Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

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Items 101–200 of 389

  1. From Systems to Structure: Bridging Networks and Mechanism
    James S. Fraser, John D. Gross, Nevan J. Krogan · 2013 · Molecular Cell
  2. Protein function prediction: towards integration of similarity metrics
    Serkan Erdin, Andreas Martin Lisewski, Olivier Lichtarge · 2011 · Current Opinion in Structural Biology
  3. Biological Diversity and Molecular Plasticity of FIC Domain Proteins
    Alexander Harms, Frédéric V. Stanger, Christoph Dehio · 2016 · Annual Review of Microbiology
  4. Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli
    James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland R. Arnold, Alla G. Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar et al. · 2014 · Bioinformatics
  5. Systems biology of pathogen‐host interaction: Networks of protein‐protein interaction within pathogens and pathogen‐human interactions in the post‐genomic era
    Saliha Durmuş Tekir, Kutlu Ö. Ülgen · 2012 · Biotechnology Journal
  6. Essentiality and centrality in protein interaction networks revisited
    Sawsan Khuri, Stefan Wuchty · 2015 · BMC Bioinformatics
  7. GENIES: gene network inference engine based on supervised analysis
    Masaaki Kotera, Yoshihiro Yamanishi, Yuki Moriya · 2012 · Nucleic Acids Research
  8. Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli
    Jens Hör, Silvia Di Giorgio, Milan Gerovac, Elisa Venturini, Konrad U. Förstner, Jörg Vogel · 2020 · Nucleic Acids Research
  9. Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing
    Ghadie, Mohamed Ali, Lambourne, Luke, Vidal, Marc, Xia, Yu · 2017 · PLOS Computational Biology
  10. Handbook of systems biology : concepts and insights
    Albertha J.M. Walhout, Marc Vidal, Job Dekker · 2013 · The Journal of the American Medical Association (JAMA) Network (American Medical Association)
  11. Prediction and Analysis of the Protein Interactome in Pseudomonas aeruginosa to Enable Network-Based Drug Target Selection
    Minlu Zhang, Shengchang Su, Raj Bhatnagar, Daniel J. Hassett, Long Jason Lu · 2012 · PLoS ONE
  12. Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation
    Jean-Karim Hèriché, Jonathan Gill Lees, Ian Morilla, Thomas Walter, Boryana Petrova, M. Julia Roberti, M. Julius Hossain, Priit Adler, José M. Fernández, Martin Krallinger et al. · 2014 · Molecular Biology of the Cell
  13. Novel function discovery through sequence and structural data mining
    Briallen Lobb, Andrew C. Doxey · 2016 · Current Opinion in Structural Biology
  14. Genomics of apicomplexan parasites
    Lakshmipuram S. Swapna, John Parkinson · 2017 · Critical Reviews in Biochemistry and Molecular Biology
  15. A journey into the regulatory secrets of the de novo purine nucleotide biosynthesis
    Nour Ayoub, Antoine Gedeon, Hélène Munier‐Lehmann · 2024 · Frontiers in Pharmacology
  16. EcoliNet: a database of cofunctional gene network for Escherichia coli
    Hanhae Kim, Jung Eun Shim, Junha Shin, Insuk Lee · 2015 · Database
  17. Structural Coupling between RNA Polymerase Composition and DNA Supercoiling in Coordinating Transcription: a Global Role for the Omega Subunit?
