Article
Computer Science, Hardware & Architecture
Xiaojie Zhu, Erman Ayday, Roman Vitenberg
Summary: Due to the privacy concerns of genomic and phenotype data, data owners often outsource their data to cloud service providers (CSPs) for storage and analysis. In this work, we propose a solution that enables privacy-preserving search and analysis over encrypted genomic and phenotype data owned by multiple hospitals. We introduce encryption mechanisms for phenotype data and multi-key fully homomorphic encryption for genomic data, allowing efficient identification of case/control groups and computation of GWAS statistics without privacy violations.
IEEE TRANSACTIONS ON DEPENDABLE AND SECURE COMPUTING
(2023)
Article
Genetics & Heredity
Maria Alvarellos, Hadley E. Sheppard, Ingrid Knarston, Craig Davison, Nathaniel Raine, Thorben Seeger, Pablo Prieto Barja, Maria Chatzou Dunford
Summary: Since the first sequencing of the human genome, the cost of sequencing has decreased, resulting in a massive amount of genomic data. However, this data is not widely distributed due to strict governance and privacy policies, with most of the clinical-genomic data being inaccessible. Federated data platforms are emerging as a solution to this issue, allowing secure data sharing without physically transferring the data. These platforms enable global collaboration, improve representation, and have the potential to facilitate research in the long term.
FRONTIERS IN GENETICS
(2023)
Article
Quantum Science & Technology
Yao Ma, Elham Kashefi, Myrto Arapinis, Kaushik Chakraborty, Marc Kaplan
Summary: This article introduces a secure hardware device called QEnclave, which can secure the remote execution of quantum operations using classical controls. By attaching QEnclave to a quantum computer, a remote client can securely delegate its computation to the server using classical communication. The security of QEnclave is investigated and it is shown to enable blind delegated quantum computing with perfect security.
NPJ QUANTUM INFORMATION
(2022)
Article
Pediatrics
Gregory D. Zimet, Ross D. Silverman, Robert A. Bednarczyk, Abigail English
Summary: Adolescent self-consent for HPV vaccination is a potential approach to increasing access and improving vaccination coverage, but legal, healthcare provider, and adolescent awareness barriers still exist.
JOURNAL OF PEDIATRICS
(2021)
Article
Computer Science, Theory & Methods
Jie Cui, Bei Li, Hong Zhong, Geyong Min, Yan Xu, Lu Liu
Summary: This article presents a bidirectional fine-grained access control scheme for cloud data sharing, which can restrict the capabilities of both senders and receivers. By combining the cloud side and the edge side in a data sharing framework, and utilizing attribute-based encryption and proxy re-encryption algorithms, efficient access control is achieved.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2022)
Editorial Material
Medicine, General & Internal
Holland Kaplan, Marc Robinson, Astrid Grouls
Summary: This article discusses the ethical and legal considerations of respecting patients' rights for surrogate decision making, specifically when the selected surrogate is incarcerated, and provides practical suggestions for healthcare teams and systems in such situations.
ANNALS OF INTERNAL MEDICINE
(2023)
Article
Obstetrics & Gynecology
Lisa A. Rinehart
Summary: The cryopreservation of reproductive material has significantly improved clinical outcomes for patients worldwide, but has also brought significant legal, ethical, and practical challenges to physicians and practices. Freezer failures can result in material loss, while improper transportation or receipt of gametes or embryos can pose risks to a practice. Managing abandoned embryos remains a widely publicized conundrum.
FERTILITY AND STERILITY
(2021)
Article
Computer Science, Theory & Methods
Junsong Fu, Na Wang, Baojiang Cui, Bharat K. Bhargava
Summary: This paper presents a new encrypted document retrieval system that integrates a proxy server to alleviate data owner's workload and improve the system's security level. By constructing different index trees and utilizing suitable algorithms, efficient search with multiple parameters is achieved.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2022)
Article
Computer Science, Information Systems
Zaheer Abbas, Seunghwan Myeong
Summary: Cloud computing has transformed data storage, processing, and access in industries. However, the increased adoption of cloud technology raises concerns about data security. This paper explores the use of machine learning techniques to enhance cloud computing security and identifies gaps in their application in cloud cyber security. The research emphasizes the potential of machine learning algorithms in improving cloud computing security for industries and the need for continued research and development.
