Inspired by: Edward Wallace
Ribosome profiling, or Ribo-Seq (also named ribosome footprinting), is an adaptation of a technique developed by Joan Steitz and Marilyn Kozak almost 50 years ago that Nicholas Ingolia and Jonathan Weissman adapted to work with next generation sequencing that uses specialized messenger RNA (mRNA) sequencing to determine which mRNAs are being actively translated. Wikipedia (CC BY-SA 3.0)
2023 Articles
7 518 articles
Protocol for analyzing intact mRNA poly(A) tail length using nanopore direct RNA sequencing
- Koichi Ogami, Yuka Oishi, Shin-Ichi Hoshino, Koichi Ogami, Yuka Oishi, Shin-Ichi Hoshino
- STAR Protoc, 10.1016/j.xpro.2023.102340
Ribosome Profiling in the Model Diatom Thalassiosira pseudonana
- Monica Pichler, Andreas Meindl, Markus Romberger, …, Gunter Meister, Jan Medenbach, Thomas Mock
- Curr Protoc, 10.1002/cpz1.843
Rewriting the message: Harnessing RNA pseudouridylation to tackle disease
- Matias Montes, Nicole M MartÃnez, Matias Montes, Nicole M MartÃnez, Matias Montes, Nicole M MartÃnez
- Mol Cell, 10.1016/j.molcel.2023.02.001
choros: correction of sequence-based biases for accurate quantification of ribosome profiling data
- Amanda Mok, Robert Tunney, Gonzalo Benegas, …, Gonzalo Benegas, Edward W J Wallace, Liana F Lareau
- bioRxiv : the preprint server for biology, 10.1101/2023.02.21.529452
Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purification
- Hirotatsu Imai, Daisuke Utsumi, Hidetsugu Torihara, …, Kenzo Takahashi, Hidehito Kuroyanagi, Akio Yamashita
- Nucleic Acids Res, 10.1093/nar/gkad545
Protocol to measure ribosome density along mRNA transcripts of Arabidopsis thaliana tissues using Ribo-seq
- Isabel Cristina Vélez-Bermúdez, Shu-Jen Chou, Ai-Ping Chen, …, Ai-Ping Chen, Wen-Dar Lin, Wolfgang Schmidt
- STAR Protoc, 10.1016/j.xpro.2023.102520
Translational regulation by uORFs and start codon selection stringency
- Thomas E Dever, Ivaylo P Ivanov, Alan G Hinnebusch, …, Thomas E Dever, Ivaylo P Ivanov, Alan G Hinnebusch
- Genes Dev, 10.1101/gad.350752.123
Flow-Seq Method: Features and Application in Bacterial Translation Studies
- E S Komarova, O A Dontsova, D V Pyshnyi, …, D V Pyshnyi, M R Kabilov, P V Sergiev
- None, 10.32607/actanaturae.11820
uORF4u: a tool for annotation of conserved upstream open reading frames
- Artyom A Egorov, Gemma C Atkinson, Artyom A Egorov, …, Gemma C Atkinson, Artyom A Egorov, Gemma C Atkinson
- Bioinformatics, 10.1093/bioinformatics/btad323
Contributions of Ccr4 and Gcn2 to the Translational Response of C. neoformans to Host-Relevant Stressors and Integrated Stress Response Induction
- Corey M Knowles, David Goich, Amanda L M Bloom, …, Amanda L M Bloom, Murat C Kalem, John C Panepinto
- mBio, 10.1128/mbio.00196-23
2022 Articles
683 articles
BID-seq: The Quantitative and Base-Resolution Sequencing Method for RNA Pseudouridine
- Li-Sheng Zhang, Qing Dai, Chuan He, …, Li-Sheng Zhang, Qing Dai, Chuan He
- ACS Chem Biol, 10.1021/acschembio.2c00881
Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals
- Stephen J Kiniry, Dmitry E Andreev, Jonathan M Mudge, …, Dmitry E Andreev, Jonathan M Mudge, Pavel V Baranov
- Nat Commun, 10.1038/s41467-022-35595-6
Specific mechanisms of translation initiation in higher eukaryotes: the eIF4G2 story
- Ekaterina D Shestakova, Victoria V Smirnova, Ivan N Shatsky, …, Victoria V Smirnova, Ivan N Shatsky, Ilya M Terenin
- RNA, 10.1261/rna.079462.122
Discovering misannotated lncRNAs using deep learning training dynamics
- Afshan Nabi, Berke Dilekoglu, Ogun Adebali, …, Berke Dilekoglu, Ogun Adebali, Oznur Tastan
- Bioinformatics, 10.1093/bioinformatics/btac821
Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli
- Maximilian P Kohl, Maria Kompatscher, Nina Clementi, …, Nina Clementi, Lena Holl, Matthias D Erlacher
- Nucleic Acids Res, 10.1093/nar/gkac1175
Transcriptome-wide analysis of pseudouridylation in Drosophila melanogaster
- Wan Song, Ram Podicheti, Douglas B Rusch, …, Ram Podicheti, Douglas B Rusch, William Daniel Tracey
- G3 (Bethesda), 10.1093/g3journal/jkac333
Deciphering the role of RNA structure in translation efficiency
- Jianan Lin, Yang Chen, Yuping Zhang, …, Yuping Zhang, Haifan Lin, Zhengqing Ouyang
- BMC Bioinformatics, 10.1186/s12859-022-05037-7
Eukaryotic translation initiation factor eIF4G2 opens novel paths for protein synthesis in development, apoptosis and cell differentiation
- Yudi Liu, Jiuwei Cui, Andrew R Hoffman, …, Jiuwei Cui, Andrew R Hoffman, Ji-Fan Hu
- Cell Prolif, 10.1111/cpr.13367
Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process of ribosome scanning
- Ke Li, Jinhui Kong, Shuo Zhang, …, Shuo Zhang, Tong Zhao, Wenfeng Qian
- Genome Biol, 10.1186/s13059-022-02829-1
The Emerging Role of uORF-Encoded uPeptides and HLA uLigands in Cellular and Tumor Biology
- Lara Jürgens, Klaus Wethmar, Lara Jürgens, Klaus Wethmar
- None, 10.3390/cancers14246031