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1. Engineering the Magnetic Transition Temperatures and the Rare Earth Exchange Interaction in Oxide Heterostructures

Author

Spring, Jonathan, Fedorova, Natalya, Georgescu, Alexandru B., Vogel, Alexander, De Luca, Gabriele, Jöhr, Simon, Piamonteze, Cinthia, Rossell, Marta D., Íñiguez-González, Jorge, and Gibert, Marta

Subjects
Condensed Matter - Materials Science, Condensed Matter - Strongly Correlated Electrons
Abstract

The properties of functional oxide heterostructures are strongly influenced by the physics governing their interfaces. Modern deposition techniques allow us to accurately engineer the interface physics through the growth of atomically precise heterostructures. This enables minute control over the electronic, magnetic, and structural characteristics. Here, we investigate the magnetic properties of tailor-made superlattices employing the ferromagnetic and insulating double perovskites RE$_2$NiMnO$_6$ (RE = La, Nd), featuring distinct Curie temperatures. Adjusting the superlattice periodicity at the unit cell level allows us to engineer their magnetic phase diagram. Large periodicity superlattices conserve the individual para- to ferromagnetic transitions of the La$_2$NiMnO$_6$ and Nd$_2$NiMnO$_6$ parent compounds. As the superlattice periodicity is reduced, the Curie temperatures of the superlattice constituents converge and, finally, collapse into one single transition for the lowest period samples. This is a consequence of the magnetic order parameter propagating across the superlattice interfaces, as supported by a minimal Landau theory model. Further, we find that the Nd-Ni/Mn exchange interaction can be enhanced by the superlattice interfaces. This leads to a field-induced reversal of the Nd magnetic moments, as confirmed by synchrotron X-ray magnetic circular dichroism measurements and supported by first-principles calculations. Our work demonstrates how superlattice engineering can be employed to fine-tune the magnetic properties in oxide heterostructures and broadens our understanding of magnetic interfacial effects.

Published
2024

3. Adversarial Machine Learning and Cybersecurity: Risks, Challenges, and Legal Implications

Author

Musser, Micah, Lohn, Andrew, Dempsey, James X., Spring, Jonathan, Kumar, Ram Shankar Siva, Leong, Brenda, Liaghati, Christina, Martinez, Cindy, Grant, Crystal D., Rohrer, Daniel, Frase, Heather, Elliott, Jonathan, Bansemer, John, Rodriguez, Mikel, Regan, Mitt, Chowdhury, Rumman, and Hermanek, Stefan

Subjects
Computer Science - Cryptography and Security, Computer Science - Artificial Intelligence, Computer Science - Computers and Society
Abstract

In July 2022, the Center for Security and Emerging Technology (CSET) at Georgetown University and the Program on Geopolitics, Technology, and Governance at the Stanford Cyber Policy Center convened a workshop of experts to examine the relationship between vulnerabilities in artificial intelligence systems and more traditional types of software vulnerabilities. Topics discussed included the extent to which AI vulnerabilities can be handled under standard cybersecurity processes, the barriers currently preventing the accurate sharing of information about AI vulnerabilities, legal issues associated with adversarial attacks on AI systems, and potential areas where government support could improve AI vulnerability management and mitigation. This report is meant to accomplish two things. First, it provides a high-level discussion of AI vulnerabilities, including the ways in which they are disanalogous to other types of vulnerabilities, and the current state of affairs regarding information sharing and legal oversight of AI vulnerabilities. Second, it attempts to articulate broad recommendations as endorsed by the majority of participants at the workshop.

Published
2023
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4. An Analysis of How Many Undiscovered Vulnerabilities Remain in Information Systems

Author

Spring, Jonathan M

Subjects
Computer Science - Cryptography and Security
Abstract

Vulnerability management strategy, from both organizational and public policy perspectives, hinges on an understanding of the supply of undiscovered vulnerabilities. If the number of undiscovered vulnerabilities is small enough, then a reasonable investment strategy would be to focus on finding and removing the remaining undiscovered vulnerabilities. If the number of undiscovered vulnerabilities is and will continue to be large, then a better investment strategy would be to focus on quick patch dissemination and engineering resilient systems. This paper examines a paradigm, namely that the number of undiscovered vulnerabilities is manageably small, through the lens of mathematical concepts from the theory of computing. From this perspective, we find little support for the paradigm of limited undiscovered vulnerabilities. We then briefly support the notion that these theory-based conclusions are relevant to practical computers in use today. We find no reason to believe undiscovered vulnerabilities are not essentially unlimited in practice and we examine the possible economic impacts should this be the case. Based on our analysis, we recommend vulnerability management strategy adopts an approach favoring quick patch dissemination and engineering resilient systems, while continuing good software engineering practices to reduce (but never eliminate) vulnerabilities in information systems.

Published
2023
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5. On managing vulnerabilities in AI/ML systems

Author

Spring, Jonathan M., Galyardt, April, Householder, Allen D., and VanHoudnos, Nathan

Subjects
Computer Science - Cryptography and Security, Computer Science - Artificial Intelligence, Computer Science - Machine Learning
Abstract

This paper explores how the current paradigm of vulnerability management might adapt to include machine learning systems through a thought experiment: what if flaws in machine learning (ML) were assigned Common Vulnerabilities and Exposures (CVE) identifiers (CVE-IDs)? We consider both ML algorithms and model objects. The hypothetical scenario is structured around exploring the changes to the six areas of vulnerability management: discovery, report intake, analysis, coordination, disclosure, and response. While algorithm flaws are well-known in the academic research community, there is no apparent clear line of communication between this research community and the operational communities that deploy and manage systems that use ML. The thought experiments identify some ways in which CVE-IDs may establish some useful lines of communication between these two communities. In particular, it would start to introduce the research community to operational security concepts, which appears to be a gap left by existing efforts., Comment: 16 pages. New Security Paradigms Workshop

Published
2021
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6. Magnetotransport of dirty-limit van Hove singularity quasiparticles

Author

Xu, Yang, Herman, František, Granata, Veronica, Destraz, Daniel, Das, Lakshmi, Vonka, Jakub, Gerber, Simon, Spring, Jonathan, Gibert, Marta, Schilling, Andreas, Zhang, Xiaofu, Li, Shiyan, Fittipaldi, Rosalba, Fischer, Mark H., Vecchione, Antonio, and Chang, Johan

Subjects
Condensed Matter - Strongly Correlated Electrons
Abstract

Tuning of electronic density-of-states singularities is a common route to unconventional metal physics. Conceptually, van Hove singularities are realized only in clean two-dimensional systems. Little attention has therefore been given to the disordered (dirty) limit. Here, we provide a magnetotransport study of the dirty metamagnetic system calcium-doped strontium ruthenate. Fermi liquid properties persist across the metamagnetic transition, but with an unusually strong variation of the Kadowaki-Woods ratio. This is revealed by a strong decoupling of inelastic electron scattering and electronic mass inferred from density-of-state probes. We discuss this Fermi liquid behavior in terms of a magnetic field tunable van Hove singularity in the presence of disorder. More generally, we show how dimensionality and disorder control the fate of transport properties across metamagnetic transitions.

