Guilt-by-association goes global

Cited by (559)

Items 201–300 of 559

1. Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression
   Stephen J. Bush, Mary E. B. McCulloch, Charity Muriuki, Mazdak Salavati, Gemma M. Davis, Iseabail Farquhar, Zofia M. Lisowski, Alan L. Archibald, David Arthur Hume, Emily L. Clark · 2018 · G3 Genes Genomes Genetics
2. Integration and mining of malaria molecular, functional and pharmacological data: how far are we from a chemogenomic knowledge space?
   Lyn‐Marié Birkholtz, Olivier Bastien, Gordon A. Wells, Delphine Grando, Fourie Joubert, Vinod Kasam, Marc Zimmermann, Philippe Ortet, Nicolas Jacq, Nadia Saïdani et al. · 2006 · Malaria Journal
3. DTI-Voodoo: machine learning over interaction networks and ontology-based background knowledge predicts drug–target interactions
   Tilman Hinnerichs, Robert Hoehndorf · 2021 · Bioinformatics
4. 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
5. A human gene encoding a protein homologous to ribosomal protein L39 is normally expressed in the testis and derepressed in multiple cancer cells
   Daita Nadano, Tomomi Notsu, Tsukasa Matsuda, Takaaki Sato · 2002 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
6. High-precision high-coverage functional inference from integrated data sources
   Bolan Linghu, Evan S. Snitkin, Dustin T. Holloway, Adam M Gustafson, Yu Xia, Charles DeLisi · 2008 · BMC Bioinformatics
7. Interactions between PBEF and oxidative stress proteins – A potential new mechanism underlying PBEF in the pathogenesis of acute lung injury
   Li Qin Zhang, Djanybek M. Adyshev, Patrick A. Singleton, Hailong Li, Javier Cepeda, Sheng-You Huang, Xiaoqin Zou, Alexander D. Verin, Jiancheng Tu, Joe G. N. Garcia et al. · 2008 · FEBS Letters
8. Content Disputes in Wikipedia Reflect Geopolitical Instability
   Gordana Apic, Matthew J. Betts, Robert B. Russell · 2011 · PLoS ONE
9. Development of a computational framework for the analysis of protein correlation profiling and spatial proteomics experiments
   Nichollas E. Scott, L. Brown, Anders Riis Kristensen, Leonard J. Foster · 2014 · Journal of Proteomics
10. Mapping Protein-Protein Interaction Using High-Throughput Yeast 2-Hybrid
    Jessica A. Lopez, M. Shahid Mukhtar · 2017 · Methods in molecular biology
11. Weighted Gene Correlation Network Meta-Analysis Reveals Functional Candidate Genes Associated with High- and Sub-Fertile Reproductive Performance in Beef Cattle
    Pablo Augusto de Souza Fonseca, Aroa Suárez‐Vega, Ángela Cánovas · 2020 · Genes
12. Distinct leaf transcriptomic response of water deficient Eucalyptus grandis submitted to potassium and sodium fertilization
    Bénédicte Favreau, Marie Denis, Raphaël Ployet, Fabien Mounet, Hana Peireira da Silva, Lívia Maria Franceschini, Jean‐Paul Laclau, Carlos Alberto Labate, Helaine Carrer · 2019 · PLoS ONE
13. Integrative genomics analysis of various omics data and networks identify risk genes and variants vulnerable to childhood-onset asthma