    Marcel Geertz, ANDREW A. TRAVERS, Sanja Mehandziska, Patrick Sobetzko, Sarath Chandra Janga, Nobuo Shimamoto, Georgi Muskhelishvili · 2011 · mBio
  18. The genetic and transcriptional basis of short and long term adaptation across multiple stresses in Escherichia coli
    Violeta Zorraquino, Minseung Kim, Navneet Rai, Ilias Tagkopoulos · 2016 · Molecular Biology and Evolution
  19. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation
    John R. Houser, Craig S. Barnhart, Daniel R. Boutz, Sean M. Carroll, Aurko Dasgupta, Joshua K. Michener, Brittany D. Needham, Ophelia Papoulas, Viswanadham Sridhara, Dariya K. Sydykova et al. · 2015 · PLoS Computational Biology
  20. A comparison and optimization of yeast two-hybrid systems
    John Harry Caufield, Neha Sakhawalkar, Peter Uetz · 2012 · Methods
  21. A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large
    Selma Waaijers, Javier Muñoz, Christian W. H. Berends, João Jacob Ramalho, Soenita S. Goerdayal, Teck Yew Low, Adja Damba Zoumaro-Djayoon, Michael Hoffmann, Thijs Koorman, Roderick P. Tas et al. · 2016 · BMC Biology
  22. Large-scale protein interactome mapping: strategies and opportunities
    Sam Lievens, Sven Eyckerman, Irma H. Lemmens, Jan H. Tavernier · 2010 · Expert Review of Proteomics
  23. Escherichia coli as a Model Organism and Its Application in Biotechnology
    Vargas-Maya Naurú Idalia, Franco Bernardo · 2017 · InTech eBooks
  24. Mitochondrial and plastidial COG0354 proteins have folate-dependent functions in iron–sulphur cluster metabolism
    Jeffrey C. Waller, Kenneth W. Ellens, Sophie Alvarez, Karen Loizeau, Stéphane Ravanel, Andrew D. Hanson · 2011 · Journal of Experimental Botany
  25. From proteomes to complexomes in the era of systems biology
    Trevor Clancy, Eivind J. Hovig · 2013 · PROTEOMICS
  26. Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics
    Laura Carro · 2018 · Beilstein Journal of Organic Chemistry
  27. Mechanisms of Cotranslational Protein Maturation in Bacteria
    Jiří Koubek, Jaro L. Schmitt, Carla V. Galmozzi, Günter Krämer · 2021 · Frontiers in Molecular Biosciences
  28. Remote homology and the functions of metagenomic dark matter
    Briallen Lobb, Daniel A. Kurtz, Gabriel Moreno‐Hagelsieb, Andrew C. Doxey · 2015 · Frontiers in Genetics
  29. Are Antisense Proteins in Prokaryotes Functional?
    Zachary Ardern, Klaus Neuhaus, Siegfried Scherer · 2020 · Frontiers in Molecular Biosciences
  30. PheNetic: network-based interpretation of unstructured gene lists in E. coli
    Dries De Maeyer, Joris Renkens, Lore Cloots · 2013 · Molecular BioSystems
  31. High-throughput Isolation and Characterization of Untagged Membrane Protein Complexes: Outer Membrane Complexes of Desulfovibrio vulgaris
    Peter J. Walian, Simon Allen, Maxim Shatsky, Lucy Zeng, Evelin D. Szakal, Haichuan Liu, Steven C. Hall, Susan J. Fisher, Bonita R. Lam, Mary E. Singer et al. · 2012 · Journal of Proteome Research
  32. Switch of metabolic status: redirecting metabolic flux for acetoin production from glycerol by activating a silent glycerol catabolism pathway
    Yu Wang, Fei Tao, Bo Xin, Hongyu Liu, Yanyan Gao, Ning‐Yi Zhou, Ping Xu · 2016 · Metabolic Engineering
  33. Experimental determination of evolutionary barriers to horizontal gene transfer
    Hande Acar Kirit, Mato Lagator, Jonathan P. Bollback · 2020 · BMC Microbiology
  34. Identifying and characterizing Hfq–RNA interactions
