Web cookies (also called HTTP cookies, browser cookies, or simply cookies) are small pieces of data that websites store on your device (computer, phone, etc.) through your web browser. They are used to remember information about you and your interactions with the site.
Purpose of Cookies:
Session Management:
Keeping you logged in
Remembering items in a shopping cart
Saving language or theme preferences
Personalization:
Tailoring content or ads based on your previous activity
Tracking & Analytics:
Monitoring browsing behavior for analytics or marketing purposes
Types of Cookies:
Session Cookies:
Temporary; deleted when you close your browser
Used for things like keeping you logged in during a single session
Persistent Cookies:
Stored on your device until they expire or are manually deleted
Used for remembering login credentials, settings, etc.
First-Party Cookies:
Set by the website you're visiting directly
Third-Party Cookies:
Set by other domains (usually advertisers) embedded in the website
Commonly used for tracking across multiple sites
Authentication cookies are a special type of web cookie used to identify and verify a user after they log in to a website or web application.
What They Do:
Once you log in to a site, the server creates an authentication cookie and sends it to your browser. This cookie:
Proves to the website that you're logged in
Prevents you from having to log in again on every page you visit
Can persist across sessions if you select "Remember me"
What's Inside an Authentication Cookie?
Typically, it contains:
A unique session ID (not your actual password)
Optional metadata (e.g., expiration time, security flags)
Analytics cookies are cookies used to collect data about how visitors interact with a website. Their primary purpose is to help website owners understand and improve user experience by analyzing things like:
How users navigate the site
Which pages are most/least visited
How long users stay on each page
What device, browser, or location the user is from
What They Track:
Some examples of data analytics cookies may collect:
Page views and time spent on pages
Click paths (how users move from page to page)
Bounce rate (users who leave without interacting)
User demographics (location, language, device)
Referring websites (how users arrived at the site)
Here’s how you can disable cookies in common browsers:
1. Google Chrome
Open Chrome and click the three vertical dots in the top-right corner.
Go to Settings > Privacy and security > Cookies and other site data.
Choose your preferred option:
Block all cookies (not recommended, can break most websites).
Block third-party cookies (can block ads and tracking cookies).
2. Mozilla Firefox
Open Firefox and click the three horizontal lines in the top-right corner.
Go to Settings > Privacy & Security.
Under the Enhanced Tracking Protection section, choose Strict to block most cookies or Custom to manually choose which cookies to block.
3. Safari
Open Safari and click Safari in the top-left corner of the screen.
Go to Preferences > Privacy.
Check Block all cookies to stop all cookies, or select options to block third-party cookies.
4. Microsoft Edge
Open Edge and click the three horizontal dots in the top-right corner.
Go to Settings > Privacy, search, and services > Cookies and site permissions.
Select your cookie settings from there, including blocking all cookies or blocking third-party cookies.
5. On Mobile (iOS/Android)
For Safari on iOS: Go to Settings > Safari > Privacy & Security > Block All Cookies.
For Chrome on Android: Open the app, tap the three dots, go to Settings > Privacy and security > Cookies.
Be Aware:
Disabling cookies can make your online experience more difficult. Some websites may not load properly, or you may be logged out frequently. Also, certain features may not work as expected.
Zhang, Chenyu, Pujan Joshi, Honglin Wang, Seung-Hyun Hong, Riqiang Yan, and Dong-Guk Shin. Pola Viz Reveals Microglia Polarization at Single Cell Level in Alzheimer’s Disease.2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2022. PDF
Wang, Honglin, Pujan Joshi, Seung-Hyun Hong, Peter F. Maye, David W. Rowe, and Dong-Guk Shin. Predicting the targets of IRF8 and NFATc1 during osteoclast differentiation using the machine learning method framework cTAP.BMC genomics 23, no. 1 (2022): 1-18. PMID:34991467
Joshi P, Basso B, Wang H, Hong SH, Giardina C, Shin DG. rPAC: Route based pathway analysis for cohorts of gene expression data sets. Methods. 2022 Feb;198:76-87. doi: 10.1016/j.ymeth.2021.10.002. Epub 2021 Oct 7. PMID: 34628030; PMCID: PMC8792230.
Wang, Honglin, Pujan Joshi, Seung-Hyun Hong, Peter F. Maye, David W. Rowe, and Dong-Guk Shin. cTAP: A Machine Learning Framework for Predicting Target Genes of a Transcription Factor using a Cohort of Gene Expression Data Sets. In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 164-167. IEEE, 2020. PDF
Hoang TH, Zhao Y, Lam Y, Piekos S, Han YC, Reilly C, Joshi P, Hong SH, Sung CO, Giardina C, Shin DG. BioTarget: A Computational Framework Identifying Cancer Type Specific Transcriptional Targets of Immune Response Pathways. Sci Rep. 2019 Jun 21;9(1):9029. doi: 10.1038/s41598-019-45304-x. PMID:31227749.
Zhao Y, Shin DG. Deep Pathway Analysis V2.0: A Pathway Analysis Framework Incorporating Multi-dimensional Omics Data.IEEE/ACM Trans Comput Biol Bioinform 2019 Oct 7. PMID: 31603796 doi: 10.1109/TCBB.2019.2945959.
