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Publications | Mémoires et thèses

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50 publications

En préparation
 
The tidyomics ecosystem: Enhancing omic data analyses.
Hutchison William J., Keyes Timothy J., Crowell Helena L., Serizay Jacques, Soneson Charlotte, Davis Eric S., Sato Noriaki, Moses Lambda, Tarlinton Boyd, Nahid Abdullah A. et al..
[DOI][Pmid][serval:BIB_2E7F8476CE75]
2024
 
Long term T cell response and safety of a tetravalent dengue vaccine in healthy children.
Mandaric S., Friberg H., Saez-Llorens X., Borja-Tabora C., Biswal S., Escudero I., Faccin A., Gottardo R., Brose M., Roubinis N. et al., 2024/10/17. NPJ vaccines, 9 (1) p. 192. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_421259B77384]
 
Histone marks identify novel transcription factors that parse CAR-T subset-of-origin, clinical potential and expansion.
Fiorenza S., Zheng Y., Purushe J., Bock T.J., Sarthy J., Janssens D.H., Sheih A.S., Kimble E.L., Kirchmeier D., Phi T.D. et al., 2024/09/27. Nature communications, 15 (1) p. 8309. Peer-reviewed.
[DOI][Pmid][serval:BIB_63C2526F1F8E]
 
EAES/SAGES evidence-based recommendations and expert consensus on optimization of perioperative care in older adults.
Keller D.S., Curtis N., Burt H.A., Ammirati C.A., Collings A.T., Polk H.C., Carrano F.M., Antoniou S.A., Hanna N., Piotet L.M. et al., 2024/08. Surgical endoscopy, 38 (8) pp. 4104-4126. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_713D7F881D3F]
 
ADTnorm: Robust Integration of Single-cell Protein Measurement across CITE-seq Datasets
Gottardo Raphael, Zheng Ye, Caron Daniel, Kim Ju, Jun Seong, Tian Yuan, Mair Florian, Stuart Kenneth, Sims Peter, 2024/07/08..
[DOI][Pmid][serval:BIB_8A286CBE32FB]
 
Long-term Remissions Following CD20-Directed Chimeric Antigen Receptor-Adoptive T-cell Therapy.
Mo G., Lee S.Y., Coffey D.G., Voillet V., Kirsch I.R., Gottardo R., Smythe K.S., Yeung CCS, Greenbaum A., Green D.J. et al., 2024/07/01. Blood cancer discovery, 5 (4) pp. 258-266. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F35F15A30130]
 
The tidyomics ecosystem: enhancing omic data analyses.
Hutchison W.J., Keyes T.J., tidyomics Consortium, Crowell H.L., Serizay J., Soneson C., Davis E.S., Sato N., Moses L., Tarlinton B. et al., 2024/07. Nature methods, 21 (7) pp. 1166-1170. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D2FD0777383A]
Assessing the perioperative gain of weight (Δweight) as a determinant of morbidity after kidney transplantation: a retrospective exploratory study.
Carbonell B.B., Zingg T., Matter M., Joliat G.R., Martin D., Pascual M., Demartines N., Golshayan D., Cano L., Labgaa I., 2024/06/11. Scientific reports, 14 (1) p. 13384. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7D2856ED2C2A]
 
Cost-efficiency of outpatient colectomy in a tertiary center - A projected economic evaluation
Deslarzes Philippe, Grass Fabian, Hübner Martin, Demartines Nicolas, Agri Fabio, 2024/05/31. dans Swiss Knife 2023;20:Special Edition / Swiss College of Surgeons Annual meeting 2023. Peer-reviewed.
[serval:BIB_8BEC42261972]
 
Spatially‐nested hierarchical species distribution models to overcome niche truncation in national‐scale studies
Goicolea T., Adde A., Broennimann O., García-Viñas J.I., Gastón A., José Aroca-Fernández M., Guisan A., G. Mateo R., 2024/05/21. Ecography pp. e07328. Peer-reviewed.
[DOI][WoS][serval:BIB_5E95C69F4A48]
Physical activity and lung function association in a healthy community-dwelling European population.
Collaud S., Touilloux B., von Garnier C., Marques-Vidal P., Kraege V., 2024/04/08. BMC pulmonary medicine, 24 (1) p. 169. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_01DBEEFBDF7F]
Signaling via a CD27-TRAF2-SHP-1 axis during naive T cell activation promotes memory-associated gene regulatory networks.
Jaeger-Ruckstuhl C.A., Lo Y., Fulton E., Waltner O.G., Shabaneh T.B., Simon S., Muthuraman P.V., Correnti C.E., Newsom O.J., Engstrom I.A. et al., 2024/02/13. Immunity, 57 (2) pp. 287-302.e12. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A730B5E1D986]
 
