Immunology, Genetics and Pathology, IGP

IGP Research Cancer Precision Medicine Cecilia Lindskog Bergström Publications Publications in Diva Lindskog

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Publications in DiVA – Cecilia Lindskog Bergström

Inhibiting the glycerophosphodiesterase EDI3 in ER-HER2+breast cancer cells resistant to HER2-targeted therapy reduces viability and tumour growth

Keller, Magdalena; Rohlf, Katharina; Glotzbach, Annika; Leonhardt, Gregor et al.

Part of Journal of Experimental & Clinical Cancer Research, 2023.

DOI for Inhibiting the glycerophosphodiesterase EDI3 in ER-HER2+breast cancer cells resistant to HER2-targeted therapy reduces viability and tumour growth Download full text (pdf) of Inhibiting the glycerophosphodiesterase EDI3 in ER-HER2+breast cancer cells resistant to HER2-targeted therapy reduces viability and tumour growth

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The human protein atlas-Integrated omics for single cell mapping of the human proteome

Digre, Andreas; Lindskog, Cecilia

Part of Protein Science, 2023.

DOI for The human protein atlas-Integrated omics for single cell mapping of the human proteome Download full text (pdf) of The human protein atlas-Integrated omics for single cell mapping of the human proteome

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A human adipose tissue cell-type transcriptome atlas

Norreen-Thorsen, Marthe; Struck, Eike Christopher; Oling, Sofia; Zwahlen, Martin et al.

Part of Cell reports, 2022.

DOI for A human adipose tissue cell-type transcriptome atlas Download full text (pdf) of A human adipose tissue cell-type transcriptome atlas

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A human adipose tissue cell-type transcriptome atlas

Norreen-Thorsen, Marthe; Struck, Eike Christopher; Öling, Sofia; Zwahlen, Martin et al.

Part of Cell reports, p. 111046-111046, 2022.

DOI for A human adipose tissue cell-type transcriptome atlas
AGPAT1 as a Novel Colonic Biomarker for Discriminating Between Ulcerative Colitis With and Without Primary Sclerosing Cholangitis

Vessby, Johan; Wisniewski, Jacek R.; Lindskog, Cecilia; Eriksson, Niclas et al.

Part of Clinical and Translational Gastroenterology, 2022.

DOI for AGPAT1 as a Novel Colonic Biomarker for Discriminating Between Ulcerative Colitis With and Without Primary Sclerosing Cholangitis
Antibody Validation for Estrogen Receptor Beta

Birgersson, Madeleine; Katona, Borbala; Lindskog, Cecilia; Pontén, Fredrik et al.

Part of Methods in Molecular Biology, p. 1-23, 2022.

DOI for Antibody Validation for Estrogen Receptor Beta
Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

Wang, Fei; Ding, Peiwen; Liang, Xue; Ding, Xiangning et al.

Part of Nature Communications, 2022.

DOI for Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level
Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level (vol 13, 3620, 2022)

Wang, Fei; Ding, Peiwen; Liang, Xue; Ding, Xiangning et al.

Part of Nature Communications, 2022.

DOI for Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level (vol 13, 3620, 2022) Download full text (pdf) of Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level (vol 13, 3620, 2022)

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Author Correction: Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

Garcia-Alonso, Luz; Handfield, Louis-François; Roberts, Kenny; Nikolakopoulou, Konstantina et al.

Part of Nature Genetics, 2022.

DOI for Author Correction: Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

Mahdessian, Diana; Cesnik, Anthony J.; Gnann, Christian; Danielsson, Frida et al.

Part of Nature, p. E32-E32, 2022.

DOI for Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

Wang, Fei; Ding, Peiwen; Liang, Xue; Ding, Xiangning et al.

Part of Nature Communications, 2022.

DOI for Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level Download full text (pdf) of Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

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Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction

Olsson, Henrik; Kartasalo, Kimmo; Mulliqi, Nita; Capuccini, Marco et al.

Part of Nature Communications, 2022.

DOI for Estimating diagnostic uncertainty in artificial intelligence assisted pathology using conformal prediction
Genome-wide annotation of protein-coding genes in pig

Karlsson, Max; Sjöstedt, Evelina; Oksvold, Per; Sivertsson, Asa et al.

Part of BMC Biology, 2022.

DOI for Genome-wide annotation of protein-coding genes in pig Download full text (pdf) of Genome-wide annotation of protein-coding genes in pig

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Genomic Multiple Sclerosis Risk Variants Modulate the Expression of the ANKRD55-IL6ST Gene Region in Immature Dendritic Cells

Mena, Jorge; Alloza, Iraide; Tulloch Navarro, Raquel; Aldekoa, Ane et al.

Part of Frontiers in Immunology, 2022.