Published
2020
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7. Learning the Associations of MITRE ATT&CK Adversarial Techniques

Author

Al-Shaer, Rawan, Spring, Jonathan M., and Christou, Eliana

Subjects
Computer Science - Cryptography and Security, Computer Science - Artificial Intelligence
Abstract

The MITRE ATT&CK Framework provides a rich and actionable repository of adversarial tactics, techniques, and procedures (TTP). However, this information would be highly useful for attack diagnosis (i.e., forensics) and mitigation (i.e., intrusion response) if we can reliably construct technique associations that will enable predicting unobserved attack techniques based on observed ones. In this paper, we present our statistical machine learning analysis on APT and Software attack data reported by MITRE ATT&CK to infer the technique clustering that represents the significant correlation that can be used for technique prediction. Due to the complex multidimensional relationships between techniques, many of the traditional clustering methods could not obtain usable associations. Our approach, using hierarchical clustering for inferring attack technique associations with 95% confidence, provides statistically significant and explainable technique correlations. Our analysis discovers 98 different technique associations (i.e., clusters) for both APT and Software attacks. Our evaluation results show that 78% of the techniques associated by our algorithm exhibit significant mutual information that indicates reasonably high predictability., Comment: 13 pages, 15 figures. Pre-print / expanded version of paper accepted for publication at IEEE CNS 2020

Published
2020

8. Review of human decision-making during computer security incident analysis

Author

Spring, Jonathan M. and Illari, Phyllis

Subjects
Computer Science - Computers and Society, Computer Science - Cryptography and Security
Abstract

We review practical advice on decision-making during computer security incident response. Scope includes standards from the IETF, ISO, FIRST, and the US intelligence community. To focus on human decision-making, the scope is the evidence collection, analysis, and reporting phases of response. The results indicate both strengths and gaps. A strength is available advice on how to accomplish many specific tasks. However, there is little guidance on how to prioritize tasks in limited time or how to interpret, generalize, and convincingly report results. Future work should focus on these gaps in explication and specification of decision-making during incident analysis., Comment: 58 pages, 45 pages excluding bibliography and glossary

Published
2019

9. Human decision-making in computer security incident response

Author

Spring, Jonathan Michael, Pym, D., and Illari, P.

Subjects
004
Abstract

Background: Cybersecurity has risen to international importance. Almost every organization will fall victim to a successful cyberattack. Yet, guidance for computer security incident response analysts is inadequate. Research Questions: What heuristics should an incident analyst use to construct general knowledge and analyse attacks? Can we construct formal tools to enable automated decision support for the analyst with such heuristics and knowledge? Method: We take an interdisciplinary approach. To answer the first question, we use the research tradition of philosophy of science, specifically the study of mechanisms. To answer the question on formal tools, we use the research tradition of program verification and logic, specifically Separation Logic. Results: We identify several heuristics from biological sciences that cybersecurity researchers have re-invented to varying degrees. We consolidate the new mechanisms literature to yield heuristics related to the fact that knowledge is of clusters of multi-field mechanism schema on four dimensions. General knowledge structures such as the intrusion kill chain provide context and provide hypotheses for filling in details. The philosophical analysis answers this research question, and also provides constraints on building the logic. Finally, we succeed in defining an incident analysis logic resembling Separation Logic and translating the kill chain into it as a proof of concept. Conclusion: These results benefits incident analysis, enabling it to expand from a tradecraft or art to also integrate science. Future research might realize our logic into automated decision-support. Additionally, we have opened the field of cybersecuity to collaboration with philosophers of science and logicians.

Published
2019

10. The Matsu Wheel: A Cloud-based Framework for Efficient Analysis and Reanalysis of Earth Satellite Imagery

Author

Patterson, Maria T, Anderson, Nikolas, Bennett, Collin, Bruggemann, Jacob, Grossman, Robert, Handy, Matthew, Ly, Vuong, Mandl, Dan, Pederson, Shane, Pivarski, Jim, Powell, Ray, Spring, Jonathan, and Wells, Walt

Subjects
Computer Science - Distributed, Parallel, and Cluster Computing, Astrophysics - Instrumentation and Methods for Astrophysics
Abstract

Project Matsu is a collaboration between the Open Commons Consortium and NASA focused on developing open source technology for the cloud-based processing of Earth satellite imagery. A particular focus is the development of applications for detecting fires and floods to help support natural disaster detection and relief. Project Matsu has developed an open source cloud-based infrastructure to process, analyze, and reanalyze large collections of hyperspectral satellite image data using OpenStack, Hadoop, MapReduce, Storm and related technologies. We describe a framework for efficient analysis of large amounts of data called the Matsu "Wheel." The Matsu Wheel is currently used to process incoming hyperspectral satellite data produced daily by NASA's Earth Observing-1 (EO-1) satellite. The framework is designed to be able to support scanning queries using cloud computing applications, such as Hadoop and Accumulo. A scanning query processes all, or most of the data, in a database or data repository. We also describe our preliminary Wheel analytics, including an anomaly detector for rare spectral signatures or thermal anomalies in hyperspectral data and a land cover classifier that can be used for water and flood detection. Each of these analytics can generate visual reports accessible via the web for the public and interested decision makers. The resultant products of the analytics are also made accessible through an Open Geospatial Compliant (OGC)-compliant Web Map Service (WMS) for further distribution. The Matsu Wheel allows many shared data services to be performed together to efficiently use resources for processing hyperspectral satellite image data and other, e.g., large environmental datasets that may be analyzed for many purposes., Comment: 10 pages, accepted for presentation to IEEE BigDataService 2016

Published
2016
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12. Building General Knowledge of Mechanisms in Information Security

Author

Spring, Jonathan M. and Illari, Phyllis

Subjects
Oxford University Press (Oxford, England) -- Safety and security measures, Philosophy -- Analysis, Spyware -- Analysis, Book publishing -- Analysis, Library and information science, Science and technology, Social sciences
Abstract

We show how more general knowledge can be built in information security, by the building of knowledge of mechanism clusters, some of which are multifield. By doing this, we address in a novel way the longstanding philosophical problem of how, if at all, we come to have knowledge that is in any way general, when we seem to be confined to particular experiences. We also address the issue of building knowledge of mechanisms by studying an area that is new to the mechanisms literature: the methods of what we shall call mechanism discovery in information security. This domain offers a fascinating novel constellation of challenges for building more general knowledge. Specifically, the building of stable communicable mechanistic knowledge is impeded by the inherent changeability of software, which is deployed by malicious actors constantly changing how their software attacks, and also by an ineliminable secrecy concerning the details of attacks not just by attackers (black hats), but also by information security defenders (white hats) as they protect their methods from both attackers and commercial competitors. We draw out ideas from the work of the mechanists Darden, Craver, and Glennan to yield an approach to how general knowledge of mechanisms can be painstakingly built. We then use three related examples of active research problems from information security (botnets, computer network attacks, and malware analysis) to develop philosophical thinking about building general knowledge using mechanisms, and also apply this to develop insights for information security. We show that further study would be instructive both for practitioners (who might welcome the help in conceptualizing what they do) and for philosophers (who will find novel insights into building general knowledge of a highly changeable domain that has been neglected within philosophy of science)., Author(s): Jonathan M. Spring [sup.1], Phyllis Illari [sup.2] Author Affiliations: (1) grid.83440.3b, 0000000121901201, Computer Science, University College London, , WC1E 6BT, London, England (2) grid.83440.3b, 0000000121901201, Science and Technology Studies, [...]

Published
2019
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13. Paramagnetic Nd sublattice and thickness-dependent ferromagnetism in Nd2NiMnO6 double perovskite thin films

Author

Swiss National Science Foundation, Agencia Estatal de Investigación (España), Spring, Jonathan [0000-0003-2447-3075], Luca, Gabriele de [0000-0003-3757-3761], Herrero Martín, Javier [0000-0003-1986-8128], Guillemard, Charles [0000-0002-3347-0047], Piamonteze, Cinthia [0000-0002-8416-9668], Rosário, Carlos M.M. [0000-0002-3285-2027], Hilgenkamp, Hans [0000-0001-6109-8804], Gibert, Marta [0000-0001-8856-6831], Spring, Jonathan, Luca, Gabriele de, Jöhr, Simon, Herrero Martín, Javier, Guillemard, Charles, Piamonteze, Cinthia, Rosário, Carlos M.M., Hilgenkamp, Hans, Gibert, Marta, Swiss National Science Foundation, Agencia Estatal de Investigación (España), Spring, Jonathan [0000-0003-2447-3075], Luca, Gabriele de [0000-0003-3757-3761], Herrero Martín, Javier [0000-0003-1986-8128], Guillemard, Charles [0000-0002-3347-0047], Piamonteze, Cinthia [0000-0002-8416-9668], Rosário, Carlos M.M. [0000-0002-3285-2027], Hilgenkamp, Hans [0000-0001-6109-8804], Gibert, Marta [0000-0001-8856-6831], Spring, Jonathan, Luca, Gabriele de, Jöhr, Simon, Herrero Martín, Javier, Guillemard, Charles, Piamonteze, Cinthia, Rosário, Carlos M.M., Hilgenkamp, Hans, and Gibert, Marta

Abstract

We investigate ferromagnetic and insulating thin films of the B-site ordered double perovskite Nd2NiMnO6 (NNMO) grown by radio frequency off-axis magnetron sputtering. The films grow epitaxially strained on a selection of substrates and display a strain-independent and bulklike TC of 200K at a thickness of 30 unit cells. We explore the thickness dependence of the NNMO/SrTiO3(001) system and find ferromagnetism down to ultralow thicknesses of only 3 unit cells (∼1.2nm). Below 10 unit cells, the magnetic properties deteriorate due to an interfacial charge transfer caused by the polar discontinuity at the NNMO/SrTiO3 interface. A detailed x-ray magnetic circular dichroism study allows us to separate the magnetic components into a robust ferromagnetic Ni/Mn sublattice and a paramagnetic Nd sublattice.

