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An alternative model of amino acid replacement
2004
Bioinformatics
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The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. ...
The resulting dynamical model of independent replacements drawn from heterogeneous backgrounds is simple and consistent, and provides a unified homology match score for sequence-sequence, sequence-profile ...
SEB is a Searle Scholar (1-L-110). ...
doi:10.1093/bioinformatics/bti109
pmid:15531614
fatcat:dc5o47k5b5bwbkdf47jdrvmkhe
Online Transitivity Clustering of Biological Data with Missing Values
2012
German Conference on Bioinformatics
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By means of identifying protein (super)families from incomplete all-vs-all BLAST results we demonstrate the robustness of our approach. ...
While many approaches for biomedical data clustering exist, most methods neglect two important problems: (1) Computing the similarity matrix might not be trivial but resource-intense. (2) A clustering ...
Acknowledgement JB and RR are grateful for financial support from the Cluster of Excellence on Multimodal Computing and Interaction of the German Research Foundation (DFG). ...
doi:10.4230/oasics.gcb.2012.57
dblp:conf/gcb/RottgerKVWB12
fatcat:jefnovuol5avfehuubgstq4qfi
Placental stem cells pre-treated with a hyaluronan mixed ester of butyric and retinoic acid to cure infarcted pig hearts: a multimodal study
2011
Cardiovascular Research
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Moreover, proteomic analysis of the border zone in the HBR-FMhMSCs group and the FMhMSCs group indicated, respectively, 45 and 30% phenotypic homology with healthy tissue, while this homology was only ...
Our aim was to test FMhMSCs in a large-animal model by employing a novel combination of in vivo and ex vivo analyses. ...
Acknowledgements We are grateful to Drs Silvia Burchielli and Elena Olivi for their excellent technical assistance. ...
doi:10.1093/cvr/cvr018
pmid:21257613
fatcat:6r653we4obcabjva5v35z7qngu
Pretrained Transformers as Universal Computation Engines
[article]
2021
arXiv
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We consider such a model, which we call a Frozen Pretrained Transformer (FPT), and study finetuning it on a variety of sequence classification tasks spanning numerical computation, vision, and protein ...
Additionally, we perform an analysis of the architecture, comparing the performance of a random initialized transformer to a random LSTM. ...
We would also like to thank members of the community for providing feedback online on an earlier version of this paper. ...
arXiv:2103.05247v2
fatcat:x5itsles5zal3csrb6axwgdhg4
Frozen Pretrained Transformers as Universal Computation Engines
2022
PROCEEDINGS OF THE THIRTIETH AAAI CONFERENCE ON ARTIFICIAL INTELLIGENCE AND THE TWENTY-EIGHTH INNOVATIVE APPLICATIONS OF ARTIFICIAL INTELLIGENCE CONFERENCE
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We consider such a model, which we call a Frozen Pretrained Transformer (FPT), and study finetuning it on a variety of sequence classification tasks spanning numerical computation, vision, and protein ...
Additionally, we perform an analysis of the architecture, comparing the performance of a random initialized transformer to a random LSTM. ...
Acknowledgments We would like to thank Luke Metz, Kimin Lee, Fangchen Liu, Roshan Rao, Aravind Srinivas, Nikita Kitaev, Daniel Freeman, Marc'Aurelio Ranzato, Jacob Andreas, and Ashish Vaswani for valuable ...
doi:10.1609/aaai.v36i7.20729
fatcat:qokbybk3lrgc7d4c4wmdizokky
The directional atomic solvation energy: An atom-based potential for the assignment of protein sequences to known folds
2002
Proceedings of the National Academy of Sciences of the United States of America
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The DASEY has been developed to align and score a probe amino acid sequence to a library of template protein structures for fold assignment. ...
Database of Aligned Protein Structures (DAPS). A database of aligned protein structures was derived from the domain database. ...
We also thank BER-Department of Energy, National Institutes of Health, and Howard Hughes Medical Institute for support. ...
doi:10.1073/pnas.252626399
pmid:12461172
pmcid:PMC138561
fatcat:cscyexnljzdhbpmvqp53rnjk2u
Integrated Computational Approaches and Tools for Allosteric Drug Discovery
2020
International Journal of Molecular Sciences
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The proliferation of novel computational approaches for predictingligand–protein interactions and binding using dynamic and network-centric perspectives has ledto new insights into allosteric mechanisms ...
In this article,we review computational approaches for allosteric drug discovery and discuss how these tools can beutilized to develop consensus workflows for in silico identification of allosteric sites ...
As a last resort for target domains with no detectable homologs, ab initio modelling may be an option [172, 173] . ...
doi:10.3390/ijms21030847
pmid:32013012
pmcid:PMC7036869
fatcat:y2z5vnsylnduhc7gntjkpcoslq
Serial Noninvasive In Vivo Positron Emission Tomographic Tracking of Percutaneously Intramyocardially Injected Autologous Porcine Mesenchymal Stem Cells Modified for Transgene Reporter Gene Expression
2008
Circulation Cardiovascular Imaging
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Background-Porcine bone marrow-derived mesenchymal stem cells (MSCs) were stably transfected with a lentiviral vector for transgene expression of the trifusion protein renilla luciferase, red fluorescent ...
protein and herpes simplex truncated thymidine kinase (LV-RL-RFP-tTK; positron emission tomography [PET] reporter gene) for in vivo noninvasive tracking of the intramyocardially delivered MSC fate. ...
