Correlation between gene expression profiles and protein-protein interactions within and across genomes

Bhardwaj, N., Lu, H.·2005·Bioinformatics
DOI 10.1093/bioinformatics/bti398

Cited by (185)

Items 101–185 of 185

  1. Predicting protein–protein interactions in the post synaptic density
    Ossnat Bar-Shira, Gal Chechik · 2013 · Molecular and Cellular Neuroscience
  2. msiDBN: A Method of Identifying Critical Proteins in Dynamic PPI Networks
    Yuan Zhang, Nan Du, Kang Li, Jinchao Feng, Kebin Jia, Aidong Zhang · 2014 · BioMed Research International
  3. Computational Methods to Predict Protein Interaction Partners
    Alfonso Valencia, Florencio Pazos · 2008 · Computational biology
  4. Predicting protein complexes via the integration of multiple biological information
    Xiwei Tang, Jianxin Wang, Yi Feng Pan · 2012 · IEEE International Conference on Systems Biology
  5. Employing conservation of co-expression to improve functional inference
    Carsten O. Daub, Erik L. L. Sonnhammer · 2008 · BMC Systems Biology
  6. Describing the Orthology Signal in a PPI Network at a Functional, Complex Level
    Pavol Jancura, Eleftheria Mavridou, Beatriz Pontes, Elena Marchiori · 2011 · Lecture notes in computer science
  7. Systems-Based Approach to the Analyses of Plant Functions: Conceptual Understanding, Implementation, and Analysis
    Brijesh Singh Yadav, Amit Kumar Singh, Sandeep Kumar Kushwaha · 2017 · Springer eBooks
  8. Predicting Gene Expression Divergence between Single-Copy Orthologs in Two Species
    Antara Anika Piya, Michael DeGiorgio, Raquel Assis · 2023 · Genome Biology and Evolution
  9. Predicting physiologically relevant SH3 domain mediated protein–protein interactions in yeast
    Shobhit Jain, Gary D. Bader · 2016 · Bioinformatics
  10. Analyzing Protein Interaction Networks
    Johannes B. Goll, Peter Uetz · 2007
  11. Co-regulated protein functional modules with varying activities in dynamic PPI networks
    Yuan Zhang, Nan Du, Kang Li, Kebin Jia, Aidong Zhang · 2013 · Tsinghua Science & Technology
  12. LinkedPPI: enabling intuitive, integrative protein-protein interaction discovery
    Laleh Kazemzadeh, Maulik R. Kamdar, Oya Beyan, Stefan Decker, Frank Barry · 2014
  13. Protein – Protein Etkileşimi Tespit Yöntemleri, Veri Tabanları ve Veri Güvenilirliği
    Volkan Altuntaş, Murat Gök · 2020 · European Journal of Science and Technology
  14. Prediction, Analysis, Visualization, and Storage of Protein–Protein Interactions Using Computational Approaches
    Krishna Mohan Poluri, Khushboo Gulati, Sharanya Sarkar · 2021 · Springer eBooks
  15. Predicting receptor-ligand pairs through kernel learning
    Ernesto Iacucci, Fabian Ojeda, Bart De Moor, Yves Moreau · 2011 · BMC Bioinformatics
  16. Protein Evolutionary Rates Correlate with Expression Independently of Synonymous Substitutions in Helicobacter pylori
    Björn Sällström, Ramy Arnaout, Wagied Davids, Pär Bjelkmar, Siv G. E. Andersson · 2006 · Journal of Molecular Evolution
  17. Signaling Pathway Activities Improve Prognosis for Breast Cancer
    Yunlong Jiao, Marta R. Hidalgo, Cankut Çubuk, Alicia Amadoz, José Carbonell‐Caballero, Jean‐Philippe Vert, Joaquı́n Dopazo · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  18. Trees on networks: resolving statistical patterns of phylogenetic similarities among interacting proteins
    William Kelly, Michael P. H. Stumpf · 2010 · BMC Bioinformatics
  19. AVERON notebook to discover actionable cancer vulnerabilities enabled by neomorph protein-protein interactions
    Hongyue Chen, Brian Revennaugh, Haian Fu, Andrey A. Ivanov · 2024 · iScience
  20. Comparative Analysis of Classification Methods for Protein Interaction Verification System
    Min Su Lee, Seung Soo Park · 2006 · Lecture notes in computer science
  21. A generative model of identifying informative proteins from dynamic PPI networks
    Yuan Zhang, Yue Cheng, Kebin Jia, Aidong Zhang · 2014 · Science China Life Sciences
  22. A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae
    Wei-Sheng Wu, Ming-Liang Wei, Chia-Ming Yeh, Darby Tien-Hao Chang · 2014 · BMC Systems Biology
  23. Learning functional embedding of genes governed by pair-wised labels
    Jingjun Cao, Zhengli Wu, Wenting Ye, Haohan Wang · 2017 · International Conference on Computational Intelligence and Applications (ICCIA)
  24. Validating text mining results on protein-protein interactions using gene expression profiles
    Deyu Zhou, Yulan He, Chee Keong Kwoh · 2006 · Open Research Online - ORO (The Open University)
  25. Genome Wide Identification and Characterization of LIM Domain Associated Gene Superfamily in Common Bean ( Phaseolus vulgaris L.)