DOI for Genomic Multiple Sclerosis Risk Variants Modulate the Expression of the ANKRD55-IL6ST Gene Region in Immature Dendritic Cells Download full text (pdf) of Genomic Multiple Sclerosis Risk Variants Modulate the Expression of the ANKRD55-IL6ST Gene Region in Immature Dendritic Cells

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Outcome in PCNSL patients and its association with PD-L1+leukocytes in the tumor microenvironment

Abdulla, Maysaa; Hollander, Peter; Lindskog, Cecilia; Sundström, Christer et al.

Part of Acta Oncologica, p. 824-829, 2022.

DOI for Outcome in PCNSL patients and its association with PD-L1+leukocytes in the tumor microenvironment
Protein Expression Profile of ACE2 in the Normal and COVID-19-Affected Human Brain.

Lindskog, Cecilia; Méar, Loren; Virhammar, Johan; Fällmar, David et al.

Part of Journal of Proteome Research, p. 2137-2145, 2022.

DOI for Protein Expression Profile of ACE2 in the Normal and COVID-19-Affected Human Brain. Download full text (pdf) of Protein Expression Profile of ACE2 in the Normal and COVID-19-Affected Human Brain.

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Spatial Proteomics for Further Exploration of Missing Proteins: A Case Study of the Ovary

Méar, Loren; Sutantiwanichkul, Thanadol; Östman, Josephine; Damdimopoulou, Pauliina et al.

Part of Journal of Proteome Research, 2022.

DOI for Spatial Proteomics for Further Exploration of Missing Proteins: A Case Study of the Ovary
Stemness and clinical features in relation to the subventricular zone in diffuse lower-grade glioma: an exploratory study

Corell, Alba; Vecchio, Tomas Gomez; Vega, Sandra Ferreyra; Denes, Anna et al.

Part of NEURO-ONCOLOGY ADVANCES, 2022.

DOI for Stemness and clinical features in relation to the subventricular zone in diffuse lower-grade glioma: an exploratory study Download full text (pdf) of Stemness and clinical features in relation to the subventricular zone in diffuse lower-grade glioma: an exploratory study

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The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Omenn, Gilbert S.; Lane, Lydie; Overall, Christopher M.; Pineau, Charles et al.

Part of Journal of Proteome Research, 2022.

DOI for The 2022 Report on the Human Proteome from the HUPO Human Proteome Project
A Diffusion-like Process Accommodates New Crypts During Clonal Expansion in Human Colonic Epithelium

Olpe, Cora; Khamis, Doran; Chukanova, Maria; Skoufou-Papoutsaki, Nefeli et al.

Part of Gastroenterology, p. 548-559, 2021.

DOI for A Diffusion-like Process Accommodates New Crypts During Clonal Expansion in Human Colonic Epithelium Download full text (pdf) of A Diffusion-like Process Accommodates New Crypts During Clonal Expansion in Human Colonic Epithelium

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A Diffusion-like Process Accommodates New Crypts During Clonal Expansion in Human Colonic Epithelium

Olpe, Cora; Khamis, Doran; Chukanova, Maria; Skoufou-Papoutsaki, Nefeli et al.

Part of Gastroenterology, p. 548-559.e23, 2021.

DOI for A Diffusion-like Process Accommodates New Crypts During Clonal Expansion in Human Colonic Epithelium
A single-cell type transcriptomics map of human tissues

Karlsson, Max; Zhang, Cheng; Méar, Loren; Zhong, Wen et al.

Part of Science Advances, 2021.

DOI for A single-cell type transcriptomics map of human tissues Download full text (pdf) of A single-cell type transcriptomics map of human tissues

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Combined RNA/tissue profiling identifies novel Cancer/testis genes

Jamin, Soazik P.; Hikmet, Feria; Mathieu, Romain; Jégou, Bernard et al.

Part of Molecular Oncology, p. 3003-3023, 2021.

DOI for Combined RNA/tissue profiling identifies novel Cancer/testis genes Download full text (pdf) of Combined RNA/tissue profiling identifies novel Cancer/testis genes

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DeepHistoClass: A Novel Strategy for Confident Classification of Immunohistochemistry Images Using Deep Learning

Ghoshal, Biraja; Hikmet Noraddin, Feria; Pineau, Charles; Tucker, Allan et al.

Part of Molecular & Cellular Proteomics, p. 100140-100140, 2021.

DOI for DeepHistoClass: A Novel Strategy for Confident Classification of Immunohistochemistry Images Using Deep Learning
Infiltration of NK and plasma cells is associated with a distinct immune subset in non‐small cell lung cancer

Backman, Max; La Fleur, Linnea; Kurppa, Pinja; Djureinovic, Dijana et al.

