Lista de obras - Alicia Oshlack - Dominio Público Uruguay

3D organoid-derived human glomeruli for personalised podocyte disease modelling and drug screening

artículo científico publicado en 2018

A 10-step guide to party conversation for bioinformaticians

artículo científico publicado en 2013

A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data.

artículo científico publicado en 2017

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway

artículo científico publicado en 2008

A comparison of background correction methods for two-colour microarrays

artículo científico publicado en 2007

A comparison of control samples for ChIP-seq of histone modifications

artículo científico publicado en 2014

A cross-package Bioconductor workflow for analysing methylation array data

artículo científico publicado en 2016

A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders

artículo científico publicado en 2016

A scaling normalization method for differential expression analysis of RNA-seq data

artículo científico publicado en 2010

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

artículo científico publicado en 2021

Accuracy of short tandem repeats genotyping tools in whole exome sequencing data

artículo científico publicado en 2020

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy

artículo científico publicado en 2013

Array-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosis

artículo científico publicado en 2008

Bazam: A rapid method for read extraction and realignment of high throughput sequencing data

Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data

Bpipe: a tool for running and managing bioinformatics pipelines

artículo científico publicado en 2012

Cell-type-specific transcriptional profiles of the dimorphic pathogen Penicillium marneffei reflect distinct reproductive, morphological, and environmental demands

artículo científico publicado en 2013

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

artículo científico publicado en 2011

Clinker: visualising fusion genes detected in RNA-seq data

article

Clinker: visualizing fusion genes detected in RNA-seq data

article

Clustering trees: a visualization for evaluating clusterings at multiple resolutions

scholarly article by Luke Zappia & Alicia Oshlack published 1 July 2018 in GigaScience

Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing

artículo científico publicado en 2017

Condensin I associates with structural and gene regulatory regions in vertebrate chromosomes

artículo científico publicado en 2013

Cord Blood CD8+ T Cells Have a Natural Propensity to Express IL-4 in a Fatty Acid Metabolism and Caspase Activation-Dependent Manner.

artículo científico publicado en 2018

Correction: Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures.

artículo científico publicado en 2009

Correction: Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk (doi:10.1242/dev.178673)

scientific article published on 11 July 2019

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes

artículo científico publicado en 2014

Cpipe: a shared variant detection pipeline designed for diagnostic settings

artículo científico publicado en 2015

Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions.

artículo científico publicado en 2017

Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy.

artículo científico publicado en 2017

DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging

artículo científico publicado en 2014

Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design

scholarly article published 22 September 2011

Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros.

artículo científico publicado en 2016

Direct reprogramming to human nephron progenitor-like cells using inducible piggyBac transposon expression of SNAI2-EYA1-SIX1

scientific article published on 28 February 2019

Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort

artículo científico publicado en 2016

Erratum to: 'Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq'.

artículo científico publicado en 2016

Erratum to: SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

artículo científico publicado en 2017

Evaluation of variability in human kidney organoids

artículo científico publicado en 2018

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

article

Expression discordance of monozygotic twins at birth: effect of intrauterine environment and a possible mechanism for fetal programming

artículo científico publicado en 2011

Expression profiling in primates reveals a rapid evolution of human transcription factors

artículo científico publicado en 2006

Fast and accurate differential transcript usage by testing equivalence class counts

scholarly article by Marek Cmero et al published 2019 in F1000Research

From RNA-seq reads to differential expression results

artículo científico publicado en 2010

Functionally distinct roles for different miR-155 expression levels through contrasting effects on gene expression, in acute myeloid leukaemia

artículo científico publicado en 2016

Gene length and detection bias in single cell RNA sequencing protocols

artículo científico publicado en 2017

Gene ontology analysis for RNA-seq: accounting for selection bias

artículo científico publicado en 2010

Gene regulation in primates evolves under tissue-specific selection pressures

artículo científico publicado en 2008

Gene set enrichment analysis for genome-wide DNA methylation data

artículo científico publicado en 2021

Genome-wide DNA methylation analysis identifies hypomethylated genes regulated by FOXP3 in human regulatory T cells

artículo científico publicado en 2013

Genomics in 2011: challenges and opportunities

artículo científico publicado en 2011

Genotyping microsatellites in next-generation sequencing data.

