RAS Mutations Affect Tumor Necrosis Factor–Induced Apoptosis in Colon Carcinoma Cells via ERK-Modulatory Negative and Positive Feedback Circuits Along with Non-ERK Pathway Effects... by Kreeger, Pamela K., Mandhana, Roli, Haigis, Kevin M., Hughes-Alford, Shannon Kay, Lauffenburger, Douglas A

“…A quantitative computational model based on weighted linear combinations of these pathway activities successfully predicted not only the spectrum of cell death responses but also the corresponding chemokine production responses. …”
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ADAM-10 and -17 regulate endometriotic cell migration via concerted ligand and receptor shedding feedback on kinase signaling by Miller, Miles Aaron, Meyer, Aaron Samuel, Beste, Michael T., Lasisi, Zainab A., Reddy, Sonika N., Jeng, Karen, Griffith, Linda G., Lauffenburger, Douglas A., Chen, Chia-Hung, Han, Jongyoon, Isaacson, Keith B.

“…This study uses combined measurement and computational modeling to examine how various growth factor environments influence sheddase activity and cell migration in the invasive disease of endometriosis. …”
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Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures by Kilchherr, F., Dietz, H., Kim, Do-Nyun, Bathe, Mark

“…Here, we significantly extend and experimentally validate a computational modeling framework for DNA origami previously presented as CanDo [Castro,C.E., Kilchherr,F., Kim,D.…”
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Cellular defense processes regulated by pathogen-elicited receptor signaling by Wu, Rongcong, Goldsipe, Arthur C., Schauer, David B., Lauffenburger, Douglas A.

“…We have developed over the past half-decade a "data-driven" computational modeling approach, on a 'cue-signal-response' combined experiment/computation paradigm, to elucidate key multi-variate signaling relationships governing the cell responses. …”
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Evaporation kinetics of nano water droplets using coarse-grained molecular dynamic simulations by Kieu, Hieu Trung, Tsang, Anson Yung Chak, Zhou, Kun, Law, Adrian Wing-Keung

“…In particular, computational modeling studies using molecular dynamic (MD) simulations had been extensively performed for this objective. …”
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Semi-supervised learning of functional connectome for disease classification by Yew, Wei Chee

“…Overfitting is a common problem when computational models are applied on neuroimaging datasets, which are high-dimensional and small in terms of sample sizes, resulting in poor inferences such as ungeneralizable biomarkers. …”
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Metaverse's stochastic optimization for enhanced computation and communication by Ng, Wei Chong

“…Furthermore, the thesis delves into advanced computational models, with a particular emphasis on BERT. …”
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Influence of histone tails and H4 tail acetylations on nucleosome–nucleosome interactions by Liu, Ying, Lu, Chenning, Yang, Ye, Fan, Yanping, Yang, Renliang, Liu, Chuan Fa, Korolev, Nikolay, Nordenskiöld, Lars

“…The experimental data were compared with the results of coarse-grained computer modeling for NCP solutions with explicit presence of mobile ions.…”
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From numerical model to computational intelligence: the digital transition of urban energy system by Zhang, Chuan, Romagnoli, Alessandro, Zhou, Li, Kraft, Markus

“…More specifically, numerous computational models have been proposed by the scientific community to mimic the dynamics of various components at various levels in the urban energy system. …”
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The role of the circle of Willis in internal carotid artery stenosis and anatomical variations: a computational study based on a patient-specific three-dimensional model by Zhu, Guangyu, Yuan, Qi, Yang, Jian, Yeo, Joon Hock

“…Methods: In the current study, a patient-specific three-dimensional computational model of the CoW was reconstructed based on the computed tomography (CT) images. …”
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Quantification of restitution dispersion from the dynamic changes of the T-wave peak to end, measured at the surface ECG. by Mincholé, A, Pueyo, E, Rodríguez, J, Zacur, E, Doblaré, M, Laguna, P

“…The capability of the proposed estimate to reflect APDR dispersion is assessed using a combination of ECG signal processing, and computational modeling and simulation. Specifically, ECG recordings of control subjects undergoing a tilt test trial are used to measure that estimate, while its capability to provide a quantification of APDR dispersion at tissue level is assessed by using a 2-D ventricular tissue simulation. …”

