Research Explorer

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Researcher

Francisco Avila Cobos

Awards & Distinctions

49 Results

2024

Subpar reporting of pre-analytical variables in RNA-focused blood plasma studies

Céleste Van Der SchuerenPhilippe DecruyenaereFrancisco Avila CobosJohanna BultJill DeleuLydia DipaloHetty HelsmoortelEva HulstaertAnnelien MorlionElena Ramos Varas et al.

Subpar reporting of pre‐analytical variables in RNA‐focused blood plasma studies

Céleste Van Der SchuerenPhilippe DecruyenaereFrancisco Avila CobosJohanna BultJill DeleuLydia DipaloHetty HelsmoortelEva HulstaertAnnelien MorlionElena Ramos Varas et al.

A1 Journal Article in MOLECULAR ONCOLOGY

2023

Dramatic impact of blood collection tube and RNA purification method on extracellular RNA transcriptomes

Jasper AnckaertFrancisco Avila CobosAnneleen DecockPhilippe DecruyenaereJill DeleuKatleen De PreterOlivier De WeverJilke De WildeBert DhondtThibaut D'huyvetter et al.

Performance evaluation of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

Anneleen DecockOlivier De WeverCeline EveraertHetty HelsmoortelAn HendrixPieter MestdaghAnnelien MorlionJo VandesompeleRuben Van PaemelFrancisco Avila Cobos et al.

Performance evaluation of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

Anneleen DecockOlivier De WeverCeline EveraertHetty HelsmoortelAn HendrixPieter MestdaghAnnelien MorlionJo VandesompeleRuben Van PaemelFrancisco Avila Cobos et al.

Reporting of pre-analytical variables in RNA-focused blood plasma studies : a prerequisite for quality assessment and replication

Céleste Van Der SchuerenPhilippe DecruyenaereFrancisco Avila CobosJill DeleuHetty HelsmoortelEva HulstaertAnnelien MorlionKathleen SchoofsEveline Vanden EyndeKimberly Verniers et al.

2022

Comprehensive RNA dataset of tissue and plasma from patients with esophageal cancer or precursor lesions

Kathleen SchoofsAnnouck PhilippronFrancisco Avila CobosJan KosterSteve LefeverJasper AnckaertDanny De LoozeJo VandesompelePiet PattynKatleen De Preter

A1 Journal Article in SCIENTIFIC DATA

Performance evaluation of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

Jasper AnckaertFrancisco Avila CobosAnneleen DecockPhilippe DecruyenaereJill DeleuKatleen De PreterOlivier De WeverJilke De WildeBert DhondtThibaut D'huyvetter et al.

2021

DECONbench : a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification

Clémentine DecampsAlexis ArnaudFlorent PetitprezMira AyadiAurélia BaurèsLucile ArmenoultN. AlcalaA. ArnaudFrancisco Avila CobosLuciana Batista et al.

A1 Journal Article in BMC BIOINFORMATICS

Robust sequential biophysical fractionation of blood plasma to study variations in the biomolecular landscape of systemically circulating extracellular vesicles across clinical conditions

Glenn VergauwenJoeri TulkensCláudio PinheiroFrancisco Avila CobosSandor DedeyneMarie-Angélique De ScheerderLinos VandekerckhoveFrancis ImpensIlkka MiinalainenGeert Braems et al.

A1 Journal Article in JOURNAL OF EXTRACELLULAR VESICLES

Substantial performance differences among RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

Anneleen DecockOlivier De WeverCeline EveraertHetty HelsmoortelAn HendrixPieter MestdaghAnnelien MorlionJo VandesompeleRuben Van PaemelFrancisco Avila Cobos et al.

Substantial performance differences among RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study

Anneleen DecockOlivier De WeverCeline EveraertHetty HelsmoortelAn HendrixPieter MestdaghAnnelien MorlionJo VandesompeleRuben Van PaemelFrancisco Avila Cobos et al.

The RNA Atlas expands the catalog of human non-coding RNAs

Lucia LorenziHua-Sheng ChiuFrancisco Avila CobosStephen GrossPieter-Jan VoldersRobrecht CannoodtJustine NuytensKatrien VanderheydenJasper AnckaertSteve Lefever et al.

A1 Journal Article in NATURE BIOTECHNOLOGY

The RNA Atlas expands the catalog of human non-coding RNAs (June, 10.1038/s41587-021-00936-1, 2021)

Lucia LorenziHua-Sheng ChiuFrancisco Avila CobosStephen GrossPieter-Jan VoldersRobrecht CannoodtJustine NuytensKatrien VanderheydenJasper AnckaertSteve Lefever et al.

