Publications - BioMe

  • comprehensive analysis of core polyadenylation sequences and regulation by microRNAs in a set of cancer predisposition genes

    07/10/2019
    Herein, we characterized PAS and CS sequences in a set of cancer predisposition genes (CPGs) and performed an in silico investigation of microRNAs (miRNAs) regulation to identify potential tumor-suppressive and oncogenic miRNAs. NCBI and alternative polyadenylation databases were queried to characterize CPE...
  • On the impact of the pangenome and annotation discrepancies while building protein sequence databases for bacteria proteogenomics

    07/10/2019
    We show that by using an approach where database size is controlled by removing repeated identical tryptic sequences across strains/species, computational time can be reduced drastically as database complexity increases.
  • Gain of transcription factor binding sites is associated to changes in the expression signature of human brain and testis and is correlated to genes with higher expression breadth

    04/26/2019
    Genes associated with TFBS-HS were enriched in gene ontology categories related to transcriptional regulation, signaling, differentiation/development and nervous system. Furthermore, genes associated with TFBS-HS present a higher expression breadth when compared to genes in general.
  • A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers

    05/03/2016
    Gross chromosomal rearrangements (GCRs) play an important role in human diseases, including cancer. The identity of all Genome Instability Suppressing (GIS) genes is not currently known.
  • Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans

    02/01/2013
  • Modeling tumor evolutionary dynamics

    03/01/2013
  • Domain shuffling and the increasing complexity of biological networks.

    08/01/2012
  • SPLOOCE: A new portal for the analysis of human splicing variants

    11/01/2012
  • Evolutionary history of exon shuffling

    06/01/2012
  • SurfaceomeDB: a cancer-orientated database for genes encoding cell curface proteins.

    12/03/2012
  • IID510g52, a monoclonal antibody against platelet membrane glycoprotein IIIa is a suitable tool for the determination of functional domains within integrin cell surface receptors

    01/01/1992
  • Collagen-binding site in collagenase can be determined using the concept of sense-antisense peptide interactions

    01/01/1992
  • Anti-platelets auto-antibodies from ITP patients recognize an epitope in GP IIb/IIIa deduced by complementary hydropathy

    01/01/1992
  • Regulation of extracellular matrix-degrading proteases

    01/01/1993
  • Extracellular matrix components of the mouse thymic microenviroment, III Thymic epithelial cells express the VLA6 complex that is involved in laminin-mediated interactions with thymocytes

    01/01/1993
  • Sequence Homology Between a Bacterial Metalloproteinase and Eukaryotic Matrix Metalloproteinases

    01/01/1993
  • A monoclonal Autoantibody against a Complementary Peptide Recognizes Interstitial Collagenase

    01/01/1994
  • On the struture / function relationship of polymorphonuclear-leukocyte collagenase

    01/01/1994
  • Evolution of the intron-exon structure of euKaryotic gene

    01/01/1995
  • Intron positions correlate with module bondaries in anciet proteins

    01/01/1996
  • Introns and gene evolution

    01/01/1996
  • Exon shuffing and the origin of the mitochondrial targenting function in plant cytochrome c1 precursor

    01/01/1996
  • Polymorphonuclear Leukocytes Present Laminin Peptides in Endocytic Compartments

    01/01/1996
  • Colagen/ collagenase interaction: Does the enzyme mimic the conformation of its own substrate?

    01/01/1996
  • The origin and evolution of introns: a debate

    01/01/1997
  • The correlation between introns and the three-dimensional structure of proteins

    01/01/1997
  • The yeast splice site revisited: A new exon consensus from genome analysis

    01/01/1997
  • Complementary hydropathy identifies a cellular prion protein receptor

    01/01/1997
  • Origin of Genes

    01/01/1997
  • Delta- Interacting Protein A and the Origin of Hepatitis Delta Antigen

    01/01/1997
  • Intron-Exon Strutures: From Molecular to Population Biology

    01/01/1998
  • Toward a resolution of the introns early / late debate: Only phase zero introns are correlated with the structure of ancient proteins

    01/01/1998
  • Relationship between proto-splice sites and intron phase: Evidence from dicodon analysis

    01/01/1998
  • Introns and the RNA World

    01/01/1999
  • Centripetal modules and ancient introns

    01/01/1999
  • Identification of human chromosome 22 trascribed sequences with ORF expressed sequence tags

    01/01/2000
  • IEKb- An Exon intron Knowledge base from database

    01/01/2000
  • NABC1 (BCAS1): Alternative Splicing and Downregulation in Colorectal Tumors

    01/01/2000
  • Shotgun sequencing of the human transcriptome with Open ORF expressed sequence tags

    01/01/2000
  • ExInt: an Exon/Intron database

    01/01/2000
  • The Contribution of 700,000 ORF Sequence tags to the definition of the human transcriptome

    01/01/2001
  • Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns

    01/01/2001
  • Alternative spliced transcriptas cancer markers

    01/01/2001
  • Definition of the gene content of the human genome: the need for deep experimental verification

    01/01/2001
  • Human Semaphorin 6B [(HSA) SEMAB], A Novel Human Class 6 Semaphorin Gene: Alternative Splicing and All-Trans-Retinoic Acid-Dependent Downregulation in Glioblastoma Cell Lines

    01/01/2001
  • Geration of a database cotainning discordant intron positions in euKaryotic gene (MIDB)

    01/01/2001
  • An anatomy of normal and malignant gene expression

    01/01/2002
  • Long-Range Heterogeneity at the 3´ Ends of Human mRNAs

    01/01/2002
  • Nineteen Additional Unpredicted Transcripts from Human Chromosome 21

    01/01/2002
  • An international database and integrated analysis tools for the study of cancer gene expression

    01/01/2002
  • Do introns favor or avoid regions of amino acid conservation?

