@c_elfmann

@IMPRS_GS PhD student in bioinformatics at the @JorgStulke lab of @UniGoettingen, currently working on SubtiWiki's newest iteration

 Göttingen, Germany
subtiwiki.uni-goettingen.de/
Joined January 2022
  • Tweets51
  • Following61
  • Followers99
23Media
Finally fixed some issues with PTMs for the PAE Viewer! Instead of the per-atom PAE which #AlphaFold outputs for modified amino acids, the average per-residue PAE is now displayed. subtiwiki.uni-goettingen.de/…
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Now you can also find me on @bluesky (bsky.app/profile/c-elfmann.b…) and @joinmastodon (academiccloud.social/@elfman…)!
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Try out our integration of the amazing protein structure search tool #Foldseek on #SubtiWiki (subtiwiki.uni-goettingen.de/…)! Just upload a structure or use PDB/AlphaFoldDB entries to find similar structures. @IMPRS_GS @uniGoettingen #alphafold #bacillus #subtilis
A screenshot of the results table of a Foldseek search on SubtiWiki. It shows multiple entries and corresponding metrics. One of the rows is expanded, revealing a 3D visualization of a superimposition of the target and the query structure corresponding to the search hit.

ALT A screenshot of the results table of a Foldseek search on SubtiWiki. It shows multiple entries and corresponding metrics. One of the rows is expanded, revealing a 3D visualization of a superimposition of the target and the query structure corresponding to the search hit.

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Thanks a lot to Michel van Kempen, Stephanie Kim, @schnamori, @SoedingL, and @thesteinegger for the development of Foldseek! Also check out the fantastic search.foldseek.com by @milot_mirdita, which we used as a blueprint. It boosts more options and detailed evaluation!
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And of course many thanks to @clmgilchrist and Woosub Kim for their work on the search server and on Foldseek-Multimer, respectively, which was used in our implementation!
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The PAE Viewer (subtiwiki.uni-goettingen.de/…) now supports evaluation of ligands and PTMs in your AlphaFold predictions, and the display of DNAs/RNAs is improved! @IMPRS_GS @uniGoettingen #alphafold #subtiwiki
Screenshot of the PAE Viewer web page. A complex structure is displayed, which contains the protein DnaA of Bacillus subtilis, ATP, and a DNA double strand encoding the DnaA box. The page shows the sequence of amino acids, atoms and nucleotides, a 3D rendering of the structure, and a matrix of the PAE. A selection was performed using the interactive PAE matrix, and thus the corresponding parts of the structure are highlighted in the sequences and 3D display.

ALT Screenshot of the PAE Viewer web page. A complex structure is displayed, which contains the protein DnaA of Bacillus subtilis, ATP, and a DNA double strand encoding the DnaA box. The page shows the sequence of amino acids, atoms and nucleotides, a 3D rendering of the structure, and a matrix of the PAE. A selection was performed using the interactive PAE matrix, and thus the corresponding parts of the structure are highlighted in the sequences and 3D display.

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I've created an offline version of the PAE Viewer with a basic CLI via Python, which you can use in your scripts. It just takes the input and opens the page in the browser with the data preloaded. Check out the new "Offline version" tab for instructions! subtiwiki.uni-goettingen.de/…
A screenshot of the top of the PAE Viewer page, with the new "Offline version" tab highlighted and expanded.

ALT A screenshot of the top of the PAE Viewer page, with the new "Offline version" tab highlighted and expanded.

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Proudly announcing the early release of SubtiWiki v5 (subtiwiki.uni-goettingen.de/)! It has many new features which we hope you'll like. It also still might have some bugs / missing data, so please don't hesitate to let us know! #subtiwiki #bacillus #subtilis @IMPRS_GS @JorgStulke
The logo of SubtiWiki v5.

ALT The logo of SubtiWiki v5.

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Don't worry if you're missing some features in this newest version, the last version is still accessible. Editing of data is also currently only possible in the last version. Many thanks to @VincenzDuMont, Tim van den Berg, Tom Nowak, Janne Pauline Winsemann and many more!
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Check out the new BLAST search for SubtiWiki's new beta release: subtiwiki.uni-goettingen.de/…! You can now BLAST your nucleotide/protein sequence against SubtiWiki's coding sequences. Thank you Dmytro Boiko from @UAM_Poznan for your work on it! #subtiwiki #bacillus
Screenshot of the new BLAST search page on SubtiWiki v5 beta. A form with the query sequence as well as a table of hits with alignments is shown.

ALT Screenshot of the new BLAST search page on SubtiWiki v5 beta. A form with the query sequence as well as a table of hits with alignments is shown.

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Thank you @DmytroBoik86434 !
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Christoph Elfmann retweeted
Jörg Stülke@JorgStulke25 Sep 2024
Congratulations, ⁦@DennisWicke⁩ , on receiving the thesis award of the Göttingen Center for Molecular Biosciences! ⁦@uniGoettingen⁩ #bacillus #subtiwiki #proudPI
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👉 Registration is now open! Please RT and distribute this information among your colleagues! rim2024.uni-hohenheim.de #VAAM #RIM2024 @UniHohenheim
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Christoph Elfmann retweeted
Jörg Stülke@JorgStulke3 Jun 2024
Good evening from Würzburg! I am very much enjoying the @VAAM_Microbes conference with many friends and colleagues. Even presented the poster of @c_elfmann to @CommichauM this afternoon! #subtiwiki
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Christoph Elfmann retweeted
Jen Herman 🌪️@JukeBaRosh13 May 2024
There will be 2 opportunities to attend an in-person SubtiWiki workshop at #Grampositive2024 #subtiwiki
Jen Herman 🌪️@JukeBaRosh2 May 2024
📌Deadlines approaching Consideration for: ⚫️Oral Presentation - 05/15/2024 ⚫️Poster - 06/01/2024 See website for list of confirmed speakers & daily schedule Hope to meet you in Bloomington! grampositivebloomington.iu.e… #Grampositive2024
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You can now find a hashtag feed on the sidebar of any gene page! Just use the #subtiwiki hashtag and your Tweet will pop up there!
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However, the feed is only synced once a day, so it can take a while for the newest Tweets to show up.
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An interactive visualization of conserved gene neighborhoods now on corewiki.uni-goettingen.de/ (#SubtiWiki's next version)! It features clusters created with @webflags1 . Big thanks to Tom Nowak for his work and @gem__atkinson for the great FlaGs tool! @IMPRS_GS #bacillus #MOTY
Gene neighborhoods of rnpM across different organisms.

ALT Gene neighborhoods of rnpM across different organisms.

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Christoph Elfmann retweeted
Jörg Stülke@JorgStulke5 Dec 2023
Finally online: @DennisWicke's paper on a strongly conserved bacterial protein that interacts with RNase P and modulates its activity in Bacillus subtilis! @uniGoettingen 🤝@uni_mr #moty @NAR_Open academic.oup.com/nar/article…

The previously uncharacterized RnpM (YlxR) protein modulates the activity of ribonuclease P in...

Abstract. Even though Bacillus subtilis is one of the most studied organisms, no function has been identified for about 20% of its proteins. Among these un

academic.oup.com
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SubtiWiki's gene pages now feature charts of the relative fitness of deletion mutants for various conditions and media! This can provide interesting insights into the gene's role. Data from Koo et al. (2017, doi.org/10.1016/j.cels.2016.…). Screenshot shows ΔguaB fitness.
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The visualization uses the Apache ECharts library (echarts.apache.org), just like our Expression Browser!
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