List of works - Nicolai Juul Birkbak

A breast cancer meta-analysis of two expression measures of chromosomal instability reveals a relationship with younger age at diagnosis and high risk histopathological variables

scientific article published on July 2011

A clonal expression biomarker associates with lung cancer mortality

scientific article published on 07 October 2019

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution

scientific article published on 21 October 2017

An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer

scientific article published on 16 April 2021

Artificial intelligence in cancer imaging: Clinical challenges and applications

scholarly article by Wenya Linda Bi et al published 1 March 2019 in CA

Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials

scientific article

Assessment of pharmacogenomic agreement

scientific article

BCL9L Dysfunction Impairs Caspase-2 Expression Permitting Aneuploidy Tolerance in Colorectal Cancer

scientific article

CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid-specific cancer cell death through autophagy induction

scientific article published on 19 October 2011

Characterization of in vitro chlamydial cultures in low-oxygen atmospheres

scientific article published on 13 July 2007

Chromosomal instability confers intrinsic multidrug resistance.

scientific article

Chromosomal instability drives metastasis through a cytosolic DNA response

scientific article published on 17 January 2018

Circulating tumor DNA analyses reveal novel resistance mechanisms to CDK inhibition in metastatic breast cancer

scientific article published on 17 January 2018

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

scientific article published on 03 March 2016

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution

scientific article

Computational optimisation of targeted DNA sequencing for cancer detection.

scientific article published on 3 December 2013

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response

scientific article

Constraints in cancer evolution

scientific article published on February 2017

Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

scientific article published in Nature

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

scientific article published on 11 April 2018

Early stage NSCLC - challenges to implementing ctDNA-based screening and MRD detection

scientific article published on 01 September 2018

Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer

scientific article

Enhancing reproducibility in cancer drug screening: how do we move forward?

scientific article

Evolution and clinical impact of co-occurring genetic alterations in advanced-stage EGFR-mutant lung cancers.

scientific article published on 6 November 2017

Evolutionary Precision Medicine: A Role for Repeat Epidermal Growth Factor Receptor Analysis in ALK-Rearranged Lung Adenocarcinoma?

scientific article

Expression of regulators of mitotic fidelity are associated with intercellular heterogeneity and chromosomal instability in primary breast cancer

scientific article published on 7 October 2014

Extreme chromosomal instability forecasts improved outcome in ER-negative breast cancer: a prospective validation cohort study from the TACT trial

scientific article published on 23 May 2015

Genomic instability in mutant p53 cancer cells upon entotic engulfment

scientific article published in Nature Communications

Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome

scientific article published on 2 March 2015

HELQ promotes RAD51 paralogue-dependent repair to avert germ cell loss and tumorigenesis

scientific article published on 04 September 2013

Heterogeneity Among Liver Cancer—A Hurdle to Optimizing Therapy

scientific article published on 26 February 2016

Inconsistency in large pharmacogenomic studies

scientific article

Increased Soluble PD-1 Predicts Response to Nivolumab plus Ipilimumab in Melanoma

scientific article published in 2022

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis

scientific article published on 07 July 2017

Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution

scientific article published on 05 March 2020

Intratumoural evolutionary landscape of high-risk prostate cancer: the PROGENY study of genomic and immune parameters

scientific article published in October 2017

Jetset: selecting the optimal microarray probe set to represent a gene

scientific article

MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy

scientific article published on 6 November 2015

Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer.

scientific article

Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status

scientific article

Neoantigen-directed immune escape in lung cancer evolution

scientific article published on 20 March 2019

Oncogenic PIK3CA induces centrosome amplification and tolerance to genome doubling.

scientific article

Overexpression of BLM promotes DNA damage and increased sensitivity to platinum salts in triple negative breast and serous ovarian cancers

scientific article published on 14 February 2018

Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs

scientific article

Paradoxical relationship between chromosomal instability and survival outcome in cancer

scientific article

Parallel evolution of tumour subclones mimics diversity between tumours

scientific article published in August 2013

Pervasive chromosomal instability and karyotype order in tumour evolution

scientific article published on 02 September 2020

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

scientific article

Predicting Response to Cancer Immunotherapy using Non-invasive Radiomic Biomarkers

scientific article published on 01 June 2019

Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome

scientific article

Proteolytic cleavage of the Chlamydia pneumoniae major outer membrane protein in the absence of Pmp10.

scientific article published on December 2007

Publisher Correction: A clonal expression biomarker associates with lung cancer mortality

scientific article published on 03 June 2020

Publisher Correction: Genomic instability in mutant p53 cancer cells upon entotic engulfment

scientific article published in Nature Communications

Publisher Correction: Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

scientific article published on 03 June 2020

Quantification of within-sample genetic heterogeneity from SNP-array data.

scientific article

Relationship of extreme chromosomal instability with long-term survival in a retrospective analysis of primary breast cancer

scientific article

Revisiting inconsistency in large pharmacogenomic studies

scientific article published on 16 September 2016

SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair

scientific article

STAT3 induction of miR-146b forms a feedback loop to inhibit the NF-κB to IL-6 signaling axis and STAT3-driven cancer phenotypes

scientific article

Safikhani et al. reply

scientific article

Safikhani et al. reply

scientific article published in Nature

Safikhani et al. reply

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.