    Xiuqing Ma, Peilan Wang, Guobing Xu, Fang Yu, Yunlong Ma · 2020 · BMC Medical Genomics
14. Functional genomics of trypanosomatids
    Jungmin Choi, Najib M. El-Sayed · 2011 · Parasite Immunology
15. Modelling Self-Organization in Complex Networks Via a Brain-Inspired Network Automata Theory Improves Link Reliability in Protein Interactomes
    Carlo Vittorio Cannistraci · 2018 · Scientific Reports
16. A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus)
    Charity Muriuki, Stephen J. Bush, Mazdak Salavati, Mary E. B. McCulloch, Zofia M. Lisowski, Morris K. Agaba, Appolinaire Djikeng, David Arthur Hume, Emily L. Clark · 2019 · Frontiers in Genetics
17. An integrated method for the identification of novel genes related to oral cancer
    Lei Chen, Jing Yang, Zhihao Xing, Fei Yuan, Yang Shu, Yunhua Zhang, Xiangyin Kong, Tao Huang, Haipeng Li, Yu‐Dong Cai · 2017 · PLoS ONE
18. Computational Prediction of Polycomb-Associated Long Non-Coding RNAs
    Galina V. Glazko, Boris L. Zybailov, Igor B. Rogozin · 2012 · PLoS ONE
19. Cancer module genes ranking using kernelized score functions
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20. Network Analysis for Complex Neurodegenerative Diseases
    Claudia Manzoni, Patrick Alfryn Lewis, Raffaele Ferrari · 2020 · Current Genetic Medicine Reports
21. Mrc1, a non-essential DNA replication protein, is required for telomere end protection following loss of capping by Cdc13, Yku or telomerase
    Nathalie Grandin, Michel Charbonneau · 2007 · Molecular Genetics and Genomics
22. Network-assisted analysis of GWAS data identifies a functionally-relevant gene module for childhood-onset asthma
    Yuanlong Liu, Myriam Brossard, Chloé Sarnowski, Amaury Vaysse, MF Moffatt, Patricia Margaritte‐Jeannin, Felipe Llinares-López, Marie‐Hélène Dizier, Mark G. Lathrop, William Cookson et al. · 2017 · Scientific Reports
23. Determination of Genes Related to Uveitis by Utilization of the Random Walk with Restart Algorithm on a Protein–Protein Interaction Network
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24. Selection of Expression Reference Genes with Demonstrated Stability in Barley among a Diverse Set of Tissues and Cultivars
    Michael Gines, Thomas T. Baldwin, Abdur Rashid, Phil Bregitzer, Peter J. Maughan, Eric N. Jellen, Kathy Esvelt Klos · 2017 · Crop Science
25. Identifying Genes Involved in Alkaloid Biosynthesis in Vinca minor through Transcriptomics and Gene Co-Expression Analysis
    Emily Amor Stander, Liuda Johana Sepúlveda, Thomas Dugé de Bernonville, Inês Carqueijeiro, Konstantinos Koudounas, Pamela Lemos Cruz, Sébastien Besseau, Arnaud Lanoue, Nicolas Papon, Nathalie Giglioli‐Guivarc’h et al. · 2020 · Biomolecules
26. Proteomics: Advanced Technology for the Analysis of Cellular Function
    Nobuhiro Takahashi, Hiroyuki Kaji, Mitsuaki Yanagida, Toshiya Hayano, Toshiaki Isobe · 2003 · Journal of Nutrition
