Method development

Cellular responses to silencing of PDIA3 (protein disulphide-isomerase A3): Effects on proliferation, migration, and genes in control of active vitamin D

Kermpatsou, Despoina; Olsson, Frida; Wåhlén, Erik; Söderberg, Ola et al.

Part of Journal of Steroid Biochemistry and Molecular Biology, 2024

• DOI for Cellular responses to silencing of PDIA3 (protein disulphide-isomerase A3): Effects on proliferation, migration, and genes in control of active vitamin D
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The method developer's guide to oligonucleotide design

Wenson, Leonie; Leino, Mattias; Jarvius, Malin; Heldin, Johan et al.

Part of Expert Review of Proteomics, p. 65-80, 2024

• DOI for The method developer's guide to oligonucleotide design
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Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling

Bivehed, Erik; Hellman, Björn; Wenson, Leonie; Stenerlöw, Bo et al.

Part of Nucleic Acids Research, 2024

• DOI for Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling
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Activated EGFR and PDGFR internalize in separate vesicles and downstream AKT and ERK1/2 signaling are differentially impacted by cholesterol depletion

Wåhlén, Erik; Olsson, Frida; Raykova, Doroteya; Söderberg, Ola et al.

Part of Biochemical and Biophysical Research Communications - BBRC, p. 195-201, 2023

• DOI for Activated EGFR and PDGFR internalize in separate vesicles and downstream AKT and ERK1/2 signaling are differentially impacted by cholesterol depletion
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Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs

Mihalič, Filip; Simonetti, Leandro; Giudice, Girolamo; Rubin Sander, Marie et al.

Part of Nature Communications, 2023

• DOI for Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
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Purification of DNA oligonucleotides to improve hybridization chain reaction performance

Leino, Mattias; Söderberg, Ola

Part of New Biotechnology, p. 33-40, 2023

• DOI for Purification of DNA oligonucleotides to improve hybridization chain reaction performance
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A method for Boolean analysis of protein interactions at a molecular level

Raykova, Doroteya; Kermpatsou, Despoina; Malmqvist, Tony; Harrison, Philip J et al.

Part of Nature Communications, 2022

• DOI for A method for Boolean analysis of protein interactions at a molecular level
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Differential impact of lipid raft depletion on platelet-derived growth factor (PDGF)-induced ERK1/2 MAP-kinase, SRC and AKT signaling

Wåhlén, Erik; Olsson, Frida; Söderberg, Ola; Lennartsson, Johan et al.

Part of Cellular Signalling, 2022

• DOI for Differential impact of lipid raft depletion on platelet-derived growth factor (PDGF)-induced ERK1/2 MAP-kinase, SRC and AKT signaling
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In Situ Rolling Circle Amplification Förster Resonance Energy Transfer (RCA-FRET) for Washing-Free Real-Time Single-Protein Imaging

Frances-Soriano, Laura; Leino, Mattias; Dos Santos, Marcelina Cardoso; Kovacs, Daniel et al.

Part of Analytical Chemistry, p. 1842-1850, 2021

• DOI for In Situ Rolling Circle Amplification Förster Resonance Energy Transfer (RCA-FRET) for Washing-Free Real-Time Single-Protein Imaging

Flash-comet: Significantly improved speed and sensitivity of the comet assay through the introduction of lithium-based solutions and a more gentle lysis

Bivehed, Erik; Söderberg, Ola; Hellman, Björn

Part of Mutation research. Genetic toxicology and environmental mutagenesis, 2020

• DOI for Flash-comet: Significantly improved speed and sensitivity of the comet assay through the introduction of lithium-based solutions and a more gentle lysis

Dynamin inhibitors impair platelet-derived growth factor beta-receptor dimerization and signaling

Heldin, Johan; Rubin Sander, Marie; Leino, Mattias; Thomsson, Sara et al.

Part of Experimental Cell Research, p. 69-79, 2019

• DOI for Dynamin inhibitors impair platelet-derived growth factor beta-receptor dimerization and signaling
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In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation

Wu, Chi-Chih; Klaesson, Axel; Buskas, Julia; Ranefall, Petter et al.

Part of Journal of Experimental Biology, 2019

• DOI for In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation

Optimization of proximity-dependent initiation of hybridization chain reaction for improved performance

Leino, Mattias; Heldin, Johan; Rubin Sander, Marie; Kermpatsou, Despoina et al.

