Michael Tress

Summary

Country: Spain

Publications

  1. pmc Determination and validation of principal gene products
    Michael L Tress
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
    Bioinformatics 24:11-7. 2008
  2. pmc The implications of alternative splicing in the ENCODE protein complement
    Michael L Tress
    Structural Computational Biology Programme, Spanish National Cancer Research Centre, E 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 104:5495-500. 2007
  3. pmc Target domain definition and classification in CASP8
    Michael L Tress
    Structural and Computational Biology Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Proteins 77:10-7. 2009
  4. pmc An analysis of the Sargasso Sea resource and the consequences for database composition
    Michael L Tress
    Protein Design Group, CNB CSIC, Calle Darwin, Cantoblanco 28049 Madrid, Spain
    BMC Bioinformatics 7:213. 2006
  5. pmc Proteomics studies confirm the presence of alternative protein isoforms on a large scale
    Michael L Tress
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, C, Melchor Fernandez Almagro, Madrid 28029, Spain
    Genome Biol 9:R162. 2008
  6. ncbi request reprint Assessment of predictions submitted for the CASP7 domain prediction category
    Michael Tress
    Structural and Biological Computation Programme, Spanish National Cancer Research Centre, Madrid, Spain
    Proteins 69:137-51. 2007
  7. doi request reprint Predicted residue-residue contacts can help the scoring of 3D models
    Michael L Tress
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Proteins 78:1980-91. 2010
  8. ncbi request reprint Assessment of predictions submitted for the CASP6 comparative modeling category
    Michael Tress
    Protein Design Group, CNB CSIC, Cantoblanco, Madrid, Spain
    Proteins 61:27-45. 2005
  9. ncbi request reprint Domain definition and target classification for CASP6
    Michael Tress
    Protein Design Group, CNB CSIC, Calle Darwin, 28049 Cantoblanco, Spain
    Proteins 61:8-18. 2005
  10. ncbi request reprint Scoring docking models with evolutionary information
    Michael Tress
    Protein Design Group, CNB CSIC, Cantoblanco, Madrid, Spain
    Proteins 60:275-80. 2005

