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Thanks both.</div>
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I think this is very helpful/useful.</div>
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Kind Regards,</div>
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Alan Roseman<span style="font-family: monospace; font-size: 18px;"><br>
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</span><span style="font-family: monospace; font-size: 10pt; background-color: rgba(0, 0, 0, 0);">Alan Roseman (PhD)</span></div>
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<div style="font-family: monospace; color: rgb(0, 0, 0);"><span style="font-size: 10pt; background-color: rgba(0, 0, 0, 0);">Co-Director -- MSC Life Sciences Programmes</span><span style="font-size: 18px;"><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Alex Noble <anoble@nysbc.org><br>
<b>Sent:</b> 15 July 2024 20:12<br>
<b>To:</b> Ludtke, Steven J. <sludtke@bcm.edu><br>
<b>Cc:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> Re: [3dem] New cryoEM papers (#cryoem_papers)</font>
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Hi Steve,</div>
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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.</div>
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Best,</div>
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-Alex</div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Ludtke, Steven J. <sludtke@bcm.edu><br>
<b>Sent:</b> Monday, July 15, 2024 2:46 PM<br>
<b>To:</b> Alex Noble <anoble@nysbc.org><br>
<b>Cc:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> Re: [3dem] New cryoEM papers (#cryoem_papers)</font>
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<div>Hi Alex,</div>
<div>maybe you aren’t aware, but Carlos-Oscar started a separate mailing list for exactly this purpose, with each post a separate paper:</div>
<div><a href="https://urldefense.com/v3/__https://listas.csic.es/cnb/wws/arc/3demmethods__;!!Mih3wA!EtPxs8zW6kAWatatcqvmOcAaJDFLFuk1JiHE0yvqwmgPm-DZR2napEplebUtZryyWJudqQD4SzVtSXgJ2A$">https://listas.csic.es/cnb/wws/arc/3demmethods</a></div>
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<div>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...</div>
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<div><font face="Courier New"><span style="font-size:14px">---</span></font></div>
<div><font face="Courier New"><span style="font-size:14px">Steven Ludtke, Ph.D. <sludtke@bcm.edu> Baylor College of Medicine<br>
Charles C. Bell Jr., Professor of Structural Biology Dept. of Biochemistry <br>
Deputy Director, Advanced Technology Cores and Molecular Pharmacology<br>
Academic Director, CryoEM Core<br>
Co-Director CIBR Center<br>
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<div>On Jul 15, 2024, at 2:39 PM, Alex Noble <anoble@nysbc.org> wrote:</div>
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<div><font size="2" style="font-family:Helvetica; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; text-decoration:none"><b>***CAUTION:***
This email is not from a BCM Source. Only click links or open attachments you know are safe.</b></font><span style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important"></span>
<hr style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; text-decoration:none">
<span style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">Hi
cool people,</span><span style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important"></span>
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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.=)</div>
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There used to be a twitter bot that (<a href="https://urldefense.com/v3/__https://x.com/cryoem_papers__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKv2MOaadg$" id="OWA20ca7e5d-600d-95a2-7160-370d5e81d410" class="x_x_OWAAutoLink" title="https://x.com/cryoem_papers">@cryoem_papers</a>)
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.</div>
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I'll aim to post new papers every Monday. Here's the first batch covering the past 2 weeks:</div>
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<li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
<div>CryoViT: Efficient Segmentation of Cryogenic Electron Tomograms with Vision Foundation Models<br>
<a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.26.600701v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuohK-LOA$" id="OWA4acf074a-7ee4-8bb4-14f5-cb69b1c4d559" class="x_x_OWAAutoLink">https://www.biorxiv.org/content/10.1101/2024.06.26.600701v1</a></div>
</li><li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
<div>Accurate size-based protein localization from cryo-ET tomograms<br>
<a href="https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S2590152424000096__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsRSTmqcQ$" id="OWAc4020475-30b2-6587-73c0-30b188cf05a6" class="x_x_OWAAutoLink">https://www.sciencedirect.com/science/article/pii/S2590152424000096</a></div>
</li><li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
<div>Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information<br>
<a href="https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49858-x__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvoT7cSNw$" id="OWA3da89294-c457-b39f-e216-41323c4edc11" class="x_x_OWAAutoLink">https://www.nature.com/articles/s41467-024-49858-x</a></div>
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<div>OPUS-TOMO: Deep Learning Framework for Structural Heterogeneity Analysis in Cryo-electron Tomography</div>
<div><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.30.601442v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKt1ojRpCw$" id="OWAacc40924-489a-a674-835d-c7dc7513fdd9" class="x_x_OWAAutoLink">https://www.biorxiv.org/content/10.1101/2024.06.30.601442v1</a></div>
