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New week, new papers and software:<br>
(also, I'll include papers that I missed starting from June)</div>
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<div>Cryo-electron microscopy in the study of virus entry and infection<br>
<a href="https://urldefense.com/v3/__https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2024.1429180/full__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtdLPOD9Q$" id="OWAb2fae1a6-5577-4659-138f-940696715525" class="OWAAutoLink">https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2024.1429180/full</a></div>
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<div>An image processing pipeline for electron cryo-tomography in RELION-5<br>
<a href="https://urldefense.com/v3/__https://febs.onlinelibrary.wiley.com/doi/10.1002/2211-5463.13873__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuqCeIPfg$" id="OWA0d3d6a77-214e-6656-d48f-229281ea0b10" class="OWAAutoLink">https://febs.onlinelibrary.wiley.com/doi/10.1002/2211-5463.13873</a></div>
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<div class="elementToProof">JPEG Tomogram (reduce tomogram size by ~90% for visualization, annotation, sharing)<br>
<a href="https://urldefense.com/v3/__https://github.com/alexjnoble/jpeg_tomogram__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuxgkZW3A$" id="OWA16d7a73f-3c3b-acb6-a4f8-48fe949e58dc" class="OWAAutoLink">https://github.com/alexjnoble/jpeg_tomogram</a></div>
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<div>A versatile correlative light and electron microscopy protocol for human brain and other biological models<br>
<a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.11.598271v2__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODu8pz4mYg$" id="OWA0b3671ab-af0d-1ca4-c4b2-574979da0cda" class="OWAAutoLink">https://www.biorxiv.org/content/10.1101/2024.06.11.598271v2</a></div>
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<div>The dynamic duo: cryo-EM teams up with machine learning to visualize biomolecules in motion<br>
<a href="https://urldefense.com/v3/__https://www.tandfonline.com/doi/full/10.1080/07366205.2024.2355771__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODsE9NgPUw$" id="OWA23e48274-9c56-dda1-b716-f666df792c65" class="OWAAutoLink">https://www.tandfonline.com/doi/full/10.1080/07366205.2024.2355771</a></div>
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<div>Determining Protein Secondary Structures in Heterogeneous Medium-Resolution Cryo-EM Images Using CryoSSESeg<br>
<a href="https://urldefense.com/v3/__https://pubs.acs.org/doi/full/10.1021/acsomega.4c02608__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvM-TJ5Ag$" id="OWA80a5ac56-55b6-ef12-bd5a-e4a48a78857c" class="OWAAutoLink">https://pubs.acs.org/doi/full/10.1021/acsomega.4c02608</a></div>
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<div>MDFF_NM: Improved Molecular Dynamics Flexible Fitting into Cryo-EM Density Maps with a Multireplica Normal Mode-Based Search<br>
<a href="https://urldefense.com/v3/__https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c02007__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvfWdZdyw$" id="OWA3640ab63-3252-8151-ab92-452277976576" class="OWAAutoLink">https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c02007</a></div>
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Best wishes,</div>
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Alex Noble</div>
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<div id="divRplyFwdMsg" dir="ltr" style="color: inherit;"><span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Alex Noble <anoble@nysbc.org><br>
<b>Sent:</b> Monday, August 12, 2024 10:54 AM<br>
<b>To:</b> 3dem@ncmir.ucsd.edu <3dem@ncmir.ucsd.edu><br>
<b>Subject:</b> Re: New cryoEM papers (#cryoem_papers)</span>
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New papers:</div>
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<div style="direction: ltr;">Bayesian reweighting of biomolecular structural ensembles using heterogeneous cryo-EM maps with the cryoENsemble method</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.nature.com/articles/s41598-024-68468-7__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvlD8S4Kg$" id="OWA2ab72e4f-89e2-6976-a22f-705feddb5d13" class="x_OWAAutoLink" data-auth="NotApplicable">https://www.nature.com/articles/s41598-024-68468-7</a></div>
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<div style="direction: ltr;">Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.04.606536v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtSDFVsug$" id="OWA3af95691-5337-5120-f279-a1d1026712cf" class="x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.08.04.606536v1</a></div>
