Integrating physical and genetic maps: from genomes to interaction networks

Cited by (207)

Items 101–200 of 207

1. Unravelling the complexity of signalling networks in cancer: A review of the increasing role for computational modelling
   John M. Garland · 2017 · Critical Reviews in Oncology/Hematology
2. Explorations in topology–delving underneath the surface of genetic interaction maps
   Michal Breker, Maya Schuldiner · 2009 · Molecular BioSystems
3. A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization
   Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli Nevalainen, Tero A. Aittokallio · 2012 · BioData Mining
4. Knowledge-guided differential dependency network learning for detecting structural changes in biological networks
   Ye Tian, Bai Zhang, Ie‐Ming Shih, Yue Wang · 2011 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
5. A protein network-guided screen for cell cycle regulators in Drosophila
   Stephen T. Guest, Jingkai Yu, Dongmei Liu, Julie A. Hines, Maria A Kashat, Russell L. Finley · 2011 · BMC Systems Biology
6. Tutorial on biological networks
   Francisco G Vital-Lopez, Vesna Memišević, Bhaskar Dutta · 2012 · Wiley Interdisciplinary Reviews Data Mining and Knowledge Discovery
7. Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes
   Katherine James, Anil Wipat, Jennifer Susan Hallinan · 2009 · Lecture notes in computer science
8. Recovering key biological constituents through sparse representation of gene expression
   Yosef Prat, Menachem Fromer, Nathan Linial, Michal Linial B · 2011 · Bioinformatics
9. Next generation sequencing technologies (NGST) development and applications
   Zsuzsanna Mihály, Balázs Győrffy · 2010 · Orvosi Hetilap
10. Predicting Quantitative Genetic Interactions by Means of Sequential Matrix Approximation
    Aki P. Järvinen, Jukka Hiissa, Laura L. Elo, Tero A. Aittokallio · 2008 · PLoS ONE
11. A network-based method for predicting gene–nutrient interactions and its application to yeast amino-acidmetabolism
    Idit Diamant, Yonina C. Eldar, Oleg Rokhlenko, Eytan Ruppin, Tomer Shlomi · 2009 · Molecular BioSystems
12. Interaction networks: Lessons from large‐scale studies in yeast
    Gerard Cagney · 2009 · PROTEOMICS
13. Integrative analysis of cancer genes in a functional interactome
    Matthew H. Ung, Chun-Chi Liu, Chao Cheng · 2016 · Scientific Reports
14. Fish Evo-Devo: Moving Toward Species-Specific and Knowledge-Based Interactome.
    E. P. Ahi · 2025 · Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
15. Assigning Confidence Scores to Protein–Protein Interactions
    Jingkai Yu, Thilakam Murali, Russell L. Finley · 2011 · Methods in molecular biology
16. ASSOCIATION OF SINGLE NUCLEOTIDE POLYMORPHISMS IN CANDIDATE GENES WITH ECONOMICALLY USEFUL TRAITS IN CHICKENS (Gallus gallus domesticus L.) (review)
    Л. Г. Коршунова · 2023 · Sel skokhozyaistvennaya Biologiya
17. Topological Characteristics of Molecular Networks
    Tijana Milenković, Nataša Pržulj · 2011 · Springer eBooks
18. Comparative Study of Computational Methods for Reconstructing Genetic Networks of Cancer-Related Pathways
    Nafiseh Sedaghat, Takumi Saegusa, Timothy W. Randolph, Ali Shojaie · 2014 · Cancer Informatics
19. ce‐Subpathway: Identification of ce RNA ‐mediated subpathways via joint power of ce RNA s and pathway topologies
    Chenchen Feng, Chao Song, Ziyu Ning, Bo Ai, Qiuyu Wang, Yong Jie Xu, Meng Li, Xuefeng Bai, Jianmei Zhao, Yuejuan Liu et al. · 2018 · Journal of Cellular and Molecular Medicine
20. Predicting schizophrenia by fusing networks from SNPs, DNA methylation and fMRI data
    Su-Ping Deng, Dongdong Lin, Vince D. Calhoun, Yu-Ping Wang · 2016 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
21. Detection of COPB2 as a KRAS synthetic lethal partner through integration of functional genomics screens
