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Reactome diagram viewer: data structures and strategies to boost performance

Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Pablo Marin-Garcia, Peipei Ping, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob, Janet Kelso
2017 Bioinformatics  
Through the use of highly optimized data structures and algorithms, Reactome has boosted the performance and usability of the new pathway diagram viewer, providing a robust, scalable and easy-to-integrate  ...  Results: The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s.  ...  Results and discussion The new pathway diagram viewer combines the set of strategies and data structures described above to improve performance and to include new features that aim to address the shortcomings  ... 
doi:10.1093/bioinformatics/btx752 pmid:29186351 pmcid:PMC6030826 fatcat:j4wrfd3v7fcwjb2ykhitis3apa

Bioinformatics: A Way Forward to Explore "Plant Omics" [chapter]

Mehboob-ur Rahman, Tayyaba Shaheen, Mahmood-ur Rahman, Muhammad Atif Iqbal, Yusuf Zafar
2016 Bioinformatics - Updated Features and Applications  
Second, the huge genomic data can be assembled to acquire maximum information from a voluminous "omics" data.  ...  In addition, the rapid expansion of sequencing data restricts the potential of acquisitioning, storing, distributing, and analyzing the genomic information.  ...  To find out similar sequences from databases, BLAST variations according to sequence retrieval could be performed.  ... 
doi:10.5772/64043 fatcat:w3cwexdezvf27e5adz3gfos4v4

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

R. Burke Squires, Jyothi Noronha, Victoria Hunt, Adolfo García-Sastre, Catherine Macken, Nicole Baumgarth, David Suarez, Brett E. Pickett, Yun Zhang, Christopher N. Larsen, Alvin Ramsey, Liwei Zhou (+5 others)
2012 Influenza and Other Respiratory Viruses  
Results To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented.  ...  transmission, and to facilitate development of vaccines, diagnostics, and therapeutics.  ...  Acknowledgements First and foremost, we would like to acknowledge the contribution of all providers of data to public database resources like GenBank and IRD.  ... 
doi:10.1111/j.1750-2659.2011.00331.x pmid:22260278 pmcid:PMC3345175 fatcat:wdhncwqhtbehxiqbplxkwk3ry4

Characterization and evolutionary origin of novel C2H2 zinc finger protein (ZNF648) required for both erythroid and megakaryocyte differentiation in humans

Daniel C. J. Ferguson, Juraidah Haji Mokim, Marjolein Meinders, Edmund R. R. Moody, Tom A. Williams, Sarah Cooke, Kongtana Trakarnsanga, Deborah E. Daniels, Ivan Ferrer-Vicens, Deborah Shoemark, Chartsiam Tipgomut, Katherine A. Macinnes (+3 others)
2020 Haematologica  
Its nuclear localisation and structure indicate it is likely a DNA-binding protein.  ...  Using a combination of ZNF648 overexpression in an iPSC line and primary adult erythroid cells, ZNF648 knockdown in primary adult erythroid cells and megakaryocytes, comparative proteomics and transcriptomics  ...  Acknowledgements The authors would like to thank Dr Kate Heesom, Director of the Bristol University Proteomic Facility, UK for performing Mass Spectrometry, the University of Bristol Genomics Facility,  ... 
doi:10.3324/haematol.2020.256347 pmid:33054117 pmcid:PMC8561289 fatcat:efxgycqkgjhghcjv2gdf2gul7a

Next-Generation Bioinformatics Approaches and Resources for Coronavirus Vaccine Discovery and Development—A Perspective Review

Rahul Chatterjee, Mrinmoy Ghosh, Susrita Sahoo, Santwana Padhi, Namrata Misra, Visakha Raina, Mrutyunjay Suar, Young-Ok Son
2021 Vaccines  
As genome sequencing projects for several coronavirus strains have been completed, a detailed investigation of the functions of the proteins and their 3D structures has gained increasing attention.  ...  To fight this pandemic, which has caused a massive death toll around the globe, researchers are putting efforts into developing an effective vaccine against the pathogen.  ...  Acknowledgments: We would like to acknowledge Krishn Kumar Verma for his support of the scientific visualization; and the School of Biotechnology, Kalinga Institute of Industrial Technology, and KIIT Technology  ... 
doi:10.3390/vaccines9080812 pmid:34451937 pmcid:PMC8402397 fatcat:urw75khyavfqrozw4kwaryvwo4

