Katarzyna Kedzierska
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View article: PULSAR: a Foundation Model for Multi-scale and Multicellular Biology
PULSAR: a Foundation Model for Multi-scale and Multicellular Biology Open
Biology emerges from interactions across physical scales, where molecular interactions drive cellular states, which in turn orchestrate multicellular tissue functions that collectively define health and disease. However, current computatio…
View article: Zero-shot evaluation reveals limitations of single-cell foundation models
Zero-shot evaluation reveals limitations of single-cell foundation models Open
Foundation models such as scGPT and Geneformer have not been rigorously evaluated in a setting where they are used without any further training (i.e., zero-shot). Understanding the performance of models in zero-shot settings is critical to…
View article: Assessing the limits of zero-shot foundation models in single-cell biology
Assessing the limits of zero-shot foundation models in single-cell biology Open
The advent and success of foundation models such as GPT has sparked growing interest in their application to single-cell biology. Models like Geneformer and scGPT have emerged with the promise of serving as versatile tools for this special…
View article: Functional analysis reveals driver cooperativity and novel mechanisms in endometrial carcinogenesis
Functional analysis reveals driver cooperativity and novel mechanisms in endometrial carcinogenesis Open
View article: Data from Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer
Data from Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer Open
Optimum risk stratification in early-stage endometrial cancer combines clinicopathologic factors and the molecular endometrial cancer classification defined by The Cancer Genome Atlas (TCGA). It is unclear whether analysis of intratumoral …
View article: Supplementary Data from Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer
Supplementary Data from Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer Open
Supplementary Tables 1-14 and Supplementary Figures 1-4
View article: Data from Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer
Data from Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer Open
Optimum risk stratification in early-stage endometrial cancer combines clinicopathologic factors and the molecular endometrial cancer classification defined by The Cancer Genome Atlas (TCGA). It is unclear whether analysis of intratumoral …
View article: Supplementary Data from Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer
Supplementary Data from Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer Open
Supplementary Tables 1-14 and Supplementary Figures 1-4
View article: Data used for demo of the code accompanying the <i>Assessing the limits of zero-shot foundation models in single-cell biology</i> paper.
Data used for demo of the code accompanying the <i>Assessing the limits of zero-shot foundation models in single-cell biology</i> paper. Open
This data consists of:the pancreas dataset described in the scIB manuscript,weights for scGPT human version of the model (version created on 23 Jun 2023, downloaded from authors GDrive), andweights for Geneformer (6 Layers version) accesse…
View article: Additional file 2 of Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift
Additional file 2 of Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift Open
Additional file 2.
View article: 2022-RA-1449-ESGO The prognostic value of serum CA125 and HE4 in endometrial cancers stratified by molecular subgroup
2022-RA-1449-ESGO The prognostic value of serum CA125 and HE4 in endometrial cancers stratified by molecular subgroup Open
View article: Discordant prognosis of mismatch repair deficiency in colorectal and endometrial cancer reflects variation in antitumour immune response and immune escape
Discordant prognosis of mismatch repair deficiency in colorectal and endometrial cancer reflects variation in antitumour immune response and immune escape Open
Defective DNA mismatch repair (dMMR) causes elevated tumour mutational burden (TMB) and microsatellite instability (MSI) in multiple cancer types. dMMR/MSI colorectal cancers (CRCs) have enhanced T‐cell infiltrate and favourable outcome; h…
View article: Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift
Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift Open
View article: Identification of Multi-Omics Cell Signatures of Early Liver Injury
Identification of Multi-Omics Cell Signatures of Early Liver Injury Open
Background Liver fibrosis is a wound-healing response to tissue injury and inflammation hallmarked by the extracellular matrix (ECM) protein deposition in the liver parenchyma and tissue remodelling. Different cell types of the liver are k…
View article: Correction to: The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
Correction to: The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability Open
View article: Additional file 2 of Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift
Additional file 2 of Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift Open
Additional file 2.
View article: The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability (vol 12, 102, 2020)
The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability (vol 12, 102, 2020) Open
View article: Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer
Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer Open
Optimum risk stratification in early-stage endometrial cancer combines clinicopathologic factors and the molecular endometrial cancer classification defined by The Cancer Genome Atlas (TCGA). It is unclear whether analysis of intratumoral …
View article: The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability Open
View article: Additional file 2 of The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
Additional file 2 of The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability Open
Additional file 2: Supplementary figure 2. Results of meta-analysis of all MSI cases versus controls (from ANECS – Illumina genotyped, ANECS – iCOGS genotyped, RENDOCAS, MCCS; MSI n = 225, controls n = 13,582) showing association statistic…
View article: Corrigendum: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
Corrigendum: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development Open
The authors would like to correct an omission in the Methods section of the above-mentioned article under the "CM collection by fluorescence-activated cell sorting (FACS)"
View article: Additional file 3 of The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability
Additional file 3 of The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability Open
Additional file 3: Supplementary figure 3. Results of meta-analysis of cases with loss of MLH1/PMS2 protein expression only versus controls (from ANECS – Illumina genotyped, ANECS – iCOGS genotyped, RENDOCAS, MCCS; MLH1 loss cases n = 157,…
View article: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development Open
Organogenesis involves dynamic regulation of gene transcription and complex multipathway interactions. Despite our knowledge of key factors regulating various steps of heart morphogenesis, considerable challenges in understanding its mecha…
View article: Dynamics of Cardiomyocyte Transcriptome and Chromatin Landscape Demarcates Key Events of Heart Development
Dynamics of Cardiomyocyte Transcriptome and Chromatin Landscape Demarcates Key Events of Heart Development Open
The development of an organ involves dynamic regulation of gene transcription and complex multipathway interactions. To better understand transcriptional regulatory mechanism driving heart development and the consequences of its disruption…
View article: Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
Genomic analysis of DNA repair genes and androgen signaling in prostate cancer Open
Our data supports the view that crosstalk between androgen signaling and DNA repair occurs at multiple levels, and that DNA repair enzymes in addition to PARPs, could be actionable targets in prostate cancer.
View article: SONiCS: PCR stutter noise correction in genome-scale microsatellites
SONiCS: PCR stutter noise correction in genome-scale microsatellites Open
Motivation Massively parallel capture of short tandem repeats (STRs, or microsatellites) provides a strategy for population genomic and demographic analyses at high resolution with or without a reference genome. However, the high Polymeras…
View article: Additional file 9: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
Additional file 9: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer Open
Table S7. DNA damage response genes associated with androgen treatment in prostate cancer cell lines determined by WGCNA. (XLSX 9 kb)
View article: Additional file 1: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
Additional file 1: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer Open
Table S1. DNA damage response gene variants in prostate cancer cell lines. (XLSX 16 kb)
View article: Additional file 5: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
Additional file 5: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer Open
Table S4. DNA damage response genes differentially regulated by androgen associated with Fig. 5a. (XLSX 10 kb)
View article: Additional file 8: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
Additional file 8: of Genomic analysis of DNA repair genes and androgen signaling in prostate cancer Open
Table S6. Top 10 WikiPathways for the gene sets from Modules I, II, XIV, and XV determined by Enrichr. (XLSX 11 kb)