    Raiyyan Abdur Rahim, Maria Chowdhory, Mahmuda Akhter Hasi, Fabiha Haque, Arif Hasan Khan Robin · 2025 · International Journal of Genomics
  26. The protein kinases of Dictyostelia and their incorporation into a signalome
    Koryu Kin, Zhi-hui Chen, Gillian Forbes, Hajara Lawal, Christina Schilde, Reema Singh, Christian Cole, Geoffrey J. Barton, Pauline Schaap · 2023 · Cellular Signalling
  27. ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato
    Laura Miozzi, Paolo Provero, Gian Paolo Accotto · 2010 · Plant Molecular Biology
  28. A practical prognostic lncRNA signature for lung squamous cell carcinoma
    Xiaoshun Shi, Fuxi Huang, Xiaobing Le, Xiaoxiang Li, Kailing Huang, Baoxin Liu, Viola Yingjun Luo, Yanhui Liu, Zhuolin Wu, Allen Menglin Chen et al. · 2017 · Translational Medicine Communications
  29. A nonparametric Bayesian test of dependence
    Yimin Kao, Brian J. Reich, Howard D. Bondell · 2015 · arXiv (Cornell University)
  30. Oncogene Coexpression in Mesenchymal Neoplasia Correlates with EGF Transcription
    David E. Joyner, Timothy A. Damron, Albert J. Aboulafia, Robert Lor Randall · 2007 · Clinical Orthopaedics and Related Research
  31. Predicting evolutionary targets and parameters of gene deletion from expression data
    André Luiz Campelo dos Santos, Michael DeGiorgio, Raquel Assis · 2024 · Bioinformatics Advances
  32. A graph-based integrative method of detecting consistent protein functional modules from multiple data sources
    Yuan Zhang, Yue Cheng, Liang Ge, Nan Du, Kebin Jia, Aidong Zhang · 2015 · International Journal of Data Mining and Bioinformatics
  33. Critical protein detection in dynamic PPI networks with multi-source integrated deep belief nets
    Yuan Zhang, Nan Du, Kang Li, Jinchao Feng, Kebin Jia, Aidong Zhang · 2013 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
  34. Improvement of GNs inference through biological data integration
    Fábio Fernandes da Rocha Vicente, Fabrício Martins Lopes, Ronaldo F. Hashimoto · 2011 · IEEE International Workshop on Genomic Signal Processing and Statistics
  35. Hierarchical Parallelization of Gene Differential Association Analysis
    Mark Needham, Rui Hu, Sandhya Dwarkadas, Xing Qiu · 2011 · BMC Bioinformatics
  36. Evaluating the designing perspective of Protein-Protein Interaction network using evolutionary algorithm
    Pratyusha Rakshit, Archana Chowdhury, Amit Konar, Atulya K. Nagar · 2012 · World Congress on Nature and Biologically Inspired Computing (NaBIC)
  37. Evolutionary approach for designing protein-protein interaction network using artificial bee colony optimization
    Pratyusha Rakshit, Pratyusha Das, Archana Chowdhury, Amit Konar, R. Janarthanan · 2012 · International Conference on Computing, Communication and Networking Technologies (ICCCNT)
  38. A Network Systems Approach to Identify Functional Epigenetic Drivers in Cancer
    A. Teschendorff, M. Widschwendter · 2013 · Translational bioinformatics
  39. Protocol to analyze dysregulation of the eIF4F complex in human cancers using R software and large public datasets
    Su Wu, Gerhard Wagner · 2022 · STAR Protocols
  40. Finding the pathology of major depression through effects on gene interaction networks
    Chris Gaiteri · 2011 · D-Scholarship@Pitt (University of Pittsburgh)
  41. EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery
    Wijeratne, H.R. Sagara, Runnebohm, Avery M., Barron, Monica P., Hampton, Ariana J., Li, Rudong, Peck Justice, Sarah A., Lenceski, Sophia H., Rooney, James D., Smith-Kinnaman, Whitney R., Chang, Gina S. et al. · 2026
  42. Narrow funnel-like interaction energy distribution is an indicator of specific protein interaction partner
    Choi, Juyoung · 2023 · iScience
  43. Computational interference of gene regulatory networks on the growth and development of millets
    Lipsa Leena Panigrahi, Gayatri Mishra, Dhaneswar Swain, Gyana Ranjan Rout · 2025 · Plant Gene
  44. Salt stress and the wheat curl mite (Aceria tosichella) infestation reprograms barley nitrogen metabolism via nitric oxide signaling
    Jakub Graska, Justyna Fidler, Ewa Muszyńska, Marta Gietler, Małgorzata Nykiel, Beata Prabucka, Mariusz Lewandowski, Mateusz Labudda · 2026 · Planta