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<div style="direction: ltr;">Tensorial template matching for fast cross-correlation with rotations and its application for tomography</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2408.02398__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODs_rhcfOg$" id="OWA63257c4b-08e9-cf07-7d31-c7f8db0673f0" class="x_OWAAutoLink" data-auth="NotApplicable">https://arxiv.org/abs/2408.02398</a></div>
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<div style="direction: ltr;">Multi-species cryoEM calibration and workflow verification standard</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.08.05.606612v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODu5pII4WQ$" id="OWA05568a7e-0ab1-e53b-393b-2b1d4673f913" class="x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.08.05.606612v1</a></div>
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<div style="direction: ltr;">SPOT-RASTR—A cryo-EM specimen preparation technique that overcomes problems with preferred orientation and the air/water interface <br>
<a href="https://urldefense.com/v3/__https://academic.oup.com/pnasnexus/article/3/8/pgae284/7727607__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvs9l5qyw$" id="OWAec74c2c9-24e5-48f7-01e1-055a72262c66" class="x_OWAAutoLink" data-auth="NotApplicable">https://academic.oup.com/pnasnexus/article/3/8/pgae284/7727607</a></div>
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<div style="direction: ltr;">Smart parallel automated cryo-electron tomography<br>
<a href="https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02373-9__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODt0Ol3N4w$" id="OWA742d0458-6815-c036-4575-29b59a054713" class="x_OWAAutoLink" data-auth="NotApplicable">https://www.nature.com/articles/s41592-024-02373-9</a></div>
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<div style="direction: ltr;">DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images<br>
<a href="https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02377-5__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODsxciaUCA$" id="OWA58445450-2ae0-a4b3-58ec-a101798c210c" class="x_OWAAutoLink" data-auth="NotApplicable">https://www.nature.com/articles/s41592-024-02377-5</a></div>
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<div style="direction: ltr;">Challenges, advances, and opportunities in RNA structural biology by Cryo-EM<br>
<a href="https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24001210__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuro9RxHg$" id="OWAe135f2be-6c32-054e-4f1b-27cac1a51e51" class="x_OWAAutoLink" data-auth="NotApplicable">https://www.sciencedirect.com/science/article/pii/S0959440X24001210</a></div>
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<div id="x_divRplyFwdMsg" dir="ltr" style="color: inherit;"><span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Alex Noble <<a href="mailto:anoble@nysbc.org" id="OWAe79fe3c1-6776-3421-7203-1d300c5b1792" class="x_linkificator-ext OWAAutoLink" title="Linkificator: mailto:anoble@nysbc.org">anoble@nysbc.org</a>><br>
<b>Sent:</b> Monday, August 5, 2024 3:50 PM<br>
<b>To:</b> <a href="mailto:3dem@ncmir.ucsd.edu" id="OWA92fd5e33-38f2-4a9b-c95c-cc518e011d09" class="x_linkificator-ext OWAAutoLink" title="Linkificator: mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a> <<a href="mailto:3dem@ncmir.ucsd.edu" id="OWAfc23d289-e461-1360-f6dd-d35b33c02421" class="x_linkificator-ext OWAAutoLink" title="Linkificator: mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>><br>
<b>Subject:</b> Re: New cryoEM papers (#cryoem_papers)</span>
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Hi cool people,</div>
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Below is this past week's installment of new cryoEM papers and related software - it was a slow week!</div>
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<div style="direction: ltr;">Automated fiducial-based alignment of cryo-electron tomography tilt series in Dynamo</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.cell.com/structure/fulltext/S0969-2126(24)00241-7__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuTz7kHeA$" id="OWA1427c27f-6a71-c399-5f85-e405683e49a0" class="x_x_OWAAutoLink" data-auth="NotApplicable">https://www.cell.com/structure/fulltext/S0969-2126(24)00241-7</a></div>
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<div style="direction: ltr;">Segment Anything Model 2 (SAM 2)<br>
<a href="https://urldefense.com/v3/__https://ai.meta.com/sam2/__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtT1bgfMw$" id="OWA6d13d4ba-f177-4368-63ab-f4d995babef6" class="x_x_OWAAutoLink" data-auth="NotApplicable">https://ai.meta.com/sam2/</a></div>