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<div>Frontiers in integrative structural biology: modeling disordered proteins and utilizing in situ data</div>
<div><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2407.00566__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsbFlkRLQ$" id="OWA239e0481-2e39-8e7c-60e1-173ae7a7d140" class="x_x_OWAAutoLink">https://arxiv.org/abs/2407.00566</a></div>
</li><li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
<div>Direct Measurement of the Critical Cooling Rate for the Vitrification of Water</div>
<div><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2407.01087__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKudON1_dg$" id="OWAb0628469-c032-df2a-74ab-18151abdd9c3" class="x_x_OWAAutoLink">https://arxiv.org/abs/2407.01087</a></div>
</li><li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
<div>DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map</div>
<div><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2404.02465__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsAc0GjxA$" id="OWAf1f975fa-ec0e-6b0d-e8b5-3358a3804308" class="x_x_OWAAutoLink">https://arxiv.org/abs/2404.02465</a></div>
</li><li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
<div>Einstein from Noise: Statistical Analysis</div>
<div><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvOHxAOOQ$" id="OWA2eb72f8a-c0f4-de0f-b202-6cde95b7d36d" class="x_x_OWAAutoLink">https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1</a></div>
</li><li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
<div>Advances in cryo-ET data processing: meeting the demands of visual proteomics</div>
<div><a href="https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000885__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuZU9NwEA$" id="OWAd517611e-5f78-30ea-8e83-b5b56b34e2cd" class="x_x_OWAAutoLink">https://www.sciencedirect.com/science/article/pii/S0959440X24000885</a></div>
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<div>Expanding insights from in situ cryo-EM</div>
<div><a href="https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsKNZgq3w$" id="OWAf1f15a88-ce1d-0f28-d49f-461374b690b0" class="x_x_OWAAutoLink">https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X</a></div>
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<div>High-resolution real-space reconstruction of cryo-EM structures using a neural field network</div>
<div><a href="https://urldefense.com/v3/__https://www.nature.com/articles/s42256-024-00870-2__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKsLNiVZcQ$" id="OWAedef2c38-223b-f28b-736c-bc2f3e8237af" class="x_x_OWAAutoLink">https://www.nature.com/articles/s42256-024-00870-2</a></div>
</li><li style="font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
<div>Nanobody-assisted cryoEM structural determination for challenging proteins</div>
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<div>De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM<br>
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<div>Training-free CryoET Tomogram Segmentation</div>
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<div>Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference</div>
<div><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuSxH98uw$" id="OWA8292bb57-c9e3-fb28-7dc8-b90079dd0a29" class="x_x_OWAAutoLink">https://arxiv.org/abs/2406.10455v1</a></div>
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<div>CryoJAM: Automating Protein Homolog Fitting in Medium Resolution Cryo-EM Density Maps</div>
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<div>Ais: streamlining segmentation of cryo-electron tomography datasets<br>
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<div>Cryo-electron tomography pipeline for plasma membranes</div>
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<div>DeepOrientation: Deep Orientation Estimation of Macromolecules in Cryo-electron tomography</div>
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<div>Graphene in cryo-EM specimen optimization</div>
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<div>FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer</div>
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<div>Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for Cryo-Electron Subtomogram Segmentation with Denoised Pseudo Labeling</div>
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<div>Visualizing the translation landscape in human cells at high resolution</div>
<div><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.02.601723v1__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKuurcX15w$" id="OWA0e7f5916-e7f3-6e5b-625b-dddde29120f4" class="x_x_OWAAutoLink">https://www.biorxiv.org/content/10.1101/2024.07.02.601723v1</a></div>
</li></ul>
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Best wishes,</div>
<div style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
-Alex Noble</div>
<div style="font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; font-family:Aptos,Aptos_EmbeddedFont,Aptos_MSFontService,Calibri,Helvetica,sans-serif; font-size:12pt">
SEMC/NYSBC</div>
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X:<span class="x_x_Apple-converted-space"> </span><u><a href="https://urldefense.com/v3/__https://x.com/alexjamesnoble__;!!Mih3wA!HPvc31Hr1YVapoG6ycZEQD84QfpJl9JVWlLYzSWoNyJsAKXU2A5b3J4k6Y5ILofe5XcofQHgtKvYuXYvdg$" id="OWAabb3cc11-e308-85bc-0dcf-af777310aed8" class="x_x_OWAAutoLink" title="https://x.com/alexjamesnoble">@alexjamesnoble</a></u></div>
<span style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br style="font-family:Helvetica; font-size:12px; font-style:normal; font-variant-caps:normal; font-weight:400; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
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