Drugs predicted by computational ligand docking to bind COVID19 proteins from Wu et al 2020, Kandeel et al 2020, Joshi et al 2020, Adem et al 2020 articles
Knowledge graph applications for cosmetics industryAnton Yuryev
This document summarizes three use cases for Elsevier's deep reading AI and biology knowledge graph. The first use case identifies UV-absorbing compounds for skin care by annotating over 684,000 compounds with relevant cell processes and diseases. The second use case identifies compounds that can modulate estrogen production by analyzing relevant metabolic pathways and regulation networks. The third use case performs transcriptomics analysis of androgenic alopecia to build a regulatory network model and identify new drug targets using differential expression analysis and sub-network enrichment.
Five drug development strategies to combat SARS-CoV2Anton Yuryev
Slides were presented at webinar on “Opportunities & Challenges in Drug Discovery and Development” organised by Elsevier in collaboration with Dr Reddy’s Institute of Life Sciences, Hyderabad on July 16th,2020
Genetic variations linked to Acute Respiratory Distress syndromeAnton Yuryev
The list of rs Identifiers linked by to ARDS in peer-reviewed scientific literature. This list can help determine individuals at risk to develop severe symptoms from COVID19 infection
AAK1 GAK inhibitors for anti-COVID19 therapyAnton Yuryev
BenevolentAI has reported three AAK1 and GAK kinase inhibitors effective against #coronavirus #COVID19. I publish the list of 35 approved drugs and lead compounds that can inhibit AAK1 and GAK kinases and therefore can be effective against #COVID19. Drugs were found in #Elsevier #PathwayStudio and #Reaxys knowledgebases. To find more drugs that can be effective against #COVID19 please visit #Elsevier Coronavirus Information Center or read my blog about atrategies to find more drugs for #coronavirus
Drug re-positioning for tuberculosis infection in HIV/ADS patients Anton Yuryev
Tuberculosis infection is #1 cause of death among HIV patients in the developing countries. Drugs must not only inhibit tuberculosis but also inhibit HIV infection. Sophisticated searches in #Elsevier #PathwayStudio knowledge graph revealed that several FDA approved drugs have appropriate therapeutic profile.
Patient microbiome analysis using Elsevier text miningAnton Yuryev
This presentation demonstrates how to use Elsevier Text Mining to analyze a patient's microbiome profile from Aperiomics and interpret the results. Multiple Search is used to identify bacterial species from the patient's throat and stool that have been linked to her lung and bowel problems in medical literature. Species linked to her conditions include Streptococcus pneumoniae, Streptococcus pyogenes, Haemophilus parainfluenzae, and Fusobacterium nucleatum in her throat and Bacteroides vulgatus in her stool. Multiple Search also identifies protective species in her stool like Bifidobacterium longum and Faecalibacterium prausnitzii. Antibiotics and probiotics are then suggested
The document analyzes the tumor transcriptomics profile of a patient with stage IV gallbladder cancer. It identifies the top 200 most significantly activated expression regulators in the patient's tumor using sub-network enrichment analysis software. Key regulators identified include histone deacetylases and DNA methyltransferases. The analysis suggests treatment with the HDAC inhibitor vorinostat and discusses how activated regulators like HDACs, PDCD1, and CTLA4 may be contributing to tumor proliferation and immune evasion. Graphical summaries show pathways enriched with active regulators in the tumor related to cancer hallmarks like histone modification and immune response evasion.
OMICs data analysis using Pathway StudioAnton Yuryev
This document provides summaries of 32 publications from 2018-2019 that used Pathway Studio software for OMICs data analysis. The publications covered a wide range of topics including Alzheimer's disease, stress response genes in Drosophila, gene expression following radiotherapy exposure, miRNA and mRNA profiling in horse satellite cells, and proteome changes in plant somatic embryogenesis. Figures from each publication are also presented.
Knowledge graph applications for cosmetics industryAnton Yuryev
This document summarizes three use cases for Elsevier's deep reading AI and biology knowledge graph. The first use case identifies UV-absorbing compounds for skin care by annotating over 684,000 compounds with relevant cell processes and diseases. The second use case identifies compounds that can modulate estrogen production by analyzing relevant metabolic pathways and regulation networks. The third use case performs transcriptomics analysis of androgenic alopecia to build a regulatory network model and identify new drug targets using differential expression analysis and sub-network enrichment.
