Single-RNA counting reveals alternative modes of gene expression in yeast
Cited by (683)
Items 201–300 of 683
- Noise and Information Transmission in Promoters with Multiple Internal StatesGeorg Rieckh, Gašper Tkačik · 2014 · Biophysical Journal
- Theory in Biology: Figure 1 or Figure 7?Rob Phillips · 2015 · Trends in Cell Biology
- Promoter-specific dynamics of TATA-binding protein association with the human genomeYuko Hasegawa, Jason D. Lieb, Kevin Struhl · 2019 · Genome Research
- Estimating selection on synonymous codon usage from noisy experimental dataWallace, Edward W.J., Airoldi, Edoardo M., Drummond, D. Allan · 2013 · Molecular Biology and Evolution
- Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional burstsJosé Viñuelas, Gaël Kaneko, Antoine Coulon, Elodie Vallin, Valérie Morin, Camila Mejia-Pous, Jean-Jacques Kupiec, Guillaume Beslon, Olivier Gandrillon · 2013 · BMC Biology
- The extent of ribosome queuing in budding yeastAlon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava, Tamir Tuller · 2018 · PLoS Computational Biology
- Measuring transcription at a single gene copy reveals hidden drivers of bacterial individualityMengyu Wang, Jing Zhang, Heng Xu, Ido Golding · 2019 · Nature Microbiology
- Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysisZach Hensel, Haidong Feng, Bo Han, Christine L. Hatem, Jin Wang, Jie Xiao · 2012 · Nature Structural & Molecular Biology
- Two steps forward—one step back: Advances in affinity purification mass spectrometry of macromolecular complexesMarlene Oeffinger · 2012 · PROTEOMICS
- RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3′-end processing in Saccharomyces cerevisiaeRoss D. Alexander, J. David Barrass, Beatriz Solange Dichtl, Martin Koš, Tomasz Obtułowicz, Marie-Cécile Robert, Michał Koper, Iwona Karkusiewicz, Luisa Mariconti, David W. Tollervey et al. · 2010 · RNA
- BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cellsMariana Gómez-Schiavon, Liangfu Chen, Anne E. West, Nicolas E. G. Buchler · 2017 · Genome biology
- Antisense transcription‐dependent chromatin signature modulates sense transcript dynamicsTom Brown, Françoise S. Howe, Struan C. Murray, Meredith Wouters, Philipp Lorenz, Emily Seward, Scott Rata, Andrew Angel, Jane Mellor · 2018 · Molecular Systems Biology
- Modeling the dynamic behavior of biochemical regulatory networksJohn J. Tyson, Teeraphan Laomettachit, Pavel Kraikivski · 2018 · Journal of Theoretical Biology
- A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeastJudith B. Zaugg, Nicholas M. Luscombe · 2011 · Genome Research
- Analyzing mRNA Expression Using Single mRNA Resolution Fluorescent In Situ HybridizationDaniel R. Zenklusen, Robert H. Singer · 2010 · Methods in enzymology on CD-ROM/Methods in enzymology
- Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissuesKeren Bahar Halpern, Shalev Itzkovitz · 2015 · Methods
- Single-cell differences in matrix gene expression do not predict matrix depositionAllison Coté, Claire M. McLeod, Megan J. Farrell, Patrick D. McClanahan, Margaret C. Dunagin, Arjun Raj, Robert L. Mauck · 2016 · Nature Communications
- Shadow enhancers can suppress input transcription factor noise through distinct regulatory logicRachel Waymack, Alvaro Fletcher, Germán Enciso, Zeba Wunderlich · 2020 · eLife
- Coverage-dependent bias creates the appearance of binary splicing in single cellsCarlos F. Buen Abad Najar, Nir Yosef, Liana F. Lareau · 2020 · eLife
- Frequency Domain Analysis of Fluctuations of mRNA and Protein Copy Numbers within a Cell Lineage: Theory and Experimental ValidationChen Jia, Ramon Grima · 2021 · Physical Review X