Part of Journal of Pathology, p. 243-256, 2021.

DOI for Infiltration of NK and plasma cells is associated with a distinct immune subset in non‐small cell lung cancer Download full text (pdf) of Infiltration of NK and plasma cells is associated with a distinct immune subset in non‐small cell lung cancer

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Interobserver reproducibility of perineural invasion of prostatic adenocarcinoma in needle biopsies

Egevad, Lars; Delahunt, Brett; Samaratunga, Hemamali; Tsuzuki, Toyonori et al.

Part of Virchows Archiv, p. 1109-1116, 2021.

DOI for Interobserver reproducibility of perineural invasion of prostatic adenocarcinoma in needle biopsies Download full text (pdf) of Interobserver reproducibility of perineural invasion of prostatic adenocarcinoma in needle biopsies

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Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

Garcia-Alonso, Luz; Handfield, Louis-Francois; Roberts, Kenny; Nikolakopoulou, Konstantina et al.

Part of Nature Genetics, p. 1698-, 2021.

DOI for Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro Download full text (pdf) of Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

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Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

Garcia-Alonso, Luz; Handfield, Louis-François; Roberts, Kenny; Nikolakopoulou, Konstantina et al.

Part of Nature Genetics, p. 1698-1711, 2021.

DOI for Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro
Mechanistic insights into COVID-19 by global analysis of the SARS-CoV-2 3CL(pro) substrate degradome

Pablos, Isabel; Machado, Yoan; de Jesus, Hugo C. Ramos; Mohamud, Yasir et al.

Part of Cell reports, 2021.

DOI for Mechanistic insights into COVID-19 by global analysis of the SARS-CoV-2 3CL(pro) substrate degradome Download full text (pdf) of Mechanistic insights into COVID-19 by global analysis of the SARS-CoV-2 3CL(pro) substrate degradome

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PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS

Abdulla, Maysaa; Alexsson, Andrei; Sundström, Christer; Ladenvall, Claes et al.

Part of Acta Oncologica, p. 531-538, 2021.

DOI for PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS Download full text (pdf) of PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS

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Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

Omenn, Gilbert S.; Lane, Lydie; Overall, Christopher M.; Paik, Young-Ki et al.

Part of Journal of Proteome Research, p. 5227-5240, 2021.

DOI for Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

Mahdessian, Diana; Cesnik, Anthony J.; Gnann, Christian; Danielsson, Frida et al.

Part of Nature, p. 649-654, 2021.

DOI for Spatiotemporal dissection of the cell cycle with single-cell proteogenomics
The Human Protein Atlas - Spatial localization of the human proteome in health and disease

Digre, Andreas; Lindskog, Cecilia

Part of Protein Science, p. 218-233, 2021.

DOI for The Human Protein Atlas - Spatial localization of the human proteome in health and disease
The Human Protein Atlas and Antibody-Based Tissue Profiling in Clinical Proteomics

Katona, Borbala; Lindskog, Cecilia

Part of Methods in Molecular Biology, p. 191-206, 2021.

DOI for The Human Protein Atlas and Antibody-Based Tissue Profiling in Clinical Proteomics
The prognostic impact of the tumour stroma fraction: A machine learning-based analysis in 16 human solid tumour types

Micke, Patrick; Strell, Carina; Mattsson, Johanna Sofia Margareta; Martin-Bernabe, Alfonso et al.

Part of EBioMedicine, 2021.

DOI for The prognostic impact of the tumour stroma fraction: A machine learning-based analysis in 16 human solid tumour types Download full text (pdf) of The prognostic impact of the tumour stroma fraction: A machine learning-based analysis in 16 human solid tumour types

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The prognostic impact of the tumour stroma fraction: A machine learning-based analysis in 16 human solid tumour types

Micke, Patrick; Strell, Carina; Mattsson, Johanna; Martín-Bernabé, Alfonso et al.

Part of EBioMedicine, p. 103269-103269, 2021.

DOI for The prognostic impact of the tumour stroma fraction: A machine learning-based analysis in 16 human solid tumour types
A high-stringency blueprint of the human proteome

Adhikari, Subash; Nice, Edouard C.; Deutsch, Eric W.; Lane, Lydie et al.

Part of Nature Communications, 2020.

DOI for A high-stringency blueprint of the human proteome Download full text (pdf) of A high-stringency blueprint of the human proteome

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An atlas of the protein-coding genes in the human, pig, and mouse brain

Sjostedt, Evelina; Zhong, Wen; Fagerberg, Linn; Karlsson, Max et al.

Part of Science, p. 1090-+, 2020.