    Eleni G. Christodoulou, Hai Yang, Franziska Lademann, Christian P. Pilarsky, Andreas Beyer, Michael Schroeder · 2017 · Oncotarget
22. Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates
    Daniel Boloc, Sergio Castillo-Lara, Gemma Marfany, Roser Gonzàlez‐Duarte, Josep F. Abril · 2015 · PLoS ONE
23. A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC) libraries using High Resolution Melt analysis
    Giang T. H. Vu, Peter D.S. Caligari, M. J. Wilkinson · 2010 · BMC Genomics
24. Selection of Higher Order Regression Models in the Analysis of Multi-Factorial Transcription Data
    Olivia Prazeres da Costa, Arthur W. Hoffman, Johannes Wilhelm Rey, Ulrich Mansmann, Thorsten Buch, Achim Tresch · 2014 · PLoS ONE
25. Triangle network motifs predict complexes by complementing high-error interactomes with structural information
    Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder · 2009 · BMC Bioinformatics
26. Breaking Free from the Chains of Pathway Annotation: de Novo Pathway Discovery for the Analysis of Disease Processes
    Benjamin C. Lehne, Thomas Schlitt · 2012 · Pharmacogenomics
27. Prioritizing Genes for Pathway Impact Using Network Analysis
    Aaron N. Chang · 2009 · Methods in molecular biology
28. Mapping Metabolomic Quantitative Trait Loci (mQTL): A Link Between Metabolome-Wide Association Studies and Systems Biology
    M. Dumas, D. Gauguier · 2012 · Springer eBooks
29. The AERO System: A 3D-Like Approach for Recording Gene Expression Patterns in the Whole Mouse Embryo
    Hirohito Shimizu, Atsushi Kubo, Kenta Uchibe, Megumi Hashimoto, Shigetoshi Yokoyama, Shuji Takada, Kazuhiko Mitsuoka, Hiroshi Asahara · 2013 · PLoS ONE
30. Testing the Domino Theory of Gene Loss in Buchnera aphidicola: The Relevance of Epistatic Interactions
    David J. Martínez-Cano, Gil Bor, Andrés Moyá, Luis Delaye · 2018 · Life
31. Expanding interactome analyses beyond model eukaryotes
    Katherine James, Anil Wipat, Simon Cockell · 2022 · Briefings in Functional Genomics
32. Identification of response-modulated genetic interactions by sensitivity-based epistatic analysis
    Cory Batenchuk, Lioudmila Tepliakova, Mads Kærn · 2010 · BMC Genomics
33. Accounting for Redundancy when Integrating Gene Interaction Databases
    Antigoni L Elefsinioti, Marit Ackermann, Andreas Beyer · 2009 · PLoS ONE
34. Computational Biology
    Thomas Lengauer, Mario Albrecht, Francisco S. Domingues · 2012 · Wiley-VCH eBooks
35. Computational systems biology approaches to cellular aging—Integrating network maps and dynamical models
    Hetian Su, Nan Hao · 2025 · Quantitative Biology
36. Repurposing the memory-promoting meclofenoxate hydrochloride as a treatment for Parkinson’s disease through integrative multi-omics analysis
    Huasong Zhang, Cong Fan, Ling Li, Feiyi Liu, Shaoying Li, Linyun Ma, Yuanhao Yang, D.N. Cooper, Yuedong Yang, Ronggui Hu et al. · 2025 · npj Parkinson s Disease
37. Discovery and Expansion of Gene Modules by Seeking Isolated Groups in a Random Graph Process
    Jochen Brumm, Elizabeth Conibear, Wyeth W. Wasserman, Jennifer Bryan · 2008 · PLoS ONE
38. Investigating the Network Basis of Negative Genetic Interactions in Saccharomyces cerevisiae with Integrated Biological Networks and Triplet Motif Analysis
    Chi Nam Ignatius Pang, Apurv Goel, Marc Ronald Wilkins · 2018 · Journal of Proteome Research
39. Preparation and Characterization of Bacterial Protein Complexes for Structural Analysis
    Allan Matte, Guennadi Kozlov, Jean‐François Trempe, Mark A. Currie, David L. Burk, Zongchao Jia, Kalle Gehring, Irena H. Ekiel, Albert Marinus Berghuis, Mirosław Cygler · 2009 · Advances in protein chemistry and structural biology
40. Understanding type 1 diabetes genetics - approaches for identification of susceptibility genes in multi-factorial diseases.