Face au désenchantement des étudiants en médecine, les facultés sont prêtes à innover.
Geissbühler A., Pascual M., 2024/01/17. Revue medicale suisse, 20 (856-7) pp. 5-8. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_9DDE7D621604]
 
Cost Analysis of Outpatient Colectomy in a Tertiary Center: A Projected Medico-Economic Evaluation.
Agri F., Möller W., Deslarzes P., Vogel C.A., Hahnloser D., Hubner M., Demartines N., Grass F., 2024. Health services insights, 17 p. 11786329241284400. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6F8C35ECE6CA]
Day Admission Surgery Program in a Prospective Payment System: What Are the Financial Incentives?
Grass F., Roth-Kleiner M., Demartines N., Agri F., 2024. Health services insights, 17 p. 11786329231222970. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F3FE03311165]
2023
Complementary and Integrative Medicine: a plea for a better resource allocation by the SwissDRG grouping algorithm.
Grass F., Berna C., Vogel C.A., Demartines N., Agri F., 2023/10/03. Swiss medical weekly, 153 p. 40130. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0B65591CF4D4]
 
Single-cell protein expression profiling resolves circulating and resident memory T cell diversity across tissues and infection contexts.
Evrard M., Becht E., Fonseca R., Obers A., Park S.L., Ghabdan-Zanluqui N., Schroeder J., Christo S.N., Schienstock D., Lai J. et al., 2023/07/11. Immunity, 56 (7) pp. 1664-1680.e9. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_203407FABD48]
2022
The Immune Signatures data resource, a compendium of systems vaccinology datasets.
Diray-Arce J., Miller HER, Henrich E., Gerritsen B., Mulè M.P., Fourati S., Gygi J., Hagan T., Tomalin L., Rychkov D. et al., 2022/10/20. Scientific data, 9 (1) p. 635. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FDA7293F77B9]
 
Cohort Profile: Swiss BioRef: The building blocks of a nationwide IT infrastructure in Switzerland for generating precise reference intervals
Blatter Tobias U., Witte Harald, Fasquelle-Lopez Jules, Raisaro Jean Louis, Leichtle Alexander B., 2022/08/31..
[DOI][serval:BIB_49A8D897D896]
An Ontology and Data Converter from RDF to the i2b2 Data Model
Fasquelle-Lopez Jules, Louis Raisaro Jean, 2022/05/25. pp. 372-376 dans Challenges of Trustable AI and Added-Value on Health, IOS Press.
[URN][DOI][Pmid][serval:BIB_72539EF61E24]
Generation and Evaluation of Synthetic Data in a University Hospital Setting
Kaabachi Bayrem, Despraz Jérémie, Meurers Thierry, Prasser Fabian, Raisaro Jean Louis, 2022/05/25. pp. 141-142 dans Challenges of Trustable AI and Added-Value on Health, IOS Press.
[URN][DOI][Pmid][serval:BIB_FF74F4A9D504]
 
Multiple early factors anticipate post-acute COVID-19 sequelae.
Su Y., Yuan D., Chen D.G., Ng R.H., Wang K., Choi J., Li S., Hong S., Zhang R., Xie J. et al., 2022/03/03. Cell, 185 (5) pp. 881-895.e20. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_296B705072A0]
IDEAS: individual level differential expression analysis for single-cell RNA-seq data.
Zhang M., Liu S., Miao Z., Han F., Gottardo R., Sun W., 2022/01/24. Genome biology, 23 (1) p. 33. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B48AF13F6F91]
Transcriptional correlates of malaria in RTS,S/AS01-vaccinated African children: a matched case-control study.
Moncunill G., Carnes J., Chad Young W., Carpp L., De Rosa S., Campo J.J., Nhabomba A., Mpina M., Jairoce C., Finak G. et al., 2022/01/21. eLife, 11 pp. e70393. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_807A74E7EF22]
 