2020

A comprehensive custom panel evaluation for routine hereditary cancer testing : improving the yield of germline mutation detection

C VelázquezE LastraFrancisco Avila CobosL AbellaV de la CruzBA HernandoL HernándezN MartínezM InfanteM Durán

A1 Journal Article in JOURNAL OF TRANSLATIONAL MEDICINE

Addressing challenges in transcriptome annotation and cell-type heterogeneity through integration of omics datasets and computational deconvolution

Francisco Avila CobosKatleen De PreterPieter Mestdagh

Benchmarking of cell type deconvolution pipelines for transcriptomics data

Francisco Avila CobosJosé Alquicira-HernandezJoseph E. PowellPieter MestdaghKatleen De Preter

A1 Journal Article in NATURE COMMUNICATIONS

Charting extracellular transcriptomes in the human biofluid RNA atlas

Eva HulstaertAnnelien MorlionFrancisco Avila CobosKimberly VerniersJustine NuytensEveline Vanden EyndeNurten YigitJasper AnckaertAnja GeertsPieter Hindryckx et al.

A1 Journal Article in CELL REPORTS

Germline genetic findings which may impact therapeutic decisions in families with a presumed predisposition for hereditary breast and ovarian cancer

Carolina VelázquezKim De LeeneerEva M. Esteban-CardeñosaFrancisco Avila CobosEnrique LastraLuis E. AbellaVirginia de la CruzCarmen D. LobatónKathleen ClaesMercedes Durán et al.

A1 Journal Article in CANCERS

Substantial performance differences among RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control study-important considerations for liquid biopsies

Anneleen DecockJasper AnckaertCeline EveraertJustine NuytensScott KuerstenAn HendrixJo VandesompelePieter MestdaghBert DhondtRuben Van Paemel et al.

The role of miR-155 in cigarette smoke-induced pulmonary inflammation and COPD

Elise De SmetHannelore Van EeckhoutteFrancisco Avila CobosEvy BlommeFien VerhammeSharen ProvoostSTIJN VERLEDENKoen VenkenTania MaesGuy Joos et al.

A1 Journal Article in MUCOSAL IMMUNOLOGY

2019

A neuronal enhancer network upstream of MEF2C is compromised in patients with Rett-like characteristics

Eva D'haeneReut Bar-YaacovInbar BariahLies VantommeSien Van LooFrancisco Avila CobosKaren VerboomReut EshelRawan AlatawnaBjörn Menten et al.

A1 Journal Article in HUMAN MOLECULAR GENETICS

Benchmarking the impact of data transformation, pre-processing and choice of method in the computational deconvolution of transcriptomics data

Francisco Avila CobosJosé Alquicira-HernandezJo VandesompeleJoseph PowellPieter MestdaghKatleen De Preter

Dramatic differences in RNA purification kit performance in the extracellular RNA quality control study : important considerations for liquid biopsies

Annelien MorlionJasper AnckaertFrancisco Avila CobosAnneleen DecockOlivier De WeverBert DhondtCeline EveraertCarolina FierroHetty HelsmoortelAn Hendrix et al.

Dramatic differences in RNA purification kit performance in the extracellular RNA quality control study : important considerations for liquid biopsies

Annelien MorlionJasper AnckaertFrancisco Avila CobosAnneleen DecockOlivier De WeverBert DhondtCeline EveraertCarolina FierroHetty HelsmoortelAn Hendrix et al.

Evaluating the impact of RNA purification kit and blood collection tube in the extracellular RNA quality control study : important considerations for liquid biopsies

Annelien MorlionJasper AnckaertFrancisco Avila CobosAnneleen DecockJill DeleuOlivier De WeverBert DhondtCeline EveraertCarolina FierroHetty Helsmoortel et al.

Long noncoding RNA expression profiling in cancer : challenges and opportunities

Lucia LorenziFrancisco Avila CobosAnneleen DecockCeline EveraertHetty HelsmoortelSteve LefeverKaren VerboomPieter-Jan VoldersFranki SpelemanJo Vandesompele et al.

A1 Journal Article in GENES CHROMOSOMES & CANCER

Noncoding structural variants disrupt the regulatory architecture of Rett genes

Eva D'haeneReut Bar-YaacovInbar BariahLies VantommeSien Van LooFrancisco Avila CobosKaren VerboomReut EshelRawan AlatawnaBjörn Menten et al.

Noncoding structural variants disrupt the regulatory architecture of Rett genes

Eva D'haeneReut Bar-YaacovInbar BariahLies VantommeSien Van LooFrancisco Avila CobosKaren VerboomReut EshelRawan AlatawnaBjörn Menten et al.

The RNA Atlas, a single nucleotide resolution map of the human transcriptome

Lucia LorenziHua-Sheng ChiuFrancisco Avila CobosStephen GrossPieter-Jan VoldersRobrecht CannoodtJustine NuytensKatrien VanderheydenJasper AnckaertSteve Lefever et al.

2018

A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing

Karen VerboomWouter Van LoockePieter-Jan VoldersBieke DecaestekerFrancisco Avila CobosSimon BornscheinCharles E de BockZeynep Kalender AtakEmmanuelle ClappierStein Aerts et al.

A1 Journal Article in HAEMATOLOGICA

A neuronal enhancer network upstream of MEF2C is compromised in patients with Rett-like characteristics

Eva D'haeneReut Bar-YaacovInbar BariahLies VantommeSien Van LooFrancisco Avila CobosKaren VerboomReut EshelRawan AlatawnaBjörn Menten et al.