scientific article

Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

scientific article published on 07 October 2019

Systematic evaluation of the prognostic impact and intratumour heterogeneity of clear cell renal cell carcinoma biomarkers

scientific article published on 19 July 2014

Targeting chromosomal instability and tumour heterogeneity in HER2-positive breast cancer

scientific article

Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents

scientific article published on 22 March 2012

Tracking genomic cancer evolution for precision medicine: the lung TRACERx study

scientific article

Tracking the Evolution of Non-Small-Cell Lung Cancer

scientific article published on 26 April 2017

Tracking the genomic evolution of esophageal adenocarcinoma through neoadjuvant chemotherapy

scientific article published on 23 May 2015

Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations

scientific article

TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

scientific article (publication date: October 2015)

List of works by Nicolai Juul Birkbak

A breast cancer meta-analysis of two expression measures of chromosomal instability reveals a relationship with younger age at diagnosis and high risk histopathological variables

A clonal expression biomarker associates with lung cancer mortality

Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution

An integrated multi-omics analysis identifies prognostic molecular subtypes of non-muscle-invasive bladder cancer

Artificial intelligence in cancer imaging: Clinical challenges and applications

Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials

Assessment of pharmacogenomic agreement

BCL9L Dysfunction Impairs Caspase-2 Expression Permitting Aneuploidy Tolerance in Colorectal Cancer

CERT depletion predicts chemotherapy benefit and mediates cytotoxic and polyploid-specific cancer cell death through autophagy induction

Characterization of in vitro chlamydial cultures in low-oxygen atmospheres

Chromosomal instability confers intrinsic multidrug resistance.

Chromosomal instability drives metastasis through a cytosolic DNA response

Circulating tumor DNA analyses reveal novel resistance mechanisms to CDK inhibition in metastatic breast cancer

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution

Computational optimisation of targeted DNA sequencing for cancer detection.

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response

Constraints in cancer evolution

Corrigendum: Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

Early stage NSCLC - challenges to implementing ctDNA-based screening and MRD detection

Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer

Enhancing reproducibility in cancer drug screening: how do we move forward?

Evolution and clinical impact of co-occurring genetic alterations in advanced-stage EGFR-mutant lung cancers.

Evolutionary Precision Medicine: A Role for Repeat Epidermal Growth Factor Receptor Analysis in ALK-Rearranged Lung Adenocarcinoma?

Expression of regulators of mitotic fidelity are associated with intercellular heterogeneity and chromosomal instability in primary breast cancer

Extreme chromosomal instability forecasts improved outcome in ER-negative breast cancer: a prospective validation cohort study from the TACT trial

Genomic instability in mutant p53 cancer cells upon entotic engulfment

Glioblastoma adaptation traced through decline of an IDH1 clonal driver and macro-evolution of a double-minute chromosome

HELQ promotes RAD51 paralogue-dependent repair to avert germ cell loss and tumorigenesis

Heterogeneity Among Liver Cancer—A Hurdle to Optimizing Therapy

Inconsistency in large pharmacogenomic studies

Increased Soluble PD-1 Predicts Response to Nivolumab plus Ipilimumab in Melanoma

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis

Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution

Intratumoural evolutionary landscape of high-risk prostate cancer: the PROGENY study of genomic and immune parameters

Jetset: selecting the optimal microarray probe set to represent a gene

MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy

Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer.

Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status

Neoantigen-directed immune escape in lung cancer evolution

Oncogenic PIK3CA induces centrosome amplification and tolerance to genome doubling.

Overexpression of BLM promotes DNA damage and increased sensitivity to platinum salts in triple negative breast and serous ovarian cancers

Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs

Paradoxical relationship between chromosomal instability and survival outcome in cancer

Parallel evolution of tumour subclones mimics diversity between tumours

Pervasive chromosomal instability and karyotype order in tumour evolution

Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution

Predicting Response to Cancer Immunotherapy using Non-invasive Radiomic Biomarkers

Profiles of genomic instability in high-grade serous ovarian cancer predict treatment outcome

Proteolytic cleavage of the Chlamydia pneumoniae major outer membrane protein in the absence of Pmp10.

Publisher Correction: A clonal expression biomarker associates with lung cancer mortality

Publisher Correction: Genomic instability in mutant p53 cancer cells upon entotic engulfment

Publisher Correction: Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

Quantification of within-sample genetic heterogeneity from SNP-array data.

Relationship of extreme chromosomal instability with long-term survival in a retrospective analysis of primary breast cancer

Revisiting inconsistency in large pharmacogenomic studies

SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair

STAT3 induction of miR-146b forms a feedback loop to inhibit the NF-κB to IL-6 signaling axis and STAT3-driven cancer phenotypes

Safikhani et al. reply

Safikhani et al. reply

Safikhani et al. reply

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.

Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer

Systematic evaluation of the prognostic impact and intratumour heterogeneity of clear cell renal cell carcinoma biomarkers

Targeting chromosomal instability and tumour heterogeneity in HER2-positive breast cancer

Telomeric allelic imbalance indicates defective DNA repair and sensitivity to DNA-damaging agents

Tracking genomic cancer evolution for precision medicine: the lung TRACERx study

Tracking the Evolution of Non-Small-Cell Lung Cancer

Tracking the genomic evolution of esophageal adenocarcinoma through neoadjuvant chemotherapy

Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations

TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

Whole Genome Doubling mitigates Muller's Ratchet in Cancer Evolution: Supplementary figures