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-source 'https://rubygems.org'
-group :jekyll_plugins do
- gem 'jekyll'
- gem 'jekyll-archives'
- gem 'jekyll-diagrams'
- gem 'jekyll-email-protect'
- gem 'jekyll-feed'
- gem 'jekyll-imagemagick'
- gem 'jekyll-minifier'
- gem 'jekyll-paginate-v2'
- gem 'jekyll-scholar'
- gem 'jekyll-sitemap'
- gem 'jekyll-link-attributes'
- gem 'jekyll-twitter-plugin'
- gem 'jemoji'
- gem 'mini_racer'
- gem 'unicode_utils'
- gem 'webrick'
-end
-group :other_plugins do
- gem 'httparty'
- gem 'feedjira'
-end
diff --git a/_bibliography/WeisseGroup.bib b/_bibliography/WeisseGroup.bib
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-
-@inproceedings{weisse2006,
- title = {Adaptive approach for modelling variability in pharmacokinetics},
- isbn = {3-540-45767-4},
- abstract = {We present an improved adaptive approach for studying systems of ODEs affected by parameter variability and state space uncertainty. Our approach is based on a reformulation of the ODE problem as a transport problem of a probability density describing the evolution of the ensemble of systems in time. The resulting multidimensional problem is solved by representing the probability density w.r.t. an adaptively chosen Galerkin ansatz space of Gaussian densities. Due to our improvements in adaptivity control, we substantially improved the overall performance of the original algorithm and moreover inherited to the numerical scheme the theoretical property that the number of Gaussian distributions remains constant for linear ODEs. We illustrate the approach in application to dynamical systems describing the pharmacokinetics of drugs and xenobiotics, where variability in physiological parameters is important to be considered.},
- booktitle = {{CompLife}},
- author = {Weiße, Andrea Y and Horenko, Illia and Huisinga, Wilhelm},
- year = {2006},
- keywords = {weisse2006.png},
- pages = {194--204},
-}
-
-@incollection{perkins2012,
- title = {3. {Chance} and memory},
- isbn = {978-1-4398-2722-2},
- booktitle = {Quantitative {Biology}: {From} {Molecular} to {Cellular} {Systems}},
- publisher = {CRC Press},
- author = {Perkins, Theodore J and Weiße, Andrea Y and Swain, Peter S},
- year = {2012},
- keywords = {perkins2012.png},
- pages = {1--22},
-}
-
-@inproceedings{weisse2010b,
- title = {Global sensitivity analysis of {ODEs} via the solution of the associated {Fokker}-{Planck} equation},
- booktitle = {Proceedings of the 6th {Workshop} on {Computation} of {Biochemical} {Pathways} and {Genetic} {Networks}},
- publisher = {Logos Verlag Berlin},
- author = {Weiße, Andrea Y and Huisinga, Wilhelm},
- year = {2010},
- pages = {43--52},
-}
-
-@inproceedings{weisse2015b,
- title = {Quantifying host-circuit interactions with a mechanistic chassis model},
- booktitle = {Synthetic {Biology}: {Engineering}, {Evolution}, and {Design} {Conference} 2015, {SEED} 2015},
- publisher = {AIChE},
- author = {Weiße, Andrea},
- year = {2015},
- pages = {40--49},
-}
-
-@article{weisse2015a,
- title = {Mechanistic links between cellular trade-offs, gene expression, and growth},
- volume = {112},
- issn = {0027-8424, 1091-6490},
- url = {https://pnas.org/doi/full/10.1073/pnas.1416533112},
- doi = {10.1073/pnas.1416533112},
- abstract = {Significance
- Cells have finite resources. Committing resources to one task therefore reduces the amount of resources available to others. These trade-offs are often overlooked but potentially modify all cellular processes. Building a mathematical cell model that respects such trade-offs and describes the mechanisms of protein synthesis and how cells extract resources from their environment, we quantitatively recover the typical behavior of an individual growing cell and of a population of cells. As trade-offs are experienced by all cells and because growth largely determines cellular fitness, a predictive understanding of how biochemical processes affect others and affect growth is important for diverse applications, such as the use of microbes for biotechnology, the inhibition of antibiotic resistance, and the growth of cancers.
- ,
- Intracellular processes rarely work in isolation but continually interact with the rest of the cell. In microbes, for example, we now know that gene expression across the whole genome typically changes with growth rate. The mechanisms driving such global regulation, however, are not well understood. Here we consider three trade-offs that, because of limitations in levels of cellular energy, free ribosomes, and proteins, are faced by all living cells and we construct a mechanistic model that comprises these trade-offs. Our model couples gene expression with growth rate and growth rate with a growing population of cells. We show that the model recovers Monod’s law for the growth of microbes and two other empirical relationships connecting growth rate to the mass fraction of ribosomes. Further, we can explain growth-related effects in dosage compensation by paralogs and predict host–circuit interactions in synthetic biology. Simulating competitions between strains, we find that the regulation of metabolic pathways may have evolved not to match expression of enzymes to levels of extracellular substrates in changing environments but rather to balance a trade-off between exploiting one type of nutrient over another. Although coarse-grained, the trade-offs that the model embodies are fundamental, and, as such, our modeling framework has potentially wide application, including in both biotechnology and medicine.},
- language = {en},
- number = {9},
- urldate = {2023-05-25},
- journal = {Proceedings of the National Academy of Sciences},
- author = {Weiße, Andrea Y. and Oyarzún, Diego A. and Danos, Vincent and Swain, Peter S.},
- month = mar,
- year = {2015},
- keywords = {weisse2015a.png},
-}
-
-@inproceedings{hunt2023,
- address = {Baltimore, MD, USA},
- title = {Investigating the relationship between cue immersion and the strength of motor imagery during hand and wrist movements},
- isbn = {978-1-66546-292-1},
- url = {https://ieeexplore.ieee.org/document/10123823/},
- doi = {10.1109/NER52421.2023.10123823},
- abstract = {Virtual reality (VR) has gained popularity as a modality for motor imagery (MI) cue presentation for brain-computer interfaces due to the increased cortical activity caused by the immersiveness of the medium. In this work, we show that increased immersion alone is not sufficient to generate a greater cortical response during MI. We demonstrate this relationship through a MI protocol performed using three modalities of cue presentation, Image, Video, and VR, wherein intact limb participants were instructed to imagine the prompted hand and wrist movements as their own. Cue presentation using static images outperformed cue presentation using both traditional videos and immersive VR simulations (p {\textless} 0.05) in terms of percent change in relative alpha power. These results imply that providing more immersive cues may sometimes reduce the effectiveness of MI, possibly by inducing action observation rather than mental simulation.},
- urldate = {2023-05-25},
- booktitle = {2023 11th {International} {IEEE}/{EMBS} {Conference} on {Neural} {Engineering} ({NER})},
- publisher = {IEEE},
- author = {Hunt, Christopher L. and Ding, Keqin and Wagner, Christoph S. and Berberich, Nicolas and Yilmazer, Karahan and Gonzalez-Fernandez, Marlis and Cheng, Gordon and Thakor, Nitish V.},
- month = apr,
- year = {2023},
- keywords = {hunt2023.png},
- pages = {1--4},
-}
-
-@techreport{myall2021a,
- type = {preprint},
- title = {Characterising contact in disease outbreaks via a network model of spatial-temporal proximity},
- url = {http://medrxiv.org/lookup/doi/10.1101/2021.04.07.21254497},
- abstract = {ABSTRACT
- Contact tracing is a key tool in epidemiology to identify and control outbreaks of infectious diseases. Existing contact tracing methodologies produce contact maps of individuals based on a binary definition of contact which can be hampered by missing data and indirect contacts. Here, we present a Spatial-temporal Epidemiological Proximity (StEP) model to recover contact maps in disease outbreaks based on movement data. The StEP model accounts for imperfect data by considering probabilistic contacts between individuals based on spatial-temporal proximity of their movement trajectories, creating a robust movement network despite possible missing data and unseen transmission routes. Using real-world data we showcase the potential of StEP for contact tracing with outbreaks of multidrug-resistant bacteria and COVID-19 in a large hospital group in London, UK. In addition to the core structure of contacts that can be recovered using traditional methods of contact tracing, the StEP model reveals missing contacts that connect seemingly separate outbreaks. Comparison with genomic data further confirmed that these recovered contacts indeed improve characterisation of disease transmission and so highlights how the StEP framework can inform effective strategies of infection control and prevention.},
- language = {en},
- urldate = {2023-05-25},
- institution = {Epidemiology},
- author = {Myall, Ashleigh and Peach, Robert L. and Wan, Yu and Mookerjee, Siddharth and Jauneikaite, Elita and Bolt, Frankie and Price, James and Davies, Frances and Weiße, Andrea Y. and Holmes, Alison and Barahona, Mauricio},
- month = apr,
- year = {2021},
- keywords = {myall2021a.jpg},
-}
-
-@article{oyarzun2013,
- title = {Cumulative {Signal} {Transmission} in {Nonlinear} {Reaction}-{Diffusion} {Networks}},
- volume = {8},
- issn = {1932-6203},
- url = {https://dx.plos.org/10.1371/journal.pone.0062834},
- doi = {10.1371/journal.pone.0062834},
- language = {en},
- number = {5},
- urldate = {2023-05-25},
- journal = {PLoS ONE},
- author = {Oyarzún, Diego A. and López-Caamal, Fernando and García, Míriam R. and Middleton, Richard H. and Weiße, Andrea Y.},
- editor = {Kurths, Jürgen},
- month = may,
- year = {2013},
- keywords = {oyarzun2013.png},
- pages = {e62834},
-}
-
-@article{otter2020,
- title = {Detecting carbapenemase-producing {Enterobacterales} ({CPE}): an evaluation of an enhanced {CPE} infection control and screening programme in acute care},
- volume = {75},
- issn = {0305-7453, 1460-2091},
- shorttitle = {Detecting carbapenemase-producing {Enterobacterales} ({CPE})},
- url = {https://academic.oup.com/jac/article/75/9/2670/5849541},
- doi = {10.1093/jac/dkaa192},
- abstract = {Abstract
-
- Objectives
- The transmission of carbapenemase-producing Enterobacterales (CPE) poses an increasing healthcare challenge. A range of infection prevention activities, including screening and contact precautions, are recommended by international and national guidelines. We evaluated the introduction of an enhanced screening programme in a multisite London hospital group.
-
-
- Methods
- In June 2015, an enhanced CPE policy was launched in response to a local rise in CPE detection. This increased infection prevention measures beyond the national recommendations, with enhanced admission screening, contact tracing and environmental disinfection, improved laboratory protocols and staff/patient education. We report the CPE incidence and trends of CPE in screening and clinical cultures and the adoption of enhanced CPE screening. All non-duplicate CPE isolates identified between April 2014 and March 2018 were included.
-
-
- Results
- The number of CPE screens increased progressively, from 4530 in July 2015 to 10 589 in March 2018. CPE detection increased from 18 patients in July 2015 (1.0 per 1000 admissions) to 50 patients in March 2018 (2.7 per 1000 admissions). The proportion of CPE-positive screening cultures remained at approximately 0.4\% throughout, suggesting that whilst the CPE carriage rate was unchanged, carrier identification increased. Also, 123 patients were identified through positive CPE clinical cultures over the study period; there was no significant change in the rate of CPE from clinical cultures per 1000 admissions (P = 0.07).