artículo científico publicado en 2015

Haploinsufficiency for the Six2 gene increases nephron progenitor proliferation promoting branching and nephron number

artículo científico publicado en 2017

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

artículo científico publicado en 2016

Human yolk sac-like haematopoiesis generates RUNX1- and GFI1/1B-dependent blood and SOX17-positive endothelium

artículo científico publicado en 2020

Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq

artículo científico publicado en 2015

Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing

artículo científico publicado en 2013

Identification, expression, and regulation of anti-Müllerian hormone type-II receptor in the embryonic chicken gonad

artículo científico publicado en 2014

JAFFA: High sensitivity transcriptome-focused fusion gene detection

artículo científico publicado en 2015

JAFFAL: detecting fusion genes with long-read transcriptome sequencing

artículo científico publicado en 2022

Jarid2 regulates hematopoietic stem cell function by acting with polycomb repressive complex 2.

artículo científico publicado en 2015

Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells

article

Limb patterning genes and heterochronic development of the emu wing bud.

artículo científico publicado en 2016

MCM3AP in recessive Charcot-Marie-Tooth neuropathy and mild intellectual disability

artículo científico publicado en 2017

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

artículo científico publicado en 2021

MLL-TFE3: a novel and aggressive KMT2A fusion identified in infant leukemia

artículo científico publicado en 2020

NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network.

artículo científico publicado en 2018

Natural selection on gene expression

artículo científico publicado en 2006

Near Infrared Micro-variability of Radio-loud Quasars

scholarly article

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.

artículo científico publicado en 2018

Nephron progenitor commitment is a stochastic process influenced by cell migration

scholarly article by Kynan T Lawlor et al published 24 January 2019 in eLife

Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes

artículo científico publicado en 2007

Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips

artículo científico publicado en 2010

Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms

Publisher Correction: The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAome

artículo científico publicado en 2019

Purification and Transcriptomic Analysis of Mouse Fetal Leydig Cells Reveals Candidate Genes for Specification of Gonadal Steroidogenic Cells

artículo científico publicado en 2015

RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome

artículo científico publicado en 2013

RUNX1 AND GROUP F SOX GENES ARE REQUIRED AT DISTINCT STAGES FOR HUMAN HAEMATOPOIETIC DEVELOPMENT

scholarly article

Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data

artículo científico publicado en 2015

SFPQ-ABL1 and BCR-ABL1 use different signaling networks to drive B-cell acute lymphoblastic leukemia

artículo científico publicado en 2022

STRetch: detecting and discovering pathogenic short tandem repeat expansions

artículo científico publicado en 2018

STRetch: detecting and discovering pathogenic short tandem repeats expansions

SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips

artículo científico publicado en 2012

Segmental duplications contribute to gene expression differences between humans and chimpanzees

artículo científico publicado en 2009

Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor

artículo científico publicado en 2021

Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period

artículo científico publicado en 2018

Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data

artículo científico publicado en 2020

Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk

artículo científico publicado en 2019

Single-cell analysis reveals congruence between kidney organoids and human fetal kidney

scholarly article by Alexander N Combes et al published 23 January 2019 in Genome Medicine

Sixty years of genome biology

artículo científico publicado en 2013

Splatter: simulation of single-cell RNA sequencing data

artículo científico publicado en 2017

Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis

artículo científico publicado en 2006

SuperFreq: Integrated mutation detection and clonal tracking in cancer

article published in 2018

SuperFreq: Integrated mutation detection and clonal tracking in cancer

artículo científico publicado en 2020

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

artículo científico

Susceptibility to acute rheumatic fever based on differential expression of genes involved in cytotoxicity, chemotaxis, and apoptosis

artículo científico publicado en 2013

THE NATURE OF THE OPTICAL EMISSION IN RADIO-SELECTED AGN

Targeted therapy and disease monitoring in CNTRL-FGFR1-driven leukaemia

scientific article published on 28 June 2019

The Dose-Dependent Effects of Microrna-155 in Acute Myeloid Leukemia ⬇️

scholarly article

The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia

artículo científico publicado en 2020

The polycomb repressive complex 2 governs life and death of peripheral T cells

scientific article published on 20 June 2014

The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAome

artículo científico publicado en 2019

The spectral energy distribution of PKS 2004-447: a compact steep-spectrum source and possible radio-loud narrow-line Seyfert 1 galaxy

artículo científico publicado en 2006

Transcript length bias in RNA-seq data confounds systems biology

artículo científico publicado en 2009

Transcriptional profiles for distinct aggregation states of mutant Huntingtin exon 1 protein unmask new Huntington's disease pathways

artículo científico publicado en 2017

Using DNA microarrays to study gene expression in closely related species

artículo científico publicado en 2007

Whole exome sequencing in systemic juvenile idiopathic arthritis

Whole exome sequencing in systemic juvenile idiopathic arthritis.

artículo científico publicado en 2015

Women in Science

artículo científico publicado en 2012

Ximmer: A system for improving accuracy and consistency of CNV calling from exome data

article by Simon P Sadedin et al published 6 September 2018 in GigaScience

miRNA-Seq normalization comparisons need improvement

artículo científico publicado en 2013

missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform

artículo científico publicado en 2015

Lista de obras de Alicia Oshlack

3D organoid-derived human glomeruli for personalised podocyte disease modelling and drug screening

A 10-step guide to party conversation for bioinformaticians

A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data.