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Since it's a slow week, how about a discussion on cryoEM papers: Peer-review is a process that helps keep guard-rails on papers (which is good) but it also significantly slows down research compared to the computer science field, for example, which primarily
uses preprints to rapidly increment progress. In contrast, it's common in my experience as an author and peer-reviewer for editors and reviewers to stymie progress in our field's development due to minor misunderstandings; e.g. a paper being rejected because
a reviewer wrongly claims that a method is not novel and the editor accepting that claim.<br>
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To avoid many of these unnecessary issues, I decided late last year to only peer-review a paper if the editor allows for open discussion between myself and the authors by email (with the editor cc'ed). Have others used this method as well, or have another solution
to this problem? Is this a problem?</div>
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Best wishes,</div>
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Alex Noble</div>
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<div id="x_x_divRplyFwdMsg" dir="ltr" style="color: inherit;"><span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Alex Noble <<a href="mailto:anoble@nysbc.org" id="OWAa52177d1-d8a1-74a8-0a9a-49bc8fd7227a" class="x_x_linkificator-ext x_x_OWAAutoLink" title="Linkificator: mailto:anoble@nysbc.org">anoble@nysbc.org</a>><br>
<b>Sent:</b> Monday, July 29, 2024 9:39 AM<br>
<b>To:</b> <a href="mailto:3dem@ncmir.ucsd.edu" id="OWAdcdb9524-8443-9e5f-ad80-c11a08120742" class="x_x_linkificator-ext x_x_OWAAutoLink" title="Linkificator: mailto:3dem@ncmir.ucsd.edu">
3dem@ncmir.ucsd.edu</a> <<a href="mailto:3dem@ncmir.ucsd.edu" id="OWA6ee0b44f-0605-447d-9a61-8bff3f6b6b51" class="x_x_linkificator-ext x_x_OWAAutoLink" title="Linkificator: mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>><br>
<b>Subject:</b> Re: New cryoEM papers (#cryoem_papers)</span>
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Hi cool people,</div>
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Below is this past week's installment of new cryoEM papers. There are many short M&M papers - they're not listed here for space reasons; the first link has a full list.</div>
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<div style="direction: ltr;">M&M papers:<br>
<a href="https://urldefense.com/v3/__https://academic.oup.com/mam/issue/30/Supplement_1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvYHxHuuA$" id="OWAd43b7a40-4932-423d-ab16-c3573f1070db" class="x_x_x_OWAAutoLink" data-auth="NotApplicable">https://academic.oup.com/mam/issue/30/Supplement_1</a></div>
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<div style="direction: ltr;">Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using (an)aerobic blot-free vitrification</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.19.604374v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtZH9eZMQ$" id="OWAfa67f911-c69e-4689-ee47-f17220ffc2ee" class="x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.19.604374v1</a></div>
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<div style="direction: ltr;">Amortized template-matching of molecular conformations from cryo-electron microscopy images using simulation-based inference</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.23.604154v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODv70hYZQQ$" id="OWA31f5792d-6393-e8fd-b3d3-a5eb18a27b40" class="x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.23.604154v1</a></div>
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<div style="direction: ltr;">Cryo-EM Screening of Apoferritin at 100 kV Using Hitachi’s HT7800 Thermionic Transmission Electron Microscope<br>
<a href="https://urldefense.com/v3/__https://academic.oup.com/mam/article/30/Supplement_1/ozae044.379/7720487__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvPXAJxyQ$" id="OWA5d1714ce-1fa8-2cec-83f4-00ad6872b88b" class="x_x_x_OWAAutoLink" data-auth="NotApplicable">https://academic.oup.com/mam/article/30/Supplement_1/ozae044.379/7720487</a></div>
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<div style="direction: ltr;">All atom molecular dynamics simulations enable ensemble refinement of flexible and mismodelled cryo-EM derived RNA structures</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.24.604258v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODshLERdTg$" id="OWAce0b3fed-1a36-0fee-4ccc-1949cd05a2e5" class="x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.24.604258v1</a></div>
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<div style="direction: ltr;">Likelihood-based interactive local docking into cryo-EM maps in ChimeraX<br>