-
-
- Conclusions
- Our findings suggest that whilst the enhanced screening programme identified a previously undetected reservoir of CPE colonization in our patient population, the rate of detection of CPE in clinical cultures did not increase.},
- language = {en},
- number = {9},
- urldate = {2023-05-25},
- journal = {Journal of Antimicrobial Chemotherapy},
- author = {Otter, Jonathan A and Mookerjee, Siddharth and Davies, Frances and Bolt, Frances and Dyakova, Eleonora and Shersing, Yeeshika and Boonyasiri, Adhiratha and Weiße, Andrea Y and Gilchrist, Mark and Galletly, Tracey J and Brannigan, Eimear T and Holmes, Alison H},
- month = sep,
- year = {2020},
- keywords = {otter2020.jpg},
- pages = {2670--2676},
-}
-
-@article{price2021,
- title = {Development and {Delivery} of a {Real}-time {Hospital}-onset {COVID}-19 {Surveillance} {System} {Using} {Network} {Analysis}},
- issn = {1058-4838, 1537-6591},
- url = {https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa892/5868508},
- doi = {10.1093/cid/ciaa892},
- abstract = {Abstract
-
- Background
- Understanding nosocomial acquisition, outbreaks, and transmission chains in real time will be fundamental to ensuring infection-prevention measures are effective in controlling coronavirus disease 2019 (COVID-19) in healthcare. We report the design and implementation of a hospital-onset COVID-19 infection (HOCI) surveillance system for an acute healthcare setting to target prevention interventions.
-
-
- Methods
- The study took place in a large teaching hospital group in London, United Kingdom. All patients tested for SARS-CoV-2 between 4 March and 14 April 2020 were included. Utilizing data routinely collected through electronic healthcare systems we developed a novel surveillance system for determining and reporting HOCI incidence and providing real-time network analysis. We provided daily reports on incidence and trends over time to support HOCI investigation and generated geotemporal reports using network analysis to interrogate admission pathways for common epidemiological links to infer transmission chains. By working with stakeholders the reports were co-designed for end users.
-
-
- Results
- Real-time surveillance reports revealed changing rates of HOCI throughout the course of the COVID-19 epidemic, key wards fueling probable transmission events, HOCIs overrepresented in particular specialties managing high-risk patients, the importance of integrating analysis of individual prior pathways, and the value of co-design in producing data visualization. Our surveillance system can effectively support national surveillance.
-
-
- Conclusions
- Through early analysis of the novel surveillance system we have provided a description of HOCI rates and trends over time using real-time shifting denominator data. We demonstrate the importance of including the analysis of patient pathways and networks in characterizing risk of transmission and targeting infection-control interventions.},
- language = {en},
- urldate = {2023-05-25},
- journal = {Clinical Infectious Diseases},
- author = {Price, James Richard and Mookerjee, Siddharth and Dyakova, Eleonora and Myall, Ashleigh and Leung, Wendy and Weiße, Andrea Yeong and Shersing, Yeeshika and Brannigan, Eimear Therese and Galletly, Tracey and Muir, David and Randell, Paul and Davies, Frances and Bolt, Frances and Barahona, Mauricio and Otter, Jonathan Ashley and Holmes, Alison H},
- month = jul,
- year = {2020},
- keywords = {price2021.jpg},
- pages = {ciaa892},
-}
-
-@article{weisse2011,
- title = {Error-controlled global sensitivity analysis of ordinary differential equations},
- volume = {230},
- issn = {00219991},
- url = {https://linkinghub.elsevier.com/retrieve/pii/S0021999111003159},
- doi = {10.1016/j.jcp.2011.05.011},
- language = {en},
- number = {17},
- urldate = {2023-05-25},
- journal = {Journal of Computational Physics},
- author = {Weiße, Andrea Y. and Huisinga, Wilhelm},
- month = jul,
- year = {2011},
- pages = {6824--6842},
-}
-
-@phdthesis{weisse2009,
- title = {Adaptive {Dichtepropagation} mit {Approximate} {ApproximationsGlobal} sensitivity analysis of ordinary differential equations: adaptive density propagation using approximate approximations},
- shorttitle = {Adaptive {Dichtepropagation} mit {Approximate} {ApproximationsGlobal} sensitivity analysis of ordinary differential equations},
- url = {https://refubium.fu-berlin.de/handle/fub188/9586},
- abstract = {Gewöhnliche Differentialgleichungen nehmen eine essentielle Stellung in der mathematischen Modellierung ein. Als Voraussetzung für zuverlässige Resultate muss sowohl in der Modellbildung als auch in der Analyse des Modells der Einfluss von Unsicherheit und/oder Variabilität in den Eingabedaten berücksichtigt werden. Mit Hilfe von Sensitivitätsanalyse wird untersucht, wie sich Unsicherheit und Variabilität durch die Modelldynamik ausbreiten und sich somit auf die Ausgabedaten auswirken. Globale Sensitivitätsanalyse untersucht die Auswirkungen von Abweichungen in den Eingabedaten, die sich möglicherweise über den gesamten Zustandsraum erstrecken. Zwei Probleme, die die globale Analyse erschweren, sind hohe Dimensionen und eine Kontrolle der Genauigkeit, mit der die Ausgabeunsicherheit geschätzt wird. Die meisten numerischen Ansätze konzentrieren sich derzeitig darauf, die Analyse von hoch- dimensionalen Problemen effizienter zu gestalten. Inwiefern die geschätzte Ausgabeunsicherheit dabei der tatsächlichen Ausgabeunsicherheit entspricht, bleibt jedoch meist unklar. In dieser Arbeit wird ein neuer Ansatz zur globalen Sensitivitätsanalyse von gewöhnlichen Differentialgleichungen vorgestellt. Hauptmerkmal dieses Ansatzes ist eine adaptive Schätzung der Ausgabeunsicherheit, bei der der Approximationsfehler automatisch kontrolliert wird. Dafür bedienen wir uns einer äquivalenten Formulierung des Problems, in der die zeitliche Entwicklung der Wahrscheinlichkeitsdichte der unsicheren Zustandsvariablen durch eine partielle Differentialgleichung beschrieben wird. Zur Lösung dieser Differentialgleichung kombinieren wir neue Ansätze aus Numerik und Approximationstheorie. Die hier vorgestellte Methode kontrolliert den Approximationsfehler, indem sowohl die Zeit- als auch die Ortsdiskretisierung angepasst wird. Wir verwenden ein Rothe-Verfahren, das einen angemessenen Kontext für die separate Schätzung von Zeit- und Ortsfehlern schafft, so dass die Diskretisierung entsprechend adaptiert werden kann. Für die Ortsdiskretisierung verwenden wir Approximate Approximations, eine neu eingeführte Approximationsmethode, die hier zum ersten Mal im Rahmen eines adaptiven Rothe-Verfahrens eingesetzt wird. Wir analysieren die Konvergenz des Verfahrens und untersuchen, wie sich Approximate Approximations für die adaptive Lösung der Ortsprobleme eignen. Wir zeigen, dass das Verfahren konvergiert. Darüber hinaus geben die theoretischen Resultate direkt Aufschluss darüber, wie eine effiziente Implementierung realisiert werden kann. Die Ergebnisse werden anhand von numerischen Beispielen illustriert, die auch zeigen, dass das Verfahren eine hohe Genauigkeit bei der Schätzung der Ausgabeunsicherheiten erzielt. Desweiteren erweisen sich Approximate Approximations als vorteilhaft innerhalb des adaptiven Verfahrens, da sowohl Fehlerschätzer als auch Approximationen hoher Ordnung zu vertretbaren Rechenzeiten verfügbar sind. Aktuelle Fortschritte in der Theorie von Approximate Approximations, beruhend auf einer gitterfreien Diskretisierung, lassen außerdem darauf hoffen, dass sich das in dieser Arbeit vorgestellte Konzept auch auf höher-dimensionale Probleme übertragen lässt.},
- urldate = {2023-05-25},
- school = {Freie Universität Berlin},
- author = {Weiße, Andrea Yeong},
- collaborator = {Universitätsbibliothek Der FU Berlin and Universitätsbibliothek Der FU Berlin},
- year = {2009},
- keywords = {weisse2009.png},
-}
-
-@article{nikolados2019,
- title = {Growth {Defects} and {Loss}-of-{Function} in {Synthetic} {Gene} {Circuits}},
- volume = {8},
- issn = {2161-5063, 2161-5063},
- url = {https://pubs.acs.org/doi/10.1021/acssynbio.8b00531},
- doi = {10.1021/acssynbio.8b00531},
- language = {en},
- number = {6},
- urldate = {2023-05-25},
- journal = {ACS Synthetic Biology},
- author = {Nikolados, Evangelos-Marios and Weiße, Andrea Y. and Ceroni, Francesca and Oyarzún, Diego A.},
- month = jun,
- year = {2019},
- keywords = {nikolados2019.jpg},
- pages = {1231--1240},
-}
-
-@article{myall2022b,
- title = {Improved contact tracing using network analysis and spatial-temporal proximity},
- volume = {116},
- issn = {12019712},
- url = {https://linkinghub.elsevier.com/retrieve/pii/S1201971221009395},
- doi = {10.1016/j.ijid.2021.12.047},
- language = {en},
- urldate = {2023-05-25},
- journal = {International Journal of Infectious Diseases},
- author = {Myall, A. and Peach, R. and Wan, Y. and Mookerjee, S. and Jauneikaite, E. and Bolt, F. and Price, J. and Davies, F. and Weisse, A. and Holmes, A.H. and Barahona, M.},
- month = mar,
- year = {2022},
- pages = {S20},
-}
-
-@article{ming2021,
- title = {Informing antimicrobial management in the context of {COVID}-19: understanding the longitudinal dynamics of {C}-reactive protein and procalcitonin},
- volume = {21},
- issn = {1471-2334},
- shorttitle = {Informing antimicrobial management in the context of {COVID}-19},
- url = {https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-021-06621-7},
- doi = {10.1186/s12879-021-06621-7},
- abstract = {Abstract
-
- Background
- To characterise the longitudinal dynamics of C-reactive protein (CRP) and Procalcitonin (PCT) in a cohort of hospitalised patients with COVID-19 and support antimicrobial decision-making.
-
-
- Methods
- Longitudinal CRP and PCT concentrations and trajectories of 237 hospitalised patients with COVID-19 were modelled. The dataset comprised of 2,021 data points for CRP and 284 points for PCT. Pairwise comparisons were performed between: (i) those with or without significant bacterial growth from cultures, and (ii) those who survived or died in hospital.
-
-
- Results
- CRP concentrations were higher over time in COVID-19 patients with positive microbiology (day 9: 236 vs 123 mg/L, p {\textless} 0.0001) and in those who died (day 8: 226 vs 152 mg/L, p {\textless} 0.0001) but only after day 7 of COVID-related symptom onset. Failure for CRP to reduce in the first week of hospital admission was associated with significantly higher odds of death. PCT concentrations were higher in patients with COVID-19 and positive microbiology or in those who died, although these differences were not statistically significant.
-
-
- Conclusions
- Both the absolute CRP concentration and the trajectory during the first week of hospital admission are important factors predicting microbiology culture positivity and outcome in patients hospitalised with COVID-19. Further work is needed to describe the role of PCT for co-infection. Understanding relationships of these biomarkers can support development of risk models and inform optimal antimicrobial strategies.},
- language = {en},
- number = {1},
- urldate = {2023-05-25},
- journal = {BMC Infectious Diseases},
- author = {Ming, Damien K. and Myall, Ashleigh C. and Hernandez, Bernard and Weiße, Andrea Y. and Peach, Robert L. and Barahona, Mauricio and Rawson, Timothy M. and Holmes, Alison H.},
- month = dec,
- year = {2021},
- keywords = {ming2021.jpg},
- pages = {932},
-}
-
-@techreport{boonyasiri2021,
- type = {preprint},
- title = {Integrated patient network and genomic plasmid analysis reveal a regional, multi-species outbreak of carbapenemase-producing {Enterobacterales} carrying both \textit{bla} $_{\textrm{{IMP}}}$ and \textit{mcr-9} genes},
- url = {http://medrxiv.org/lookup/doi/10.1101/2021.10.28.21265436},
- abstract = {Abstract
- The incidence of carbapenemase-producing Enterobacterales (CPE) is rising globally, yet Imipenemase (IMP) carbapenemases remain relatively rare. This study describes an investigation of the emergence of IMP-encoding CPE amongst diverse Enterobacterales species between 2016 and 2019 in patients across a London regional hospital network.
