Publications

1.- (2016) Riadi, G., Ossandón, F., Larraín, J., Melo, F. “Towards the bridging of molecular genetics data across Xenopus species” BMC Genomics 17(1):161.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/26925848)]

2.- (2016) Gutiérrez, F.I., Rodríguez-Valenzuela, F., Ibarra, I.L., Devos, D.P. and Melo, F. “Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner.” BMC Bioinformatics 17(1):20, 1-13.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/26732380)][Software (http://melolab NULL.org/supmat/moma/download NULL.html)][SupMat Page]

3.- (2015) Ribeiro, J., Melo, F. and Schüller A “PDIviz: analysis and visualization of protein–DNA binding interfaces” Bioinformatics 31, 2751-2753.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/25886981)][Software (http://melolab NULL.org/pdiviz/)]

4.- (2015) Tapia-Rojas, C., Schüller, A., Lindsay, C.B., Ureta, R.C., Mejías-Reyes, C., Hancke, J., Melo, F. and Inestrosa, N.C. “Andrographolide activates the canonical Wnt signalling pathway by a mechanism that implicates the non-ATP competitive inhibition of GSK-3β: autoregulation of GSK-3β in vivo” Biochem J. 466, 415-430.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/25423492)]

5.- (2014) Montecinos-Oliva, C., Schüller, A., Parodi, J., Melo, F. and Inestrosa, N.C. “Effects of Tetrahydrohyperforin in Mouse Hippocampal Slices: Neuroprotection, Long-term Potentiation and TRPC Channels” Curr Med Chem 21, 3494-3506.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/25039785)]

6.- (2014) Lee-Liu, D., Moreno, M., Almonacid, L.I., Tapia, V.S., Muñoz, R., Edwards-Faret, G., von Márees, J., Gaete, M., Melo, F. and Larraín, J. “Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages” Neural Development 22, 9-12.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/24885550)]

7.- (2014) Wiederstein, M., Gruber, M., Frank, K., Melo, F. and Sippl, M.J. “Structure-Based Characterization of Multiprotein Complexes” Structure 22, 1063-1070.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/24954616)]

8.- (2014) Orelllana, M., Aceituno, F., Slater, A.W., Almonacid, L.I., Melo, F. and Agosin, E. “Metabolic and transcriptomic response of the wine yeast Saccharomyces cerevisiae strain EC1118 after an oxygen impulse under carbon sufficient, nitrogen-limited fermentative conditions” FEMS Yeast Research 14, 412-424.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/24387769)]

9.- (2013) Norambuena T., Cares, J.F., Capriotti, E. and Melo, F. “WebRASP: a server for computing energy scores to assess the accuracy and stability of RNA 3D structures” Bioinformatics 29, 2649-2650.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/23929030)][Server]

10.- (2013) Slater, A.W., Castellanos, J.I., Sippl, M.J. and Melo, F. “Towards the development of standardized comparison, ranking and evaluation of structure alignments” Bioinformatics 29, 47-53.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/23060612)][SupMat Page]

11.- (2012) Aceituno, F.F., Orellana, M., Torres, J., Mendoza, S., Slater, A.W., Vidal, E.A., Melo, F. and Agosin, E. “Oxygen response of the wine yeast Saccharomyces cerevisiae EC1118 strain grown under carbon-sufficient, nitrogen-limited oenological conditions” Applied and Environmental Microbiology 78, 8340-52.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/23001663)]

12.- (2012) Lee-Liu, D. Almonacid, L. I., Melo, F., Larraín J. “Transcriptomics Using Next Generation Sequencing Technologies” Xenopus Protocols: Methods in Molecular Biology 917, 293-317.

13.- (2012) Faunes F., Almonacid L.I., Melo F., Larraín J. “Characterization of small RNAs in Xenopus tropicalis gastrulae” Genesis 50,260-70.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/22253037)]

14.- (2012) Schüller A., Slater A.W., Norambuena T., Cifuentes J.J., Almonacid L.I., Melo F. “Computer-Based Annotation of Putative AraC/XylS-Family Transcription Factors of Known Structure but Unknown Function” Journal of Biomedicine and Biotechnology 2012,103132.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/22505803)][SupMat PDF (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pmc/articles/PMC3312330/bin/103132 NULL.f1 NULL.docx)]

15.- (2012) Cabello-Verrugio C., Santander C., Cofré C., Acuña M.J., Melo F., Brandan E. “The internal region leucine-rich repeat 6 of decorin interacts with low density lipoprotein receptor-related protein-1, modulates transforming growth factor (TGF)-beta-dependent signaling, and inhibits TGF-beta-dependent fibrotic response in skeletal muscles” Journal of Biological Chemistry 287,6773-87.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/22203668)]

16.- (2012) Vergara I.A., Villouta P., Herrera S., Melo F. “Autosomal STR allele frequencies for the CODIS system from a large random population sample in Chile” Forensic Science International: Genetics 6,e83-5.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/21813345)]

