 1
Published: over 3 years ago
10.1242/bio.056515
A glucose-supplemented diet enhances gut barrier integrity in <i>Drosophila</i>Cited by: 8
Author(s): Anthony Galenza, Edan Foley
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0228730
Codon and amino acid content are associated with mRNA stability in mammalian cellsCited by: 47
Author(s): Megan E. Forrest, Otis Pinkard, Sophie Martin, Thomas J. Sweet, Gavin Hanson, Jeff Coller
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pone.0194581
Transcriptome analysis of genetically matched human induced pluripotent stem cells disomic or trisomic for chromosome 21Cited by: 32
Author(s): Patrick Gonzales, Christine M. Roberts, Virginia Fonte, Connor Jacobsen, Gretchen H. Stein, Christopher D. Link
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pbio.3000638
Bacterially produced metabolites protect C. elegans neurons from degenerationCited by: 44
Author(s): Arlés Urrutia, Víctor Antonio García-Angulo, Andrés Fuentes-Flores, Mauricio Caneo, Marcela Legüe, Sebastián Urquiza, Scarlett E. Delgado, Juan A. Ugalde, Paula Burdisso, Andrea Calixto
Software Mentions: 1
Published: over 4 years ago
10.1186/s12967-019-1942-z
Akt-activated endothelium promotes ovarian cancer proliferation through notch activationCited by: 17
Author(s): Jessica Hoarau-Véchot, Cyril Touboul, Najeeb Halabi, Morgane Blot-Dupin, Raphaël Lis, Charbel Abi Khalil, Shahin Rafii, Arash Rafii, Jennifer Pasquier
Software Mentions: 1
Published: over 5 years ago
10.1038/s41598-017-11312-y
Molecular insights into photosynthesis and carbohydrate metabolism in Jatropha curcas grown under elevated CO2 using transcriptome sequencing and assemblyCited by: 17
Author(s): S. Kumar, Rachapudi Venkata Sreeharsha, Shalini Mudalkar, Prasad M Sarashetti, A. Ramachandra Reddy
Software Mentions: 1
Published: about 7 years ago
10.1038/s41598-018-33072-z
Human serum albumin alters specific genes that can play a role in survival and persistence in Acinetobacter baumanniiCited by: 40
Author(s): Brettni Quinn, Nyah Rodman, Eugenio Jara, Jennifer S. Fernandez, Jasmine Martinez, Germán Matías Traglia, Sabrina Montaña, Virginia Cantera, Kori Place, Robert A. Bonomo, Andrés Iriarte, María Soledad Ramírez
Software Mentions: 1
Published: about 6 years ago
10.1186/s13075-019-1894-y
RNA sequencing of mesenchymal stem cells reveals a blocking of differentiation and immunomodulatory activities under inflammatory conditions in rheumatoid arthritis patientsCited by: 11
Author(s): José Ramón Lamas, Benjamín Fernández-Gutiérrez, Arkaitz Mucientes, Fernando Marco, Yaiza Lópiz, Lydia Abásolo, Luis Rodríguez‐Rodríguez
Software Mentions: 1
Published: over 5 years ago
10.1038/s41598-019-42005-3
Cell cycle genes are downregulated after adipogenic triggering in human adipose tissue-derived stem cells by regulation of mRNA abundanceCited by: 22
Author(s): Bruna Hilzendeger Marcon, Patrícia Shigunov, Lucía Spangenberg, Isabela Tiemy Pereira, Alessandra Melo de Aguiar, Rocío Amorín, Carmen K. Rebelatto, Alejandro Correa, Bruno Dallagiovanna
Software Mentions: 1
Published: over 5 years ago
10.14814/phy2.13183
Interaction between plasma fetuin-A and free fatty acids predicts changes in insulin sensitivity in response to long-term exerciseCited by: 30
Author(s): Sindre Lee, Frode Norheim, Hanne Løvdal Gulseth, Torgrim M. Langleite, Kristoffer Jensen Kolnes, Daniel S. Tangen, Hans Kristian Stadheim, Gregor D. Gilfillan, Torgeir Holen, Kåre I. Birkeland, Jørgen Jensen, Christian A. Drevon
Software Mentions: 1
Published: over 7 years ago
10.3390/genes11030267
A Comprehensive Transcriptomics Analysis Reveals Long Non-Coding RNA to Be Involved in the Key Metabolic Pathway in Response to Waterlogging Stress in MaizeCited by: 24
Author(s): Feng Yu, Zengdong Tan, Fang Tian, Kaizhi Tang, Kun Liang, Fazhan Qiu
Software Mentions: 1
Published: over 4 years ago
10.1038/s41598-019-52280-9
The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAomeCited by: 3
Author(s): Deevina Arasaratnam, Katrina M. Bell, Choon Boon Sim, Kathy Koutsis, David J. Anderson, Elizabeth Qian, Edouard G. Stanley, Michael Cheung, Alicia Oshlack, Anthony J. White, Charbel Abi Khalil, James E. Hudson, Enzo R. Porrello, David A. Elliott
Software Mentions: 1
Published: about 5 years ago
10.1534/g3.119.400249
Maternal Experience Leads to Lasting Gene Expression Changes in Some Regions of the Mouse BrainCited by: 8
Author(s): Michelle N. Arbeitman
Software Mentions: 1
Published: over 5 years ago