Alex Lederer
@alexlederer19
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Systems biologist working at the interface of biology and computation. Single-cell genomics, transcriptional dynamics, development, and Python! PhD @EPFL
Lausanne, Switzerland
Joined September 2019
I’m very happy to share that a major piece of my PhD work is now online @naturemethods! #VeloCycle is a Bayesian framework for the statistically-robust estimation of RNA velocity during the cell cycle, written in Pyro. For more details, please see my LinkedIn post and the paper.
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2 new papers from the labs of @Brainmind_EPFL professors @GioeleLaManno & @EpiGN_Lab 👇 Lederer AR...Naef F, La Manno G. Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations. Nature Methods 2024 https://t.co/3veyoYJhUj
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VeloCycle, developed by the team of @GioeleLaManno and @NaefLab is a manifold-constrained RNA velocity framework for uncovering cell cycle dynamics. https://t.co/9fiJ5CVxvL
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I'm happy and honored to announce the publication of my research on co-infections and the role of host innate immune signaling in mediating pathogen-pathogen interactions in @NatureComms: https://t.co/2kkF3bJ8D5 You can find a look behind the paper here: https://t.co/snVrrOty1V
communities.springernature.com
We’re happy and proud to share the most recent work from our group which was spearheaded by @philipp_walch and is now published online at @NatureComms: https://t.co/1ZgBVXFOmP
@DIB_UNIL @FBM_UNIL @unil
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We’re happy and proud to share the most recent work from our group which was spearheaded by @philipp_walch and is now published online at @NatureComms: https://t.co/1ZgBVXFOmP
@DIB_UNIL @FBM_UNIL @unil
nature.com
Nature Communications - By systematically screening viral and bacterial pathogens during co-infection in macrophages, the authors identify and characterize altered host cell entry and suppressed...
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Interested in navigating #metabolism in space and time? Meet uMAIA (the Unified Mass Imaging Analyzer) - a framework developed in collaboration with @Gio_Dangel0 & @OatesLab @epflSV led by @HSchede & @Leila_Alieh
#omics #lipidtime #MALDI
https://t.co/Z0mp9P7A6J 1/N
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I feel compelled to share my take. TL;DR: (1) the first iteration of anything cannot be perfect, (2) a one-size-fits-all path can be a minefield, (3) let's value diverse voices, (4) let’s prioritize rigorous tools even if, on the surface, it looks like they achieve less. [1/19]
Kudos to @nimwegenlab for pushing back. We all need to keep pushing back on this state of affairs. The RNA velocity figure at the top of the thread is from: https://t.co/5CqRSto52M 6/6
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Founded half a century ago, Europe’s life sciences laboratory continues to champion innovative scientific research, services, technology development, & training, with support of its member states. Join us as we celebrate our birthday this week #EMBL50🎂 https://t.co/bvLtAd7Vn1
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@GioeleLaManno My thesis is now publicly available, feel free to check it out here: https://t.co/zBL0t5ZFGn
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On June 13th, I was officially awarded my PhD! My colleagues designed a clever hat, capturing the themes of my research: retinal degeneration and cell state transition modeling. Thanks to @GioeleLaManno, I also now have a wonderful painting of Joseph Fourier to hang in my office!
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Thank you @alexlederer19 (@GioeleLaManno lab) for a great presentation of VeloCycle at our NYU Single-Cell Club. VeloCycle is a new implementation of RNA velocity that combines velocity field and manifold estimation, tailored for the cell cycle.
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SIB Training Course 📣 Single-Cell Transcriptomics with Python 📷 27 - 29 May 2024 📷@alexlederer19
@geertvangeest and Tania Wyss in person, Bern #bioinformatics #training #SIB #Python #SingleCell @ISBSIB @SIBTraining Apply here:🚨
sib.swiss
Overview Single-cell RNA sequencing (scRNA-seq) can measure the gene expression of complex biological systems at the level of individual cells, enabli
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Our latest preprint, @mukundkabbe's single-cell epigenomics (scATAC & Nano-Cut&Tag) of the adult human central nervous system, finding developmental epigenetic memory at HOX clusters in adult oligodendroglia! @karolinskainst
biorxiv.org
The adult human central nervous system (CNS) is remarkably complex, with neural cells displaying extensive transcriptional heterogeneity. However, how different layers of epigenetic regulation...
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Have you been meaning to learn how to analyze your latest single-cell RNA seq experiment, but don't know where to start? Join us for "Single-Cell Transcriptomics" in Bern next month for a three day intro analysis course! It's the first time the SIB offers this course in Python!
📢 Single-Cell Transcriptomics with Python 👉27 - 29 May 2024 📍 Bern Trainers: @alexlederer19 @geertvangeest and Tania Wyss #bioinformatics #training #SIB #Python #SingleCell #transcriptomics
@ISBSIB 🚨 Apply here:
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Thank you @GioeleLaManno for placing trust in me and for our many (still ongoing) scientific discussions and inspiration!
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It took time to sink in, but I'm happy to share I recently passed my private defense with great feedback from the examiners! The path as a first PhD student is bumpy, but I did it! Excited about the future and to celebrate again with family & friends at the public defense in June
I am so proud of @alexlederer19 who today brilliantly passed his private doctoral defense! Dr. Lederer is the first graduate from my lab. Congratulations Alex! Thank you the exceptional examiners @bayraktar_lab @GrayCampLab Anne-Flo Bitbol & Pierre Göngzy
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I’m proud & excited to share the first major preprint of my postdoc in @broz_lab, @unil. We systematically mapped interactions during bacterial-viral co-infection: https://t.co/VpjuiuUVOz Thanks to @EMBO, @FBM_UNIL, and all my colleagues at @DIB_UNIL & mentors for the support.
researchsquare.com
Understanding how pathogens cause and maintain infection is essential to develop novel therapeutics and prevent outbreaks of emerging diseases. While the broadening of accessible methodologies has...
Excited to share our latest preprint on mapping host-pathogen interactions during co-infection: https://t.co/JmeBJuENve Congratulations to @philipp_walch for spearheading such an ambitious project, encompassing both unbiased screening & mechanistic characterization. @DIB_UNIL
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