17.- (2011) Capriotti, E., Norambuena, T., Marti-Renom, M. A., Melo, F. “All-atom knowledge-based potential for RNA structure prediction and assessment” Bioinformatics 27,1086-93.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/21349865)][SupMat Page]

18.- (2011) Faunes F., Sánchez N., Moreno M., Olivares G.H., Lee-Liu D., Almonacid L., Slater A.W., Norambuena T., Taft R.J., Mattick J.S., Melo F., Larraí­n J. “Expression of transposable elements in neural tissues during Xenopus development” PLoS One 6,e22569.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/21818339)]

19.- (2010) Gazitúa, M.C., Slater, A.W., Melo, F., González, B. “Novel alpha-ketoglutarate dioxygenase tfdA-related genes are found in soil DNA after exposure to phenoxyalkanoic herbicides” Environmental Microbiology 12,2411-25.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/20406281)][SupMat Page]

20.- (2010) Benadof, D., San Martín, M., Aguirre, J., Paredes, L., Malig, R., Melo, F., Lehouque, G. “A new multiplex PCR assay for the simultaneous detection of vancomycin-resistant enterococci from rectal swabs” The Journal of Infection 60,354-9.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/20211201)]

21.- (2010) Ibarra, I., Melo, F. “Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming” Bioinformatics 26,1664-1665.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=2887054&tool=pmcentrez&rendertype=abstract)][Software]

22.- (2010) Norambuena, T., Melo, F. “The Protein-DNA Interface database” BMC Bioinformatics 11,262.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/20482798)][Database]

23.- (2009) Ferrada, E., Melo, F. “Effective knowledge-based potentials” Protein Science 18,1469-1485.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=2775215&tool=pmcentrez&rendertype=abstract)][SupMat Page]

24.- (2009) Faunes, F., Sánchez, N., Castellanos, J., Vergara, Ismael A, Melo, F., Larraí­n, J. “Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression” Genome Biology 10,R15.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=2688288&tool=pmcentrez&rendertype=abstract)][SupMat Page]

25.- (2008) Panjkovich, A., Melo, F., Marti-Renom, M. A. “Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs” Genome Biology 9,R68.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=2643939&tool=pmcentrez&rendertype=abstract)][SupMat Page (http://sgt NULL.cnag NULL.cat/www/software/)]

26.- (2008) Vergara, I. A., Norambuena, T., Ferrada, E., Slater, A., Melo, F. “StAR: a simple tool for the statistical comparison of ROC curves” BMC Bioinformatics 9,265.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=2435548&tool=pmcentrez&rendertype=abstract)][Server]

27.- (2008) Melo F., Feytmans E. “Scoring functions for protein structure predictions” Computational Structural Biology (Book chapter) 3, 61-88 (T. Schwede and M. Peitsch, Editors) .
[Google Book (http://books NULL.google NULL.cl/books?id=aZLpHRteWtIC&lpg=PR10&ots=XZkSTWrzR1&dq=Computational%20Structural%20Biology%20T NULL.%20Schwede%20and%20M NULL.%20Peitsch&pg=PA61#v=onepage&q&f=false)]

28.- (2008) Lehouque, G., Sanhueza, R., Melo F. “MultiTAAG: an automated genotyping system for Eucalyptus species using multiplex amplification of microsatellite markers” CIDEU 6-7, 25-34.
[Pubmed (http://protein NULL.bio NULL.puc NULL.cl/cardex/publications/files/cideu2008 NULL.pdf)]

29.- (2007) Melo, Francisco, Sali, Andrej, “Fold assessment for comparative protein structure modeling” Protein Science 16,2412-2426.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=2211691&tool=pmcentrez&rendertype=abstract)][SupMat Page]

30.- (2007) Norambuena, T., Malig, R., Melo, F. “SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation” Nucleic Acids Research 35,W163.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=1933165&tool=pmcentrez&rendertype=abstract)][Server]

31.- (2007) Ferrada, E., Melo, F. “Non-bonded terms extrapolated from nonlocal knowledge-based energy functions improve error detection in near-native protein structure models” Protein Science 16,1410.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=2206707&tool=pmcentrez&rendertype=abstract)][SupMat Page]

32.- (2007) Larrondo, L. F., Canessa, P., Melo, F., Polanco, R., Vicuña, R. “Cloning and characterization of the genes encoding the high-affinity iron-uptake protein complex Fet3/Ftr1 in the basidiomycete Phanerochaete chrysosporium” Microbiology 153,1772.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/17526834)][SupMat PDF]

33.- (2007) Ferrada, E., Vergara, I. A., Melo, F. “A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations” Cell Biochemistry and Biophysics 49,111.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/17906366)][SupMat Page]

34.- (2006) Larraín-Linton, J., De La Iglesia, R., Melo, F., González, B. “Molecular and population analyses of a recombination event in the catabolic plasmid pJP4.” Journal of Bacteriology 188,6793.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=1595507&tool=pmcentrez&rendertype=abstract)]