<a href="https://urldefense.com/v3/__https://journals.iucr.org/d/issues/2024/08/00/id5013/index.html__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvyXQVMpw$" id="OWA5e61a78a-1137-1f5f-5ba7-116c1d757fbf" class="x_x_OWAAutoLink" data-auth="NotApplicable">https://journals.iucr.org/d/issues/2024/08/00/id5013/index.html</a></div>
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Cheers,</div>
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Alex Noble</div>
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<div id="x_x_x_divRplyFwdMsg" dir="ltr" style="color: inherit;"><span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Alex Noble <<a href="mailto:anoble@nysbc.org" id="OWA814e8c07-bcff-3e6f-db91-3c67eb2b5b89" class="x_x_x_linkificator-ext x_x_x_OWAAutoLink" title="Linkificator: mailto:anoble@nysbc.org">anoble@nysbc.org</a>><br>
<b>Sent:</b> Monday, July 22, 2024 12:18 PM<br>
<b>To:</b> <a href="mailto:3dem@ncmir.ucsd.edu" id="OWA4b2932f3-a2b1-e051-71db-3ee1094aeef1" class="x_x_x_linkificator-ext x_x_x_OWAAutoLink" title="Linkificator: mailto:3dem@ncmir.ucsd.edu">
3dem@ncmir.ucsd.edu</a> <<a href="mailto:3dem@ncmir.ucsd.edu" id="OWAe089deea-172f-366c-0f28-9fb156bc0d70" class="x_x_x_linkificator-ext x_x_x_OWAAutoLink" title="Linkificator: mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>><br>
<b>Subject:</b> Re: New cryoEM papers (#cryoem_papers)</span>
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Hi cool people,</div>
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Here is this past week's installment of new cryoEM papers (which will now also include new software):</div>
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<div style="direction: ltr;">MarkerDetector: A method for robust fiducial marker detection in electron micrographs using wavelet-based template</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S1047847723001077__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtGY814Mg$" id="OWAbcf2f1ba-44da-7e9c-846d-ecb82d6d14a9" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.sciencedirect.com/science/article/abs/pii/S1047847723001077</a></div>
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<div style="direction: ltr;">CryoEM Workflow Acceleration with Feret Signatures</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.mdpi.com/1422-0067/25/14/7593__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuxMSuXXA$" id="OWA7ab7ae14-582c-28c6-d51e-d2ebb5409248" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.mdpi.com/1422-0067/25/14/7593</a></div>
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<div style="direction: ltr;">St Jude's EMHub software for facility organization</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://x.com/StJudeStructBio/status/1813236681388032326__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuYhntgzA$" id="OWA72ba479c-d0af-0bac-2948-fd6ae46b765b" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://x.com/StJudeStructBio/status/1813236681388032326</a><br>
<a href="https://urldefense.com/v3/__https://github.com/3dem/emhub__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODt0ZQk-lg$" id="OWAdddee85a-d6ce-235a-1762-ba3e4bc2692a" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://github.com/3dem/emhub</a></div>
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<div style="direction: ltr;">CryoSamba: self-supervised deep volumetric denoising for cryo-electron tomography data</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.11.603117v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvwKL-x7Q$" id="OWAeba65176-39d0-b4e2-1362-dc0e0435ac7e" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.11.603117v1</a></div>
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<div style="direction: ltr;">Denoising, Deblurring, and optical Deconvolution for cryo-ET and light microscopy with a physics-informed deep neural network DeBCR</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.12.603278v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtreReaSQ$" id="OWAaac2005d-b76a-6ade-8dbf-006136d20d01" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.12.603278v1</a></div>
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<div style="direction: ltr;">Vesicle Picker: A tool for efficient identification of membrane protein complexes in vesicles</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.15.603622v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvfPWwpJw$" id="OWA29db3975-0daa-ed0b-d360-af79be9e5831" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.15.603622v1</a></div>
