Publications
Info about publications here
2012
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2012. MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. Bioinformatics. 28:487–494.
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2012. Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee.. BMC Bioinformatics. 13 Suppl 4:S1. Abstract
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2012. Use of ChIP-Seq data for the design of a multiple promoter-alignment method.. Nucleic Acids Res.. 40:e52. Abstract
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2012. AMPA: an automated web server for prediction of protein antimicrobial regions.. Bioinformatics. 28:130–131. Abstract
2011
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2011. Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters. PloS one. 6:e24279.
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2011. BlastR–fast and accurate database searches for non-coding RNAs.. Nucleic Acids Res.. 39:6886–6895. Abstract
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2011. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.. Nat Protoc. 6:1669–1682. Abstract
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2011. STRIKE: evaluation of protein MSAs using a single 3D structure.. Bioinformatics. 27:3385–3391. Abstract
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2011. The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences.. Mol. Biol. Evol.. 28:3213–3223. Abstract
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2011. Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.. BMC Genomics. 12:552. Abstract
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2011. A user-friendly web portal for T-Coffee on supercomputers.. BMC Bioinformatics. 12:150. Abstract
2010
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2010. A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis.. Genes Dev.. 24:129–134. Abstract
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2010. T-RMSD: a fine-grained, structure-based classification method and its application to the functional characterization of TNF receptors.. J. Mol. Biol.. 400:605–617. Abstract
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2010. Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite proliferation and viability.. PLoS Negl Trop Dis. 4:e729. Abstract
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2010. Computing multiple sequence/structure alignments with the T-coffee package.. Curr Protoc Bioinformatics. Chapter 3:Unit3.8.1–Unit3.825. Abstract
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2010. Predicting phenotypic traits of prokaryotes from protein domain frequencies.. BMC Bioinformatics. 11:481. Abstract
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2010. Long Noncoding RNAs with Enhancer-like Function in Human Cells. Cell. 143:46–58. Abstract
2009
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2009. The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion. Genome research. 19:611–625.
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2009. Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions.. Stem Cells. 27:300–306. Abstract
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2009. Upcoming challenges for multiple sequence alignment methods in the high-throughput era.. Bioinformatics. 25:2455–2465. Abstract
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2009. How much does it cost? Optimization of costs in sequence analysis of social science data Sociological Methods and Research. Volume 38:Pages197-231.
2008
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2008. Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast. Molecular Biology of the Cell. 19:2193–2207.
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2008. R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res. 36:W10-3. Abstract
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2008. R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res. 36:e52. Abstract
2007
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2007. Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time. BMC Genomics. 8:398. Abstract
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2007. The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res. 35:W645-8. Abstract
2006
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2006. APDB: a web server to evaluate the accuracy of sequence alignments using structural information. Bioinformatics. 22:2439-40. Abstract
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2006. The iRMSD: a local measure of sequence alignment accuracy using structural information. Bioinformatics. 22:e35-9. Abstract
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2006. PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Res. 34:W600-3. Abstract
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2006. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res. 34:W604-8. Abstract
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2006. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 34:1692-9. Abstract
2004
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2004. 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res. 32:W37-40. Abstract
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2004. CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res. 32:W606-9. Abstract
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2004. Computing multiple sequence/structure alignments with the T-coffee package. Curr Protoc Bioinformatics. Chapter 3:Unit38. Abstract
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2004. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol. 340:385-95. Abstract
2003
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2003. Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J Struct Funct Genomics. 4:141-57. Abstract
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2003. APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics. 19 Suppl 1:i215-21. Abstract
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2003. Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. 31:3503-6. Abstract
2002
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2002. Recent progress in multiple sequence alignment: a survey. Pharmacogenomics. 3:131-44. Abstract
2001
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2001. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res. 29:55-7. Abstract
2000
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2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 302:205-17. Abstract
1998
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1998. COFFEE: an objective function for multiple sequence alignments. Bioinformatics. 14:407-22. Abstract
1997
1996