- Elimination of cap structures generated by mRNA decay involves the new scavenger mRNA decapping enzyme Aph1/FHIT together with DcpSValério Taverniti, Bertrand Séraphin · 2014 · Nucleic Acids Research
- Transimulation - Protein Biosynthesis Web ServiceSiwiak, Marlena, Zielenkiewicz, Piotr · 2013 · PLoS ONE
- Abundance and distribution of RNA polymerase II in Arabidopsis interphase nucleiVeit Schubert, Klaus Weißhart · 2015 · Journal of Experimental Botany
- The architecture of eukaryotic translationDominique Chu, Tobias von der Haar · 2012 · Nucleic Acids Research
- Single molecule fluorescence in situ hybridisation for quantitating post-transcriptional regulation in Drosophila brainsLu Yang, Josh Titlow, Darragh Ennis, Carlas Smith, Jessica H. Mitchell, Florence L. Young, Scott Waddell, David Ish‐Horowicz, Ilan Davis · 2017 · Methods
- Interactions between HIV-1 Gag and Viral RNA Genome Enhance Virion AssemblyKari A. Dilley, Olga A. Nikolaitchik, Andrea Galli, Ryan C. Burdick, Louis Levine, Kelvin Li, Alan R. Rein, Vinay K. Pathak, Wei-Shau Hu · 2017 · Journal of Virology
- Transcriptional Regulation of Lineage Commitment - A Stochastic Model of Cell Fate DecisionsJose Teles, Cristina Pina, Patrik Edén, Mattias Ohlsson, Tariq Enver, Carsten Peterson · 2013 · PLoS Computational Biology
- Complex dynamics of transcription regulationDiana A. Stavreva, Lyuba Varticovski, Gordon L. Hager · 2012 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- Discriminating cellular heterogeneity using microwell-based RNA cytometryIvan K. Dimov, Rong Lu, Eric P. Lee, Jun Seita, Debashis Sahoo, Seung-min Park, Irving L. Weissman, Luke P. Lee · 2014 · Nature Communications
- Genome architecture and the role of transcriptionArgyris Papantonis, Peter R. Cook · 2010 · Current Opinion in Cell Biology
- Quantitative analysis of the transcription control mechanismChanghui Mao, Christopher R. Brown, Elena Falkovskaia, Shawfeng Dong, Eva Hrabeta‐Robinson, Lauren Wenger, Hinrich Boeger · 2010 · Molecular Systems Biology
- Exploring transcription regulation through cell-to-cell variabilityRuty Rinott, Ariel Jaimovich, Nir Friedman · 2011 · Proceedings of the National Academy of Sciences
- Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributionsXiaoming Fu, Heta Patel, Stefano Coppola, Libin Xu, Zhixing Cao, Tineke Laura Lenstra, Ramon Grima · 2022 · eLife
- Oscillatory control of signalling moleculesPawel Paszek, Dean Andrew Jackson, Michael White · 2010 · Current Opinion in Genetics & Development
- Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanismsDonna Garvey Brickner, Varun Sood, Evelina Tutucci, Robert Coukos, Kayla Viets, Robert H. Singer, Jason H. Brickner · 2016 · Molecular Biology of the Cell
- Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kineticsSonghao Luo, Zihao Wang, Zhenquan Zhang, Tianshou Zhou, Jiajun Zhang · 2022 · Nucleic Acids Research
- A Nutrient-Responsive Pathway that Determines M Phase Timing through Control of B-Cyclin mRNA StabilityVincent Messier, Daniel Zenklusen, Stephen W. Michnick · 2013 · Cell
- Writing a wrong: Coupled RNA polymerase II transcription and RNA quality controlSarah A. Peck Justice, Katlyn D. Hughes, Jose F. Victorino, Amber L. Mosley · 2019 · Wiley Interdisciplinary Reviews - RNA
- Visualizing the translation and packaging of HIV-1 full-length RNAJianbo Chen, Yang Liu, Bin Wu, Olga A. Nikolaitchik, Preeti R. Mohan, Jiji Chen, Vinay K. Pathak, Wei-Shau Hu · 2020 · Proceedings of the National Academy of Sciences
- Transcriptional bursting: stochasticity in deterministic developmentEmilia A. Leyes Porello, Robert T. Trudeau, Bomyi Lim · 2023 · Development