Part of Molecular Systems Design & Engineering, p. 1058-1065, 2019

• DOI for Optimization of proximity-dependent initiation of hybridization chain reaction for improved performance
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Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes

Klaesson, Axel; Grannas, Karin; Ebai, Tonge; Heldin, Johan et al.

Part of Scientific Reports, 2018

• DOI for Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes
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Detection of Extracellular Vesicles Using Proximity Ligation Assay with Flow Cytometry Readout – ExoPLA: In Print

Löf, Liza; Arngården, Linda; Ebai, Tonge; Landegren, Ulf et al.

Part of Current Protocol in Cytometry, 2017

• DOI for Detection of Extracellular Vesicles Using Proximity Ligation Assay with Flow Cytometry Readout – ExoPLA: In Print

Flow Cytometric Measurement of Blood Cells with BCR-ABL1 Fusion Protein in Chronic Myeloid Leukemia

Löf, Liza; Arngården, Linda; Olsson-Strömberg, Ulla; Siart, Benjamin et al.

Part of Scientific Reports, p. 1-9, 2017

• DOI for Flow Cytometric Measurement of Blood Cells with BCR-ABL1 Fusion Protein in Chronic Myeloid Leukemia
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Insufficient antibody validation challenges oestrogen receptor beta research

Andersson, Sandra; Sundberg, Mårten; Pristovsek, Nusa; Ibrahim, Ahmed et al.

Part of Nature Communications, 2017

• DOI for Insufficient antibody validation challenges oestrogen receptor beta research
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Protein Diagnostics by Proximity Ligation: Combining Multiple Recognition and DNA Amplification for Improved Protein Analyses

Cane, Gaëlle; Leuchowius, Karl-Johan; Söderberg, Ola; Kamali-Moghaddam, Masood et al.

Part of Molecular Diagnostics (Third Edition), p. 219-231, Academia Press, 2017

Antagonists of IGF: Vitronectin Interactions Inhibit IGF-I-Induced Breast Cancer Cell Functions

Kashyap, Abhishek S.; Shooter, Gary K.; Shokoohmand, Ali; McGovern, Jacqui et al.

Part of Molecular Cancer Therapeutics, p. 1602-1613, 2016

• DOI for Antagonists of IGF: Vitronectin Interactions Inhibit IGF-I-Induced Breast Cancer Cell Functions

Clinical Relevance Of Recurrent Allele-Specific Recombination Expressing The Wnt10Bivs1 Allele Variant In Acute Myeloid Leukemia

Beghini, A.; Lazzaroni, F.; Del Giacco, L.; Söderberg, Ola et al.

Part of Haematologica, p. 668-669, 2016

Detecting individual extracellular vesicles using a multicolor in situ proximity ligation assay with flow cytometric readout

Löf, Liza; Ebai, Tonge; Dubois, Louise; Wik, Lotta et al.

Part of Scientific Reports, 2016

• DOI for Detecting individual extracellular vesicles using a multicolor in situ proximity ligation assay with flow cytometric readout
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Let There Be Light!

Raykova, Doroteya; Koos, Bjoern; Asplund, Anna; Gelleri, Marton et al.

Part of Proteomes, 2016

• DOI for Let There Be Light!
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Single Chain Antibodies as Tools to Study transforming growth factor--Regulated SMAD Proteins in Proximity Ligation-Based Pharmacological Screens

Blokzijl, Andries; Zieba, Agata; Hust, Michael; Schirrmann, Thomas et al.

Part of Molecular & Cellular Proteomics, p. 1848-1856, 2016

• DOI for Single Chain Antibodies as Tools to Study transforming growth factor--Regulated SMAD Proteins in Proximity Ligation-Based Pharmacological Screens

The protein kinase LKB1 negatively regulates bone morphogenetic protein receptor signaling

Raja, Erna; Tzavlaki, Kalliopi; Vuilleumier, Robin; Edlund, Karolina et al.

Part of Oncotarget, p. 1120-1143, 2016

• DOI for The protein kinase LKB1 negatively regulates bone morphogenetic protein receptor signaling
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Visualization of Borna Disease Virus Protein Interactions with Host Proteins using in situ Proximity Ligation Assay

Johansson Wensman, Jonas; Leuchowius, Karl-Johan; Yan, Jiting; Berg, Anna-Lena et al.

Part of British journal of virology, p. 11-23, 2016

• DOI for Visualization of Borna Disease Virus Protein Interactions with Host Proteins using in situ Proximity Ligation Assay

Closing in on life - proximity dependent methods for life sciences

Koos, Björn; Söderberg, Ola

Part of Oncotarget, p. 17867-17868, 2015

Compaction of rolling circle amplification products increases signal integrity and signal–to–noise ratio

Clausson, Carl-Magnus; Arngården, Linda; Ishaq, Omer; Klaesson, Axel et al.