Detail Information

Publications22

  1. pmc Determination and validation of principal gene products
    Michael L Tress
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
    Bioinformatics 24:11-7. 2008
    ..For many computational applications and for experimental research, it is important to be able to concentrate on the isoform that retains the core biological function. For many genes this is far from clear...
  2. pmc The implications of alternative splicing in the ENCODE protein complement
    Michael L Tress
    Structural Computational Biology Programme, Spanish National Cancer Research Centre, E 28029 Madrid, Spain
    Proc Natl Acad Sci U S A 104:5495-500. 2007
    ....
  3. pmc Target domain definition and classification in CASP8
    Michael L Tress
    Structural and Computational Biology Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Proteins 77:10-7. 2009
    ..The targets submitted for CASP8 confirmed a trend that has been apparent since CASP5: targets submitted to the CASP experiments are becoming easier to predict...
  4. pmc An analysis of the Sargasso Sea resource and the consequences for database composition
    Michael L Tress
    Protein Design Group, CNB CSIC, Calle Darwin, Cantoblanco 28049 Madrid, Spain
    BMC Bioinformatics 7:213. 2006
    ....
  5. pmc Proteomics studies confirm the presence of alternative protein isoforms on a large scale
    Michael L Tress
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, C, Melchor Fernandez Almagro, Madrid 28029, Spain
    Genome Biol 9:R162. 2008
    ..Although there is extensive evidence for large scale alternative splicing at the transcript level, there have been no comparable studies demonstrating the existence of alternatively spliced protein isoforms...
  6. ncbi request reprint Assessment of predictions submitted for the CASP7 domain prediction category
    Michael Tress
    Structural and Biological Computation Programme, Spanish National Cancer Research Centre, Madrid, Spain
    Proteins 69:137-51. 2007
    ..Two thirds of the targets submitted were single domains and hence regarded as easy to predict. Even those targets defined as having multiple domains always had at least one domain with a similar template structure...
  7. doi request reprint Predicted residue-residue contacts can help the scoring of 3D models
    Michael L Tress
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Proteins 78:1980-91. 2010
    ..Despite the well-known low accuracy of residue-residue contact predictions, it is clear that the predictive power of contacts can be useful in 3D model prediction strategies...
  8. ncbi request reprint Assessment of predictions submitted for the CASP6 comparative modeling category
    Michael Tress
    Protein Design Group, CNB CSIC, Cantoblanco, Madrid, Spain
    Proteins 61:27-45. 2005
    ..In addition we investigated the ability of predictors to build models that improve on the structural template and reached some tentative conclusions from comparisons with the previous CASP experiment...
  9. ncbi request reprint Domain definition and target classification for CASP6
    Michael Tress
    Protein Design Group, CNB CSIC, Calle Darwin, 28049 Cantoblanco, Spain
    Proteins 61:8-18. 2005
    ....
  10. ncbi request reprint Scoring docking models with evolutionary information
    Michael Tress
    Protein Design Group, CNB CSIC, Cantoblanco, Madrid, Spain
    Proteins 60:275-80. 2005
    ..Here we detail our successes and highlight several of the limitations and problems that we faced while dealing with particular docking cases...
  11. pmc TreeDet: a web server to explore sequence space
    Angel Carro
    Protein Design Group, CNB CSIC C Darwin n 3, 28049, Madrid, Spain
    Nucleic Acids Res 34:W110-5. 2006
    ..An additional method is provided to highlight the reliability of the position in the alignments. The server is available at http://www.pdg.cnb.uam.es/servers/treedet...
  12. ncbi request reprint CASP6 assessment of contact prediction
    Osvaldo Grana
    Protein Design Group, Centro Nacional de Biotecnologia CNB CSIC, C Darwin 3, Cantoblanco, Madrid, Spain
    Proteins 61:214-24. 2005
    ..Comparisons of the predictions of the three best methods with those of CASP5/CAFASP3 suggested some improvement, although there were not enough targets in the comparisons to make this statistically significant...
  13. ncbi request reprint Assessment of predictions submitted for the CASP7 function prediction category
    Gonzalo Lopez
    Structural and Computational Biology Programme, Spanish National Cancer Research Centre, Almagro, Madrid, Spain
    Proteins 69:165-74. 2007
    ..After CASP 6 and 7 the need to organize a more effective blind function prediction category is obvious, even if it means focusing on binding site prediction as the only category that can be truly assessed in the CASP spirit...
  14. pmc Assessment of ligand binding residue predictions in CASP8
    Gonzalo Lopez
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Proteins 77:138-46. 2009
    ....
  15. ncbi request reprint SQUARE--determining reliable regions in sequence alignments
    Michael L Tress
    CNB CSIC, Calle Darwin, Cantoblanco, 28049 Madrid, Spain
    Bioinformatics 20:974-5. 2004
    ..In addition, the scores can be compared against template secondary structure, conserved residues and important sites...
  16. ncbi request reprint Predicting reliable regions in protein alignments from sequence profiles
    Michael L Tress
    Protein Design Group, Centro Nacional de Biotechnologia, CNB CSIC, Cantoblanco, 28049 Madrid, Spain
    J Mol Biol 330:705-18. 2003
    ..This suggests that many binding sites that are present in both target and template sequences are in sequence-conserved regions and that there is the possibility of translating reliability to binding site prediction...
  17. pmc Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts
    Milana Frenkel-Morgenstern
    Structural Biology and Biocomputing Program, Spanish National Cancer Research Centre, Madrid, Spain
    Genome Res 22:1231-42. 2012
    ..Taken together, these findings establish that some chimeric RNAs are translated into potentially functional proteins in humans...
  18. ncbi request reprint Assessment of intramolecular contact predictions for CASP7
    Jose M G Izarzugaza
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, 3E 28029 Madrid, Spain
    Proteins 69:152-8. 2007
    ..In general, contacts inferred from 3D structural predictions are similar in accuracy to those predicted by contact prediction methods. However, contact prediction methods were more accurate for some targets...
  19. doi request reprint Progress and challenges in predicting protein-protein interaction sites
    Iakes Ezkurdia
    Centro Nacional de Biotechnolgia, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Brief Bioinform 10:233-46. 2009
    ..We provide suggestions for effective feature selection, and make it clear that community standards for testing, training and performance measures are necessary for progress in the field...
  20. pmc firestar--prediction of functionally important residues using structural templates and alignment reliability
    Gonzalo Lopez
    Structural Biology and Biocomputing Program, Spanish National Cancer Research Centre CNIO Melchor Fernández Almagro, 3, E 28029, Madrid, Spain
    Nucleic Acids Res 35:W573-7. 2007
    ..We found this facility particularly useful during the recent assessment of CASP7 function prediction. Availability: http://firedb.bioinfo.cnio.es/Php/FireStar.php...
  21. doi request reprint Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8
    Iakes Ezkurdia
    Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre CNIO, Madrid, Spain
    Proteins 77:196-209. 2009
    ..Despite this small success, the lack of free modeling targets makes it unlikely that either category will be included in their present form in CASP9...
  22. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...