[3dem] New cryoEM papers (#cryoem_papers)
Carlos Oscar Sorzano
coss at cnb.csic.es
Mon Jul 15 22:42:20 PDT 2024
Dear all,
as Steve points out, anyone is free to register in the list and the wiki
(https://urldefense.com/v3/__https://3demmethods.i2pc.es/index.php/Main_Page__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvW2pbfjCQ$ ) and post any mail.
Still, Alex contribution is also welcome and I will try to keep the wiki
updated with this information.
Cheers, Carlos Oscar
El 15/07/2024 a las 21:12, Alex Noble escribió:
> Hi Steve,
>
> Thanks. I hadn't heard of this resource from Carlos. I just checked
> the past week of papers between our two collections and see some in
> common and some not in common, so it looks like both collections are
> useful.
>
> Best,
> -Alex
> ------------------------------------------------------------------------
> *From:* Ludtke, Steven J. <sludtke at bcm.edu>
> *Sent:* Monday, July 15, 2024 2:46 PM
> *To:* Alex Noble <anoble at nysbc.org>
> *Cc:* 3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
> *Subject:* Re: [3dem] New cryoEM papers (#cryoem_papers)
> Hi Alex,
> maybe you aren’t aware, but Carlos-Oscar started a separate mailing
> list for exactly this purpose, with each post a separate paper:
> https://urldefense.com/v3/__https://listas.csic.es/cnb/wws/arc/3demmethods__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvU_rr_p-A$
> <https://urldefense.com/v3/__https://listas.csic.es/cnb/wws/arc/3demmethods__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzVtSXgJ2A$>
>
> I’ve been following it for years, and he does a nice job of fining
> good methods papers. I haven’t seen others posting, but since it’s a
> mailing list I can’t see anything preventing it either...
>
> ---
> Steven Ludtke, Ph.D. <sludtke at bcm.edu> Baylor
> College of Medicine
> Charles C. Bell Jr., Professor of Structural Biology Dept. of
> Biochemistry
> Deputy Director, Advanced Technology Cores and
> Molecular Pharmacology
> Academic Director, CryoEM Core
> Co-Director CIBR Center
>
>
>> On Jul 15, 2024, at 2:39 PM, Alex Noble <anoble at nysbc.org> wrote:
>>
>> ****CAUTION:*** This email is not from a BCM Source. Only click links
>> or open attachments you know are safe.*
>> ------------------------------------------------------------------------
>> Hi cool people,
>>
>> I've been finding new cryoEM papers that are interesting to me
>> (methods/new tech, machine learning, cryoFIB/SEM-ET, etc.; typically
>> no biology-focused papers) for our internal Slack channel for years
>> and decided to share them with the community as well. Many papers
>> fall through the cracks, so I think it would be good to have the
>> whole cryoEM community on the same page. Hopefully it will make the
>> community more productive and speed up the pace of developments.=)
>>
>> There used to be a twitter bot that (@cryoem_papers
>> <https://urldefense.com/v3/__https://x.com/cryoem_papers__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKv2MOaadg$>)
>> that did this work. I'll add #cryoem_papers to this recurrent email
>> so it's easy for you to filter them as you wish.
>>
>> I'll aim to post new papers every Monday. Here's the first batch
>> covering the past 2 weeks:
>>
>> *
>> CryoViT: Efficient Segmentation of Cryogenic Electron Tomograms
>> with Vision Foundation Models
>> https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.26.600701v1__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvVAQr1GDQ$
>> <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.26.600701v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuohK-LOA$>
>> *
>> Accurate size-based protein localization from cryo-ET tomograms
>> https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S2590152424000096__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvUuAok-UA$
>> <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S2590152424000096__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsRSTmqcQ$>
>> *
>> Accurate Prediction of Protein Structural Flexibility by Deep
>> Learning Integrating Intricate Atomic Structures and Cryo-EM
>> Density Information
>> https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49858-x__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvU7p__8xw$
>> <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49858-x__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvoT7cSNw$>
>> *
>> OPUS-TOMO: Deep Learning Framework for Structural Heterogeneity
>> Analysis in Cryo-electron Tomography
>> https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.30.601442v1__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvVfwR4QPg$
>> <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.30.601442v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKt1ojRpCw$>
>> *
>> Frontiers in integrative structural biology: modeling disordered
>> proteins and utilizing in situ data
>> https://urldefense.com/v3/__https://arxiv.org/abs/2407.00566__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvVg_tRHSw$
>> <https://urldefense.com/v3/__https://arxiv.org/abs/2407.00566__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsbFlkRLQ$>
>> *
>> Direct Measurement of the Critical Cooling Rate for the
>> Vitrification of Water
>> https://urldefense.com/v3/__https://arxiv.org/abs/2407.01087__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvWiiSIj-g$
>> <https://urldefense.com/v3/__https://arxiv.org/abs/2407.01087__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKudON1_dg$>
>> *
>> DiffFit: Visually-Guided Differentiable Fitting of Molecule
>> Structures to a Cryo-EM Map
>> https://urldefense.com/v3/__https://arxiv.org/abs/2404.02465__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvW5zAtzCw$
