About
Jose Maria Carazo Garcia (h factor = 59, 12861 citations (ISI Web of Science-July 05, 2024), h factor = 72, 18946 (Google Scholar, July 05, 2024))), born in 1959, studied Physics at University of Granada, Spain, and obtained his PhD in Biology at University Autonoma, Madrid, Spain (1984). After the post-doc period at Wadsworth Center of the NYS Department of Health (USA) with Nobel Laureate Prof. Joachim Frank, he joined the National Center of Biotechnology as head of the Biocomputing Unit in 1989, where he was appointed full professor of the Spanish National Research Council (CSIC) in 2005.
Professor Carazo has a sustained experience in the field of Three-dimensional Electron Microscopy under cryogenic conditions (cryo-EM), especially in the methods development area. His laboratory has opened whole new areas in the field, naming just as example the successful family of Maximum Likelihood algorithms (developed in Madrid from 2007 to 2011) or the very much used EMDataBank (started from the European Union project “Bioimage” that he Coordinated from 1996 to 1999). At the level of software developments, his laboratory develops and support software packages like Xmipp and Scipion, who are been actively used by more than 1700 users in more than 13000 projects distributed throughout the world, as well as web services, like 3DBionotes, with close than 1600 new users just in 2022. Note that a specific version of Scipion developed for cryoEM facilities is currently being at the heart of some key resources, such as the European Synchrotron (ESRF), in Grenoble, and SciLab and soon the French Synchrotron Soleil.
On the technology transfer area, he founded the spin-off “Integromics”, winner of the first National Prize of La Caixa Emprendedor XXI (2007) and the Frost & Sullivan award to the Most Innovative Bioinformatics Company in Europe (2008). Integromics was acquired by the US multinational Perkin-Elmer in 2014.
He has supervised and co-supervised almost 30 postdocs and 90 graduate students. Some of them have already become key scientists in their own right, such as Sjors Scheres, who is currently at the LMB-MRC. Others have held influential positions in the private sector, such as Alberto Pascual, who serves as Product Portfolio Leader for Signals Workflows at Revvity Signals, and Carlos Oscar Sorzano, who is Co-PI of the Biocomputing Unit located at the National Center for Biotechnology – CSIC.
Selected recent publications
1485676
{1485676:D66Y2AXK},{1485676:FQZQFCAZ},{1485676:DW64G6H4},{1485676:268BDTKC},{1485676:SZUQWUXT},{1485676:DTB9847B}
1
nature
50
date
1
324
https://biophysicsworkshop.co.za/wp-content/plugins/zotpress/
%7B%22status%22%3A%22success%22%2C%22updateneeded%22%3Afalse%2C%22instance%22%3Afalse%2C%22meta%22%3A%7B%22request_last%22%3A0%2C%22request_next%22%3A0%2C%22used_cache%22%3Atrue%7D%2C%22data%22%3A%5B%7B%22key%22%3A%22DTB9847B%22%2C%22library%22%3A%7B%22id%22%3A1485676%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Schwalbe%20et%20al.%22%2C%22parsedDate%22%3A%222024-10-03%22%2C%22numChildren%22%3A2%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%202%3B%20%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%20style%3D%5C%22clear%3A%20left%3B%20%5C%22%3E%5Cn%20%20%20%20%3Cdiv%20class%3D%5C%22csl-left-margin%5C%22%20style%3D%5C%22float%3A%20left%3B%20padding-right%3A%200.5em%3B%20text-align%3A%20right%3B%20width%3A%201em%3B%5C%22%3E1.%3C%5C%2Fdiv%3E%3Cdiv%20class%3D%5C%22csl-right-inline%5C%22%20style%3D%5C%22margin%3A%200%20.4em%200%201.5em%3B%5C%22%3ESchwalbe%2C%20H.%20%3Ci%3Eet%20al.%3C%5C%2Fi%3E%20The%20future%20of%20integrated%20structural%20biology.%20%3Ci%3EStructure%3C%5C%2Fi%3E%20%3Cb%3E32%3C%5C%2Fb%3E%2C%201563%26%23×2013%3B1580%20%282024%29.