List of works by Sandro José de Souza

A New Approach for Identification of Cancer-related Pathways using Protein Networks and Genomic Data.

scientific article

A bioinformatics analysis of alternative exon usage in human genes coding for extracellular matrix proteins

scientific article

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

scientific article published on 21 June 2019

A comprehensive in silico expression analysis of RNA binding proteins in normal and tumor tissue: Identification of potential players in tumor formation.

scientific article

A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers

scientific article published on 13 April 2016

A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease.

scientific article

A possible role of exon-shuffling in the evolution of signal peptides of human proteins.

scientific article

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

scientific article

A tool for integrating genetic and mass spectrometry-based peptide data: Proteogenomics Viewer: PV: A genome browser-like tool, which includes MS data visualization and peptide identification parameters

scientific article

A transcript finishing initiative for closing gaps in the human transcriptome

scientific article

AMIN domains have a predicted role in localization of diverse periplasmic protein complexes.

scientific article published on 21 August 2008

Alternative spliced transcripts as cancer markers

scientific article

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

scientific article

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

scientific article

Alternative splicing: a bioinformatics perspective

scientific article

An anatomy of normal and malignant gene expression

scientific article

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

scientific article published in February 2011

Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression

scientific article published on 21 November 2019

Assessment of somatic mutations in urine and plasma of Wilms tumor patients

scientific article published on 26 June 2020

Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data.

scientific article

Bioinformatics Analysis of the Human Surfaceome Reveals New Targets for a Variety of Tumor Types

scientific article published on 14 November 2016

Bioinformatics construction of the human cell surfaceome.

scientific article published on 15 September 2009

Building comprehensive MS-friendly databases for proteomic analysis of bacterial species of unknown genetic background

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

scientific article

Complex Landscape of Germline Variants in Brazilian Patients With Hereditary and Early Onset Breast Cancer.

scientific article published on 7 May 2018

Definition of the gene content of the human genome: the need for deep experimental verification

scientific article

Delta-interacting protein A and the origin of hepatitis delta antigen

scientific article (publication date: 2 May 1997)

Detection and evaluation of intron retention events in the human transcriptome.

scientific article published in May 2004

Different evolutionary strategies for the origin of caspase-1 inhibitors

scientific article published on 14 May 2008

Dissecting the human spliceosome through bioinformatics and proteomics approaches

scientific article published on 01 January 2004

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

scientific article (publication date: August 2011)

Distribution and linkage disequilibrium of the enhancer SNP rs5758550 among Latin American populations: influence of continental ancestry

scientific article published on 16 March 2020

Do introns favor or avoid regions of amino acid conservation?

scientific article published in April 2002

Domain shuffling and the increasing complexity of biological networks

scientific article published on 23 April 2012

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

scientific article published on 13 August 2019

Evidence of Sleep Cycle Analogous to Vertebrate SWS/REM Alternation in the Octopus ⬇️

scholarly article from 'SSRN Electronic Journal' published in 2020

Evolutionary history of exon shuffling

scientific article published on 01 June 2012

Exome Sequencing of Native Populations From the Amazon Reveals Patterns on the Peopling of South America

scientific article published on 29 October 2020

Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor

scientific article published on July 1996

Exploiting ESTs in human health

scientific article published on January 2009

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

scientific article published on 22 March 2019

Gene copy-number polymorphism caused by retrotransposition in humans

scientific article

Gene expression arrays in cancer research: methods and applications

scientific article

Genome-wide identification of cancer/testis genes and their association with prognosis in a pan-cancer analysis

scientific article published on 10 October 2017

High-throughput sequencing of a South American Amerindian

scientific article

Human gene discovery through experimental definition of transcribed regions of the human genome

scientific article

Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences.

scientific article

Identification of 9 novel transcripts and two RGSL genes within the hereditary prostate cancer region (HPC1) at 1q25.

scientific article published in May 2003

Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis.

scientific article published on 18 June 2009

Identification of NUDT15 gene variants in Amazonian Amerindians and admixed individuals from northern Brazil

scientific article published on 15 April 2020

Identification of human exons overexpressed in tumors through the use of genome and expressed sequence data

scientific article

Identification of new genes associated to senescent and tumorigenic phenotypes in mesenchymal stem cells.

