-
2021GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells., Nucleic Acids Res 2021 Dec; (): .
-
2021The oxidative stress response of pathogenic Leptospira is controlled by two peroxide stress regulators which putatively cooperate in controlling virulence., PLoS Pathog 2021 Dec; 17(12): e1009087.
-
2020The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress., PLoS Pathog 2020 Oct; 16(10): e1008904.
-
2020Targeting Macrophage Histone H3 Modification as a Leishmania Strategy to Dampen the NF-κB/NLRP3-Mediated Inflammatory Response., Cell Rep 2020 02; 30(6): 1870-1882.e4.
-
2019Trans-Atlantic Spill Over: Deconstructing the Ecological Adaptation of Leishmania infantum in the Americas., Genes (Basel) 2019 12; 11(1): .
-
2018Leishmania Genome Dynamics during Environmental Adaptation Reveal Strain-Specific Differences in Gene Copy Number Variation, Karyotype Instability, and Telomeric Amplification., mBio 2018 11; 9(6): .
-
2018Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis, Curr. Biol. 2018 11;28(22):3547-3561.e9.
-
2017Haplotype selection as an adaptive mechanism in the protozoan pathogen Leishmania donovani, Nat Ecol Evol 2017 Dec;1(12):1961-1969.
-
2017Modulation of Aneuploidy in during Adaptation to Different and Environments and Its Impact on Gene Expression, mBio 2017 05;8(3).
-
2017Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution, EMBO Rep. 2017 07;18(7):1231-1247.
-
2016Intron retention-dependent gene regulation in Cryptococcus neoformans, Sci Rep 2016 08;6:32252.
-
2016Improved definition of the mouse transcriptome via targeted RNA sequencing, Genome Res. 2016 05;26(5):705-16.
-
2015Multiple sequence alignment modeling: methods and applications, Brief. Bioinformatics 2016 11;17(6):1009-1023.
-
2015CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis, J. Mol. Cell. Cardiol. 2015 Dec;89(Pt A):98-112.
-
2015Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing, Nat. Methods 2015 Apr;12(4):339-42.
-
2015Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression, Nat Commun 2015 Jan;6:5903.
-
2014Principles of regulatory information conservation between mouse and human, Nature 2014 Nov;515(7527):371-375.
-
2014A comparative encyclopedia of DNA elements in the mouse genome, Nature 2014 Nov;515(7527):355-64.
-
2014SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments, Nucleic Acids Res. 2014 Jul;42(Web Server issue):W356-60.
-
2014T-Coffee: Tree-based consistency objective function for alignment evaluation, Methods Mol. Biol. 2014;1079:117-29.
-
2013Detecting and comparing non-coding RNAs in the high-throughput era, Int J Mol Sci 2013 Jul;14(8):15423-58.
-
2013Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package, Bioinformatics 2013 May;29(9):1112-9.
-
2012An integrated encyclopedia of DNA elements in the human genome, Nature 2012 Sep;489(7414):57-74.
-
2012The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res. 2012 Sep;22(9):1775-89.
-
2012Use of ChIP-Seq data for the design of a multiple promoter-alignment method, Nucleic Acids Res. 2012 Apr;40(7):e52.
-
2011Exploring the gonad transcriptome of two extreme male pigs with RNA-seq, BMC Genomics 2011 Nov;12:552.
-
2011Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures, Nat Protoc 2011 Nov;6(11):1669-82.
-
2011BlastR–fast and accurate database searches for non-coding RNAs, Nucleic Acids Res. 2011 Sep;39(16):6886-95.
-
2010Long noncoding RNAs with enhancer-like function in human cells, Cell 2010 Oct;143(1):46-58.
-
2010A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis, Genes Dev. 2010 Jan;24(2):129-34.
-
2008The MoVIN server for the analysis of protein interaction networks, BMC Bioinformatics 2008 Mar;9 Suppl 2:S11.