Five drug development strategies to combat SARS-CoV2Anton Yuryev
Slides were presented at webinar on “Opportunities & Challenges in Drug Discovery and Development” organised by Elsevier in collaboration with Dr Reddy’s Institute of Life Sciences, Hyderabad on July 16th,2020
Genetic variations linked to Acute Respiratory Distress syndromeAnton Yuryev
The list of rs Identifiers linked by to ARDS in peer-reviewed scientific literature. This list can help determine individuals at risk to develop severe symptoms from COVID19 infection
AAK1 GAK inhibitors for anti-COVID19 therapyAnton Yuryev
BenevolentAI has reported three AAK1 and GAK kinase inhibitors effective against #coronavirus #COVID19. I publish the list of 35 approved drugs and lead compounds that can inhibit AAK1 and GAK kinases and therefore can be effective against #COVID19. Drugs were found in #Elsevier #PathwayStudio and #Reaxys knowledgebases. To find more drugs that can be effective against #COVID19 please visit #Elsevier Coronavirus Information Center or read my blog about atrategies to find more drugs for #coronavirus
Drug re-positioning for tuberculosis infection in HIV/ADS patients Anton Yuryev
Tuberculosis infection is #1 cause of death among HIV patients in the developing countries. Drugs must not only inhibit tuberculosis but also inhibit HIV infection. Sophisticated searches in #Elsevier #PathwayStudio knowledge graph revealed that several FDA approved drugs have appropriate therapeutic profile.
Patient microbiome analysis using Elsevier text miningAnton Yuryev
This presentation demonstrates how to use Elsevier Text Mining to analyze a patient's microbiome profile from Aperiomics and interpret the results. Multiple Search is used to identify bacterial species from the patient's throat and stool that have been linked to her lung and bowel problems in medical literature. Species linked to her conditions include Streptococcus pneumoniae, Streptococcus pyogenes, Haemophilus parainfluenzae, and Fusobacterium nucleatum in her throat and Bacteroides vulgatus in her stool. Multiple Search also identifies protective species in her stool like Bifidobacterium longum and Faecalibacterium prausnitzii. Antibiotics and probiotics are then suggested
The document analyzes the tumor transcriptomics profile of a patient with stage IV gallbladder cancer. It identifies the top 200 most significantly activated expression regulators in the patient's tumor using sub-network enrichment analysis software. Key regulators identified include histone deacetylases and DNA methyltransferases. The analysis suggests treatment with the HDAC inhibitor vorinostat and discusses how activated regulators like HDACs, PDCD1, and CTLA4 may be contributing to tumor proliferation and immune evasion. Graphical summaries show pathways enriched with active regulators in the tumor related to cancer hallmarks like histone modification and immune response evasion.
OMICs data analysis using Pathway StudioAnton Yuryev
This document provides summaries of 32 publications from 2018-2019 that used Pathway Studio software for OMICs data analysis. The publications covered a wide range of topics including Alzheimer's disease, stress response genes in Drosophila, gene expression following radiotherapy exposure, miRNA and mRNA profiling in horse satellite cells, and proteome changes in plant somatic embryogenesis. Figures from each publication are also presented.
Analysis of gene expression microarray data of patients with Spinal Muscular ...Anton Yuryev
This document compares two approaches for identifying potential gene expression regulators from experimental data: Sub-Network Enrichment Analysis (SNEA) in Pathway Studio and Causal Reasoning in Ingenuity Pathway Analysis (IPA). It analyzes a publicly available dataset on Spinal Muscular Atrophy. SNEA identified biological functions and expression regulators more specifically related to neurogenesis, the key process affected in SMA. It produced results with greater relevance to the disease compared to IPA. Mapping genes to a motor neuron differentiation model also showed SNEA results were more consistent with SMN1 knockout.
Analysis of Functional Magnetic Resonance Imaging (fMRI) data from human brai...Anton Yuryev
The presentation from National Institute of Mental Health shows how to use Pathway Studio data for analysis of fMRI from schizophrenia patients. It finds novel proteins that can be used as biomarkers or drug targets for schizophrenia.
Elsevier helps malaria research with comprehensive Plasmodium biology databaseAnton Yuryev
Elsevier professional services constructed the most comprehensive knowledgebase for network and pathway analysis of Plasmodium genome using deep reading NLP technology from thousands scientific publications about Plasmodium parasite. The database allows pathway reconstruction by data-mining human-parasite protein interactions, network enrichment analysis of OMICs data-sets, search for compounds modulating human immune response to parasite or inhibiting Plasmodium proteins. This slide presentation shows some of key features and statistics for this database.