Article
Biochemistry & Molecular Biology
Belen Jimenez-Mena, Hugo Flavio, Romina Henriques, Alice Manuzzi, Miguel Ramos, Dorte Meldrup, Janette Edson, Snaebjorn Palsson, Gudbjorg Asta Olafsdottir, Jennifer R. Ovenden, Einar Eg Nielsen
Summary: This research presents specific guidelines and considerations for designing capture sequencing experiments for population genetics, focusing on neutral genomic regions and regions subject to selection. The bait design process for three fish species was described, and the performance of the approach was evaluated across historical and modern samples. The supeRbaits R-package, which implements the workflow used for designing the bait sets, is user-friendly and versatile.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Computer Science, Hardware & Architecture
Yandong Zheng, Rongxing Lu, Yunguo Guan, Jun Shao, Hui Zhu
Summary: This article proposes a practical and privacy-preserving multi-dimensional range query (PRQ) scheme, which utilizes R-tree and lightweight matrix encryption technique to address the issues of single-dimensional privacy leakage, inefficiency, and the requirement of two cloud servers in existing solutions.
IEEE TRANSACTIONS ON DEPENDABLE AND SECURE COMPUTING
(2022)
Article
Computer Science, Information Systems
Jiayi Li, Jianfeng Ma, Yinbin Miao, Ruikang Yang, Ximeng Liu, Kim-Kwang Raymond Choo
Summary: This article proposes an efficient and privacy-preserving multi-keyword ranked search scheme that achieves highly accurate ciphertext retrieval by combining coordinate matching with TF-IDF and improving the secure kNN method. It also effectively refines users' search privileges through a polynomial-based access strategy.
IEEE TRANSACTIONS ON CLOUD COMPUTING
(2022)
Article
Genetics & Heredity
William Cross, Iben Lyskjaer, Tom Lesluyes, Steven Hargreaves, Anna-Christina Strobl, Christopher Davies, Sara Waise, Shadi Hames-Fathi, Dahmane Oukrif, Hongtao Ye, Fernanda Amary, Roberto Tirabosco, Craig Gerrand, Toby Baker, David Barnes, Christopher Steele, Ludmil Alexandrov, Gareth Bond, Genomics England Research Consortium, Paul Cool, Nischalan Pillay, Peter Van Loo, Adrienne M. Flanagan
Summary: This study aimed to improve the accuracy of prognostication for central conventional chondrosarcoma patients by examining IDH1, IDH2, and TERT mutations. The results showed significant differences in the relationship and prognosis of IDH1 and IDH2 mutant tumors with TERT mutations.
Article
Oncology
Chie Kikutake, Mikita Suyama
Summary: This study elucidated the mechanism by which whole-genome doubling (WGD) affects prognosis in cancer patients using sequencing data. It was found that WGD was associated with longer LOH regions and LOH in chr17, which were in turn associated with poor prognosis. In non-WGD samples, the number of mutations in tumor suppressor genes was also associated with prognosis. Different treatment strategies may be needed for WGD and non-WGD samples.
