====== Privacy in Pangenomics ======
\\
| [[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=427117679 | 392232]] | Schönhuth | Winter 2023/2024 | Thu 10-12 in U2-232 (S) |
==== Papers ====
\\
| | **Title** | **Authors** | **Year** | **Journal** |
| |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/a_framework_for_adaptive_differential_privacy.pdf |A Framework for Adaptive Differential Privacy]] |Daniel Winograd-Cort et al.|2017|Proceedings of the ACM on Programming Languages|
| Amadeus Beckmann |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/a_survey_on_homomorphic_encryption_schemes_theory_and_implementation.pdf|A Survey on Homomorphic Encryption Schemes: Theory and Implementation]]| Abbas Acar et al.| 2018| ACM Computing Surveys|
| Annalena Franz |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/blockchain-enabled_federated_learning_a_survey.pdf|Blockchain-enabled Federated Learning: A Survey]]|Cheng Li, Yong Yuan, Fei-Yue Wang|2021|IEEE International Conference on Digital Twins and Parallel Intelligence (DTPI)|
| Vignesh Natarajan |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/blockchain_meets_federated_learning_in_healthcare_a_systematic_review_with_challenges_and_opportunities.pdf|Blockchain Meets Federated Learning
in Healthcare: A Systematic Review
With Challenges and Opportunities]]|Raushan Myrzashova et al.|2023|IEEE INTERNET OF THINGS JOURNAL|
| Mumtaz Hussain |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/cloud-based_secure_health_monitoring_optimizing_fully-homomorphic_encryption_for_streaming_algorithms.pdf|Cloud-based Secure Health Monitoring: Optimizing Fully-Homomorphic Encryption for Streaming Algorithms]]|Alex Page et al.|2014|2014 IEEE Globecom Workshops (GC Wkshps)|
| |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/deep_learning_with_differential_privacy.pdf|Deep Learning with Differential Privacy]]|Martín Abadi et al|2016|Proceedings of the 2016 ACM SIGSAC Conference on Computer and Communications Security|
| Marvin Mrowka |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/flimma-privacy-differentialanalysis.pdf|Flimma: a federated and privacy-aware tool for differential gene expression analysis]]|Olga Zolotareva et al.| 2021 |Genome Biology|
| |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/gaussian_differential_privacy.pdf|Gaussian differential privacy]]|Jinshuo Dong et al.| 2022 |Journal of the Royal Statistical Society Series B: Statistical Methodology|
| Khaled Bagh |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/hidingsensitivegenotypescho.pdf|Mechanisms for Hiding Sensitive Genotypes With Information-Theoretic Privacy]]|Fangwei Ye et al.| 2022 |IEEE Transactions on Information Theory|
| Mika Sempert |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/privacychallengesandresearchopportunitiesforgenomicdatasharing.pdf|Privacy challenges and research opportunities for genomic data sharing]]|Luca Bonomi et al.|2020|Nature GeNetics|
| Aya Benzine |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/privacyfunctionalgenomics.pdf|Functional genomics data: privacy risk assessment and technological mitigation]]|Gamze Gürsoy et al. |2022|Nature Reviews |
| |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/privacypreservingimputationcenk.pdf|Privacy-preserving genotype imputation in a trusted execution environment]]|Natnatee Dokmai et al.| 2021 |Cell Systems|
| |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature s/securehumanactionrecognition.pdf|Secure human action recognition by encrypted neural network inference]]|Miran Kim et al.| 2022 |Nature Communications|
| Johanna Pries |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/sequrebiomedicaldatasharing.pdf|Sequre: a high‑performance framework for secure multiparty computation enables biomedical data sharing]]|Haris Smajlović et al.| 2023 |Genome Biology|
| Anna-Lena Rinke |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/sociotechnicalsafeguardsforgenomicdataprivacy.pdf|Sociotechnical safeguards for genomic data privacy]]|Zhiyu Wan et al.|2022|Nature Reviews |
| Vali Florinel Craciun |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/swarm-afederatedcloudframeworkforlarge-scalevariantanalysis.pdf|Swarm: A federated cloud framework for large-scale variant analysis]]|Amir Bahmani|2021|PLOS Computational Biology|
| Kristin Willms |[[https://gds.techfak.uni-bielefeld.de/_media/teaching/literature/swarmlearningfordecentralizedandconfidentialclinicalmachinelearning.pdf|Swarm Learning for decentralized and confidential clinical machine learning]]|Stefanie Warnat-Herresthal|2021|Nature|
| Nils Witznick |AUTOENCODING VARIATIONAL INFERENCE FOR TOPIC MODELS|Akash Srivastava et al.|2017| ICLR |
:!: You need to login in order to view the literature.
==== Time table lecture====
| **Date** | **Topic** |
|12.10.2023 |Introduction ({{teaching:2023winter:pangenomics:Introduction-121023.pdf|slides}}) | [[:teaching:2023winter:privacy|Privacy in Healthcare]] |
|19.10.2023 | How to present ({{teaching:2023winter:pangenomics:howtopresent.pdf|slides}})| [[:teaching:2023winter:present|Presentations: Guidelines]] |
|26.10.2023 | How to write Reports |
|02.05.2023 | |
|02.11.2023 | |
|09.11.2023 | |
|16.11.2023 | Deadline paper selection |
|23.11.2023 | |
|30.11.2023 | |
|14.12.2023 | Anna-Lena Rinke |
|21.12.2023 | Khaled Bagh, Vignesh Natarajan |
|11.01.2024 | Aya Benzine, Annalena Franz, Mumtaz Hussain|
|18.01.2024 | Marvin Mrowka, Kristin Willms, Nils Witznick |
|25.01.2024 | Johanna Pries, Vali Florinel Craciun, Amadeus Beckmann |
|01.02.2024 | Mumtaz Hussain |
Presentations each start at 9:30 AM.