    Martha Faner, Andrew L. Feig · 2013 · Methods
  35. Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)
    Klaus Neuhaus, Richard Landstorfer, Lea Fellner, Svenja Simon, Andrea Schafferhans, Tatyana Goldberg, Harald Marx, Olga N. Ozoline, Burkhard Rost, Bernhard Küster et al. · 2016 · BMC Genomics
  36. Uropathogenic Escherichia coli: An Ideal Resource for DNA Microarray Probe Designing
    Payam Behzadi, Elham Behzadi · 2017 · Lecture notes in computer science
  37. Systems-level approaches for identifying and analyzing genetic interaction networks in Escherichia coli and extensions to other prokaryotes
    Mohan Babu, Gabriel A. Musso, J. Javier Díaz-Mejía, Gareth P. Butland, Jack F. Greenblatt, Andrew Emili · 2009 · Molecular BioSystems
  38. Protein annotation from protein interaction networks and Gene Ontology
    Cao Nguyen, Katheleen Gardiner, Krzysztof J. Cios · 2011 · Journal of Biomedical Informatics
  39. Loss of YhcB results in dysregulation of coordinated peptidoglycan, LPS and phospholipid synthesis during Escherichia coli cell growth
    Emily C. A. Goodall, Georgia L. Isom, Jessica L. Rooke et al. · 2021 · PLoS Genetics
  40. A systematic study of genome context methods: calibration, normalization and combination
    Luciana Ferrer, Joseph M. Dale, Peter D. Karp · 2010 · BMC Bioinformatics
  41. Studying protein complexes by the yeast two-hybrid system
    Seesandra Venkatappa Rajagopala, Patricia M. Sikorski, John Harry Caufield, Andrey Tovchigrechko, Peter Uetz · 2012 · Methods
  42. The use of evolutionary patterns in protein annotation
    Angela D. Wilkins, Benjamin J. Bachman, Serkan Erdin, Olivier Lichtarge · 2012 · Current Opinion in Structural Biology
  43. The Role of the Environment in Horizontal Gene Transfer
    Hande Acar Kirit, Jonathan P. Bollback, Mato Lagator · 2022 · Molecular Biology and Evolution
  44. General organisational principles of the transcriptional regulation system: a tree or a circle?
    Georgi Muskhelishvili, Patrick Sobetzko, Marcel Geertz, Michael Berger · 2010 · Molecular BioSystems
  45. Effect of Reference Genome Selection on the Performance of Computational Methods for Genome-Wide Protein-Protein Interaction Prediction
    V. Muley, A. Ranjan · 2012 · PLoS ONE
  46. Novel MntR-Independent Mechanism of Manganese Homeostasis in Escherichia coli by the Ribosome-Associated Protein HflX
    Gursharan Kaur, Sandeepan Sengupta, Vineet Kumar, Aruna Kumari, Aditi Ghosh, Pradeep Parrack, Dipak Dutta · 2014 · Journal of Bacteriology
  47. An Outer Membrane Protein YiaD Contributes to Adaptive Resistance of Meropenem in Acinetobacter baumannii
    Lei Han, Yiyuan Gao, Yuqing Liu, Siyu Yao, Shuyan Zhong, Sirui Zhang, Jingdan Wang, Peng Mi, Yurong Wen, Zhenlin Ouyang et al. · 2022 · Microbiology Spectrum
  48. Mono-dimensional blue native-PAGE and bi-dimensional blue native/urea-PAGE or/SDS-PAGE combined with nLC–ESI-LIT-MS/MS unveil membrane protein heteromeric and homomeric complexes in Streptococcus thermophilus
    Anna Maria Salzano, Gianfranco Novi, Stefania Arioli, Silvia Corona, Diego Mora, Andrea Scaloni · 2013 · Journal of Proteomics
  49. Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria
    Lore Cloots, Kathleen Marchal · 2011 · Current Opinion in Microbiology
  50. Growing trend of CE at the omics level: The frontier of systems biology – An update