-
- A network analysis approach to patient pathways, using routinely collected electronic health records, identified previously unrecognised contacts between patients who were IMP CPE positive on screening, implying potential bacterial transmission events. Whole genome sequencing of 85 Enterobacterales isolates from these patients revealed that 86\% (73/85) were diverse species (predominantly
- Klebsiella
- spp,
- Enterobacter
- spp,
- E. coli
- ) and harboured an IncHI2 plasmid, which carried both
- bla
- IMP
- and the putative mobile colistin resistance gene
- mcr-9
- . Detailed phylogenetic analysis identified two distinct IncHI2 plasmid lineages, A and B, both of which showed significant association with patient movements between four hospital sites and across medical specialities.
-
-
- Combined, our patient network and plasmid analyses demonstrate an interspecies, plasmid-mediated outbreak of
- bla
- IMP
- CPE, which remained unidentified during standard microbiology and infection control investigations. With whole genome sequencing (WGS) technologies and large-data incorporation, the outbreak investigation approach proposed here provides a framework for real-time identification of key factors causing pathogen spread. Analysing outbreaks at the plasmid level reveals that resistance may be wider spread than suspected, allowing more targetted interventions to stop the transmission of resistance within hospital networks.},
- language = {en},
- urldate = {2023-05-25},
- institution = {Infectious Diseases (except HIV/AIDS)},
- author = {Boonyasiri, Adhiratha and Myall, Ashleigh C. and Wan, Yu and Bolt, Frances and Ledda, Alice and Mookerjee, Siddharth and Weiße, Andrea Y. and Turton, Jane F. and Abbas, Hala and Prakapaite, Ruta and Sabnis, Akshay and Abdolrasouli, Alireza and Malpartida-Cardenas, Kenny and Miglietta, Luca and Donaldson, Hugo and Gilchrist, Mark and Hopkins, Katie L. and Ellington, Matthew J and Otter, Jonathan A. and Larrouy-Maumus, Gerald and Edwards, Andrew M. and Rodriguez-Manzano, Jesus and Didelot, Xavier and Barahona, Mauricio and Holmes, Alison H. and Jauneikaite, Elita and Davies, Frances},
- month = oct,
- year = {2021},
- keywords = {boonyasiri2021.jpg},
-}
-
-@article{myall2021b,
- title = {Network memory in the movement of hospital patients carrying antimicrobial-resistant bacteria},
- volume = {6},
- issn = {2364-8228},
- url = {https://appliednetsci.springeropen.com/articles/10.1007/s41109-021-00376-5},
- doi = {10.1007/s41109-021-00376-5},
- abstract = {Abstract
- Hospitals constitute highly interconnected systems that bring into contact an abundance of infectious pathogens and susceptible individuals, thus making infection outbreaks both common and challenging. In recent years, there has been a sharp incidence of antimicrobial-resistance amongst healthcare-associated infections, a situation now considered endemic in many countries. Here we present network-based analyses of a data set capturing the movement of patients harbouring antibiotic-resistant bacteria across three large London hospitals. We show that there are substantial memory effects in the movement of hospital patients colonised with antibiotic-resistant bacteria. Such memory effects break first-order Markovian transitive assumptions and substantially alter the conclusions from the analysis, specifically on node rankings and the evolution of diffusive processes. We capture variable length memory effects by constructing a lumped-state memory network, which we then use to identify individually import wards and overlapping communities of wards. We find these wards align closely to known hotspots of transmission and commonly followed pathways patients. Our framework provides a means to focus infection control efforts and cohort outbreaks of healthcare-associated infections.},
- language = {en},
- number = {1},
- urldate = {2023-05-25},
- journal = {Applied Network Science},
- author = {Myall, Ashleigh C. and Peach, Robert L. and Weiße, Andrea Y. and Mookerjee, Siddharth and Davies, Frances and Holmes, Alison and Barahona, Mauricio},
- month = dec,
- year = {2021},
- keywords = {myall2021b.jpg},
- pages = {34},
-}
-
-@incollection{nikolados2021,
- address = {New York, NY},
- title = {Prediction of {Cellular} {Burden} with {Host}–{Circuit} {Models}},
- volume = {2229},
- isbn = {978-1-07-161031-2 978-1-07-161032-9},
- url = {https://link.springer.com/10.1007/978-1-0716-1032-9_13},
- language = {en},
- urldate = {2023-05-25},
- booktitle = {Synthetic {Gene} {Circuits}},
- publisher = {Springer US},
- author = {Nikolados, Evangelos-Marios and Weiße, Andrea Y. and Oyarzún, Diego A.},
- editor = {Menolascina, Filippo},
- year = {2021},
- keywords = {nikolados2021.jpg},
- pages = {267--291},
-}
-
-@article{myall2022a,
- title = {Prediction of hospital-onset {COVID}-19 using networks of patient contact: an observational study},
- volume = {116},
- issn = {12019712},
- shorttitle = {Prediction of hospital-onset {COVID}-19 using networks of patient contact},
- url = {https://linkinghub.elsevier.com/retrieve/pii/S1201971221011504},
- doi = {10.1016/j.ijid.2021.12.258},
- language = {en},
- urldate = {2023-05-25},
- journal = {International Journal of Infectious Diseases},
- author = {Myall, A. and Price, J. and Peach, R. and Abbas, M. and Mookerjee, S. and Ahmad, I. and Ming, D. and Zhu, N.J. and Ramzan, F. and Weisse, A. and Holmes, A.H. and Barahona, M.},
- month = mar,
- year = {2022},
- pages = {S109--S110},
-}
-
-@article{weisse2010a,
- title = {Quantifying uncertainty, variability and likelihood for ordinary differential equation models},
- volume = {4},
- issn = {1752-0509},
- url = {https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-144},
- doi = {10.1186/1752-0509-4-144},
- language = {en},
- number = {1},
- urldate = {2023-05-25},
- journal = {BMC Systems Biology},
- author = {Weiße, Andrea Y and Middleton, Richard H and Huisinga, Wilhelm},
- month = dec,
- year = {2010},
- keywords = {weisse2010a.png},
- pages = {144},
-}
-
-@article{karwacki-neisius2013,
- title = {Reduced {Oct4} {Expression} {Directs} a {Robust} {Pluripotent} {State} with {Distinct} {Signaling} {Activity} and {Increased} {Enhancer} {Occupancy} by {Oct4} and {Nanog}},
- volume = {12},
- issn = {19345909},
- url = {https://linkinghub.elsevier.com/retrieve/pii/S1934590913001598},
- doi = {10.1016/j.stem.2013.04.023},
- language = {en},
- number = {5},
- urldate = {2023-05-25},
- journal = {Cell Stem Cell},
- author = {Karwacki-Neisius, Violetta and Göke, Jonathan and Osorno, Rodrigo and Halbritter, Florian and Ng, Jia Hui and Weiße, Andrea Y. and Wong, Frederick C.K. and Gagliardi, Alessia and Mullin, Nicholas P. and Festuccia, Nicola and Colby, Douglas and Tomlinson, Simon R. and Ng, Huck-Hui and Chambers, Ian},
- month = may,
- year = {2013},
- keywords = {karwacki-neisius2013.jpg},
- pages = {531--545},
-}
-
-@article{veron2009,
- title = {Retention of gene products in syncytial spermatids promotes non-{Mendelian} inheritance as revealed by the \textit{t complex responder}},
- volume = {23},
- issn = {0890-9369, 1549-5477},
- url = {http://genesdev.cshlp.org/lookup/doi/10.1101/gad.553009},
- doi = {10.1101/gad.553009},
- abstract = {The
- t complex responder
- (
- Tcr
- ) encoded by the mouse
- t
- haplotype is able to cause phenotypic differences between
- t
- and + sperm derived from
- t
- /+ males, leading to non-Mendelian inheritance. This capability of
- Tcr
- contradicts the concept of phenotypic equivalence proposed for sperm cells, which develop in a syncytium and actively share gene products. By analyzing a
- Tcr
- minigene in hemizygous transgenic mice, we show that
- Tcr
- gene products are post-meiotically expressed and are retained in the haploid sperm cells. The wild-type allele of
- Tcr
- ,
- sperm motility kinase-1
- (
- Smok1
- ), behaves in the same manner, suggesting that
- Tcr
- /
- Smok
- reveal a common mechanism prone to evolve non-Mendelian inheritance in mammals.},
- language = {en},
- number = {23},
- urldate = {2023-05-25},
- journal = {Genes \& Development},
- author = {Véron, Nathalie and Bauer, Hermann and Weiße, Andrea Y. and Lüder, Gerhild and Werber, Martin and Herrmann, Bernhard G.},
- month = dec,
- year = {2009},
- keywords = {veron2009.jpg},
- pages = {2705--2710},
-}
-
-@article{weisse2016,
- title = {Signaling {Tug}-of-{War} {Delivers} the {Whole} {Message}},
- volume = {3},
- issn = {24054712},
- url = {https://linkinghub.elsevier.com/retrieve/pii/S2405471216303672},
- doi = {10.1016/j.cels.2016.11.003},
- language = {en},
- number = {5},
- urldate = {2023-05-25},
- journal = {Cell Systems},
- author = {Weiße, Andrea Y. and Mannan, Ahmad A. and Oyarzún, Diego A.},
- month = nov,
- year = {2016},
- keywords = {weisse2016.jpg},
- pages = {414--416},
-}
-
-@article{thomas2018,
- title = {Sources, propagation and consequences of stochasticity in cellular growth},
- volume = {9},
- issn = {2041-1723},
- url = {https://www.nature.com/articles/s41467-018-06912-9},
- doi = {10.1038/s41467-018-06912-9},
- abstract = {Abstract
- Growth impacts a range of phenotypic responses. Identifying the sources of growth variation and their propagation across the cellular machinery can thus unravel mechanisms that underpin cell decisions. We present a stochastic cell model linking gene expression, metabolism and replication to predict growth dynamics in single bacterial cells. Alongside we provide a theory to analyse stochastic chemical reactions coupled with cell divisions, enabling efficient parameter estimation, sensitivity analysis and hypothesis testing. The cell model recovers population-averaged data on growth-dependence of bacterial physiology and how growth variations in single cells change across conditions. We identify processes responsible for this variation and reconstruct the propagation of initial fluctuations to growth and other processes. Finally, we study drug-nutrient interactions and find that antibiotics can both enhance and suppress growth heterogeneity. Our results provide a predictive framework to integrate heterogeneous data and draw testable predictions with implications for antibiotic tolerance, evolutionary and synthetic biology.},
- language = {en},
- number = {1},
- urldate = {2023-05-25},
- journal = {Nature Communications},
- author = {Thomas, Philipp and Terradot, Guillaume and Danos, Vincent and Weiße, Andrea Y.},
- month = oct,
- year = {2018},
- keywords = {thomas2018.png},
