Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins
Hu, Pingzhao, Janga, Sarath Chandra, Babu, Mohan, Díaz-Mejía, J. Javier, Butland, Gareth, Yang, Wenhong, Pogoutse, Oxana, Guo, Xinghua, Phanse, Sadhna, Wong, Peter, Chandran, Shamanta, Christopoulos, Constantine, Nazarians-Armavil, Anaies, Nasseri, Negin Karimi, Musso, Gabriel, Ali, Mehrab, Nazemof, Nazila, Eroukova, Veronika, Golshani, Ashkan, Paccanaro, Alberto, Greenblatt, Jack F, Moreno-Hagelsieb, Gabriel, Emili, Andrew·2009·PLoS Biology
Cited by (389)
Items 301–389 of 389
- Screening, Optimization and Assembly of Key Pathway Enzymes in Metabolic EngineeringYanfeng Liu, Long Liu · 2019 · Springer eBooks
- Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living CellsSamuel Rochette, Guillaume Diss, Marie Filteau, Jean‐Baptiste Leducq, Alexandre K. Dubé, Christian R. Landry · 2015 · Journal of Visualized Experiments
- Analyses of Complex Genome-Scale Biological NetworksVijaykumar Yogesh Muley, Vishal Acharya · 2012 · SpringerBriefs in systems biology
- Characterization of Escherichia coli Single-gene Deletion Mutants Impaired in Bacteriophage ReproductionKelly Reimer · 2013 · TSpace (University of Toronto)
- Predicting direct physical interactions in multimeric proteins with deep learningMu Gao, Davi Nakajima An, Jerry M. Parks, Jeffrey Skolnick · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- The protein interactome of Escherichia coli carbohydrate metabolismShomeek Chowdhury, Stephen S. Fong, Peter Uetz · 2025 · PLoS ONE
- Four Ab Initio Whole Cell Kinetic Models of Bacillus subtilis 168 (bsuLL25) 6051-HGW (bshSM25), N33 (bsuN33SS25), FUA2231 (bsuGR25)Maurice HT Ling · 2025 · Journal of Clinical Immunology & Microbiology
- Applications of Protein Interaction NetworksVijaykumar Yogesh Muley, Vishal Acharya · 2012 · SpringerBriefs in systems biology
- Genomic and Transcriptomic Analyses of Foodborne Bacterial PathogensWei Zhang, Edward G. Dudley, Joseph T. Wade · 2010 · Springer eBooks
- Lateral Genetic Transfer and Cellular NetworksElizabeth Skippington, Mark A. Ragan · 2013 · Springer eBooks
- Quantitative and Systems-Based Approaches for Deciphering Bacterial Membrane Interactome and Gene FunctionViktor Deineko, Ashwani Kumar, James Vlasblom, Mohan Babu · 2015 · Advances in experimental medicine and biology
- Recent advances in the techniques of protein-protein interaction studyMingqiang Wang, Jinxia Wu, Yuhong Zhang · 2013 · Hereditas (Beijing)
- Proteomics Defines Protein Interaction Network of Signaling PathwaysShitao Li · 2012 · Translational bioinformatics
- Advantages and Applications of Gel-Free Proteomic Approaches in the Study of ProkaryotesJohn Phillip Bowman · 2014 · Comprehensive analytical chemistry
- Genetic Interaction Scoring Procedure for Bacterial SpeciesOmar Wagih, Leopold Parts · 2015 · Advances in experimental medicine and biology
- Prediction of Intra‐ and Interspecies Protein–Protein Interactions Facilitating Systems Biology StudiesSylvia Schleker, Seshan Ananthasubramanian, Judith Klein‐Seetharaman, Madhavi K. Ganapathiraju · 2013 · Methods and principles in medicinal chemistry
- Computational Prediction of Gene Function From High-throughput Data SourcesSara Mostafavi · 2011 · TSpace (University of Toronto)
- C 4 -dicarboxylate metabolons: Interaction of C 4 -dicarboxylate transporters of Escherichia coli with cytosolic enzymesChristopher Schubert, Gottfried Unden · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
- Regulatory interactions of enzymes of the citric acid cycle in Bacillus subtilisFrederik M. Meyer · 2013 · eDiss (Georg-August-Universität Göttingen)
- Faculty Opinions recommendation of HMCES Maintains Genome Integrity by Shielding Abasic Sites in Single-Strand DNA.Houra Merrikh · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
