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Alexander Kel

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Bioinformatics, systems biology, personalized medicine.TRANSFAC database. Search for TF binding sites and analysis of promoters and enhancers. Search for master regulators in signal transduction networks.

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York University

Sheffield Hallam University

Sheila Macrine, Ph.D.

University of Massachusetts, Dartmouth

University College Copenhagen

Rajamangala University of Technology Thanyaburi

Indera Syahrul Mat Radzuan

Universiti Tun Hussein Onn Malaysia

Landmark University

Babcock University

Irini Dermitzaki

UNIVERSITY OF THESSALY, GREECE

Mauricio Archila Neira

Universidad Nacional de Colombia (National University of Colombia)

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Papers by Alexander Kel

Comparative analysis of deeply phenotyped GBM cohorts of ‘short-term’ and ‘long-term’ survivors

Glioblastoma (GBM) is an aggressive brain cancer that typically results in death in the first 15 ... more Glioblastoma (GBM) is an aggressive brain cancer that typically results in death in the first 15 months after diagnosis. There have been limited advances in finding new treatments for GBM. In this study, we investigated molecular differences between patients with extremely short (≤9 months, Short term survivors, STS) and long survival (≥36 months, Long term survivors, LTS). Patients were selected from an in-house cohort (GLIOTRAIN-cohort), using defined inclusion criteria (Karnofsky score >70; age <70 years old; Stupp protocol as first line treatment, IDH wild type), and a multi-omic analysis of LTS and STS GBM samples was performed. Transcriptomic analysis of tumour samples identified cilium gene signatures enriched in LTSs. Immunohistochemical analysis confirmed the presence of cilia in the tumours of LTSs. Notably, reverse phase protein array analysis (RPPA) demonstrated increased phosphorylated GAB1 (Y627), SRC (Y527), BCL2 (S70) and RAF (S338) protein expression in STS co...

Epigenome-Wide Changes in the Cell Layers of the Vein Wall When Exposing the Venous Endothelium to Oscillatory Shear Stress

Epigenomes, Mar 20, 2023

Supplementary Table 2 from Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-Cell Acute Lymphoblastic Leukemia by Remote 3′-BCL11B Enhancers and Coregulation by PU.1 and HMGA1

Supplementary Table 2 from Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-Cell Acute Lymphob... more

Supplementary Table 1 from Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-Cell Acute Lymphoblastic Leukemia by Remote 3′-BCL11B Enhancers and Coregulation by PU.1 and HMGA1

Supplementary Table 1 from Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-Cell Acute Lymphob... more

DOP80 Multi-omic sequencing reveals distinctive gene expression and DNA methylation alterations as potential predictors of primary sclerosing cholangitis development in treatment-naïve paediatric ulcerative colitis

Journal of Crohn's and Colitis

Background Primary sclerosing cholangitis (PSC) is a progressive choleostatic disease and up to 8... more Background Primary sclerosing cholangitis (PSC) is a progressive choleostatic disease and up to 80% of patients also have ulcerative colitis (PSC-UC). This presents a clinical challenge owing to difficulty in diagnosis and increased risk for developing cancer. While several multifactorial processes including inflammation and microbial dysbiosis have been associated with PSC-UC pathogenesis, the precise molecular factors that regulate the phenotype of this disease subtype remain unknown. Methods Here, we applied methyl-capture sequencing and mRNA sequencing to colonic mucosal biopsies to identify transcriptomic and epigenetic alterations differentiating UC from PSC-UC. Samples were taken from 3 groups of treatment-naïve children at diagnosis who participated in the DOCHAS study (GEN-193/11) - UC (n=10), PSC-UC (n=10) and healthy controls(n=10). Results Differential gene expression between UC and PSC-UC identified disease-associated genes that were either up- or down-regulated in UC o...