Article
Computer Science, Theory & Methods
Sang-Hoon Choi, Ki-Woong Park
Summary: Given the increasing importance of stability and security in cloud computing services, this article proposes a method called Cloud-BlackBox that records the memory of VM swarms running on cloud platforms and enables large-scale analysis. By clustering memory and using cognitive-scale bitmaps, the approach reduces storage and improves performance, making it applicable in various fields.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
(2022)
Correction
Biotechnology & Applied Microbiology
Sergei Yakneen, Sebastian M. Waszak, Michael Gertz, Jan O. Korbel, Brice Aminou, Javier Bartolome, Keith A. Boroevich, Rich Boyce, Angela N. Brooks, Alex Buchanan, Ivo Buchhalter, Adam P. Butler, Niall J. Byrne, Andy Cafferkey, Peter J. Campbell, Zhaohong Chen, Sunghoon Cho, Wan Choi, Peter Clapham, Brandi N. Davis-Dusenbery, Francisco M. De La Vega, Jonas Demeulemeester, Michelle T. Dow, Lewis Jonathan Dursi, Juergen Eils, Roland Eils, Kyle Ellrott, Claudiu Farcas, Francesco Favero, Nodirjon Fayzullaev, Vincent Ferretti, Paul Flicek, Nuno A. Fonseca, Josep Ll. Gelpi, Gad Getz, Bob Gibson, Robert L. Grossman, Olivier Harismendy, Allison P. Heath, Michael C. Heinold, Julian M. Hess, Oliver Hofmann, Jongwhi H. Hong, Thomas J. Hudson, Barbara Hutter, Carolyn M. Hutter, Daniel Hubschmann, Seiya Imoto, Sinisa Ivkovic, Seung-Hyup Jeon, Wei Jiao, Jongsun Jung, Rolf Kabbe, Andre Kahles, Jules N. A. Kerssemakers, Hyung-Lae Kim, Hyunghwan Kim, Jihoon Kim, Youngwook Kim, Kortine Kleinheinz, Michael Koscher, Antonios Koures, Milena Kovacevic, Chris Lawerenz, Ignaty Leshchiner, Jia Liu, Dimitri Livitz, George L. Mihaiescu, Sanja Mijalkovic, Ana Mijalkovic Lazic, Satoru Miyano, Naoki Miyoshi, Hardeep K. Nahal-Bose, Hidewaki Nakagawa, Mia Nastic, Steven J. Newhouse, Jonathan Nicholson, Brian D. O'Connor, David Ocana, Kazuhiro Ohi, Lucila Ohno-Machado, Larsson Omberg, B. F. Francis Ouellette, Nagarajan Paramasivam, Marc D. Perry, Todd D. Pihl, Manuel Prinz, Montserrat Puiggros, Petar Radovic, Keiran M. Raine, Esther Rheinbay, Mara Rosenberg, Romina Royo, Gunnar Ratsch, Gordon Saksena, Matthias Schlesner, Solomon I. Shorser, Charles Short, Heidi J. Sofia, Jonathan Spring, Lincoln D. Stein, Adam J. Struck, Grace Tiao, Nebojsa Tijanic, David Torrents, Peter Van Loo, Miguel Vazquez, David Vicente, Jeremiah A. Wala, Zhining Wang, Sebastian M. Waszak, Joachim Weischenfeldt, Johannes Werner, Ashley Williams, Youngchoon Woo, Adam J. Wright, Qian Xiang, Liming Yang, Denis Yuen, Christina K. Yung, Junjun Zhang, Jan O. Korbel
NATURE BIOTECHNOLOGY
(2023)
Correction
Genetics & Heredity
Yuan Yuan, Young Seok Ju, Youngwook Kim, Jun Li, Yumeng Wang, Christopher J. Yoon, Yang Yang, Inigo Martincorena, Chad J. Creighton, John N. Weinstein, Yanxun Xu, Leng Han, Hyung-Lae Kim, Hidewaki Nakagawa, Keunchil Park, Peter J. Campbell, Han Liang
Article
Biochemistry & Molecular Biology
Nikos Sidiropoulos, Balca R. Mardin, F. German Rodriguez-Gonzalez, Ivan D. Bochkov, Shilpa Garg, Adrian M. Stuetz, Jan O. Korbel, Erez Lieberman Aiden, Joachim Weischenfeldt
Summary: The study reveals that the occurrence and formation of genomic structural variants are influenced by 3D chromatin architecture, with SVs having a tendency to occur between similar chromatin compartments and replication timing regions, and impacting gene regulation.