    Regine Bergholdt · 2009 · PubMed
41. Protein-protein interactions are a major source of epistasis in genetic interaction networks
    Xavier Castellanos-Girouard, Adrian W.R. Serohijos, Stephen W. Michnick · 2026 · Nature Communications
42. Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancer
    Dequan Liu, Lei Liu, Xiangyu Che, Guangzhen Wu · 2025 · Frontiers in Cell and Developmental Biology
43. Observation of significant biomarkers in osteosarcoma via integrating module- identification method with attract
    Jie Qi, Liang Ma, Xiaogang Wang, Ying Li, Kejun Wang · 2017 · Cancer Biomarkers
44. Bioinformatics in Agriculture: Translating Alphabets for Transformation in the Field
    Ratna Prabha, Mukesh Kumar Verma, Dhananjaya Pratap Singh · 2017 · Springer eBooks
45. Genome-Wide Scoring of Positive and Negative Epistasis through Decomposition of Quantitative Genetic Interaction Fitness Matrices
    Ville-Pekka Eronen, Rolf Lindén, Anna Lindroos, Mirella Kanerva, Tero A. Aittokallio · 2010 · PLoS ONE
46. TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information
    Yongsoo Kim, Jin-Hyeok Jang, Seungjin Choi, Daehee Hwang · 2014 · Bioinformatics
47. Improved functional overview of protein complexes using inferred epistatic relationships
    Colm J. Ryan, Derek Greene, Aude Guénolé, Haico van Attikum, Nevan J. Krogan, Pádraig Cunningham, Gerard Cagney · 2011 · BMC Systems Biology
48. A Publish-Subscribe Model of Genetic Networks
    Brett Calcott, Duygu Balcan, Paul A. Hohenlohe · 2008 · PLoS ONE
49. Does the study of genetic interactions help predict the function of mitochondrial proteins in Saccharomyces cerevisiae?
    Jelena Ostojić, Annie Glatigny, Christopher J. Herbert, Geneviève Dujardin, Nathalie Bonnefoy · 2013 · Biochimie
50. From Topology to Phenotype in Protein–Protein Interaction Networks
    Nataša Pržulj · 2010 · Springer eBooks
51. A Systems Perspective of Signalling Networks in Host–Pathogen Interactions
    Kalyani Korla, Nagasuma R Chandra · 2017 · Journal of the Indian Institute of Science
52. Network-Based Models in Molecular Biology
    Andreas Beyer · 2009 · Birkhäuser Boston eBooks
53. Identifying Genes Relevant to Specific Biological Conditions in Time Course Microarray Experiments
    Nitesh Kumar Singh, Dirk Repsilber, Volkmar Liebscher, Leila Taher, Georg Fuellen · 2013 · PLoS ONE
54. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs
    Fergal Casey, Nevan J. Krogan, Denis C. Shields, Gerard Cagney · 2011 · BMC Systems Biology
55. Analysis of the Growth Control Network Specific for Human Lung Adenocarcinoma Cells
    Guillaume Pinna, Andrei Y. Zinovyev, N. Araujo, Nadya Morozova, Annick Harel‐Bellan · 2012 · Mathematical Modelling of Natural Phenomena
56. Differential Dependency Network Analysis to Identify Topological Changes in Biological Networks
    Bai Zhang, Huai Li, Robert C. Clarke, Leena A Hilakivi-Clarke, Yue Wang · 2010
57. Characterisation of protein-protein interaction network base on ℓ1-norm optimisation
    Benjamin Yee Shing Li, Lam Fat Yeung, Choujun Zhan, Genke Yang · 2013 · IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
58. Role of Next Generation Sequencing in Trait Identification, Genetic Mapping, and Crop Improvement
    Sidak Minocha, Sakshi Vats, Amit Kumar Bhatt, Vijaya R. Chitnis, Ramesha B. Thimmappa, Manoj Kumar · 2023 · Springer eBooks
59. On the integration of protein-protein interaction networks with gene expression and 3D structural data: What can be gained?
    Paola Bertolazzi, Mary Ellen Bock, Concettina Guerra, Paola Paci, Daniele Santoni · 2014 · The European Physical Journal Plus
60. Module network rewiring in response to therapy
    Tao Zeng, Ruozhao Wang, Luonan Chen · 2012 · IEEE International Conference on Systems Biology
61. Integrating “Omics” Data for Quantitative and Systems Pharmacology in Translational Oncology
    Erica L. Bradshaw‐Pierce, Aik Choon Tan · 2012 · Springer eBooks
62. Gene Networks in Neuropsychiatric Disease
    Neelroop Parikshak, Daniel H. Geschwind · 2016 · Elsevier eBooks
63. Bridging the gap between high-throughput genetic and transcriptional data reveals cellular pathways responding to alpha-synuclein toxicity
    Esti Yeger‐Lotem, Laura Riva, Linhui Julie Su, Aaron D. Gitler, Anil G. Cashikar, Oliver D. King, Pavan Kumar Auluck, Melissa L. Geddie, Julie S. Valastyan, David Ron Karger et al. · 2009
64. Microsatellite Development and Potential Application in Authentication, Conservation, and Genetic Improvement of Chinese Medicinal Plants
    Jianjun Chen, Ying Wang · 2015 · Chinese Herbal Medicines
65. Constructing Reliable Protein-Protein Interaction (PPI) Networks
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
66. Correction: Module Discovery by Exhaustive Search for Densely Connected, Co-Expressed Regions in Biomolecular Interaction Networks
