Publications - BioMe

  • Essential Saccharomyces cerevisiae genome instability suppressing genes identify potential human tumor suppressors

    11/20/2019
    Gross Chromosomal Rearrangements (GCRs) play an important role in human diseases, including cancer. Although most of the nonessential Genome Instability Suppressing (GIS) genes in Saccharomyces cerevisiae are known, the essential genes in which mutations can cause increased GCR rates are not well...
  • Influence of BRCA1 germline mutations in the somatic mutational burden of triple-negative breast cancer

    11/20/2019
    The data presented here indicate that in the absence of BRCA1 germline mutations, a higher number of driver mutations are required for tumor development and that different defective processes are operating in the tumorigenesis of hereditary and sporadic TNBC in young women....
  • 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