0000000000105464

AUTHOR

Alfonso Valencia

showing 35 related works from this author

Modular organization in the reductive evolution of protein-protein interaction networks

2006

Analysis of the reduction in genome size of Buchnera aphidicola from its common ancestor E. coli shows that the organization of networks into modules is the property that seems to be directly related with the evolutionary process of genome reduction.

Systems biologyComplex systemComputational biologyBiologyGenomeProtein protein interaction networkProtein–protein interactionBuchneraInteraction networkProtein Interaction MappingEscherichia coliAnimalsHumansDatabases ProteinGeneticsbusiness.industrySystems BiologyResearchbiochemical phenomena metabolism and nutritionModular designbiology.organism_classificationBiological EvolutionProtein Structure TertiaryStructural Homology ProteinMultiprotein ComplexesBuchnerabusinessAlgorithmsGenome BacterialGenome Biology
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Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

2019

Este es el artículo que se ha publicado de forma definitiva en: https://molecularautism.biomedcentral.com/articles/10.1186/s13229-019-0262-8 En este artículo también participa Joan Climent, Vera Pancaldi, Lourdes Fañanás, Celso Arango, Mara Parellada, Anaïs Baudot, Daniel Vogt, John L. Rubenstein, Alfonso Valencia y Rafael Tabarés-Seisdedos. Background: Epidemiological and clinical evidence points to cancer as a comorbidity in people with autism spectrum disorders (ASD). A significant overlap of genes and biological processes between both diseases has also been reported. Methods: Here, for the first time, we compared the gene expression profiles of ASD frontal cortex tissues and 22 cancer t…

Autism.AutismComorbidityBioinformaticsAutismo.lcsh:RC346-429Expresión génica.TranscriptomeAfectividad - Trastornos.0302 clinical medicineNeoplasmsGene expression2.1 Biological and endogenous factorsAetiologyCàncerCáncer - Aspectos genéticos.ComputingMilieux_MISCELLANEOUSCancer0303 health sciencesProstate CancerBrainAffective disorders.3. Good healthPsychiatry and Mental healthMental HealthSignal transductionSignal TransductionBiotechnologyUrologic DiseasesIntellectual and Developmental Disabilities (IDD)1.1 Normal biological development and functioningClinical SciencesBiologyASDBiological pathway03 medical and health sciencesDevelopmental NeuroscienceUnderpinning researchmental disordersGeneticsmedicineHumansAutistic DisorderIntellectual and Developmental DisabilitiesGeneMolecular Biologylcsh:Neurology. Diseases of the nervous systemPI3K/AKT/mTOR pathwayCancer - Genetic aspects.030304 developmental biologyResearchNeurosciencesMultimorbidityCancermedicine.diseaseExpressió gènicaHuman geneticsBrain DisordersMeta-analysisGene expression.AutismGene expressionAutisme[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]TranscriptomeKidney cancer030217 neurology & neurosurgeryDevelopmental BiologyMolecular Autism
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Transcriptomic and Genetic Associations between Alzheimer's Disease, Parkinson's Disease, and Cancer.

2021

Simple Summary Epidemiological studies have identified a link between neurodegenerative disorders and a reduced risk of overall cancer. Increases and decreases in the risk of site-specific cancers have also been reported. However, it is still unknown whether these associations arise due to shared genetic and molecular factors or are explained by other phenomena (e.g., biases in epidemiological studies or the use of medication). In this study, we aimed to investigate the potential molecular, genetic, and pharmacological links between Alzheimer’s and Parkinson’s diseases and a large panel of 22 cancer types. To examine the overlapping involvement of genes and pathways, we obtained differentia…

