Alicia Oshlack
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Australian bioinformatician
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Alicia Oshlackbiology Degrees
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Bioinformatics
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Computational Biology
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Biology
Alicia Oshlack's Degrees
- Bachelors Bioinformatics University of Melbourne
- PhD Bioinformatics University of Melbourne
Why Is Alicia Oshlack Influential?
(Suggest an Edit or Addition)According to Wikipedia, Alicia Yinema Kate Nungarai Oshlack is an Australian bioinformatician and is Co-Head of Computational Biology at the Peter MacCallum Cancer Centre in Melbourne, Victoria, Australia. She is best known for her work developing methods for the analysis of transcriptome data as a measure of gene expression. She has characterized the role of gene expression in human evolution by comparisons of humans, chimpanzees, orangutans, and rhesus macaques, and works collaboratively in data analysis to improve the use of clinical sequencing of RNA samples by RNAseq for human disease diagnosis.
Alicia Oshlack's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- A scaling normalization method for differential expression analysis of RNA-seq data (2010) (5704)
- Gene ontology analysis for RNA-seq: accounting for selection bias (2010) (4811)
- A comparison of background correction methods for two-colour microarrays (2007) (952)
- SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips (2012) (722)
- From RNA-seq reads to differential expression results (2010) (711)
- Transcript length bias in RNA-seq data confounds systems biology (2009) (538)
- Splatter: simulation of single-cell RNA sequencing data (2017) (493)
- missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform (2016) (461)
- Corset: enabling differential gene expression analysis for de novo assembled transcriptomes (2014) (399)
- Expression profiling in primates reveals a rapid evolution of human transcription factors (2006) (322)
- A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders (2016) (309)
- Clustering trees: a visualization for evaluating clusterings at multiple resolutions (2018) (272)
- ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity (2011) (270)
- Diagnostic Impact and Cost-effectiveness of Whole-Exome Sequencing for Ambulant Children With Suspected Monogenic Conditions (2017) (229)
- Array-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosis. (2008) (227)
- Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips (2010) (221)
- Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort (2016) (218)
- Natural selection on gene expression. (2006) (207)
- Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database (2017) (192)
- Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures (2008) (152)
- Evaluation of variability in human kidney organoids (2018) (143)
- Bpipe: a tool for running and managing bioinformatics pipelines (2012) (140)
- Patient-iPSC-Derived Kidney Organoids Show Functional Validation of a Ciliopathic Renal Phenotype and Reveal Underlying Pathogenetic Mechanisms. (2018) (129)
- 3D organoid-derived human glomeruli for personalised podocyte disease modelling and drug screening (2018) (127)
- Single-cell analysis reveals congruence between kidney organoids and human fetal kidney (2019) (126)
- JAFFA: High sensitivity transcriptome-focused fusion gene detection (2015) (125)
- Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros (2016) (119)
- Identification of recurrent FGFR3 fusion genes in lung cancer through kinome‐centred RNA sequencing (2013) (119)
- goseq: Gene Ontology testing for RNA-seq datasets (2014) (115)
- Genome-wide DNA methylation analysis identifies hypomethylated genes regulated by FOXP3 in human regulatory T cells. (2013) (113)
- Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy (2013) (111)
- A cross-package Bioconductor workflow for analysing methylation array data (2016) (99)
- The polycomb repressive complex 2 governs life and death of peripheral T cells. (2014) (95)
- STRetch: detecting and discovering pathogenic short tandem repeat expansions (2017) (95)
- RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome (2013) (92)
- Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk (2019) (85)
- DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging (2014) (80)
- Cpipe: a shared variant detection pipeline designed for diagnostic settings (2015) (79)
- SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes (2016) (77)
- Kidney micro-organoids in suspension culture as a scalable source of human pluripotent stem cell-derived kidney cells (2019) (73)
- Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes (2007) (71)
- Using DNA microarrays to study gene expression in closely related species (2007) (70)
- A Very Radio Loud Narrow-Line Seyfert 1: PKS 2004–447 (2001) (69)
- NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network (2018) (67)
- Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data (2015) (67)
- Expression discordance of monozygotic twins at birth: Effect of intrauterine environment and a possible mechanism for fetal programming (2011) (65)
- Black Hole Mass Estimates of Radio-selected Quasars (2002) (63)
- A cross-package Bioconductor workflow for analysing methylation array data. (2016) (58)
- The spectral energy distribution of PKS 2004–447: a compact steep-spectrum source and possible radio-loud narrow-line Seyfert 1 galaxy (2006) (56)
- Gene length and detection bias in single cell RNA sequencing protocols (2017) (51)
- Condensin I associates with structural and gene regulatory regions in vertebrate chromosomes (2013) (51)
- A Combination of Genomic Approaches Reveals the Role of FOXO1a in Regulating an Oxidative Stress Response Pathway (2008) (47)
- Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data (2019) (47)
- Gene set enrichment analysis for genome-wide DNA methylation data (2020) (46)
- Nephron progenitor commitment is a stochastic process influenced by cell migration (2018) (41)
- Functionally distinct roles for different miR-155 expression levels through contrasting effects on gene expression, in acute myeloid leukaemia (2017) (40)
- Jarid2 regulates hematopoietic stem cell function by acting with polycomb repressive complex 2. (2015) (39)
- Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy (2017) (37)
- Purification and Transcriptomic Analysis of Mouse Fetal Leydig Cells Reveals Candidate Genes for Specification of Gonadal Steroidogenic Cells1 (2015) (36)
- The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia. (2020) (34)
- SuperFreq: Integrated mutation detection and clonal tracking in cancer (2018) (33)
- A comparison of control samples for ChIP-seq of histone modifications (2014) (31)
- A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines (2021) (31)
- miRNA-Seq normalization comparisons need improvement. (2013) (29)
- Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq (2015) (28)
- Corset: enabling differential gene expression analysis for (2014) (28)
- Sex-Specific Control of Human Heart Maturation by the Progesterone Receptor (2021) (28)
- Segmental Duplications Contribute to Gene Expression Differences Between Humans and Chimpanzees (2009) (26)
- Cell-Type–Specific Transcriptional Profiles of the Dimorphic Pathogen Penicillium marneffei Reflect Distinct Reproductive, Morphological, and Environmental Demands (2013) (25)
- Ximmer: a system for improving accuracy and consistency of CNV calling from exome data (2018) (24)
- Haploinsufficiency for the Six2 gene increases nephron progenitor proliferation promoting branching and nephron number. (2017) (24)
- Identification, Expression, and Regulation of Anti-Müllerian Hormone Type-II Receptor in the Embryonic Chicken Gonad1 (2014) (23)
- Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis (2006) (23)
- Transcriptional profiles for distinct aggregation states of mutant Huntingtin exon 1 protein unmask new Huntington's disease pathways (2017) (23)
- MCM3AP in recessive Charcot-Marie-Tooth neuropathy and mild intellectual disability (2017) (23)
- Erratum to: ‘Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq’ (2015) (21)
- A clinically driven variant prioritization framework outperforms purely computational approaches for the diagnostic analysis of singleton WES data (2017) (21)
- Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants (2021) (20)
- 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) (2019) (20)
- Accuracy of short tandem repeats genotyping tools in whole exome sequencing data (2020) (19)
- Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing (2017) (19)
- Direct reprogramming to human nephron progenitor-like cells using inducible piggyBac transposon expression of SNAI2-EYA1-SIX1. (2019) (18)
- High throughput single cell RNA-seq of developing mouse kidney and human kidney organoids reveals a roadmap for recreating the kidney (2017) (18)
- Susceptibility to Acute Rheumatic Fever Based on Differential Expression of Genes Involved in Cytotoxicity, Chemotaxis, and Apoptosis (2013) (18)
- 3 D organoid-derived human glomeruli for personalised podocyte disease modelling and drug screening (2018) (17)
- propeller: testing for differences in cell type proportions in single cell data (2021) (16)
- Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design (2012) (15)
- Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design (2012) (15)
- JAFFAL: detecting fusion genes with long-read transcriptome sequencing (2021) (13)
- MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data (2020) (12)
- Genotyping microsatellites in next-generation sequencing data (2014) (11)
- Human yolk sac-like haematopoiesis generates RUNX1-, GFI1- and/or GFI1B-dependent blood and SOX17-positive endothelium (2020) (11)
- Limb patterning genes and heterochronic development of the emu wing bud (2016) (11)
- ALLSorts: an RNA-Seq subtype classifier for B-cell acute lymphoblastic leukemia (2022) (11)
- A cross-package Bioconductor workflow for analysing methylation array data (2016) (10)
- Cord Blood CD8+ T Cells Have a Natural Propensity to Express IL-4 in a Fatty Acid Metabolism and Caspase Activation-Dependent Manner (2018) (10)
- Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data (2018) (10)
- Clinker: visualizing fusion genes detected in RNA-seq data (2018) (10)
- Corset: enabling differential gene expression analysis for de novoassembled transcriptomes (2014) (9)
- Detecting copy number alterations in RNA-Seq using SuperFreq (2020) (9)
- RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken embryos and allows comprehensive annotation of W-chromosome genes (2013) (9)
- A comparison of control samples for ChIP-seq of histone modifications (2014) (8)
- Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia. (2022) (8)
- Sixty years of genome biology (2013) (8)
- Gene set enrichment analysis for genome-wide DNA methylation data (2021) (7)
- Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability (2022) (7)
- Using equivalence class counts for fast and accurate testing of differential transcript usage (2019) (7)
- Necklace: combining reference and assembled transcriptomes for more comprehensive RNA-Seq analysis (2017) (6)
- STRetch: detecting and discovering pathogenic short tandem repeat expansions (2018) (5)
- Targeted therapy and disease monitoring in CNTRL‐FGFR1‐driven leukaemia (2019) (5)
- Statistical solutions to modern problems : proceedings of the 20th International Workshop on Statistical Modelling, Sydney, Australia, July 10-15, 2005 (2005) (5)
- Erratum to: SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes (2017) (5)
- Human yolk sac-like haematopoiesis generates RUNX1- and GFI1/1B-dependent blood and SOX17-positive endothelium. (2020) (4)
- Near Infrared Micro-variability of Radio-loud Quasars (2001) (4)
- The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAome (2019) (3)
- MLL-TFE3: a novel and aggressive KMT2A fusion identified in infant leukemia. (2020) (3)
- MCM 3 AP in recessive Charcot-Marie-Tooth neuropathy and mild intellectual disability (3)
- Human genome meeting 2016 (2016) (3)
- HEMATOPOIESIS AND STEM CELLS Jarid 2 regulates hematopoietic stem cell function by acting with polycomb repressive complex 2 (2015) (3)
- Transcriptional evaluation of the developmental accuracy, reproducibility and robustness of kidney organoids derived from human pluripotent stem cells (2017) (3)
- splatPop: simulating population scale single-cell RNA sequencing data (2021) (3)