Prediction of EVT6-NTRK3-dependent papillary thyroid cancer using expression profile of ten key genes

Bulletin of Experimental Biology and Medicine, 2022

Systemic Changes of Gene Expression in Venous Tissue Leading to Varicose Vein Disease Could Be Potentially Treated by Targeting PSMA7 and DUSP9 Genes’ Activity

Journal of Vascular Surgery: Venous and Lymphatic Disorders, 2022

Additional file 4: of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

Table S9. List of 71 genes encoding TFs linked to PWMs that were found overrepresented in the gen... more Table S9. List of 71 genes encoding TFs linked to PWMs that were found overrepresented in the genomic regions around CpGs whose methylation was negatively of positively correlated with gene expression. These TF genes were identified independently by three independent algorithms: by classical CMA analysis (of NEG and POS sets versus control), by CMAcorrel as well as by F-Match of enriched single PWMs. (XLSX 76â kb)

Additional file 6: Table S5. of Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3

List of 62 genes up-regulated in Nutlin-3 insensitive cell lines and matching the disease categor... more

Significance of miR-146a quantification in human blood plasma for the diagnosis of colorectal cancer

Bulletin of Russian State Medical University, 2017

Оценка значимости определения количества miR-146a в плазме крови человека для диагностики колоректального рака

Cyclonet - a database on cell cycle regulation ?

Cyclonet is a database on cell cycle regulation in eukaryotes. It con tains information about spe... more Cyclonet is a database on cell cycle regulation in eukaryotes. It con tains information about specific genes, proteins ant their complexes, models of cell cycle regulation and results of their analysis, microarray data, literature references and other related resources. Using Cyclonet database we are demonstrating that BioUML and BeanExplorer Enterprise Edition technologies can be used for formal description, visualisation and simulation of complex biological systems. BioUML workbench is used to query and edit the database content as well as for visual modelling. BeanExplorer Enterprise Edition provides web interface for access to Cyclonet database.

Увеличение экспрессии цитокинов, сопровождающее старение фибробластов человека in vitro

P003 Identification of a novel therapeutic agent for treating Crohn’s disease guided by systems medicine

Journal of Crohn's and Colitis, Jan 16, 2018

OTU-001 Identification of a novel therapeutic agent for treating IBD guided by systems medicine

IBD, 2018

Towards a European health research and innovation cloud (HRIC)

Genome Medicine, 2020

The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) ai... more The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action p...

One-click personalized medicine: automatic identification of a therapeutic target by patient’s DNA and RNA

Laboratory and production, 2019

Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data

EuPA Open Proteomics, 2016

Deep insights into the response of human cervical carcinoma cells to a new cyano enone-bearing triterpenoid soloxolone methyl: a transcriptome analysis

Oncotarget, 2019

BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes

Computational Biology and Chemistry, 2018

Comparative analysis of deeply phenotyped GBM cohorts of ‘short-term’ and ‘long-term’ survivors

Glioblastoma (GBM) is an aggressive brain cancer that typically results in death in the first 15 ... more Glioblastoma (GBM) is an aggressive brain cancer that typically results in death in the first 15 months after diagnosis. There have been limited advances in finding new treatments for GBM. In this study, we investigated molecular differences between patients with extremely short (≤9 months, Short term survivors, STS) and long survival (≥36 months, Long term survivors, LTS). Patients were selected from an in-house cohort (GLIOTRAIN-cohort), using defined inclusion criteria (Karnofsky score >70; age <70 years old; Stupp protocol as first line treatment, IDH wild type), and a multi-omic analysis of LTS and STS GBM samples was performed. Transcriptomic analysis of tumour samples identified cilium gene signatures enriched in LTSs. Immunohistochemical analysis confirmed the presence of cilia in the tumours of LTSs. Notably, reverse phase protein array analysis (RPPA) demonstrated increased phosphorylated GAB1 (Y627), SRC (Y527), BCL2 (S70) and RAF (S338) protein expression in STS co...

Epigenome-Wide Changes in the Cell Layers of the Vein Wall When Exposing the Venous Endothelium to Oscillatory Shear Stress

Epigenomes, Mar 20, 2023

Supplementary Table 2 from Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-Cell Acute Lymphoblastic Leukemia by Remote 3′-BCL11B Enhancers and Coregulation by PU.1 and HMGA1

Supplementary Table 2 from Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-Cell Acute Lymphob... more

Supplementary Table 1 from Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-Cell Acute Lymphoblastic Leukemia by Remote 3′-BCL11B Enhancers and Coregulation by PU.1 and HMGA1

Supplementary Table 1 from Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-Cell Acute Lymphob... more

