@BenjaminMayro

NCI K00 Fellow at UTSW in the Tagliabracci lab. Interested in cool enzymes and PTMs

Joined October 2019
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I am excited and humbled to share that I have been awarded an NCI F99K00. This fellowship will provide up to two years of funding for me to finish my PhD studying tyrosine kinase signaling networks during hypoxia, and four additional years of post-doctoral funding. 1/2
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🧬 Big Data Phylogeny & Comparative Methods course (23–26 June, online) Learn to build and interpret phylogenetic trees, analyse trait evolution, and apply comparative genomics to real data physalia-courses.org/courses…

Big Data Phylogeny and Comparative Methods: From Theory to Practice

Figure: https://doi.org/10.1098/rspb.2024.1412

physalia-courses.org
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🧬Collinearity Analysis is here in #gbdraw v0.11.0! You can easily detect and visualize synteny and collinearity blocks using LOSATP. You can instantly align the entire diagram based on a shared ortholog! Try it now: gbdraw.app/ #bioinformatics #genomics #microbiology
Collinearity analysis of Hepatoplasmataceae, a group of mollicutes associated with isopod crustaceans. Inverted syntenic blocks are colored in dark red.

ALT Collinearity analysis of Hepatoplasmataceae, a group of mollicutes associated with isopod crustaceans. Inverted syntenic blocks are colored in dark red.

Synteny of lividomycin-like aminoglycoside biosynthetic gene clusters. The diagrams are aligned based on livE gene (see next figure for the command)

ALT Synteny of lividomycin-like aminoglycoside biosynthetic gene clusters. The diagrams are aligned based on livE gene (see next figure for the command)

Dialog box for the livE gene in the record BGC0000708. Click "Align" to align the records based on the shared livE orthologs, as seen in the previous figure.

ALT Dialog box for the livE gene in the record BGC0000708. Click "Align" to align the records based on the shared livE orthologs, as seen in the previous figure.

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📣Nominations are now open for the following awards: -Outstanding Postdoc at Duke (nominate here: duke.qualtrics.com/jfe/form/…) -Outstanding Postdoc Mentor at Duke (nominate here: duke.qualtrics.com/jfe/form/…) Deadline to nominate: 9/10/25 at noon More info: research.duke.edu/postdoc/aw…
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Benjamin Mayro retweeted
Cancer Discovery@CD_AACR5 Mar 2025
Read the paper featured on the cover of this month’s Cancer Discovery: PKN2 Is a Dependency of the Mesenchymal-like Cancer Cell State brnw.ch/21wR7NC By Shane Killarney, @kcw00d, and colleagues @Duke_PCB @DukeCancer
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An accomplished scientist who studies the role of protein tyrosine kinases, Ann Marie Pendergast, PhD, finds mentoring easy because she focuses on it full time. She meets weekly with students in her lab and outside of that, her office is always open. pcb.duke.edu/news/mentor-spo…

Mentor Spotlight: Ann Marie Pendergast, PhD

“Mentoring is fun because you can see students make a big impact. Many of them branch into different areas outside of the field they trained in. It’s nice to see how this training impacts their...

pcb.duke.edu
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Exciting findings in a study led by Shane Killarney in the @kcw00d lab: Mesenchymal-like cancer cells depend on PKN2 kinase for survival, offering a potential therapeutic target against drug resistance. A cool collaboration with the Pendergast and McDonnell labs ⬇️ @DukeCancer
Elizabeth McKenna@ElizSMcKenna20 Nov 2024
Now online in @CD_AACR: PKN2 Is a Dependency of the Mesenchymal-like Cancer Cell State - by Shane Killarney, @kcw00d, and colleagues doi.org/10.1158/2159-8290.CD… @Duke_PCB
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I'm excited to announce that I've accepted a TT faculty position @VanderbiltCDB and @VUMC_Cancer! Thrilled to join @VanderbiltU! The Mudumbi Lab opens January 2025. We will use single-molecule microscopy to study the kinetics of RTK signaling, with a focus on biased signaling!
Man standing in front of a wall with the Vanderbilt seal arms crossed.