Published
2023

14. Towards Scientific Incident Response

Author

Spring, Jonathan M., Pym, David, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Bushnell, Linda, editor, Poovendran, Radha, editor, and Başar, Tamer, editor

Published
2018
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16. Why Separation Logic Works

Author

Pym, David, Spring, Jonathan M., and O'Hearn, Peter

Subjects
Memory (Computers), Computer science, Semiconductor memory, Library and information science, Science and technology, Social sciences
Abstract

One might poetically muse that computers have the essence both of logic and machines. Through the case of the history of Separation Logic, we explore how this assertion is more than idle poetry. Separation Logic works because it merges the software engineer's conceptual model of a program's manipulation of computer memory with the logical model that interprets what sentences in the logic are true, and because it has a proof theory which aids in the crucial problem of scaling the reasoning task. Scalability is a central problem, and some would even say the central problem, in appli- cations of logic in computer science. Separation Logic is an interesting case because of its widespread success in verification tools. For these two senses of model-the engineering/conceptual and the logical-to merge in a genuine sense, each must maintain their norms of use from their home disciplines. When this occurs, both the logic and engineering benefit greatly. Seeking this intersection of two different senses of model provides a strategy for how computer scientists and logicians may be successful. Furthermore, the history of Separation Logic for analysing programs provides a novel case for philosophers of science of how software engineers and computer scientists develop models and the components of such models. We provide three contributions: an exploration of the extent of models merging that is necessary for success in computer science; an introduction to the technical details of Separation Logic, which can be used for reasoning about other exhaustible resources; and an introduction to (a subset of) the problems, process, and results of computer scientists for those outside the field., Author(s): David Pym [sup.1] , Jonathan M. Spring [sup.1] , Peter O'Hearn [sup.1] Author Affiliations: (Aff1) 0000000121901201, grid.83440.3b, Computer Science, University College London, , Gower Street, WC1E 6BT, London, UK [...]

Published
2019
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17. On Malfunction, Mechanisms and Malware Classification

Author

Primiero, Giuseppe, Solheim, Frida J., and Spring, Jonathan M.

Subjects
Data security -- Methods -- Social aspects, Spyware -- Identification and classification -- Control -- Social aspects, Data security issue, Library and information science, Science and technology, Social sciences
Abstract

Malware has been around since the 1980s and is a large and expensive security concern today, constantly growing over the past years. As our social, professional and financial lives become more digitalised, they present larger and more profitable targets for malware. The problem of classifying and preventing malware is therefore urgent, and it is complicated by the existence of several specific approaches. In this paper, we use an existing malware taxonomy to formulate a general, language independent functional description of malware as transformers between states of the host system and described by a trust relation with its components. This description is then further generalised in terms of mechanisms, thereby contributing to a general understanding of malware. The aim is to use the latter in order to present an improved classification method for malware., Author(s): Giuseppe Primiero [sup.1] , Frida J. Solheim [sup.2] , Jonathan M. Spring [sup.3] Author Affiliations: (Aff1) 0000 0004 1757 2822, grid.4708.b, Department of Philosophy, University of Milan, , Via [...]

Published
2019
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19. Competition between Carrier Injection and Structural Distortions in Electron‐Doped Perovskite Nickelate Thin Films

Author

Hadjimichael, Marios, primary, Mundet, Bernat, additional, Domínguez, Claribel, additional, Waelchli, Adrien, additional, De Luca, Gabriele, additional, Spring, Jonathan, additional, Jöhr, Simon, additional, McKeown Walker, Siobhan, additional, Piamonteze, Cinthia, additional, Alexander, Duncan T. L., additional, Triscone, Jean‐Marc, additional, and Gibert, Marta, additional

Published
2023
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20. Author Correction: The NCI Genomic Data Commons

Author

Heath, Allison P., Ferretti, Vincent, Agrawal, Stuti, An, Maksim, Angelakos, James C., Arya, Renuka, Bajari, Rosita, Baqar, Bilal, Barnowski, Justin H. B., Burt, Jeffrey, Catton, Ann, Chan, Brandon F., Chu, Fay, Cullion, Kim, Davidsen, Tanja, Do, Phuong-My, Dompierre, Christian, Ferguson, Martin L., Fitzsimons, Michael S., Ford, Michael, Fukuma, Miyuki, Gaheen, Sharon, Ganji, Gajanan L., Garcia, Tzintzuni I., George, Sameera S., Gerhard, Daniela S., Gerthoffert, Francois, Gomez, Fauzi, Han, Kang, Hernandez, Kyle M., Issac, Biju, Jackson, Richard, Jensen, Mark A., Joshi, Sid, Kadam, Ajinkya, Khurana, Aishmit, Kim, Kyle M. J., Kraft, Victoria E., Li, Shenglai, Lichtenberg, Tara M., Lodato, Janice, Lolla, Laxmi, Martinov, Plamen, Mazzone, Jeffrey A., Miller, Daniel P., Miller, Ian, Miller, Joshua S., Miyauchi, Koji, Murphy, Mark W., Nullet, Thomas, Ogwara, Rowland O., Ortuño, Francisco M., Pedrosa, Jesús, Pham, Phuong L., Popov, Maxim Y., Porter, James J., Powell, Raymond, Rademacher, Karl, Reid, Colin P., Rich, Samantha, Rogel, Bessie, Sahni, Himanso, Savage, Jeremiah H., Schmitt, Kyle A., Simmons, Trevar J., Sislow, Joseph, Spring, Jonathan, Stein, Lincoln, Sullivan, Sean, Tang, Yajing, Thiagarajan, Mathangi, Troyer, Heather D., Wang, Chang, Wang, Zhining, West, Bedford L., Wilmer, Alex, Wilson, Shane, Wu, Kaman, Wysocki, William P., Xiang, Linda, Yamada, Joseph T., Yang, Liming, Yu, Christine, Yung, Christina K., Zenklusen, Jean Claude, Zhang, Junjun, Zhang, Zhenyu, Zhao, Yuanheng, Zubair, Ariz, Staudt, Louis M., and Grossman, Robert L.

Published
2021
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21. Competition between Carrier Injection and Structural Distortions in Electron‐Doped Perovskite Nickelate Thin Films

Author

Hadjimichael, Marios; https://orcid.org/0000-0001-6618-8075, Mundet, Bernat; https://orcid.org/0000-0003-0608-2070, Domínguez, Claribel; https://orcid.org/0000-0002-1438-0230, Waelchli, Adrien, De Luca, Gabriele; https://orcid.org/0000-0003-3757-3761, Spring, Jonathan; https://orcid.org/0000-0002-3645-8908, Jöhr, Simon, McKeown Walker, Siobhan, Piamonteze, Cinthia; https://orcid.org/0000-0002-8416-9668, Alexander, Duncan T L; https://orcid.org/0000-0003-4350-8587, Triscone, Jean‐Marc; https://orcid.org/0000-0002-9067-701X, Gibert, Marta; https://orcid.org/0000-0001-8856-6831, Hadjimichael, Marios; https://orcid.org/0000-0001-6618-8075, Mundet, Bernat; https://orcid.org/0000-0003-0608-2070, Domínguez, Claribel; https://orcid.org/0000-0002-1438-0230, Waelchli, Adrien, De Luca, Gabriele; https://orcid.org/0000-0003-3757-3761, Spring, Jonathan; https://orcid.org/0000-0002-3645-8908, Jöhr, Simon, McKeown Walker, Siobhan, Piamonteze, Cinthia; https://orcid.org/0000-0002-8416-9668, Alexander, Duncan T L; https://orcid.org/0000-0003-4350-8587, Triscone, Jean‐Marc; https://orcid.org/0000-0002-9067-701X, and Gibert, Marta; https://orcid.org/0000-0001-8856-6831