Single-cell immunology of SARS-CoV-2 infection.
Tian Y., Carpp L.N., Miller HER, Zager M., Newell E.W., Gottardo R., 2022/01. Nature biotechnology, 40 (1) pp. 30-41. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F4C681A1F5A5]
The deficiency in Th2-like Tfh cells affects the maturation and quality of HIV-specific B cell response in viremic infection.
Noto A., Suffiotti M., Joo V., Mancarella A., Procopio F.A., Cavet G., Leung Y., Corpataux J.M., Cavassini M., Riva A. et al., 2022. Frontiers in immunology, 13 p. 960120. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3A9147719CB5]
2021
New interpretable machine-learning method for single-cell data reveals correlates of clinical response to cancer immunotherapy.
Greene E., Finak G., D'Amico L.A., Bhardwaj N., Church C.D., Morishima C., Ramchurren N., Taube J.M., Nghiem P.T., Cheever M.A. et al., 2021/12/10. Patterns, 2 (12) p. 100372. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4AF9E6EB0D95]
Author Correction: Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption
Froelicher David, Troncoso-Pastoriza Juan R., Raisaro Jean Louis, Cuendet Michel A., Sousa Joao Sa, Cho Hyunghoon, Berger Bonnie, Fellay Jacques, Hubaux Jean-Pierre, 2021/12. Nature Communications, 12 (1). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BA7A4545F831]
Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption.
Froelicher D., Troncoso-Pastoriza J.R., Raisaro J.L., Cuendet M.A., Sousa J.S., Cho H., Berger B., Fellay J., Hubaux J.P., 2021/10/11. Nature communications, 12 (1) p. 5910. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3683F2C63090]
 
Use and Effectiveness of Sperm Cryopreservation for Adolescents and Young Adults: A 37-Year Bicentric Experience.
Adam C., Deffert C., Leyvraz C., Primi M.P., Simon J.P., Beck Popovic M., Bénard J., Bouthors T., Girardin C., Streuli I. et al., 2021/02. Journal of adolescent and young adult oncology, 10 (1) pp. 78-84. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_11FA9C76B3DF]
2020
SCOR: A secure international informatics infrastructure to investigate COVID-19.
Raisaro J.L., Marino F., Troncoso-Pastoriza J., Beau-Lejdstrom R., Bellazzi R., Murphy R., Bernstam E.V., Wang H., Bucalo M., Chen Y. et al., 2020/11/01. Journal of the American Medical Informatics Association, 27 (11) pp. 1721-1726. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7D30526235EB]
 
Promotion de la vaccination antigrippale durant la visite médicale d'embauche
Currat Michael, Lazor-Blanchet Catherine, Zanetti Giorgio, 2020/10/01. dans Archives des maladies professionnelles et de l'environnement.
[serval:BIB_45BBE6F51E10]
GenoShare: Supporting Privacy-Informed Decisions for Sharing Individual-Level Genetic Data.
Raisaro J.L., Troncoso-Pastoriza J.R., El-Zein Y., Humbert M., Troncoso C., Fellay J., Hubaux J.P., 2020/06/16. pp. 238-241 dans Digital Personalized Health and Medicine, IOS Press.
[URN][DOI][WoS][Pmid][serval:BIB_E4D4CB80455C]
SPHN/PHRT - MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery.
Raisaro J.L., Troncoso-Pastoriza J.R., Pradervand S., Cuendet M., Misbach M., Sa J., Marino F., Freundler N., Rosat N., Cavin D. et al., 2020/06/16. pp. 1161-1162 dans Digital Personalized Health and Medicine, IOS Press.
[URN][DOI][Pmid][serval:BIB_3077196DA0EB]
MedCo2: Privacy-Preserving Cohort Exploration and Analysis.
Froelicher David, Mickaël Misbach, Troncoso-Pastoriza Juan Ramon, Raisaro Jean Louis, Hubaux Jean-Pierre, 2020/06/01. pp. 317-321 dans Digital Personalized Health and Medicine, IOS Press.
[URN][DOI][Pmid][serval:BIB_D0C4C9C55DD4]
Data protection and ethics requirements for multisite research with health data: a comparative examination of legislative governance frameworks and the role of data protection technologies.
Scheibner J., Ienca M., Kechagia S., Troncoso-Pastoriza J.R., Raisaro J.L., Hubaux J.P., Fellay J., Vayena E., 2020. Journal of law and the biosciences, 7 (1) pp. lsaa010. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E81CB33F863F]
2019
 
MedCo: Enabling Secure and Privacy-Preserving Exploration of Distributed Clinical and Genomic Data
Raisaro Jean Louis, Troncoso-Pastoriza Juan Ramon, Misbach Mickael, Sousa Joao Sa, Pradervand Sylvain, Missiaglia Edoardo, Michielin Olivier, Ford Bryan, Hubaux Jean-Pierre, 2019/07/01. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16 (4) pp. 1328-1341. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_EB26A9E809D5]
2018
 