Zhao Y, Joshi P, Shin DG. Recurrent Neural Network for Gene Regulation Network construction on Time Series Expression Data. IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2019), Nov. 18-21, San Diego, CA, USA. PDF
Thibodeau A, Shin DG, TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators, Bioinformatics 2019 Aug 1; 35(15), Oxford University Press. PMID: 30566622.
Zhao Y, Piekos S, Hoang TH, Shin DG. A Framework using Topological Pathways for Deeper Analysis of Transcriptome Data.BMC Special Issue of ISBRA. 2019 (To Be Published) PDF
Shin DJ, Joshi P, Shin DG, Wang L. Genome-Wide Analysis for Identifying FOXO Protein-Binding Sites.Methods Mol Biol. 2019;1890:193-203. doi: 10.1007/978-1-4939-8900-3_16.PubMed PMID: 30414155.
Bae M, Lee Y, Park YK, Shin DG, Joshi P, Hong SH, Alder N, Koo SI, Lee JY. Astaxanthin attenuates the increase in mitochondrial respiration during the activation of hepatic stellate cells. J Nutr Biochem. 2019 Sep;71:82-89. doi: 10.1016/j.jnutbio.2019.06.001. Epub 2019 Jun 20. PMID: 31302374
Hong BY, Sobue T, Choquette L, Dupuy AK, Thompson A, Burleson JA, Salner AL, Schauer PK, Joshi P, Fox E, Shin DG, Weinstock GM, Strausbaugh LD, Dongari-Bagtzoglou A, Peterson DE, Diaz PI. Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis.Microbiome.2019 Apr 25;7(1):66. doi: 10.1186/s40168-019-0679-5. PubMed PMID: 31018870; PubMed Central PMCID: PMC6482518.
Becker T, Lee WP, Leone J, Zhu Q, Zhang C, Liu S, Sargent J, Shanker K, Mil-Homens A, Cerveira E, Ryan M, Cha J, Navarro FCP, Galeev T, Gerstein M, Mills RE, Shin DG, Lee C, Malhotra A. FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods. Genome Biol. 2018 Mar 20; 19(1):38. doi: 10.1186/s13059-018-1404-6. PMID: 29559002
Zhao Y, Hoang TH, Joshi P, Hong SH, Giardina C, Shin DG. A route-based pathway analysis framework integrating mutation information and gene expression data. Methods. 2017 Jul 15;124:3-12. PMID: 28647608
Thibodeau A, Márquez EJ, Shin DG, Vera-Licona P, Ucar D. Chromatin interaction networks revealed unique connectivity patterns of broad H3K4me3 domains and super enhancers in 3D chromatin. Sci Rep. 2017 Oct 31;7(1):14466. PMID: 29089515 PMCID: PMC5663946
Thibodeau A, Márquez EJ, Luo O, Ruan Y, Menghi F, Shin DG, Stitzel ML, Vera-Licona P, Ucar D. QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. PLoS Comput Biol. 2016 Jun 23;12(6) PMCID: 27336171 PMCID: PMC491905
Lieberman R, Kranzler HR, Joshi P, Shin DG, Covault J, GABRA2 Alcohol Dependence Risk Allele is Associated with Reduced Expression of Chromosome 4p12 GABAA Subunit Genes in Human Neural Cultures. Alcohol Clin Exp Res. 2015 Sep;39(9):1654-64. doi: 10.1111/acer.12807. Epub 2015 Aug 6 PMID: 26250693 PMCID: PMC4558268
Bayarsaihan D, Shin DG. Epigenetic drug therapy based on bromodomain inhibition.Epigenomics. 2014;6(5):473-6. doi: 10.2217/epi.14.45.PubMed PMID: 25431940.
Zhao Y, Chen MH, Pei B, Rowe D, Shin DG, Xie W, Yu F, Kuo L. A Bayesian Approach to Pathway Analysis by Integrating Gene-Gene Functional Directions and Microarray Data. Stat Biosci 2012;4(1):105-31.PMID:23482678.
Pei B, Shin DG. Reconstruction of biological networks by incorporating prior knowledge into Bayesian network models. Journal of computational biology: a journal of computational molecular cell biology. 2012; 19(12):1324-34. PMID: 23210479 PMCID: PMC3513982
Shin, DG., Kazmi, S., Baikang, P. Kim, Y-A., Maddox, J., Nori. R. Wong, A., Krueger, W., and Rowe, D. Computing Consistencies between Microarray Data and Known Gene Regulation Relationships”, IEEE Transactions on Information Technology in Biomedicine, 2009; 13(6):1075-82, PMID: 19783507
Selected Skeletal Image Processing Related Publications
Rowe DW, Adams DJ, Hong SH, Zhang C, Shin DG. Renata RC, Chen L, Wu Z, Garland G, Godfrey DA, Sundberg JP, Ackert-Bicknell C, Screening Gene Knockout Mice for Variation in Bone Mass: Analysis by μCT and Histomorphometry, Current Osteoporosis Reports, 2018, 1-18, doi: 10.1007/s11914-018-0421-4. PMID: 29508144
