|
|
| Num |
Reference |
Sup. Mat. |
File |
| 37 |
"All-atom knowledge-based potential for RNA structure prediction and assessment"
(2010) (submitted)
Capriotti, E., Norambuena, T., Marti-Renom, M.A. and Melo, F.
|
Sup.
Mat. |
n.a. |
| 36 |
"The Protein-DNA interface database"
(2010) (submitted)
Norambuena, T. and Melo, F.
|
Database |
n.a. |
| 35 |
"A new multiplex PCR assay for the simultaneous detection of vancomycin-resistant enterococci from rectal swabs"
(2010) Journal of Infection (accepted)
Benadof, D., San Martin, M., Aguirre, J., Paredes, L., Vasquez, C., Malig, R., Melo, F. and Lehouque, G.
|
n.a. |
n.a. |
| 34 |
"Novel -ketoglutarate dioxygenase tfdA related genes are found in soil DNA after exposure to phenoxyalkanoic herbicides"
(2010) Environmental Microbiology and Environmental Microbiology Reports (accepted)
Gacitua, M.C., Slater, A.W., Melo, F., Gonzalez, B.
|
Sup.
Mat. |
n.a. |
| 33 |
"Effective knowledge-based potentials"
(2009) Protein Science 18, 1469-1485.
Ferrada, E. and Melo, F.
|
Sup.
Mat. |
PubMed |
| 32 |
"Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression (SAGE)"
(2009) Genome Biology 10, R15, 1-16
Faunes, F., Sanchez, N., Castellanos, J., Vergara, I.A., Melo, F. and Larrain, J.
|
Sup.
Mat. |
PubMed |
| 31 |
"MultiTAAG: an automated genotyping system for Eucalyptus species using multiplex amplification of microsatellite markers"
(2008) CIDEU 6-7, 25-34
Lehouque, G., Sanhueza, R. and Melo, F.
|
n.a. |
|
| 30 |
"StAR: a simple tool for the statistical comparison of ROC curves"
(2008) BMC Bioinformatics 9, 265, 1-11
Vergara, I.A, Norambuena, T., Ferrada, E., Slater, A.W. and Melo, F.
|
Server |
PubMed |
| 29 |
"Scoring functions for protein structure prediction"
(2008) Computational Structural Biology (book chapter) 3, 61-88. (T. Schwede and M. Peitsch, Editors)
Melo, F. and Feytmans, E.
|
n.a. |
GoogleBooks |
| 28 |
"Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs"
(2008) Genome Biology 9, R68, 1-11
Panjkovich, A., Melo, F. and Marti-Renom, M.A.
|
Sup.
Mat. |
PubMed |
| 27 |
"Fold assessment for comparative protein structure modeling"
(2007) Protein Science 16, 2412-2426.
Melo, F. and Sali, A.
|
Sup.
Mat. |
PubMed |
| 26 |
"A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations"
(2007) Cell Biochemistry and Biophysics 49, 111-124.
Ferrada, E., Vergara, I.A. and Melo, F.
|
Sup.
Mat. |
PubMed |
| 25 |
"SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation"
(2007) Nucleic Acids Research 35, 163-168
Norambuena, T., Malig, R. and Melo, F..
|
Server |
PubMed |
| 24 |
"Non-bonded terms extrapolated from non-local knowledge based energy functions improve error detection in near native protein structure models"
(2007) Protein Science 16, 1410-1421.
Ferrada, E. and Melo, F.
|
Sup.
Mat. |
PubMed |
| 23 |
"Cloning and characterization of the genes encoding the high affinity iron uptake protein complex Fet3/Ftr1 in the basidiomycete Phanerochaete chrysosporium"
(2007) Microbiology 153, 1772-1780.
Larrondo, L.F., Canessa, P., Melo, F., Polanco, R. and Vicuña, R.
|
Sup.
Mat. |
PubMed |
| 22 |
"Accurate and unambiguous tag-to-gene mapping in SAGE by a hierarchical gene assignment procedure"
(2006) BMC Bioinformatics 7, 487-508.
Malig, R., Varela, C., Agosin, E. and Melo, F..
|
Sup.
Mat. |
|
| 21 |
"Molecular and population analyses of a recombination event in the catabolic plasmid pJP4"
(2006) Journal of Bacteriology 188, 6793-6801.
Larrain-Linton, J., De la Iglesia, R., Melo, F. and Gonzalez, B.
|
n.a. |
PubMed |
| 20 |
"A composite score for predicting errors in protein structure models"
(2006) Protein Science 15, 1653-1666.
Eramian, D.,Shen, M.Y., Devos, D., Melo, F., Sali, A. and Marti-Renom, M.A.
|
n.a. |
PubMed |
| 19 |
"Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets"
(2006) Proteins: Function, Structure and Bioinformatics 63, 986-995.