Are privacy-enhancing technologies for genomic data ready for the clinic? A survey of medical experts of the Swiss HIV Cohort Study.
Raisaro J.L., McLaren P.J., Fellay J., Cavassini M., Klersy C., Hubaux J.P., Swiss HIV Cohort Study, 2018/03. Journal of biomedical informatics, 79 pp. 1-6. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AA11676A72A9]
Feasibility of Homomorphic Encryption for Sharing I2B2 Aggregate-Level Data in the Cloud.
Raisaro J.L., Klann J.G., Wagholikar K.B., Estiri H., Hubaux J.P., Murphy S.N., 2018. AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science, 2017 pp. 176-185. Peer-reviewed.
[URN][Pmid][serval:BIB_FDEFCDEC84BD]
 
Protecting Privacy and Security of Genomic Data in i2b2 with Homomorphic Encryption and Differential Privacy.
Raisaro J.L., Gwangbae Choi, Pradervand S., Colsenet R., Jacquemont N., Rosat N., Mooser V., Hubaux J.P., 2018. IEEE/ACM transactions on computational biology and bioinformatics, 15 (5) pp. 1413-1426. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_77895CA6B07B]
2017
 
UnLynx: A Decentralized System for Privacy-Conscious Data Sharing
Froelicher David, Egger Patricia, Sousa João Sá, Raisaro Jean Louis, Huang Zhicong, Mouchet Christian, Ford Bryan, Hubaux Jean-Pierre, 2017/10/01. Proceedings on Privacy Enhancing Technologies, 2017 (4) pp. 232-250. Peer-reviewed.
[DOI][serval:BIB_B0D7721A18A6]
Efficient and secure outsourcing of genomic data storage.
Sousa J.S., Lefebvre C., Huang Z., Raisaro J.L., Aguilar-Melchor C., Killijian M.O., Hubaux J.P., 2017/07/26. BMC medical genomics, 10 (Suppl 2) p. 46. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_33015E73AFE3]
Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks.
Raisaro J.L., Tramèr F., Ji Z., Bu D., Zhao Y., Carey K., Lloyd D., Sofia H., Baker D., Flicek P. et al., 2017/07/01. Journal of the American Medical Informatics Association, 24 (4) pp. 799-805. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B1775430E24D]
2015
COMPASS identifies T-cell subsets correlated with clinical outcomes.
Lin L., Finak G., Ushey K., Seshadri C., Hawn T.R., Frahm N., Scriba T.J., Mahomed H., Hanekom W., Bart P.A. et al., 2015/06. Nature biotechnology, 33 (6) pp. 610-616. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8FADB11D7063]
 
Privacy Threats and Practical Solutions for Genetic Risk Tests
Barman Ludovic, Elgraini Mohammed-Taha, Raisaro Jean Louis, Hubaux Jean-Pierre, Ayday Erman, 2015/05. dans 2015 IEEE Security and Privacy Workshops. Peer-reviewed, IEEE.
[DOI][serval:BIB_8DDC312D0DF5]
2014
 
Patient privacy in the genomic era.
Raisaro J.L., Ayday E., Hubaux J.P., 2014/05/07. Praxis, 103 (10) pp. 579-586. Peer-reviewed.
[DOI][Pmid][serval:BIB_73FA5E278D80]
 
Privacy-Preserving Processing of Raw Genomic Data
Ayday Erman, Raisaro Jean Louis, Hengartner Urs, Molyneaux Adam, Hubaux Jean-Pierre, 2014. pp. 133-147 dans Data Privacy Management and Autonomous Spontaneous Security, Springer Berlin Heidelberg.
[DOI][serval:BIB_E50F64F54A6C]
2013
 
Personal use of the genomic data: Privacy vs. storage cost
Ayday Erman, Raisaro Jean Louis, Hubaux Jean-Pierre, 2013/12. dans 2013 IEEE Global Communications Conference (GLOBECOM). Peer-reviewed, IEEE.
[DOI][serval:BIB_FF4AEBDCF4F9]
 
Protecting and evaluating genomic privacy in medical tests and personalized medicine
Ayday Erman, Raisaro Jean Louis, Hubaux Jean-Pierre, Rougemont Jacques, 2013/11/04. dans Proceedings of the 12th ACM workshop on Workshop on privacy in the electronic society. Peer-reviewed, ACM.
[DOI][serval:BIB_D5DF60F60F90]
 
Privacy-Preserving Computation of Disease Risk by Using Genomic, Clinical, and Environmental Data
Ayday Erman, Raisaro Jean Louis, McLaren Paul J, Fellay Jacques, Hubaux Jean-Pierre, 2013. dans Proceedings of the 2013 USENIX Conference on Safety, Security, Privacy and Interoperability of Health Information Technologies. Peer-reviewed.
[serval:BIB_048635477FF8]
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