Part of Scientific Reports, 2015

• DOI for Compaction of rolling circle amplification products increases signal integrity and signal–to–noise ratio

Crosstalk between Hippo and TGF beta: Subcellular Localization of YAP/TAZ/Smad Complexes

Grannas, Karin; Arngården, Linda; Lönn, Peter; Mazurkiewicz, Magdalena et al.

Part of Journal of Molecular Biology, p. 3407-3415, 2015

• DOI for Crosstalk between Hippo and TGF beta: Subcellular Localization of YAP/TAZ/Smad Complexes

Detection of glyco-mucin profiles improves specificity of MUC16 and MUC1 biomarkers in ovarian serous tumours

Ricardo, Sara; Marcos-Silva, Lara; Pereira, Daniela; Pinto, Rita et al.

Part of Molecular Oncology, p. 503-512, 2015

• DOI for Detection of glyco-mucin profiles improves specificity of MUC16 and MUC1 biomarkers in ovarian serous tumours

E-cadherin can limit the transforming properties of activating beta-catenin mutations

Huels, David J.; Ridgway, Rachel A.; Radulescu, Sorina; Leushacke, Marc et al.

Part of EMBO Journal, p. 2321-2333, 2015

• DOI for E-cadherin can limit the transforming properties of activating beta-catenin mutations

Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia

Mansouri, Larry; Sutton, Lesley-Ann; Ljungström, Viktor; Bondza, Sina et al.

Part of Journal of Experimental Medicine, p. 833-843, 2015

• DOI for Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia
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Next-Generation Pathology: Surveillance of Tumor Microecology

Koos, Björn; Kamali-Moghaddam, Masood; David, Leonor; Sobrinho-Simoes, Manuel et al.

Part of Journal of Molecular Biology, p. 2013-2022, 2015

• DOI for Next-Generation Pathology: Surveillance of Tumor Microecology

Proximity-dependent initiation of hybridization chain reaction

Koos, Björn; Cane, Gaëlle; Grannas, Karin; Löf, Liza et al.

Part of Nature Communications, 2015

• DOI for Proximity-dependent initiation of hybridization chain reaction
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Analysis of protein interactions in situ by proximity ligation assays

Koos, Björn; Andersson, Linda; Clausson, Carl-Magnus; Grannas, Karin et al.

Part of High-Dimensional Single Cell Analysis, p. 111-26, Springer, 2014

• DOI for Analysis of protein interactions in situ by proximity ligation assays

Fine-Tuning of Smad Protein Function by Poly(ADP-Ribose) Polymerases and Poly(ADP-Ribose) Glycohydrolase during Transforming Growth Factor β Signaling

Dahl, Markus; Maturi, Varun; Lönn, Peter; Papoutsoglou, Panagiotis et al.

Part of PLOS ONE, 2014

• DOI for Fine-Tuning of Smad Protein Function by Poly(ADP-Ribose) Polymerases and Poly(ADP-Ribose) Glycohydrolase during Transforming Growth Factor β Signaling
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Recurrent Mutations within the Nfkbie gene: A Novel Mechanism for NF-kappa B Deregulation in Aggressive Chronic Lymphocytic Leukemia

Mansouri, Larry; Sutton, Lesley-Ann; Ljungström, Viktor; Bondza, Sina et al.

Part of Blood, 2014

Association of the Protein-Tyrosine Phosphatase DEP-1 with Its Substrate FLT3 Visualized by In Situ Proximity Ligation Assay

Bohmer, Sylvia-Annette; Weibrecht, Irene; Söderberg, Ola; Bohmer, Frank-D.

Part of PLOS ONE, 2013

• DOI for Association of the Protein-Tyrosine Phosphatase DEP-1 with Its Substrate FLT3 Visualized by In Situ Proximity Ligation Assay
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In situ detection of individual mRNA molecules and protein complexes or post-translational modifications using padlock probes combined with the in situ proximity ligation assay

Weibrecht, Irene; Lundin, Elin; Kiflemariam, Sara; Mignardi, Marco et al.