- Defining the Fetal Gene Program at Single-Cell Resolution in Pediatric Dilated Cardiomyopathy (2022) (3)
- Pooled-parent exome sequencing to prioritise de novo variants in genetic disease (2019) (2)
- STRipy: A graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data (2021) (2)
- Clinker: visualising fusion genes detected in RNA-seq data (2017) (2)
- JAFFAL: detecting fusion genes with long-read transcriptome sequencing (2022) (2)
- Splatter: simulation of single-cell RNA sequencing data (2017) (2)
- A 10-step guide to party conversation for bioinformaticians (2013) (2)
- Shifts in ovine cardiopulmonary microRNA expression in late gestation and the perinatal period (2018) (2)
- The Dose-Dependent Effects of Microrna-155 in Acute Myeloid Leukemia (2016) (1)
- JAFFA: High sensitivity transcriptome-focused fusion gene detection (2015) (1)
- Slinker: Visualising novel splicing events in RNA-Seq data (2021) (1)
- Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq (2015) (1)
- Correction: Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures (2009) (1)
- Limb patterning genes and heterochronic development of the emu wing bud (2016) (1)
- DiffVar: a new method for detecting differential variability with application to methylation in cancer and aging (2014) (1)
- ALLSorts: a RNA-Seq classifier for B-Cell Acute Lymphoblastic Leukemia (2021) (1)
- SFPQ-ABL1 and BCR-ABL1 use different signaling networks to drive B-cell acute lymphoblastic leukemia (2022) (1)
- splatPop: simulating population scale single-cell RNA sequencing data (2021) (1)
- Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data (2020) (1)
- Multimodal single cell analysis of the paediatric lower airway reveals novel immune cell phenotypes in early life health and disease (2022) (1)
- Co-option of the cardiac transcription factor Nkx2.5 during development of the emu wing (2017) (1)
- SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips (2012) (1)
- Disorders of sex development: insights from targeted gene sequencing of a large international patient cohort (2016) (1)
- Fast and accurate differential transcript usage by testing equivalence class counts (2018) (1)
- ASCIA-P74: AUSTRALIAN AUTOINFLAMMATORY DISEASES REGISTRY (AADRY): A NATIONAL APPROACH TO THE GENETIC AND IMMUNOLOGICAL EVALUATION OF PATIENTS WITH SUSPECTED AUTOINFLAMMATORY DISEASE (2016) (1)
- DNA Methylation Profiles of Purified Cell Types in Bronchoalveolar Lavage: Applications for Mixed Cell Paediatric Pulmonary Studies (2021) (1)
- NKX2-5 regulates human cardiomyogenesis via a HEY2 dependent transcriptional network (2018) (1)
- Genomics in 2011: challenges and opportunities (2011) (1)
- Bazam: a rapid method for read extraction and realignment of high-throughput sequencing data (2019) (1)
- Cpipe: a shared variant detection pipeline designed for diagnostic settings (2015) (1)
- RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome (2013) (1)
- Year : 2013 miRNA-Seq normalization comparisons need improvement (2017) (1)
- Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy (2013) (1)
- Benchmarking single-cell hashtag oligo demultiplexing methods (2023) (1)
- SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes (2017) (0)
- Evaluation of variability in human kidney organoids (2018) (0)
- Erratum to: ‘Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq’ (2016) (0)
- Genotyping microsatellites in next-generation sequencing data (2015) (0)
- Optimisation of Kidney Organoids as a Reproducible and Developmentally Accurate Model of Human Kidney Development and Disease (2018) (0)
- Whole exome sequencing in systemic juvenile idiopathic arthritis (2015) (0)
- Stochastic modelling of congestion control algorithms (2005) (0)
- Haploinsufficiency for SIX2 increases nephron progenitorproliferation leading to elevated branching and nephron number (2019) (0)
- MCM3AP in recessive axonal neuropathy and mild intellectual disability (2018) (0)
- High Resolution Spectroscopy of `Red' Flat-Spectrum Radio-Quasars (2008) (0)
- TALLSorts: a T-cell acute lymphoblastic leukaemia subtype classifier using RNA-seq expression data (2023) (0)