27. Are scale-free networks robust to measurement errors?
    Nan Lin, Hongyu Zhao · 2005 · BMC Bioinformatics
28. TAWFN: a deep learning framework for protein function prediction
    Lu Meng, Xiaoran Wang · 2024 · Bioinformatics
29. A network perspective on unraveling the role of TRP channels in biology and disease
    Jung Nyeo Chun, Jin Muk Lim, Young Ae Kang, Eung Hee Kim, Young-Cheul Shin, Hong‐Gee Kim, Dayk Jang, Dongseop Kwon, Soo-Yong Shin, Insuk So et al. · 2013 · Pflügers Archiv - European Journal of Physiology
30. From protein interactions to functional annotation: graph alignment in Herpes
    Michal Kolář, Michael Lässig, Johannes Berg · 2008 · BMC Systems Biology
31. Cluster-based assessment of protein-protein interaction confidence
    Atanas Kamburov, Arndt Großmann, Ralf Herwig, Ulrich Stelzl · 2012 · BMC Bioinformatics
32. A TRPV2 interactome-based signature for prognosis in glioblastoma patients
    Pau Doñate‐Macian, Antonio Gómez, Irene Roman Degano, Alex Perálvarez‐Marín · 2018 · Oncotarget
33. Implications for domain fusion protein-protein interactions based on structural information
    Jer-Ming Chia, Prasanna R. Kolatkar · 2004 · BMC Bioinformatics
34. Exploring Mouse Protein Function via Multiple Approaches
    Guohua Huang, Chen Chu, Tao Huang, Xiangyin Kong, Yunhua Zhang, Ning Zhang, Yu‐Dong Cai · 2016 · PLoS ONE
35. Identification of growth regulators using cross-species network analysis in plants
    Pasquale Luca Curci, Jie Zhang, Niklas Mähler, Carolin Seyfferth, Chanaka Mannapperuma, Tim Diels, Tom Van Hautegem, David Jonsen, Nathaniel Robert Street, Torgeir Rhoden Hvidsten et al. · 2022 · PLANT PHYSIOLOGY
36. Metagenomic Guilt by Association: An Operonic Perspective
    Gregory Vey · 2013 · PLoS ONE
37. Identification and characterization of NIF3L1 BP1, a novel cytoplasmic interaction partner of the NIF3L1 protein
    Sèmi Tascou, Tae-Ho Kang, Ralf Ulrich Trappe, Wolfgang Engel, Peter Burfeind · 2003 · Biochemical and Biophysical Research Communications
38. Identification of VIMP as a Gene Inhibiting Cytokine Production in Human CD4+ Effector T Cells
    Christophe Capelle, Ni Zeng, Egle Danileviciute, Sabrina Freitas Rodrigues, Markus W. Ollert, Rudi Balling, Feng Q. HeFeng · 2020 · iScience
39. MOLECULAR NETWORKS IN MODEL SYSTEMS
    Timothy Galitski · 2004 · Annual Review of Genomics and Human Genetics
40. Exploring functional genomics for drug target and therapeutics discovery in Plasmodia.
    L. Birkholtz, A. V. Van Brummelen, Katherine Clark, J. Niemand, Éric Maréchal, Manuel Llinás, Abraham I. Louw · 2008 · Acta Tropica
41. A Hybrid Computational Method for the Discovery of Novel Reproduction-Related Genes
    Lei Chen, Chen Chu, Xiangyin Kong, Guohua Huang, Tao Huang, Yu‐Dong Cai · 2015 · PLoS ONE
42. Functional 5′ UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks
    Mathieu Lavallée‐Adam, Philippe Cloutier, Benoit Coulombe, Mathieu Blanchette · 2017 · Nucleic Acids Research
43. Convergent and distributed effects of the 3q29 deletion on the human neural transcriptome
    Esra Sefik, Ryan H. Purcell, The Emory 3q29 Project, Katrina Aberizk, Hallie Averbach, Emily Black, Teresa Lindsey Burrell, Shanthi Cambala, Grace Carlock, Tamara Caspary et al. · 2021 · Translational Psychiatry
44. Yeast Mitochondrial Protein–Protein Interactions Reveal Diverse Complexes and Disease-Relevant Functional Relationships
    Ke Jin, Gabriel A. Musso, James Vlasblom, Matthew Jessulat, Viktor Deineko, Jacopo Negroni, Roberto Mosca, Ramy Habashy Malty, Diem‐Hang Nguyen‐Tran, Hiroyuki Aoki et al. · 2014 · Journal of Proteome Research
45. Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm
    Yunhua Zhang, Li Dai, Ying Liu, Yuhang Zhang, Shaopeng Wang · 2017 · PLoS ONE
46. Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system
    Andrea Hildebrandt, Gregorio Alanis‐Lobato, Andrea Voigt, Kathi Zarnack, Miguel Angel Andrade-Navarro, Petra Beli, Julian König · 2017 · Scientific Reports
47. Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling
    Anis Karimpour‐Fard, Lawrence Hunter, Ryan T. Gill · 2007 · BMC Genomics
48. Genotype to phenotype: a technological challenge
    Ian D. Wilson, Gary Barker, Keith J. Edwards · 2003 · Annals of Applied Biology
49. Identifying Spurious Interactions and Predicting Missing Interactions in the Protein-Protein Interaction Networks via a Generative Network Model
    Yuan Zhu, Xiaofei Zhang, Dao‐Qing Dai, Mengyun Wu · 2012 · IEEE Transactions on Computational Biology and Bioinformatics
50. Protein–Protein Interaction (PPI) Network of Zebrafish Oestrogen Receptors: A Bioinformatics Workflow
    Rabiatul‐Adawiah Zainal‐Abidin, Nor Afiqah‐Aleng, Muhammad‐Redha Abdullah‐Zawawi, Sarahani Harun, Zeti‐Azura Mohamed‐Hussein · 2022 · Life
51. Mining protein interactomes to improve their reliability and support the advancement of network medicine
    Gregorio Alanis‐Lobato · 2015 · Frontiers in Genetics
52. Multitask Protein Function Prediction through Task Dissimilarity
    Marco Frasca, Nicolò Cesa‐Bianchi · 2017 · IEEE Transactions on Computational Biology and Bioinformatics
53. Interaction networks as a tool to investigate the mechanisms of aging
    Émilie Chautard, Nicolas Thierry‐Mieg, Sylvie Ricard‐Blum · 2010 · Biogerontology
54. Computational Network Inference for Bacterial Interactomics
    Katherine James, José Muñoz-Muñoz · 2022 · mSystems
55. Computational Prediction of Protein Complexes from Protein Interaction Networks
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
56. Multidimensional patterns of metabolic response in abiotic stress-induced growth of Arabidopsis thaliana
    Brijesh Singh Yadav, Tamar Lahav, Eli Reuveni, Daniel Chamovitz, Shiri Freilich · 2016 · Plant Molecular Biology
57. [22] Visualizing Networks
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58. Evolutionary Computation for the Interpretation of Metabolomic Data
    Royston Goodacre, Douglas Bruce Kell · 2003 · Springer eBooks
59. Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry
    Michael A. Skinnider, Mopelola O. Akinlaja, Leonard J. Foster · 2023 · Nature Communications
60. Prioritization of candidate disease genes by enlarging the seed set and fusing information of the network topology and gene expression
    Shao‐Wu Zhang, Dong-Dong Shao, Song-Yao Zhang, Yibin Wang · 2014 · Molecular BioSystems
61. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation
    Douglas Bruce Kell · 2021 · Advances in microbial physiology/Advances in Microbial Physiology
62. The Reconstruction and Analysis of Gene Regulatory Networks
    Guangyong Zheng, Tao Huang · 2018 · Methods in molecular biology
63. Genome-wide analysis of signaling domain function
    Jong W. Yu, Mark A. Lemmon · 2003 · Current Opinion in Chemical Biology
64. Protein-Protein Docking Methods
    Garland R. Marshall, Ilya A. Vakser · 2006 · Springer eBooks
65. Prioritizing Disease Candidate Proteins in Cardiomyopathy-Specific Protein-Protein Interaction Networks Based on “Guilt by Association” Analysis
    Li Wan, Lina Chen, Weiming He, Weiguo Li, Xiaoli Qu, Binhua Liang, Qianping Gao, Chenchen Feng, Jia Xu, Yana Lv et al. · 2013 · PLoS ONE