Article
Genetics & Heredity
Michelle D. Noyes, William T. Harvey, David Porubsky, Arvis Sulovari, Ruiyang Li, Nicholas R. Rose, Peter A. Audano, Katherine M. Munson, Alexandra P. Lewis, Kendra Hoekzema, Tuomo Mantere, Tina A. Graves-Lindsay, Ashley D. Sanders, Sara Goodwin, Melissa Kramer, Younes Mokrab, Michael C. Zody, Alexander Hoischen, Jan O. Korbel, W. Richard McCombie, Evan E. Eichler
Summary: This study utilized long-read sequencing and a more complete reference genome to identify more de novo mutations, providing a more comprehensive catalog compared to previous short-read data studies.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Oncology
Paulina Richter-Pechanska, Joachim B. Kunz, Tobias Rausch, Busra Erarslan-Uysal, Beat Bornhauser, Viktoras Frismantas, Yassen Assenov, Martin Zimmermann, Margit Happich, Caroline von Knebel-Doeberitz, Nils von Neuhoff, Rolf Kohler, Martin Stanulla, Martin Schrappe, Gunnar Cario, Gabriele Escherich, Renate Kirschner-Schwabe, Cornelia Eckert, Smadar Avigad, Stefan M. Pfister, Martina U. Muckenthaler, Jean-Pierre Bourquin, Jan O. Korbel, Andreas E. Kulozik
Summary: This study investigates the mechanisms of T-ALL relapse and reveals fundamentally different mechanisms driving type-1 and type-2 relapses. Type-1 relapses are characterized by IL7R upregulation, while type-2 relapses involve constitutional cancer predisposition gene mutations, genetic and epigenetic remodeling, and somatic hypermutator phenotypes. The study also finds that T-ALLs that later develop into type-2 relapses already have complex subclonal architecture even at the time of initial diagnosis.
Article
Genetics & Heredity
Jana Ebler, Peter Ebert, Wayne E. Clarke, Tobias Rausch, Peter A. Audano, Torsten Houwaart, Yafei Mao, Jan O. Korbel, Evan E. Eichler, Michael C. Zody, Alexander T. Dilthey, Tobias Marschall
Summary: PanGenie is an alignment-free, k-mer-based tool that uses a haplotype-resolved pangenome reference and k-mer counts from short-read sequencing data to perform fast and accurate genotyping of a wide range of genetic variants. It outperforms mapping-based approaches in terms of speed and genotype concordance, especially for large insertions and variants in repetitive regions.
Article
Biochemistry & Molecular Biology
Ludovica Mercuri, Donato Palmisano, Alberto L'Abbate, Pietro D'Addabbo, Francesco Montinaro, Claudia Rita Catacchio, Patrick Hasenfeld, Mario Ventura, Jan O. Korbel, Ashley D. Sanders, Flavia Angela Maria Maggiolini, Francesca Antonacci
Summary: This study provides a comprehensive analysis of the southern white-cheeked gibbon genome, revealing a large number of small-scale inversions and suggesting their involvement in the rapid evolution and high diversity of gibbons. The study also identifies assembly errors in the current reference genome and lists candidate genes potentially involved in gibbon diversification and speciation.