scientific article published on 19 December 2017

Identification of rare alternative splicing events in MS/MS data reveals a significant fraction of alternative translation initiation sites

scientific article

In silico comparison of the transcriptome derived from purified normal breast cells and breast tumor cell lines reveals candidate upregulated genes in breast tumor cells

scientific article published on 01 February 2002

Influence of BRCA1 Germline Mutations in the Somatic Mutational Burden of Triple-Negative Breast Cancer

scientific article published on 13 August 2019

Insights into gliomagenesis: systems biology unravels key pathways

scientific article published on 27 October 2009

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

scientific article

Intron positions correlate with module boundaries in ancient proteins

scientific article published on December 1996

Long-range heterogeneity at the 3' ends of human mRNAs

scientific article

Modeling cancer: integration of "omics" information in dynamic systems

scientific article published on August 2007

Modeling tumor evolutionary dynamics

scientific article published on January 2012

Mutation Detection in Tumor-Derived Cell Free DNA Anticipates Progression in a Patient With Metastatic Colorectal Cancer

article published in 2018

NFAT1 transcription factor regulates cell cycle progression and cyclin E expression in B lymphocytes

scientific article published on 11 July 2016

Nineteen additional unpredicted transcripts from human chromosome 21

scientific article (publication date: June 2002)

ORESTES are enriched in rare exon usage variants affecting the encoded proteins.

scientific article published in October 2003

On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics

scientific article published on 20 June 2019

Origin of Genes ⬇️

scientific article published on July 22, 1997

PVALB, a new Hürthle adenoma diagnostic marker identified through gene expression

scientific article

Populational landscape of INDELs affecting transcription factor-binding sites in humans

scientific article published on 22 July 2015

Relationship between "proto-splice sites" and intron phases: evidence from dicodon analysis

scientific article published on January 1998

Resveratrol decreases the expression of genes involved in inflammation through transcriptional regulation

article

S-score: a scoring system for the identification and prioritization of predicted cancer genes

scientific article

SPLOOCE: a new portal for the analysis of human splicing variants.

scientific article published on 12 October 2012

Sense-antisense pairs in mammals: functional and evolutionary considerations

scientific article

Sequence features responsible for intron retention in human

scientific article

Sex-biased gene expression in the frontal cortex of common marmosets (Callithrix jacchus) and potential behavioral correlates

article

Shotgun sequencing of the human transcriptome with ORF expressed sequence tags

scientific article

Signs of ancient and modern exon-shuffling are correlated to the distribution of ancient and modern domains along proteins

scientific article published on 18 July 2005

Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data

scientific article

Splicing factors are differentially expressed in tumors

scientific article published on 30 December 2004

SurfaceomeDB: a cancer-orientated database for genes encoding cell surface proteins

scientific article

Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing

scientific article

Testing for natural selection in human exonic splicing regulators associated with evolutionary rate shifts

scientific article published on 26 March 2013

The FAPESP/LICR Human Cancer Genome Project: Perspectives on Integration

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

scientific article

The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms

scientific article

The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome.

scientific article

The correlation between introns and the three-dimensional structure of proteins

scientific article

The emergence of a synthetic theory of intron evolution

scientific article

The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags

scientific article published on 30 October 2003

The human cell surfaceome of breast tumors

scientific article published on 9 September 2013

The impact of SNPs on the interpretation of SAGE and MPSS experimental data

scientific article

The role of exon shuffling in shaping protein-protein interaction networks

scientific article

The yeast splice site revisited: new exon consensus from genomic analysis

scientific article published on 01 December 1997

Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line

scholarly article

Uncovering association networks through an eQTL analysis involving human miRNAs and lincRNAs ⬇️

scientific article published in Scientific Reports

Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades

scientific article published on 01 September 2018

XPA deficiency affects the ubiquitin-proteasome system function

scientific article published on 16 July 2020

neoANT-HILL: an integrated tool for identification of potential neoantigens

scientific article published on 22 February 2020

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