    Eunmi Ban, Soo Hyun Park, Min‐Jung Kang, Hyun‐Jung Lee, Eun Joo Song, Young Sook Yoo · 2011 · Electrophoresis
  51. Prediction of Protein Complexes in Trypanosoma brucei by Protein Correlation Profiling Mass Spectrometry and Machine Learning
    Thomas W. M. Crozier, Michele Tinti, Mark Larance, Angus I. Lamond, Michael A. J. Ferguson · 2017 · Molecular & Cellular Proteomics
  52. Genome-scale genetic manipulation methods for exploring bacterial molecular biology
    Alla G. Gagarinova, Andrew Emili · 2012 · Molecular BioSystems
  53. Protein-protein Interaction Networks of E. coli and S. cerevisiae are similar
    Stefan Wuchty, Peter Uetz · 2014 · Scientific Reports
  54. Small molecule-mediated targeting of microRNAs for drug discovery: Experiments, computational techniques, and disease implications
    Jianfeng Sun, Miaoer Xu, Jinlong Ru, Anna James-Bott, Dapeng Xiong, Xia Wang, Adam P. Cribbs · 2023 · European Journal of Medicinal Chemistry
  55. Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli
    Irina A. Rodionova, Ye Gao, Anand V. Sastry · 2021 · Communications Biology
  56. The diversity of microbial aldo/keto reductases from Escherichia coli K12
    Adrian Jonathan Lapthorn, Xiaofeng Zhu, Elizabeth M. Ellis · 2012 · Chemico-Biological Interactions
  57. YgfZ contributes to secretion of cytotoxic necrotizing factor 1 into outer-membrane vesicles in Escherichia coli
    Hao Yu, Kwang Sik Kim · 2011 · Microbiology
  58. Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported
    Maxim Shatsky, Simon Allen, B. Gold, Nancy L. Liu, Thomas R. Juba, Sonia A. Reveco, Dwayne A. Elias, Ramadevi Prathapam, Jennifer He, Wenhong Yang et al. · 2016 · Molecular & Cellular Proteomics
  59. ESCHERICHIA COLI AS A MODEL ORGANISM
    Muhammad Kamran Taj, Zohra Samreen, Ji Xiu Ling · 2016
  60. Knowledge-guided inference of domain–domain interactions from incomplete protein–protein interaction networks
    Mei Liu, Xuewen Chen, Raja Jothi · 2009 · Bioinformatics
  61. Characterization of a Protein Interactome by Co-Immunoprecipitation and Shotgun Mass Spectrometry
    Giuseppina Maccarrone, Juán José Bonfiglio, Susana Silberstein, Christoph W. Turck, Daniel Martins‐de‐Souza · 2016 · Methods in molecular biology
  62. Comparative evolutionary analysis of protein complexes in E. coli and yeast
    Adam James Reid, Juan A. G. Ranea, Christine Anne Orengo · 2010 · BMC Genomics
  63. NrdR Transcription Regulation: Global Proteome Analysis and Its Role in Escherichia coli Viability and Virulence
    Naveen Vankadari, Chwan‐Deng Hsiao · 2016 · PLoS ONE
  64. Bacterial protein meta-interactomes predict cross-species interactions and protein function
    John Harry Caufield, Christopher Wimble, Semarjit Shary, Stefan Wuchty, Peter Uetz · 2017 · BMC Bioinformatics
  65. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead
    Pedro Escudeiro, Christopher S. Henry, Ricardo Pedro Moreira Dias · 2022 · Current Research in Microbial Sciences
  66. Links between critical proteins drive the controllability of protein interaction networks
    Stefan Wuchty, Toni A. Boltz, Hande Küçük‐McGinty · 2017 · PROTEOMICS
  67. Lateral Gene Transfer in Evolution
    Uri Gophna · 2013 · Springer eBooks
  68. Uncharacterized ORF HUR1 influences the efficiency of non-homologous end-joining repair in Saccharomyces cerevisiae
    Katayoun Omidi, Matthew Jessulat, Mohsen Hooshyar, Daniel. J. Burnside, Andrew Schoenrock, Thomas David Daniel Kazmirchuk, Maryam Hajikarimlou, Mary Daniel, Houman Moteshareie, Urvi Bhojoo et al. · 2017 · Gene
