OrthoClust: an orthology-based network framework for clustering data across multiple species
暂无分享,去创建一个
[1] Karen Spärck Jones. A statistical interpretation of term specificity and its application in retrieval , 2021, J. Documentation.
[2] D. S. Gross,et al. Chromatin , 2020, Definitions.
[3] Peter J. Bickel,et al. Comparative analysis of regulatory information and circuits across distant species , 2014, Nature.
[4] Mark Gerstein,et al. OrthoClust: an orthology-based network framework for clustering data across multiple species , 2014, Genome Biology.
[5] Peter J. Bickel,et al. Comparative Analysis of the Transcriptome across Distant Species , 2014, Nature.
[6] Mona Singh,et al. Computational solutions for omics data , 2013, Nature Reviews Genetics.
[7] Michael P Snyder,et al. High-throughput sequencing for biology and medicine , 2013, Molecular systems biology.
[8] Paul C. Leyland,et al. FlyBase: improvements to the bibliography , 2012, Nucleic Acids Res..
[9] Nadav S. Bar,et al. Landscape of transcription in human cells , 2012, Nature.
[10] D. Bartel,et al. Long noncoding RNAs in C. elegans , 2012, Genome research.
[11] Mark Gerstein,et al. TIP: A probabilistic method for identifying transcription factor target genes from ChIP-seq binding profiles , 2011, Bioinform..
[12] J. Kleinman,et al. Spatiotemporal transcriptome of the human brain , 2011, Nature.
[13] Matko Bosnjak,et al. REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.
[14] Haifeng Li,et al. Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation , 2011, PLoS Comput. Biol..
[15] F. Feltus,et al. Gene Coexpression Network Alignment and Conservation of Gene Modules between Two Grass Species: Maize and Rice[C][W][OA] , 2011, Plant Physiology.
[16] Shuli Kang,et al. Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network , 2011, Nucleic acids research.
[17] Mark Gerstein,et al. Measuring the Evolutionary Rewiring of Biological Networks , 2011, PLoS Comput. Biol..
[18] Mark Gerstein,et al. Getting Started in Gene Orthology and Functional Analysis , 2010, PLoS Comput. Biol..
[19] Weixiong Zhang,et al. A general co-expression network-based approach to gene expression analysis: comparison and applications , 2010, BMC Systems Biology.
[20] Kimberly Van Auken,et al. WormBase: a comprehensive resource for nematode research , 2009, Nucleic Acids Res..
[21] Jukka-Pekka Onnela,et al. Community Structure in Time-Dependent, Multiscale, and Multiplex Networks , 2009, Science.
[22] Julie A. Dickerson,et al. Arabidopsis gene co-expression network and its functional modules , 2009, BMC Bioinformatics.
[23] Michael F. Lin,et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.
[24] S. Horvath,et al. WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.
[25] V. Traag,et al. Community detection in networks with positive and negative links. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.
[26] Bonnie Berger,et al. Global alignment of multiple protein interaction networks with application to functional orthology detection , 2008, Proceedings of the National Academy of Sciences.
[27] Paul Pavlidis,et al. Gene Ontology term overlap as a measure of gene functional similarity , 2008, BMC Bioinformatics.
[28] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[29] M. Long,et al. The evolution of courtship behaviors through the origination of a new gene in Drosophila , 2008, Proceedings of the National Academy of Sciences.
[30] Jean-Loup Guillaume,et al. Fast unfolding of communities in large networks , 2008, 0803.0476.
[31] Brad T. Sherman,et al. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists , 2007, Genome Biology.
[32] Mark Gerstein,et al. Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications , 2007, Bioinform..
[33] Anita Burgun-Parenthoine,et al. A transversal approach to predict gene product networks from ontology-based similarity , 2007, BMC Bioinformatics.
[34] Haiyuan Yu,et al. Developing a similarity measure in biological function space , 2007 .
[35] Jacques van Helden,et al. Evaluation of clustering algorithms for protein-protein interaction networks , 2006, BMC Bioinformatics.
[36] Budapest University of Technology,et al. Limited resolution in complex network community detection with Potts model approach , 2006, cond-mat/0610370.
[37] S. Fortunato,et al. Resolution limit in community detection , 2006, Proceedings of the National Academy of Sciences.
[38] Johannes Berg,et al. Cross-species analysis of biological networks by Bayesian alignment. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[39] M E J Newman,et al. Modularity and community structure in networks. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[40] E. Koonin,et al. Conservation and coevolution in the scale-free human gene coexpression network. , 2004, Molecular biology and evolution.
[41] M. Newman. Analysis of weighted networks. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.
[42] M. Gerstein,et al. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. , 2004, Genome research.
[43] B. Snel,et al. The yeast coexpression network has a small‐world, scale‐free architecture and can be explained by a simple model , 2004, EMBO reports.
[44] J. Reichardt,et al. Detecting fuzzy community structures in complex networks with a Potts model. , 2004, Physical review letters.
[45] Joshua M. Stuart,et al. A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.
[46] U. Alon. Biological Networks: The Tinkerer as an Engineer , 2003, Science.
[47] R. Karp,et al. Conserved pathways within bacteria and yeast as revealed by global protein network alignment , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[48] Carole A. Goble,et al. Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation , 2003, Bioinform..
[49] E. Domany,et al. Potts ferromagnets on coexpressed gene networks: identifying maximally stable partitions. , 2003, Physical review letters.
[50] Joseph T. Chang,et al. Spectral biclustering of microarray data: coclustering genes and conditions. , 2003, Genome research.
[51] W. Wong,et al. Transitive functional annotation by shortest-path analysis of gene expression data , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[52] K. Sneppen,et al. Specificity and Stability in Topology of Protein Networks , 2002, Science.
[53] M. Newman,et al. Random graphs with arbitrary degree distributions and their applications. , 2000, Physical review. E, Statistical, nonlinear, and soft matter physics.
[54] S. Oliver. Proteomics: Guilt-by-association goes global , 2000, Nature.
[55] J. Hopfield,et al. From molecular to modular cell biology , 1999, Nature.
[56] J. Mesirov,et al. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[57] D. Botstein,et al. Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[58] P. Doreian,et al. A partitioning approach to structural balance , 1996 .
[59] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[60] J. Mattick,et al. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. , 2006, Trends in genetics : TIG.
[61] F. Y. Wu. The Potts model , 1982 .