bioconductor: QuasR | Projects | Ecosyste.ms: Papers

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: over 8 years ago

Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans
Cited by: 43
Author(s): Milou W.M. Meeuse, Yannick P Hauser, Lucas J Morales Moya, Gert‐Jan Hendriks, Jan Eglinger, Guy Bogaarts, Charisios D. Tsiairis, Helge Großhans
Software Mentions: 14
Published: over 4 years ago

10.1371/journal.pgen.1007102

Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content
Cited by: 16
Author(s): Daniele Colombo, Lukas Burger, Tuncay Baubec, Dirk Schübeler
Software Mentions: 10
Published: about 7 years ago

10.1128/mBio.02683-20

The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral UL4 / UL5 Transcripts
Cited by: 23
Author(s): Ana Cristina Gonzalez-Perez, Markus Stempel, Emanuel Wyler, Christian Urban, Antonio Piras, Thomas Hennig, Sabina Ganskih, Yuanjie Wei, Albert Heim, Markus Landthaler, Andreas Pichlmair, Lars Dölken, Mathias Munschauer, Florian Erhard, Melanie M. Brinkmann
Software Mentions: 6
Published: over 3 years ago

10.26508/lsa.201800175

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
Cited by: 16
Author(s): Charlotte Soneson, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D. Robinson
Software Mentions: 6
Published: almost 6 years ago

10.18632/oncotarget.16493

ERK signalling modulates epigenome to drive epithelial to mesenchymal transition
Cited by: 20
Author(s): Mohit Navandar, Angela Garding, Sanjeeb Kumar Sahu, Abhijeet Pataskar, Sandra Schick, Vijay Tiwari
Software Mentions: 5
Published: almost 8 years ago

10.15252/emmm.202013162

The NFIB‐ERO1A axis promotes breast cancer metastatic colonization of disseminated tumour cells
Cited by: 23
Author(s): Federica Zilli, Pedro Marques Ramos, Priska Auf der Maur, Charly Jehanno, Atul Sethi, Marie–May Coissieux, Tobias Eichlisberger, Loïc Sauteur, Adelin Rouchon, Laura Bonapace, Joana Couto, Roland Rad, Michael Rugaard Jensen, Andrea Banfi, Michael Stadler, Mohamed Bentires‐Alj
Software Mentions: 5
Published: almost 4 years ago

10.7554/eLife.64932

Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci
Cited by: 41
Author(s): Victoria J Sugrue, Joseph A. Zoller, Pritika Narayan, Ake T. Lu, Oscar Ortega‐Recalde, Megan Grant, C. Simon Bawden, Skye R. Rudiger, Amin Haghani, Donna M. Bond, Reuben R Hore, Michael Garratt, Karen E. Sears, Nan Wang, Xiangdong Yang, Russell G. Snell, Timothy A Hore, Steve Horvath
Software Mentions: 5
Published: over 3 years ago

10.1126/sciadv.aaz4012

Three-dimensional chromatin interactions remain stable upon CAG/CTG repeat expansion
Cited by: 13
Author(s): Gustavo A. Ruiz Buendía, Marion Leleu, Flavia Marzetta, Ludovica Vanzan, Jennifer Y. Tan, Victor Ythier, Emma Randall, Ana C. Marques, Tuncay Baubec, Rabih Murr, Ioannis Xénarios, Vincent Dion
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-021-07845-2

ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw
Cited by: 4
Author(s): Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro Shimizu, Rie Shimizu‐Inatsugi, Mark D. Robinson
Software Mentions: 4
Published: over 3 years ago

10.7554/eLife.31437

The formation of the light-sensing compartment of cone photoreceptors coincides with a transcriptional switch
Cited by: 29
Author(s): Janine M Daum, Özkan Keles, Sjoerd J.B. Holwerda, Hubertus Kohler, Filippo M. Rijli, Michael Stadler, Botond Roska
Software Mentions: 4
Published: about 7 years ago

10.3390/cells9081846

Caenorhabditis elegans Deficient in DOT-1.1 Exhibit Increases in H3K9me2 at Enhancer and Certain RNAi-Regulated Regions
Cited by: 6
Author(s): Ruben Esse, Alla Grishok
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pgen.1004143

DNA Sequence Explains Seemingly Disordered Methylation Levels in Partially Methylated Domains of Mammalian Genomes
Cited by: 62
Author(s): Dimos Gaidatzis, Lukas Burger, Rabih Murr, Anita Lerch, Sophie Dessus-Babus, Dirk Schübeler, Michael Stadler
Software Mentions: 3
Published: almost 11 years ago

10.15252/embj.201797038

Isoform‐specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands
Cited by: 88
Author(s): Massimiliano Manzo, Joël Wirz, Christina M. Ambrosi, Rodrigo Villaseñor, Bernd Roschitzki, Tuncay Baubec
Software Mentions: 3
Published: about 7 years ago

10.3389/fgene.2018.00485

A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples
Cited by: 35
Author(s): Pierre R. Bushel, Richard S. Paules, Scott S. Auerbach
Software Mentions: 3
Published: about 6 years ago

10.3389/fpubh.2021.694834

A Modern Genotoxicity Testing Paradigm: Integration of the High-Throughput CometChip® and the TGx-DDI Transcriptomic Biomarker in Human HepaRG™ Cell Cultures
Cited by: 14
Author(s): Julie K. Buick, Andrew Williams, Matthew J. Meier, Carol D. Swartz, Leslie Recio, Rémi Gagné, Stephen S. G. Ferguson, Bevin P. Engelward, Carole Yauk
Software Mentions: 3
Published: over 3 years ago