- pages = {4528},
-}
-
-@article{terradot2018,
- title = {Survival of the {Fattest}: {Evolutionary} {Trade}-offs in {Cellular} {Resource} {Storage}},
- volume = {335},
- issn = {15710661},
- shorttitle = {Survival of the {Fattest}},
- url = {https://linkinghub.elsevier.com/retrieve/pii/S1571066118300136},
- doi = {10.1016/j.entcs.2018.03.010},
- language = {en},
- urldate = {2023-05-25},
- journal = {Electronic Notes in Theoretical Computer Science},
- author = {Terradot, Guillaume and Beica, Andreea and Weiße, Andrea and Danos, Vincent},
- month = apr,
- year = {2018},
- keywords = {terradot2018.png},
- pages = {91--112},
-}
diff --git a/_bibliography/addPreview.py b/_bibliography/addPreview.py
deleted file mode 100644
index b5e38da9d002..000000000000
--- a/_bibliography/addPreview.py
+++ /dev/null
@@ -1,20 +0,0 @@
-from pybtex.database import parse_file, BibliographyData, Entry
-from pybtex.database.input.bibtex import Parser
-
-nuParser = Parser()
-bib_data = parse_file('WeisseGroup.bib')
-
-for pprKey in bib_data.entries:
- print(pprKey)
- ppr = bib_data.entries[pprKey]
-
- fieldsDict = dict(ppr.fields)
- if "abstract" in fieldsDict.keys():
- fieldsDict.pop('abstract')
- if "keywords" in fieldsDict.keys():
- fieldsDict['preview'] = fieldsDict['keywords']
- fieldsDict.pop('keywords')
- nuEntry = Entry(ppr.type, fields=fieldsDict, persons=ppr.persons)
- nuParser.data.add_entry(pprKey, nuEntry)
-
-nuParser.data.to_file('papers.bib', bib_format='bibtex')
diff --git a/_bibliography/papers.bib b/_bibliography/papers.bib
deleted file mode 100644
index 30edfb007098..000000000000
--- a/_bibliography/papers.bib
+++ /dev/null
@@ -1,377 +0,0 @@
-@inproceedings{weisse2006,
- author = "Weiße, Andrea Y and Horenko, Illia and Huisinga, Wilhelm",
- title = "Adaptive approach for modelling variability in pharmacokinetics",
- isbn = "3-540-45767-4",
- booktitle = "{CompLife}",
- year = "2006",
- pages = "194--204",
- preview = "weisse2006.png"
-}
-
-@incollection{perkins2012,
- author = "Perkins, Theodore J and Weiße, Andrea Y and Swain, Peter S",
- title = "3. {Chance} and memory",
- isbn = "978-1-4398-2722-2",
- booktitle = "Quantitative {Biology}: {From} {Molecular} to {Cellular} {Systems}",
- publisher = "CRC Press",
- year = "2012",
- pages = "1--22",
- preview = "perkins2012.png"
-}
-
-@inproceedings{weisse2010b,
- author = "Weiße, Andrea Y and Huisinga, Wilhelm",
- title = "Global sensitivity analysis of {ODEs} via the solution of the associated {Fokker}-{Planck} equation",
- booktitle = "Proceedings of the 6th {Workshop} on {Computation} of {Biochemical} {Pathways} and {Genetic} {Networks}",
- publisher = "Logos Verlag Berlin",
- year = "2010",
- pages = "43--52"
-}
-
-@inproceedings{weisse2015b,
- author = "Weiße, Andrea",
- title = "Quantifying host-circuit interactions with a mechanistic chassis model",
- booktitle = "Synthetic {Biology}: {Engineering}, {Evolution}, and {Design} {Conference} 2015, {SEED} 2015",
- publisher = "AIChE",
- year = "2015",
- pages = "40--49"
-}
-
-@article{weisse2015a,
- author = "Weiße, Andrea Y. and Oyarzún, Diego A. and Danos, Vincent and Swain, Peter S.",
- title = "Mechanistic links between cellular trade-offs, gene expression, and growth",
- volume = "112",
- issn = "0027-8424, 1091-6490",
- url = "https://pnas.org/doi/full/10.1073/pnas.1416533112",
- doi = "10.1073/pnas.1416533112",
- language = "en",
- number = "9",
- urldate = "2023-05-25",
- journal = "Proceedings of the National Academy of Sciences",
- month = "March",
- year = "2015",
- preview = "weisse2015a.png"
-}
-
-@inproceedings{hunt2023,
- author = "Hunt, Christopher L. and Ding, Keqin and Wagner, Christoph S. and Berberich, Nicolas and Yilmazer, Karahan and Gonzalez-Fernandez, Marlis and Cheng, Gordon and Thakor, Nitish V.",
- address = "Baltimore, MD, USA",
- title = "Investigating the relationship between cue immersion and the strength of motor imagery during hand and wrist movements",
- isbn = "978-1-66546-292-1",
- url = "https://ieeexplore.ieee.org/document/10123823/",
- doi = "10.1109/NER52421.2023.10123823",
- urldate = "2023-05-25",
- booktitle = "2023 11th {International} {IEEE}/{EMBS} {Conference} on {Neural} {Engineering} ({NER})",
- publisher = "IEEE",
- month = "April",
- year = "2023",
- pages = "1--4",
- preview = "hunt2023.png"
-}
-
-@techreport{myall2021a,
- author = "Myall, Ashleigh and Peach, Robert L. and Wan, Yu and Mookerjee, Siddharth and Jauneikaite, Elita and Bolt, Frankie and Price, James and Davies, Frances and Weiße, Andrea Y. and Holmes, Alison and Barahona, Mauricio",
- type = "preprint",
- title = "Characterising contact in disease outbreaks via a network model of spatial-temporal proximity",
- url = "http://medrxiv.org/lookup/doi/10.1101/2021.04.07.21254497",
- language = "en",
- urldate = "2023-05-25",
- institution = "Epidemiology",
- month = "April",
- year = "2021",
- preview = "myall2021a.jpg"
-}
-
-@article{oyarzun2013,
- author = "Oyarzún, Diego A. and López-Caamal, Fernando and García, Míriam R. and Middleton, Richard H. and Weiße, Andrea Y.",
- editor = "Kurths, Jürgen",
- title = "Cumulative {Signal} {Transmission} in {Nonlinear} {Reaction}-{Diffusion} {Networks}",
- volume = "8",
- issn = "1932-6203",
- url = "https://dx.plos.org/10.1371/journal.pone.0062834",
- doi = "10.1371/journal.pone.0062834",
- language = "en",
- number = "5",
- urldate = "2023-05-25",
- journal = "PLoS ONE",
- month = "May",
- year = "2013",
- pages = "e62834",
- preview = "oyarzun2013.png"
-}
-
-@article{otter2020,
- author = "Otter, Jonathan A and Mookerjee, Siddharth and Davies, Frances and Bolt, Frances and Dyakova, Eleonora and Shersing, Yeeshika and Boonyasiri, Adhiratha and Weiße, Andrea Y and Gilchrist, Mark and Galletly, Tracey J and Brannigan, Eimear T and Holmes, Alison H",
- title = "Detecting carbapenemase-producing {Enterobacterales} ({CPE}): an evaluation of an enhanced {CPE} infection control and screening programme in acute care",
- volume = "75",
- issn = "0305-7453, 1460-2091",
- shorttitle = "Detecting carbapenemase-producing {Enterobacterales} ({CPE})",
- url = "https://academic.oup.com/jac/article/75/9/2670/5849541",
- doi = "10.1093/jac/dkaa192",
- language = "en",
- number = "9",
- urldate = "2023-05-25",
- journal = "Journal of Antimicrobial Chemotherapy",
- month = "September",
- year = "2020",
- pages = "2670--2676",
- preview = "otter2020.jpg"
-}
-
-@article{price2021,
- author = "Price, James Richard and Mookerjee, Siddharth and Dyakova, Eleonora and Myall, Ashleigh and Leung, Wendy and Weiße, Andrea Yeong and Shersing, Yeeshika and Brannigan, Eimear Therese and Galletly, Tracey and Muir, David and Randell, Paul and Davies, Frances and Bolt, Frances and Barahona, Mauricio and Otter, Jonathan Ashley and Holmes, Alison H",
- title = "Development and {Delivery} of a {Real}-time {Hospital}-onset {COVID}-19 {Surveillance} {System} {Using} {Network} {Analysis}",
- issn = "1058-4838, 1537-6591",
- url = "https://academic.oup.com/cid/advance-article/doi/10.1093/cid/ciaa892/5868508",
- doi = "10.1093/cid/ciaa892",
- language = "en",
- urldate = "2023-05-25",
- journal = "Clinical Infectious Diseases",
- month = "July",
- year = "2020",
- pages = "ciaa892",
- preview = "price2021.jpg"
-}
-
-@article{weisse2011,
- author = "Weiße, Andrea Y. and Huisinga, Wilhelm",
- title = "Error-controlled global sensitivity analysis of ordinary differential equations",
- volume = "230",
- issn = "00219991",
- url = "https://linkinghub.elsevier.com/retrieve/pii/S0021999111003159",
- doi = "10.1016/j.jcp.2011.05.011",
- language = "en",
- number = "17",
- urldate = "2023-05-25",
- journal = "Journal of Computational Physics",
- month = "July",
- year = "2011",
- pages = "6824--6842"
-}
-
-@phdthesis{weisse2009,
- author = "Weiße, Andrea Yeong",
- title = "Adaptive {Dichtepropagation} mit {Approximate} {ApproximationsGlobal} sensitivity analysis of ordinary differential equations: adaptive density propagation using approximate approximations",
- shorttitle = "Adaptive {Dichtepropagation} mit {Approximate} {ApproximationsGlobal} sensitivity analysis of ordinary differential equations",
- url = "https://refubium.fu-berlin.de/handle/fub188/9586",
- urldate = "2023-05-25",
- school = "Freie Universität Berlin",
- collaborator = "Universitätsbibliothek Der FU Berlin and Universitätsbibliothek Der FU Berlin",
- year = "2009",
- preview = "weisse2009.png"
-}
-
-@article{nikolados2019,
- author = "Nikolados, Evangelos-Marios and Weiße, Andrea Y. and Ceroni, Francesca and Oyarzún, Diego A.",
- title = "Growth {Defects} and {Loss}-of-{Function} in {Synthetic} {Gene} {Circuits}",
- volume = "8",
- issn = "2161-5063, 2161-5063",
- url = "https://pubs.acs.org/doi/10.1021/acssynbio.8b00531",
- doi = "10.1021/acssynbio.8b00531",
- language = "en",
- number = "6",
- urldate = "2023-05-25",
- journal = "ACS Synthetic Biology",
- month = "June",
- year = "2019",
- pages = "1231--1240",
- preview = "nikolados2019.jpg"
-}
-
-@article{myall2022b,
- author = "Myall, A. and Peach, R. and Wan, Y. and Mookerjee, S. and Jauneikaite, E. and Bolt, F. and Price, J. and Davies, F. and Weisse, A. and Holmes, A.H. and Barahona, M.",
- title = "Improved contact tracing using network analysis and spatial-temporal proximity",
- volume = "116",
- issn = "12019712",
- url = "https://linkinghub.elsevier.com/retrieve/pii/S1201971221009395",
- doi = "10.1016/j.ijid.2021.12.047",
- language = "en",
- urldate = "2023-05-25",
- journal = "International Journal of Infectious Diseases",
- month = "March",
- year = "2022",
- pages = "S20"
-}
-
-@article{ming2021,
- author = "Ming, Damien K. and Myall, Ashleigh C. and Hernandez, Bernard and Weiße, Andrea Y. and Peach, Robert L. and Barahona, Mauricio and Rawson, Timothy M. and Holmes, Alison H.",
- title = "Informing antimicrobial management in the context of {COVID}-19: understanding the longitudinal dynamics of {C}-reactive protein and procalcitonin",
- volume = "21",
- issn = "1471-2334",
- shorttitle = "Informing antimicrobial management in the context of {COVID}-19",
- url = "https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-021-06621-7",
- doi = "10.1186/s12879-021-06621-7",
- language = "en",
- number = "1",
- urldate = "2023-05-25",
- journal = "BMC Infectious Diseases",
- month = "December",
- year = "2021",
- pages = "932",
- preview = "ming2021.jpg"
-}
-
-@techreport{boonyasiri2021,