    01/01/2002
  • In Silico Comparison of the Ttranscriptome Derived from Purified Normal Breast Cells and Breast Tumor Cell Lines Reveals Candidate Upreguated Genes in Breast Tumor Cells

    01/01/2002
  • Human gene discovery through experimental definition of transcribed regions of the human genome

    01/01/2002
  • ExInt: an Exon intron Database

    01/01/2002
  • The generation and utilization of a cancer oriented representation of the human transcriptome using expressed sequence tags.

    01/01/2003
  • ORESTES are enriched in rare exon usage variants affecting the encoded proteins

    01/01/2003
  • Identification of 9 novel transcripts and two RGSL gene within the hereditary prostate cancer region (HPC1) at 1q25

    01/01/2003
  • The emergence of a synthetic theory of intron evolution

    01/01/2003
  • pp-Blast: a pseudo-parallel Blast

    01/01/2003
  • The impact of SNPs on the interpretation of SAGE and MPSS experimental data

    01/01/2004
  • A bioinformatics analysis of alternative exon usage in human genes coding for extracellular matrix proteins

    01/01/2004
  • Splicing factors are differentially expressed in tumors

    01/01/2004
  • Identification and characterization of new human genes through the use of mouse orthologs and testis cDNA sequences

    01/01/2004
  • The use of Open Reading Frame ESTs (ORESTES) for analysis of the honeybee transcriptome

    01/01/2004
  • A transcript finishing initiative for closing gaps in the human transcriptome

    01/01/2004
  • Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

    01/01/2004
  • Detection and evaluation of intron retention events in the human transcriptome

    01/01/2004
  • Dissecting the Human Spliceosome Through Bioinformatics and Proteomics Approaches

    01/01/2004
  • Identification of human exons over-expressed in tumors through the use of genome and expressed sequence data

    01/01/2005
  • The FAPESP/LICR Human Cancer Genome Project: perspectives on integration

    01/01/2005
  • Chasing the elusive cellular prion receptor

    01/01/2005
  • Signs of ancient and modern exon shuffling are correlated to the distribution of ancient and modern domains along proteins

    01/01/2005
  • ExInt - An Exon Intron database

    01/01/2005
  • Gene expression arrays in Cancer Research: Methods and Applications

    01/01/2005
  • Using ORESTES ESTs to mine gene cancer expression data

    01/01/2005
  • The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv Integrative Display of Human Gene Expression across Disparate Technologies and Platforms

    02/07/2005
  • A possible role of exon-shuffling in the evolution of signal peptides of human proteins

    01/01/2006
  • Characterization of a cancer/testis (CT) antigen gene family capable of eliciting humoral response in cancer patients

    01/01/2006
  • Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury

    01/01/2007
  • Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS datav

    01/01/2007
  • Sequence features responsible for intron retention in human.

    01/01/2007
  • Sense-antisense pairs in mammals: functional and evolutionary considerations

    01/01/2007
  • Alternative splicing: a bioinformatics perspective.

    01/01/2007
  • Modeling cancer: integration of

    01/01/2007
  • Different evolutionary strategies for the origin of caspase-1 inhibitors

    01/01/2008
  • Heteroduplex formation and S1 digestion for mapping alternative splicing sites

    01/01/2008
  • AMIN domains have a predicted role in localization of diverse periplasmic protein complexes

    01/01/2008
  • The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

    01/01/2008
  • A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

    01/01/2009
  • A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue; identification of potential players in tumor formation

    01/01/2009
  • Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis?

    01/01/2009
  • Insights into gliomagenesis: systems biology unravels key pathways.

    01/01/2009
  • Bioinformatics construction of the human cell surfaceome

    01/01/2009
  • Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. PNAS

    01/01/2009
  • Exploiting EST in human health

    01/01/2009
  • The role of exon shuffling in shaping protein-protein interaction networks

    01/01/2010
  • Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing

    01/01/2010
  • Alternative splicing enriched cDNA libraries to identify breast cancer associated transcripts

    01/01/2010
  • Temporal blastemal cell gene expression analysis in the kidney reveals new Wnt and related signaling pathway genes to be essential for Wilms' tumor onset.

    01/01/2011
  • Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders

    01/01/2011
  • a New Hurthle Adenoma Diagnostic Marker Identified through Gene Expression

    01/01/2011
  • Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual

    01/01/2011
  • Analysis of allelic differential expression in the human genome using allele-specific serial analysis of gene expression tags

    01/01/2011
  • Systematic detection of putative tumor suppressor genes throuh the combined use of exome and transcriptome sequencing

    01/01/2011