Search
Results
-
A missense variant effect prediction and annotation resource for SARS-CoV-2
(2021)bioRxivThe COVID19 pandemic is a global crisis severely impacting many people across the world. An important part of the response is monitoring viral variants and determining the impact they have on viral properties, such as infectivity, disease severity and interactions with drugs and vaccines. In this work we generate and make available computational variant effect predictions for all possible single amino-acid substitutions to SARS-CoV-2 in ...Working Paper -
Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival
(2021)bioRxivGenetic alterations in cancer cells trigger oncogenic transformation, a process largely mediated by the dysregulation of kinase and transcription factor (TF) activities. While the mutational profiles of thousands of tumours has been extensively characterized, the measurements of protein activities has been technically limited until recently. We compiled public data of matched genomics and (phospho)proteomics measurements for 1,110 tumours ...Working Paper -
Nektar++: Design and implementation of an implicit, spectral/hp element, compressible flow solver using a Jacobian-free Newton Krylov approach
(2020)arXivAt high Reynolds numbers, the use of explicit in time compressible flow simulations with spectral/hp element discretization can become significantly limited by time step. To alleviate this limitation we extend the capability of the spectral/hp element open-source software framework, Nektar++, to include an implicit discontinuous Galerkin compressible flow solver. The integration in time is carried out by a singly diagonally implicit ...Working Paper -
Network expansion of genetic associations defines a pleiotropy map of human cell biology
(2021)bioRxivProteins that interact within molecular networks tend to have similar functions and when perturbed influence the same organismal traits. Interaction networks can be used to expand the list of likely trait associated genes from genome-wide association studies (GWAS). Here, we used improvements in SNP-to-gene mapping to perform network based expansion of trait associated genes for 1,002 human traits showing that this recovers known disease ...Working Paper -
Hydrologic predictions in a changing environment: behavioral modeling
(2010)Hydrology and Earth System Sciences DiscussionsMost hydrological models are valid at most only in a few places and cannot be rea-sonably transferred to other places or to far distant time periods. Transfer in space isdifficult because the models are conditioned on past observations at particular placesto define parameter values and unobservable processes that are needed to fully characterize the structure and functioning of the landscape. Transfer in time has to deal withthe likely ...Working Paper -
Electricity Planning for Sustainable Development in the MENA Region
(2017)MENA-SELECT Working PaperWorking Paper -
A structural biology community assessment of AlphaFold 2 applications
(2021)bioRxivWorking Paper -
Modeling Electrical Resistance Drift with Ultrafast Saturation of OTS Selectors
(2021)arXivCrossbar array architecture is an essential design element for densely connected Non-Volatile Memory(NVM) applications. To overcome intrinsic sneak current problem of crossbar arrays, each memory unit is serially attached to a selector unit with highly nonlinear current-voltage (I-V) characteristics. Recently, Ovonic Threshold Switching (OTS) materials are preferred as selectors due to their fabrication compatibility with PRAM, MRAM or ...Working Paper -
Towards a structurally resolved human protein interaction network
(2021)bioRxivAll cellular functions are governed by complex molecular machines that assemble through protein-protein interactions. Their atomic details are critical to the study of their molecular mechanisms but fewer than 5% of hundreds of thousands of human interactions have been structurally characterized. Here, we test the potential and limitations of recent progress in deep-learning methods using AlphaFold2 to predict structures for 65,484 human ...Working Paper -
The distribution of plasmid fitness effects explains plasmid persistence in bacterial communities
(2020)bioRxivPlasmid persistence in bacterial populations is strongly influenced by the fitness effects associated with plasmid carriage. However, plasmid fitness effects in wild-type bacterial hosts remain largely unexplored. In this study, we determined the distribution of fitness effects (DFE) for the major antibiotic resistance plasmid pOXA-48 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. Our results ...Working Paper