- author = "Boonyasiri, Adhiratha and Myall, Ashleigh C. and Wan, Yu and Bolt, Frances and Ledda, Alice and Mookerjee, Siddharth and Weiße, Andrea Y. and Turton, Jane F. and Abbas, Hala and Prakapaite, Ruta and Sabnis, Akshay and Abdolrasouli, Alireza and Malpartida-Cardenas, Kenny and Miglietta, Luca and Donaldson, Hugo and Gilchrist, Mark and Hopkins, Katie L. and Ellington, Matthew J and Otter, Jonathan A. and Larrouy-Maumus, Gerald and Edwards, Andrew M. and Rodriguez-Manzano, Jesus and Didelot, Xavier and Barahona, Mauricio and Holmes, Alison H. and Jauneikaite, Elita and Davies, Frances",
- type = "preprint",
- title = "Integrated patient network and genomic plasmid analysis reveal a regional, multi-species outbreak of carbapenemase-producing {Enterobacterales} carrying both \textit{bla} $\_{\textrm{{IMP}}}$ and \textit{mcr-9} genes",
- url = "http://medrxiv.org/lookup/doi/10.1101/2021.10.28.21265436",
- language = "en",
- urldate = "2023-05-25",
- institution = "Infectious Diseases (except HIV/AIDS)",
- month = "October",
- year = "2021",
- preview = "boonyasiri2021.jpg"
-}
-
-@article{myall2021b,
- author = "Myall, Ashleigh C. and Peach, Robert L. and Weiße, Andrea Y. and Mookerjee, Siddharth and Davies, Frances and Holmes, Alison and Barahona, Mauricio",
- title = "Network memory in the movement of hospital patients carrying antimicrobial-resistant bacteria",
- volume = "6",
- issn = "2364-8228",
- url = "https://appliednetsci.springeropen.com/articles/10.1007/s41109-021-00376-5",
- doi = "10.1007/s41109-021-00376-5",
- language = "en",
- number = "1",
- urldate = "2023-05-25",
- journal = "Applied Network Science",
- month = "December",
- year = "2021",
- pages = "34",
- preview = "myall2021b.jpg"
-}
-
-@incollection{nikolados2021,
- author = "Nikolados, Evangelos-Marios and Weiße, Andrea Y. and Oyarzún, Diego A.",
- editor = "Menolascina, Filippo",
- address = "New York, NY",
- title = "Prediction of {Cellular} {Burden} with {Host}–{Circuit} {Models}",
- volume = "2229",
- isbn = "978-1-07-161031-2 978-1-07-161032-9",
- url = "https://link.springer.com/10.1007/978-1-0716-1032-9\_13",
- language = "en",
- urldate = "2023-05-25",
- booktitle = "Synthetic {Gene} {Circuits}",
- publisher = "Springer US",
- year = "2021",
- pages = "267--291",
- preview = "nikolados2021.jpg"
-}
-
-@article{myall2022a,
- author = "Myall, A. and Price, J. and Peach, R. and Abbas, M. and Mookerjee, S. and Ahmad, I. and Ming, D. and Zhu, N.J. and Ramzan, F. and Weisse, A. and Holmes, A.H. and Barahona, M.",
- title = "Prediction of hospital-onset {COVID}-19 using networks of patient contact: an observational study",
- volume = "116",
- issn = "12019712",
- shorttitle = "Prediction of hospital-onset {COVID}-19 using networks of patient contact",
- url = "https://linkinghub.elsevier.com/retrieve/pii/S1201971221011504",
- doi = "10.1016/j.ijid.2021.12.258",
- language = "en",
- urldate = "2023-05-25",
- journal = "International Journal of Infectious Diseases",
- month = "March",
- year = "2022",
- pages = "S109--S110"
-}
-
-@article{weisse2010a,
- author = "Weiße, Andrea Y and Middleton, Richard H and Huisinga, Wilhelm",
- title = "Quantifying uncertainty, variability and likelihood for ordinary differential equation models",
- volume = "4",
- issn = "1752-0509",
- url = "https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-4-144",
- doi = "10.1186/1752-0509-4-144",
- language = "en",
- number = "1",
- urldate = "2023-05-25",
- journal = "BMC Systems Biology",
- month = "December",
- year = "2010",
- pages = "144",
- preview = "weisse2010a.png"
-}
-
-@article{karwacki-neisius2013,
- author = "Karwacki-Neisius, Violetta and Göke, Jonathan and Osorno, Rodrigo and Halbritter, Florian and Ng, Jia Hui and Weiße, Andrea Y. and Wong, Frederick C.K. and Gagliardi, Alessia and Mullin, Nicholas P. and Festuccia, Nicola and Colby, Douglas and Tomlinson, Simon R. and Ng, Huck-Hui and Chambers, Ian",
- title = "Reduced {Oct4} {Expression} {Directs} a {Robust} {Pluripotent} {State} with {Distinct} {Signaling} {Activity} and {Increased} {Enhancer} {Occupancy} by {Oct4} and {Nanog}",
- volume = "12",
- issn = "19345909",
- url = "https://linkinghub.elsevier.com/retrieve/pii/S1934590913001598",
- doi = "10.1016/j.stem.2013.04.023",
- language = "en",
- number = "5",
- urldate = "2023-05-25",
- journal = "Cell Stem Cell",
- month = "May",
- year = "2013",
- pages = "531--545",
- preview = "karwacki-neisius2013.jpg"
-}
-
-@article{veron2009,
- author = "Véron, Nathalie and Bauer, Hermann and Weiße, Andrea Y. and Lüder, Gerhild and Werber, Martin and Herrmann, Bernhard G.",
- title = "Retention of gene products in syncytial spermatids promotes non-{Mendelian} inheritance as revealed by the \textit{t complex responder}",
- volume = "23",
- issn = "0890-9369, 1549-5477",
- url = "http://genesdev.cshlp.org/lookup/doi/10.1101/gad.553009",
- doi = "10.1101/gad.553009",
- language = "en",
- number = "23",
- urldate = "2023-05-25",
- journal = "Genes \\& Development",
- month = "December",
- year = "2009",
- pages = "2705--2710",
- preview = "veron2009.jpg"
-}
-
-@article{weisse2016,
- author = "Weiße, Andrea Y. and Mannan, Ahmad A. and Oyarzún, Diego A.",
- title = "Signaling {Tug}-of-{War} {Delivers} the {Whole} {Message}",
- volume = "3",
- issn = "24054712",
- url = "https://linkinghub.elsevier.com/retrieve/pii/S2405471216303672",
- doi = "10.1016/j.cels.2016.11.003",
- language = "en",
- number = "5",
- urldate = "2023-05-25",
- journal = "Cell Systems",
- month = "November",
- year = "2016",
- pages = "414--416",
- preview = "weisse2016.jpg"
-}
-
-@article{thomas2018,
- author = "Thomas, Philipp and Terradot, Guillaume and Danos, Vincent and Weiße, Andrea Y.",
- title = "Sources, propagation and consequences of stochasticity in cellular growth",
- volume = "9",
- issn = "2041-1723",
- url = "https://www.nature.com/articles/s41467-018-06912-9",
- doi = "10.1038/s41467-018-06912-9",
- language = "en",
- number = "1",
- urldate = "2023-05-25",
- journal = "Nature Communications",
- month = "October",
- year = "2018",
- pages = "4528",
- preview = "thomas2018.png"
-}
-
-@article{terradot2018,
- author = "Terradot, Guillaume and Beica, Andreea and Weiße, Andrea and Danos, Vincent",
- title = "Survival of the {Fattest}: {Evolutionary} {Trade}-offs in {Cellular} {Resource} {Storage}",
- volume = "335",
- issn = "15710661",
- shorttitle = "Survival of the {Fattest}",
- url = "https://linkinghub.elsevier.com/retrieve/pii/S1571066118300136",
- doi = "10.1016/j.entcs.2018.03.010",
- language = "en",
- urldate = "2023-05-25",
- journal = "Electronic Notes in Theoretical Computer Science",
- month = "April",
- year = "2018",
- pages = "91--112",
- preview = "terradot2018.png"
-}
diff --git a/_config.yml b/_config.yml
deleted file mode 100644
index 766f320c0568..000000000000
--- a/_config.yml
+++ /dev/null
@@ -1,382 +0,0 @@
-# -----------------------------------------------------------------------------
-# Site settings
-# -----------------------------------------------------------------------------
-
-title: Biomedical Computation Group # the website title (if blank, full name will be used instead)
-first_name: Andrea
-middle_name: Yeong
-last_name: Weisse
-email:
-description: > # the ">" symbol means to ignore newlines until "footer_text:"
- Virtual domain of our splendid computation team in the beautiful Edinburgh
-footer_text: >
- Powered by Jekyll with al-folio theme.
- Hosted by GitHub Pages.
-keywords: jekyll, jekyll-theme, academic-website, portfolio-website # add your own keywords or leave empty
-
-lang: en # the language of your site (for example: en, fr, cn, ru, etc.)
-icon: ⚛️ # the emoji used as the favicon (alternatively, provide image name in /assets/img/)
-
-url: https://chwag.github.io # the base hostname & protocol for your site
-baseurl: # the subpath of your site, e.g. /blog/
-last_updated: true # set to true if you want to display last updated in the footer
-impressum_path: # set to path to include impressum link in the footer, use the same path as permalink in a page, helps to conform with EU GDPR
-
-# -----------------------------------------------------------------------------
-# Theme
-# -----------------------------------------------------------------------------
-
-# code highlighter theme
-highlight_theme_light: github # https://github.com/jwarby/jekyll-pygments-themes
-highlight_theme_dark: native # https://github.com/jwarby/jekyll-pygments-themes
-
-# repo color theme
-repo_theme_light: default # https://github.com/anuraghazra/github-readme-stats/blob/master/themes/README.md
-repo_theme_dark: dark # https://github.com/anuraghazra/github-readme-stats/blob/master/themes/README.md
-
-# -----------------------------------------------------------------------------
-# RSS Feed
-# -----------------------------------------------------------------------------
-# will use title and url fields
-# Take a look to https://github.com/jekyll/jekyll-feed for more customization
-
-rss_icon: false
-
-# -----------------------------------------------------------------------------
-# Layout
-# -----------------------------------------------------------------------------
-
-navbar_fixed: true
-footer_fixed: false
-
-# Dimensions
-max_width: 800px
-
-# TODO: add layout settings (single page vs. multi-page)
-
-# -----------------------------------------------------------------------------
-# Open Graph & Schema.org
-# -----------------------------------------------------------------------------
-# Display links to the page with a preview object on social media.
-serve_og_meta: false # Include Open Graph meta tags in the HTML head
-serve_schema_org: false # Include Schema.org in the HTML head
-og_image: # The site-wide (default for all links) Open Graph preview image
-
-# -----------------------------------------------------------------------------
-# Social integration
-# -----------------------------------------------------------------------------
-
-github_username: # your GitHub user name
-gitlab_username: # your GitLab user name
-twitter_username: # your Twitter handle
-mastodon_username: # your mastodon instance+username in the format instance.tld/@username
-linkedin_username: # your LinkedIn user name
-telegram_username: # your Telegram user name
-scholar_userid: # your Google Scholar ID
-semanticscholar_id: # your Semantic Scholar ID
-whatsapp_number: # your WhatsApp number (full phone number in international format. Omit any zeroes, brackets, or dashes when adding the phone number in international format.)
