[3dem] New cryoEM papers (#cryoem_papers)

Alex Noble anoble at nysbc.org
Mon Jul 15 12:12:20 PDT 2024 

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!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!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzVflz4r6w$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.26.600701v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuohK-LOA$>
  *
Accurate size-based protein localization from cryo-ET tomograms
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S2590152424000096__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzVcXXUJMg$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S2590152424000096__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsRSTmqcQ$>
  *
Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49858-x__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzU1aKxttQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49858-x__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvoT7cSNw$>
  *
OPUS-TOMO: Deep Learning Framework for Structural Heterogeneity Analysis in Cryo-electron Tomography
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.30.601442v1__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzWA1oeouQ$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.30.601442v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKt1ojRpCw$>
  *
Frontiers in integrative structural biology: modeling disordered proteins and utilizing in situ data
https://urldefense.com/v3/__https://arxiv.org/abs/2407.00566__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzU4DcouyA$ <https://urldefense.com/v3/__https://arxiv.org/abs/2407.00566__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsbFlkRLQ$>
  *
Direct Measurement of the Critical Cooling Rate for the Vitrification of Water
https://urldefense.com/v3/__https://arxiv.org/abs/2407.01087__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzWgcrfBpw$ <https://urldefense.com/v3/__https://arxiv.org/abs/2407.01087__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKudON1_dg$>
  *
DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map
https://urldefense.com/v3/__https://arxiv.org/abs/2404.02465__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzWS1r5geQ$ <https://urldefense.com/v3/__https://arxiv.org/abs/2404.02465__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsAc0GjxA$>
  *
Einstein from Noise: Statistical Analysis
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzWnB-sRWw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvOHxAOOQ$>
  *
Advances in cryo-ET data processing: meeting the demands of visual proteomics
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000885__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzX1yqAHtg$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000885__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuZU9NwEA$>
  *
Expanding insights from in situ cryo-EM
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzUem-hu2g$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsKNZgq3w$>
  *
High-resolution real-space reconstruction of cryo-EM structures using a neural field network
https://urldefense.com/v3/__https://www.nature.com/articles/s42256-024-00870-2__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzWunNkPPg$ <https://urldefense.com/v3/__https://www.nature.com/articles/s42256-024-00870-2__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsLNiVZcQ$>
  *
Nanobody-assisted cryoEM structural determination for challenging proteins
https://urldefense.com/v3/__https://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(24)00136-1__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzXrCOiXcg$ <https://urldefense.com/v3/__https://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(24)00136-1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuCSE_NrQ$>
  *
De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM
https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49647-6__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzVBzDDPkQ$ <https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49647-6__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKv7UOYzog$>
  *
Training-free CryoET Tomogram Segmentation
https://urldefense.com/v3/__https://www.arxiv.org/abs/2407.06833__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzV9QVlZ6A$ <https://urldefense.com/v3/__https://www.arxiv.org/abs/2407.06833__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuwOMxByw$>
  *
Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference
https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455v1__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzVQ6cR62g$ <https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuSxH98uw$>
  *
CryoJAM: Automating Protein Homolog Fitting in Medium Resolution Cryo-EM Density Maps
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.10.602952v1__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzUULzPC3A$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.10.602952v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKtwRefPZA$>
  *
Ais: streamlining segmentation of cryo-electron tomography datasets
https://urldefense.com/v3/__https://elifesciences.org/reviewed-preprints/98552__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzX94X0Zfw$ <https://urldefense.com/v3/__https://elifesciences.org/reviewed-preprints/98552__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsVogSXzQ$>
  *
Cryo-electron tomography pipeline for plasma membranes
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.27.600657v1__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzUSyCeclg$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.27.600657v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKth_101CQ$>
  *
DeepOrientation: Deep Orientation Estimation of Macromolecules in Cryo-electron tomography
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.12.603241v1__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzXN1W8_2Q$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.12.603241v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsFGRQwPA$>
  *
Graphene in cryo-EM specimen optimization
https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000502__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzWOgShWZg$ <https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000502__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvyMFyQlw$>
  *
FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer
https://urldefense.com/v3/__https://arxiv.org/abs/2304.02011__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzUdNXpxcw$ <https://urldefense.com/v3/__https://arxiv.org/abs/2304.02011__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKt4snzGwQ$>
  *
Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for Cryo-Electron Subtomogram Segmentation with Denoised Pseudo Labeling
https://urldefense.com/v3/__https://arxiv.org/abs/2406.18610__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzXAyeZUdg$ <https://urldefense.com/v3/__https://arxiv.org/abs/2406.18610__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsLmJzU3g$>
  *
Visualizing the translation landscape in human cells at high resolution
https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.02.601723v1__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzVdiELbFw$ <https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.02.601723v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuurcX15w$>

Best wishes,
-Alex Noble
SEMC/NYSBC
X: @alexjamesnoble<https://urldefense.com/v3/__https://x.com/alexjamesnoble__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvYuXYvdg$>
_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=Uj7V_MoJXBrlxlLbnOffA9f7MbLqDs7ywnT4VexbRRUKevmhPJ7CRJxV5y43hzHp&s=ECFXBO0X0Gb0-xS7fdqtk9K39V24JWNs0-H0LjPsO2c&e=

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20240715/0d077efa/attachment.html>

More information about the 3dem mailing list