0301 basic medicineOncologyCancer ResearchParkinson's diseaseGenetic correlationsGenome-wide association studyDiseaseComorbidityParkinson Enfermedad de - Aspectos genéticos.chemistry.chemical_compound0302 clinical medicineExemestaneParkinson's disease - Genetic aspects.MedicineParkinsonCáncer - Aspectos genéticos.Càncer -- Aspectes genèticsRC254-282Alzheimer's disease - Genetic aspects.NeurodegenerationNeoplasms. Tumors. Oncology. Including cancer and carcinogensCódigo genético.comorbidityOncology:Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC]medicine.medical_specialtyGenetic code.Alzheimer Enfermedad de - Aspectos genéticos.Article03 medical and health sciencesInternal medicineParkinson Malaltia dePI3K/AKT/mTOR pathwaygenetic correlationsCancer - Genetic aspects.business.industryCancertranscriptomicmedicine.diseaseComorbidityAlzheimer Malaltia d'030104 developmental biologychemistryTranscriptomicmeta-analysesMeta-analysesNeurodegenerative disordersAlzheimerGene expressionbusiness030217 neurology & neurosurgeryCancers
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Abstract A22: PanDrugsDB: Identifying druggable genetic dependencies for personalized cancer therapy

2015

Abstract The paradigm of personalized medicine is the identification of the appropriate drug for the right patient, using molecular profiles. In Oncology, it is well established that the anticancer drugs are effective in only a small subset of patients. Moreover, many of the new targeted therapies inhibit specific proteins, and they are only effective in tumors that are genetically altered. Consequently, the success of personalized treatment depends on each individual molecular profile, which a priori can be considered as very heterogeneous. Here, we present a new computational approach (PanDrugsDB) based on the analysis and integration of genomic data (mutations, copy number variations or …

Cancer Researchbusiness.industryGenomic dataDruggabilityCancer therapyCancermedicine.diseaseBioinformaticsOncologyTumor progressionmedicineIdentification (biology)Copy-number variationPersonalized medicinebusinessMolecular Cancer Therapeutics
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Unveiling the molecular basis of disease co-occurrence: towards personalized comorbidity profiles

2018

AbstractComorbidity is an impactful medical problem that is attracting increasing attention in healthcare and biomedical research. However, little is known about the molecular processes leading to the development of a specific disease in patients affected by other conditions. We present a disease interaction network inferred from similarities in patients’ molecular profiles, which significantly recapitulates epidemiologically documented comorbidities, providing the basis for their interpretation at a molecular level. Furthermore, expanding on the analysis of subgroups of patients with similar molecular profiles, our approach discovers comorbidity relations not previously described, implicat…

Molecular levelbusiness.industryInteraction networkCo-occurrenceMedicineIn patientDiseaseComputational biologybusinessmedicine.diseaseComorbidity
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No paradox, no progress: inverse cancer comorbidity in people with other complex diseases.

2011

Salvador Martínez [et al.]. 5 p., 2 tables and references.

medicine.medical_specialtyDown syndromeAnorexia NervosaNeuregulin-1DiseaseComorbidity03 medical and health sciences0302 clinical medicineAlzheimer DiseaseNeoplasmsEpidemiologymedicineHumansGenetic Predisposition to DiseasePsychiatryComputingMilieux_MISCELLANEOUS030304 developmental biology0303 health sciencesbusiness.industryCancerParkinson Diseasemedicine.disease[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]Comorbidity3. Good healthOncologySchizophreniaAnorexia nervosa (differential diagnoses)SchizophreniaAlzheimer's diseaseDown Syndromebusiness030217 neurology & neurosurgeryChromosomes Human Pair 8The Lancet. Oncology
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Association of Anorexia Nervosa With Risk of Cancer: A Systematic Review and Meta-analysis

2019

This systematic review and meta-analysis evaluates the association of anorexia nervosa with the cancer incidence and mortality among study populations with anorexia nervosa compared with the general population or those without anorexia nervosa.

AdultMalemedicine.medical_specialtyAnorexia NervosaPopulationbehavioral disciplines and activitiesYoung Adult03 medical and health sciences0302 clinical medicineBreast cancerNeoplasmsInternal medicineObservational studymental disordersHumansMedicine030212 general & internal medicineSex DistributionYoung adulteducationOriginal InvestigationAgedCancereducation.field_of_studybusiness.industryResearchMortality ratedigestive oral and skin physiologyCancerGeneral MedicineMiddle Agedmedicine.disease3. Good healthOnline OnlyMeta-analysisOncologyAnorexia nervosa (differential diagnoses)030220 oncology & carcinogenesisMeta-analysisSystematic reviewFemaleEpidemiologic Methodsbusinesshormones hormone substitutes and hormone antagonistsCohort study
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2006

Current usage of gene nomenclature is ambiguous and impairs the efficient handling of scientific information. Therefore it is important to propose guidelines to deal with this problem. This study attempts to evaluate the success of HUGO nomenclature for human genes. The results indicate that HUGO guidelines are not supported by the scientific community.