10.1038/s41438-020-0241-4

A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.)
Cited by: 27
Author(s): Kousuke Seki, Kenji Kono, Keisuke Tanaka, Masahiro Hiraga, Hiromi Kajiya‐Kanegae, Hideo Matsumura, Yuichi Uno
Software Mentions: 3
Published: almost 5 years ago

10.1093/jxb/erw386

Post-transcriptional regulation of photosynthetic genes is a key driver of C4leaf ontogeny
Cited by: 15
Author(s): Niklaus Fankhauser, Sylvain Aubry
Software Mentions: 3
Published: about 8 years ago

10.1038/s41598-019-45058-6

Zebrafish macroH2A variants have distinct embryo localization and function
Cited by: 5
Author(s): Elena González-Muñoz, Yohanna Arboleda-Estudillo, S. K. Chanumolu, H. H. Otu, José B. Cibelli
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1007238

EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum
Cited by: 68
Author(s): Seijiro Ono, Hua Liu, Katsutoshi Tsuda, Eigo Fukai, Keisuke Tanaka, Takuji Sasaki, Ken–Ichi Nonomura
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pgen.1005461

Silencing of X-Linked MicroRNAs by Meiotic Sex Chromosome Inactivation
Cited by: 30
Author(s): Hélène Royo, Hervé Seitz, Elias ElInati, Antoine H.F.M. Peters, Michael Stadler, James M. A. Turner
Software Mentions: 2
Published: about 9 years ago

10.1242/dev.173328

Molecular signatures identify immature mesenchymal progenitors in early mouse limb buds that respond differentially to morphogen signaling
Cited by: 27
Author(s): Robert M. Reinhardt, Fabiana Gullotta, Gretel Nusspaumer, Erkan Ünal, Robert Ivánek, Aimée Zúñiga, Rolf Zeller
Software Mentions: 2
Published: almost 6 years ago

10.15252/embj.201798518

Strong homeostatic TCR signals induce formation of self‐tolerant virtual memory CD8 T cells
Cited by: 56
Author(s): Ales Drobek, Alena Moudrá, Daniel L. Mueller, Martina Huranová, Veronika Horková, Michaela Přibíková, Robert Ivánek, Susanne Oberle, Dietmar Zehn, Kathleen McCoy, Peter Dráber, Ondřej Štěpánek
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21072562

Asynchronous Embryo Transfer Followed by Comparative Transcriptomic Analysis of Conceptus Membranes and Endometrium Identifies Processes Important to the Establishment of Equine Pregnancy
Cited by: 6
Author(s): Charlotte Gibson, Marta de Ruijter-Villani, Stefan Bauersachs, T.A.E. Stout
Software Mentions: 2
Published: over 4 years ago

10.1093/bioinformatics/btu781

QuasR: quantification and annotation of short reads in R
Cited by: 241
Author(s): Dimos Gaidatzis, Anita Lerch, Florian Hahne, Michael Stadler
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.ppat.1004579

Macrophage-Derived Human Resistin Is Induced in Multiple Helminth Infections and Promotes Inflammatory Monocytes and Increased Parasite Burden
Cited by: 43
Author(s): Jessica Jang, Gang Chen, Spencer H. Wang, Mark Barnes, Josiah I. Chung, Mali Camberis, Graham Le Gros, Philip J. Cooper, Cathy Steel, Thomas B. Nutman, Mitchell A. Lazar, Meera G. Nair
Software Mentions: 2
Published: almost 10 years ago

10.1038/s41598-018-36124-6

Transcriptome analysis of the anhydrobiotic cell line Pv11 infers the mechanism of desiccation tolerance and recovery
Cited by: 13
Author(s): Takahiro Yamada, Yoshitaka Suetsugu, Ruslan Deviatiiarov, Oleg Gusev, Richard Cornette, А. А. Несмелов, Noriko Hiroi, Takahiro Kikawada, Akira Funahashi
Software Mentions: 1
Published: about 6 years ago

10.26508/lsa.201900405

HELZ directly interacts with CCR4–NOT and causes decay of bound mRNAs
Cited by: 13
Author(s): Aoife Hanet, Felix Räsch, Ramona Weber, Vincenzo Ruscica, Maria Fauser, Tobias Raisch, Duygu Kuzuoğlu-Öztürk, Chung Te Chang, Dipankar Bhandari, Cátia Igreja, Lara Wohlbold
Software Mentions: 1
Published: about 5 years ago

10.12688/wellcomeopenres.14730.2

UK circulating strains of human parainfluenza 3: an amplicon based next generation sequencing method and phylogenetic analysis
Cited by: 5
Author(s): Anna Smielewska, Edward Emmott, Kyriaki Ranellou, A.I. Popay, Ian Goodfellow, Hamid Jalal
Software Mentions: 1
Published: about 6 years ago

10.3390/jof7020091

Acid pH Strategy Adaptation through NRG1 in Ustilago maydis
Cited by: 3
Author(s): José Alejandro Sánchez-Arreguín, José Ruíz-Herrera, F. de Jesus Mares-Rodriguez, Claudia Geraldine León-Ramírez, Lino Sánchez-Segura, Patricio Adrián Zapata-Morín, Jordan Coronado-Gallegos, Elva Teresa Aréchiga-Carvajal
Software Mentions: 1
Published: almost 4 years ago

Ecosyste.ms: Papers

Projects: bioconductor: QuasR

Papers Mentioning QuasR 30