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Global quantification of mammalian gene expression control

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  1. Ji Min Lee & Henrik M. Hammarén & Mikhail M. Savitski & Sung Hee Baek, 2023. "Control of protein stability by post-translational modifications," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  2. Marvin Hering & Alaa Madi & Roger Sandhoff & Sicong Ma & Jingxia Wu & Alessa Mieg & Karsten Richter & Kerstin Mohr & Nora Knabe & Diana Stichling & Gernot Poschet & Felix Bestvater & Larissa Frank & J, 2024. "Sphinganine recruits TLR4 adaptors in macrophages and promotes inflammation in murine models of sepsis and melanoma," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  3. Mohammad Soltani & Cesar A Vargas-Garcia & Duarte Antunes & Abhyudai Singh, 2016. "Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes," PLOS Computational Biology, Public Library of Science, vol. 12(8), pages 1-23, August.
  4. Jonathan J. Swietlik & Stefanie Bärthel & Chiara Falcomatà & Diana Fink & Ankit Sinha & Jingyuan Cheng & Stefan Ebner & Peter Landgraf & Daniela C. Dieterich & Henrik Daub & Dieter Saur & Felix Meissn, 2023. "Cell-selective proteomics segregates pancreatic cancer subtypes by extracellular proteins in tumors and circulation," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  5. Rune B Jakobsen & Esben Østrup & Xiaolan Zhang & Tarjei S Mikkelsen & Jan E Brinchmann, 2014. "Analysis of the Effects of Five Factors Relevant to In Vitro Chondrogenesis of Human Mesenchymal Stem Cells Using Factorial Design and High Throughput mRNA-Profiling," PLOS ONE, Public Library of Science, vol. 9(5), pages 1-13, May.
  6. Beatrice T. Laudenbach & Karsten Krey & Quirin Emslander & Line Lykke Andersen & Alexander Reim & Pietro Scaturro & Sarah Mundigl & Christopher Dächert & Katrin Manske & Markus Moser & Janos Ludwig & , 2021. "NUDT2 initiates viral RNA degradation by removal of 5′-phosphates," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
  7. Claude Gérard & Laurane De Mot & Sabine Cordi & Jonathan van Eyll & Frédéric P Lemaigre, 2021. "Temporal dynamics of a CSF1R signaling gene regulatory network involved in epilepsy," PLOS Computational Biology, Public Library of Science, vol. 17(4), pages 1-20, April.
  8. Ryosuke Ishimura & Afnan H. El-Gowily & Daisuke Noshiro & Satoko Komatsu-Hirota & Yasuko Ono & Mayumi Shindo & Tomohisa Hatta & Manabu Abe & Takefumi Uemura & Hyeon-Cheol Lee-Okada & Tarek M. Mohamed , 2022. "The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  9. Ralda Nehme & Olli Pietiläinen & Mykyta Artomov & Matthew Tegtmeyer & Vera Valakh & Leevi Lehtonen & Christina Bell & Tarjinder Singh & Aditi Trehan & John Sherwood & Danielle Manning & Emily Peirent , 2022. "The 22q11.2 region regulates presynaptic gene-products linked to schizophrenia," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
  10. Yan Li & Bing Wang & Wentao Yang & Fahan Ma & Jianling Zou & Kai Li & Subei Tan & Jinwen Feng & Yunzhi Wang & Zhaoyu Qin & Zhiyu Chen & Chen Ding, 2024. "Longitudinal plasma proteome profiling reveals the diversity of biomarkers for diagnosis and cetuximab therapy response of colorectal cancer," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
  11. Kaslik, Eva & Rădulescu, Ileana Rodica, 2022. "Stability and bifurcations in fractional-order gene regulatory networks," Applied Mathematics and Computation, Elsevier, vol. 421(C).
  12. Viviana Volta & Sandra Pérez-Baos & Columba Parra & Olga Katsara & Amanda Ernlund & Sophie Dornbaum & Robert J. Schneider, 2021. "A DAP5/eIF3d alternate mRNA translation mechanism promotes differentiation and immune suppression by human regulatory T cells," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
  13. McNutt Patrick & Gut Ian & Hubbard Kyle & Beske Phil, 2015. "A novel method to prioritize RNAseq data for post-hoc analysis based on absolute changes in transcript abundance," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 14(3), pages 227-241, June.
