Grzegorz Kudla

发表

Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

D. Tollervey, A. Helwak, Grzegorz Kudla, 2013, Cell.

Evidence for the biogenesis of more than 1,000 novel human microRNAs

Xavier Estivill, Justo González, Marc R Friedländer, 2014, Genome Biology.

Synonymous but not the same: the causes and consequences of codon bias

J. Plotkin, Grzegorz Kudla, 2011, Nature Reviews Genetics.

Rate-Limiting Steps in Yeast Protein Translation

J. Plotkin, Premal Shah, Grzegorz Kudla, 2013, Cell.

High Guanine and Cytosine Content Increases mRNA Levels in Mammalian Cells

A. Helwak, Grzegorz Kudla, M. Żylicz, 2006, PLoS biology.

Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast

David Tollervey, Sander Granneman, D. Tollervey, 2011, Proceedings of the National Academy of Sciences.

Codon usage influences fitness through RNA toxicity

Joshua B. Plotkin, J. Plotkin, Grzegorz Kudla, 2018, Proceedings of the National Academy of Sciences.

Coding-Sequence Determinants of Gene Expression in Escherichia coli

David Tollervey, Joshua B Plotkin, A. Murray, 2009, Science.

Evidence for strong mutation bias towards, and selection against, T/U content in SARS-CoV2: implications for attenuated vaccine design

L. Hurst, Grzegorz Kudla, S. Mühlhausen, 2020, bioRxiv.

Rok 1 helicase A pre-ribosomal RNA interaction network involving snoRNAs and the

Grzegorz Kudla, E. Schleiff, M. Bohnsack, 2014 .

Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing

D. Tollervey, Grzegorz Kudla, R. V. van Nues, 2011, The EMBO journal.

Global mapping of RNA homodimers in living cells

Y. Crow, Grzegorz Kudla, R. O’Keefe, 2022, Genome research.

RNA Conformation Capture by Proximity Ligation.

A. Helwak, Grzegorz Kudla, Y. Wan, 2020, Annual review of genomics and human genetics.

RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression

Grzegorz Kudla, Ronan K. Carroll, P. Arede, 2022, Nature Communications.

Edinburgh Rate-limiting steps in yeast protein translation

J. Plotkin, Premal Shah, Grzegorz Kudla, 2017 .

Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E

D. Tollervey, M. Wilkins, N. Deshpande, 2016, The EMBO journal.

Hsp 90 chaperones wild-type p 53 tumor suppressor protein

J. Boros, A. Helwak, Grzegorz Kudla, 2022 .

Codon optimization of antigen coding sequences improves the immune potential of DNA vaccines against avian influenza virus H5N1 in mice and chickens

Grzegorz Kudla, A. Sirko, A. Stachyra, 2016, Virology Journal.

The PIN domain endonuclease Utp24 cleaves pre-ribosomal RNA at two coupled sites in yeast and humans

D. Tollervey, Grzegorz Kudla, K. Sloan, 2016, Nucleic acids research.

The RNA-Binding Landscape of HAX1 Protein Indicates Its Involvement in Translation and Ribosome Assembly

D. Tollervey, A. Helwak, Grzegorz Kudla, 2022, Cells.

Causes and Consequences of Purifying Selection on SARS-CoV-2

L. Hurst, Grzegorz Kudla, S. Mühlhausen, 2021, Genome biology and evolution.

RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit

Ross D. Alexander, D. Tollervey, J. Rappsilber, 2017, eLife.

N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing

Stepanka Vanacova, Š. Vaňáčová, Grzegorz Kudla, 2017, Nucleic acids research.

The human nuclear exosome targeting complex is loaded onto newly synthesized RNA to direct early ribonucleolysis.

T. Jensen, Grzegorz Kudla, M. Lubas, 2015, Cell reports.

Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target

D. Tollervey, A. Helwak, Grzegorz Kudla, 2011, Proceedings of the National Academy of Sciences.

Network of epistatic interactions within a yeast snoRNA

Guido Sanguinetti, Botond Cseke, David Tollervey, 2016, Science.

Codon Usage and Splicing Jointly Influence mRNA Localization

Martin S. Taylor, Robert S. Young, L. Hurst, 2020, Cell systems.

Splicing buffers suboptimal codon usage in human cells

Martin S. Taylor, Robert S. Young, L. Hurst, 2019, bioRxiv.

Gene conversion and GC-content evolution in mammalian Hsp70.

Leszek Lipinski, A. Helwak, Grzegorz Kudla, 2004, Molecular biology and evolution.

Theory Rate-Limiting Steps in Yeast Protein Translation

Joshua B. Plotkin, Premal Shah, J. Plotkin, 2013 .

Transcription, mRNA Export, and Immune Evasion Shape the Codon Usage of Viruses

L. Hurst, Grzegorz Kudla, M. Liss, 2021, Genome biology and evolution.

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

D. Tollervey, Grzegorz Kudla, Wiebke Wlotzka, 2011 .

The nuclear RNA polymerase II surveillance system targets polymerase III transcripts

D. Tollervey, Grzegorz Kudla, Wiebke Wlotzka, 2011, The EMBO journal.

The PIN domain endonuclease Utp24 cleaves pre-ribosomal RNA at two coupled sites in yeast and humans

David Tollervey, Nicholas J. Watkins, Claudia Schneider, 2016, Nucleic acids research.

The Destabilization of Lipid Membranes Induced by the C-terminal Fragment of Caspase 8-cleaved Bid Is Inhibited by the N-terminal Fragment*

Grzegorz Kudla, J. Martinou, B. Antonsson, 2000, The Journal of Biological Chemistry.