Personalized Medicine: Matching cancer drugs with mechanism (AAPS webinar)Anton Yuryev
Anton Yuryev describes how to identify optimal molecular targets and drugs for personalized cancer treatment using network and pathway analysis of transcriptomics profiles from tumor biopsies. The approach involves determining the most active targets using network analysis, finding cancer hallmark pathways enriched with these targets, and identifying FDA-approved drugs targeting the most active hallmarks. Sub-Network Enrichment Analysis is used to calculate regulator activity from downstream targets in patient profiles. Pathway Studio contains cancer pathway models built from literature to map patient profiles and find druggable targets. The approach is validated for stage IV cancer patients and aims to optimize treatment by targeting multiple identified regulators with drug combinations.
Presentation at Rare Disease conference in San-AntonioAnton Yuryev
Elsevier has significantly reduced the cost of drug development for rare diseases through drug repurposing. They have brought together knowledge about drug targets, effects, and disease biology to identify drugs and nutraceuticals approved by the FDA that could potentially be repositioned to treat rare diseases, eliminating the need for new drug development and clinical trials. Using automated queries of Elsevier knowledgebases, they can provide summaries of potential treatments for a given rare disease, including key researchers and institutions, relevant drug targets, and approved drugs that may be effective - reducing the cost of repositioning existing drugs to under $500,000.
Profiling how Immune inhibitors Secreted by Melanoma affect NK & other immune...Anton Yuryev
The document summarizes how Elsevier's solutions can help identify novel immunotherapy targets for melanoma by integrating data from multiple sources. It describes using natural language processing to extract information on immune mechanisms from over 20,000 articles, identifying 226 proteins secreted by melanoma that inhibit immune activation and 142 that activate immune tolerance. This approach found many potential immunotherapy targets, including examples of novel targets and opportunities for drug repurposing. Integrating these insights could help create models for combinatorial treatments and better match patients to treatments.
Profiling how Immune inhibitors Secreted by Melanoma affect NK & other immune...Anton Yuryev
The document summarizes how Elsevier's solutions can help identify novel immunotherapy targets for melanoma by integrating data from multiple sources. It describes using natural language processing to extract information on immune mechanisms from over 20,000 articles, identifying 226 proteins secreted by melanoma that inhibit immune activation and 142 that activate immune tolerance. This approach found many potential immunotherapy targets, including examples of novel targets and opportunities for drug repurposing. Integrating these insights could help create models for combinatorial treatments and better match patients to treatments.
This document summarizes a presentation by Timothy Hoctor, VP of Professional Services at Elsevier, about Elsevier's strategic vision and professional services. The key points are:
1) Elsevier aims to increase R&D productivity by linking data across the development spectrum and increase return on information through enhanced search and visualization tools.
2) Elsevier's Professional Services team leverages Elsevier's capabilities to provide customized data management and analysis solutions.
3) Elsevier's strategic objective is to become a leading collaborator in R&D data management through services like data mapping, gap analysis, data governance, and integrated data management.
Pathway analysis for personalized oncologyAnton Yuryev
1) The document discusses using pathway analysis and pathway activity signatures to enable more personalized cancer treatment. It outlines calculating major expression regulators from patient omics data and mapping them to cancer pathways to determine activated pathways.
2) Calculating pathway activity signatures which are short allows better patient classification compared to single targets. Pathway activity also allows selection of drugs that inhibit the active pathway.
3) An example shows a patient's tumor signaling pathway was identified and treatment with drugs targeting the pathway led to no cancer metastasis. The approach aims to continue validating with more medical collaborators.
Construction of cancer pathways for personalized medicineAnton Yuryev
This document discusses constructing cancer pathways for personalized medicine using sub-network enrichment analysis (SNEA). SNEA calculates the transcriptional activity of upstream regulators using differentially expressed genes and regulatory knowledgebases. This identifies key expression regulators in specific cancer patients. Mapping these regulators onto known pathways builds personalized cancer pathways for each patient. Analyzing pathways from multiple patients provides insights into common cancer biology and identifies potential drug targets in a personalized manner.
Analysis of gene expression microarray data of patients with Spinal Muscular ...Anton Yuryev
This document compares two approaches for identifying potential gene expression regulators from experimental data: Sub-Network Enrichment Analysis (SNEA) in Pathway Studio and Causal Reasoning in Ingenuity Pathway Analysis (IPA). It analyzes a publicly available dataset on Spinal Muscular Atrophy. SNEA identified biological functions and expression regulators more specifically related to neurogenesis, the key process affected in SMA. It produced results with greater relevance to the disease compared to IPA. Mapping genes to a motor neuron differentiation model also showed SNEA results were more consistent with SMN1 knockout.
Analysis of Functional Magnetic Resonance Imaging (fMRI) data from human brai...Anton Yuryev
The presentation from National Institute of Mental Health shows how to use Pathway Studio data for analysis of fMRI from schizophrenia patients. It finds novel proteins that can be used as biomarkers or drug targets for schizophrenia.
