“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks
Gillis, Jesse, Pavlidis, Paul·2012·PLoS Computational Biology
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Items 101–200 of 216
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- Constraints in the Design of the Synthetic Bacterial ChassisAntoine Danchin, Agnieszka Sekowska · 2013 · Methods in microbiology
- Visualizing high dimensional datasets using parallel coordinates: Application to gene prioritizationThomas Boogaerts, Léon-Charles Tranchevent, Georgios A. Pavlopoulos, Jan A Aerts, Joos P. L. Vandewalle · 2012 · IEEE International Conference on Bioinformatics and Bioengineering (BIBE)
- Metals and methylotrophy: Via global gene expression studiesZachary J. Johnson, Dennis D. Krutkin, Pavlo Bohutskyi, Marina Kalyuzhnaya · 2021 · Methods in enzymology on CD-ROM/Methods in enzymology
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- CINPER: An Interactive Web System for Pathway Prediction for ProkaryotesXizeng Mao, Xin Chen, Yu Zhang, Spencer Pangle, Ying Xu · 2012 · PLoS ONE
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- Integrating rare variant genetics and brain transcriptome data implicates novel schizophrenia putative risk genesShengtong Han, Marieke R. Gilmartin, Wenhui Sheng, Victor X. Jin · 2025 · Schizophrenia Research
- Aberration hubs in protein interaction networks highlight actionable targets in cancerMehran Karimzadeh, Pouria Jandaghi, Andreas Ioannis Papadakis, Sebastian Trainor, Johan Rung, Mar Gonzàlez-Porta, Ghislaine Scélo, Naveen S. Vasudev, Alvis Brāzma, Sidong Huang et al. · 2018 · Oncotarget
- Prediction of key gene function in spinal muscular atrophy using guilt by association method based on network and gene ontologyWenjiu Yang, Jing Han, Jinfeng Ma, Yujie Feng, Qingxian Hou, Zhijie Wang, Tengbo Yu · 2019 · Experimental and Therapeutic Medicine
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- Network centrality approaches used to uncover and classify most influential nodes with their related miRNAs in cardiovascular diseasesMohd Murshad Ahmed, Safia Tazyeen, Rafat Ali, Aftab Alam, Nikhat Imam, Md. Zubbair Malik, Shahnawaz Ali, Romana Ishrat · 2022 · Gene Reports
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- Inferring novel genes related to colorectal cancer via random walk with restart algorithmSheng Lu, Zhenggang Zhu, Wencong Lu · 2019 · Gene Therapy
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- A method for estimating coherence of molecular mechanisms in major human disease and traitsMikhail G. Dozmorov, Kellen G. Cresswell, Silviu‐Alin Bacanu, Carl F. Craver, Mark Reimers, Kenneth S. Kendler · 2020 · BMC Bioinformatics
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- A survey of disease connections for CD4+ T cell master genes and their directly linked genesWentian Li, Jesús Espinal Enríquez, Kim R. Simpfendorfer, Enrique Hernandez Lemus · 2015 · Computational Biology and Chemistry
- The 4th Schizophrenia International Research Society Conference, 5–9 April 2014, Florence, Italy: A summary of topics and trendsOlukayode Abayomi, Davide Amato, C. C. Bailey, Byron K.Y. Bitanihirwe, Lynneice Bowen, Shimon Burshtein, Alexis E. Cullen, Montserrat Fusté, Ana Paula Herrmann, Babak Khodaie et al. · 2014 · Schizophrenia Research
- A methodology for disease gene association using centrality measuresAshkan Entezari Heravi, Sheridan K. Houghten · 2016 · IEEE Congress on Evolutionary Computation (CEC)
- Knowledge-guided gene prioritization reveals new insights into the mechanisms of chemoresistanceAmin Emad, Carl R. Woese, Junmei Cairns, Krishna R. Kalari, Liewei Wang, M.D., Saurabh Sinha · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