-orcid_id: # your ORCID ID
-medium_username: # your Medium username
-quora_username: # your Quora username
-publons_id: # your ID on Publons
-research_gate_profile: # your profile on ResearchGate
-blogger_url: # your blogger URL
-work_url: # work page URL
-keybase_username: # your keybase user name
-wikidata_id: # your wikidata id
-dblp_url: # your DBLP profile url
-stackoverflow_id: # your stackoverflow id
-kaggle_id: # your kaggle id
-lastfm_id: # your lastfm id
-spotify_id: # your spotify id
-pinterest_id: # your pinterest id
-unsplash_id: # your unsplash id
-instagram_id: # your instagram id
-facebook_id: # your facebook id
-youtube_id: # your youtube channel id (youtube.com/@)
-discord_id: # your discord id (18-digit unique numerical identifier)
-
-contact_note: >
- For any enquiries, please reach out by mail at andrea[dot]weisse[at]ed.ac.uk
-
-# -----------------------------------------------------------------------------
-# Analytics and search engine verification
-# -----------------------------------------------------------------------------
-
-google_analytics: # your Goole Analytics measurement ID (format: G-XXXXXXXXXX)
-panelbear_analytics: # panelbear analytics site ID (format: XXXXXXXXX)
-
-google_site_verification: # your google-site-verification ID (Google Search Console)
-bing_site_verification: # out your bing-site-verification ID (Bing Webmaster)
-
-# -----------------------------------------------------------------------------
-# Blog
-# -----------------------------------------------------------------------------
-
-blog_name: # blog_name will be displayed in your blog page
-blog_nav_title: # your blog must have a title for it to be displayed in the nav bar
-blog_description: a simple whitespace theme for academics
-permalink: /blog/:year/:title/
-
-# Pagination
-pagination:
- enabled: true
-
-# Giscus comments (RECOMMENDED)
-# Follow instructions on https://giscus.app/ to setup for your repo to fill out
-# the information below.
-giscus:
- repo: alshedivat/al-folio # /
- repo_id: MDEwOlJlcG9zaXRvcnk2MDAyNDM2NQ==
- category: Comments # name of the category under which discussions will be created
- category_id: DIC_kwDOA5PmLc4CTBt6
- mapping: title # identify discussions by post title
- strict: 1 # use strict identification mode
- reactions_enabled: 1 # enable (1) or disable (0) emoji reactions
- input_position: bottom # whether to display input form below (bottom) or above (top) the comments
- theme: preferred_color_scheme # name of the color scheme (preferred works well with al-folio light/dark mode)
- emit_metadata: 0
- lang: en
-
-# Disqus comments (DEPRECATED)
-disqus_shortname: al-folio # put your disqus shortname
-# https://help.disqus.com/en/articles/1717111-what-s-a-shortname
-
-# External sources.
-# If you have blog posts published on medium.com or other exteranl sources,
-# you can display them in your blog by adding a link to the RSS feed.
-external_sources:
- - name: medium.com
- rss_url: https://medium.com/@al-folio/feed
-
-# -----------------------------------------------------------------------------
-# Collections
-# -----------------------------------------------------------------------------
-
-collections:
- news:
- defaults:
- layout: post
- output: true
- permalink: /news/:path/
- projects:
- output: true
- permalink: /projects/:path/
- people:
- output: true
- permalink: /people/:path/
-
-news_scrollable: true # adds a vertical scroll bar if there are more than 3 news items
-news_limit: 5 # leave blank to include all the news in the `_news` folder
-
-# -----------------------------------------------------------------------------
-# Jekyll settings
-# -----------------------------------------------------------------------------
-
-# Markdown and syntax highlight
-markdown: kramdown
-highlighter: rouge
-kramdown:
- input: GFM
- syntax_highlighter_opts:
- css_class: 'highlight'
- span:
- line_numbers: false
- block:
- line_numbers: false
- start_line: 1
-
-# Includes & excludes
-include: ['_pages']
-exclude:
- - bin
- - Gemfile
- - Gemfile.lock
- - vendor
-keep_files:
- - CNAME
- - .nojekyll
- - .git
-
-# Plug-ins
-plugins:
- - jekyll-archives
- - jekyll-diagrams
- - jekyll-email-protect
- - jekyll-feed
- - jekyll-imagemagick
- - jekyll-minifier
- - jekyll-paginate-v2
- - jekyll/scholar
- - jekyll-sitemap
- - jekyll-link-attributes
- - jekyll-twitter-plugin
- - jemoji
-
-# Sitemap settings
-defaults:
- - scope:
- path: "assets/**/*.*"
- values:
- sitemap: false
-
-# -----------------------------------------------------------------------------
-# Jekyll Minifier
-# -----------------------------------------------------------------------------
-
-jekyll-minifier:
- exclude: ['robots.txt']
- uglifier_args:
- harmony: true
-
-# -----------------------------------------------------------------------------
-# Jekyll Archives
-# -----------------------------------------------------------------------------
-
-jekyll-archives:
- enabled: [year, tags, categories] # enables year, tag and category archives (remove if you need to disable one of them).
- layouts:
- year: archive-year
- tag: archive-tag
- category: archive-category
- permalinks:
- year: '/blog/:year/'
- tag: '/blog/tag/:name/'
- category: '/blog/category/:name/'
-
-display_tags: ['formatting', 'images', 'links', 'math', 'code'] # this tags will be dispalyed on the front page of your blog
-
-# -----------------------------------------------------------------------------
-# Jekyll Scholar
-# -----------------------------------------------------------------------------
-
-scholar:
-
- last_name:
- first_name:
-
- style: apa
- locale: en
-
- source: /_bibliography/
- bibliography: papers.bib
- bibliography_template: bib
- # Note: if you have latex math in your bibtex, the latex filter
- # preprocessing may conflict with MathJAX if the latter is enabled.
- # See https://github.com/alshedivat/al-folio/issues/357.
- bibtex_filters: [latex, smallcaps, superscript]
-
- replace_strings: true
- join_strings: true
-
- details_dir: bibliography
- details_layout: bibtex.html
- details_link: Details
-
- query: "@*"
-
-badges: # Display different badges for your pulications
- altmetric_badge: false # Altmetric badge (https://www.altmetric.com/products/altmetric-badges/)
- dimensions_badge: false # Dimensions badge (https://badge.dimensions.ai/)
-
-# Filter out certain bibtex entry keywords used internally from the bib output
-filtered_bibtex_keywords: [abbr, abstract, arxiv, bibtex_show, html, pdf, selected, supp, blog, code, poster, slides, website, preview, altmetric]
-
-# Maximum number of authors to be shown for each publication (more authors are visible on click)
-max_author_limit: 5 # leave blank to always show all authors
-more_authors_animation_delay: 10 # more authors are revealed on click using animation; smaller delay means faster animation
-
-
-# -----------------------------------------------------------------------------
-# Jekyll Link Attributes
-# -----------------------------------------------------------------------------
-
-# These are the defaults
-external_links:
- enabled: true
- rel: external nofollow noopener
- target: _blank
- exclude:
-
-
-# -----------------------------------------------------------------------------
-# Responsive WebP Images
-# -----------------------------------------------------------------------------
-
-imagemagick:
- enabled: true # enables responsive images for your site (recomended, see https://github.com/alshedivat/al-folio/issues/537)
- widths:
- - 480
- - 800
- - 1400
- input_directories:
- - assets/img/
- input_formats:
- - ".jpg"
- - ".jpeg"
- - ".png"
- - ".tiff"
- output_formats:
- webp: "-resize 800x"
-
-# -----------------------------------------------------------------------------
-# Jekyll Diagrams
-# -----------------------------------------------------------------------------
-
-jekyll-diagrams:
- # configuration, see https://github.com/zhustec/jekyll-diagrams.
- # feel free to comment out this section if not using jekyll diagrams.
-
-
-# -----------------------------------------------------------------------------
-# Optional Features
-# -----------------------------------------------------------------------------
-
-enable_google_analytics: false # enables google analytics
-enable_panelbear_analytics: false # enables panelbear analytics
-enable_google_verification: false # enables google site verification
-enable_bing_verification: false # enables bing site verification
-enable_masonry: true # enables automatic project cards arangement
-enable_math: true # enables math typesetting (uses MathJax)
-enable_tooltips: false # enables automatic tooltip links generated
- # for each section titles on pages and posts
-enable_darkmode: true # enables switching between light/dark modes
-enable_navbar_social: false # enables displaying social links in the
- # navbar on the about page
-enable_project_categories: false # enables categorization of projects into
- # multiple categories
-enable_people_categories: false # enables categorization of people into multiple categories
-enable_medium_zoom: true # enables image zoom feature (as on medium.com)
-enable_progressbar: true # enables a horizontal progress bar linked to the vertical scroll position
-
-# -----------------------------------------------------------------------------
-# Library versions
-# -----------------------------------------------------------------------------
-
-academicons:
- version: "1.9.1"
- integrity: "sha256-i1+4qU2G2860dGGIOJscdC30s9beBXjFfzjWLjBRsBg="
-bootstrap:
- version: "4.6.1"
- integrity:
- css: "sha256-DF7Zhf293AJxJNTmh5zhoYYIMs2oXitRfBjY+9L//AY="
- js: "sha256-fgLAgv7fyCGopR/gBNq2iW3ZKIdqIcyshnUULC4vex8="
-fontawesome:
- version: "5.15.4"
- integrity: "sha256-mUZM63G8m73Mcidfrv5E+Y61y7a12O5mW4ezU3bxqW4="
-jquery:
- version: "3.6.0"
- integrity: "sha256-/xUj+3OJU5yExlq6GSYGSHk7tPXikynS7ogEvDej/m4="
-mathjax:
- version: "3.2.0"
-masonry:
- version: "4.2.2"
- integrity: "sha256-Nn1q/fx0H7SNLZMQ5Hw5JLaTRZp0yILA/FRexe19VdI="
-mdb:
- version: "4.20.0"
- integrity:
- css: "sha256-jpjYvU3G3N6nrrBwXJoVEYI/0zw8htfFnhT9ljN3JJw="
- js: "sha256-NdbiivsvWt7VYCt6hYNT3h/th9vSTL4EDWeGs5SN3DA="
-medium_zoom:
- version: "1.0.8"
- integrity: "sha256-7PhEpEWEW0XXQ0k6kQrPKwuoIomz8R8IYyuU1Qew4P8="
diff --git a/_data/coauthors.yml b/_data/coauthors.yml
deleted file mode 100644
index 8ed521248d81..000000000000
--- a/_data/coauthors.yml
+++ /dev/null
@@ -1,34 +0,0 @@
-"Adams":
- - firstname: ["Edwin", "E.", "E. P.", "Edwin Plimpton"]
- url: https://en.wikipedia.org/wiki/Edwin_Plimpton_Adams
-
-"Podolsky":
- - firstname: ["Boris", "B.", "B. Y.", "Boris Yakovlevich"]
- url: https://en.wikipedia.org/wiki/Boris_Podolsky
-
-"Rosen":
- - firstname: ["Nathan", "N."]
- url: https://en.wikipedia.org/wiki/Nathan_Rosen
-
-"Bach":
- - firstname: ["Johann Sebastian", "J. S."]
- url: https://en.wikipedia.org/wiki/Johann_Sebastian_Bach
-
- - firstname: ["Carl Philipp Emanuel", "C. P. E."]
- url: https://en.wikipedia.org/wiki/Carl_Philipp_Emanuel_Bach
-
-"Przibram":
- - firstname: ["Karl"]
- url: https://link.springer.com/article/10.1007/s00016-019-00242-z
-
-"Schrödinger":
- - firstname: ["Erwin"]
- url: https://en.wikipedia.org/wiki/Erwin_Schr%C3%B6dinger
-
-"Lorentz":
- - firstname: ["Hendrik Antoon"]
- url: https://en.wikipedia.org/wiki/Hendrik_Lorentz
-
-"Planck":
- - firstname: ["Max"]
- url: https://en.wikipedia.org/wiki/Max_Planck
diff --git a/_data/cv.yml b/_data/cv.yml
deleted file mode 100644
index 5b1157240e07..000000000000
--- a/_data/cv.yml
+++ /dev/null
@@ -1,97 +0,0 @@
-- title: General Information
- type: map
- contents:
- - name: Full Name
- value: Albert Einstein
- - name: Date of Birth
- value: 14th March 1879
- - name: Languages
- value: English, German
-
-- title: Education
- type: time_table
- contents:
- - title: PhD
- institution: University of Zurich, Zurich, Switzerland
- year: 1905
- description:
- - Description 1.