Elsevier helps malaria research with comprehensive Plasmodium biology databaseAnton Yuryev
Elsevier professional services constructed the most comprehensive knowledgebase for network and pathway analysis of Plasmodium genome using deep reading NLP technology from thousands scientific publications about Plasmodium parasite. The database allows pathway reconstruction by data-mining human-parasite protein interactions, network enrichment analysis of OMICs data-sets, search for compounds modulating human immune response to parasite or inhibiting Plasmodium proteins. This slide presentation shows some of key features and statistics for this database.
Personalized Medicine: Matching cancer drugs with mechanism (AAPS webinar)Anton Yuryev
Anton Yuryev describes how to identify optimal molecular targets and drugs for personalized cancer treatment using network and pathway analysis of transcriptomics profiles from tumor biopsies. The approach involves determining the most active targets using network analysis, finding cancer hallmark pathways enriched with these targets, and identifying FDA-approved drugs targeting the most active hallmarks. Sub-Network Enrichment Analysis is used to calculate regulator activity from downstream targets in patient profiles. Pathway Studio contains cancer pathway models built from literature to map patient profiles and find druggable targets. The approach is validated for stage IV cancer patients and aims to optimize treatment by targeting multiple identified regulators with drug combinations.
Presentation at Rare Disease conference in San-AntonioAnton Yuryev
Elsevier has significantly reduced the cost of drug development for rare diseases through drug repurposing. They have brought together knowledge about drug targets, effects, and disease biology to identify drugs and nutraceuticals approved by the FDA that could potentially be repositioned to treat rare diseases, eliminating the need for new drug development and clinical trials. Using automated queries of Elsevier knowledgebases, they can provide summaries of potential treatments for a given rare disease, including key researchers and institutions, relevant drug targets, and approved drugs that may be effective - reducing the cost of repositioning existing drugs to under $500,000.
Profiling how Immune inhibitors Secreted by Melanoma affect NK & other immune...Anton Yuryev
The document summarizes how Elsevier's solutions can help identify novel immunotherapy targets for melanoma by integrating data from multiple sources. It describes using natural language processing to extract information on immune mechanisms from over 20,000 articles, identifying 226 proteins secreted by melanoma that inhibit immune activation and 142 that activate immune tolerance. This approach found many potential immunotherapy targets, including examples of novel targets and opportunities for drug repurposing. Integrating these insights could help create models for combinatorial treatments and better match patients to treatments.
Profiling how Immune inhibitors Secreted by Melanoma affect NK & other immune...Anton Yuryev
The document summarizes how Elsevier's solutions can help identify novel immunotherapy targets for melanoma by integrating data from multiple sources. It describes using natural language processing to extract information on immune mechanisms from over 20,000 articles, identifying 226 proteins secreted by melanoma that inhibit immune activation and 142 that activate immune tolerance. This approach found many potential immunotherapy targets, including examples of novel targets and opportunities for drug repurposing. Integrating these insights could help create models for combinatorial treatments and better match patients to treatments.
This document summarizes a presentation by Timothy Hoctor, VP of Professional Services at Elsevier, about Elsevier's strategic vision and professional services. The key points are:
1) Elsevier aims to increase R&D productivity by linking data across the development spectrum and increase return on information through enhanced search and visualization tools.
2) Elsevier's Professional Services team leverages Elsevier's capabilities to provide customized data management and analysis solutions.
3) Elsevier's strategic objective is to become a leading collaborator in R&D data management through services like data mapping, gap analysis, data governance, and integrated data management.
Pathway analysis for personalized oncologyAnton Yuryev
1) The document discusses using pathway analysis and pathway activity signatures to enable more personalized cancer treatment. It outlines calculating major expression regulators from patient omics data and mapping them to cancer pathways to determine activated pathways.
2) Calculating pathway activity signatures which are short allows better patient classification compared to single targets. Pathway activity also allows selection of drugs that inhibit the active pathway.
3) An example shows a patient's tumor signaling pathway was identified and treatment with drugs targeting the pathway led to no cancer metastasis. The approach aims to continue validating with more medical collaborators.
Construction of cancer pathways for personalized medicineAnton Yuryev
This document discusses constructing cancer pathways for personalized medicine using sub-network enrichment analysis (SNEA). SNEA calculates the transcriptional activity of upstream regulators using differentially expressed genes and regulatory knowledgebases. This identifies key expression regulators in specific cancer patients. Mapping these regulators onto known pathways builds personalized cancer pathways for each patient. Analyzing pathways from multiple patients provides insights into common cancer biology and identifies potential drug targets in a personalized manner.