DOI for An atlas of the protein-coding genes in the human, pig, and mouse brain
Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study

Strom, Peter; Kartasalo, Kimmo; Olsson, Henrik; Solorzano, Leslie et al.

Part of The Lancet Oncology, p. 222-232, 2020.

DOI for Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study
ASCL1 promotes tumor progression through cell-autonomous signaling and immune modulation in a subset of lung adenocarcinoma

Miyashita, Naoya; Horie, Masafumi; Mikami, Yu; Urushiyama, Hirokazu et al.

Part of Cancer Letters, p. 121-132, 2020.

DOI for ASCL1 promotes tumor progression through cell-autonomous signaling and immune modulation in a subset of lung adenocarcinoma
Candidate protein biomarkers in pancreatic neuroendocrine neoplasms grade 3

Ali, Abir Salwa; Perren, Aurel; Lindskog, Cecilia; Welin, Staffan et al.

Part of Scientific Reports, 2020.

DOI for Candidate protein biomarkers in pancreatic neuroendocrine neoplasms grade 3 Download full text (pdf) of Candidate protein biomarkers in pancreatic neuroendocrine neoplasms grade 3

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Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins

Sivertsson, Åsa; Lindström, Emil; Oksvold, Per; Katona, Borbala et al.

Part of Journal of Proteome Research, p. 4766-4781, 2020.

DOI for Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins Download full text (pdf) of Enhanced Validation of Antibodies Enables the Discovery of Missing Proteins

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Estimating Uncertainty in Deep Learning for Reporting Confidence: An Application on Cell Type Prediction in Testes Based on Proteomics

Ghoshal, Biraja; Lindskog, Cecilia; Tucker, Allan

Part of Lecture Notes in Computer Science, p. 223-234, 2020.

DOI for Estimating Uncertainty in Deep Learning for Reporting Confidence: An Application on Cell Type Prediction in Testes Based on Proteomics
Marginal zone lymphoma expression of histidine-rich glycoprotein correlates with improved survival

Persson Skare, Tor; Sjöberg, Elin; Berglund, Mattias; Smith, Ross O. et al.

Part of eJHaem, p. 199-207, 2020.

DOI for Marginal zone lymphoma expression of histidine-rich glycoprotein correlates with improved survival

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Perivascular Neuropilin-1 expression is an independent marker of improved survival in renal cell carcinoma

Morin, Eric; Lindskog, Cecilia; Johansson, Martin; Egevad, Lars et al.

Part of Journal of Pathology, p. 387-396, 2020.

DOI for Perivascular Neuropilin-1 expression is an independent marker of improved survival in renal cell carcinoma Download full text (pdf) of Perivascular Neuropilin-1 expression is an independent marker of improved survival in renal cell carcinoma

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Proximity Ligation Assay as a Tool for Antibody Validation in Human Tissues

Lindskog, Cecilia; Backman, Max; Zieba, Agata; Asplund, Anna et al.

Part of Journal of Histochemistry and Cytochemistry, p. 515-529, 2020.

DOI for Proximity Ligation Assay as a Tool for Antibody Validation in Human Tissues
Research on the Human Proteome Reaches a Major Milestone: > 90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project

Omenn, Gilbert S.; Lane, Lydie; Overall, Christopher M.; Cristea, Ileana M. et al.

Part of Journal of Proteome Research, p. 4735-4746, 2020.

DOI for Research on the Human Proteome Reaches a Major Milestone: > 90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project
Somatostatin receptor expression and mTOR pathway activation in glioneuronal tumours of childhood

Ehrstedt, Christoffer; Ahlsten, Gunnar; Strömberg, Bo; Lindskog, Cecilia et al.

Part of Seizure, p. 123-130, 2020.

DOI for Somatostatin receptor expression and mTOR pathway activation in glioneuronal tumours of childhood
Systematic analysis reveals a functional role for STAMBPL1 in the epithelial-mesenchymal transition process across multiple carcinomas

Ambroise, Gorbatchev; Yu, Ting-ting; Zhang, Boxi; Kacal, Merve et al.

Part of British Journal of Cancer, p. 1164-1177, 2020.

DOI for Systematic analysis reveals a functional role for STAMBPL1 in the epithelial-mesenchymal transition process across multiple carcinomas
TGFBR3L-An Uncharacterised Pituitary Specific Membrane Protein Detected in the Gonadotroph Cells in Non-Neoplastic and Tumour Tissue.

Sjöstedt, Evelina; Kolnes, Anders J; Olarescu, Nicoleta C; Mitsios, Nicholas et al.

Part of Cancers, 2020.

DOI for TGFBR3L-An Uncharacterised Pituitary Specific Membrane Protein Detected in the Gonadotroph Cells in Non-Neoplastic and Tumour Tissue.

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