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fbiophysicsworkshop.co.za%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D1485676%26amp%3Bitem_key%3DDTB9847B%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%20%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22The%20future%20of%20integrated%20structural%20biology%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Harald%22%2C%22lastName%22%3A%22Schwalbe%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pauline%22%2C%22lastName%22%3A%22Audergon%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Natalie%22%2C%22lastName%22%3A%22Haley%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Claudia%20Alen%22%2C%22lastName%22%3A%22Amaro%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jon%22%2C%22lastName%22%3A%22Agirre%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marc%22%2C%22lastName%22%3A%22Baldus%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lucia%22%2C%22lastName%22%3A%22Banci%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Wolfgang%22%2C%22lastName%22%3A%22Baumeister%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Martin%22%2C%22lastName%22%3A%22Blackledge%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jose%20Maria%22%2C%22lastName%22%3A%22Carazo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kristina%20Djinovic%22%2C%22lastName%22%3A%22Carugo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Patrick%22%2C%22lastName%22%3A%22Celie%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Isabella%22%2C%22lastName%22%3A%22Felli%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Darren%20J.%22%2C%22lastName%22%3A%22Hart%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Thomas%22%2C%22lastName%22%3A%22Hau%5Cu00df%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lari%22%2C%22lastName%22%3A%22Lehti%5Cu00f6%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Kresten%22%2C%22lastName%22%3A%22Lindorff-Larsen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jos%5Cu00e9%22%2C%22lastName%22%3A%22M%5Cu00e1rquez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Andr%5Cu00e9%22%2C%22lastName%22%3A%22Matagne%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Roberta%22%2C%22lastName%22%3A%22Pierattelli%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Antonio%22%2C%22lastName%22%3A%22Rosato%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Frank%22%2C%22lastName%22%3A%22Sobott%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sridhar%22%2C%22lastName%22%3A%22Sreeramulu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jan%22%2C%22lastName%22%3A%22Steyaert%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Joel%20L.%22%2C%22lastName%22%3A%22Sussman%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lukas%22%2C%22lastName%22%3A%22Trantirek%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Manfred%20S.%22%2C%22lastName%22%3A%22Weiss%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Matthias%22%2C%22lastName%22%3A%22Wilmanns%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222024-10-03%22%2C%22language%22%3A%22English%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.str.2024.08.014%22%2C%22ISSN%22%3A%220969-2126%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.cell.com%5C%2Fstructure%5C%2Fabstract%5C%2FS0969-2126%2824%2900331-9%22%2C%22collections%22%3A%5B%22EENXQ3XN%22%5D%2C%22dateModified%22%3A%222024-10-20T19%3A59%3A10Z%22%7D%7D%2C%7B%22key%22%3A%22D66Y2AXK%22%2C%22library%22%3A%7B%22id%22%3A1485676%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Herreros%20et%20al.%22%2C%22parsedDate%22%3A%222024-09-19%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%202%3B%20%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%20style%3D%5C%22clear%3A%20left%3B%20%5C%22%3E%5Cn%20%20%20%20%3Cdiv%20class%3D%5C%22csl-left-margin%5C%22%20style%3D%5C%22float%3A%20left%3B%20padding-right%3A%200.5em%3B%20text-align%3A%20right%3B%20width%3A%201em%3B%5C%22%3E1.%3C%5C%2Fdiv%3E%3Cdiv%20class%3D%5C%22csl-right-inline%5C%22%20style%3D%5C%22margin%3A%200%20.4em%200%201.5em%3B%5C%22%3EHerreros%2C%20D.%20%3Ci%3Eet%20al.%3C%5C%2Fi%3E%20Real-space%20heterogeneous%20reconstruction%2C%20refinement%2C%20and%20disentanglement%20of%20CryoEM%20conformational%20states%20with%20HetSIREN.%20Preprint%20at%20%3Ca%20class%3D%27zp-DOIURL%27%20href%3D%27https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1101%5C%2F2024.09.16.613176%27%3Ehttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1101%5C%2F2024.09.16.613176%3C%5C%2Fa%3E%20%282024%29.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fbiophysicsworkshop.co.za%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D1485676%26amp%3Bitem_key%3DD66Y2AXK%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%20%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22preprint%22%2C%22title%22%3A%22Real-space%20heterogeneous%20reconstruction%2C%20refinement%2C%20and%20disentanglement%20of%20CryoEM%20conformational%20states%20with%20HetSIREN%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22D.%22%2C%22lastName%22%3A%22Herreros%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22C.%20P.%22%2C%22lastName%22%3A%22Mata%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22C.%22%2C%22lastName%22%3A%22Noddings%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22D.%22%2C%22lastName%22%3A%22Irene%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.%22%2C%22lastName%22%3A%22Krieger%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22D.%20A.%22%2C%22lastName%22%3A%22Agard%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22M.-D.%22%2C%22lastName%22%3A%22Tsai%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22C.%20O.%20S.%22%2C%22lastName%22%3A%22Sorzano%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.%20M.%22%2C%22lastName%22%3A%22Carazo%22%7D%5D%2C%22abstractNote%22%3A%22Single-particle%20analysis%20by%20Cryo-electron%20microscopy%20%28CryoEM%29%20provides%20direct%20access%20to%20the%20conformation%20of%20each%20macromolecule.%20However%2C%20the%20image%5Cu2019s%20signal-to-noise%20ratio%20is%20low%2C%20and%20some%20form%20of%20classification%20is%20usually%20performed%20at%20the%20image%20processing%20level%20to%20allow%20structural%20modeling.%20Classical%20classification%20methods%20imply%20the%20existence%20of%20a%20discrete%20number%20of%20structural%20conformations.%20However%2C%20new%20heterogeneity%20algorithms%20introduce%20a%20novel%20reconstruction%20paradigm%2C%20where%20every%20state%20is%20represented%20by%20a%20lower%20number%20of%20particles%2C%20potentially%20just%20one%2C%20allowing%20the%20estimation%20of%20conformational%20landscapes%20representing%20the%20different%20structural%20states%20a%20biomolecule%20explores.%20In%20this%20work%2C%20we%20present%20a%20novel%20deep%20learning-based%20method%20called%20HetSIREN.%20HetSIREN%20can%20fully%20reconstruct%20or%20refine%20a%20CryoEM%20volume%20in%20real%20space%20based%20on%20the%20structural%20information%20summarized%20in%20a%20conformational%20latent%20space.%20The%20unique%20characteristics%20that%20set%20HetSIREN%20apart%20start%20with%20the%20definition%20of%20the%20approach%20as%20a%20real%20space-based%20only%20method%2C%20a%20fact%20that%20allows%20spatially%20focused%20analysis%2C%20but%20also%20the%20introduction%20of%20a%20novel%20network%20architecture%20specifically%20designed%20to%20make%20use%20of%20meta-sinusoidal%20activations%2C%20with%20proven%20high%20analytics%20capacities.%20Continuing%20with%20innovations%2C%20HetSIREN%20can%20also%20refine%20the%20pose%20parameters%20of%20the%20images%20at%20the%20same%20time%20that%20it%20conditions%20the%20network%20with%20prior%20information%5C%2Fconstraints%20on%20the%20maps%2C%20such%20as%20Total%20Variation%20and%20L1%20denoising%2C%20ultimately%20yielding%20cleaner%20volumes%20with%20high-quality%20structural%20features.%20Finally%2C%20but%20very%20importantly%2C%20HetSIREN%20addresses%20one%20of%20the%20most%20confusing%20issues%20in%20heterogeneity%20analysis%2C%20as%20it%20is%20the%20fact%20that%20real%20structural%20heterogeneity%20estimation%20is%20entangled%20with%20pose%20estimation%20%28and%20to%20a%20lesser%20extent%20with%20CTF%20estimation%29%2C%20in%20this%20way%2C%20HetSIREN%20introduces%20a%20novel%20encoding%20architecture%20able%20to%20decouple%20pose%20and%20CTF%20information%20from%20the%20conformational%20landscape%2C%20resulting%20in%20more%20accurate%20and%20interpretable%20conformational%20latent%20spaces.%20We%20present%20results%20on%20computer-simulated%20data%2C%20public%20data%20from%20EMPIAR%2C%20and%20data%20from%20experimental%20systems%20currently%20being%20studied%20in%20our%20laboratories.%20An%20important%20finding%20is%20the%20sensitivity%20of%20the%20structure%20and%20dynamics%20of%20the%20SARS-CoV-2%20Spike%20protein%20on%20the%20storage%20temperature.%22%2C%22genre%22%3A%22%22%2C%22repository%22%3A%22bioRxiv%22%2C%22archiveID%22%3A%22%22%2C%22date%22%3A%222024-09-19%22%2C%22DOI%22%3A%2210.1101%5C%2F2024.09.16.613176%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.biorxiv.org%5C%2Fcontent%5C%2F10.1101%5C%2F2024.09.16.613176v1%22%2C%22language%22%3A%22en%22%2C%22collections%22%3A%5B%22EENXQ3XN%22%5D%2C%22dateModified%22%3A%222024-10-20T20%3A01%3A41Z%22%7D%7D%2C%7B%22key%22%3A%22SZUQWUXT%22%2C%22library%22%3A%7B%22id%22%3A1485676%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Zarrabeitia%20et%20al.%22%2C%22parsedDate%22%3A%222024-05%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%202%3B%20%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%20style%3D%5C%22clear%3A%20left%3B%20%5C%22%3E%5Cn%20%20%20%20%3Cdiv%20class%3D%5C%22csl-left-margin%5C%22%20style%3D%5C%22float%3A%20left%3B%20padding-right%3A%200.5em%3B%20text-align%3A%20right%3B%20width%3A%201em%3B%5C%22%3E1.%3C%5C%2Fdiv%3E%3Cdiv%20class%3D%5C%22csl-right-inline%5C%22%20style%3D%5C%22margin%3A%200%20.4em%200%201.5em%3B%5C%22%3EZarrabeitia%2C%20O.%20L.%2C%20Ram%26%23xED%3Brez-Aportela%2C%20E.%2C%20Carazo%2C%20J.%20M.%20%26amp%3B%20Sorzano%2C%20C.%20O.%20S.%20Fast%20Global%20Image%20Alignment%20Algorithm%20for%20CryoEM%20through%20Vector%20Compression.%20in%20%3Ci%3E2024%20IEEE%20International%20Symposium%20on%20Biomedical%20Imaging%20%28ISBI%29%3C%5C%2Fi%3E%201%26%23×2013%3B4%20%282024%29.%20%3Ca%20class%3D%27zp-DOIURL%27%20href%3D%27http%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1109%5C%2FISBI56570.2024.10635352%27%3Ehttp%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1109%5C%2FISBI56570.2024.10635352%3C%5C%2Fa%3E.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fbiophysicsworkshop.co.za%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D1485676%26amp%3Bitem_key%3DSZUQWUXT%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%20%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22conferencePaper%22%2C%22title%22%3A%22Fast%20Global%20Image%20Alignment%20Algorithm%20for%20CryoEM%20through%20Vector%20Compression%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22O.L.%22%2C%22lastName%22%3A%22Zarrabeitia%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22E.%22%2C%22lastName%22%3A%22Ram%5Cu00edrez-Aportela%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.M.%22%2C%22lastName%22%3A%22Carazo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22C.O.S.%22%2C%22lastName%22%3A%22Sorzano%22%7D%5D%2C%22abstractNote%22%3A%22In%20cryo-electron%20microscopy%20%28Cryo-EM%29%2C%20single-particle%20analysis%20involves%20aligning%20two-dimensional%20images%20of%20individual%20protein%20molecules.%20These%20particles%20are%20flash-frozen%20and%20imaged%20in%20various%20orientations.%20The%20goal%20of%20image%20alignment%20is%20to%20computationally%20determine%20the%20relative%20orientations%20and%20positions%20of%20the%20particles%20in%20each%20image.%20It%20is%20possible%20to%20reconstruct%20a%20high-resolution%20three-dimensional%20molecule%20model%20by%20doing%20so.%20This%20process%20is%20critical%20for%20understanding%20molecular%20structure%20and%20function.%20This%20study%20introduces%20a%20novel%20fast%20alignment%20algorithm%20designed%20explicitly%20for%20Cryo-Electron%20Microscopy%20%28CryoEM%29%20images%2C%20leveraging%20the%20efficiency%20of%20vector%20compression%20techniques%20such%20as%20PCA%20and%20IVF-PQ%20to%20accelerate%20the%20alignment%20process.%20Experimental%20evaluations%20on%20diverse%20CryoEM%20datasets%20demonstrate%20the%20algorithm%5Cu2019s%20efficacy%20in%20improving%20alignment%20speed%20with%20a%20slight%20compromise%20in%20accuracy.%20Thus%2C%20we%20state%20that%20this%20algorithm%20is%20particularly%20interesting%20during%20the%20preliminary%20stages%20of%203D%20refinement%2C%20where%20computational%20efficiency%20is%20paramount%2C%20and%20the%20observed%20slight%20accuracy%20degradation%20is%20deemed%20acceptable.%22%2C%22date%22%3A%222024-05%22%2C%22proceedingsTitle%22%3A%222024%20IEEE%20International%20Symposium%20on%20Biomedical%20Imaging%20%28ISBI%29%22%2C%22conferenceName%22%3A%222024%20IEEE%20International%20Symposium%20on%20Biomedical%20Imaging%20%28ISBI%29%22%2C%22language%22%3A%22%22%2C%22DOI%22%3A%2210.1109%5C%2FISBI56570.2024.10635352%22%2C%22ISBN%22%3A%22%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fieeexplore.ieee.org%5C%2Fabstract%5C%2Fdocument%5C%2F10635352%22%2C%22collections%22%3A%5B%22EENXQ3XN%22%5D%2C%22dateModified%22%3A%222024-10-20T20%3A01%3A04Z%22%7D%7D%2C%7B%22key%22%3A%22268BDTKC%22%2C%22library%22%3A%7B%22id%22%3A1485676%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Cacho-Navas%20et%20al.%22%2C%22parsedDate%22%3A%222024-04-10%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%202%3B%20%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%20style%3D%5C%22clear%3A%20left%3B%20%5C%22%3E%5Cn%20%20%20%20%3Cdiv%20class%3D%5C%22csl-left-margin%5C%22%20style%3D%5C%22float%3A%20left%3B%20padding-right%3A%200.5em%3B%20text-align%3A%20right%3B%20width%3A%201em%3B%5C%22%3E1.%3C%5C%2Fdiv%3E%3Cdiv%20class%3D%5C%22csl-right-inline%5C%22%20style%3D%5C%22margin%3A%200%20.4em%200%201.5em%3B%5C%22%3ECacho-Navas%2C%20C.%20%3Ci%3Eet%20al.%3C%5C%2Fi%3E%20ICAM-1%20nanoclusters%20regulate%20hepatic%20epithelial%20cell%20polarity%20by%20leukocyte%20adhesion-independent%20control%20of%20apical%20actomyosin.%20%3Ci%3EeLife%3C%5C%2Fi%3E%20%3Cb%3E12%3C%5C%2Fb%3E%2C%20RP89261%20%282024%29.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fbiophysicsworkshop.co.za%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D1485676%26amp%3Bitem_key%3D268BDTKC%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%20%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22ICAM-1%20nanoclusters%20regulate%20hepatic%20epithelial%20cell%20polarity%20by%20leukocyte%20adhesion-independent%20control%20of%20apical%20actomyosin%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Cristina%22%2C%22lastName%22%3A%22Cacho-Navas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Carmen%22%2C%22lastName%22%3A%22L%5Cu00f3pez-Pujante%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Natalia%22%2C%22lastName%22%3A%22Reglero-Real%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Natalia%22%2C%22lastName%22%3A%22Col%5Cu00e1s-Algora%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Ana%22%2C%22lastName%22%3A%22Cuervo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jose%20Javier%22%2C%22lastName%22%3A%22Conesa%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Susana%22%2C%22lastName%22%3A%22Barroso%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Gema%22%2C%22lastName%22%3A%22de%20Rivas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sergio%22%2C%22lastName%22%3A%22Ciordia%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alberto%22%2C%22lastName%22%3A%22Paradela%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Gianluca%22%2C%22lastName%22%3A%22D%27Agostino%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Carlo%22%2C%22lastName%22%3A%22Manzo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jorge%22%2C%22lastName%22%3A%22Feito%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Germ%5Cu00e1n%22%2C%22lastName%22%3A%22Andr%5Cu00e9s%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Francisca%22%2C%22lastName%22%3A%22Molina-Jim%5Cu00e9nez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pedro%22%2C%22lastName%22%3A%22Majano%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Isabel%22%2C%22lastName%22%3A%22Correas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jos%5Cu00e9-Maria%22%2C%22lastName%22%3A%22Carazo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sussan%22%2C%22lastName%22%3A%22Nourshargh%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Meritxell%22%2C%22lastName%22%3A%22Huch%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jaime%22%2C%22lastName%22%3A%22Mill%5Cu00e1n%22%7D%2C%7B%22creatorType%22%3A%22editor%22%2C%22firstName%22%3A%22Pramod%20K%22%2C%22lastName%22%3A%22Mistry%22%7D%5D%2C%22abstractNote%22%3A%22Epithelial%20intercellular%20adhesion%20molecule%20%28ICAM%29-1%20is%20apically%20polarized%2C%20interacts%20with%2C%20and%20guides%20leukocytes%20across%20epithelial%20barriers.%20Polarized%20hepatic%20epithelia%20organize%20their%20apical%20membrane%20domain%20into%20bile%20canaliculi%20and%20ducts%2C%20which%20are%20not%20accessible%20to%20circulating%20immune%20cells%20but%20that%20nevertheless%20confine%20most%20of%20ICAM-1.%20Here%2C%20by%20analyzing%20ICAM-1_KO%20human%20hepatic%20cells%2C%20liver%20organoids%20from%20ICAM-1_KO%20mice%20and%20rescue-of-function%20experiments%2C%20we%20show%20that%20ICAM-1%20regulates%20epithelial%20apicobasal%20polarity%20in%20a%20leukocyte%20adhesion-independent%20manner.%20ICAM-1%20signals%20to%20an%20actomyosin%20network%20at%20the%20base%20of%20canalicular%20microvilli%2C%20thereby%20controlling%20the%20dynamics%20and%20size%20of%20bile%20canalicular-like%20structures.%20We%20identified%20the%20scaffolding%20protein%20EBP50%5C%2FNHERF1%5C%2FSLC9A3R1%2C%20which%20connects%20membrane%20proteins%20with%20the%20underlying%20actin%20cytoskeleton%2C%20in%20the%20proximity%20interactome%20of%20ICAM-1.%20EBP50%20and%20ICAM-1%20form%20nano-scale%20domains%20that%20overlap%20in%20microvilli%2C%20from%20which%20ICAM-1%20regulates%20EBP50%20nano-organization.%20Indeed%2C%20EBP50%20expression%20is%20required%20for%20ICAM-1-mediated%20control%20of%20BC%20morphogenesis%20and%20actomyosin.%20Our%20findings%20indicate%20that%20ICAM-1%20regulates%20the%20dynamics%20of%20epithelial%20apical%20membrane%20domains%20beyond%20its%20role%20as%20a%20heterotypic%20cell%5Cu2013cell%20adhesion%20molecule%20and%20reveal%20potential%20therapeutic%20strategies%20for%20preserving%20epithelial%20architecture%20during%20inflammatory%20stress.%22%2C%22date%22%3A%222024-04-10%22%2C%22language%22%3A%22%22%2C%22DOI%22%3A%2210.7554%5C%2FeLife.89261%22%2C%22ISSN%22%3A%222050-084X%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fdoi.org%5C%2F10.7554%5C%2FeLife.89261%22%2C%22collections%22%3A%5B%22EENXQ3XN%22%5D%2C%22dateModified%22%3A%222024-10-20T20%3A01%3A24Z%22%7D%7D%2C%7B%22key%22%3A%22DW64G6H4%22%2C%22library%22%3A%7B%22id%22%3A1485676%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22de%20Isidro-G%5Cu00f3mez%20et%20al.%22%2C%22parsedDate%22%3A%222024-03-01%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%202%3B%20%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%20style%3D%5C%22clear%3A%20left%3B%20%5C%22%3E%5Cn%20%20%20%20%3Cdiv%20class%3D%5C%22csl-left-margin%5C%22%20style%3D%5C%22float%3A%20left%3B%20padding-right%3A%200.5em%3B%20text-align%3A%20right%3B%20width%3A%201em%3B%5C%22%3E1.%3C%5C%2Fdiv%3E%3Cdiv%20class%3D%5C%22csl-right-inline%5C%22%20style%3D%5C%22margin%3A%200%20.4em%200%201.5em%3B%5C%22%3Ede%20Isidro-G%26%23xF3%3Bmez%2C%20F.%20P.%2C%20Vilas%2C%20J.%20L.%2C%20Losana%2C%20P.%2C%20Carazo%2C%20J.%20M.%20%26amp%3B%20Sorzano%2C%20C.%20O.%20S.%20A%20deep%20learning%20approach%20to%20the%20automatic%20detection%20of%20alignment%20errors%20in%20cryo-electron%20tomographic%20reconstructions.%20%3Ci%3EJ%20Struct%20Biol%3C%5C%2Fi%3E%20%3Cb%3E216%3C%5C%2Fb%3E%2C%20108056%20%282024%29.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fbiophysicsworkshop.co.za%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D1485676%26amp%3Bitem_key%3DDW64G6H4%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%20%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22A%20deep%20learning%20approach%20to%20the%20automatic%20detection%20of%20alignment%20errors%20in%20cryo-electron%20tomographic%20reconstructions%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22F.%20P.%22%2C%22lastName%22%3A%22de%20Isidro-G%5Cu00f3mez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.%20L.%22%2C%22lastName%22%3A%22Vilas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22P.%22%2C%22lastName%22%3A%22Losana%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.%20M.%22%2C%22lastName%22%3A%22Carazo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22C.%20O.%20S.%22%2C%22lastName%22%3A%22Sorzano%22%7D%5D%2C%22abstractNote%22%3A%22Electron%20tomography%20is%20an%20imaging%20technique%20that%20allows%20for%20the%20elucidation%20of%20three-dimensional%20structural%20information%20of%20biological%20specimens%20in%20a%20very%20general%20context%2C%20including%20cellular%20in%20situ%20observations.%20The%20approach%20starts%20by%20collecting%20a%20set%20of%20images%20at%20different%20projection%20directions%20by%20tilting%20the%20specimen%20stage%20inside%20the%20microscope.%20Therefore%2C%20a%20crucial%20preliminary%20step%20is%20to%20precisely%20define%20the%20acquisition%20geometry%20by%20aligning%20all%20the%20tilt%20images%20to%20a%20common%20reference.%20Errors%20introduced%20in%20this%20step%20will%20lead%20to%20the%20appearance%20of%20artifacts%20in%20the%20tomographic%20reconstruction%2C%20rendering%20them%20unsuitable%20for%20the%20sample%20study.%20Focusing%20on%20fiducial-based%20acquisition%20strategies%2C%20this%20work%20proposes%20a%20deep-learning%20algorithm%20to%20detect%20misalignment%20artifacts%20in%20tomographic%20reconstructions%20by%20analyzing%20the%20characteristics%20of%20these%20fiducial%20markers%20in%20the%20tomogram.%20In%20addition%2C%20we%20propose%20an%20algorithm%20designed%20to%20detect%20fiducial%20markers%20in%20the%20tomogram%20with%20which%20to%20feed%20the%20classification%20algorithm%20in%20case%20the%20alignment%20algorithm%20does%20not%20provide%20the%20location%20of%20the%20markers.%20This%20open-source%20software%20is%20available%20as%20part%20of%20the%20Xmipp%20software%20package%20inside%20of%20the%20Scipion%20framework%2C%20and%20also%20through%20the%20command-line%20in%20the%20standalone%20version%20of%20Xmipp.%22%2C%22date%22%3A%222024-03-01%22%2C%22language%22%3A%22%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.jsb.2023.108056%22%2C%22ISSN%22%3A%221047-8477%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.sciencedirect.com%5C%2Fscience%5C%2Farticle%5C%2Fpii%5C%2FS1047847723001193%22%2C%22collections%22%3A%5B%22EENXQ3XN%22%5D%2C%22dateModified%22%3A%222024-10-20T20%3A05%3A44Z%22%7D%7D%2C%7B%22key%22%3A%22FQZQFCAZ%22%2C%22library%22%3A%7B%22id%22%3A1485676%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Krieger%20et%20al.%22%2C%22parsedDate%22%3A%222024-02-08%22%2C%22numChildren%22%3A0%7D%2C%22bib%22%3A%22%3Cdiv%20class%3D%5C%22csl-bib-body%5C%22%20style%3D%5C%22line-height%3A%202%3B%20%5C%22%3E%5Cn%20%20%3Cdiv%20class%3D%5C%22csl-entry%5C%22%20style%3D%5C%22clear%3A%20left%3B%20%5C%22%3E%5Cn%20%20%20%20%3Cdiv%20class%3D%5C%22csl-left-margin%5C%22%20style%3D%5C%22float%3A%20left%3B%20padding-right%3A%200.5em%3B%20text-align%3A%20right%3B%20width%3A%201em%3B%5C%22%3E1.%3C%5C%2Fdiv%3E%3Cdiv%20class%3D%5C%22csl-right-inline%5C%22%20style%3D%5C%22margin%3A%200%20.4em%200%201.5em%3B%5C%22%3EKrieger%2C%20J.%20M.%20%3Ci%3Eet%20al.%3C%5C%2Fi%3E%20Scipion%20flexibility%20hub%20and%20Scipion%20chem%3A%20New%20frameworks%20coupling%20computational%20biophysics%20of%20protein%20dynamics%20and%20virtual%20screening%20to%20cryo-electron%20microscopy.%20%3Ci%3EBiophys%20J%3C%5C%2Fi%3E%20%3Cb%3E123%3C%5C%2Fb%3E%2C%2014a%26%23×2013%3B15a%20%282024%29.%20%3Ca%20title%3D%27Cite%20in%20RIS%20Format%27%20class%3D%27zp-CiteRIS%27%20href%3D%27https%3A%5C%2F%5C%2Fbiophysicsworkshop.co.za%5C%2Fwp-content%5C%2Fplugins%5C%2Fzotpress%5C%2Flib%5C%2Frequest%5C%2Frequest.cite.php%3Fapi_user_id%3D1485676%26amp%3Bitem_key%3DFQZQFCAZ%27%3ECite%3C%5C%2Fa%3E%20%3C%5C%2Fdiv%3E%5Cn%20%20%3C%5C%2Fdiv%3E%5Cn%3C%5C%2Fdiv%3E%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Scipion%20flexibility%20hub%20and%20Scipion%20chem%3A%20New%20frameworks%20coupling%20computational%20biophysics%20of%20protein%20dynamics%20and%20virtual%20screening%20to%20cryo-electron%20microscopy%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22James%20M.%22%2C%22lastName%22%3A%22Krieger%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22David%22%2C%22lastName%22%3A%22Herreros%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Daniel%20del%22%2C%22lastName%22%3A%22Hoyo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yunior%22%2C%22lastName%22%3A%22Fonseca%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marcos%22%2C%22lastName%22%3A%22Gragera%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Carlos%20P.%22%2C%22lastName%22%3A%22Mata%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alba%22%2C%22lastName%22%3A%22Lomas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Eugenia%22%2C%22lastName%22%3A%22Ulzurrun%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Nuria%20E.%22%2C%22lastName%22%3A%22Campillo%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pablo%22%2C%22lastName%22%3A%22Conesa%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Carlos%20Oscar%20S.%22%2C%22lastName%22%3A%22Sorzano%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jose%20Maria%22%2C%22lastName%22%3A%22Carazo%22%7D%5D%2C%22abstractNote%22%3A%22%22%2C%22date%22%3A%222024-02-08%22%2C%22language%22%3A%22English%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.bpj.2023.11.207%22%2C%22ISSN%22%3A%220006-3495%22%2C%22url%22%3A%22https%3A%5C%2F%5C%2Fwww.cell.com%5C%2Fbiophysj%5C%2Fabstract%5C%2FS0006-3495%2823%2900907-4%22%2C%22collections%22%3A%5B%22EENXQ3XN%22%5D%2C%22dateModified%22%3A%222024-10-20T20%3A05%3A56Z%22%7D%7D%5D%7D
1.
Schwalbe, H.
et al. The future of integrated structural biology.
Structure 32, 1563–1580 (2024).
Cite
1.
Zarrabeitia, O. L., Ramírez-Aportela, E., Carazo, J. M. & Sorzano, C. O. S. Fast Global Image Alignment Algorithm for CryoEM through Vector Compression. in
2024 IEEE International Symposium on Biomedical Imaging (ISBI) 1–4 (2024).
http://doi.org/10.1109/ISBI56570.2024.10635352.
Cite
1.
Cacho-Navas, C.
et al. ICAM-1 nanoclusters regulate hepatic epithelial cell polarity by leukocyte adhesion-independent control of apical actomyosin.
eLife 12, RP89261 (2024).
Cite
1.
de Isidro-Gómez, F. P., Vilas, J. L., Losana, P., Carazo, J. M. & Sorzano, C. O. S. A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions.
J Struct Biol 216, 108056 (2024).
Cite
1.
Krieger, J. M.
et al. Scipion flexibility hub and Scipion chem: New frameworks coupling computational biophysics of protein dynamics and virtual screening to cryo-electron microscopy.
Biophys J 123, 14a–15a (2024).
Cite