A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway

A comparison of background correction methods for two-colour microarrays

A comparison of control samples for ChIP-seq of histone modifications

A cross-package Bioconductor workflow for analysing methylation array data

A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders

A scaling normalization method for differential expression analysis of RNA-seq data

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

Accuracy of short tandem repeats genotyping tools in whole exome sequencing data

Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy

Array-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosis

Bazam: A rapid method for read extraction and realignment of high throughput sequencing data

Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data

Bpipe: a tool for running and managing bioinformatics pipelines

Cell-type-specific transcriptional profiles of the dimorphic pathogen Penicillium marneffei reflect distinct reproductive, morphological, and environmental demands

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

Clinker: visualising fusion genes detected in RNA-seq data

Clinker: visualizing fusion genes detected in RNA-seq data

Clustering trees: a visualization for evaluating clusterings at multiple resolutions

Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing

Condensin I associates with structural and gene regulatory regions in vertebrate chromosomes

Cord Blood CD8+ T Cells Have a Natural Propensity to Express IL-4 in a Fatty Acid Metabolism and Caspase Activation-Dependent Manner.

Correction: Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures.

Correction: Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk (doi:10.1242/dev.178673)

Corset: enabling differential gene expression analysis for de novo assembled transcriptomes

Cpipe: a shared variant detection pipeline designed for diagnostic settings

Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions.

Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy.

DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging

Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design

Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros.

Direct reprogramming to human nephron progenitor-like cells using inducible piggyBac transposon expression of SNAI2-EYA1-SIX1

Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort

Erratum to: 'Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq'.

Erratum to: SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes

Evaluation of variability in human kidney organoids

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Expression discordance of monozygotic twins at birth: effect of intrauterine environment and a possible mechanism for fetal programming

Expression profiling in primates reveals a rapid evolution of human transcription factors

Fast and accurate differential transcript usage by testing equivalence class counts

From RNA-seq reads to differential expression results

Functionally distinct roles for different miR-155 expression levels through contrasting effects on gene expression, in acute myeloid leukaemia

Gene length and detection bias in single cell RNA sequencing protocols

Gene ontology analysis for RNA-seq: accounting for selection bias

Gene regulation in primates evolves under tissue-specific selection pressures

Gene set enrichment analysis for genome-wide DNA methylation data

Genome-wide DNA methylation analysis identifies hypomethylated genes regulated by FOXP3 in human regulatory T cells

Genomics in 2011: challenges and opportunities

Genotyping microsatellites in next-generation sequencing data.

Haploinsufficiency for the Six2 gene increases nephron progenitor proliferation promoting branching and nephron number

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

Human yolk sac-like haematopoiesis generates RUNX1- and GFI1/1B-dependent blood and SOX17-positive endothelium

Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq

Identification of recurrent FGFR3 fusion genes in lung cancer through kinome-centred RNA sequencing

Identification, expression, and regulation of anti-Müllerian hormone type-II receptor in the embryonic chicken gonad

JAFFA: High sensitivity transcriptome-focused fusion gene detection

JAFFAL: detecting fusion genes with long-read transcriptome sequencing

Jarid2 regulates hematopoietic stem cell function by acting with polycomb repressive complex 2.

Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells

Limb patterning genes and heterochronic development of the emu wing bud.

MCM3AP in recessive Charcot-Marie-Tooth neuropathy and mild intellectual disability

MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data

MLL-TFE3: a novel and aggressive KMT2A fusion identified in infant leukemia

NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network.

Natural selection on gene expression

Near Infrared Micro-variability of Radio-loud Quasars

Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis.

Nephron progenitor commitment is a stochastic process influenced by cell migration

Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes

Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips

Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms

Publisher Correction: The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAome

Purification and Transcriptomic Analysis of Mouse Fetal Leydig Cells Reveals Candidate Genes for Specification of Gonadal Steroidogenic Cells

RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome

RUNX1 AND GROUP F SOX GENES ARE REQUIRED AT DISTINCT STAGES FOR HUMAN HAEMATOPOIETIC DEVELOPMENT

Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data

SFPQ-ABL1 and BCR-ABL1 use different signaling networks to drive B-cell acute lymphoblastic leukemia