Hyb: A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data

D. Tollervey, A. Travis, A. Helwak, 2014, Methods.

Hsp90 Chaperones Wild-type p53 Tumor Suppressor Protein*

J. Boros, A. Helwak, Grzegorz Kudla, 2004, Journal of Biological Chemistry.

Mutually Exclusive CBC-Containing Complexes Contribute to RNA Fate

T. Jensen, Michal Domanski, Grzegorz Kudla, 2017, Cell reports.

Escherichia coliin Coding-Sequence Determinants of Gene Expression

A. Murray, J. Plotkin, D. Tollervey, 2009 .

Transcriptome-wide Analysis of Exosome Targets

D. Tollervey, A. Tuck, Grzegorz Kudla, 2012, Molecular cell.

Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs

David Tollervey, Sander Granneman, E. Petfalski, 2009, Proceedings of the National Academy of Sciences.

Integrity of SRP RNA is ensured by La and the nuclear RNA quality control machinery

D. Tollervey, A. Tuck, Grzegorz Kudla, 2014, Nucleic acids research.

The RNA-binding landscape of HAX1 protein indicates its involvement in ribosome biogenesis and translation

D. Tollervey, A. Helwak, Grzegorz Kudla, 2022, bioRxiv.

In vivo structure and dynamics of the SARS-CoV-2 RNA genome

Youliang Wang, Grzegorz Kudla, Youzhi Mao, 2021, Nature Communications.

A pre-ribosomal RNA interaction network involving snoRNAs and the Rok1 helicase

Grzegorz Kudla, E. Schleiff, M. Bohnsack, 2014, RNA.

Evidence in disease and non-disease contexts that nonsense mutations cause altered splicing via motif disruption

L. Hurst, Grzegorz Kudla, Rosina Savisaar, 2021, Nucleic acids research.

Genome Landscapes and Bacteriophage Codon Usage

Joshua B. Plotkin, Julius B. Lucks, David R. Nelson, 2007, PLoS Comput. Biol..

Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design

L. Hurst, Grzegorz Kudla, S. Mühlhausen, 2020, Molecular biology and evolution.

Loss of the Yeast SR Protein Npl3 Alters Gene Expression Due to Transcription Readthrough

L. Steinmetz, D. Tollervey, C. Guthrie, 2015, PLoS genetics.

Strand-specific , high-resolution mapping of modified RNA polymerase II

G. Sanguinetti, E. Petfalski, D. Tollervey, 2016 .

In vivo structure and dynamics of the RNA genome of SARS-Cov-2

Grzegorz Kudla, M. Jin, Zhihu Zhao, 2021, bioRxiv.

The Human Nuclear Exoso me Targeting Complex Is Loaded onto Newly Synthesized RNA to Direct Early Ribonucleolysis Graphical

T. Jensen, Grzegorz Kudla, M. Lubas, 2015 .

PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast

Grzegorz Kudla, Shaun Webb, S. Granneman, 2014, Genome Biology.

Nrd 1-Nab 3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast

Grzegorz Kudla, Shaun Webb, S. Granneman, 2013 .

Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity

E. Miska, I. Ulitsky, Grzegorz Kudla, 2021, bioRxiv.

Global mapping of RNA homodimers in living cells

Grzegorz Kudla, Marta M Gabryelska, 2021, bioRxiv.

COMRADES determines in vivo RNA structures and interactions

Aaron T. L. Lun, J. Marioni, I. MacRae, 2018, Nature Methods.

Inducible Heat Shock Protein 70 Promotes Myelin Autoantigen Presentation by the HLA Class II1

Jacek Szymanski, C. Brosnan, K. Selmaj, 2004, The Journal of Immunology.

Brr2p-mediated conformational rearrangements in the spliceosome during activation and substrate repositioning.

D. Tollervey, Grzegorz Kudla, J. Beggs, 2012, Genes & development.

Deep mutational scanning quantifies DNA binding and predicts clinical outcomes of PAX6 variants

J. Marsh, Grzegorz Kudla, H. N. Hall, 2023, bioRxiv.

Genotype-phenotype map of an RNA-ligand complex

J. Bujnicki, G. Whyte, D. Oyarzún, 2020, bioRxiv.

Codon optimization of antigen coding sequences improves the immune potential of DNA vaccines against avian influenza virus H5N1 in mice and chickens

Grzegorz Kudla, A. Sirko, A. Stachyra, 2016, Virology Journal.

COMRADES determines in vivo RNA structures and interactions

Aaron T. L. Lun, Ian Goodfellow, John C Marioni, 2018, Nature Methods.

Maf1-mediated regulation of yeast RNA polymerase III is correlated with CCA addition at the 3′ end of tRNA precursors

W. Karłowski, Grzegorz Kudla, M. Żywicki, 2017, Gene.

Strand-specific , high-resolution mapping of modified RNA polymerase II

G. Sanguinetti, E. Petfalski, D. Tollervey, 2016 .

The human nuclear exosome targeting complex is loaded onto newly synthesized RNA to direct early ribonucleolysis.

T. Jensen, Grzegorz Kudla, M. Lubas, 2015, Cell reports.

References and Notes Supporting Online Material Coding-sequence Determinants of Gene Expression in Escherichia Coli

A. Murray, M. Heisenberg, J. Plotkin, 2022 .

Selection on synonymous sites: the unwanted transcript hypothesis.

Z. Izsvák, Grzegorz Kudla, Sofia Radrizzani, 2024, Nature reviews. Genetics.

Lighting up protein design

Grzegorz Kudla, Marcin Plech, 2022, eLife.

Escherichia coliin Coding-Sequence Determinants of Gene Expression

J. Plotkin, D. Tollervey, Grzegorz Kudla, 2009 .