>> <https://urldefense.com/v3/__https://arxiv.org/abs/2404.02465__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsAc0GjxA$>
>> *
>> Einstein from Noise: Statistical Analysis
>> https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvUd51OIVQ$
>> <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvOHxAOOQ$>
>> *
>> Advances in cryo-ET data processing: meeting the demands of
>> visual proteomics
>> https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000885__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvUhubm1ng$
>> <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000885__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuZU9NwEA$>
>> *
>> Expanding insights from in situ cryo-EM
>> https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvUmqljBng$
>> <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsKNZgq3w$>
>> *
>> High-resolution real-space reconstruction of cryo-EM structures
>> using a neural field network
>> https://urldefense.com/v3/__https://www.nature.com/articles/s42256-024-00870-2__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvVVrNtWlw$
>> <https://urldefense.com/v3/__https://www.nature.com/articles/s42256-024-00870-2__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsLNiVZcQ$>
>> *
>> Nanobody-assisted cryoEM structural determination for challenging
>> proteins
>> https://urldefense.com/v3/__https://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(24)00136-1__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvXu1RuhRA$
>> <https://urldefense.com/v3/__https://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(24)00136-1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuCSE_NrQ$>
>> *
>> De novo atomic protein structure modeling for cryoEM density maps
>> using 3D transformer and HMM
>> https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49647-6__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvUq2WUMTA$
>> <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49647-6__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKv7UOYzog$>
>> *
>> Training-free CryoET Tomogram Segmentation
>> https://urldefense.com/v3/__https://www.arxiv.org/abs/2407.06833__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvVcmGa13g$
>> <https://urldefense.com/v3/__https://www.arxiv.org/abs/2407.06833__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuwOMxByw$>
>> *
>> Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized
>> Pose Inference
>> https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455v1__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvWblm71Kg$
>> <https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuSxH98uw$>
>> *
>> CryoJAM: Automating Protein Homolog Fitting in Medium Resolution
>> Cryo-EM Density Maps
>> https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.10.602952v1__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvXUEUSg-Q$
>> <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.10.602952v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKtwRefPZA$>
>> *
>> Ais: streamlining segmentation of cryo-electron tomography datasets
>> https://urldefense.com/v3/__https://elifesciences.org/reviewed-preprints/98552__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvVTTOSMtA$
>> <https://urldefense.com/v3/__https://elifesciences.org/reviewed-preprints/98552__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsVogSXzQ$>
>> *
>> Cryo-electron tomography pipeline for plasma membranes
>> https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.27.600657v1__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvWLSQlUCw$
>> <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.27.600657v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKth_101CQ$>
>> *
>> DeepOrientation: Deep Orientation Estimation of Macromolecules in
>> Cryo-electron tomography
>> https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.12.603241v1__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvW0lRHjzw$
>> <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.12.603241v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsFGRQwPA$>
>> *
>> Graphene in cryo-EM specimen optimization
>> https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000502__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvXq0hugxQ$
>> <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000502__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvyMFyQlw$>
>> *
>> FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer
>> https://urldefense.com/v3/__https://arxiv.org/abs/2304.02011__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvXhItjL6Q$
>> <https://urldefense.com/v3/__https://arxiv.org/abs/2304.02011__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKt4snzGwQ$>
>> *
>> Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for
>> Cryo-Electron Subtomogram Segmentation with Denoised Pseudo Labeling
>> https://urldefense.com/v3/__https://arxiv.org/abs/2406.18610__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvWP8hmHBw$
>> <https://urldefense.com/v3/__https://arxiv.org/abs/2406.18610__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsLmJzU3g$>
>> *
>> Visualizing the translation landscape in human cells at high
>> resolution
>> https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.02.601723v1__;!!Mih3wA!A7l1tDeXP1DrwVye8Lo_0WY_WTm3Qk0vkLu5e9htfGureAK3jgPCQaUftdyGgg6iO2fp2fMGZvUyTFHKFA$
>> <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.02.601723v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuurcX15w$>
>>
>>
>> Best wishes,
>> -Alex Noble
>> SEMC/NYSBC
>> X:_ at alexjamesnoble
>> <https://urldefense.com/v3/__https://x.com/alexjamesnoble__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvYuXYvdg$>_
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