BOKEI: Bayesian optimization using knowledge of correlated torsions and expected improvement for conformer generation​ by Chan, L, Hutchison, GR, Morris, G

“…Increasing our understanding of the conformational preferences of molecules will help improve our ability to find low energy conformers efficiently, which will have impact in a wide range of computational modeling applications.…”

Not all predictions are equal: 'What' and 'When' predictions modulate activity in auditory cortex through different mechanisms by Auksztulewicz, R, Schwiedrzik, C, Thesen, T, Doyle, W, Devinsky, O, Devinsky, O, De Ozorio Nobre, A, Schroeder, C, Friston, K, Melloni, L

“…Here, to elucidate the neural mechanisms of predictions, we combine invasive electrophysiological recordings (human electrocorticography in 4 females and 2 males) with computational modelling while manipulating predictions about content (‘what’) and time (‘when’). …”

Temporal regularity in audition by Rajendran, V

“…I combine human psychoacoustics, rodent electrophysiology, and computational modelling to demonstrate that rhythmic sound patterns are easier to detect than arrhythmic ones, that adaptation in the auditory system may be a mechanism by which information about temporal structure at the rhythm timescale is encoded and made available to higher structures, and that low-level auditory processing may play a substantial part in shaping complex percepts such as where and how clearly we feel the beat in music.…”

Integrating single-cell and spatial transcriptomics in a computational multiscale model of triple negative breast cancer by Victori, P

“…<p>This thesis presents a multiscale computational model of tumour growth, microCJ. microCJ models cells as independent agents, each with their own genetic identity and state. …”

VEGF signals induce trailblazer cell identity that drives neural crest migration. by McLennan, R, Schumacher, L, Morrison, J, Teddy, J, Ridenour, D, Box, A, Semerad, C, Li, H, McDowell, W, Kay, D, Maini, P, Baker, R, Kulesa, P

“…Timed addition and removal of VEGF in culture reveals the changes in neural crest cell gene expression are rapid. A computational model incorporating an integrate-and-switch mechanism between cellular phenotypes predicts migration efficiency is influenced by the timescale of cell behavior switching. …”

Effects of ranolazine on the arrhythmic substrate in hypertrophic cardiomyopathy by Coleman, JA, Doste, R, Beltrami, M, Argirò, A, Coppini, R, Olivotto, I, Raman, B, Bueno Orovio, A

“…</p> <br> <p><strong>Methods:</strong> Computational models of human tissue and ventricles were used to simulate the electrophysiological behaviour of diseased HCM myocardium for variable degrees of repolarisation impairment, validated against in vitro and clinical recordings. …”

Novel fingerprinting method characterises the necessary and sufficient structural connectivity from deep brain stimulation electrodes for a successful outcome by Fernandes, H, Van Hartvelt, T, Boccard, S, Green, A, FitzGerald, J, Aziz, T, Kringelbach, M

“…Ultimately, our novel fingerprinting method could be combined with advanced whole-brain computational modelling of the spontaneous dynamics arising from the structural changes in disease, to provide new insights and potentially new targets for hitherto impenetrable neuropsychiatric disorders.…”

Effective connectivity of the subthalamic nucleus-globus pallidus network during Parkinsonian oscillations. by Nevado-Holgado, A, Mallet, N, Magill, P, Bogacz, R

“…We recorded the activities of STN, Type-I GP (GP-TI) and Type-A GP (GP-TA) neurons in anaesthetised Parkinsonian rats during such oscillations to constrain a series of computational models that systematically explored the effective connections and physiological parameters underlying neuronal rhythmic firing and phase preferences in vivo. …”

The short-term plasticity of VIP interneurons in motor cortex by McFarlan, AR, Gomez, I, Chou, CYC, Alcolado, A, Costa, RP, Sjöström, PJ

“…Surprisingly, unlike VIP IN outputs, E → VIP IN synapses exhibited heterogeneous short-term dynamics, which we attributed to the target VIP IN cell rather than the input. Computational modeling furthermore linked the diversity in short-term dynamics at VIP IN inputs to a wide variability in probability of release. …”