Abstract

The discovery of superconductivity in doped infinite‐layer nickelate thin films has brought increased attention to the behavior of the doped perovskite phase. Despite this interest, the majority of existing studies pertain to hole‐doped perovskite rare‐earth nickelate thin films, while most electron‐doping studies have been performed on bulk materials so far. To tackle this imbalance, a detailed study that addresses doping of NdNiO$_{3}$ thin films using A‐site substitution is presented, using Pb as a dopant and taking advantage of its valence‐skipping nature. Through a combination of complementary techniques including X‐ray diffraction, transport measurements, X‐ray absorption spectroscopy, electron energy‐loss spectroscopy and scanning transmission electron microscopy, the valence of Pb in the Nd$_{1−x}$Pb$_{x}$NiO$_{3}$ structure is confirmed to be 4+, and the behavior of the doped thin films is found to be controlled by a competition between carrier injection and structural distortions, which respectively reduce and increase the metal‐to‐insulator transition temperature. This work provides a systematic study of electron doping in NdNiO$_{3}$, demonstrating that A‐site substitution with Pb is an appropriate method for such doping in perovskite rare‐earth nickelate systems.

Published
2023

22. Cyber Security via Signaling Games: Toward a Science of Cyber Security

Author

Casey, William, Morales, Jose A., Nguyen, Thomson, Spring, Jonathan, Weaver, Rhiannon, Wright, Evan, Metcalf, Leigh, Mishra, Bud, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, and Natarajan, Raja, editor

Published
2014
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23. NRXN1 is associated with enlargement of the temporal horns of the lateral ventricles in psychosis

Author

Alliey-Rodriguez, Ney, Grey, Tamar A., Shafee, Rebecca, Asif, Huma, Lutz, Olivia, Bolo, Nicolas R., Padmanabhan, Jaya, Tandon, Neeraj, Klinger, Madeline, Reis, Katherine, Spring, Jonathan, Coppes, Lucas, Zeng, Victor, Hegde, Rachal R., Hoang, Dung T., Bannai, Deepthi, Nawaz, Uzma, Henson, Philip, Liu, Siyuan, Gage, Diane, McCarroll, Steven, Bishop, Jeffrey R., Hill, Scot, Reilly, James L., Lencer, Rebekka, Clementz, Brett A., Buckley, Peter, Glahn, David C., Meda, Shashwath A., Narayanan, Balaji, Pearlson, Godfrey, Keshavan, Matcheri S., Ivleva, Elena I., Tamminga, Carol, Sweeney, John A., Curtis, David, Badner, Judith A., Keedy, Sarah, Rapoport, Judith, Liu, Chunyu, and Gershon, Elliot S.

Published
2019
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25. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

Author

Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, 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Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian

Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.

Published
2023
Full Text
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26. Combined burden and functional impact tests for cancer driver discovery using DriverPower

Author

Shuai, Shimin, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Barenboim, Jonathan, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lawrence, Michael S, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Marchal, Kathleen, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Paczkowska, Marta, Park, Keunchil, Park, Kiejung, Pedersen, Jakob Skou, Pons, Tirso, Pulido-Tamayo, Sergio, Raphael, Benjamin J, Reimand, Jüri, Reyes-Salazar, Iker, Reyna, Matthew A, Rheinbay, Esther, Rubin, Mark A, Rubio-Perez, Carlota, Sahinalp, S Cenk, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shrestha, Raunak, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Stuart, Joshua M, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, Uusküla-Reimand, Liis, Valencia, Alfonso, Vazquez, Miguel, Verbeke, Lieven PC, Wadelius, 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Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.

Published
2023
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27. Integrative pathway enrichment analysis of multivariate omics data

Author

Paczkowska, Marta, Barenboim, Jonathan, Sintupisut, Nardnisa, Fox, Natalie S, Zhu, Helen, Abd-Rabbo, Diala, Mee, Miles W, Boutros, Paul C, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Brunak, Søren, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Dhingra, Priyanka, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Getz, Gad, Gonzalez-Perez, Abel, Guo, Qianyun, Gut, Ivo G, Haan, David, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Izarzugaza, Jose MG, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kahraman, Abdullah, Kellis, Manolis, Khurana, Ekta, Kim, Jaegil, Kim, Jong K, Kim, 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Vijver, Marc J, and Veer, L van’t

Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an integrative method that discovers significantly enriched pathways across multiple datasets using statistical data fusion, rationalizes contributing evidence and highlights associated genes. As part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumor types, we integrated genes with coding and non-coding mutations and revealed frequently mutated pathways and additional cancer genes with infrequent mutations. We also analyzed prognostic molecular pathways by integrating genomic and transcriptomic features of 1780 breast cancers and highlighted associations with immune response and anti-apoptotic signaling. Integration of ChIP-seq and RNA-seq data for master regulators of the Hippo pathway across normal human tissues identified processes of tissue regeneration and stem cell regulation. ActivePathways is a versatile method that improves systems-level understanding of cellular organization in health and disease through integration of multiple molecular datasets and pathway annotations.

Published
2023
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28. Pathway and network analysis of more than 2500 whole cancer genomes

Author

Reyna, Matthew A, Haan, David, Paczkowska, Marta, Verbeke, Lieven PC, Vazquez, Miguel, Kahraman, Abdullah, Pulido-Tamayo, Sergio, Barenboim, Jonathan, Wadi, Lina, Dhingra, Priyanka, Shrestha, Raunak, Getz, Gad, Lawrence, Michael S, Pedersen, Jakob Skou, Rubin, Mark A, Wheeler, David A, Brunak, Søren, Izarzugaza, Jose MG, Khurana, Ekta, Marchal, Kathleen, von Mering, Christian, Sahinalp, S Cenk, Valencia, Alfonso, Abascal, Federico, Amin, Samirkumar B, Bader, Gary D, Bandopadhayay, Pratiti, Beroukhim, Rameen, Bertl, Johanna, Boroevich, Keith A, Busanovich, John, Campbell, Peter J, Carlevaro-Fita, Joana, Chakravarty, Dimple, Chan, Calvin Wing Yiu, Chen, Ken, Choi, Jung Kyoon, Deu-Pons, Jordi, Diamanti, Klev, Feuerbach, Lars, Fink, J Lynn, Fonseca, Nuno A, Frigola, Joan, Gambacorti-Passerini, Carlo, Garsed, Dale W, Gerstein, Mark, Guo, Qianyun, Gut, Ivo G, Hamilton, Mark P, Haradhvala, Nicholas J, Harmanci, Arif O, Helmy, Mohamed, Herrmann, Carl, Hess, Julian M, Hobolth, Asger, Hodzic, Ermin, Hong, Chen, Hornshøj, Henrik, Isaev, Keren, Johnson, Rory, Johnson, Todd A, Juul, Malene, Juul, Randi Istrup, Kahles, Andre, Kellis, Manolis, Kim, Jaegil, Kim, Jong K, Kim, Youngwook, Komorowski, Jan, Korbel, Jan O, Kumar, Sushant, Lanzós, Andrés, Larsson, Erik, Lee, Donghoon, Lehmann, Kjong-Van, Li, Shantao, Li, Xiaotong, Lin, Ziao, Liu, Eric Minwei, Lochovsky, Lucas, Lou, Shaoke, Madsen, Tobias, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, McGillivray, Patrick D, Meyerson, William, Muiños, Ferran, Mularoni, Loris, Nakagawa, Hidewaki, Nielsen, Morten Muhlig, Park, Keunchil, Park, Kiejung, Pons, Tirso, Reyes-Salazar, Iker, Rheinbay, Esther, Rubio-Perez, Carlota, Saksena, Gordon, Salichos, Leonidas, Sander, Chris, Schumacher, Steven E, Shackleton, Mark, Shapira, Ofer, Shen, Ciyue, Shuai, Shimin, Sidiropoulos, Nikos, Sieverling, Lina, Sinnott-Armstrong, Nasa, Stein, Lincoln D, Tamborero, David, Tiao, Grace, Tsunoda, Tatsuhiko, Umer, Husen M, 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Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding mutations, most notably TERT promoter mutations, have been reported. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancer across 38 tumor types, we perform multi-faceted pathway and network analyses of non-coding mutations across 2583 whole cancer genomes from 27 tumor types compiled by the ICGC/TCGA PCAWG project that was motivated by the success of pathway and network analyses in prioritizing rare mutations in protein-coding genes. While few non-coding genomic elements are recurrently mutated in this cohort, we identify 93 genes harboring non-coding mutations that cluster into several modules of interacting proteins. Among these are promoter mutations associated with reduced mRNA expression in TP53, TLE4, and TCF4. We find that biological processes had variable proportions of coding and non-coding mutations, with chromatin remodeling and proliferation pathways altered primarily by coding mutations, while developmental pathways, including Wnt and Notch, altered by both coding and non-coding mutations. RNA splicing is primarily altered by non-coding mutations in this cohort, and samples containing non-coding mutations in well-known RNA splicing factors exhibit similar gene expression signatures as samples with coding mutations in these genes. These analyses contribute a new repertoire of possible cancer genes and mechanisms that are altered by non-coding mutations and offer insights into additional cancer vulnerabilities that can be investigated for potential therapeutic treatments.

