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An alternative model of amino acid replacement

G. E. Crooks, S. E. Brenner
2004 Bioinformatics  
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

Richard Röttger, Christoph Kreutzer, Thuy Duong Vu, Tobias Wittkop, Jan Baumbach, Marc Herbstritt
2012 German Conference on Bioinformatics  
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

Anca Simioniuc, Manuela Campan, Vincenzo Lionetti, Martina Marinelli, Giovanni D. Aquaro, Claudia Cavallini, Sabrina Valente, Dario Di Silvestre, Silvia Cantoni, Fabio Bernini, Claudia Simi, Silvia Pardini (+5 others)
2011 Cardiovascular Research  
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]

Kevin Lu, Aditya Grover, Pieter Abbeel, Igor Mordatch
2021 arXiv   pre-print
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

Kevin Lu, Aditya Grover, Pieter Abbeel, Igor Mordatch
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

P. Mallick, R. Weiss, D. Eisenberg
2002 Proceedings of the National Academy of Sciences of the United States of America  
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

Sheik Amamuddy, Veldman, Manyumwa, Khairallah, Agajanian, Oluyemi, Verkhivker, Tastan Bishop
2020 International Journal of Molecular Sciences  
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

M. Gyongyosi, J. Blanco, T. Marian, L. Tron, O. Petnehazy, Z. Petrasi, R. Hemetsberger, J. Rodriguez, G. Font, I. J. Pavo, I. Kertesz, L. Balkay (+8 others)
2008 Circulation Cardiovascular Imaging  
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

Gesa Hartwigsen, Lukas J. Volz
2020 NeuroImage  
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

Cheng-gen Qian, Yu-lei Chen, Pei-jian Feng, Xuan-zhong Xiao, Mei Dong, Ji-cheng Yu, Quan-yin Hu, Qun-dong Shen, Zhen Gu
2017 Acta Pharmacologica Sinica  
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

Thomas Edmund Cope, Rimona Sharon Weil, Emrah Düzel, Bradford C Dickerson, James Benedict Rowe
2021 Journal of Neurology, Neurosurgery and Psychiatry  
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

Melcy Philip, Tyrone Chen, Sonika Tyagi
2021 Non-Coding RNA  
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]

Jan Hsiao, Lola Chenxi Deng, Sreekanth H Chalasani, Eric Edsinger
2021 bioRxiv   pre-print
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

Zachary R. Stromberg, Will Fischer, Steven B. Bradfute, Jessica Z. Kubicek-Sutherland, Peter Hraber
2020 Vaccines  
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

J. Reithler, J.C. Peters, A.T. Sack
2011 Progress in Neurobiology  
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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