    Recep Çolak, Flavia Moser, Jeffrey Shih-Chieh Chu, Alexander Schönhuth, Nansheng Chen, Martin Ester · 2010 · PLoS ONE
67. The DNA Damage Road Map
    Nir Friedman, Maya Schuldiner · 2010 · Science
68. Forging New Ties between E. coli Genes
    Trey E. Ideker · 2008 · Cell
69. Protein-protein interaction is a major source of epistasis in genetic interaction networks
    Xavier Castellanos-Girouard, Adrian W.R. Serohijos, Stephen W. Michnick · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
70. The Use ofSaccharomyces cerevisiaeto Study the Mechanism of pre‐mRNA Splicing
    Brian C. Rymond · 2012 · Wiley eBooks
71. Systems Biology of Human Immunity and Disease
    2011 · SpringerReference
72. Reverse engineering biological networks: computational approaches for modeling biological systems from perturbation data
    Yungil Kim · 2013 · University of Minnesota Digital Conservancy (University of Minnesota)
73. Core module network construction for breast cancer metastasis
    Ruoting Yang, Bernie J. Daigle, Linda Ruth Petzold, Francis J. Doyle · 2012 · World Congress on Intelligent Control and Automation
74. Detection of complex genetic effects in genome-wide association studies
    Li Ma · 2010 · University of Minnesota Digital Conservancy (University of Minnesota)
75. Methods for Identifying Pathway Epistasis and the Effects of Aging on the Human Methylome
    Gregory Hannum · 2012 · eScholarship (California Digital Library)
76. Modular Algorithms for Biomolecular Network Alignment
    Fadi Towfic · 2011
77. Computational identification and analysis of evolutionary breakpoint regions in amniote genomes
    Jitendra Narayan · 2014
78. System biology modeling : the insights for computational drug discovery
    Hui Huang · 2014 · IUScholarWorks (Indiana University)
79. In vitro evaluation of cytotoxicity caused by carbamazepine and its metabolites in association to carbamazepine-induced hypersensitivity reactions
    Philippe T. Marlot · 2016 · University of Liverpool
80. Introduction to GRNs
    U. Ala, C. Damasco · 2010 · IGI Global eBooks
81. In silicoanalysis strategies and resources for psychiatric genetics research
    Ali Torkamani, Trygve E. Bakken, Nicholas J. Schork · 2012 · Cambridge University Press eBooks
82. Genetic interactions and network reliability
    Edgar Delgado‐Eckert, Niko Beerenwinkel · 2015 · Cambridge University Press eBooks
83. Transcriptional Dynamics of the Eukaryotic Cell
    Cory Batenchuk · 2011 · Library and Archives Canada (Government of Canada)
84. Identifying Evolutionarily Conserved Protein Complexes
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
85. Protein Complex Prediction in the Era of Systems Biology
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
86. Introduction to Protein Complex Prediction
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
87. Evaluating Protein Complex Prediction Methods
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
88. Computational Methods for Protein Complex Prediction from PPI Networks
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
89. Open Challenges in Protein Complex Prediction
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
90. Identifying Dynamic Protein Complexes
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
91. Mapping Genetic Interaction Networks in Yeast
    Anastasija Baryshnikova · 2013 · TSpace (University of Toronto)
92. Classifying Schizophrenia Subjects by Fusing Networks From Single-Nucleotide Polymorphisms, DNA Methylation, and Functional Magnetic Resonance Imaging Data
    Su-Ping Deng, De-Shuang Huang, Dongdong Lin, Vince D. Calhoun, Yu‐Ping Wang · 2018 · Elsevier eBooks
93. PanoromiX: a time-course network medicine platform integrating molecular assays and pathophenotypic data
    Ruoting Yang, Daniel Watson, Joshua Williams, Raina Kumar, Ross Campbell, Uma S. Mudunuri, Rasha Hammamieh, Marti Jett · 2018 · BMC Bioinformatics
94. Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate
    Katherine Licon, John Paul Shen, Brenton P. Munson, Manuel Michaca, Cole Fassino, Luke Fassino, Jason F. Kreisberg, Trey E. Ideker · 2019 · Methods in molecular biology
95. Quantitative Genetic Screens for Mapping Bacterial Pathways and Functional Networks
    Alla G. Gagarinova, Ali Hosseinnia, Mohan Babu · 2021 · Methods in molecular biology
96. Conclusion
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
97. References
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
98. Preface
    Sriganesh Srihari, Chern Han Yong, Limsoon Wong · 2017
99. Integration of probabilistic functional networks without an external Gold Standard
    Katherine James, Aoesha Alsobhe, Simon Cockell, Anil Wipat, Matthew Pocock · 2022 · BMC Bioinformatics
100. Systems Biology of Human Immunity and Disease
     Jared C. Roach · 2009 · Encyclopedia of Complexity and Systems Science