  45. NTreceptorDB: a Database of Polymorphisms and Disease-Gene Associations in Behavioral Disorders
    Aliyu Musa, Ekrem Varoğlu, Bahar Taneri · 2013 · Eastern Mediterranean University Institutional Repository (Eastern Mediterranean University)
  46. A Method of Pathway Enrichment Analysis Based Gene Expression Variability
    XiaoDong Jia, XiuJie CHEN, Xin Wu, Jiankai Xu, Fujian Tan, Xiangqiong Liu, Lei Liu, Ruizhi Yang · 2013 · ACTA AGRONOMICA SINICA
  47. The protease web
    Wolfgang Esser‐Skala, Nikolaus Fortelny · 2021 · Elsevier eBooks
  48. Network Analytics Enabled by Generating a Pool of Network Variants from Noisy Data
    Aamir Mandviwalla, Amr Elsisy, Muhammad Saad Atique, Konstantin Kuzmin, Chris Gaiteri, Boleslaw Karol Szymanski · 2023 · Entropy
  49. Stress-Induced Constraint on Expression Noise of Essential Genes in E. coli
    Perry A. LaBoone, Raquel Assis · 2024 · Journal of Molecular Evolution
  50. Are protein hubs faster folders? Exploration based on Escherichia coli proteome
    Hongrui Xu, Jun-Feng Cheng, Xiao-Pan Hu, Ying-Ying Chu, Bin‐Guang Ma · 2016 · Amino Acids
  51. Network-Guided Key Gene Discovery for a Given Cellular Process
    Feng Q. HeFeng, Markus W. Ollert · 2016 · Advances in biochemical engineering, biotechnology
  52. Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation
    Jun-Xiao Ma, Yi Yang, Guang Li, Bin‐Guang Ma · 2021 · International Journal of Molecular Sciences
  53. Interacting partners of Brassica juncea regulator of G-protein signaling protein suggest its role in cell wall metabolism and cellular signaling
    Roshan Kumar, Naveen Chandra Bisht · 2022 · Bioscience Reports
  54. Prediction of Intra‐ and Interspecies Protein–Protein Interactions Facilitating Systems Biology Studies
    Sylvia Schleker, Seshan Ananthasubramanian, Judith Klein‐Seetharaman, Madhavi K. Ganapathiraju · 2013 · Methods and principles in medicinal chemistry
  55. Computational approaches in high-throughput proteomics data analysis
    Anna‐Maria Lahesmaa‐Korpinen · 2012 · Työväentutkimus Vuosikirja
  56. Protein-protein interactions more conserved within than across species
    Sven Mika, Burkhard Rost · 2005 · PLoS Computational Biology
  57. Multi-task analysis of gene expression data on cancer public datasets
    Yasmmin Martins · 2023 · medRxiv
  58. Computational Approaches to Elucidating Transient Protein-Protein Interactions, Predicting Receptor-Ligand Pairings
    Ernesto Iacucci, Samuel Xavier‐de‐Souza, Yves Moreau · 2012 · IntechOpen eBooks
  59. Towards Better Receptor-Ligand Prioritization: How Machine Learning on Protein-Protein Interaction Data Can Provide Insight Into Receptor-Ligand Pairs
    Ernesto Iacucci, Yves Moreau · 2010 · Lecture notes in computer science
  60. Discovering domain-domain interactions toward genome-wide protein interaction and function predictions
    Xuewen Chen, Mei Liu · 2009
  61. The Role of Neurotransmitter Receptors in Mental and Behavioral Disorders: a Biomedical Text Mining Approach
    Aliyu Musa · 2012 · Eastern Mediterranean University Institutional Repository (Eastern Mediterranean University)
  62. Similarity of Transcription Profiles for Genes in Gene Sets
    Marko Toplak, Tomaž Curk, Blaž Zupan · 2011 · Lecture notes in computer science
  63. Analysis of incomplete gene expression dataset through protein-protein interaction information
    Raimon Massanet Vila, Teresa Padró, A. Cardus, Lina Badimón, P. Caminal, Alexandre Perera-Lluna · 2011 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
  64. Identifying changed protein-protein interactions in biological processes by gene coexpression analysis
    Ting Zhang, Xuegong Zhang, Zhirong Sun · 2010 · Chinese Science Bulletin
  65. Protein-Protein Interaction Reliability Enhancement System based on Feature Selection and Classification Technique
    Minsu Lee, Seung-Soo Park, Sangho Lee, Hwan-Seung Yong, Sung-Hee Kang · 2006 · The KIPS Transactions PartB
  66. NETWORKS IN EPIGENETICS
    Kuljeet Singh Sandhu · 2010 · Figshare
  67. Vertical integration of high-throughput measurements to derive functional and regulatory interactions in S. cerevisiae