- - Description 2.
- - title: Description 3.
- contents:
- - Sub-description 1.
- - Sub-description 2.
- - title: Federal teaching diploma
- institution: Eidgenössische Technische Hochschule, Zurich, Switzerland
- year: 1900
- description:
- - Description 1.
- - Description 2.
-
-- title: Experience
- type: time_table
- contents:
- - title: Professor of Theoretical Physics
- institution: Institute for Advanced Study, Princeton University
- year: 1933 - 1955
- description:
- - Description 1.
- - Description 2.
- - title: Description 3.
- contents:
- - Sub-description 1.
- - Sub-description 2.
- - title: Visiting Professor
- institution: California Institute of Technology, Pasadena, California, US
- year: 1933
- description:
- - Description 1.
- - Description 2.
-
- - title: Director
- institution: Kaiser Wilhelm Institute for Physics, Berlin, Germany.
- year: 1917-1933
-
- - title: Professor of Theoretical Physics
- institution: Karl-Ferdinand University, Prague, Czechoslovakia
- year: 1911 - 1917
- description:
-
- - title: Associate Professor of Theoretical Physics
- institution: University of Zurich, Zurich, Switzerland
- year: 1909 - 1911
-
-- title: Open Source Projects
- type: time_table
- contents:
- - title: al-folio
- year: 2015-now
- description: A beautiful, simple, clean, and responsive Jekyll theme for academics.
-
-- title: Honors and Awards
- type: time_table
- contents:
- - year: 1921
- items:
- - Nobel Prize in Physics
- - Matteucci Medal
- - year: 2029
- items:
- - Max Planck Medal
-
-- title: Academic Interests
- type: nested_list
- contents:
- - title: Topic 1.
- items:
- - Description 1.
- - Description 2.
- - title: Topic 2.
- items:
- - Description 1.
- - Description 2.
-
-- title: Other Interests
- type: list
- contents:
- - Hobbies: Hobby 1, Hobby 2, etc.
diff --git a/_data/repositories.yml b/_data/repositories.yml
deleted file mode 100644
index 5205c9f6f7e9..000000000000
--- a/_data/repositories.yml
+++ /dev/null
@@ -1,12 +0,0 @@
-github_users:
- - torvalds
- - alshedivat
-
-github_repos:
- - alshedivat/al-folio
- - twbs/bootstrap
- - jekyll/jekyll
- - jquery/jquery
- - FortAwesome/Font-Awesome
- - jpswalsh/academicons
- - mathjax/MathJax
diff --git a/_data/venues.yml b/_data/venues.yml
deleted file mode 100644
index 6c16ad5dcbdf..000000000000
--- a/_data/venues.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-"AJP":
- url: https://aapt.scitation.org/journal/ajp
- color: "#00369f"
-
-"PhysRev":
- url: https://journals.aps.org/
diff --git a/_includes/cv/list.html b/_includes/cv/list.html
deleted file mode 100644
index 7562585916d3..000000000000
--- a/_includes/cv/list.html
+++ /dev/null
@@ -1,5 +0,0 @@
-
- {% for content in entry.contents %}
-
{{ content }}
- {% endfor %}
-
\ No newline at end of file
diff --git a/_includes/cv/map.html b/_includes/cv/map.html
deleted file mode 100644
index e0d1983ef0ee..000000000000
--- a/_includes/cv/map.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
- {% for content in entry.contents %}
-
-
{{ content.name }}
-
{{ content.value }}
-
- {% endfor %}
-
\ No newline at end of file
diff --git a/_includes/cv/nested_list.html b/_includes/cv/nested_list.html
deleted file mode 100644
index 4778aca07ff1..000000000000
--- a/_includes/cv/nested_list.html
+++ /dev/null
@@ -1,14 +0,0 @@
-
- {% for content in entry.contents %}
-
-
{{ content.title }}
- {% if content.items %}
-
- {% for subitem in content.items %}
-
{{ subitem }}
- {% endfor %}
-
- {% endif %}
-
- {% endfor %}
-
\ No newline at end of file
diff --git a/_includes/cv/time_table.html b/_includes/cv/time_table.html
deleted file mode 100644
index 123b9d099fde..000000000000
--- a/_includes/cv/time_table.html
+++ /dev/null
@@ -1,59 +0,0 @@
-
- {% for content in entry.contents %}
-
-
- {% if content.year %}
-
-
- {{ content.year }}
-
-
- {% endif %}
-
- {% if content.title %}
-
{{content.title}}
- {% endif %}
- {% if content.institution %}
-
{{content.institution}}
- {% endif %}
- {% if content.description %}
-
- {% for item in content.description %}
-
- {% if item.contents %}
- {{ item.title }}
-
- {% for subitem in item.contents %}
-
{{ subitem }}
- {% endfor %}
-
- {% else %}
- {{ item }}
- {% endif %}
-
- {% endfor %}
-
- {% endif %}
- {% if content.items %}
-
- {% for item in content.items %}
-
- {% if item.contents %}
- {{ item.title }}
-
- {% for subitem in item.contents %}
-
{{ subitem }}
- {% endfor %}
-
- {% else %}
- {{ item }}
- {% endif %}
-
- {% endfor %}
-
- {% endif %}
-
-
-
- {% endfor %}
-
\ No newline at end of file
diff --git a/_includes/disqus.html b/_includes/disqus.html
deleted file mode 100644
index 73fe9538d0dc..000000000000
--- a/_includes/disqus.html
+++ /dev/null
@@ -1,13 +0,0 @@
-
- {{ year }}
- {%- if tags != "" %}
- ·
- {% for tag in page.tags -%}
-
- {{ tag }}
- {% endfor -%}
- {% endif %}
-
- {%- if categories != "" %}
- ·
- {% for category in page.categories -%}
-
- {{ category }}
- {% endfor -%}
- {% endif %}
-
-
-
-
-
- {{ content }}
-
-
- {%- if site.disqus_shortname and page.disqus_comments -%}
- {% include disqus.html %}
- {%- endif %}
- {%- if site.giscus.repo and page.giscus_comments -%}
- {% include giscus.html %}
- {%- endif -%}
-
-
diff --git a/_news/announcement_0.md b/_news/announcement_0.md
deleted file mode 100644
index f506751fc1fa..000000000000
--- a/_news/announcement_0.md
+++ /dev/null
@@ -1,7 +0,0 @@
----
-layout: post
-date: 2023-03-30 15:59:00-0400
-inline: true
----
-
-First test news. Update this, when the website goes live!
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diff --git a/_news/announcement_1.md b/_news/announcement_1.md
deleted file mode 100644
index b0a1db0f82c8..000000000000
--- a/_news/announcement_1.md
+++ /dev/null
@@ -1,7 +0,0 @@
----
-layout: post
-date: 2023-05-24 15:59:00-0400
-inline: true
----
-
-Christoph's recent work on the effect of immersive motor prompts on motor imagery was published in the proceedings of the 11th International IEEE/EMBS Conference on Neural Engineering - congratulations, Christoph!
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diff --git a/_pages/about.md b/_pages/about.md
deleted file mode 100644
index 3a8795400ee2..000000000000
--- a/_pages/about.md
+++ /dev/null
@@ -1,13 +0,0 @@
----
-layout: about
-title: about
-permalink: /
-subtitle: @University of Edinburgh
-
-news: true # includes a list of news items
-selected_papers: false # includes a list of papers marked as "selected={true}"
-social: false # includes social icons at the bottom of the page
----
-
-Our group focuses on computational systems analyses of biological processes. We use mechanistic computational models to integrate heterogenous data into predictive models. We have a particular interest in mechanisms that promote the emergence and spread of antimicrobial resistance, which we study at the cellular and population level as well as across patients.
- I held postdoctoral positions at the University of Edinburgh (with Peter Swain and Vincent Danos) and Imperial College London (with Alison Holmes, OBE).
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diff --git a/_people/ashleighMyall.md b/_people/ashleighMyall.md
deleted file mode 100644
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----
-layout: page
-title: Ashleigh Myall
-description: PhD student
-img:
-importance: 1
-category: PhD students
----
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diff --git a/_people/christophWagner.md b/_people/christophWagner.md
deleted file mode 100644
index a811c72ab589..000000000000
--- a/_people/christophWagner.md
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----
-layout: page
-title: Christoph Wagner
-description: PhD student
-img: assets/img/profiles/christophWagner_cropped.png
-importance: 1
-category: PhD students
----
-
-
-
-
-
- I joined the university in 2022, to do my PhD with Andrea, co-supervised with Nadanai Laohakunakorn. We are interested in the ability of cells to self-regenerate. To study this, we run cell-free transcription-translation (TXTL) experiments in a microfluidics chip, wherein a gene expression machinery produces its own proteins. The gathered data is then used to generate a model of TXTL self-regeneration.
- Understanding and controlling the ability of a TXTL system to self-regenerate would mark a milestone on the path towards synthetic cells, which to me is the holy grail of synthetic biology. Everything from basic science to industry would benefit greatly from achieving to build fully synthetic cells. It's just a bummer, how very complicated that is...
- Aside my PhD, I like to spend my time dancing traditional Scottish dances, writing science communication articles on my blog and sometimes running around in circles.
-
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diff --git a/_people/elenaGarcia.md b/_people/elenaGarcia.md
deleted file mode 100644
index 482abec46e3b..000000000000
--- a/_people/elenaGarcia.md
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----
-layout: page
-title: Elena Pascual Garcia
-description: PhD student
-img:
-importance: 1
-category: PhD students
----
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diff --git a/_people/hollieHindley.md b/_people/hollieHindley.md
deleted file mode 100644
index 595ca94d1a5e..000000000000
--- a/_people/hollieHindley.md
+++ /dev/null
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----
-layout: page
-title: Hollie Hindley
-description: PhD student
-img: assets/img/profiles/hollieHindley_cropped.png
-importance: 1
-category: PhD students
----
-
-
-
-
-
- I joined the group in 2021 when I started my PhD in mathematical modelling of RNA repair. I’ve always had an interest in antimicrobial resistance and have completed projects in my BSc and MSc on antibiotic resistance at the University of Bristol where I studied biochemistry. My PhD also has an AMR focus through modelling of a gene system in bacteria, which is implicated in antibiotic tolerance. This system is highly conserved across all domains of life, highlighting its importance and our interest in discovering more about why it causes tolerance and how we can potentiate antibiotic treatments in the future.
- Outside of my PhD I am a competitive triathlete and I love exploring the amazing outdoors we have on our doorstep in Edinburgh!
-
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diff --git a/_people/rohanGorantla.md b/_people/rohanGorantla.md
deleted file mode 100644
index 29b148931e25..000000000000
--- a/_people/rohanGorantla.md
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----
-layout: page
-title: Rohan Gorantla
-description: PhD student
-img:
-importance: 1
-category: PhD students
----
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diff --git a/_people/sandyNelson.md b/_people/sandyNelson.md
deleted file mode 100644
index 13f26165150e..000000000000
--- a/_people/sandyNelson.md
+++ /dev/null
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----
-layout: page
-title: Sandy Nelson
-description: PhD student
-img: assets/img/profiles/sandyNelson_cropped.png
-importance: 1
-category: PhD students
----
-
-
-
-
-
- Sandy Nelson is a PhD student funded by the CDT in Biomedical AI. He is researching robust biodesign for cell-free systems using probabilistic approaches, working jointly with the Gutmann group (Informatics), the Laohakunakorn group and the Weiße group (IQB3). He studied physics and experimental psychology at Durham University then a PhD in cognitive science at Edinburgh University. While there, he was involved in research projects at the School of Informatics on computational models of memory and text processing.
