pypi: pyCRAC | Projects | Ecosyste.ms: Papers

10.1016/j.molcel.2020.06.002

Nascent Transcript Folding Plays a Major Role in Determining RNA Polymerase Elongation Rates
Cited by: 41
Author(s): Tomasz W. Turowski, Elisabeth Petfalski, Benjamin D. Goddard, Sarah L. French, Aleksandra Helwak, David Tollervey
Software Mentions: 8
Published: over 4 years ago

10.15252/msb.20188689

Defining the <scp>RNA</scp> interactome by total <scp>RNA</scp> ‐associated protein purification
Cited by: 103
Author(s): Vadim Shchepachev, Stefan Bresson, Christos Spanos, Elisabeth Petfalski, Lutz Fischer, Juri Rappsilber, David Tollervey
Software Mentions: 7
Published: over 5 years ago

10.1016/j.molcel.2020.09.021

Stress-Induced Translation Inhibition through Rapid Displacement of Scanning Initiation Factors
Cited by: 49
Author(s): Stefan Bresson, Vadim Shchepachev, Christos Spanos, Tomasz W. Turowski, Juri Rappsilber, David Tollervey
Software Mentions: 7
Published: about 4 years ago

10.1016/j.molcel.2020.01.007

Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to Translation
Cited by: 74
Author(s): Alex Tuck, Aneliya Rankova, Alaaddin Bulak Arpat, Luz Angélica Liechti, Daniel Heß, Vytautas Iešmantavičius, Violeta Castelo-Szekely, David Gatfield, Marc Bühler
Software Mentions: 7
Published: over 4 years ago

10.7554/eLife.54655

Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation
Cited by: 58
Author(s): Ira Alexandra Iosub, Rob W. van Nues, Stuart McKellar, Karen Jule Nieken, Marta Marchioretto, Brandon Sy, Jai J. Tree, Gabriella Viero, Sander Granneman
Software Mentions: 6
Published: over 4 years ago

10.1080/15476286.2020.1827784

The mRNA derived MalH sRNA contributes to alternative carbon source utilization by tuning maltoporin expression in E. coli
Cited by: 10
Author(s): Ira Alexandra Iosub, Marta Marchioretto, Rob W. van Nues, Stuart McKellar, Gabriella Viero, Sander Granneman
Software Mentions: 5
Published: about 4 years ago

10.1016/j.celrep.2019.02.012

Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control
Cited by: 56
Author(s): Lee Davidson, Laura Francis, Ross A. Cordiner, Joshua D. Eaton, Chris Estell, Sara Macías, Javier F. Cáceres, Steven West
Software Mentions: 4
Published: over 5 years ago

10.1186/s13059-015-0848-1

Transcriptome-wide RNA processing kinetics revealed using extremely short 4tU labeling
Cited by: 59
Author(s): J. David Barrass, Jane E. A. Reid, Yuanhua Huang, Ralph D. Hector, Guido Sanguinetti, Jean D. Beggs, Sander Granneman
Software Mentions: 4
Published: almost 9 years ago

10.15252/msb.20166869

Strand‐specific, high‐resolution mapping of modified RNA polymerase II
Cited by: 46
Author(s): Laura Milligan, Vân Anh Huynh-Thu, Clémentine Delan-Forino, Alex Tuck, Elisabeth Petfalski, Rodrigo Lombraña, Guido Sanguinetti, Grzegorz Kudla, David Tollervey
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-021-02379-y

diffBUM-HMM: a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data
Cited by: 4
Author(s): Paolo Marangio, Ka Ying Toby Law, Guido Sanguinetti, Sander Granneman
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.27082

RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit
Cited by: 14
Author(s): Laura Milligan, Camille Sayou, Alex Tuck, Tatsiana Auchynnikava, Jane E. A. Reid, Ross D. Alexander, Flávia de Lima Alves, Robin C. Allshire, Christos Spanos, Juri Rappsilber, Jean D. Beggs, Grzegorz Kudla, David Tollervey
Software Mentions: 3
Published: about 7 years ago

10.1128/MCB.00165-17

RNA Binding by Histone Methyltransferases Set1 and Set2
Cited by: 27
Author(s): Camille Sayou, Gonzalo Millán-Zambrano, Helena Santos‐Rosa, Elisabeth Petfalski, Samuel Robson, Jonathan Houseley, Tony Kouzarides, David Tollervey
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pbio.1001669

An RNA-Binding Complex Involved in Ribosome Biogenesis Contains a Protein with Homology to tRNA CCA-Adding Enzyme
Cited by: 32
Author(s): Jinzhong Lin, Jing Lü, Yingang Feng, Mengyi Sun, Keqiong Ye
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pgen.1005735

Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough
Cited by: 19
Author(s): Rebecca K. Holmes, Alex Tuck, Chenchen Zhu, Hywel Dunn-Davies, Grzegorz Kudla, Sandra Clauder‐Münster, Sander Granneman, Lars M. Steinmetz, Christine Guthrie, David Tollervey
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.molcel.2017.01.005

Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast
Cited by: 53
Author(s): Stefan Bresson, Alex Tuck, Desislava P. Staneva, David Tollervey
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pgen.1006699

Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex
Cited by: 37
Author(s): Clémentine Delan-Forino, Claudia Schneider, David Tollervey
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0178752

Structural basis for 5'-ETS recognition by Utp4 at the early stages of ribosome biogenesis
Cited by: 3
Author(s): Fabiola R. Calviño, Markus Kornprobst, Géza Schermann, Fabienne Birkle, Klemens Wild, Tamás Fischer, Ed Hurt, Yasar Luqman Ahmed, Irmgard Sinning
Software Mentions: 2
Published: over 7 years ago

10.1016/j.cell.2013.07.047

A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs
Cited by: 201
Author(s): Alex Tuck, David Tollervey
Software Mentions: 2
Published: over 11 years ago

10.1038/celldisc.2017.40

Binding to RNA regulates Set1 function
Cited by: 27
Author(s): Pierre Luciano, Jongcheol Jeon, Abdessamad El-Kaoutari, Drice Challal, Amandine Bonnet, Mara Barucco, Tito Candelli, Frédéric Jourquin, Pascale Lesage, Jae-Hoon Kim, Domenico Libri, Vincent Géli
Software Mentions: 2
Published: about 7 years ago

10.15252/embj.2019101548

Termination of non‐coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD‐mimicking region in Sen1
Cited by: 21
Author(s): Zhong Chao Han, Olga Jasnovidova, Nouhou Haidara, Agnieszka Tudek, Karel Kubíček, Domenico Libri, Richard Štefl, Odil Porrúa
Software Mentions: 2
Published: over 4 years ago

10.1186/gb-2014-15-1-r8

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast
Cited by: 153
Author(s): Shaun Webb, Ralph D. Hector, Grzegorz Kudla, Sander Granneman
Software Mentions: 2
Published: almost 11 years ago

10.1128/mBio.01041-21

Burning the Candle at Both Ends: Have Exoribonucleases Driven Divergence of Regulatory RNA Mechanisms in Bacteria?
Cited by: 9
Author(s): Daniel G. Mediati, David Lalaouna, Jai J. Tree
Software Mentions: 2
Published: about 3 years ago

10.1186/s12915-017-0444-9

RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination
Cited by: 118
Author(s): Nila Roy Choudhury, Gregory Heikel, Maryia Trubitsyna, Peter Kubík, Jakub Stanislaw Nowak, Shaun Webb, Sander Granneman, Christos Spanos, Juri Rappsilber, Alfredo Castelló, Gracjan Michlewski
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pbio.1002083

The DEAH-box Helicase Dhr1 Dissociates U3 from the Pre-rRNA to Promote Formation of the Central Pseudoknot
Cited by: 69
Author(s): Richa Sardana, Xin Liu, Sander Granneman, Jian Zhu, Michael Gill, Ophelia Papoulas, Edward M. Marcotte, David Tollervey, Carl C. Correll, Arlen Johnson
Software Mentions: 1
Published: over 9 years ago

10.1074/jbc.RA117.000300

Ribosome maturation by the endoribonuclease YbeY stabilizes a type 3 secretion system transcript required for virulence of enterohemorrhagic Escherichia coli
Cited by: 23
Author(s): Sean P. McAteer, Brandon Sy, Julia L. Wong, David Tollervey, David L. Gally, Jai J. Tree
Software Mentions: 1
Published: over 6 years ago

10.12688/wellcomeopenres.10724.2

RNA substrate length as an indicator of exosome interactions in vivo
Cited by: 6
Author(s): Clémentine Delan-Forino, Claudia Schneider, David Tollervey
Software Mentions: 1
Published: over 7 years ago

10.1038/s42003-021-01963-z

The RelA hydrolase domain acts as a molecular switch for (p)ppGpp synthesis
Cited by: 10
Author(s): Anurag Kumar Sinha, Kristoffer Skovbo Winther
Software Mentions: 1
Published: over 3 years ago

10.1016/j.molcel.2013.10.017

Rrp5 Binding at Multiple Sites Coordinates Pre-rRNA Processing and Assembly
Cited by: 63
Author(s): Simon Lebaron, Åsa Segerstolpe, Sarah L. French, Tatiana Dudnakova, Flávia de Lima Alves, Sander Granneman, Juri Rappsilber, Ann L. Beyer, Lars Wieslander, David Tollervey
Software Mentions: 1
Published: almost 11 years ago

10.1016/j.molcel.2014.05.006

Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli
Cited by: 197
Author(s): Jai J. Tree, Sander Granneman, Sean P. McAteer, David Tollervey, David L. Gally
Software Mentions: 1
Published: over 10 years ago

Ecosyste.ms: Papers

Projects: pypi: pyCRAC

Papers Mentioning pyCRAC 29