66. A Systematic Analysis on the Genes and Their Interaction Underlying the Comorbidity of Alzheimer's Disease and Major Depressive Disorder
    Pan Guo, Shasha Chen, Hao Wang, Yaogang Wang, Ju Wang · 2022 · Frontiers in Aging Neuroscience
67. PROSNET: INTEGRATING HOMOLOGY WITH MOLECULAR NETWORKS FOR PROTEIN FUNCTION PREDICTION
    Sheng Wang, Meng Qu, Jian Peng · 2016 · Pacific Symposium on Biocomputing (PSB)
68. Gene gravity-like algorithm for disease gene prediction based on phenotype-specific network
    Limei Lin, Tinghong Yang, Ling Fang, Jian Yang, Fan Yang, Jing Zhao · 2017 · BMC Systems Biology
69. Interactomics and tick vaccine development: new directions for the control of tick-borne diseases
    Sara Artigas-Jerónimo, José de la Fuente, Margarita Villar · 2018 · Expert Review of Proteomics
70. Unrevealing functional candidate genes for bovine fertility through RNA sequencing meta-analysis and regulatory elements networks of co-expressed genes and lncRNAs
    Pablo Augusto de Souza Fonseca, Aroa Suárez‐Vega, Ángela Cánovas · 2022 · Functional & Integrative Genomics
71. Multiomic investigation of Sugarcane mosaic virus resistance in sugarcane
    Ricardo José Gonzaga Pimenta, Alexandre Hild Aono, Roberto Carlos Villavicencio Burbano, Marcel Fernando da Silva, Ivan Antônio dos Anjos, Marcos Guimarães de Andrade Landell, Marcos César Gonçalves, Luciana Rossini Pinto, Anete Pereira de Souza · 2023 · The Crop Journal
72. Proteomics profiling of interactome dynamics by colocalisation analysis (COLA)
    Faraz K. Mardakheh, Heba Sailem, Sandra Kuemper, Christopher J. Tape, Ryan R. McCully, Angela Paul, Sara Anjomani‐Virmouni, Claus Jørgensen, George Poulogiannis, Christopher J. Marshall et al. · 2016 · Molecular BioSystems
73. Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
    Phillip M. Seitzer, A. Jeanniard, Fang-Rui Ma, J. van Etten, M. Facciotti, D. Dunigan · 2018 · Viruses
74. Role of the Putative Structural Protein Sed1p in Mitochondrial Genome Maintenance
    Naina Phadnis, Elaine Ayres Sia · 2004 · Journal of Molecular Biology
75. Protein-protein interactions of the hyperthermophilic archaeon Pyrococcus horikoshiiOT3
    Kengo Usui, Shintaro Katayama, Mutsumi Kanamori-Katayama, Chihiro Ogawa, Chikatoshi Kai, Makiko Okada, Jun Kawai, Takahiro Arakawa, Piero Carninci, Masayoshi Itoh et al. · 2005 · Genome biology
76. Genome-wide analysis of the context-dependence of regulatory networks.
    Balázs Papp, Stephen G. Oliver · 2005 · Genome biology
77. Computational function prediction of bacteria and phage proteins
    Susanna R. Grigson, George Spyro Bouras, Bas E. Dutilh, Robert Olson, Robert Alan Edwards · 2025 · Microbiology and Molecular Biology Reviews
78. Inferring biosynthetic and gene regulatory networks from Artemisia annua RNA sequencing data on a credit card-sized ARM computer
    Qiao Wen Tan, Marek Mutwil · 2019 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
79. Fibrinaloid Microclots and Atrial Fibrillation
    Douglas Bruce Kell, Gregory Y.H. Lip, Etheresia Pretorius · 2024 · Biomedicines
80. Advances in Parkinson’s disease research – A computational network pharmacological approach
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81. Exploitation of genetic interaction network topology for the prediction of epistatic behavior
    Gregorio Alanis‐Lobato, Carlo Vittorio Cannistraci, Timothy Ravasi · 2013 · Genomics
82. Automated gene function prediction through gene multifunctionality in biological networks