  14. Jasjot Singh & Hadeer Elhabashy & Pathma Muthukottiappan & Markus Stepath & Martin Eisenacher & Oliver Kohlbacher & Volkmar Gieselmann & Dominic Winter, 2022. "Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  15. Suran Kim & Sungjin Min & Yi Sun Choi & Sung-Hyun Jo & Jae Hun Jung & Kyusun Han & Jin Kim & Soohwan An & Yong Woo Ji & Yun-Gon Kim & Seung-Woo Cho, 2022. "Tissue extracellular matrix hydrogels as alternatives to Matrigel for culturing gastrointestinal organoids," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
  16. Sébastien Durand & Marion Bruelle & Fleur Bourdelais & Bigitha Bennychen & Juliana Blin-Gonthier & Caroline Isaac & Aurélia Huyghe & Sylvie Martel & Antoine Seyve & Christophe Vanbelle & Annie Adrait , 2023. "RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  17. Jingbo Qie & Yang Liu & Yunzhi Wang & Fan Zhang & Zhaoyu Qin & Sha Tian & Mingwei Liu & Kai Li & Wenhao Shi & Lei Song & Mingjun Sun & Yexin Tong & Ping Hu & Tao Gong & Xiaqiong Wang & Yi Huang & Bolo, 2022. "Integrated proteomic and transcriptomic landscape of macrophages in mouse tissues," Nature Communications, Nature, vol. 13(1), pages 1-23, December.
  18. Michelle M. Kameda-Smith & Helen Zhu & En-Ching Luo & Yujin Suk & Agata Xella & Brian Yee & Chirayu Chokshi & Sansi Xing & Frederick Tan & Raymond G. Fox & Ashley A. Adile & David Bakhshinyan & Kevin , 2022. "Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
  19. Marzieh Marzbany & Fatemeh Ghassemi & Mahsa Rasekhian, 2019. "Application of the 3'-Untranslated Region of Messenger RNA from Measles Virus Matrix Protein as an RNA Stabilizer: Implications in Pharmaceutical Biotechnology," Journal of Molecular Biology Research, Canadian Center of Science and Education, vol. 9(1), pages 1-53, December.
  20. Anna Trenaman & Michele Tinti & Richard J. Wall & David Horn, 2024. "Post-transcriptional reprogramming by thousands of mRNA untranslated regions in trypanosomes," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
  21. Yuping Chen & Jo-Hsi Huang & Connie Phong & James E. Ferrell, 2024. "Viscosity-dependent control of protein synthesis and degradation," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  22. Mengyi Yin & Wenhua Kuang & Qianran Wang & Xi Wang & Chuanfei Yuan & Zhe Lin & Huanyu Zhang & Fei Deng & Haobo Jiang & Peng Gong & Zhen Zou & Zhihong Hu & Manli Wang, 2022. "Dual roles and evolutionary implications of P26/poxin in antagonizing intracellular cGAS-STING and extracellular melanization immunity," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
  23. Johan Kerkhofs & Liesbet Geris, 2015. "A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-23, June.
  24. Lingling Li & Dongxian Jiang & Qiao Zhang & Hui Liu & Fujiang Xu & Chunmei Guo & Zhaoyu Qin & Haixing Wang & Jinwen Feng & Yang Liu & Weijie Chen & Xue Zhang & Lin Bai & Sha Tian & Subei Tan & Chen Xu, 2023. "Integrative proteogenomic characterization of early esophageal cancer," Nature Communications, Nature, vol. 14(1), pages 1-28, December.
  25. Hirofumi Nagao & Ashok Kumar Jayavelu & Weikang Cai & Hui Pan & Jonathan M. Dreyfuss & Thiago M. Batista & Bruna B. Brandão & Matthias Mann & C. Ronald Kahn, 2023. "Unique ligand and kinase-independent roles of the insulin receptor in regulation of cell cycle, senescence and apoptosis," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
  26. Thomas C. J. Tan & Van Kelly & Xiaoyan Zou & David Wright & Tony Ly & Rose Zamoyska, 2022. "Translation factor eIF5a is essential for IFNγ production and cell cycle regulation in primary CD8+ T lymphocytes," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  27. Gábor Csárdi & Alexander Franks & David S Choi & Edoardo M Airoldi & D Allan Drummond, 2015. "Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast," PLOS Genetics, Public Library of Science, vol. 11(5), pages 1-32, May.
  28. Katharina Clemm von Hohenberg & Sandra Müller & Sibylle Schleich & Matthias Meister & Jonathan Bohlen & Thomas G. Hofmann & Aurelio A. Teleman, 2022. "Cyclin B/CDK1 and Cyclin A/CDK2 phosphorylate DENR to promote mitotic protein translation and faithful cell division," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  29. Sajib Chakraborty & Hossain Uddin Shekhar, 2017. "Applications of Mass-Spectrometry Based Quantitative Proteomics to Understand Complex Cellular Functions and Cell Fate Decisions," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 1(1), pages 169-171, June.
  30. Lingling Li & Dongxian Jiang & Hui Liu & Chunmei Guo & Rui Zhao & Qiao Zhang & Chen Xu & Zhaoyu Qin & Jinwen Feng & Yang Liu & Haixing Wang & Weijie Chen & Xue Zhang & Bin Li & Lin Bai & Sha Tian & Su, 2023. "Comprehensive proteogenomic characterization of early duodenal cancer reveals the carcinogenesis tracks of different subtypes," Nature Communications, Nature, vol. 14(1), pages 1-24, December.