Deeper insights into long-term survival heterogeneity of Pancreatic Ductal Adenocarcinoma (PDAC) patients using integrative individual- and group-level transcriptome network analyses [article]

Archana Bhardwaj, Claire Josse, Daniel Van Daele, Christophe Poulet, Marcela Chavez, Ingrid Struman, Kristel Van Steen
2020 bioRxiv   pre-print
Data (NetICS) to integrate group-based and individual-specific perturbed genes in relation to PDAC LT survival.  ...  Method: Using a discovery cohort of 19 PDAC patients from CHU-Liege (Belgium), we first performed differential gene expression (DGE) analysis comparing LT to ST survivor.  ...  This will boost cancer prognosis and treatment in the context of personalized medicine.  ... 
doi:10.1101/2020.06.01.116194 fatcat:at46sigm3vh4naqy2qinsbmo3i

Visualizing the drug target landscape

Stephen J. Campbell, Anna Gaulton, Jason Marshall, Dmitri Bichko, Sid Martin, Cory Brouwer, Lee Harland
2010 Drug Discovery Today  
A retrospective on how the application of data integration and visualisation has been used to connect disparate information sources into a drug-discovery focused, decision making environment.  ...  Acknowledgements The authors acknowledge the guidance of Enoch Huang and substantial input from Robert Hernandez, Markella Skempri, Dave  ...  strategies [3] .  ... 
doi:10.1016/j.drudis.2009.09.011 pmid:19840866 fatcat:csd4hsaokjgbjjbq4azwdnf24q

Visualizing the drug target landscape

Stephen J. Campbell, Anna Gaulton, Jason Marshall, Dmitri Bichko, Sid Martin, Cory Brouwer, Lee Harland
2012 Drug Discovery Today  
A retrospective on how the application of data integration and visualisation has been used to connect disparate information sources into a drug-discovery focused, decision making environment.  ...  Acknowledgements The authors acknowledge the guidance of Enoch Huang and substantial input from Robert Hernandez, Markella Skempri, Dave  ...  In addition, collaboration and discussion between companies might enable industry to speak with a common voice on key issues and could boost initiatives such as the adoption of data standards.  ... 
doi:10.1016/j.drudis.2011.12.005 pmid:22178891 fatcat:qvdkemacwbaibb42sb4om6dxke

EMBnet.journal 18 Suppl. B

EMBnet Journal
2012 EMBnet journal  
Acknowledgements The authors are partially supported by the FLAGSHIP "InterOmics" project (PB.P05) funded by the Italian MIUR and CNR institutions, and by the cooperative programme 2010-2012 between the  ...  Carlo Bernasconi and the Collegio Ghislieri in Pavia for their active support.  ...  short oral CommuniCations EMBnet.journal 18.B set of highly related SNPs and genes to a new query disease to boost further research.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q

XVII Congress of the Italian Society of Experimental Hematology, Roma, Italy, March 31 – April 1-2, 2022

The Editors
2022 Haematologica  
Data analysis was carried out referring to available databases (UCSC, NCBI, Data of Genomic Variants, Biocarta, KEGG, Reactome).  ...  STAT5B amplicon sequencing was performed through the Illumina platform and results were analyzed with Integrative Genome Viewer (IGV).  ...  PCR for NPM1, WT1 expression and GeneScan PCR for FLT3-ITD mutations were performed according to the national and international guidelines.  ... 
doi:10.3324/haematol.2022.s1 fatcat:s55yahndtzaq5avyg2bgofh4ze

