|
|
| Num |
Reference |
Sup. Mat. |
File |
| 47 |
"Effective atomic interactions for the characterization of protein-ligand binding interfaces"
(2012) (submitted)
Slater, A.W., Ferrada, E. and Melo, F.
|
Sup.
Mat. |
n.a. |
| 46 |
"Standardized ranking of protein structure alignments"
(2012) (submitted)
Slater, A.W, Castellanos, J.I., Sippl, M.J. and Melo, F.
|
Sup.
Mat. |
n.a. |
| 45 |
"Receiver Operating Characteristic Curve"
(2012) Encyclopedia of Systems Biology (in press) (Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho and Hiroki Yokota). Springer, Heidelberg, Germany.
Melo, F.
|
n.a. |
n.a. |
| 44 |
"Xenopus Methods in Molecular Biology Transcriptomics Using Next Generation Sequencing Technologies"
(2012) (in press)
Lee-Liu, D, Almonacid, L.I., Melo, F. and Larrain, J.
|
n.a. |
n.a. |
| 43 |
"Annotation of putative AraC/XylS-family transcription factors of known structure but unknown function"
(2012) Journal of Biomedicine and Biotechnology 2012, 1-14. doi:10.1155/2012/103132.
Schueller, A., Slater, A.W., Norambuena, T., Cifuentes, J.J., Almonacid, L.I. and Melo, F.
|
Sup.
Mat. |
n.a. |
| 42 |
"Characterization of small RNAs in X. tropicalis gastrulae"
(2012) Genesis 50, 260-270. doi: 10.1002/dvg.22012.
Faunes, F., Almonacid, L.I., Melo, F. and Larrain, J.
|
n.a. |
n.a. |
| 41 |
"Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile"
(2012) Forensic Science International: Genetics 6, e83-e85. doi: 10.1016/j.fsigen.2011.07.002.
Vergara, I.A., Villouta, P., Herrera, S. and Melo, F.
|
n.a. |
PubMed |
| 40 |
"The Internal Region Leucine-rich Repeat 6 of Decorin Interacts with LRP-1, Modulates TGF-B Dependent Signaling and inhibits TGF-B Dependent Fibrotic Response in Skeletal Muscles"
(2012) Journal of Biological Chemistry 287, 6773-6787.
Cabello-Verrugio, C., Cristian Santander, C., Melo, F. and Brandan, E.
|
n.a. |
n.a. |
| 39 |
"Expression of Transposable Elements in Neural Tissues during Xenopus development"
(2011) PLoS One 6(7):e22569.
Faunes, F., Sanchez, N., Moreno, M., Olivares, G., Lee-Liu, D., Almonacid, L., Slater, A.W., Norambuena, T., Taft, R.J., Mattick, J.S., Melo, F. and Larrain, J.
|
n.a. |
PubMed |
| 38 |
"All-atom knowledge-based potential for RNA structure prediction and assessment"
(2011) Bioinformatics 27, 1086-1093
Capriotti, E., Norambuena, T., Marti-Renom, M.A. and Melo, F.
|
Sup.
Mat. |
PubMed |
| 37 |
"The Protein-DNA interface database"
(2010) BMC Bioinformatics 11, 262, 1-12.
Norambuena, T. and Melo, F.
|
Database |
PubMed |
| 36 |
"Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming"
(2010) Bioinformatics 26, 1664-1665.
Ibarra, I.L. and Melo, F.
|
Software |
PubMed |
| 35 |
"A new multiplex PCR assay for the simultaneous detection of vancomycin-resistant enterococci from rectal swabs"
(2010) Journal of Infection 60, 354-359
Benadof, D., San Martin, M., Aguirre, J., Paredes, L., Vasquez, C., Malig, R., Melo, F. and Lehouque, G.
|
n.a. |
PubMed |
| 34 |
"Novel-ketoglutarate dioxygenase tfdA related genes are found in soil DNA after exposure to phenoxyalkanoic herbicides"
(2010) Environmental Microbiology 12, 2411-2425.
Gacitua, M.C., Slater, A.W., Melo, F., Gonzalez, B.
|
Sup.
Mat. |
PubMed |
| 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 |
|
