Genome-wide Analysis papers 
Click on a topic to see a list of all papers associated with that topic:
| Citation | Topic(s) |
|---|---|
| Hughes AL, et al. (2012) A functional evolutionary approach to identify determinants of nucleosome positioning: a unifying model for establishing the genome-wide pattern. Mol Cell 48(1):5-15 | Omics , Other genomic analysis |
| Huo L, et al. (2012) The Rix1 (Ipi1p-2p-3p) complex is a critical determinant of DNA replication licensing independent of their roles in ribosome biogenesis. Cell Cycle 11(7):1325-39 | Large-scale phenotype analysis , Omics |
| Iben JR and Maraia RJ (2012) tRNAomics: tRNA gene copy number variation and codon use provide bioinformatic evidence of a new anticodon:codon wobble pair in a eukaryote. RNA 18(7):1358-72 | Omics , Other genomic analysis |
| Itzhaki Z and Margalit H (2012) Reduced polymorphism in domains involved in protein-protein interactions. PLoS One 7(4):e34503 | Computational analysis , Omics , Other genomic analysis |
| Jacklin N, et al. (2012) Noniterative convex optimization methods for network component analysis. IEEE/ACM Trans Comput Biol Bioinform 9(5):1472-81 | Computational analysis , Omics |
| Jackson CA, et al. (2012) Proteomic analysis of interactors for yeast protein arginine methyltransferase Hmt1 reveals novel substrate and insights into additional biological roles. Proteomics 12(22):3304-14 | Large-scale protein interaction , Omics |
| Jacobson T, et al. (2012) Arsenite interferes with protein folding and triggers formation of protein aggregates in yeast. J Cell Sci 125(Pt 21):5073-83 | Large-scale protein detection , Omics |
| Jaime MD, et al. (2012) Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics. BMC Genomics 13(1):267 | Genomic expression study , Large-scale phenotype analysis , Omics |
| Jakoby T, et al. (2012) Quantitative protease cleavage site profiling using tandem-mass-tag labeling and LC-MALDI-TOF/TOF MS/MS analysis. J Proteome Res 11(3):1812-20 | Large-scale protein modification , Omics |
| James K, et al. (2012) Is newer better?--evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae. Integr Biol (Camb) 4(7):715-27 | Computational analysis , Omics |
| Jancura P, et al. (2012) A methodology for detecting the orthology signal in a PPI network at a functional complex level. BMC Bioinformatics 13 Suppl 10():S18 | Computational analysis , Omics |
| Jay JJ, et al. (2012) A systematic comparison of genome-scale clustering algorithms. BMC Bioinformatics 13 Suppl 10():S7 | Computational analysis , Omics |
| Jiang CR, et al. (2012) Inferring Genetic Interactions via a Data-Driven Second Order Model. Front Genet 3():71 | Computational analysis , Omics |
| Jiang JQ and McQuay LJ (2012) Predicting protein function by multi-label correlated semi-supervised learning. IEEE/ACM Trans Comput Biol Bioinform 9(4):1059-69 | Computational analysis , Omics |
| Jiang JQ and Wu M (2012) Predicting multiplex subcellular localization of proteins using protein-protein interaction network: a comparative study. BMC Bioinformatics 13 Suppl 10():S20 | Computational analysis , Omics |
| Johnson ME and Edlind TD (2012) Topological and mutational analysis of Saccharomyces cerevisiae Fks1. Eukaryot Cell 11(7):952-60 | Computational analysis , Omics |
| Jol SJ, et al. (2012) System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes. PLoS Comput Biol 8(3):e1002415 | Computational analysis , Omics |
| Jones BR, et al. (2012) ANGES: reconstructing ANcestral GEnomeS maps. Bioinformatics 28(18):2388-90 | Computational analysis , Omics |
| Joshi A, et al. (2012) Post-transcriptional regulatory networks play a key role in noise reduction that is conserved from micro-organisms to mammals. FEBS J 279(18):3501-12 | Computational analysis , Omics |
| Joshi RS, et al. (2012) Topoisomerase II is required for the production of long Pol II gene transcripts in yeast. Nucleic Acids Res 40(16):7907-15 | Genomic expression study , Omics |
| Jouhten P, et al. (2012) Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis. FEBS J 279(18):3338-54 | Computational analysis , Omics |
| Jun H, et al. (2012) Comparative proteome analysis of Saccharomyces cerevisiae: A global overview of in vivo targets of the yeast activator protein 1. BMC Genomics 13(1):230 | Large-scale protein detection , Omics |
| Kaganovich M and Snyder MP (2012) Phosphorylation of yeast transcription factors correlates with the evolution of novel sequence and function. J Proteome Res 11(1):261-8 | Computational analysis , Omics |
| Kahm M, et al. (2012) Potassium starvation in yeast: mechanisms of homeostasis revealed by mathematical modeling. PLoS Comput Biol 8(6):e1002548 | Computational analysis , Omics |
| Kalli A and Hess S (2012) Effect of mass spectrometric parameters on peptide and protein identification rates for shotgun proteomic experiments on an LTQ-orbitrap mass analyzer. Proteomics 12(1):21-31 | Large-scale protein detection , Omics |
| Kaluarachchi Duffy S, et al. (2012) Exploring the yeast acetylome using functional genomics. Cell 149(4):936-48 | Large-scale genetic interaction , Large-scale protein localization , Large-scale protein modification , Omics |
| Kamburov A, et al. (2012) Cluster-based assessment of protein-protein interaction confidence. BMC Bioinformatics 13(1):262 | Computational analysis , Omics |
| Karagiannis J (2012) Decoding the Informational Properties of the RNA Polymerase II Carboxy Terminal Domain. BMC Res Notes 5(1):241 | Computational analysis , Omics |
| Karschau J, et al. (2012) Optimal placement of origins for DNA replication. Phys Rev Lett 108(5):058101 | Computational analysis , Omics |
| Katrin K, et al. (2012) Ergosterol content specifies targeting of tail-anchored proteins to mitochondrial outer membranes. Mol Biol Cell 23(20):3927-35 | Large-scale phenotype analysis , Omics |