- Appendix: Further details on the background correction models and their implementation (2007) (0)
- Erratum to: SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes (2017) (0)
- Navigating the single cell analysis landscape with application to kidney organoids (2019) (0)
- Modeling human hematopoiesis in pluripotent stem cells (2017) (0)
- Toblerone: detecting exon deletion events in cancer using RNA-seq (2022) (0)
- Single-cell analysis reveals congruence between kidney organoids and human fetal kidney (2019) (0)
- Comparing algorithms to genotype short tandem repeats in next-generation sequencing data (2015) (0)
- Unusual PDGFRB fusion reveals novel mechanism of kinase activation in Ph-like B-ALL (2023) (0)
- SuperFreq: Supplementary Methods (2020) (0)
- Immunopathology HARD-BOILED (0)
- Simplifying simulation of single-cell RNA sequencing (2016) (0)
- Publisher Correction: The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAome (2019) (0)
- MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data (2021) (0)
- Visualise Clusterings at Different Resolutions [R package clustree version 0.4.3] (2020) (0)
- A multimodal cell atlas of the pediatric lower airway (2022) (0)
- 160 Identification of fusion genes through kinome-centered RNA sequencing in different types of solid tumors (2014) (0)
- Whole exome sequencing in systemic juvenile idiopathic arthritis. (2016) (0)
- Single-cell atlas of bronchoalveolar lavage from preschool cystic fibrosis reveals new cell phenotypes (2022) (0)
- Diagnostic Utility of Multimodal Genomic Profiling for Molecular Classification and MRD Assessment in Adult B-Cell Acute Lymphoblastic Leukemia (2021) (0)
- Multi-omic profiling of lung inflammation in early life cystic fibrosis (2022) (0)
- PW287 Identification of key microRNAs involved in regulation of ovine fetal heart development (2014) (0)
- A 10-step guide to party conversation for bioinformaticians (2013) (0)
- Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability (2022) (0)
- Using clustering trees to visualise single-cell RNA-sequencing data (2018) (0)
- Heart and Lung bta‐miR‐22‐3p Decrease and bta‐miR‐125a Increase in Growth‐restricted Fetal Lambs with Sustained in utero Stress (2015) (0)
- 3D organoid-derived human glomeruli for personalised podocyte disease modelling and drug screening (2018) (0)
- Women in science. (2012) (0)
- Sixty years of genome biology (2013) (0)
- RUNX1 AND GROUP F SOX GENES ARE REQUIRED AT DISTINCT STAGES FOR HUMAN HAEMATOPOIETIC DEVELOPMENT (2019) (0)
- IMMUNOBIOLOGY Genome-wide DNA methylation analysis identi fi es hypomethylated genes regulated by FOXP 3 in human regulatory T cells (2013) (0)
- Different Classes of ABL1 Fusions Activate Different Downstream Signalling Nodes (2018) (0)
- DiffVar: a new method to test for differentially variable features (2014) (0)
- Frontiers in Perinatal Mental Health – Looking to the Future (2019) (0)
- Unravelling Active Galactic Nuclei (2000) (0)
- 1 8 M ay 2 00 0 Unravelling Active Galactic Nuclei (2000) (0)
- The Nature of the Optical Emission in Radio-Selected AGN (2004) (0)
- Abstracts From the ISTS Satellite Meeting June 20, 2016, Brisbane (2016) (0)
- Jet vs Disc: the Optical Output of Flat-Spectrum Quasars (2003) (0)
- Using equivalence classes for differential transcript usage and variant detection in RNA-seq data (2020) (0)
- SuperTranscript: a reference for the visualisation and analysis of transcriptome data. (2016) (0)
- RNAseq of amniotic fluid cell-free RNA: a discovery phase study of the pathophysiology of congenital cytomegalovirus infection. (2022) (0)
- Abstracts for the 39th Human Genetics Society of Australasia Annual Scientific Meeting Perth, Western Australia: August 8–11, 2015 (2015) (0)
- Dissecting the roles of RUNX1 and SOXF transcription factors in human hematopoiesis (2017) (0)
- AB0166 Sex-Specific Gene Expression Differences in Oligoarticular Juvenile Idiopathic Arthritis (2016) (0)
- Human genome meeting 2016 (2016) (0)
- Catchii: empowering literature review screening in healthcare (2023) (0)
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What Schools Are Affiliated With Alicia Oshlack?
Alicia Oshlack is affiliated with the following schools:
