Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Dario Amodei"'
Publikováno v:
PLoS Computational Biology, Vol 10, Iss 1, p e1003408 (2014)
Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated
Externí odkaz:
https://doaj.org/article/4fcc5451a95f4710bbe8a0154b12ba8c
Autor:
Brendan MacLean, Michael J. MacCoss, Parag Mallick, Dario Amodei, Don Marsh, Richard J. Johnson, Jarrett D. Egertson, Austin T. Keller, Olga Vitek, Gennifer E. Merrihew
Publikováno v:
Journal of the American Society for Mass Spectrometry
A major goal of proteomics research is the accurate and sensitive identification and quantification of a broad range of proteins within a sample. Data-independent acquisition (DIA) approaches that acquire MS/MS spectra independently of precursor info
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::32c804577c3e11a8ef77857db5f67ba6
http://europepmc.org/articles/PMC6445824
http://europepmc.org/articles/PMC6445824
Autor:
Ruedi Aebersold, George Rosenberger, Ben C. Collins, Brendan MacLean, Henry H N Lam, Ludovic C Gillet, Parag Mallick, Witold Wolski, Dario Amodei, Pedro Navarro, Olga T. Schubert
Publikováno v:
Nature Protocols
Schubert, O T, Gillet, L C, Collins, B C, Navarro, P, Rosenberger, G, Wolski, W E, Lam, H, Amodei, D, Mallick, P, MacLean, B & Aebersold, R 2015, ' Building high-quality assay libraries for targeted analysis of SWATH MS data ', Nature Protocols, vol. 10, no. 3, pp. 426-441 . https://doi.org/10.1038/nprot.2015.015
Schubert, O T, Gillet, L C, Collins, B C, Navarro, P, Rosenberger, G, Wolski, W E, Lam, H, Amodei, D, Mallick, P, MacLean, B & Aebersold, R 2015, ' Building high-quality assay libraries for targeted analysis of SWATH MS data ', Nature Protocols, vol. 10, no. 3, pp. 426-441 . https://doi.org/10.1038/nprot.2015.015
Targeted proteomics by selected/multiple reaction monitoring (S/MRM) or, on a larger scale, by SWATH (sequential window acquisition of all theoretical spectra) MS (mass spectrometry) typically relies on spectral reference libraries for peptide identi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0d78251acf1c3ce799c0d52c5081f93a
Autor:
Timothy E. Holy, Frederick S. Soo, Michael J. Berry, Nikhil Deshmukh, Kolia Sadeghi, Olivier Marre, Dario Amodei
Publikováno v:
The Journal of Neuroscience. 32:14859-14873
Recording simultaneously from essentially all of the relevant neurons in a local circuit is crucial to understand how they collectively represent information. Here we show that the combination of a large, dense multielectrode array and a novel, mostl
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f64ecf90ecd31e88df7145e26a148a0f
https://doi.org/10.1523/jneurosci.0723-12.2012
https://doi.org/10.1523/jneurosci.0723-12.2012
Publikováno v:
Journal of Neurophysiology
We explored the manner in which spatial information is encoded by retinal ganglion cell populations. We flashed a set of 36 shape stimuli onto the tiger salamander retina and used different decoding algorithms to read out information from a populatio
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8dc8cd52221e01973574e35aa2b5626d
https://doi.org/10.1152/jn.00564.2011
https://doi.org/10.1152/jn.00564.2011
Autor:
Thierry Mora, Michael J. Berry, Dario Amodei, Gašper Tkačik, Olivier Marre, William Bialek, Stephanie E. Palmer
Publikováno v:
Proceedings of the National Academy of Sciences of the United States of America
Proceedings of the National Academy of Sciences of the United States of America, 2015, 112 (37), pp.11508-11513. ⟨10.1073/pnas.1514188112⟩
Proceedings of the National Academy of Sciences of the United States of America, 2015, 112 (37), pp.11508-11513. ⟨10.1073/pnas.1514188112⟩
International audience; The activity of a neural network is defined by patterns of spiking and silence from the individual neurons. Because spikes are (relatively) sparse, patterns of activity with increasing numbers of spikes are less probable, but,
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e2dc436adf2e9330c14c71289990145e
https://pubmed.ncbi.nlm.nih.gov/26330611
https://pubmed.ncbi.nlm.nih.gov/26330611
Autor:
Suckau Detlev, Brent Lefebvre, David M. Creasy, Paape Rainer, Matthew C. Chambers, Laurent Gatto, Katherine Hoff, Eric W. Deutsch, James I. Langridge, Lydia M. Nuwaysir, David B. Agus, Lisa Flashner, Michael J. MacCoss, Kian Kani, Brian Connolly, Chris Moulding, Nicholas J. Shulman, Frank E. Kuhlmann, Trey Chadick, Jonathan E. Katz, David L. Tabb, Parag Mallick, Brian S. Pratt, Christopher Paulse, Robert L. Moritz, Brendan MacLean, Andreas Huhmer, Jarrett D. Egertson, Bernd Fischer, Robert Burke, Tina Hemenway, Daniel Ruderman, Steffen Neumann, Mi-Youn Brusniak, Krisztina Holly, Dario Amodei, Tahmina A Baker, Sean L. Seymour, Barbara Frewen, Joe Roark, Josh Eckels, Natalie Tasman, Darren Kessner
Publikováno v:
Nature Biotechnology
Nature biotechnology
Nature biotechnology
Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological and clinical samples1, identify pathways affected by endo
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d9379058c155d7ae7b1b2eb67cd96e06
Autor:
Ruedi Aebersold, Lars Malmström, Ben C. Collins, Dario Amodei, Hannes L. Röst, George Rosenberger, Sarah J. Parker, Vidya Venkatraman, Koen Raedschelders, Jennifer E. Van Eyk
Publikováno v:
Parker, S J, Rost, H, Rosenberger, G, Collins, B C, Malmström, L, Amodei, D, Venkatraman, V, Raedschelders, K, Eyk, J E V & Aebersold, R 2015, ' Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry ', Molecular and Cellular Proteomics, vol. 14, no. 10, pp. 2800-2813 . https://doi.org/10.1074/mcp.O114.042267
Accurate knowledge of retention time (RT) in liquid chromatography-based mass spectrometry data facilitates peptide identification, quantification, and multiplexing in targeted and discovery-based workflows. Retention time prediction is particularly
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c39843f2ac3a8018d5c355d520c4a5eb
https://pubmed.ncbi.nlm.nih.gov/26199342
https://pubmed.ncbi.nlm.nih.gov/26199342
Autor:
Joon Ho Kang, Nathan Cermak, Sangwon Byun, Monte M. Winslow, Vivian C. Hecht, Sungmin Son, Josephine Shaw, Parag Mallick, Scott R. Manalis, Tyler Jacks, Dario Amodei
Publikováno v:
Proceedings of the National Academy of Sciences of the United States of America. 110(19)
Metastasis requires the penetration of cancer cells through tight spaces, which is mediated by the physical properties of the cells as well as their interactions with the confined environment. Various microfluidic approaches have been devised to mimi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::343b4383da4e5c93e07bcfed2513b1b3
https://pubmed.ncbi.nlm.nih.gov/23610435
https://pubmed.ncbi.nlm.nih.gov/23610435
Recent work emphasizes that the maximum entropy principle provides a bridge between statistical mechanics models for collective behavior in neural networks and experiments on networks of real neurons. Most of this work has focused on capturing the me
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9f4d059fd9c97a7cab246bb717f9172e