ALT Man standing in front of a wall with the Vanderbilt seal arms crossed.

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Does anyone have a recommendation for a plasmid that allows for constitutive expression in E. Coli? #AcademicTwitter
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What are some examples of missing genes for known activities in metabolic pathways? #ScienceTwitter #AcademicChatter
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A farewell to our fantastic colleague, Jamie Baize Smith @katbaizes. The PCB students, staff and faculty thank you and we wish you all the best in your next chapter.
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Benjamin Mayro retweeted
FASEB
@FASEBorg29 Apr 2024
Are you ready for unpublished research on protein kinases and phosphorylation plus a gorgeous view of the Irish Coast? Join @bradylabupenn, @Megston8, @mbyaffe, and Vincent Tagliabracci @UTSWScience for this great program and save your space at #PPHSRC: hubs.ly/Q02v5Hs20
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Current protein models (ESM-2, AlpaFold2,...) only encode the 20 wild-type amino acids -- what about PTMs, which significantly influence the diversity of the proteome? 💁‍♂️To solve this, we present the first PTM-aware protein language model, PTM-Mamba! biorxiv.org/content/10.1101/…

PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks

Proteins serve as the workhorses of living organisms, orchestrating a wide array of vital functions. Post-translational modifications (PTMs) of their amino acids greatly influence the structural and...

biorxiv.org
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Benjamin Mayro retweeted
Ardem Patapoutian@ardemp25 Jan 2024
I'm a serial exclamation mark user, and I'm not sorry about it!
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Robert W. Sobol@rwsobol1 Dec 2023
Nice report by Keith Caldecott: Causes and consequences of DNA single-strand breaks: Trends in Biochemical Sciences cell.com/trends/biochemical-…

Causes and consequences of DNA single-strand breaks

DNA single-strand breaks (SSBs) are among the most common lesions arising in human cells, with tens to hundreds of thousands arising in each cell, each day. Cells have efficient mechanisms for the...

cell.com
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Benjamin Mayro retweeted
Turk Lab@benturklab22 Nov 2023
Our paper discovering short linear motifs #SLiMs targeted by the MAP kinases ERK and p38 is now published! Led by the incomparable Jaylissa Torres Robles, this paper resolves how these two related kinases selectively target unique substrates. pnas.org/doi/10.1073/pnas.23…
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Benjamin Mayro retweeted
Pengfei Hou@houpf043116 Nov 2023
It is not fresh to know that γ-secretases process APP to generate Aβ. But what do they cut in microglia? Why do they cut so many proteins in the meantime? Our paper just published in @MolecularCell provides new insights on these topics. Check it out: cell.com/molecular-cell/full…
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PCB Dissertation Seminar Breast cancer cells exhibit a non-linear proliferative dose response to progestins Presented by: Emma Dolan Advisors: Drs. Donald McDonnell & Susan Murphy Friday, October 27 at 9:00am LSRC A247
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🍹NEW:@ArdehaliHossein & co find a role for the #HistoneDemethylase KDM3B in sensing #ironlevels and regulating #mTORC1 via #transcriptional repression of mTORC1 pathway components. @nu_fcvrri @NUFeinbergMed @NorthwesternMed @NUMSTP rdcu.be/dnhYk nature.com/articles/s41556-0…
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Ok, Twitter, prove you are still useful: Tell me when and by whom Oct3/4, Sox2, Klf4, c-Myc were each first cloned/described? @matthewcobb @AMartinezArias @gastrulateordie @MadS100tist, an RT is appreciated.
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Elucidation of E3 ubiquitin ligase specificity through proteome-wide internal degron mapping dlvr.it/SwTj6W

Elucidation of E3 ubiquitin ligase specificity through proteome-wide internal degron mapping

Zhang et al. combined a proteome-wide screen with machine learning to identify thousands of short linear motifs (degrons) in human proteins that are associated with sequence-dependent protein...

cell.com
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