- What have single-molecule studies taught us about gene expression?Huimin Chen, Daniel R. Larson · 2016 · Genes & Development
- Mov10 and APOBEC3G Localization to Processing Bodies Is Not Required for Virion Incorporation and Antiviral ActivityTaisuke Izumi, Ryan C. Burdick, Mayu Shigemi, Sergey Y. Plisov, Wei-Shau Hu, Vinay K. Pathak · 2013 · Journal of Virology
- The Interleaved GenomeJane Mellor, Ronja Woloszczuk, Françoise S. Howe · 2015 · Trends in Genetics
- Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiaeBenjamin Neymotin, Victoria M. Ettorre, David Gresham · 2016 · G3 Genes Genomes Genetics
- Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcriptionGrace A. Rosen, Inwha Baek, Larry J. Friedman, Yoo Jin Joo, Stephen Buratowski, Jeff Gelles · 2020 · Proceedings of the National Academy of Sciences
- Inferring gene regulation from stochastic transcriptional variation across single cells at steady stateAnika Gupta, Jorge Diego Martin-Rufino, Thouis R. Jones, Vidya Subramanian, Xiaojie Qiu, Emanuelle I. Grody, Alex Bloemendal, Chen Weng, Sheng-Yong Niu, Kyung Hoi Min et al. · 2022 · Proceedings of the National Academy of Sciences
- Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual burstsDaniel Ramsköld, Gert‐Jan Hendriks, Anton J. M. Larsson, Juliane V. Mayr, Christoph Ziegenhain, Michael Hagemann-Jensen, Leonard Hartmanis, Rickard Sandberg · 2024 · Nature Cell Biology
- Digital nature of the immediate-early transcriptional responseMichelle Stevense, Tetsuya Muramoto, Iris I. Müller, Jonathan Robert Chubb · 2010 · Development
- Dynamics of HIV-1 RNA Near the Plasma Membrane during Virus AssemblyLuca Sardo, Steven C. Hatch, Jianbo Chen, Olga A. Nikolaitchik, Ryan C. Burdick, De Chen, Christopher J. Westlake, Stephen Lockett, Vinay K. Pathak, Wei-Shau Hu · 2015 · Journal of Virology
- Distribution Modes and Their Corresponding Parameter Regions in Stochastic Gene TranscriptionFeng Jiao, Qiwen Sun, Moxun Tang, Jianshe Yu, Bo Zheng · 2015 · SIAM Journal on Applied Mathematics
- Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genusYinjia Li, Sheng Zuo, Zhiliang Zhang, Zhanjie Li, Jinlei Han, Zhaoqing Chu, Robert Hasterok, Kai Wang · 2018 · The Plant Journal
- Origins and consequences of transcriptional discontinuityDavid M. Suter, Nacho Molina, Félix Naef, Ueli Schibler · 2011 · Current Opinion in Cell Biology
- Using variability in gene expression as a tool for studying gene regulationOlivia M. Padovan-Merhar, Arjun Raj · 2013 · WIREs Systems Biology and Medicine
- The Chemical Fluctuation Theorem governing gene expressionSeong Jun Park, Sanggeun Song, Gil‐Suk Yang, Philip M. Kim, Sangwoon Yoon, Ji‐Hyun Kim, Jaeyoung Sung · 2018 · Nature Communications
- HIV-1 uncoating requires long double-stranded reverse transcription productsRyan C. Burdick, Michael Morse, Ioulia F. Rouzina, Mark C. Williams, Wei-Shau Hu, Vinay K. Pathak · 2024 · Science Advances
- Transcription by the numbers redux: experiments and calculations that surpriseHernán G. García, Álvaro Sánchez, Thomas E. Kuhlman, Jané Kondev, Rob Phillips · 2010 · Trends in Cell Biology
- Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycleZhen Liu, Pu Yang, Fei Li, Clifford A. Shaffer, Stefan Hoops, John J. Tyson, Yang Cao · 2012 · The Journal of Chemical Physics
- Exploiting Natural Fluctuations to Identify Kinetic Mechanisms in Sparsely Characterized SystemsAndreas Hilfinger, Thomas M. Norman, Johan Paulsson · 2016 · Cell Systems
- Architecture and dynamics of overlapped RNA regulatory networksChristopher P. Lapointe, Melanie A. Preston, Daniel Wilinski, Harriet A. J. Saunders, Zachary T. Campbell, Marvin Wickens · 2017 · RNA