35.- (2006) Eramian, D., Shen, M., Devos, D., Melo, F., Sali, A., Marti-Renom, M. A., “A composite score for predicting errors in protein structure models” Protein science 15,1653.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=2242555&tool=pmcentrez&rendertype=abstract)]

36.- (2006) Melo, F., Marti-Renom, M. A., “Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets” Proteins 63,986.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/16506243)][SupMat Page]

37.- (2006) Malig, R., Varela, C., Agosin, E., Melo, F. “Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression by a hierarchical gene assignment procedure” BMC Bioinformatics 7,487.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=1637119&tool=pmcentrez&rendertype=abstract)][Server][SupMat Page]

38.- (2006) 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., Sali A. “ModBase, a database of annotated comparative protein structure models, and associated resources” Nucleic Acids Research 34(Database issue):D291-5.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/16381869)][Server (http://salilab NULL.org/modbase)]

39.- (2005) Panjkovich, A., Norambuena, T., Melo, F. “dnaMATE: a consensus melting temperature prediction server for short DNA sequences” Nucleic Acids Research 33,W570.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=1160140&tool=pmcentrez&rendertype=abstract)][Server][SupMat Page]

40.- (2005) Opazo, J C., Palma, R E., Melo, F., Lessa, E P. “Adaptive evolution of the insulin gene in caviomorph rodents” Molecular Biology and Evolution 22,1290.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/15728738)]

41.- (2005) Varela, C., Cárdenas, J., Melo, F., Agosin, E. “Quantitative analysis of wine yeast gene expression profiles under winemaking conditions” Yeast 22,369.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/15806604)]

42.- (2005) Panjkovich, A., Melo, F. “Comparison of different melting temperature calculation methods for short DNA sequences” Bioinformatics 21,711.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/15501913)][SupMat Page]

43.- (2003) Larrondo, L. F., Salas, L., Melo, F., Vicuña, R., Cullen, D. “A novel extracellular multicopper oxidase from Phanerochaete chrysosporium with ferroxidase activity” Applied and Environmental Microbiology 69,6257.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=201228&tool=pmcentrez&rendertype=abstract)]

44.- (2003) Santander, V., Portales, M A., Melo,  F. “A tool to assist the study of specific features at protein binding sites” Bioinformatics 19 Suppl 1,i250.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/12855466)]

45.- (2002) Melo, F., Sánchez, R., Sali, A., “Statistical potentials for fold assessment” Protein Science 11,430.
[Pubmed (http://www NULL.pubmedcentral NULL.nih NULL.gov/articlerender NULL.fcgi?artid=2373452&tool=pmcentrez&rendertype=abstract)]

46.- (2001) Martí-Renom, M.A., Stuart, A.C., Fiser, A., Sánchez, R., Melo, F., Sali, A. “Comparative protein structure modeling of genes and genomes” Annual Review of Biophysics and Biomolecular Structure 29,291.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/10940251)]

47.- (2000) Sánchez, R., Pieper, U., Melo, F., Eswar, N., Martí-Renom, M.A., Madhusudhan, M.S., Mirkovic, N., Sali, A. “Protein structure modeling for structural genomics” Nature Structural Biology 7 Suppl,986.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/11104007)]

48.- (1998) Melo, F., Feytmans, E. “Assessing protein structures with a non-local atomic interaction energy” Journal of Molecular Biology 277,1141.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/9571028)]

49.- (1997) Melo, F., Feytmans, E. “Novel knowledge-based mean force potential at atomic level” Journal of Molecular Biology 267,207.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/9096219)]

50.- (1997) Melo, F., Devos, D., Depiereux, E., Feytmans, E. “ANOLEA: a www server to assess protein structures” Proceedings in the International Conference on Intelligent Systems for Molecular Biology 5,187.
[Pubmed (http://www NULL.aaai NULL.org/Papers/ISMB/1997/ISMB97-027 NULL.pdf)][Server (http://protein NULL.bio NULL.puc NULL.cl/cardex/servers/anolea/index NULL.html)]

51.- (1997) Brandan E., Melo F., Gonzales M., Contreras M. “Significantly reduced expression of the proteoglycan decorin in Alzheimer’s disease fibroblasts” Journal of Clinical Pathology 49,351.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/16696102)]

52.- (1996) Brandan, E., Carey, D. J., Larraín, J., Melo, F., Campos, A. “Synthesis and processing of glypican during differentiation of skeletal muscle cells” European Journal of Cell Biology 71,170.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/8905294)]

53.- (1996) Melo, F., Carey, D. J., Brandan, E. “Extracellular matrix is required for skeletal muscle differentiation but not myogenin expression” Journal of Cellular Biochemistry 62,227.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/8844403)]

54.- (1993) Melo, F., Brandan, E. “Decorin is specifically solubilized by heparin from the extracellular matrix of rat skeletal muscles” FEBS letters 319,249.
[Pubmed (http://www NULL.ncbi NULL.nlm NULL.nih NULL.gov/pubmed/8458417)]