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List of works by Elia Stupka

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

scientific article

A novel function for FOXP3 in humans: intrinsic regulation of conventional T cells

scientific article

A novel truncating variant of GLI2 associated with Culler-Jones syndrome impairs Hedgehog signalling

scientific article published in PLoS ONE

A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells

scientific article published on 31 May 2007

A strong anti-inflammatory signature revealed by liver transcription profiling of Tmprss6-/- mice.

scientific article

ARNT2 mutation causes hypopituitarism, post-natal microcephaly, visual and renal anomalies

scientific article

An RNA-Seq atlas of gene expression in mouse and rat normal tissues.

scientific article published on 12 December 2017

An autoinflammatory neurological disease due to interleukin 6 hypersecretion

scientific article published on 21 February 2013

Asthma in seniors: Part 1. Evidence for underdiagnosis, undertreatment, and increasing morbidity and mortality

scientific article published on January 2009

BASC: an integrated bioinformatics system for Brassica research

scientific article published on 5 December 2006

BATLAS: Deconvoluting Brown Adipose Tissue

article

Biopipe: a flexible framework for protocol-based bioinformatics analysis

scientific article

Characterisation and validation of insertions and deletions in 173 patient exomes

scientific article

Characterization of the intronic portion of cadherin superfamily members, common cancer orchestrators

scientific article published on 8 February 2012

Common variants at the MHC locus and at chromosome 16q24.1 predispose to Barrett's esophagus

scientific article

Comparative analysis of the testis and ovary transcriptomes in zebrafish by combining experimental and computational tools

scientific article published on January 2004

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors.

scientific article

Dissecting the signaling pathways associated with the oncogenic activity of MLK3 P252H mutation

scientific article

Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

scientific article published on 03 September 2013

Ensembl 2002: accommodating comparative genomics

scientific article published on January 2003

Epigenetic regulation of survivin by Bmi1 is cell type specific during corticogenesis and in gliomas

scientific article

Epigenetics and Future Generations

scientific article published on 3 February 2015

Epigenomics of Neural Cells: REST-Induced Down- and Upregulation of Gene Expression in a Two-Clone PC12 Cell Model

scientific article published on 27 August 2015

Exome sequencing and pathway analysis for identification of genetic variability relevant for bronchopulmonary dysplasia (BPD) in preterm newborns: A pilot study

scientific article published on 8 January 2015

Gene expression analysis of the emergence of epileptiform activity after focal injection of kainic acid into mouse hippocampus

scientific article published on October 2010

Genetic factors predisposing to bronchopulmonary dysplasia. A pilot study by exome sequencing and pathways analysis.

scientific article

Genome wide identification of aberrant alternative splicing events in myotonic dystrophy type 2.

scientific article

Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts.

scientific article published on 22 August 2011

Genome-wide methylation and gene expression changes in newborn rats following maternal protein restriction and reversal by folic acid

scientific article

Genome-wide signatures of convergent evolution in echolocating mammals

scientific article

Germline CDH1 deletions in hereditary diffuse gastric cancer families

scientific article published on 24 January 2009

HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

scientific article published on 16 July 2019

Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

scientific article published on 7 February 2013

Histone Modifications in a Mouse Model of Early Adversities and Panic Disorder: Role for Asic1 and Neurodevelopmental Genes

scientific article

Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data

scientific article

Immune signature drives leukemia escape and relapse after hematopoietic cell transplantation

scientific article published on 25 March 2019

Impact of MS genetic loci on familial aggregation, clinical phenotype, and disease prediction

scientific article published on 9 July 2015

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Integrated genetic and epigenetic analysis identifies haplotype-specific methylation in the FTO type 2 diabetes and obesity susceptibility locus

scientific article

Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma

scientific article published on 22 December 2013

Large Deletion of MAGT1 Gene in a Patient with Classic Kaposi Sarcoma, CD4 Lymphopenia, and EBV Infection.

scientific article published on 21 October 2016

Large-scale open bioinformatics data resources.

scientific article

Lentiviral hematopoietic stem cell gene therapy benefits metachromatic leukodystrophy

scientific article

Lentiviral vectors escape innate sensing but trigger p53 in human hematopoietic stem and progenitor cells.

scientific article published on 30 June 2017

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat.

scientific article

Mixed lineage kinase 3 gene mutations in mismatch repair deficient gastrointestinal tumours

scientific article

Mutation of SALL2 causes recessive ocular coloboma in humans and mice

scientific article

Overexpression of facioscapulohumeral muscular dystrophy region gene 1 causes primary defects in myogenic stem cells

scientific article published on 22 March 2013

PRGdb: a bioinformatics platform for plant resistance gene analysis

scientific article

ParkDB: a Parkinson's disease gene expression database

scientific article

Phylogenomic analyses elucidate the evolutionary relationships of bats

scientific article

Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements

scientific article

REST-Governed Gene Expression Profiling in a Neuronal Cell Model Reveals Novel Direct and Indirect Processes of Repression and Up-Regulation.

scientific article published on 10 November 2015

Revealing the acute asthma ignorome: characterization and validation of uninvestigated gene networks

scientific article published on 21 April 2016

Sequence variation database project at the European Bioinformatics Institute

scientific article published on 01 January 2000

Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage

scientific article published on January 2006

Social Epigenetics and Equality of Opportunity

scientific article published on 15 July 2013

Targeted transgene integration overcomes variability of position effects in zebrafish

scientific article published on February 2014

The BioMart community portal: an innovative alternative to large, centralized data repositories

scientific article (publication date: July 2015)

The Bioperl toolkit: Perl modules for the life sciences

scientific article

The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution

scientific article

The Ensembl genome database project

scientific article

The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium

scientific article

The TATA-binding protein regulates maternal mRNA degradation and differential zygotic transcription in zebrafish

scientific article

The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones.

scientific article published on 16 October 2007

The case of an APDS patient: Defects in maturation and function and decreased in vitro anti-mycobacterial activity in the myeloid compartment

scientific article published on 27 December 2015

The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance.

scientific article published on 3 June 2014

The kinetochore protein, CENPF, is mutated in human ciliopathy and microcephaly phenotypes

scientific article

The transcriptional landscape of the mammalian genome

scientific article

Tprg, a gene predominantly expressed in skin, is a direct target of the transcription factor p63

scientific journal article

Transcription initiation arising from E-cadherin/CDH1 intron2: a novel protein isoform that increases gastric cancer cell invasion and angiogenesis

scientific article

VISPA: a computational pipeline for the identification and analysis of genomic vector integration sites

scientific article published on 3 September 2014

Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

scientific article

miR-17∼92 family clusters control iNKT cell ontogenesis via modulation of TGF-β signaling

scientific article published on 05 December 2016

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