Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.
暂无分享,去创建一个
M. Gerstein | J. Qian | Haiyuan Yu | M. Dolled-Filhart | J. Lin | H. Yu | Jimmy Lin | Jiang Qian | Jiang Qian
[1] Inhibition of yeast 1 -pyrroline-5-carboxylate dehydrogenase by common amino acids and the regulation of proline catabolism. , 1973, Biochimica et biophysica acta.
[2] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[3] M. Brandriss. Proline utilization in Saccharomyces cerevisiae: analysis of the cloned PUT2 gene , 1983, Molecular and cellular biology.
[4] M. Brandriss,et al. Primary structure of the nuclear PUT2 gene involved in the mitochondrial pathway for proline utilization in Saccharomyces cerevisiae. , 1984, Molecular and cellular biology.
[5] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[6] S. Ackerman,et al. Identification of two nuclear genes (ATP11, ATP12) required for assembly of the yeast F1-ATPase. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[7] P. Brown,et al. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. , 1996, Genome research.
[8] D. Lockhart,et al. Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.
[9] Gapped BLAST and PSI-BLAST: A new , 1997 .
[10] C. Hollenberg,et al. The molecular genetics of hexose transport in yeasts. , 1997, FEMS microbiology reviews.
[11] K. Isono,et al. Identification and characterization of the genes for mitochondrial ribosomal proteins of Saccharomyces cerevisiae. , 1997, European journal of biochemistry.
[12] M. Holcombe,et al. Information Processing in Cells and Tissues , 1998, Springer US.
[13] J. Barker,et al. Large-scale temporal gene expression mapping of central nervous system development. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[14] M. Bittner,et al. Data management and analysis for gene expression arrays , 1998, Nature Genetics.
[15] Ronald W. Davis,et al. A genome-wide transcriptional analysis of the mitotic cell cycle. , 1998, Molecular cell.
[16] M Levitt,et al. Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins , 1998, Protein science : a publication of the Protein Society.
[17] Dmitrij Frishman,et al. MIPS: a database for protein sequences and complete genomes , 1998, Nucleic Acids Res..
[18] M. Levitt,et al. A unified statistical framework for sequence comparison and structure comparison. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[19] W. Pearson. Empirical statistical estimates for sequence similarity searches. , 1998, Journal of molecular biology.
[20] P. D’haeseleer,et al. Mining the gene expression matrix: inferring gene relationships from large scale gene expression data , 1998 .
[21] M. Riley. Systems for categorizing functions of gene products. , 1998, Current Opinion in Structural Biology.
[22] M. Gerstein. Patterns of protein‐fold usage in eight microbial genomes: A comprehensive structural census , 1998, Proteins.
[23] James I. Garrels,et al. The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data , 1999, Nucleic Acids Res..
[24] P. Törönen,et al. Analysis of gene expression data using self‐organizing maps , 1999, FEBS letters.
[25] Scott A. Rifkin,et al. Microarray analysis of Drosophila development during metamorphosis. , 1999, Science.
[26] G. Church,et al. Systematic determination of genetic network architecture , 1999, Nature Genetics.
[27] D. Eisenberg,et al. A combined algorithm for genome-wide prediction of protein function , 1999, Nature.
[28] 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.
[29] C. Niehrs,et al. Synexpression groups in eukaryotes , 1999, Nature.
[30] T. Hanekamp,et al. YNT20, a bypass suppressor of yme1 yme2, encodes a putative 3′-5′ exonuclease localized in mitochondria of Saccharomyces cerevisiae , 1999, Current Genetics.
[31] 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.
[32] Laurie J. Heyer,et al. Exploring expression data: identification and analysis of coexpressed genes. , 1999, Genome research.
[33] K Sivakumar,et al. General nonlinear framework for the analysis of gene interaction via multivariate expression arrays. , 2000, Journal of biomedical optics.
[34] Nathan Linial,et al. ProtoMap: automatic classification of protein sequences and hierarchy of protein families , 2000, Nucleic Acids Res..
[35] James R. Knight,et al. A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae , 2000, Nature.
[36] T. Gaasterland,et al. Making the most of microarray data , 2000, Nature Genetics.
[37] M. Gerstein,et al. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. , 2000, Journal of molecular biology.
[38] Yudong D. He,et al. Functional Discovery via a Compendium of Expression Profiles , 2000, Cell.
[39] M Gerstein,et al. Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. , 2000, Nucleic acids research.
[40] E. Brown,et al. Genomic analysis of gene expression in C. elegans. , 2000, Science.
[41] D. Botstein,et al. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth , 2000, Nature.
[42] Michal Linial,et al. Using Bayesian Networks to Analyze Expression Data , 2000, J. Comput. Biol..
[43] D Haussler,et al. Knowledge-based analysis of microarray gene expression data by using support vector machines. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[44] M. Gerstein,et al. A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome. , 2000, Journal of molecular biology.
[45] T. Ito,et al. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[46] H. Riezman,et al. Functional interactions between the p35 subunit of the Arp2/3 complex and calmodulin in yeast. , 2000, Molecular biology of the cell.
[47] M. Gerstein,et al. The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function? , 2000, Current opinion in structural biology.
[48] Kara Dolinski,et al. Integrating functional genomic information into the Saccharomyces Genome Database , 2000, Nucleic Acids Res..
[49] M. Gerstein. Integrative database analysis in structural genomics , 2000, Nature Structural Biology.
[50] G. Church,et al. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. , 2000, Journal of molecular biology.
[51] H. Riezman,et al. Saccharomyces cerevisiae Arc35p works through two genetically separable calmodulin functions to regulate the actin and tubulin cytoskeletons. , 2000, Journal of cell science.
[52] N. Lee,et al. A concise guide to cDNA microarray analysis. , 2000, BioTechniques.
[53] M Gerstein,et al. Genome-wide analysis relating expression level with protein subcellular localization. , 2000, Trends in genetics : TIG.
[54] M. Gerstein,et al. Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome. , 2001, Nucleic acids research.
[55] H. Bussemaker,et al. Regulatory element detection using correlation with expression , 2001, Nature Genetics.
[56] Jong H. Park,et al. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. , 2001, Journal of molecular biology.
[57] R. Altman,et al. Whole-genome expression analysis: challenges beyond clustering. , 2001, Current opinion in structural biology.
[58] M. Gerstein,et al. Relating whole-genome expression data with protein-protein interactions. , 2002, Genome research.
[59] Christus,et al. A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins , 2022 .