    R. J. P. van Berlo · 2010 · Research Repository (Delft University of Technology)
  68. Can pharmacology possibly have a role for bioinformatics?
    Paul A. Whittaker · 2007 · Expert Opinion on Drug Discovery
  69. The evolution of a disease resistance pathway in tomato
    Lukasz Grzeskowiak · 2009 · Electronic Theses of LMU Munich (Ludwig-Maximilians-Universität München)
  70. Transcriptional profiling and network-based gene annotations of human malaria parasite plasmodium falciparum
    Guang An Hu · 2009
  71. Exploring gene interactions in dna microarray data
    Xintao Wu, Yong Ye · 2007
  72. Other Applications of Combinatorial Peptide Libraries
    Pier Giorgio Righetti, Egisto Boschetti · 2013 · Elsevier eBooks
  73. Mining protein complexes from protein interaction data
    Min Wu · 2011
  74. Discovering Transcriptional Regulation by Integrating Protein-Protein Interaction, Gene Expression and Transcriptional Interaction Data
    Fei Luo, Jinyan Li · 2009
  75. Protein function prediction based on protein – protein interaction networks.
    Derek D. Wang · 2016
  76. An Analysis of the Expression, Regulation and Interaction of Genes and Gene Products using Computational and Molecular Methods
    Ron Ammar · 2008 · TSpace (University of Toronto)
  77. Network Medicine in the age of biomedical big data
    Abhijeet R. Sonawane, Scott T. Weiss, Kimberly Glass, Amitabh Sharma · 2019 · arXiv (Cornell University)
  78. Predicting expression divergence and its evolutionary parameters between single-copy genes in two species
    Antara Anika Piya, Michael DeGiorgio, Raquel Assis · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  79. Statistical detecting of genes associated with PIK3C2B on lung disease
    Jiamin Wei, Hongbo Wei, Yuxuan Xing, Bin Wang, Lu Han, Liang Tong, Ying Zhou · 2023 · BIO Web of Conferences
  80. Covalent inhibition of Plasmodium falciparum Ubc13 impairs global protein synthesis
    Anna Truong, Ruitian Hu, Baiyi Quan, Morgan A. Bailey, Erin A. Schroeder, Kayla Sylvester, Gaëlle Neveu, Björn F.C. Kafsack, Michael C. Fitzgerald, Emily Rose Derbyshire · 2025 · iScience
  81. Gene Co-expression Networks are Poor Proxies for Expert-Curated Gene Regulatory Networks
    Suryadipto Sarkar, David B. Blumenthal · 2025 · Lecture notes in computer science
  82. Mechanistic Bayesian Networks for Integrating Knowledge and Data to Unravel Biological Complexity
    Abhik Shah · 2011 · Deep Blue (University of Michigan)
  83. An integrative approach to studying protein-protein interactions within the genome of Mycobacterium tuberculosis
    Kenneth Opap · 2011 · Open University of Cape Town (University of Cape Town)
  84. Gene function predicts divergence across molecular levels
    Antara Anika Piya, Ksenia Macias Calix, Raquel Assis · 2026 · Scientific Reports
  85. Generation of scRNA-seq Data by Combining Generation Adversarial Network and Label
    Xiaoshu Zhu, Tiezheng Qiao, Fei Teng, Qintong Lyu, Ya Zhou, Chunrong Xiong · 2026 · International Conference on Information Science and Technology