Acknowledgments We thank Sanjiv Sam Gambhir, MD, PhD, for receiving the trifusion gene for cell transfection in Centro de Investigación Cardiovascular (CSIC-ICCC), Barcelona, Spain. ...
doi:10.1161/circimaging.108.797449
pmid:19808526
pmcid:PMC3053595
fatcat:sjqr2naqxjfeblrggrqj6sigxa
Probing rapid network reorganization of motor and language functions via neuromodulation and neuroimaging
2020
NeuroImage
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and treatment approaches. ...
These mechanisms may allow for computational flexibility of large-scale neural networks underlying motor and cognitive functions. ...
For instance, the upregulation of a remote or homologous region after inhibitory rTMS over a specific key area might either reflect an attempt to compensate for the disruption or disinhibition of that ...
doi:10.1016/j.neuroimage.2020.117449
pmid:33059054
fatcat:bo3htmxyyndlhelnnfdnde5yyq
Conjugated polymer nanomaterials for theranostics
2017
Acta Pharmacologica Sinica
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A variety of stimuli-responsive CPN systems for drug delivery are also summarized, and the promising trends and translational challenges are discussed. ...
Specifically, CPN-based in vivo imaging techniques, including near-infrared (NIR) imaging, two-photon (TP) imaging, photoacoustic (PA) imaging, and multimodal (MM) imaging, are introduced. ...
Acknowledgements This work was supported by the National Natural Science Foundation of China (No 21174060) to Qun-dong SHEN, the Sloan Research Fellowship to Zhen GU, and Program A for Outstanding PhD ...
doi:10.1038/aps.2017.42
pmid:28552910
pmcid:PMC5520193
fatcat:4wwmjb2tkraybpywqzsstuefmm
Advances in neuroimaging to support translational medicine in dementia
2021
Journal of Neurology, Neurosurgery and Psychiatry
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In combination with large datasets, open data and artificial intelligence analysis methods, new informatics-based approaches are set to enable accurate single-subject inferences for diagnosis, prediction ...
They are especially informative when combined in multimodal studies, with model-based analyses to test precisely defined hypotheses. ...
Multimodal imaging to test disease mechanisms Multimodal studies combining PET ligands for metabolism, protein aggregation and neuroinflammation are particularly powerful to examine underlying disease ...
doi:10.1136/jnnp-2019-322402
pmid:33568448
pmcid:PMC8862738
fatcat:kfzojf7vpncq7pgln7xiaue324
A Survey of Current Resources to Study lncRNA-Protein Interactions
2021
Non-Coding RNA
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We specifically surveyed recent computational methods and databases which researchers can exploit for LPI investigation. ...
We therefore review the current state of the art in lncRNA-protein interactions. ...
Acknowledgments: We thank Yashpal Ramakrishnaiah for his proofreading and feedback on this article. The authors thank the HPC team at Monash eResearch Centre for their continuous personnel support. ...
doi:10.3390/ncrna7020033
pmid:34201302
fatcat:psr5mlwzlzgyvdbpsdnzzj6lvq
Numerous expansions in TRP ion channel diversity highlight widespread evolution of molecular sensors in animal diversification
[article]
2021
bioRxiv
pre-print
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Transient Potential Receptor (TRP) ion channels are a diverse superfamily of multimodal molecular sensors that respond to a wide variety of stimuli, including mechanical, chemical, and thermal. ...
We developed a flexible push-button bioinformatic and phylogenomic pipeline, GIGANTIC, that generated genome-based gene and species trees and enabled phylogenetic characterization of challenging remote ...
These proteins function as multimodal primary and secondary molecular sensors (mechano, thermo, and chemosensing). ...
doi:10.1101/2021.11.14.466824
fatcat:bq5mv5itmvdcjpre3v4lr3b6yi
Vaccine Advances against Venezuelan, Eastern, and Western Equine Encephalitis Viruses
2020
Vaccines
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Vaccinations are a crucial intervention in combating infectious diseases. ...
Currently, there are no licensed treatments or vaccines available for these viruses in humans. Experimental vaccines have shown variable efficacy and may cause severe adverse effects. ...
Martinez and Christine Pedersen for helpful discussions. We are grateful to the anonymous reviewers for the clarifications that improved the presentation of this work. ...
doi:10.3390/vaccines8020273
pmid:32503232
pmcid:PMC7350001
fatcat:exlni2s6kbgjhkrtwzqj6nstjy
Multimodal transcranial magnetic stimulation: Using concurrent neuroimaging to reveal the neural network dynamics of noninvasive brain stimulation
2011
Progress in Neurobiology
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Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of ...
If the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the "Taverne" license above, please follow below link for the End User ...
Moreover, due to the already mentioned intrinsic intricacies of neural circuits, a multimodal approach by concurrent use of complementary methods will also be required in this line of research (Logothetis ...
doi:10.1016/j.pneurobio.2011.04.004
pmid:21527312
fatcat:zy5l6tfp35efpgceanjkvkivt4
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