Part of Nature Protocols, p. 355-372, 2013

• DOI for In situ detection of individual mRNA molecules and protein complexes or post-translational modifications using padlock probes combined with the in situ proximity ligation assay

Parallel Visualization of Multiple Protein Complexes in Individual Cells in Tumor Tissue

Leuchowius, Karl-Johan; Clausson, Carl-Magnus; Grannas, Karin; Erbilgin, Yücel et al.

Part of Molecular & Cellular Proteomics, p. 1563-1571, 2013

• DOI for Parallel Visualization of Multiple Protein Complexes in Individual Cells in Tumor Tissue

P-cadherin functional role is dependent on E-cadherin cellular context: a proof of concept using the breast cancer model

Ribeiro, Ana Sofia; Sousa, Bárbara; Carreto, Laura; Mendes, Nuno et al.

Part of Journal of Pathology, p. 705-718, 2013

• DOI for P-cadherin functional role is dependent on E-cadherin cellular context: a proof of concept using the breast cancer model

Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation

Gu, Gucci Jijuan; Friedman, Mikaela; Jost, Christian; Johnsson, Kai et al.

Part of New Biotechnology, p. 144-152, 2013

• DOI for Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation

Specific interactions between Smad proteins and AP-1 components determine TGFβ-induced breast cancer cell invasion

Sundqvist, Anders; Zieba, Agata; Vasilaki, Eleftheria; Herrera Hidalgo, Carmen et al.

Part of Oncogene, p. 3606-3615, 2013

• DOI for Specific interactions between Smad proteins and AP-1 components determine TGFβ-induced breast cancer cell invasion

The importance of E-cadherin binding partners to evaluate the pathogenicity of E-cadherin missense mutations associated to HDGC

Figueiredo, Joana; Söderberg, Ola; Simoes-Correia, Joana; Grannas, Karin et al.

Part of European Journal of Human Genetics, p. 301-309, 2013

• DOI for The importance of E-cadherin binding partners to evaluate the pathogenicity of E-cadherin missense mutations associated to HDGC

Functional Overlap Between Chondroitin and Heparan Sulfate Proteoglycans During VEGF-Induced Sprouting Angiogenesis

Le Jan, Sébastien; Hayashi, Makoto; Kasza, Zsolt; Eriksson, Inger et al.

Part of Arteriosclerosis, Thrombosis and Vascular Biology, p. 1255-1263, 2012

• DOI for Functional Overlap Between Chondroitin and Heparan Sulfate Proteoglycans During VEGF-Induced Sprouting Angiogenesis

Identification of new cancer biomarkers based on aberrant mucin glycoforms by in situ proximity ligation

Pinto, Rita; Carvalho, Ana S.; Conze, Tim; Magalhães, Ana et al.

Part of Journal of Cellular and Molecular Medicine, p. 1474-1484, 2012

• DOI for Identification of new cancer biomarkers based on aberrant mucin glycoforms by in situ proximity ligation

Intercellular variation in signaling through the TGF-β pathway and its relation to cell densityand cell cycle phase

Zieba, Agata; Pardali, Katerina; Söderberg, Ola; Lindbom, Lena et al.

Part of Molecular & Cellular Proteomics, 2012

• DOI for Intercellular variation in signaling through the TGF-β pathway and its relation to cell densityand cell cycle phase

Methods for analysis of the cancer microenvironment and their potential for disease prediction, monitoring and personalized treatments

Clausson, Carl-Magnus; Grundberg, Ida; Weibrecht, Irene; Nilsson, Mats et al.

Part of The EPMA journal, 2012

• DOI for Methods for analysis of the cancer microenvironment and their potential for disease prediction, monitoring and personalized treatments

Molecular tools for companion diagnostics

Zieba, Agata; Grannas, Karin; Söderberg, Ola; Gullberg, Mats et al.

Part of New Biotechnology, p. 634-640, 2012

• DOI for Molecular tools for companion diagnostics

Transcriptional profiling of human glioblastoma vessels indicates a key role of VEGF-A and TGFβ2 in vascular abnormalization

Dieterich, Lothar C.; Mellberg, Sofie; Langenkamp, Elise; Zhang, Lei et al.

Part of Journal of Pathology, p. 378-390, 2012

• DOI for Transcriptional profiling of human glioblastoma vessels indicates a key role of VEGF-A and TGFβ2 in vascular abnormalization

Visualising individual sequence-specific protein-DNA interactions in situ

Weibrecht, Irene; Gavrilovic, Milan; Lindbom, Lena; Landegren, Ulf et al.

Part of New Biotechnology, p. 589-598, 2012

• DOI for Visualising individual sequence-specific protein-DNA interactions in situ