Gene nomenclatureHuman genomeComputational biologyBiologyNomenclatureHuman geneticsGenome Biology
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Molecular evidence for the inverse comorbidity between central nervous system disorders and cancers detected by transcriptomic meta-analyses.

2014

There is epidemiological evidence that patients with certain Central Nervous System (CNS) disorders have a lower than expected probability of developing some types of Cancer. We tested here the hypothesis that this inverse comorbidity is driven by molecular processes common to CNS disorders and Cancers, and that are deregulated in opposite directions. We conducted transcriptomic meta-analyses of three CNS disorders (Alzheimer's disease, Parkinson's disease and Schizophrenia) and three Cancer types (Lung, Prostate, Colorectal) previously described with inverse comorbidities. A significant overlap was observed between the genes upregulated in CNS disorders and downregulated in Cancers, as wel…

Central Nervous SystemCancer ResearchGene ExpressionDiseaseComorbidityBioinformaticsProstate cancer0302 clinical medicineNeoplasmsGenetics (clinical)0303 health sciencesWnt signaling pathwayParkinson DiseaseAlzheimer's diseasePeptidylprolyl Isomerase[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]3. Good health[SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]Alzheimer's diseaseResearch ArticleSignal Transductionlcsh:QH426-470[SDV.CAN]Life Sciences [q-bio]/CancerProtein degradationBiology03 medical and health sciencesAlzheimer Disease[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN]medicineGeneticsCancer GeneticsHumansGene NetworksMolecular BiologyBiologyEcology Evolution Behavior and Systematics030304 developmental biologyPeptidylprolyl isomeraseGene Expression ProfilingCancerComputational Biologymedicine.diseaseColorectal cancerComorbidityMalariaNIMA-Interacting Peptidylprolyl IsomeraseMeta-analysislcsh:GeneticsGene Expression RegulationImmunologySchizophrenia[SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie030217 neurology & neurosurgery
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Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies

2017

BACKGROUND: Anorexia nervosa is characterized by a severe restriction of caloric intake, low body weight, fear of gaining weight or of becoming fat, and disturbance of body image. Pathogenesis of the disorder may include genetic predisposition, hormonal changes and a combination of environmental, psychosocial, and cultural factors. Cancer is the second leading cause of death worldwide. At present, no systematic reviews and meta-analyses have evaluated the risk of cancer in people with anorexia nervosa. The objective of this study will be to evaluate the association between anorexia nervosa and the risk of developing or dying from cancer. METHODS/DESIGN: This study protocol is part of a syst…

medicine.medical_specialtyAnorexia NervosaEpidemiological studyMedicine (miscellaneous)lcsh:Medicine03 medical and health sciences0302 clinical medicineNeoplasmsEpidemiologymental disordersmedicineProtocolHumans030212 general & internal medicinePsychiatryCancerbusiness.industryIncidencelcsh:REating disorderCancerCáncermedicine.disease3. Good healthMeta-analysisSystematic reviewAnorexia nervosa (differential diagnoses)030220 oncology & carcinogenesisMeta-analysisCohortSystematic reviewbibliometríaObservational studybusinessPsychosocialanorexia nerviosaSystematic Reviews as Topic
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Risk of mortality among children, adolescents, and adults with autism spectrum disorder or attention deficit hyperactivity disorder and their first-d…

2017

BACKGROUND: Autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD) are childhood onset neurodevelopmental disorders that may persist into adulthood. ASD and ADHD tend to run in families and may have a significant negative impact on the health and longevity of those with the disorder and their relatives. The aim of this study will be to analyze the risk of mortality among children, adolescents, and adults with ASD or ADHD and their first-degree relatives. METHODS/DESIGN: We will conduct a systematic review and meta-analysis of observational studies. Searches of PubMed/MEDLINE, EMBASE, PsycINFO, SCOPUS, and ISI Web of Science will be used to identify epidemiologica…