Assessing the biological signal of different RNA fractions for computational deconvolution of healthy tissues

Francisco Avila CobosLucia LorenziJo VandesompeleGary SchrothKatleen De PreterPieter Mestdagh

Computational deconvolution of transcriptomics data from mixed cell populations

Francisco Avila CobosJo VandesompelePieter MestdaghKatleen De Preter

A1 Journal Article in BIOINFORMATICS

The MEF2C regulatory network is disrupted in patients with Rett-like characteristics

Eva D'haeneSarah VergultReut Bar-YaakovInbar BariahLies VantommeSien Van LooFrancisco Avila CobosReut EshelRowan AlatawnaRamon Birnbaum et al.

The MEF2C regulatory network is disrupted in patients with Rett-like characteristics

Eva D'haeneReut Bar-YaakovInbar BariahSien Van LooLies VantommeFrancisco Avila CobosReut EshelRowan AlatawnaBjörn MentenRamon Birnbaum et al.

The extracellular RNA quality control (exRNAQC) study : controlling pre-analytical variables of RNA sequencing in blood-based precision medicine

Francisco Avila CobosAnneleen DecockKatleen De PreterBert DhondtOlivier De WeverBram De WildeCeline EveraertCarolina FierroHetty HelsmoortelAn Hendrix et al.

The extracellular RNA quality control (exRNAQC) study : controlling pre-analytical variables of RNA sequencing in blood-based precision medicine

Francisco Avila CobosAnneleen DecockKatleen De PreterOlivier De WeverBram De WildeBert DhondtCeline EveraertCarolina FierroHetty HelsmoortelAn Hendrix et al.

The role of microRNA-155 in cigarette smoke-induced inflammation

Elise De SmetPieter MestdaghFrancisco Avila CobosEvy BlommeFien VerhammeSharen ProvoostTania MaesGuy JoosGuy BrusselleKen Bracke

Zipper plot : visualizing transcriptional activity of genomic regions

Francisco Avila CobosJasper AnckaertPieter-Jan VoldersCeline EveraertDries RombautJo VandesompeleKatleen De PreterPieter Mestdagh

2017

MicroRNA profiling reveals a role for microRNA-218-5p in the pathogenesis of chronic obstructive pulmonary disease

Griet ConickxPieter MestdaghFrancisco Avila CobosFien VerhammeTania MaesBart M VanaudenaerdeLeen SeysLies LahousseRichard Y KimAlan C Hsu et al.

A1 Journal Article in AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Zipper plot : visualizing transcriptional activity of genomic regions

Francisco Avila CobosJasper AnckaertPieter-Jan VoldersCeline EveraertDries RombautJo VandesompeleKatleen De PreterPieter Mestdagh

A1 Journal Article in BMC BIOINFORMATICS

microRNA profiling in lung tissue and bronchoalveolar lavage of cigarette smoke-exposed mice and in COPD patients : a translational approach

Griet ConickxFrancisco Avila CobosMaarten van den BergeAlen FaizWim TimensPieter S. HiemstraGuy JoosGuy BrussellePieter MestdaghKen Bracke

A1 Journal Article in SCIENTIFIC REPORTS

2016

Asthma inflammatory phenotypes show differential microRNA expression in sputum

Tania MaesFrancisco Avila CobosFlorence SchleichValentina SorbelloMonique HenketKatleen De PreterKen BrackeGriet ConickxClaire MesnilJo Vandesompele et al.

A1 Journal Article in JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

LncRNAs in the context of Chronic Obstructive Pulmonary Disease (COPD) are associated to immune response and metabolism of xenobiotics

Francisco Avila CobosKen BrackeJo VandesompeleKimberly VerniersGuy JoosKatleen De PreterGuy BrussellePieter Mestdagh

Long noncoding RNA signatures define oncogenic subtypes in T-cell acute lymphoblastic leukemia

Annelynn WallaertKaat DurinckWouter Van LoockeInge Van de WalleFilip MatthijssensPieter-Jan VoldersFrancisco Avila CobosDries RombautPieter RondouPieter Mestdagh et al.

A1 Journal Article in LEUKEMIA

Microrna-218-5p is implicated in the pathogenesis of chronic obstructive pulmonary disease

Griet ConickxPieter MestdaghFrancisco Avila CobosFien VerhammeTania MaesBM VanaudenaerdeLies LahousseGuy JoosJo VandesompeleKen Bracke et al.

Rol van microRNA in neutrofiel astma

Tania MaesFrancisco Avila CobosFlorence SchleichValentina SorbelloMonique HenketKatleen De PreterKen BrackeGriet ConickxClaire MesnilJo Vandesompele et al.

A4 Journal Article in BLOEDVATEN HART LONGEN

The chromosome 17q super-enhancer landscape in neuroblastoma

Bieke DecaestekerAnton HenssenWouter Van LoockeFrancisco Avila CobosAnneleen BeckersStein AertsJohannes SchulteKatleen De PreterFranki Speleman