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<div style="direction: ltr;">Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0304399123001997__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODv8risoNw$" id="OWAaca04bf3-0cb9-7d71-f3aa-ac693b0f45cc" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.sciencedirect.com/science/article/pii/S0304399123001997</a></div>
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<div style="direction: ltr;">CryoDRGN-ET: deep reconstructing generative networks for visualizing dynamic biomolecules inside cells<br>
<a href="https://urldefense.com/v3/__https://www.nature.com/articles/s41592-024-02340-4__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvDlw8f-w$" id="OWAab81bd57-ca40-5c39-5657-a70a5d17cdaa" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.nature.com/articles/s41592-024-02340-4</a></div>
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<div style="direction: ltr;">Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://app.jove.com/b/66310/modeling-small-molecule-ligands-in-cryoem-maps-of-macromolecules__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvKZC43jQ$" id="OWA3e9122a9-d93c-c4d8-5919-8e46206fbd85" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://app.jove.com/b/66310/modeling-small-molecule-ligands-in-cryoem-maps-of-macromolecules</a></div>
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<div style="direction: ltr;">AQuaRef: Machine learning accelerated quantum refinement of protein structures</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.21.604493v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuOQHHtOw$" id="OWA1a48a2b2-90bb-69f1-3ae9-95f2085d257e" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.21.604493v1</a></div>
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<div style="direction: ltr;">The myth of high-resolution liquid phase biological electron microscopy</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://onlinelibrary.wiley.com/doi/10.1002/pro.5125__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODs1EMhPhA$" id="OWA0205614d-ed1f-0081-b7b4-25808c64aeff" class="x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://onlinelibrary.wiley.com/doi/10.1002/pro.5125</a></div>
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Best wishes,</div>
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Alex Noble</div>
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<div id="x_x_x_x_divRplyFwdMsg" dir="ltr" style="color: inherit;"><span style="font-family: Calibri, sans-serif; font-size: 11pt; color: rgb(0, 0, 0);"><b>From:</b> Alex Noble<br>
<b>Sent:</b> Monday, July 15, 2024 2:39 PM<br>
<b>To:</b> <a href="mailto:3dem@ncmir.ucsd.edu" id="OWAcf3817e2-1fa4-4e7a-31be-8cb853f800b4" class="x_x_x_x_linkificator-ext x_x_x_OWAAutoLink" title="Linkificator: mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a> <<a href="mailto:3dem@ncmir.ucsd.edu" id="OWA0d5fd985-3654-16bf-d44b-014bbb04d694" class="x_x_x_x_linkificator-ext x_x_x_OWAAutoLink" title="Linkificator: mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>><br>
<b>Subject:</b> New cryoEM papers (#cryoem_papers)</span>
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Hi cool people,</div>
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I've been finding new cryoEM papers that are interesting to me (methods/new tech, machine learning, cryoFIB/SEM-ET, etc.; typically no biology-focused papers) for our internal Slack channel for years and decided to share them with the community as well. Many
papers fall through the cracks, so I think it would be good to have the whole cryoEM community on the same page. Hopefully it will make the community more productive and speed up the pace of developments.=)</div>
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There used to be a twitter bot that (<a href="https://urldefense.com/v3/__https://x.com/cryoem_papers__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuWHPldGA$" id="OWA4ee12708-89d7-667b-8d19-9187c0db11a6" class="x_x_x_x_x_OWAAutoLink" title="https://x.com/cryoem_papers" data-auth="NotApplicable">@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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<div style="direction: ltr;">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!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvIB5yybQ$" id="OWA0e508fb6-7edb-fac0-268a-4ad5af8398a7" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.06.26.600701v1</a></div>
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<div style="direction: ltr;">Accurate size-based protein localization from cryo-ET tomograms<br>
<a href="https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S2590152424000096__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODu9jcvs8g$" id="OWAac62db1b-e7cd-e2f9-ab75-f549deac47b9" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.sciencedirect.com/science/article/pii/S2590152424000096</a></div>