- Identification and characterization of novel genes involved in DNA double strand break repair process in the yeast Saccharomyces cerevisiaeKatayoun Omidi · 2017 · Carleton University's Institutional Repository (MacOdrum Library, Carleton University)
- Learning gene interactions and functional landscapes from entire bacterial proteomesPalash Sethi, Marc G. Chevrette, Juannan Zhou · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Mass spectrometry in clinical protein biomarker discoveryVille Parviainen · 2014 · Työväentutkimus Vuosikirja
- Inference, Orthology, and Inundation: Addressing Current Challenges in the Field of MetagenomicsGregory Vey · 2009 · Scholars Commons (Wilfrid Laurier University)
- Caracterização de cepas de Escherichia coli contendo diferentes alelos rpoS.Heloisa Galbiati · 2011
- Investigating Hfq-mRNA interactions in bacteriaMartha Faner · 2013 · Human Biology
- Biogen interacts with target discoveryTim Fulmer · 2012 · Science-Business eXchange
- A functional blueprint of E. coliAllison J. Doerr · 2009 · Nature Methods
- Interactions between rank and sparsity in penalized estimation, and detection of structured objectsPierre-André Savalle · 2014 · theses.fr (ABES)
- Interpreting the Regulatory Interplay in E. coli Metabolic PathwaysAnália Maria Garcia Lourenço, Sónia Carneiro, José P. Pinto, Miguel Rocha, Eugénio Campos Ferreira, Isabel Rocha · 2011 · Advances in intelligent and soft computing
- in Escherichia coli under complex evolutionary scenarios 2Violeta Zorraquino, Semarhy Quiñones-Soto, Minseung Kim, Navneet Rai · 2014
- On the interconnection of stable protein complexes: inter-complex hubs and their conservation in Saccharomyces cerevisiae and Homo sapiens networksConcettina Guerra · 2015 · International Journal of Bioinformatics Research and Applications
- Identification of Chromatin-Binding Protein ComplexesAlain Doucet, Daniel Figeys · 2013 · Springer eBooks
- A Combination of Protein-Protein Interaction Network Topological and Biological Process Features for Multiprotein Complex DetectionNazar Zaki, Elfadil Abdalla Mohamed · 2016 · Elsevier eBooks
- The Role of Elyc Protein in Protection Against Oxidative Stress in E. Coli CellsKhadidja Senouci‐Rezkallah · 2015 · IP International Journal of Medical Microbiology and Tropical Diseases
- Filtering and Interpreting Large-Scale Experimental Protein–Protein Interaction DataGabriel A. Musso, Andrew Emili, Zhaolei Zhang · 2011 · Methods in molecular biology
- BASIC CONCEPTS IN THE MAMMALIAN GUT MICROBIOME Meta'omic Analytic Techniques for Studying the Intestinal MicrobiomeXochitl C. Morgan, Curtis Huttenhower · 2014
- Protein-Protein Functional Linkage Predictions: Bringing Regulation to ContextAnne Hahn, Vijaykumar Yogesh Muley · 2016 · CRC Press eBooks
- Cell-free Determination of Binary Complexes That Comprise Extended Protein-Protein Interaction Networks of Yersinia pestisSarah L. Keasey, Mohan Natesan, Christine L. Pugh, Teddy Kamata, Stefan Wuchty, Robert G. Ulrich · 2016 · Molecular & Cellular Proteomics
- Incorporating Correlations among Gene Ontology Terms into Predicting Protein FunctionsPingzhao Hu, Hui Jiang, Andrew Emili · 2013 · Bioinformatics
- Exploring the Bioactive Landscape of the Gut Microbiota to Identify Metabolites Underpinning Human HealthPáraic Ó Cuív, Sriti Burman, Sian Pottenger, Mark Morrison · 2016 · Springer eBooks
- Mining into interspecific bacterial interactionsOlaf Tyc · 2016
- Two‐Hybrid and Related SystemsNeha Sakhawalkar, John Harry Caufield, Peter Uetz · 2017 · Encyclopedia of Life Sciences
- BACTERIAL CELL DIVISION IN-SIGHT: A SUPER-RESOLUTION STUDY OF THE ESCHERICHIA COLI DIVISOMEJackson A. Buss · 2013
- An Efficient Lentiviral-based Proteomics Approach Identifies Mitochondrial Complexes with Neurodegenerative FunctionSandy Kassir · 2015