  69. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation
    Zoran Minić, Tanya E. S. Dahms, Mohan Babu · 2018 · Journal of Chromatography B
  70. The power of operon rearrangements for predicting functional associations
    Gabriel Moreno‐Hagelsieb · 2015 · Computational and Structural Biotechnology Journal
  71. RecF protein targeting to post-replication (daughter strand) gaps II: RecF interaction with replisomes
    Camille Henry, Gurleen Kaur, Megan E Cherry et al. · 2023 · Nucleic Acids Research
  72. Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
    Samuel Rochette, Guillaume Diss, Marie Filteau, Jean‐Baptiste Leducq, Alexandre K. Dubé, Christian R. Landry · 2015 · Journal of Visualized Experiments
  73. Characterizing the Escherichia coli O157:H7 Proteome Including Protein Associations with Higher Order Assemblies
    Rembert Pieper, Quanshun Zhang, David J. Clark, Shih-Ting Huang, Moo‐Jin Suh, John C. Braisted, Samuel Payne, Robert D. Fleischmann, Scott N. Peterson, Saul R. Tzipori · 2011 · PLoS ONE
  74. Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli
    Patricia Espenhain Sørensen, Sharmin Baig, Marc Stegger, Hanne Ingmer, An Garmyn, Patrick Butaye · 2021 · Frontiers in Microbiology
  75. Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo
    Anneliese M. Faustino, Piyoosh A. Sharma, Edgar Manriquez‐Sandoval, Divya Yadav, Stephen D. Fried · 2023 · Analytical Chemistry
  76. Structural Evidence That Colicin A Protein Binds to a Novel Binding Site of TolA Protein in Escherichia coli Periplasm
    Chan Li, Ying Zhang, Mireille N. Vankemmelbeke · 2012 · Journal of Biological Chemistry
  77. Characterization of the Sinorhizobium meliloti HslUV and ClpXP Protease Systems in Free-Living and Symbiotic States
    Aaron J. Ogden, Jacqueline M. McAleer, Michael L. Kahn · 2019 · Journal of Bacteriology
  78. Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks
    Pierre C. Havugimana, Pingzhao Hu, Andrew Emili · 2017 · Expert Review of Proteomics
  79. His-Tagged Peptidiscs Enable Affinity Purification of the Membrane Proteome for Downstream Mass Spectrometry Analysis
    John William Young, Irvinder Singh Wason, Zhiyu Zhao, David Rattray, Leonard J. Foster, Franck Duong · 2020 · Journal of Proteome Research
  80. Global organization of protein complexome in the yeast Saccharomyces cerevisiae
    Sang Hoon Lee, Pan‐Jun Kim, Hawoong Jeong · 2011 · BMC Systems Biology
  81. Graph theory and stability analysis of protein complex interaction networks
    Huang, Chien‐Hung, Chen, Teng‐Hung, Ng, Ka‐Lok · 2016 · IET Systems Biology
  82. Multitask Protein Function Prediction through Task Dissimilarity
    Marco Frasca, Nicolò Cesa‐Bianchi · 2017 · IEEE Transactions on Computational Biology and Bioinformatics
  83. Functional Proteomics of Nuclear Proteins in Tetrahymena thermophila: A Review
    Alejandro Saettone, Syed Nabeel‐Shah, Jyoti Garg, Jean‐Philippe Lambert, Ronald E. Pearlman, Jeffrey Fillingham · 2019 · Genes
  84. Ribosome-Dependent ATPase Interacts with Conserved Membrane Protein in Escherichia coli to Modulate Protein Synthesis and Oxidative Phosphorylation
    Mohan Babu, Hiroyuki Aoki, Wasimul Q. Chowdhury, Alla G. Gagarinova, Chris Graham, Sadhna Phanse, Ben Laliberte, Noor Sunba, Matthew Jessulat, Ashkan Golshani et al. · 2011 · PLoS ONE · Retracted