- Sensitivity of mRNA TranslationGilad Poker, Michael Margaliot A, Tamir Tuller · 2015 · Scientific Reports
- Analytical Time-Dependent Distributions for Gene Expression Models With Complex Promoter Switching MechanismsChen Jia, Youming Li · 2023 · SIAM Journal on Applied Mathematics
- Transcriptional Bursting Diversifies the Behaviour of a Toggle Switch: Hybrid Simulation of Stochastic Gene ExpressionPavol Bokes, John R. King, Andrew T. A. Wood, Matthew Loose · 2013 · Bulletin of Mathematical Biology
- A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular VariabilityDebashis Barik, David A. Ball, Jean Peccoud, John J. Tyson · 2016 · PLoS Computational Biology
- Stochastic transcription in the p53‐mediated response to DNA damage is modulated by burst frequencyDhana Friedrich, Laura Friedel, Ana Finzel, Andreas Herrmann, Stephan Preibisch, Alexander Loewer · 2019 · Molecular Systems Biology
- The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-PoissonianDouglas E. Weidemann, James Holehouse, Abhyudai Singh, Ramon Grima, Silke Hauf · 2023 · Science Advances
- Single-Molecule Resolution Fluorescent In Situ Hybridization (smFISH) in the Yeast S. cerevisiaeSamir Rahman, Daniel Zenklusen · 2013 · Methods in molecular biology
- Quantifying the Effect of Ribosomal Density on mRNA StabilityShlomit Edri, Tamir Tuller · 2014 · PLoS ONE
- Population density approach for discrete mRNA distributions in generalized switching models for stochastic gene expressionAdam R. Stinchcombe, Charles S. Peskin, Daniel Tranchina · 2012 · Physical Review E
- Distinguishing between models of mammalian gene expression: telegraph-like models versus mechanistic modelsBraichenko, Svitlana, Holehouse, James, Grima, Ramon · 2021 · Journal of The Royal Society Interface
- APOBEC3 proteins can copackage and comutate HIV-1 genomesBelete Ayele Desimmie, Ryan C. Burdick, Taisuke Izumi, Hibiki Doi, Wei Shao, W. Gregory Alvord, Kei Sato, Yoshio Koyanagi, Sara Jones, Eleanor M. P. Wilson et al. · 2016 · Nucleic Acids Research
- Modelling and measuring intracellular competition for finite resources during gene expressionRenana Sabi, Tamir Tuller · 2019 · Journal of The Royal Society Interface
- m-TAG: a PCR-based genomic integration method to visualize the localization of specific endogenous mRNAs in vivo in yeastLiora Haim-Vilmovsky, Jeffrey E. Gerst · 2009 · Nature Protocols
- Polysome collapse and RNA condensation fluidize the cytoplasmYing Xie, Tong Shu, Tiewei Liu, Marie-Christin Spindler, Julia Mahamid, Glen M. Hocky, David Gresham, Liam J. Holt · 2024 · Molecular Cell
- The Low Noise Limit in Gene ExpressionRoy D. Dar, Brandon S. Razooky, Leor S. Weinberger, Chris D. Cox, Michael L. Simpson · 2015 · PLoS ONE
- Why Dom34 Stimulates Growth of Cells with Defects of 40S Ribosomal Subunit BiosynthesisArpita Bhattacharya, Kerri B. McIntosh, Ian M. Willis, Jonathan R. Warner · 2010 · Molecular and Cellular Biology
- Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing dataMaria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior S. Pachter · 2024 · Nature Methods
- Differential context-specific impact of individual core promoter elements on transcriptional dynamicsOliver Hendy, John A. Campbell, Jocelyn D. Weissman, Daniel R. Larson, Dinah S. Singer · 2017 · Molecular Biology of the Cell
- Detecting RNA base methylations in single cells by in situ hybridizationRohan T. Ranasinghe, Martin R. Challand, Kristina A. Ganzinger, Benjamin W. Lewis, Charlotte A. Softley, Wolfgang Hellmut Schmied, Mathew H. Horrocks, Nadia Shivji, Jason W. Chin, JAMES M. SPENCER et al. · 2018 · Nature Communications