COMPUTATIONAL METHODS TO STUDY KNOWN AND NOVEL PROTEIN POST-TRANSLATIONAL MODIFICATIONS BY MASS SPECTROMETRY

ENRICO MASSIGNANI
2021
Here, we apply computational methods to MS data, in order to study PTMs from two points of view. In one project, we conducted a comprehensive analysis of Arginine (R) methylation at a global level.  ...  Since all PTMs introduce a change in the proteins mass, one of the leading techniques to study PTMs is Tandem Mass Spectrometry (MS/MS), which can measure the mass of molecules with high precision and  ...  Functional enrichment analysis was performed using the "gprofiler2" R package [114] ; Gene Ontology terms, Reactome [115] and KEGG pathways, and CORUM complexes were used as data sources; only the most  ... 
doi:10.13130/massignani-enrico_phd2021-12-13 fatcat:h66fg7dixzfx5ky63ul5l52dvq

Multiomic characterization of the effects of G-quadruplex binders on R-loop homeostasis and innate immune response in human cancer cells

Marco Russo
2020
Here, through bioinformatic analysis of genomic R-loop maps and the development of a specific tool to better annotate R-loop regions to gene, we propose that stabilization of G4 structures with specific  ...  ligands leads to accumulation of DNA damage and genome instability in cancer cells and that this process is mediated by R-loop stabilization.  ...  Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, https://www.ncbi.nlm.nih.gov/geo (accession no. GSE115957). ACKNOWLEDGMENTS.  ... 
doi:10.6092/unibo/amsdottorato/9253 fatcat:z76mq6kvezhlxovztri7qfvram

DEVELOPMENT OF A HEPATITIS C VIRUS KNOWLEDGEBASE WITH COMPUTATIONAL PREDICTION OF FUNCTIONAL HYPOTHESIS OF THERAPEUTIC RELEVANCE KOJO KWOFIE SAMUEL

Vladimir Bajic, Alan Christoffels
2011 unpublished
(HCV) therapeutic and diagnostic challenges requires robust intervention strategies, including approaches that leverage the plethora of rich data published in biomedical literature to gain greater understanding  ...  genomics and molecular biology data, and cross-referenced links to canonical pathways and other essential biomedical databases.  ...  Abstract To ameliorate Hepatitis C Virus (HCV) therapeutic and diagnostic challenges requires robust intervention strategies, including approaches that leverage the plethora of rich data published in biomedical  ... 
fatcat:khbuvbkjujbk3dvhoinrnwxqq4

DEVELOPMENT OF A HEPATITIS C VIRUS KNOWLEDGEBASE WITH COMPUTATIONAL PREDICTION OF FUNCTIONAL HYPOTHESIS OF THERAPEUTIC RELEVANCE KOJO KWOFIE SAMUEL

Vladimir Bajic, Alan Christoffels
2011 unpublished
(HCV) therapeutic and diagnostic challenges requires robust intervention strategies, including approaches that leverage the plethora of rich data published in biomedical literature to gain greater understanding  ...  genomics and molecular biology data, and cross-referenced links to canonical pathways and other essential biomedical databases.  ...  Abstract To ameliorate Hepatitis C Virus (HCV) therapeutic and diagnostic challenges requires robust intervention strategies, including approaches that leverage the plethora of rich data published in biomedical  ... 
fatcat:dxh5kptlxfdojbqc7dngtunu4a

Characterization of The Functional Role of PEAK1 and PEAK3 Pseudokinases

JIANMEI HOU
2022
The three pseudokinases PEAK1, PEAK2 and the recently identified PEAK3 constitute the PEAK family. Both PEAK1 and PEAK2 function as scaffolds to regulate cell proliferation, migration and invasion.  ...  In this thesis, the role of PEAK1 in mammary gland development and PEAK3 signalling mechanisms and function were characterized.  ...  Figure 3 . 6 36 Figure 3.6 Peak1 −/− mouse mammary ductal structure. (A) Schematic diagram depicting the mammary ductal structure.  ... 
doi:10.26180/19602376.v1 fatcat:wp536aih7rb6nmdchwdgxuh5rm
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