- Characterization of Metal-binding P-loop GTPases: E. coli YeiR and M. thermoacetica AcsFJessica Andrea Flood-Garibay · 2011 · TSpace (University of Toronto)
- Escherichia coli responses to acid-stress : signal transduction and gene regulationHrishiraj Sen · 2018 · University of Birmingham Institutional Research Archive (University of Birmingham)
- An Improved Prorank Algorithm for Detection of Overlapping Protein Complexes using Protein Interaction and Gene Expression Datasets in YeastP. Manikandan, D. Ramyachitra · 2018 · IEEE/ACIS International Conference on Computer and Information Science (ICIS)
- Functional Genomics for Improving Gene Function Assessment in BacteriaWenjun Shao · 2015 · eScholarship (California Digital Library)
- The Organization and Evolution of Biological Networks in Bacteria - Elucidating Biological Pathways and Complexes Involved in Bacterial Survival and Environmental AdaptationCedoljub Bundalovic-Torma · 2018 · TSpace (University of Toronto)
- Functional Genomics in YeastMaryam Hajikarimlou · 2020
- BIOCHEMICAL PROFILE-BASED COMPUTATIONAL INFERENCE OF PROTEIN COMPLEXESHU Zhong-ming · 2020 · TSpace (University of Toronto)
- Dynamics of Proteins and Macromolecular Machines in Escherichia coliMaxime Leroux, Nicolas Soubry, Rodrigo Reyes‐Lamothe · 2021 · EcoSal Plus
- Unwrapping BacteriaKevin D. Young · 2014 · PLoS Genetics
- Quantitative Genetic Screens for Mapping Bacterial Pathways and Functional NetworksAlla G. Gagarinova, Ali Hosseinnia, Mohan Babu · 2021 · Methods in molecular biology
- Prediction and Investigation of Novel Proteins in DNA Double Stranded Break RepairMohsen Hooshyar · 2016
- Relações da estrutura de redes complexas com as dinâmicas do passeio aleatório, de transporte e de sincronizaçãoLucas Antiqueira · 2012 · Digital Library of Theses and Dissertations (Universidade de São Paulo)
- Incorporating Correlations among Gene Ontology Terms into Predicting Protein FunctionsPingzhao Hu, Hui Jiang, Andrew Emili · 2011 · IGI Global eBooks
- Chemical-genetic profiling to investigate cross-resistance and collateral sensitivity between antimicrobial peptidesPramod Kumar Jangir · 2020
- Faculty Opinions recommendation of Multiplexed gene synthesis in emulsions for exploring protein functional landscapes.Nobuhiko Tokuriki · 2019 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
- Faculty Opinions recommendation of A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies.Dario Leister, Thilo Rühle · 2021 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
- Identifying of protein complexes and functional modules in E.coli PPI networksPing Kong, Wei Liu · 2020
- Protein–protein interaction network of E. coli K‐12 has significant high‐dimensional cavities: new insights from algebraic topological studiesXiaoyan Xue, Zhou Chen, Yue Hu, Dan Nie, Hui Zhao, Xinggang Mao · 2022 · FEBS Open Bio
- Developing a CHIP-SEQ pipeline to determine function of chromatin remodeling and transcription related complexes in a model organismAlejandro Saettone · 2022
- Environment and the Evolutionary Trajectory of Horizontal Gene TransferRama P. Bhatia, Hande Acar Kirit, Cecil M. Lewis, Krithivasan Sankaranarayanan, Jonathan P. Bollback · 2022 · Access Microbiology
- Developing a CHIP-SEQ pipeline to determine function of chromatin remodeling and transcription related complexes in a model organismAlejandro Saettone · 2022
- DeepsmirUD: Precise prediction of regulatory effects on miRNA expression mediated by small molecular compounds using competing deep learning frameworksJianfeng Sun, Jinlong Ru, Zihao Chen, Fei Qi, Lorenzo Ramos‐Mucci, Suyuan Chen, Adam P. Cribbs, Li Deng, Xia Wang · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