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- Rewiring of miRNA-mRNA bipartite co-expression network as a novel way to understand the prostate cancer related playersMohammad Mehdi Naghizadeh, Behnaz Bakhshandeh, Farshid Noorbakhsh, Marjan Yaghmaie, Ali Masoudi‐Nejad · 2023 · Systems Biology in Reproductive Medicine
- Properties of Biological NetworksVlado Dančík, Amrita B Basu, Paul A. Clemons · 2013 · Springer eBooks
- Prioritizing uncharacterized genes in the search for glioma biomarkersRheal A. Towner, Jonathan D. Wren · 2014 · CNS Oncology
- Integrative Omics for Informed Drug Repurposing: Targeting CNS DisordersRammohan Shukla, Nicholas Henkel, Khaled Alganem, Abdul-Rizaq Ali Hamoud, James K. Reigle, Rawan S. Alnafisah, Hunter Eby, Ali Sajid Imami, Justin F. Creeden, Scott A. Miruzzi et al. · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
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- Proteomizer: Leveraging the Transcriptome-Proteome Mismatch to Infer Novel Gene Regulatory RelationsGiulio Deangeli, Maria Grazia Spillantini, Píetro Lió · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
- Optimized Molecular Interaction Networks for the Study of Skeletal MuscleStephen Morgan, Apostolos Malatras, Stéphanie Duguez, William John Duddy · 2021 · Journal of Neuromuscular Diseases
- Functional Annotation Routines Used by ABRF Bioinformatics Core Facilities - Observations, Comparisons, and ConsiderationsCharles A. Whittaker, Alper Küçükural, Chris Gates, Owen Michael Wilkins, George W. Bell, John N. Hutchinson, Shawn W. Polson, Julie A. Dragon · 2023 · Journal of Biomolecular Techniques JBT
- Uncovering coordinated pathway interactions through gene co-differential expression in yeastMuhammad Ibtisam Nasar, Syed Sabih Ur Rehman, S. Ott, Mohammad Tauqeer Alam · 2025 · Nucleic Acids Research
- Biological networks in Barley (Hordeum vulgare L.): From molecular interactions to systems-level understandingBahman Panahi, Hossein Abbasi Holasou, Rasmieh Hamid, Amir Ghaffar Shahriari, Zahra Ghorbanzadeh · 2026 · Current Plant Biology
- The role of protein embeddings for protein–protein interaction prediction with graph neural networksLaura Balbi, Rita T. Sousa, Pedro Giesteira Cotovio, Cátia Pesquita · 2026 · Briefings in Bioinformatics
- Depicting Gene Co-expression Networks Underlying eQTLsNathalie Vialaneix, Laurence Liaubet, Magali SanCristobal · 2016 · Springer eBooks
- EVATECH H POLYMER-MODIFIED BITUMENJ C Nicholls · 1994 · OpenGrey (Institut de l'Information Scientifique et Technique)
- CBDCEM: An effective centrality based differential co-expression method for critical gene findingManaswita Saikia, Dhruba K. Bhattacharyya, Jugal Kumar Kalita · 2022 · Gene Reports
- On functional annotation with gene co-expression networksVladimir Kunc, Jǐŕı Kléma · 2022 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- VI-VS: calibrated identification of feature dependencies in single-cell multiomicsPierre Boyeau, Stephen Bates, Can Ergen, Michael I. Jordan, Nir Yosef · 2024 · Genome biology
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- Accurate prediction of drug-protein interactions by maintaining the original topological relationships among embeddingsYanfei Li, Xiran Chen, Shuqin Wang, Jinmao Wei · 2025 · BMC Biology
- A Random Forest proximity matrix as a new measure for gene annotationJosé Antonio Seoane, Ian N.M. Day, Juan Pablo Casas, Colin Campbell, Tom R. Gaunt · 2014
- Identifying large-scale interaction atlases using probabilistic graphs and external knowledgeSree Krishna Chanumolu, Hasan H. Otu · 2022 · Journal of Clinical and Translational Science