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<div style="direction: ltr;">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!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvMMyzpMw$" id="OWA991031a8-a702-ebf5-1f16-d5e616820bf4" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.nature.com/articles/s41467-024-49858-x</a></div>
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<div style="direction: ltr;">OPUS-TOMO: Deep Learning Framework for Structural Heterogeneity Analysis in Cryo-electron Tomography</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.30.601442v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODsrpuH7xg$" id="OWA45c10786-7aa6-d63c-4fad-d9e1dc4348a4" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.06.30.601442v1</a></div>
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<div style="direction: ltr;">Frontiers in integrative structural biology: modeling disordered proteins and utilizing in situ data</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2407.00566__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvV53suSg$" id="OWA92f60f38-3351-47a1-a54d-f6aba6b50053" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://arxiv.org/abs/2407.00566</a></div>
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<div style="direction: ltr;">Direct Measurement of the Critical Cooling Rate for the Vitrification of Water</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2407.01087__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtAZe62Gw$" id="OWA01533b8e-d844-fd75-e65d-11ca8bb21045" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://arxiv.org/abs/2407.01087</a></div>
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<div style="direction: ltr;">DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2404.02465__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODv6466H5g$" id="OWA3a0c4b70-097c-3160-282c-3f217eb6b0b7" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://arxiv.org/abs/2404.02465</a></div>
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<div style="direction: ltr;">Einstein from Noise: Statistical Analysis</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODudLVcR0Q$" id="OWA4df95fdc-c310-9bb9-a26a-a5c7e201353f" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.06.602366v1</a></div>
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<div style="direction: ltr;">Advances in cryo-ET data processing: meeting the demands of visual proteomics</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000885__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvxoCBW9w$" id="OWA3ee21506-2141-6115-f3e6-a75a8816ad62" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.sciencedirect.com/science/article/pii/S0959440X24000885</a></div>
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<div style="direction: ltr;">Expanding insights from in situ cryo-EM</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtO88hsNA$" id="OWAece0e70c-70ff-a73b-dbd3-0036ee2d4fc5" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.sciencedirect.com/science/article/abs/pii/S0959440X2400112X</a></div>
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<div style="direction: ltr;">High-resolution real-space reconstruction of cryo-EM structures using a neural field network</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.nature.com/articles/s42256-024-00870-2__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtsGaY_lQ$" id="OWA0dbbf960-1ef2-550f-55a0-608a688b9c31" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.nature.com/articles/s42256-024-00870-2</a></div>
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<div style="direction: ltr;">Nanobody-assisted cryoEM structural determination for challenging proteins</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(24)00136-1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODsODGZomw$" id="OWA2f26f8e3-2490-0527-236e-b059a1647716" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.cell.com/trends/biochemical-sciences/abstract/S0968-0004(24)00136-1</a></div>
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<div style="direction: ltr;">De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM<br>
<a href="https://urldefense.com/v3/__https://www.nature.com/articles/s41467-024-49647-6__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuC0pdjtw$" id="OWAabc54fa2-a440-cc7b-215f-d5ae8a0c8154" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.nature.com/articles/s41467-024-49647-6</a></div>
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<div style="direction: ltr;">Training-free CryoET Tomogram Segmentation</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.arxiv.org/abs/2407.06833__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtLqmf_4Q$" id="OWAc4f54866-193b-773f-aa8a-ace2cf3ef86a" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.arxiv.org/abs/2407.06833</a></div>