Research designMaleEpidemiologyAutism Spectrum DisorderMedicine (miscellaneous)lcsh:MedicineTrastorns de l'atencióAdolescents0302 clinical medicineCause of DeathRisk of mortalityProtocol030212 general & internal medicineChildChild developmentNeurodevelopmental disordersAutism spectrum disorders3. Good healthAutism spectrum disorderResearch DesignMeta-analysisFemaleInfantsCohort studyAdultRiskmedicine.medical_specialtyAdolescentAttention deficit hyperactivity disorder03 medical and health sciencesBibliometriamental disordersmedicineMortalitatAttention deficit hyperactivity disorderAdultsHumansFamilyFirst-degree relativesMortalityPsychiatrybusiness.industrylcsh:Rmedicine.diseaseMeta-analysisAttention Deficit Disorder with HyperactivitySystematic reviewObservational studyAutismebusiness030217 neurology & neurosurgerySystematic Reviews as Topic
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Cancer and central nervous system disorders: protocol for an umbrella review of systematic reviews and updated meta-analyses of observational studies

2017

[Background] The objective of this study will be to synthesize the epidemiological evidence and evaluate the validity of the associations between central nervous system disorders and the risk of developing or dying from cancer.

Research designAnorexia NervosaBipolar DisorderMedicine (miscellaneous)lcsh:MedicineDisease0302 clinical medicineDown’s syndromeCentral Nervous System DiseasesNeoplasmsProtocolMedicine030212 general & internal medicineCàncerCancerDepressionIncidenceHuntington’sdiseaseAnorèxia nerviosaAutism spectrum disorders3. Good healthObservational Studies as TopicSystematic reviewResearch DesignMeta-analysisEsquizofrèniaAlzheimer’s diseaseHuntington’s diseasemedicine.medical_specialtyCentral nervous system disorderMultiple SclerosisBipolar disorderSistema nerviós central MalaltiesMEDLINEMultiple sclerosisParkinson’s Disease03 medical and health sciencesMeta-Analysis as TopicDown’s SyndromeHuntington’s DiseaseHumansAlzheimer’s DiseasePsychiatryIntensive care medicineEpilepsybusiness.industrylcsh:RAmyotrophic Lateral SclerosisCancerCentral Nervous System DisorderAnorexia nervosamedicine.diseaseAmyotrophic lateral sclerosisMeta-analysisReview Literature as TopicParkinson’s diseaseSystematic reviewSchizophreniaObservational Studies as TopicObservational studySystematic ReviewAutismebusiness030217 neurology & neurosurgerySystematic Reviews as TopicMeta-Analysis
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A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer's Disease, Glioblastoma and Lung cancer.

2017

Epidemiological studies indicate that patients suffering from Alzheimer’s disease have a lower risk of developing lung cancer, and suggest a higher risk of developing glioblastoma. Here we explore the molecular scenarios that might underlie direct and inverse co-morbidities between these diseases. Transcriptomic meta-analyses reveal significant numbers of genes with inverse patterns of expression in Alzheimer’s disease and lung cancer, and with similar patterns of expression in Alzheimer’s disease and glioblastoma. These observations support the existence of molecular substrates that could at least partially account for these direct and inverse co-morbidity relationships. A functional analy…

0301 basic medicineLung NeoplasmsMolecular biology[SDV]Life Sciences [q-bio]Gene ExpressionDiseaseCàncer--Fisiologia patològicaComorbidityTranscriptomeMedicineDinàmica molecularMultidisciplinaryQLung Cancer:Enginyeria biomèdica [Àrees temàtiques de la UPC]R3. Good healthAlzheimer's disease (AD)MedicineDisease SusceptibilityAlzheimer's diseaseSignal transductionSignal TransductionCentral Nervous System (CNS)ScienceModels BiologicalArticle03 medical and health sciencesImmune systemcáncerAlzheimer DiseaseDementia[CHIM]Chemical SciencesHumansLung cancerbusiness.industryGenetic Variationmedicine.diseaseComorbidityCNS cancerAlzheimer Malaltia d'030104 developmental biologyGliobastomas (GBM)ImmunologyCancer researchDementiabusinessGlioblastomaReactive Oxygen SpeciesNon-small-cell lung cancerBiomarkers
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Additional file 1: of Risk of mortality among children, adolescents, and adults with autism spectrum disorder or attention deficit hyperactivity diso…

2017

PRISMA-P checklist. (DOCX 24 kb)