  85. How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets?
    Сергиев Петр Владимирович, Anna Y. Golovina, Olga V. Sergeeva, Ilya А. Osterman, Mikhail V. Nesterchuk, Alexey A. Bogdanov, Olga А. Dontsova · 2012 · Nucleic Acids Research
  86. Lateral acquisition of genes is affected by the friendliness of their products
    Uri Gophna, Yanay Ofran · 2010 · Proceedings of the National Academy of Sciences
  87. Development of a Method Combining Peptidiscs and Proteomics to Identify, Stabilize, and Purify a Detergent-Sensitive Membrane Protein Assembly
    John William Young, Irvinder Singh Wason, Zhiyu Zhao, Sun‐Young Kim, Hiroyuki Aoki, Sadhna Phanse, David Rattray, Leonard J. Foster, Mohan Babu, Franck Duong · 2022 · Journal of Proteome Research
  88. Navigating the complexities of multi-domain protein folding
    Nandakumar Rajasekaran, Christian Kaiser · 2024 · Current Opinion in Structural Biology
  89. Protein Complexes in Bacteria
    John Harry Caufield, Marco Abreu, Christopher Wimble, Peter Uetz · 2015 · PLoS Computational Biology
  90. PTMOracle: A Cytoscape App for Covisualizing and Coanalyzing Post-Translational Modifications in Protein Interaction Networks
    Aidan P. Tay, Chi Nam Ignatius Pang, Daniel L. Winter, Marc Ronald Wilkins · 2017 · Journal of Proteome Research
  91. Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB
    Samridhdi Paudyal, Mercedes Alfonso‐Prieto, Vincenzo Carnevale · 2014 · Proteins Structure Function and Bioinformatics
  92. Predicting protein functions by relaxation labelling protein interaction network
    Pingzhao Hu, Hui Jiang, Andrew Emili · 2010 · BMC Bioinformatics
  93. Computational Network Inference for Bacterial Interactomics
    Katherine James, José Muñoz-Muñoz · 2022 · mSystems
  94. Array-Based Synthetic Genetic Screens to Map Bacterial Pathways and Functional Networks in Escherichia coli
    Mohan Babu, Alla G. Gagarinova, Jack F. Greenblatt, Andrew Emili · 2011 · Methods in molecular biology
  95. Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources
    Shirin Taghipour, Peyman Zarrineh, ‎Mohammad Ganjtabesh, Abbas Nowzari-Dalini · 2017 · BMC Bioinformatics
  96. Characterization of the Widely Distributed Novel ECF42 Group of Extracytoplasmic Function σ Factors in Streptomyces venezuelae
    Qiang Liu, Daniela Pinto, Thorsten Mascher · 2018 · Journal of Bacteriology
  97. Evaluation of Physical and Functional Protein-Protein Interaction Prediction Methods for Detecting Biological Pathways
    Vijaykumar Yogesh Muley, Akash Ranjan · 2013 · PLoS ONE
  98. Integrating Multimeric Threading With High-throughput Experiments for Structural Interactome of Escherichia coli
    Gong, Weikang, Guerler, Aysam, Zhang, Chengxin, Warner, Elisa, Li, Chunhua, Zhang, Yang · 2021 · Journal of Molecular Biology
  99. On the growth and form of bacterial colonies
    Rachel L. Porter, Carolina Trenado-Yuste, Alejandro Martínez-Calvo, Morgan Su, Ned S. Wingreen, Sujit Sankar Datta, Kerwyn Casey Huang · 2025 · Nature Reviews Physics
  100. Exploring interspecific interaction variability in microbiota: A review
    Zhong Yu, Zhihao Gan, Ahmed Tawfik, Fangang Meng · 2024 · Engineering Microbiology