DOP80 Multi-omic sequencing reveals distinctive gene expression and DNA methylation alterations as potential predictors of primary sclerosing cholangitis development in treatment-naïve paediatric ulcerative colitis

Journal of Crohn's and Colitis

Background Primary sclerosing cholangitis (PSC) is a progressive choleostatic disease and up to 8... more Background Primary sclerosing cholangitis (PSC) is a progressive choleostatic disease and up to 80% of patients also have ulcerative colitis (PSC-UC). This presents a clinical challenge owing to difficulty in diagnosis and increased risk for developing cancer. While several multifactorial processes including inflammation and microbial dysbiosis have been associated with PSC-UC pathogenesis, the precise molecular factors that regulate the phenotype of this disease subtype remain unknown. Methods Here, we applied methyl-capture sequencing and mRNA sequencing to colonic mucosal biopsies to identify transcriptomic and epigenetic alterations differentiating UC from PSC-UC. Samples were taken from 3 groups of treatment-naïve children at diagnosis who participated in the DOCHAS study (GEN-193/11) - UC (n=10), PSC-UC (n=10) and healthy controls(n=10). Results Differential gene expression between UC and PSC-UC identified disease-associated genes that were either up- or down-regulated in UC o...

Prediction of EVT6-NTRK3-dependent papillary thyroid cancer using expression profile of ten key genes

Bulletin of Experimental Biology and Medicine, 2022

Systemic Changes of Gene Expression in Venous Tissue Leading to Varicose Vein Disease Could Be Potentially Treated by Targeting PSMA7 and DUSP9 Genes’ Activity

Journal of Vascular Surgery: Venous and Lymphatic Disorders, 2022

Additional file 4: of Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer

Table S9. List of 71 genes encoding TFs linked to PWMs that were found overrepresented in the gen... more Table S9. List of 71 genes encoding TFs linked to PWMs that were found overrepresented in the genomic regions around CpGs whose methylation was negatively of positively correlated with gene expression. These TF genes were identified independently by three independent algorithms: by classical CMA analysis (of NEG and POS sets versus control), by CMAcorrel as well as by F-Match of enriched single PWMs. (XLSX 76â kb)

Additional file 6: Table S5. of Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3

List of 62 genes up-regulated in Nutlin-3 insensitive cell lines and matching the disease categor... more

Significance of miR-146a quantification in human blood plasma for the diagnosis of colorectal cancer

Bulletin of Russian State Medical University, 2017

Оценка значимости определения количества miR-146a в плазме крови человека для диагностики колоректального рака

Cyclonet - a database on cell cycle regulation ?

Cyclonet is a database on cell cycle regulation in eukaryotes. It con tains information about spe... more Cyclonet is a database on cell cycle regulation in eukaryotes. It con tains information about specific genes, proteins ant their complexes, models of cell cycle regulation and results of their analysis, microarray data, literature references and other related resources. Using Cyclonet database we are demonstrating that BioUML and BeanExplorer Enterprise Edition technologies can be used for formal description, visualisation and simulation of complex biological systems. BioUML workbench is used to query and edit the database content as well as for visual modelling. BeanExplorer Enterprise Edition provides web interface for access to Cyclonet database.

Увеличение экспрессии цитокинов, сопровождающее старение фибробластов человека in vitro

P003 Identification of a novel therapeutic agent for treating Crohn’s disease guided by systems medicine

Journal of Crohn's and Colitis, Jan 16, 2018

OTU-001 Identification of a novel therapeutic agent for treating IBD guided by systems medicine

IBD, 2018

Towards a European health research and innovation cloud (HRIC)

Genome Medicine, 2020

The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) ai... more The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action p...

One-click personalized medicine: automatic identification of a therapeutic target by patient’s DNA and RNA

Laboratory and production, 2019

Prediction of protein-DNA interactions of transcription factors linking proteomics and transcriptomics data

EuPA Open Proteomics, 2016

Deep insights into the response of human cervical carcinoma cells to a new cyano enone-bearing triterpenoid soloxolone methyl: a transcriptome analysis

Oncotarget, 2019

BRCA-analyzer: Automatic workflow for processing NGS reads of BRCA1 and BRCA2 genes

Computational Biology and Chemistry, 2018