3. Good health
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Additional file 3: of Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies

2017

Definitions of specific cancer-site outcomes. (DOCX 27 kb)

3. Good health
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Additional file 2: of Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies

2017

Key terms for PubMed/MEDLINE search. (DOCX 22 kb)

3. Good health
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Additional file 3: of Cancer and central nervous system disorders: protocol for an umbrella review of systematic reviews and updated meta-analyses of…

2017

Definitions of specific cancer-site outcomes (DOCX 26 kb)

3. Good health
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Additional file 1: of Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

2019

Table S1. Datasets included in our study. Table S2. Age, gender and pmi distributions between cases and control samples at each step of the preprocessing procedure at the asd defferentail gene expression meta-analysis. Table S3. Final samples included in the asd meta-analysis. Table S4. Jointly same direction derregulated genes in asd ans sddcs and jointly oposite direction derregulated genes in asd and oddcs. Table S5. Genes jointly deregulated in asd and in sddcs and oddcs. Figure S1. Comaprison of differential gene expression analysis using limma with rlog transformed data and two state of the art rnaseq differential expression metdos. Figure S2. Patient overlap in the three asd studies.…

mental disorders
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Additional file 1: of Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies

2017

PRISMA-P Checklist. (DOCX 27 kb)

3. Good health
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Additional file 2: of Risk of mortality among children, adolescents, and adults with autism spectrum disorder or attention deficit hyperactivity diso…

2017

Key terms for PubMed/MEDLINE search. (DOCX 20 kb)

3. Good health
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Additional file 1: of Cancer and central nervous system disorders: protocol for an umbrella review of systematic reviews and updated meta-analyses of…

2017

PRISMA-P Checklist (DOCX 27 kb)

3. Good health
researchProduct

Additional file 1: of Risk of mortality among children, adolescents, and adults with autism spectrum disorder or attention deficit hyperactivity diso…

2017

PRISMA-P checklist. (DOCX 24 kb)

3. Good health
researchProduct

Additional file 2: of Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies

2017

Key terms for PubMed/MEDLINE search. (DOCX 22 kb)

3. Good health
researchProduct

Additional file 1: of Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies

2017

PRISMA-P Checklist. (DOCX 27 kb)

3. Good health
researchProduct

Additional file 2: of Cancer and central nervous system disorders: protocol for an umbrella review of systematic reviews and updated meta-analyses of…

2017

Key terms for PubMed/MEDLINE search (DOCX 22 kb)

3. Good health
researchProduct

Additional file 3: of Anorexia nervosa and cancer: a protocol for a systematic review and meta-analysis of observational studies

2017

Definitions of specific cancer-site outcomes. (DOCX 27 kb)

3. Good health
researchProduct

Additional file 2: of Risk of mortality among children, adolescents, and adults with autism spectrum disorder or attention deficit hyperactivity diso…

2017

Key terms for PubMed/MEDLINE search. (DOCX 20 kb)

3. Good health
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Additional file 5: of Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

2019

Full differential gene expression meta-analysis results of cancer data. (ZIP 31237 kb)

population characteristicshuman activities
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Additional file 3: of Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

2019

Full ASD GSEA pre-ranked enrichment results for different molecular signatures (C2, H, GO_BP, GO_CC, and GO_MF). (XLSX 698 kb)

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Additional file 5: of Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

2019

Full differential gene expression meta-analysis results of cancer data. (ZIP 31237 kb)

population characteristicshuman activities
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Additional file 3: of Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

2019

Full ASD GSEA pre-ranked enrichment results for different molecular signatures (C2, H, GO_BP, GO_CC, and GO_MF). (XLSX 698 kb)

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Additional file 4: of Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

2019

gProfileR biological process overrepresentation results of the genes contained in the significant intersections of ASD, SDDCs, and ODDCs. (XLSX 233 kb)

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Additional file 2: of Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

2019

Full ASD differential gene expression meta-analysis results. (CSV 1387 kb)

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Additional file 2: of Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

2019

Full ASD differential gene expression meta-analysis results. (CSV 1387 kb)

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Additional file 4: of Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer

2019

gProfileR biological process overrepresentation results of the genes contained in the significant intersections of ASD, SDDCs, and ODDCs. (XLSX 233 kb)

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