Published
2023
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29. Divergent mutational processes distinguish hypoxic and normoxic tumours

Author

Bhandari, Vinayak, Li, Constance H, Bristow, Robert G, Boutros, Paul C, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Atwal, Gurnit, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Bailey, Peter J, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhosle, Shriram G, Biankin, Andrew V, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campbell, Peter J, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chang, David K, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooke, Susanna L, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshpande, Vikram, Deshwar, Amit G, Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C, Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Faltas, Bishoy M, Fan, Daiming, Fan, Yu, Faquin, William C, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A, Fink, J Lynn, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garraway, Levi, Garred, Øystein, Garrison, Erik, Garsed, Dale W, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstein, Mark, Gerstung, Moritz, Getz, Gad, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grimmond, Sean M, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Ivo G, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Haider, Syed, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Hamilton, Mark P, Han, Leng, Hanna, George B, Hansmann, Martin, Haradhvala, Nicholas J, Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Helmy, Mohamed, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Herrmann, Carl, Hersey, Peter, Hess, Julian M, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hoadley, Katherine A, Hobolth, Asger, Hodzic, Ermin, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Chen, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hornshøj, Henrik, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Isaev, Keren, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Izarzugaza, Jose MG, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Jiao, Wei, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Johnson, Rory, Johnson, Todd A, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Malene, Juul, Randi Istrup, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kahles, Andre, Kahraman, Abdullah, Kaiser, Vera B, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S, Katai, Hitoshi, Kato, Mamoru, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kellis, Manolis, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Khurana, Ekta, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jaegil, Kim, Jihoon, Kim, Jong K, Kim, Youngwook, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komorowski, Jan, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korbel, Jan O, Korchina, Viktoriya, Korshunov, Andrey, Koscher, Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Kiran, Kumar, Pardeep, Kumar, Sushant, Kumar, Yogesh, Kundra, Ritika, Kübler, Kirsten, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lawrence, Michael S, Lazar, Alexander J, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Lou, Shaoke, Louis, David N, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lynch, Andy G, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchal, Kathleen, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin, Sancha, Martin-Subero, Jose I, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McGillivray, Patrick D, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, Matthew, Meyerson, William, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyano, Satoru, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morris, Quaid D, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Muiños, Ferran, Mularoni, Loris, Mungall, Andrew J, Mungall, Karen, Musgrove, Elizabeth A, Mustonen, Ville, Mutch, David, Muyas, Francesc, Muzny, Donna M, Muñoz, Alfonso, Myers, Jerome, Myklebost, Ola, Möller, Peter, Nagae, Genta, Nagrial, Adnan M, Nahal-Bose, Hardeep K, Nakagama, Hitoshi, Nakagawa, Hidewaki, Nakamura, Hiromi, Nakamura, Toru, Nakano, Kaoru, Nandi, Tannistha, Nangalia, Jyoti, Nastic, Mia, Navarro, Arcadi, Navarro, Fabio CP, Neal, David E, Nettekoven, Gerd, Newell, Felicity, Newhouse, Steven J, Newton, Yulia, Ng, Alvin Wei Tian, Ng, Anthony, Nicholson, Jonathan, Nicol, David, Nie, Yongzhan, Nielsen, G Petur, Nielsen, Morten Muhlig, Nik-Zainal, Serena, Noble, Michael S, Nones, Katia, Northcott, Paul A, Notta, Faiyaz, O’Connor, Brian D, O’Donnell, Peter, O’Donovan, Maria, O’Meara, Sarah, O’Neill, Brian Patrick, O’Neill, J Robert, Ocana, David, Ochoa, Angelica, Oesper, Layla, Ogden, Christopher, Ohdan, Hideki, Ohi, Kazuhiro, Ohno-Machado, Lucila, Oien, Karin A, Ojesina, Akinyemi I, Ojima, Hidenori, Okusaka, Takuji, Omberg, Larsson, Ong, Choon Kiat, Ossowski, Stephan, Ott, German, Ouellette, BF Francis, P’ng, Christine, Paczkowska, Marta, Paiella, Salvatore, Pairojkul, Chawalit, Pajic, Marina, Pan-Hammarström, Qiang, Papaemmanuil, Elli, Papatheodorou, Irene, Paramasivam, Nagarajan, Park, Ji Wan, Park, Joong-Won, Park, Keunchil, Park, Kiejung, Park, Peter J, Parker, Joel S, Parsons, Simon L, Pass, Harvey, Pasternack, Danielle, Pastore, Alessandro, Patch, Ann-Marie, Pauporté, Iris, Pea, Antonio, Pearson, John V, Pedamallu, Chandra Sekhar, Pedersen, Jakob Skou, Pederzoli, Paolo, Peifer, Martin, Pennell, Nathan A, Perou, Charles M, Perry, Marc D, Petersen, Gloria M, Peto, Myron, Petrelli, Nicholas, Petryszak, Robert, Pfister, Stefan M, Phillips, Mark, Pich, Oriol, Pickett, Hilda A, Pihl, Todd D, Pillay, Nischalan, Pinder, Sarah, Pinese, Mark, Pinho, Andreia V, Pitkänen, Esa, Pivot, Xavier, Piñeiro-Yáñez, Elena, Planko, Laura, Plass, Christoph, Polak, Paz, Pons, Tirso, Popescu, Irinel, Potapova, Olga, Prasad, Aparna, Preston, Shaun R, Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Puiggròs, Montserrat, Pulido-Tamayo, Sergio, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Raphael, Benjamin J, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reimand, Jüri, Reis-Filho, Jorge, Reuter, Victor, Reyes-Salazar, Iker, Reyna, Matthew A, Reynolds, Sheila M, Rheinbay, Esther, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Rippe, Karsten, Roach, Jeffrey, Roberts, Lewis R, Roberts, Nicola D, Roberts, Steven A, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodriguez-Martin, Bernardo, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rubin, Mark A, Rubio-Perez, Carlota, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabarinathan, Radhakrishnan, Sabelnykova, Veronica Y, Sadeghi, Sara, Sahinalp, S Cenk, Saini, Natalie, Saito-Adachi, Mihoko, Saksena, Gordon, Salcedo, Adriana, Salgado, Roberto, Salichos, Leonidas, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sander, Chris, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlesner, Matthias, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schumacher, Steven E, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Scully, Ralph, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shackleton, Mark, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shapira, Ofer, Shelton, Troy, Shen, Ciyue, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shrestha, Raunak, Shringarpure, Suyash S, Shriver, Craig, Shuai, Shimin, Sidiropoulos, Nikos, Siebert, Reiner, Sieuwerts, Anieta M, Sieverling, Lina, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sinnott-Armstrong, Nasa, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D, Stenhouse, Alasdair, Stewart, Chip, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stuart, Joshua M, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tamborero, David, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tiao, Grace, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Torrents, David, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, MC Tubio, Jose, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Villasante, Izar, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Waddell, Nicola, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wala, Jeremiah A, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, 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Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Lixing, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yao, Xiaotong, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yoon, Sung-Soo, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zamora, Jorge, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Cheng-Zhong, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian

Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

Many primary tumours have low levels of molecular oxygen (hypoxia), and hypoxic tumours respond poorly to therapy. Pan-cancer molecular hallmarks of tumour hypoxia remain poorly understood, with limited comprehension of its associations with specific mutational processes, non-coding driver genes and evolutionary features. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we quantify hypoxia in 1188 tumours spanning 27 cancer types. Elevated hypoxia associates with increased mutational load across cancer types, irrespective of underlying mutational class. The proportion of mutations attributed to several mutational signatures of unknown aetiology directly associates with the level of hypoxia, suggesting underlying mutational processes for these signatures. At the gene level, driver mutations in TP53, MYC and PTEN are enriched in hypoxic tumours, and mutations in PTEN interact with hypoxia to direct tumour evolutionary trajectories. Overall, hypoxia plays a critical role in shaping the genomic and evolutionary landscapes of cancer.