Melo, F. and Marti-Renom, M.
|
Sup.
Mat. |
PubMed |
| 18 |
"MODBASE: a database of annotated comparative protein structure models and associated resources"
(2006) Nucleic Acids Research 33, 291-295.
Pieper, U., Eswar, N., Davis, F.P., Braberg, H., Madhusudhan, M.S., Rossi, A., Marti-Renom, M., Karchin, R., Webb, B.M., Eramian, D., Shen, M.Y., Kelly, L., Melo, F. and Sali, A.
|
Database |
|
| 17 |
"dnaMATE: a consensus melting temperature prediction server for short DNA sequences"
(2005) Nucleic Acids Research 33, 570-572.
Panjkovich, A., Norambuena, T. and Melo, F..
|
Server |
|
| 16 |
"Evolution of the insulin gene in caviomorph rodents"
(2005) Molecular Biology and Evolution 22, 1290-1298.
Opazo, J., Palma, R.E., Melo, F., and Lessa, E.P..
|
n.a. |
PubMed |
| 15 |
"Quantification of yeast gene expression profiles during the winemaking process"
(2005) Yeast 22, 369-383.
Varela, C., Cardenas, J., Melo, F., and Agosin, E.
|
SAGE data |
PubMed |
| 14 |
"Comparison of different melting temperature calculation methods for short DNA sequences"
(2005) Bioinformatics 21, 711-722.
Panjkovich, A. and Melo, F..
|
Sup.
Mat. |
PubMed |
| 13 |
"A novel extracellular multicopper oxidase from Phanerochaete chrysosporium"
(2003) Applied and Environmental Microbiology 69, 6257-6263.
Larrondo, L., Salas, L., Melo, F., Vicuña, R., and Cullen, D.
|
n.a. |
|
| 12 |
"A tool to assist the study of specific features at protein binding sites"
(2003) Bioinformatics 19, Suppl 1, I250-I251.
Santander, V., Portales, M.A., and Melo, F.
|
database |
ps
|
| 11 |
"Statistical potentials for fold assessment"
(2002) Protein Science 11, 430-448.
Melo, F., Sánchez, R., and Sali, A.
|
model dataset |
ps
|
| 10 |
"Comparative protein structure modeling"
(2001) Computational Biochemistry and Biophysics (book chapter) 11, 275-312. (M. Dekker, M. Watanabe, B. Roux, A. MacKerell, and O. Becker, editors)
Fiser, A., Sanchez, R., Melo, F. and Sali, A.
|
n.a. |
|
| 9 |
"Protein structure modeling for structural genomics"
(2000) Nature Structural Biology 7, Suppl:986-990.
Sanchez, R., Pieper U., Melo F., Eswar N., Martí-Renom, M.A., Madhusudhan M.S., Mirkovic N., and Sali, A.
|
n.a. |
ps
|
| 8 |
"Comparative protein structure modeling of genes and genomes"
(2000) Annual Reviews in Biophysics and Biomolecular Structure 29, 291-325.
Marti-Renom, M.A., Stuart, A., Fiser, A., Sanchez, R., Melo, F., and Sali, A.
|
n.a. |
ps
|
| 7 |
"Assessing protein structures with a non-local atomic interaction energy"
(1998) Journal of Molecular Biology 277, 1141-1152.
Melo, F. and Feytmans, E.
|
n.a. |
ps |
| 6 |
"Novel Knowledge-based mean force potential at atomic level"
(1997) Journal of Molecular Biology 267, 207-222.
Melo, F. and Feytmans, E.
|
n.a. |
ps |
| 5 |
"ANOLEA: a www server to assess protein structures"
(1997) Intelligent Systems for Molecular Biology 97, 187-190.
Melo, F., Devos, D., Depiereux, E. and Feytmans, E.
|
n.a. |
|
| 4 |
"Significantly reduced expression of the proteoglycan decorin in Alzheimer's disease fibroblasts"
(1997) Journal of Clinical Pathology 49, 351-356.
Brandan, E., Melo, F., Gonzalez, M. and Contreras, M.
|
n.a. |
|
| 3 |
"Synthesis and processing of glypican during differentiation of skeletal muscle cells"
(1996) European Journal of Cell Biology 71, 170-176.
Brandan, E., Carey, D.J., Larrain, J., Melo, F. and Campos, A.
|
n.a. |
PubMed |
| 2 |
"Extracellular matrix is required for skeletal muscle differentiation but not for myogenin expression"
(1996) Journal of Cellular Biochemistry 62(2), 227-239.
Melo, F., Carey, D.J. and Brandan, E.
|
n.a. |
PubMed |
| 1 |
"Decorin is specifically solubilized by heparin from the extracellular matrix of rat skeletal muscles"
(1993) FEBS Letters 319(2), 249-252.
Melo, F. and Brandan, E.
|
n.a. |
PubMed |
|