    Marco Frasca · 2015 · Neurocomputing
83. Exploring mitochondrial system properties of neurodegenerative diseases through interactome mapping
    James Vlasblom, Ke Jin, Sandy Kassir, Mohan Babu · 2013 · Journal of Proteomics
84. Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales
    Sabrina Kleeßen, Sebastian Klie, Zoran Nikoloski · 2013 · The Plant Cell
85. Deep Learning Techniques Dealing with Diabetes Mellitus: A Comprehensive Study
    Sujit Kumar Das, Pinki Roy, Arnab Kumar Mishra · 2021 · Studies in computational intelligence
86. A packed microcolumn approach to a cell-based biosensor
    Jeb H. Flemming, Helen K. Baca, Margaret Werner‐Washburne, Susan M. Brozik, Gabriel P. López · 2005 · Sensors and Actuators B Chemical
87. Molecular interaction networks for the analysis of human disease: Utility, limitations, and considerations
    Sarah‐Jane Schramm, Vivek Jayaswal, Apurv Goel, Simone S. Li, Jean Yee Hwa Yang, Graham J. Mann, Marc Ronald Wilkins · 2013 · PROTEOMICS
88. Inferring Disease Associated Phosphorylation Sites via Random Walk on Multi-Layer Heterogeneous Network
    Xiaoyi Xu, Minghui Wang · 2015 · IEEE Transactions on Computational Biology and Bioinformatics
89. Big data analytics: Solution to healthcare
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90. An integrative C. elegans protein–protein interaction network with reliability assessment based on a probabilistic graphical model
    Xiaotai Huang, Yuan Zhu, Leanne Lai Hang Chan, Zhongying Zhao, Hong Yan · 2015 · Molecular BioSystems
91. Mining for genes related to choroidal neovascularization based on the shortest path algorithm and protein interaction information
    Jian Zhang, Yan Suo, Yuhang Zhang, Qing Zhang, Xijia Chen, Xun Xu, Wencong Lu · 2016 · Biochimica et Biophysica Acta (BBA) - General Subjects
92. Signal transduction profiling using label-free biosensors
    Matthew A. Cooper · 2009 · Journal of Receptors and Signal Transduction
93. Interactome Networks
    Anne‐Ruxandra Carvunis, Frederick P. Roth, Michael A. Calderwood, Michael E. Cusick, Giulio Superti‐Furga, Marc Vidal · 2012 · Elsevier eBooks
94. Identification of circulating immune landscape in ischemic stroke based on bioinformatics methods
    Danyang Li, Lifang Li, Fei Quan, Tianfeng Wang, Si Xu, Shuang Li, Kuo Tian, Meng Feng, Ni He, Liting Tian et al. · 2022 · Frontiers in Genetics
95. The coordinated regulation mechanism of rice plant architecture and its tolerance to stress
    Huibo Zhao, Xiong Liu, Jiajia Wang, Qian Qian, Guangheng Zhang · 2022 · Frontiers in Plant Science
96. Evolutionary divergence between homologous X–Y chromosome genes shapes sex-biased biology
    Alex R. DeCasien, Kathryn Tsai, Siyuan Liu, Adam G. Thomas, Armin Raznahan · 2025 · Nature Ecology & Evolution
97. Positive and negative forms of replicability in gene network analysis
    Wim Verleyen, Sara Ballouz, Jesse A Gillis · 2015 · Bioinformatics
98. Impaired Airway Epithelial Barrier Integrity in Response to Stenotrophomonas maltophilia Proteases, Novel Insights Using Cystic Fibrosis Bronchial Epithelial Cell Secretomics
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99. Proteomics and Network Analyses Reveal Inhibition of Akt‐mTOR Signaling in CD4 + T Cells by Mycobacterium tuberculosis Mannose‐Capped Lipoarabinomannan
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100. Protein function prediction as a graph-transduction game
     Sebastiano Vascon, Marco Frasca, Rocco Tripodi, Giorgio Valentini, Marcello Pelillo · 2018 · Pattern Recognition Letters