Published
2023
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30. Genomic footprints of activated telomere maintenance mechanisms in cancer

Author

Sieverling, Lina, Hong, Chen, Koser, Sandra D, Ginsbach, Philip, Kleinheinz, Kortine, Hutter, Barbara, Braun, Delia M, Cortés-Ciriano, Isidro, Xi, Ruibin, Kabbe, Rolf, Park, Peter J, Eils, Roland, Schlesner, Matthias, Akdemir, Kadir C, Alvarez, Eva G, Baez-Ortega, Adrian, Beroukhim, Rameen, Boutros, Paul C, Bowtell, David DL, Brors, Benedikt, Burns, Kathleen H, Campbell, Peter J, Chan, Kin, Chen, Ken, Dueso-Barroso, Ana, Dunford, Andrew J, Edwards, Paul A, Estivill, Xavier, Etemadmoghadam, Dariush, Feuerbach, Lars, Fink, J Lynn, Frenkel-Morgenstern, Milana, Garsed, Dale W, Gerstein, Mark, Gordenin, Dmitry A, Haan, David, Haber, James E, Hess, Julian M, Imielinski, Marcin, Jones, David TW, Ju, Young Seok, Kazanov, Marat D, Klimczak, Leszek J, Koh, Youngil, Korbel, Jan O, Kumar, Kiran, Lee, Eunjung Alice, Lee, Jake June-Koo, Li, Yilong, Lynch, Andy G, Macintyre, Geoff, Markowetz, Florian, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Meyerson, Matthew, Miyano, Satoru, Nakagawa, 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Prinz, Manuel, Pritchard, Antonia L, Prokopec, Stephenie D, Provenzano, Elena, Puente, Xose S, Puig, Sonia, Pulido-Tamayo, Sergio, Pupo, Gulietta M, Purdie, Colin A, Quinn, Michael C, Rabionet, Raquel, Rader, Janet S, Radlwimmer, Bernhard, Radovic, Petar, Raeder, Benjamin, Raine, Keiran M, Ramakrishna, Manasa, Ramakrishnan, Kamna, Ramalingam, Suresh, Raphael, Benjamin J, Rathmell, W Kimryn, Rausch, Tobias, Reifenberger, Guido, Reimand, Jüri, Reis-Filho, Jorge, Reuter, Victor, Reyes-Salazar, Iker, Reyna, Matthew A, Reynolds, Sheila M, Rheinbay, Esther, Riazalhosseini, Yasser, Richardson, Andrea L, Richter, Julia, Ringel, Matthew, Ringnér, Markus, Rino, Yasushi, Roach, Jeffrey, Roberts, Lewis R, Robertson, A Gordon, Robertson, Alan J, Rodriguez, Javier Bartolomé, Rodríguez-González, F Germán, Roehrl, Michael HA, Rohde, Marius, Rokutan, Hirofumi, Romieu, Gilles, Rooman, Ilse, Roques, Tom, Rosebrock, Daniel, Rosenberg, Mara, Rosenstiel, Philip C, Rosenwald, Andreas, Rowe, Edward W, Royo, Romina, Rozen, Steven G, Rubanova, Yulia, Rubin, Mark A, Rubio-Perez, Carlota, Rudneva, Vasilisa A, Rusev, Borislav C, Ruzzenente, Andrea, Rätsch, Gunnar, Sabarinathan, Radhakrishnan, Sabelnykova, Veronica Y, Sadeghi, Sara, Sahinalp, S Cenk, Saini, Natalie, Saito-Adachi, Mihoko, Saksena, Gordon, Salcedo, Adriana, Salgado, Roberto, Salichos, Leonidas, Sallari, Richard, Saller, Charles, Salvia, Roberto, Sam, Michelle, Samra, Jaswinder S, Sanchez-Vega, Francisco, Sander, Chris, Sanders, Grant, Sarin, Rajiv, Sarrafi, Iman, Sasaki-Oku, Aya, Sauer, Torill, Sauter, Guido, Saw, Robyn PM, Scardoni, Maria, Scarlett, Christopher J, Scarpa, Aldo, Scelo, Ghislaine, Schadendorf, Dirk, Schein, Jacqueline E, Schilhabel, Markus B, Schlomm, Thorsten, Schmidt, Heather K, Schramm, Sarah-Jane, Schreiber, Stefan, Schultz, Nikolaus, Schwarz, Roland F, Scolyer, Richard A, Scott, David, Seethala, Raja, Segre, Ayellet V, Selander, Iris, Semple, Colin A, Senbabaoglu, Yasin, Sengupta, Subhajit, Sereni, Elisabetta, Serra, Stefano, Sgroi, Dennis C, Shah, Nimish C, Shahabi, Sagedeh, Shang, Catherine A, Shang, Ping, Shapira, Ofer, Shelton, Troy, Shen, Ciyue, Shen, Hui, Shepherd, Rebecca, Shi, Ruian, Shi, Yan, Shiah, Yu-Jia, Shibata, Tatsuhiro, Shih, Juliann, Shimizu, Eigo, Shimizu, Kiyo, Shin, Seung Jun, Shiraishi, Yuichi, Shmaya, Tal, Shmulevich, Ilya, Shorser, Solomon I, Short, Charles, Shrestha, Raunak, Shringarpure, Suyash S, Shriver, Craig, Shuai, Shimin, Siebert, Reiner, Sieuwerts, Anieta M, Signoretti, Sabina, Sikora, Katarzyna O, Simbolo, Michele, Simon, Ronald, Simons, Janae V, Simpson, Jared T, Simpson, Peter T, Singer, Samuel, Sinnott-Armstrong, Nasa, Sipahimalani, Payal, Skelly, Tara J, Smid, Marcel, Smith, Jaclyn, Smith-McCune, Karen, Socci, Nicholas D, Sofia, Heidi J, Soloway, Matthew G, Song, Lei, Sood, Anil K, Sothi, Sharmila, Sotiriou, Christos, Soulette, Cameron M, Span, Paul N, Spellman, Paul T, Sperandio, Nicola, Spillane, Andrew J, Spiro, Oliver, Spring, Jonathan, Staaf, Johan, Stadler, Peter F, Staib, Peter, Stark, Stefan G, Stebbings, Lucy, Stefánsson, Ólafur Andri, Stegle, Oliver, Stein, Lincoln D, Stenhouse, Alasdair, Stilgenbauer, Stephan, Stobbe, Miranda D, Stratton, Michael R, Stretch, Jonathan R, Struck, Adam J, Stuart, Joshua M, Stunnenberg, Henk G, Su, Hong, Su, Xiaoping, Sun, Ren X, Sungalee, Stephanie, Susak, Hana, Suzuki, Akihiro, Sweep, Fred, Szczepanowski, Monika, Sültmann, Holger, Yugawa, Takashi, Tam, Angela, Tamborero, David, Tan, Benita Kiat Tee, Tan, Donghui, Tan, Patrick, Tanaka, Hiroko, Taniguchi, Hirokazu, Tanskanen, Tomas J, Tarabichi, Maxime, Tarnuzzer, Roy, Tarpey, Patrick, Taschuk, Morgan L, Tatsuno, Kenji, Tavaré, Simon, Taylor, Darrin F, Taylor-Weiner, Amaro, Teague, Jon W, Teh, Bin Tean, Tembe, Varsha, Temes, Javier, Thai, Kevin, Thayer, Sarah P, Thiessen, Nina, Thomas, Gilles, Thomas, Sarah, Thompson, Alan, Thompson, Alastair M, Thompson, John FF, Thompson, R Houston, Thorne, Heather, Thorne, Leigh B, Thorogood, Adrian, Tiao, Grace, Tijanic, Nebojsa, Timms, Lee E, Tirabosco, Roberto, Tojo, Marta, Tommasi, Stefania, Toon, Christopher W, Toprak, Umut H, Tortora, Giampaolo, Tost, Jörg, Totoki, Yasushi, Townend, David, Traficante, Nadia, Treilleux, Isabelle, Trotta, Jean-Rémi, Trümper, Lorenz HP, Tsao, Ming, Tsunoda, Tatsuhiko, Tucker, Olga, Turkington, Richard, Turner, Daniel J, Tutt, Andrew, Ueno, Masaki, Ueno, Naoto T, Umbricht, Christopher, Umer, Husen M, Underwood, Timothy J, Urban, Lara, Urushidate, Tomoko, Ushiku, Tetsuo, Uusküla-Reimand, Liis, Valencia, Alfonso, Van Den Berg, David J, Van Laere, Steven, Van Loo, Peter, Van Meir, Erwin G, Van den Eynden, Gert G, Van der Kwast, Theodorus, Vasudev, Naveen, Vazquez, Miguel, Vedururu, Ravikiran, Veluvolu, Umadevi, Vembu, Shankar, Verbeke, Lieven PC, Vermeulen, Peter, Verrill, Clare, Viari, Alain, Vicente, David, Vicentini, Caterina, VijayRaghavan, K, Viksna, Juris, Vilain, Ricardo E, Vincent-Salomon, Anne, Visakorpi, Tapio, Voet, Douglas, Vyas, Paresh, Vázquez-García, Ignacio, Waddell, Nick M, Wadelius, Claes, Wadi, Lina, Wagener, Rabea, Wang, Jian, Wang, Jiayin, Wang, Linghua, Wang, Qi, Wang, Wenyi, Wang, Yumeng, Wang, Zhining, Waring, Paul M, Warnatz, Hans-Jörg, Warrell, Jonathan, Warren, Anne Y, Waszak, Sebastian M, Wedge, David C, Weichenhan, Dieter, Weinberger, Paul, Weinstein, John N, Weisenberger, Daniel J, Welch, Ian, Wendl, Michael C, Werner, Johannes, Whalley, Justin P, Wheeler, David A, Whitaker, Hayley C, Wigle, Dennis, Wilkerson, Matthew D, Williams, Ashley, Wilmott, James S, Wilson, Gavin W, Wilson, Julie M, Wilson, Richard K, Winterhoff, Boris, Wintersinger, Jeffrey A, Wiznerowicz, Maciej, Wolf, Stephan, Wong, Bernice H, Wong, Tina, Wong, Winghing, Woo, Youngchoon, Wood, Scott, Wouters, Bradly G, Wright, Adam J, Wright, Derek W, Wright, Mark H, Wu, Chin-Lee, Wu, Dai-Ying, Wu, Guanming, Wu, Jianmin, Wu, Kui, Wu, Yang, Wu, Zhenggang, Xi, Liu, Xia, Tian, Xiang, Qian, Xiao, Xiao, Xing, Rui, Xiong, Heng, Xu, Qinying, Xu, Yanxun, Xue, Hong, Yachida, Shinichi, Yakneen, Sergei, Yamaguchi, Rui, Yamaguchi, Takafumi N, Yamamoto, Masakazu, Yamamoto, Shogo, Yamaue, Hiroki, Yang, Fan, Yang, Huanming, Yang, Jean Y, Yang, Liming, Yang, Shanlin, Yang, Tsun-Po, Yang, Yang, Yaspo, Marie-Laure, Yates, Lucy, Yau, Christina, Ye, Chen, Ye, Kai, Yellapantula, Venkata D, Yoon, Christopher J, Yousif, Fouad, Yu, Jun, Yu, Kaixian, Yu, Willie, Yu, Yingyan, Yuan, Ke, Yuan, Yuan, Yuen, Denis, Yung, Christina K, Zaikova, Olga, Zapatka, Marc, Zenklusen, Jean C, Zenz, Thorsten, Zeps, Nikolajs, Zhang, Fan, Zhang, Hailei, Zhang, Hongwei, Zhang, Hongxin, Zhang, Jiashan, Zhang, Jing, Zhang, Junjun, Zhang, Xiuqing, Zhang, Xuanping, Zhang, Yan, Zhang, Zemin, Zhao, Zhongming, Zheng, Liangtao, Zheng, Xiuqing, Zhou, Wanding, Zhou, Yong, Zhu, Bin, Zhu, Hongtu, Zhu, Jingchun, Zhu, Shida, Zou, Lihua, Zou, Xueqing, deFazio, Anna, van As, Nicholas, van Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian

Subjects
Human Biology & Physiology, Ecology,Evolution & Ethology, Tumour Biology, Genetics & Genomics, Structural Biology & Biophysics, Computational & Systems Biology
Abstract

Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we dissect whole-genome sequencing data of over 2500 matched tumor-control samples from 36 different tumor types aggregated within the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium to characterize the genomic footprints of these mechanisms. While the telomere content of tumors with ATRX or DAXX mutations (ATRX/DAXXtrunc) is increased, tumors with TERT modifications show a moderate decrease of telomere content. One quarter of all tumor samples contain somatic integrations of telomeric sequences into non-telomeric DNA. This fraction is increased to 80% prevalence in ATRX/DAXXtrunc tumors, which carry an aberrant telomere variant repeat (TVR) distribution as another genomic marker. The latter feature includes enrichment or depletion of the previously undescribed singleton TVRs TTCGGG and TTTGGG, respectively. Our systematic analysis provides new insight into the recurrent genomic alterations associated with telomere maintenance mechanisms in cancer.

Published
2023
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33. Top‐Layer Engineering Reshapes Charge Transfer at Polar Oxide Interfaces

Author

De Luca, Gabriele, primary, Spring, Jonathan, additional, Kaviani, Moloud, additional, Jöhr, Simon, additional, Campanini, Marco, additional, Zakharova, Anna, additional, Guillemard, Charles, additional, Herrero‐Martin, Javier, additional, Erni, Rolf, additional, Piamonteze, Cinthia, additional, Rossell, Marta D., additional, Aschauer, Ulrich, additional, and Gibert, Marta, additional

Published
2022
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34. Supporting Information for Adv. Mater., DOI: 10.1002/adma.202203071 Top-Layer Engineering Reshapes Charge Transfer at Polar Oxide Interfaces

Author

Luca, Gabriele de, Spring, Jonathan, Kaviani, Moloud, Jöhr, Simon, Campanini, Marco, Zakharova, Anna, Guillemard, Charles, Herrero Martín, Javier, Erni, Rolf, Piamonteze, Cinthia, Rossell, Marta D., Aschauer, Ulrich, Gibert, Marta, Luca, Gabriele de, Spring, Jonathan, Kaviani, Moloud, Jöhr, Simon, Campanini, Marco, Zakharova, Anna, Guillemard, Charles, Herrero Martín, Javier, Erni, Rolf, Piamonteze, Cinthia, Rossell, Marta D., Aschauer, Ulrich, and Gibert, Marta

Published
2022

35. Top-layer engineering reshapes charge transfer at polar oxide interfaces

Author

Swiss National Science Foundation, Luca, Gabriele de, Spring, Jonathan, Kaviani, Moloud, Jöhr, Simon, Campanini, Marco, Zakharova, Anna, Guillemard, Charles, Herrero Martín, Javier, Erni, Rolf, Piamonteze, Cinthia, Rossell, Marta D., Aschauer, Ulrich, Gibert, Marta, Swiss National Science Foundation, Luca, Gabriele de, Spring, Jonathan, Kaviani, Moloud, Jöhr, Simon, Campanini, Marco, Zakharova, Anna, Guillemard, Charles, Herrero Martín, Javier, Erni, Rolf, Piamonteze, Cinthia, Rossell, Marta D., Aschauer, Ulrich, and Gibert, Marta

Abstract

Charge-transfer phenomena at heterointerfaces are a promising pathway to engineer functionalities absent in bulk materials but can also lead to degraded properties in ultrathin films. Mitigating such undesired effects with an interlayer reshapes the interface architecture, restricting its operability. Therefore, developing less-invasive methods to control charge transfer will be beneficial. Here, an appropriate top-interface design allows for remote manipulation of the charge configuration of the buried interface and concurrent restoration of the ferromagnetic trait of the whole film. Double-perovskite insulating ferromagnetic La2NiMnO6 (LNMO) thin films grown on perovskite oxide substrates are investigated as a model system. An oxygen-vacancy-assisted electronic reconstruction takes place initially at the LNMO polar interfaces. As a result, the magnetic properties of 2–5 unit cell LNMO films are affected beyond dimensionality effects. The introduction of a top electron-acceptor layer redistributes the electron excess and restores the ferromagnetic properties of the ultrathin LNMO films. Such a strategy can be extended to other interfaces and provides an advanced approach to fine-tune the electronic features of complex multilayered heterostructures.