- Co-translational control of protein complex formation: a fundamental pathway of cellular organization?Neal K. Williams, Bernhard Dichtl · 2018 · Biochemical Society Transactions
- Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasisChen Jia, Abhyudai Singh, Ramon Grima · 2022 · PLoS Computational Biology
- Quantifying and correcting bias in transcriptional parameter inference from single-cell dataRamon Grima, Pierre-Marie Esmenjaud · 2023 · Biophysical Journal
- Resource Sharing Controls Gene Expression BurstingPatrick M. Caveney, Sarah Elizabeth Norred, Charles W. J. Chin, Jonathan B. Boreyko, Brandon S. Razooky, Scott T. Retterer, Charles Patrick Collier, Michael L. Simpson · 2016 · ACS Synthetic Biology
- Homeostasis in the Central Dogma of molecular biology: the importance of mRNA instabilityPérez-Ortín, José E., Tordera, Vicente, Chávez, Sebastián · 2019 · RNA Biology
- Replicative aging as a source of cell heterogeneity in budding yeastДмитрий Алексеевич Кнорре, Aglaia V. Azbarova, Kseniia V. Galkina, Boris A. Feniouk, Fedor F. Severin · 2018 · Mechanisms of Ageing and Development
- Quantitative 3D Tracing of Gene-delivery Viral Vectors in Human Cells and Animal TissuesXiao, Ping-Jie, Li, Chengwen, Neumann, Aaron, Samulski, R Jude · 2012 · Molecular Therapy
- Quantitative measurement of single cell dynamicsDenise Bakstad, Antony D. Adamson, David G. Spiller, Michael White · 2011 · Current Opinion in Biotechnology
- Geometry-Induced Bursting Dynamics in Gene ExpressionB. Meyer, Olivier Bénichou, Yariv Kafri, Raphaël Voituriez · 2012 · Biophysical Journal
- Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling DataAlexey A. Gritsenko, Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder · 2015 · PLoS Computational Biology
- Uniform gene expression in embryos is achieved by temporal averaging of transcription noiseL. Carine Stapel, Christoph Zechner, Nadine L. Vastenhouw · 2017 · Genes & Development
- Data normalization for addressing the challenges in the analysis of single-cell transcriptomic datasetsRaquel Cuevas‐Díaz Durán, Haichao Wei, Jiaqian Wu · 2024 · BMC Genomics
- Transcriptional refractoriness is dependent on core promoter architectureFrançois Cesbron, Michael Oehler, Nati Ha, Gencer Sancar, Michael Brunner · 2015 · Nature Communications
- Quantifying the transcriptional output of single alleles in single living mammalian cellsSharon Yunger, Liat Rosenfeld, Yuval Garini, Yaron Shav‐Tal · 2013 · Nature Protocols
- Global and targeted approaches to single-cell transcriptome characterizationAleksandra A. Kolodziejczyk, Tapio Lönnberg · 2017 · Briefings in Functional Genomics
- Gene promoters dictate histone occupancy within genesRoberto Perales, Benjamin Erickson, Lian Zhang, Hyunmin Kim, Elan Valiquett, David L. Bentley · 2013 · The EMBO Journal
- Identification of a Plant Viral RNA Genome in the NucleusRuimin Gao, Peng Liu, Sek‐Man Wong · 2012 · PLoS ONE
- A nucleoporin, Nup60p, affects the nuclear and cytoplasmic localization of ASH1 mRNA in S. cerevisiaeErin A. Powrie, Daniel Zenklusen, Robert H. Singer · 2010 · RNA
- Nuclear Retention Prevents Premature Cytoplasmic Appearance of mRNAThomas Beuchert Kallehauge, Marie-Cécile Robert, Édouard Bertrand, Torben Heick Jensen · 2012 · Molecular Cell
- Balancing noise and plasticity in eukaryotic gene expressionDjordje Bajić, Juan F. Poyatos · 2012 · BMC Genomics
- Measuring Transcription Dynamics in Living Cells Using Fluctuation AnalysisMatthew Ferguson, Daniel R. Larson · 2013 · Methods in molecular biology
- Nascent RNA kinetics: Transient and steady state behavior of models of transcriptionSandeep Choubey · 2018 · Physical review. E