- In 2017 Sandy joined DeepMind as founding product manager for its Science Team. He program managed the application of machine learning to protein folding and problems in physics including glassy dynamics and Density Functional Theory. Before DeepMind, Sandy spent 10 years at Amazon as a Senior Software Development Manager, where he was responsible for worldwide dynamic personalised merchandising and led teams mining the product catalogue for relationships that drove features like AutoRip, movie discovery on Fire TV and music discovery on Echo.
-
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diff --git a/_plugins/external-posts.rb b/_plugins/external-posts.rb
deleted file mode 100644
index e4fd5eb69517..000000000000
--- a/_plugins/external-posts.rb
+++ /dev/null
@@ -1,36 +0,0 @@
-require 'feedjira'
-require 'httparty'
-require 'jekyll'
-
-module ExternalPosts
- class ExternalPostsGenerator < Jekyll::Generator
- safe true
- priority :high
-
- def generate(site)
- if site.config['external_sources'] != nil
- site.config['external_sources'].each do |src|
- p "Fetching external posts from #{src['name']}:"
- xml = HTTParty.get(src['rss_url']).body
- feed = Feedjira.parse(xml)
- feed.entries.each do |e|
- p "...fetching #{e.url}"
- slug = e.title.downcase.strip.gsub(' ', '-').gsub(/[^\w-]/, '')
- path = site.in_source_dir("_posts/#{slug}.md")
- doc = Jekyll::Document.new(
- path, { :site => site, :collection => site.collections['posts'] }
- )
- doc.data['external_source'] = src['name'];
- doc.data['feed_content'] = e.content;
- doc.data['title'] = "#{e.title}";
- doc.data['description'] = e.summary;
- doc.data['date'] = e.published;
- doc.data['redirect'] = e.url;
- site.collections['posts'].docs << doc
- end
- end
- end
- end
- end
-
-end
diff --git a/_plugins/hideCustomBibtex.rb b/_plugins/hideCustomBibtex.rb
deleted file mode 100644
index 4a852fde6a6e..000000000000
--- a/_plugins/hideCustomBibtex.rb
+++ /dev/null
@@ -1,15 +0,0 @@
- module Jekyll
- module HideCustomBibtex
- def hideCustomBibtex(input)
- keywords = @context.registers[:site].config['filtered_bibtex_keywords']
-
- keywords.each do |keyword|
- input = input.gsub(/^.*#{keyword}.*$\n/, '')
- end
-
- return input
- end
- end
-end
-
-Liquid::Template.register_filter(Jekyll::HideCustomBibtex)
diff --git a/_projects/1_bacterialGrowth.md b/_projects/1_bacterialGrowth.md
deleted file mode 100644
index 688baa76dfa5..000000000000
--- a/_projects/1_bacterialGrowth.md
+++ /dev/null
@@ -1,24 +0,0 @@
----
-layout: page
-title: Bacterial growth
-description: Investigating bacterial growth and how it is controlled
-img: assets/img/12.jpg
-importance: 1
-category: work
----
-
-Bacterial growth offers vital insights into life, evolution, and disease. The way bacteria grow is intricately linked
-to factors like nutrient availability, competitive interactions, and environmental challenges such as antibiotics. Our
-group focuses on two key areas:
-
-### Multi-scale models of bacterial cells
-Given the pressing rise of antibiotic resistance, we investigate mechanisms and environmental factors affecting drug
-efficacy. Our goal is to derive insights that can enhance existing antibiotic therapies by addressing the misuse and
-overuse of antibiotics.
-
---------
-
-### Emergence of antibiotic resistance
-We develop computational models to investigate bacterial growth adaptation in complex environments. Our models are
-rooted in core cellular mechanisms, which allows us to predict growth as it emerges from the dynamic interplay of
-environmental stimuli with the cell mechanisms.
\ No newline at end of file
diff --git a/_projects/2_syntheticBiology.md b/_projects/2_syntheticBiology.md
deleted file mode 100644
index 2bf3e7549aba..000000000000
--- a/_projects/2_syntheticBiology.md
+++ /dev/null
@@ -1,25 +0,0 @@
----
-layout: page
-title: Synthetic biology
-description: Understanding and optimising synthetic biological systems
-img: assets/img/7.jpg
-importance: 3
-category: work
----
-
-Synthetic biology explores the design and construction of biological components, both for understanding life's
-fundamental principles and applying them in biotechnology. Within this domain, our group is currently engaged in two
-areas:
-
-### Cell-free protein expression
-
-We develop and analyse computational models to probe conditions that drive self-regeneration within cell-free
-expression systems. We aim to both improve the efficiency and sustainability of protein production and gain deeper
-insights into hallmarks of self-regeneration underpinning living systems.
-
---------
-
-### Model inference and optimal experimental design
-
-We develop robust methods for parameter inference and optimal experimental design. These tools allow us to propose
-experiments designed to maximise the insights derived and expedite the design-build-test-learn cycle.
\ No newline at end of file
diff --git a/_projects/3_HAI.md b/_projects/3_HAI.md
deleted file mode 100644
index ce13f88047c9..000000000000
--- a/_projects/3_HAI.md
+++ /dev/null
@@ -1,18 +0,0 @@
----
-layout: page
-title: Health data science
-description: Leveraging data to improve healthcare
-img: assets/img/1.jpg
-importance: 3
-category: work
----
-
-Health data science leverages data-driven approaches for critical healthcare challenges. Our primary focus is centred
-on:
-
-### Healthcare-associated infections (HAIs)
-
-Using network analysis, we investigate transmission dynamics of HAIs among hospital patients. Our goal is to pinpoint
-outbreak clusters, elucidate transmission routes, and derive insights to guide effective infection control strategies.
-We focus on the transmission of multi-drug resistant bacteria, which complements our foundational research into factors
-driving the emergence and spread of antibiotic resistance.
\ No newline at end of file
diff --git a/_projects/6_project.md b/_projects/6_project.md
deleted file mode 100644
index 9a95d6e89d96..000000000000
--- a/_projects/6_project.md
+++ /dev/null
@@ -1,80 +0,0 @@
----
-layout: page
-title: project 6
-description: a project with no image
-img:
-importance: 4
-category: fun
----
-
-Every project has a beautiful feature showcase page.
-It's easy to include images in a flexible 3-column grid format.
-Make your photos 1/3, 2/3, or full width.
-
-To give your project a background in the portfolio page, just add the img tag to the front matter like so:
-
- ---
- layout: page
- title: project
- description: a project with a background image
- img: /assets/img/12.jpg
- ---
-
-
- Caption photos easily. On the left, a road goes through a tunnel. Middle, leaves artistically fall in a hipster photoshoot. Right, in another hipster photoshoot, a lumberjack grasps a handful of pine needles.
-
- This image can also have a caption. It's like magic.
-
-
-You can also put regular text between your rows of images.
-Say you wanted to write a little bit about your project before you posted the rest of the images.
-You describe how you toiled, sweated, *bled* for your project, and then... you reveal its glory in the next row of images.
-
-
-
- You can also have artistically styled 2/3 + 1/3 images, like these.
-
-
-
-The code is simple.
-Just wrap your images with `
` and place them inside `
` (read more about the Bootstrap Grid system).
-To make images responsive, add `img-fluid` class to each; for rounded corners and shadows use `rounded` and `z-depth-1` classes.
-Here's the code for the last row of images above:
-
-{% raw %}
-```html
-
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diff --git a/assets/alumni/allanBeveridge/index.html b/assets/alumni/allanBeveridge/index.html
new file mode 100644
index 000000000000..0e12fa8002e6
--- /dev/null
+++ b/assets/alumni/allanBeveridge/index.html
@@ -0,0 +1 @@
+ Allan Beveridge | Biomedical Computation Group
Allan Beveridge
Research Software Engineer
\ No newline at end of file
diff --git a/assets/alumni/emilyGaughan.md b/assets/alumni/emilyGaughan.md
deleted file mode 100644
index 5d157a521677..000000000000
--- a/assets/alumni/emilyGaughan.md
+++ /dev/null
@@ -1,20 +0,0 @@
----
-layout: page
-title: Emily Gaughan
-description: Honours student
-img:
-importance: 1
-category: Honours students
----
-
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\ No newline at end of file
diff --git a/assets/alumni/emilyGaughan/index.html b/assets/alumni/emilyGaughan/index.html
new file mode 100644
index 000000000000..ea30dbe037f0
--- /dev/null
+++ b/assets/alumni/emilyGaughan/index.html
@@ -0,0 +1 @@
+ Emily Gaughan | Biomedical Computation Group
Emily Gaughan
Honours student
\ No newline at end of file
diff --git a/assets/alumni/evangelosNikolados.md b/assets/alumni/evangelosNikolados.md
deleted file mode 100644
index 72c0e95642a8..000000000000
--- a/assets/alumni/evangelosNikolados.md
+++ /dev/null
@@ -1,20 +0,0 @@
----
-layout: page
-title: Evangelos Nikolados
-description: Research Assistant
-img:
-importance: 1
-category: Staff
----
-
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\ No newline at end of file
diff --git a/assets/alumni/evangelosNikolados/index.html b/assets/alumni/evangelosNikolados/index.html
new file mode 100644
index 000000000000..eb751e09fbf5
--- /dev/null
+++ b/assets/alumni/evangelosNikolados/index.html
@@ -0,0 +1 @@
+ Evangelos Nikolados | Biomedical Computation Group
Evangelos Nikolados
Research Assistant
\ No newline at end of file
diff --git a/assets/alumni/ruiboZhang.md b/assets/alumni/ruiboZhang.md
deleted file mode 100644
index 85e593208f08..000000000000
--- a/assets/alumni/ruiboZhang.md
+++ /dev/null
@@ -1,20 +0,0 @@
----
-layout: page
-title: Ruibo Zhang
-description: Honours student
-img:
-importance: 1
-category: Honours students
----
-
-
-
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-
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\ No newline at end of file
diff --git a/assets/alumni/ruiboZhang/index.html b/assets/alumni/ruiboZhang/index.html
new file mode 100644
index 000000000000..1cb07fdc5e2b
--- /dev/null
+++ b/assets/alumni/ruiboZhang/index.html
@@ -0,0 +1 @@
+ Ruibo Zhang | Biomedical Computation Group
Ruibo Zhang
Honours student
\ No newline at end of file
diff --git a/assets/alumni/seungwonKo.md b/assets/alumni/seungwonKo.md
deleted file mode 100644
index aeeffca31fe2..000000000000
--- a/assets/alumni/seungwonKo.md
+++ /dev/null
@@ -1,20 +0,0 @@
----
-layout: page
-title: Seungwon Ko
-description: Honours student
-img:
-importance: 1
-category: Honours students
----
-
-
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\ No newline at end of file
diff --git a/assets/alumni/seungwonKo/index.html b/assets/alumni/seungwonKo/index.html
new file mode 100644
index 000000000000..150e9118bb98
--- /dev/null
+++ b/assets/alumni/seungwonKo/index.html
@@ -0,0 +1 @@
+ Seungwon Ko | Biomedical Computation Group
- {%- endif -%}
- {%- elsif entry.abbr -%}
- {%- if site.data.venues[entry.abbr] -%}
- {%- assign venue_style = nil -%}
- {%- if site.data.venues[entry.abbr].color != blank -%}
- {%- assign venue_style = site.data.venues[entry.abbr].color | prepend: 'style="background-color:' | append: '"' -%}
- {%- endif -%}
- {{entry.abbr}}
- {%- else -%}
- {{entry.abbr}}
- {%- endif -%}
- {%- endif -%}
-