Published
2022

36. Toward Controlling Filament Size and Location for Resistive Switches via Nanoparticle Exsolution at Oxide Interfaces

Author

Massachusetts Institute of Technology. Department of Materials Science and Engineering, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Spring, Jonathan, Sediva, Eva, Hood, Zachary D., Gonzalez‐Rosillo, Juan Carlos, O'Leary, Willis, Kim, Kun Joong, Carrillo, Alfonso J., Rupp, Jennifer L. M., Massachusetts Institute of Technology. Department of Materials Science and Engineering, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Spring, Jonathan, Sediva, Eva, Hood, Zachary D., Gonzalez‐Rosillo, Juan Carlos, O'Leary, Willis, Kim, Kun Joong, Carrillo, Alfonso J., and Rupp, Jennifer L. M.

Published
2022

37. Top‐Layer Engineering Reshapes Charge Transfer at Polar Oxide Interfaces

Author

De Luca, Gabriele; https://orcid.org/0000-0003-3757-3761, Spring, Jonathan; https://orcid.org/0000-0003-2447-3075, Kaviani, Moloud, Jöhr, Simon, Campanini, Marco; https://orcid.org/0000-0003-4312-4794, Zakharova, Anna, Guillemard, Charles; https://orcid.org/0000-0002-3347-0047, Herrero‐Martin, Javier; https://orcid.org/0000-0003-1986-8128, Erni, Rolf; https://orcid.org/0000-0003-2391-5943, Piamonteze, Cinthia; https://orcid.org/0000-0002-8416-9668, Rossell, Marta D; https://orcid.org/0000-0001-8610-8853, Aschauer, Ulrich; https://orcid.org/0000-0002-1165-6377, Gibert, Marta; https://orcid.org/0000-0001-8856-6831, De Luca, Gabriele; https://orcid.org/0000-0003-3757-3761, Spring, Jonathan; https://orcid.org/0000-0003-2447-3075, Kaviani, Moloud, Jöhr, Simon, Campanini, Marco; https://orcid.org/0000-0003-4312-4794, Zakharova, Anna, Guillemard, Charles; https://orcid.org/0000-0002-3347-0047, Herrero‐Martin, Javier; https://orcid.org/0000-0003-1986-8128, Erni, Rolf; https://orcid.org/0000-0003-2391-5943, Piamonteze, Cinthia; https://orcid.org/0000-0002-8416-9668, Rossell, Marta D; https://orcid.org/0000-0001-8610-8853, Aschauer, Ulrich; https://orcid.org/0000-0002-1165-6377, and Gibert, Marta; https://orcid.org/0000-0001-8856-6831

Abstract

Charge-transfer phenomena at heterointerfaces are a promising pathway to engineer functionalities absent in bulk materials but can also lead to degraded properties in ultrathin films. Mitigating such undesired effects with an interlayer reshapes the interface architecture, restricting its operability. Therefore, developing less-invasive methods to control charge transfer will be beneficial. Here, an appropriate top-interface design allows for remote manipulation of the charge configuration of the buried interface and concurrent restoration of the ferromagnetic trait of the whole film. Double-perovskite insulating ferromagnetic La2NiMnO6 (LNMO) thin films grown on perovskite oxide substrates are investigated as a model system. An oxygen-vacancy-assisted electronic reconstruction takes place initially at the LNMO polar interfaces. As a result, the magnetic properties of 2–5 unit cell LNMO films are affected beyond dimensionality effects. The introduction of a top electron-acceptor layer redistributes the electron excess and restores the ferromagnetic properties of the ultrathin LNMO films. Such a strategy can be extended to other interfaces and provides an advanced approach to fine-tune the electronic features of complex multilayered heterostructures.

Published
2022

39. A State-Based Model for Multi-Party Coordinated Vulnerability Disclosure (MPCVD)

Author

Householder, Allen and Spring, Jonathan

Subjects
FOS: Computer and information sciences, 80309 Software Engineering
Abstract

Coordinated Vulnerability Disclosure (CVD) stands as a consensus response to the persistent fact of vulnerable software, yet few performance indicators have been proposed to measure its efficacy at the broadest scales. In this report, we seek to fill that gap. We begin by deriving a model of all possible CVD histories from first principles, organizing those histories into a partial ordering based on a set of desired criteria. We then compute a baseline expectation for the frequency of each desired criteria and propose a new set of performance indicators to measure the efficacy of CVD practices based on the differentiation of skill and luck in observation data. As a proof of concept, we apply these indicators to a variety of longitudinal observations of CVD practice and find evidence of significant skill to be prevalent. We conclude with reflections on how this model and its accompanying performance indicators could be used by various stakeholders (vendors, system owners, coordinators, and governments) to interpret the quality of their CVD practices.

Published
2022
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41. Exploring a mechanistic approach to experimentation in computing

Author

Hatleback, Eric and Spring, Jonathan M.

Subjects
Computer engineering -- Research, Philosophy of science -- Research, Library and information science, Science and technology, Social sciences
Abstract

The mechanistic approach in philosophy of science contributes to our understanding of experimental design. Applying the mechanistic approach to experimentation in computing is beneficial for two reasons. It connects the methodology of experimentation in computing with the methodology of experimentation in established sciences, thereby strengthening the scientific reputability of computing and the quality of experimental design therein. Furthermore, it pinpoints the idiosyncrasies of experimentation in computing: computing deals closely with both natural and engineered mechanisms. Better understanding of the idiosyncrasies, which manifest in terms of a nonstandard role for experimentation, are interesting both for computer scientists and for philosophers of science. Computer scientists can think more clearly about their experimental choices. The role of experimentation elucidated by computer science merits further study from philosophers of science generally, as it highlights a role for experimentation hitherto unrecognized by philosophers: demonstration that activities exist. Keywords Computing * Experiments * Mechanisms * Experimental method, 1 Introduction This note is largely a rejoinder to a particular portion of the work by Viola Schiaffonati and Mario Verdicchio recently published in this journal (Schiaffonati and Verdicchio 2013). [...]

Published
2014
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43. Cybersecurity Information Sharing: Analysing an Email Corpus of Coordinated Vulnerability Disclosure

Author

Sridhar, Kiran, Householder, Allen, Spring, Jonathan, and Woods, Daniel W

Abstract

Information sharing is widely held to improve cybersecurity outcomes whether its driven by market forces or by cooperation among firms and individuals. Formal institutions may be established to facilitate cooperative information sharing. This paper presents a case-study of such an institution, the CERT Coordination Center (CERT/CC), and provides quantitative insights based on the meta data of 434K emails passing through CERT/CC since 1993. Our longitudinal results show how the volume and proportion of emails about different products and vendors has varied over time. We also analyse the distributions of information sharing volume, participation, and duration across 46K vulnerabilities. Finally, we run regressions to understand how the volume of information sharing and decision to coordinate vary based on properties of the vulnerability and the affected vendors. We discuss what has changed, the appropriateness of a competitive or cooperative framing, and limitations.

Published
2021
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