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<div style="direction: ltr;">Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2406.10455v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuaSqXfBA$" id="OWAff5f4243-4602-07a7-0501-7de7aa04ac4a" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://arxiv.org/abs/2406.10455v1</a></div>
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<div style="direction: ltr;">CryoJAM: Automating Protein Homolog Fitting in Medium Resolution Cryo-EM Density Maps</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.10.602952v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuZmjuPAg$" id="OWA170dfde9-25de-9c44-0448-5bbeef60ab56" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.10.602952v1</a></div>
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<div style="direction: ltr;">Ais: streamlining segmentation of cryo-electron tomography datasets<br>
<a href="https://urldefense.com/v3/__https://elifesciences.org/reviewed-preprints/98552__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvxDI6sjA$" id="OWAa82b16b8-83af-16cf-6f57-3c4ee9936d3e" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://elifesciences.org/reviewed-preprints/98552</a></div>
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<div style="direction: ltr;">Cryo-electron tomography pipeline for plasma membranes</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.06.27.600657v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODsF31ebMA$" id="OWAc27b1f22-15c6-b297-f6e3-5b690388f930" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.06.27.600657v1</a></div>
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<div style="direction: ltr;">DeepOrientation: Deep Orientation Estimation of Macromolecules in Cryo-electron tomography</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.12.603241v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODthn9KJ0Q$" id="OWA3a564a62-b167-1edd-5a5a-3d8af258038e" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.12.603241v1</a></div>
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<div style="direction: ltr;">Graphene in cryo-EM specimen optimization</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.sciencedirect.com/science/article/pii/S0959440X24000502__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODtNOyLP6A$" id="OWA19bdaf87-1595-f68b-b41a-fc101d39624a" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.sciencedirect.com/science/article/pii/S0959440X24000502</a></div>
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<div style="direction: ltr;">FakET: Simulating Cryo-Electron Tomograms with Neural Style Transfer</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2304.02011__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODvKQ7LuzA$" id="OWAfba91001-1212-ceba-6829-54069eb93dc4" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://arxiv.org/abs/2304.02011</a></div>
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<div style="direction: ltr;">Vox-UDA: Voxel-wise Unsupervised Domain Adaptation for Cryo-Electron Subtomogram Segmentation with Denoised Pseudo Labeling</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://arxiv.org/abs/2406.18610__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODv9vIZfPA$" id="OWA90d33b90-9066-5bdb-cdb3-9e78d9a1eb56" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://arxiv.org/abs/2406.18610</a></div>
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<div style="direction: ltr;">Visualizing the translation landscape in human cells at high resolution</div>
<div style="direction: ltr;"><a href="https://urldefense.com/v3/__https://www.biorxiv.org/content/10.1101/2024.07.02.601723v1__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODt_m4crtA$" id="OWAf5bbdcc3-1033-a63b-541f-73dd7e65f4a5" class="x_x_x_x_x_OWAAutoLink" data-auth="NotApplicable">https://www.biorxiv.org/content/10.1101/2024.07.02.601723v1</a></div>
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Best wishes,</div>
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-Alex Noble</div>
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SEMC/NYSBC</div>
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X: <u><a href="https://urldefense.com/v3/__https://x.com/alexjamesnoble__;!!Mih3wA!CbUvk7_3EqANRuCiQgF7sDumHIx_wVVwv4p2LTi530LmmEM0Pd3rH8yI0mge7enfY_GB_jN1ODuYHe411w$" id="OWAf5c16287-2ac5-8533-7c0a-c80ac453df22" class="x_x_x_x_x_OWAAutoLink" title="https://x.com/alexjamesnoble" data-auth="NotApplicable">@alexjamesnoble</a></u></div>
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