  31. Yan Li & Chen Xu & Bing Wang & Fujiang Xu & Fahan Ma & Yuanyuan Qu & Dongxian Jiang & Kai Li & Jinwen Feng & Sha Tian & Xiaohui Wu & Yunzhi Wang & Yang Liu & Zhaoyu Qin & Yalan Liu & Jing Qin & Qi Son, 2022. "Proteomic characterization of gastric cancer response to chemotherapy and targeted therapy reveals potential therapeutic strategies," Nature Communications, Nature, vol. 13(1), pages 1-26, December.
  32. Wenhao Shi & Yushen Wang & Chen Xu & Yan Li & Sai Ge & Bin Bai & Kecheng Zhang & Yunzhi Wang & Nairen Zheng & Juan Wang & Shiqi Wang & Gang Ji & Jipeng Li & Yongzhan Nie & Wenquan Liang & Xiaosong Wu , 2023. "Multilevel proteomic analyses reveal molecular diversity between diffuse-type and intestinal-type gastric cancer," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
  33. B. Bojarojc-Nosowicz & P. Brym & E. Kaczmarczyk & A. Stachura & A.K. Habel, 2016. "Polymorphism and expression of the tumour necrosis factor-alpha (TNF-alpha) gene in non-infected cows and in cows naturally infected with the bovine leukaemia virus (BLV)," Veterinární medicína, Czech Academy of Agricultural Sciences, vol. 61(1), pages 1-9.
  34. Wenqi Hu & Haitao Zeng & Yanan Shi & Chuanchuan Zhou & Jiana Huang & Lei Jia & Siqi Xu & Xiaoyu Feng & Yanyan Zeng & Tuanlin Xiong & Wenze Huang & Peng Sun & Yajie Chang & Tingting Li & Cong Fang & Ke, 2022. "Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  35. Elena Grahn & Svenja V. Kaufmann & Malika Askarova & Momchil Ninov & Luisa M. Welp & Thomas K. Berger & Henning Urlaub & U.Benjamin Kaupp, 2023. "Control of intracellular pH and bicarbonate by CO2 diffusion into human sperm," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  36. Masayo Inoue & Katsuhisa Horimoto, 2017. "Relationship between regulatory pattern of gene expression level and gene function," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-14, May.
  37. Kaushik Bhattacharya & Samarpan Maiti & Szabolcs Zahoran & Lorenz Weidenauer & Dina Hany & Diana Wider & Lilia Bernasconi & Manfredo Quadroni & Martine Collart & Didier Picard, 2022. "Translational reprogramming in response to accumulating stressors ensures critical threshold levels of Hsp90 for mammalian life," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  38. Yuankun Yang & Christina E. Steidele & Clemens Rössner & Birgit Löffelhardt & Dagmar Kolb & Thomas Leisen & Weiguo Zhang & Christina Ludwig & Georg Felix & Michael F. Seidl & Annette Becker & Thorsten, 2023. "Convergent evolution of plant pattern recognition receptors sensing cysteine-rich patterns from three microbial kingdoms," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  39. Madison L. Doolittle & Dominik Saul & Japneet Kaur & Jennifer L. Rowsey & Stephanie J. Vos & Kevin D. Pavelko & Joshua N. Farr & David G. Monroe & Sundeep Khosla, 2023. "Multiparametric senescent cell phenotyping reveals targets of senolytic therapy in the aged murine skeleton," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
  40. Yunzhi Wang & Rongkui Luo & Xuan Zhang & Hang Xiang & Bing Yang & Jinwen Feng & Mengjie Deng & Peng Ran & Akesu Sujie & Fan Zhang & Jiajun Zhu & Subei Tan & Tao Xie & Pin Chen & Zixiang Yu & Yan Li & , 2023. "Proteogenomics of diffuse gliomas reveal molecular subtypes associated with specific therapeutic targets and immune-evasion mechanisms," Nature Communications, Nature, vol. 14(1), pages 1-32, December.
  41. Hasan Vatandaslar & Aitor Garzia & Cindy Meyer & Svenja Godbersen & Laura T. L. Brandt & Esther Griesbach & Jeffrey A. Chao & Thomas Tuschl & Markus Stoffel, 2023. "In vivo PAR-CLIP (viP-CLIP) of liver TIAL1 unveils targets regulating cholesterol synthesis and secretion," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
  42. Erik. T. Frank & Lucie Kesner & Joanito Liberti & Quentin Helleu & Adria C. LeBoeuf & Andrei Dascalu & Douglas B. Sponsler & Fumika Azuma & Evan P. Economo & Patrice Waridel & Philipp Engel & Thomas S, 2023. "Targeted treatment of injured nestmates with antimicrobial compounds in an ant society," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
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