Meeting Abstract
Hematology
Aino-Maija Leppae, Karen Grimes, Hyobin Jeong, Tobias Boch, Darja Karpova, Florian Gruenschlaeger, Anna Jauch, Anna Dolnik, Bernardo Rodriguez-Martin, Lars Bullinger, Alwin Kraemer, Ashley D. Sanders, Jan O. Korbel, Andreas Trumpp
Correction
Multidisciplinary Sciences
Claudia Calabrese, Natalie R. Davidson, Deniz Demircioglu, Nuno A. Fonseca, Yao He, Andre Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, Liliana Greger, Siliang Li, Dongbing Liu, Marc D. Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter Bailey, Serap Erkek, Katherine A. Hoadley, Yong Hou, Matthew R. Huska, Helena Kilpinen, Jan O. Korbel, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarstrom, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G. Stark, Hong Su, Patrick Tan, Sebastian M. Waszak, Christina Yung, Shida Zhu, Philip Awadalla, Chad J. Creighton, Matthew Meyerson, B. F. Francis Ouellette, Kui Wu, Huanming Yang, Alvis Brazma, Angela N. Brooks, Jonathan Goeke, Gunnar Raetsch, Roland F. Schwarz, Oliver Stegle, Zemin Zhang
Article
Biotechnology & Applied Microbiology
Hyobin Jeong, Karen Grimes, Kerstin K. Rauwolf, Peter-Martin Bruch, Tobias Rausch, Patrick Hasenfeld, Eva Benito, Tobias Roider, Radhakrishnan Sabarinathan, David Porubsky, Sophie A. Herbst, Busra Erarslan-Uysal, Johann-Christoph Jann, Tobias Marschall, Daniel Nowak, Jean-Pierre Bourquin, Andreas E. Kulozik, Sascha Dietrich, Beat Bornhauser, Ashley D. Sanders, Jan O. Korbel
Summary: This study introduces a computational method called scNOVA, which utilizes Strand-seq to analyze structural variations in single cells and infer gene expression. The research reveals the impact of structural variations on gene regulation and signaling pathways, and successfully applies the method to the study of chronic lymphocytic leukemia and T cell acute lymphoblastic leukemia.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
David R. Porubsky, Mitchell T. Vollger, William N. Harvey, Allison Rozanski, Peter Ebert, Glenn Hickey, Patrick D. Hasenfeld, Ashley Sanders, Catherine O. Stober, Jan Korbel, Benedict E. Paten, Tobias Marschall, Evan Eichler
Summary: There has been significant progress in phased genome assembly by combining long-read data with parental information or linked-read data. However, the typical phased genome assembly still has over 140 gaps. A detailed analysis of 182 haploid assemblies reveals that the majority of assembly gaps cluster near large and identical repeats, resulting in disrupted protein-coding genes. Misorientations and alignment discontinuities are also identified, highlighting the need for algorithmic development and pangenome representation.
Correction
Cell Biology
Adam Karoutas, Witold Szymanski, Tobias Rausch, Sukanya Guhathakurta, Eva A. Rog-Zielinska, Remi Peyronnet, Janine Seyfferth, Hui-Ru Chen, Rebecca de Leeuw, Benjamin Herquel, Hiroshi Kimura, Gerhard Mittler, Peter Kohl, Ohad Medalia, Jan O. Korbel, Asifa Akhtar
NATURE CELL BIOLOGY
(2023)
Article
Hematology
Cristina Lopez, Nikolai Schleussner, Stephan H. Bernhart, Kortine Kleinheinz, Stephanie Sungalee, Henrike L. Sczakiel, Helene Kretzmer, Umut H. Toprak, Selina Glaser, Rabea Wagener, Ole Ammerpohl, Susanne Bens, Maciej Giefing, Juan C. Gonzalez Sanchez, Gordana Apic, Daniel Huebschmann, Martin Janz, Markus Kreuz, Anja Mottok, Judith M. Mueller, Julian Seufert, Steve Hoffmann, Jan O. Korbel, Robert B. Russell, Roland Schuele, Lorenz Truemper, Wolfram Klapper, Bernhard Radlwimmer, Peter Lichter, Ralf Kueppers, Matthias Schlesner, Stephan Mathas, Reiner Siebert
Summary: Histone methylation-modifiers, including EZH2 and KMT2D, are frequently altered in B-cell lymphomas. In this study, we examined the whole genome and transcriptome data of 186 cases and identified recurrent alterations in KDM4C, a histone demethylase encoding gene on chromosome 9p24. We demonstrated that these structural variants in KDM4C result in loss-of-function and provide evidence that KDM4C can act as a tumor suppressor. Thus, our findings expand the mutational landscape of lymphomas and highlight the importance of KDM4C in B-cell derived lymphomas.
Meeting Abstract
Environmental Sciences
Jan O. Korbel
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2022)