- Assessing and Improving Protein-Protein Interaction Prediction in E. coliEric Arezza · 2022
- Clade-wise alignment integration improves co-evolutionary signals for protein-protein interaction predictionTao Fang, Damian Szklarczyk, Radja Hachilif, Christian von Mering · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- Additional file 2 of Identification of protein complexes and functional modules in E. coli PPI networksPing Kong, Huang, Gang, Wei Liu · 2020 · Figshare
- Additional file 1 of Identification of protein complexes and functional modules in E. coli PPI networksPing Kong, Huang, Gang, Wei Liu · 2020 · Figshare
- Decoding Translational Control and Gene ExpressionSara Takalloo · 2024 · Carleton University's Institutional Repository (MacOdrum Library, Carleton University)
- A statistical-based method for the construction and analysis of gene network: application to bacteriaZhiyuan Zhang, Guozhong Chen, Erguang Li · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
- Quantifying the Effects of Single Nucleotide Changes in the TATA Box of the Cauliflower Mosaic Virus 35S Promoter on Gene Expression in Arabidopsis thalianaStephanie C. Amack · 2021
- MsyB-HU Interaction Modulates a Two-Tiered Bacterial Stress Response by Regulating DNA SupercoilingHuan Chen, Yanan Yang, Xinrui Chen, Haolong Zhou, Yingli He, Mengzhe Li, Wei Lin, Zuyi Yuan, Yawen Wang, Stephen Matthews et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Exploiting network-based approaches for understanding gene regulation and functionSarath Chandra Janga · 2010 · Apollo (University of Cambridge)
- Additional file 3 of Experimental determination of evolutionary barriers to horizontal gene transferAcar Kirit, Hande, Mato Lagator, Jonathan P. Bollback · 2020 · Figshare
- Ab initio Whole Cell Kinetic Model of Desulfovibrio desulfuricans L4 (ddsAAR26)Atoshi Abirami RajKumar, Cheryl Kai Ning Kang, Sragvi Verma, Diya Nanthakumarvani, Shafeeqa Abul-Hasan, Leesha Haarshiny Perumal, Maurice HT Ling · 2026 · Journal of Clinical Immunology & Microbiology
- Ab initio Whole Cell Kinetic Model of Streptomyces murinus CR-43 (smuLA26)Aguilar Normi Luisa Cinco, Pandiyan Srinithiksha, Sohnnakshee Murugesu · 2026 · Journal of Clinical Immunology & Microbiology
- Analyses et prédictions bioinformatiques de réseaux d'interactions protéine-protéines contextualisésOussema Souiai · 2011 · theses.fr (ABES)
- Organisation moléculaire et réponse au stress de la voie de biosynthèse des phospholipides chez Esherichia coliAstrid Wahl · 2010
- Mécanismes et régulation d'une ARN hélicase essentielle chez E. coli : le facteur de terminaison de la transcription bactérienne RhoMakhlouf Rabhi · 2011
- Méthodes de classification de réseaux d'intéractions protéine-protéine et évaluations pour l'étude de la fonctionBenoît Robisson · 2013 · theses.fr (ABES)
- Diversité et biosynthèse des lipides chez les palmiersChloé Guerin · 2015 · theses.fr (ABES)
- Expanding the phenotypic and chemical space in Escherichia coliCarmen Lucia Herrera Dominguez · 2016
- Biogenèse des protéines à centre [Fe-S] et leur rôle dans la thiolation des ARNtsMarine Lénon · 2023 · theses.fr (ABES)
- Enzymes de la voie de biosynthèse de novo des nucléotides puriques chez les bactéries : caractérisation et rôle physiologiqueNour Ayoub · 2024 · theses.fr (ABES)
- Ab Initio Whole Cell Kinetic Model of Bifidobacterium breve DSM 20213 (bbrdPS26)Parkavi Subramanian, Shnan Harish Modankap, Shamsia Bte Ali, Jullean Louise Dizon Baylon, Lavanya Dhingra, Nurhaliza Mohamed Ali, Maurice HT Ling · 2026 · Journal of Clinical Immunology & Microbiology
- Prediction of Protein-Protein Interactions in Escherichia coli from Experimental Data in Treponema pallidumMarco Abreu · 2015 · VCU Scholars Compass (Virginia Commonwealth University)