Bridging Histology and Bioinformatics

1. BRIDGING HISTOLOGY AND BIOINFORMATICS Nahla Imbarak Teaching Assistant at Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University

2. • Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. • Bioinformatics combines computer science, biology, mathematics and engineering to analyze and interpret biological data. INTRODUCTION Introduction

3. • Drug discoveries • Vaccine development: synthetic vaccine or Ab. • Treatment of infectious diseases: commensal bacteria, engineered bacteriophages and sequence specific endonucleases. INTRODUCTION Bioinformatics has the potential to engineer novel diagnostic and therapeutic strategies for relatively curing medical conditions.

4. Bioinformatics hierarchy: INTRODUCTION Andrianantoandro, 2006

5. • Gene expression analysis in living cells: RNA expression levels are often approximated by measuring the intensity of fluorescent proteins expressed by genetic constructs inserted in cells 1. Two genetic constructs: to express a GFP-labeled RNA reporter protein and a target RNA fused with a reporter protein-binding site. e.g. field of regenerative medicine (Stem cells research) 2. Hybridization probes: using competitive linear probes, molecular beacons, and self-ligating probes GENE EXPRESSION

6. 4. Nanoflares: target RNA binding sequences are conjugated with gold nanoparticles . 5. Transcriptome in vivo analysis (TIVA): makes use of an engineered tag ( a TIVA tag= Cy3-Cy5 and FRET peptides) to enter specific cell types and capture mRNA molecules in living cells GENE EXPRESSION N.B.: Two RNA species can be monitored in parallel in living cells and its potential for diagnostics has been demonstrated

7. Web Indexing

8. Bioinformatics Recourses • Bioinformatics resource inventory (BIRI): An approach for automatically discovering and indexing public bioinformatics recourses. http://www.gib.fi.upm.es/biri/ WEB INDEXING

12. • BioRAT: A research assistant that given a query, autonomously find a set of papers, read them, highlights the most relevant facts in each. http://bioinf.cs.ucl.ac.uk/software_downloads/biorat/ WEB INDEXING Information Extraction Tool

13. • BioRAT: A research assistant that given a query, autonomously find a set of papers, read them, highlights the most relevant facts in each. http://bioinf.cs.ucl.ac.uk/software_downloads/biorat/ WEB INDEXING Information Extraction Tool

14. • NCBI: The NCBI advances science and health by providing access to biomedical and genomic information. https://www.ncbi.nlm.nih.gov/ WEB INDEXING National Center for Biotechnology Information

18. • MaLaCards: It is an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. http://www.malacards.org/ WEB INDEXING Database of Maladies

19. • MaLaCards: It is an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. http://www.malacards.org/ WEB INDEXING Database of Maladies

20. • MaLaCards: It is an integrated database of human maladies and their annotations, modeled on the architecture and richness of the popular GeneCards database of human genes. http://www.malacards.org/ WEB INDEXING Database of Maladies FDA approved drugs Cell-Based therapies Clinical trials Immunostaning Gene- receptor involvement Literature

21. • GeneCArds: It is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information. http://www.genecards.org/ WEB INDEXING Database of Genes

24. • Gene Recommender: It ranks genes according to how strongly they correlate with a set of query. Used for gene expression studies. https://www.bioconductor.org/packages/release/bioc/html/g eneRecommender.html WEB INDEXING Gene Recommender

25. • Gene Recommender: It ranks genes according to how strongly they correlate with a set of query. Used for gene expression studies. https://www.bioconductor.org/packages/release/bioc/html/g eneRecommender.html WEB INDEXING Gene Recommender

26. • PRIDE, PRIMER MASTER, PRIMO, PrimeArray, Primer, Prime and Web Primer : Several web-based services or stand-alone software provided to the public for primer design. Web primer : https://www.yeastgenome.org/cgi-bin/web- primer WEB INDEXING Primer Design

33. • PluriTest: Compatible assays for global gene expression profile assays enable quick and cost-effective verification of pluripotency profiling. https://www.pluritest.org/ For more information: https://www.ncbi.nlm.nih.gov/pubmed/21378979 WEB INDEXING Pluripotency Characterization Tool

37. • TaqMan hPSC Scorecard Assay: Assesses pluripotency and trilineage differentiation potential using real-time qPCR assays and intuitive data analysis software. https://www.thermofisher.com/content/dam/LifeTech/Docu ments/help/pascal-hpsc-scorecard-help-desk/index.html For more details: https://tools.thermofisher.com/content/sfs/manuals/taqman _hpsc_scorecard_man.pdf WEB INDEXING Pluripotency and Trilineage Differentiation Tool

40. • CiteAb, Linscott”s Directory, Biocompare, Abcam and Antibodypedia: It guide researchers to choose an appropriate antibody for a particular application. The resource contains information about close to 3 million antibodies towards over 19,000 human protein targets from more than 70 providers. 1. Antibodypedia: https://www.antibodypedia.com/ 2. Abcam: http://www.abcam.com/ WEB INDEXING Antibody Guide

48. • The Human Protein Atlas: The Human Protein Atlas is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues and organs using integration of various technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology. https://www.proteinatlas.org/ WEB INDEXING The Human Protein Atlas

56. • UniProt: It provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. http://www.uniprot.org/ WEB INDEXING Universal Protein Resource

61. • Protter: It’s a source tool for visualization of proteoforms. Useful for Ab design in immunohistochemistry. http://wlab.ethz.ch/protter/start/ WEB INDEXING Visualizing Protein Topology

62. • Protter: It’s a source tool for visualization of proteoforms. Useful for Ab design in immunohistochemistry. http://wlab.ethz.ch/protter/start/ WEB INDEXING Visualizing Protein Topology

63. • Protter: It’s a source tool for visualization of proteoforms. Useful for Ab design in immunohistochemistry. http://wlab.ethz.ch/protter/start/ WEB INDEXING Ab. Visualizing Protein Topology

64. • String: Single Protein by Name / Identifier. https://string-db.org/ WEB INDEXING Database of Proteins

65. • String: Single Protein by Name / Identifier. https://string-db.org/ WEB INDEXING SRY Mice Database of Proteins

68. • Cell designer: Modeling of biochemical network. http://celldesigner.org/models.html WEB INDEXING Cell Designer

72. • SimBiology - MATLAB – MathWorks: It provides a programmatic tools to model, simulate, and analyze dynamic systems.  A variety of model exploration techniques let you identify optimal dosing schedules and putative drug targets in cellular pathways.  SimBiology uses ordinary differential equations and stochastic solvers to simulate the time course profile of drug exposure, drug efficacy, and enzyme and metabolite levels. https://www.mathworks.com/products/simbiology.html WEB INDEXING Drug Database

73. • SimBiology - MATLAB – MathWorks: It provides a programmatic tools to model, simulate, and analyze dynamic systems.  A variety of model exploration techniques let you identify optimal dosing schedules and putative drug targets in cellular pathways.  SimBiology uses ordinary differential equations and stochastic solvers to simulate the time course profile of drug exposure, drug efficacy, and enzyme and metabolite levels. https://www.mathworks.com/products/simbiology.html WEB INDEXING Drug Database

74. • CaDNAno: It simplifies and enhances the process of designing three- dimensional nanostructures. http://cadnano.org/ WEB INDEXING Nanotechnology

78. • UTR Designer: Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. https://omictools.com/utr-designer-tool WEB INDEXING mRNA Translation Initiation Region Designer

81. Thank you

Bridging Histology and Bioinformatics

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