- Can machine learning aid in identifying disease genes? The case of autism spectrum disorderMargot Gunning, Paul Pavlidis · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- DeepPheno: Predicting single gene knockout phenotypesMaxat Kulmanov, Robert Hoehndorf · 2019 · King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)
- Root‐associated stress response networksJennifer P.C. To, Philip N. Benfey, Tedd D. Elich · 2013
- Degrees of separation as a statistical tool for evaluating candidate genesRonald M. Nelson, Mats E. Pettersson · 2014 · Computers in Biology and Medicine
- Bridging methodological gaps in network-based systems biologyT. M. Murali, Christopher L. Poirel · 2013 · VTechWorks (Virginia Tech)
- Data Integration Methods to Interpret Genome-Scale Data from CancersMarko Laakso · 2012 · Työväentutkimus Vuosikirja
- COMBINED PROFILING IN ASPEN A SYSTEMS BIOLOGY APPROACHOgonna Obudulu · 2015
- Gene Expression Models of Signaling PathwaysJeffrey T. Chang · 2015 · Translational bioinformatics
- Gene and protein networks in understanding cellular functionSK Lehtinen · 2015 · UCL Discovery (University College London)
- Network Medicine in the age of biomedical big dataAbhijeet R. Sonawane, Scott T. Weiss, Kimberly Glass, Amitabh Sharma · 2019 · arXiv (Cornell University)
- Semantic Prioritization of Novel Causative Genomic Variants in Mendelian and Oligogenic DiseasesImene Boudellioua · 2019 · King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)
- Revealing protein functions based on relationships of interacting proteins and GO termsZhixia Teng, Maozu Guo, Xiaoyan Liu, Zhen Tian, Kai Che · 2016 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
- DeORFanizing Candida albicans Genes using Co-ExpressionTeresa R. O’Meara, Matthew J. O’Meara · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
- Rol del gen RHBDD2 en la progresión del cáncer colorrectal frente al tratamiento neoadyuvanteSabina Palma · 2020
- On function homophily of microbial Protein-Protein Interaction Networks.Nicola Apollonio, Paolo Giulio Franciosa, Daniele Santoni · 2021 · arXiv (Cornell University)
- Peer Review #1 of "Clinicopathological value of long non-coding RNA profiles in gastrointestinal stromal tumor (v0.1)"2021 · PeerJ
- Peer Review #1 of "Clinicopathological value of long non-coding RNA profiles in gastrointestinal stromal tumor (v0.2)"2021 · PeerJ
- Identification of Genes Associated with Alzheimer's Disease using Evolutionary ComputationGuangyao Chen, James Sargant, Sheridan K. Houghten, Tyler K. Collins · 2021 · IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)
- Proceedings of the Twelfth Annual UT-ORNL-KBRIN Bioinformatics Summit 2013Eric Christian Rouchka, Robert M Flight · 2013 · BMC Bioinformatics
- Peer Review #2 of "Clinicopathological value of long non-coding RNA profiles in gastrointestinal stromal tumor (v0.2)"2021 · PeerJ
- Peer Review #2 of "Clinicopathological value of long non-coding RNA profiles in gastrointestinal stromal tumor (v0.1)"2021 · PeerJ
- Faculty Opinions recommendation of Large-scale investigation of the reasons why potentially important genes are ignored.Buzz Baum, Gautam Dey, Nitya Ramkumar · 2018 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
- Calibrated Identification of Feature Dependencies in Single-cell MultiomicsPierre Boyeau, Stephen Bates, Can Ergen, Michael I. Jordan, Nir Yosef · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- An In-Silico Identification of Anti-CRISPR Proteins by Using Descriptors Derived from the Primary StructuresSidra Liaqat, Saiqa Andleeb, Maryum Bibi, Wajid Arshad Abbasi · 2023 · International Conference on Frontiers of Information Technology (FIT)
- Additional file 2 of Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesisHong Li, Xiang Ma, Yanqiong Tang, Dan Wang, Ziding Zhang, Zhu Liu · 2021 · Figshare