[HTML][HTML] A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers

…, G MacGrogan, L Arnould, J Kielbassa… - Nature …, 2016 - nature.com
HER2-positive breast cancer has long proven to be a clinically distinct class of breast
cancers for which several targeted therapies are now available. However, resistance to the …

[HTML][HTML] Comprehensive characterization of claudin-low breast tumors reflects the impact of the cell-of-origin on cancer evolution

RM Pommier, A Sanlaville, L Tonon, J Kielbassa… - Nature …, 2020 - nature.com
Claudin-low breast cancers are aggressive tumors defined by the low expression of key
components of cellular junctions, associated with mesenchymal and stemness features. …

IFN-III is selectively produced by cDC1 and predicts good clinical outcome in breast cancer

…, J Berthet, C Rodriguez, V Ollion, J Kielbassa… - Science …, 2020 - science.org
Dendritic cells play a key role in the orchestration of antitumor immune responses. The
cDC1 (conventional dendritic cell 1) subset has been shown to be essential for antitumor …

[HTML][HTML] KIS SPLICE: de-novo calling alternative splicing events from RNA-seq data

GAT Sacomoto, J Kielbassa, R Chikhi, R Uricaru… - BMC …, 2012 - Springer
Background In this paper, we address the problem of identifying and quantifying polymorphisms
in RNA-seq data when no reference genome is available, without assembling the full …

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

…, L Brinza, C Marchet, J Kielbassa… - Nucleic Acids …, 2016 - academic.oup.com
… of allele i on the expression, β j the contribution of condition j to the total expression, and (αβ) …
In this setting, Y ijk denotes the counts of a sample k with allele i in condition j. We assume …

Ribosomal RNA 2′ O-methylation as a novel layer of inter-tumour heterogeneity in breast cancer

V Marcel, J Kielbassa, V Marchand, KS Natchiar… - NAR …, 2020 - academic.oup.com
Recent epitranscriptomics studies unravelled that ribosomal RNA (rRNA) 2′O-methylation
is an additional layer of gene expression regulation highlighting the ribosome as a novel …

[HTML][HTML] Comparative roadmaps of reprogramming and oncogenic transformation identify Bcl11b and Atoh8 as broad regulators of cellular plasticity

…, J Wang, Y Yu, N Rama, B Gibert, J Kielbassa… - Nature Cell …, 2022 - nature.com
Coordinated changes of cellular plasticity and identity are critical for pluripotent reprogramming
and oncogenic transformation. However, the sequences of events that orchestrate these …

Repurposing rotavirus vaccines for intratumoral immunotherapy can overcome resistance to immune checkpoint blockade

…, E Sivado, AC Jallas, S Depil, J Kielbassa… - Science translational …, 2019 - science.org
… A/J mice were implanted with Neuro2a tumor cells in the flank and received IT treatment
when tumors reached 0.7 to 1 cm in largest diameter, usually around day 7 after tumor …

Mutational profile of aggressive, localised prostate cancer from African Caribbean men versus European ancestry men

…, E Thomas, A Ferrari, AS Sertier, J Kielbassa… - European Urology, 2019 - Elsevier
Causes of high mortality of prostate cancer in men of African ancestry living in the French
West Indies are still debated, between suspicions of environmental factors and genetic …

[HTML][HTML] A 13-gene expression-based radioresistance score highlights the heterogeneity in the response to radiation therapy across HPV-negative HNSCC molecular …

…, L Bazire, S Ortiz-Cuaran, S Deneuve, J Kielbassa… - BMC medicine, 2017 - Springer
Background Radiotherapy for head and neck squamous cell carcinomas (HNSCC) is
associated with a substantial morbidity and inconsistent efficacy. Human papillomavirus (HPV)-…