Assistant Professor of Biostatistics, Boston University. Statistical genomics, biomedical data science, open science, R programming 🇨🇭🇦🇺
Boston, MA
Joined April 2013
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We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor” (OSTA)!
This contains extensive code examples, workflows, datasets, and discussion on data analysis workflows for spatial transcriptomics data using Bioconductor in R. Please check it out - feedback and suggestions welcome!
This was a huge effort by many contributors, in particular @helucro Estella Dong @raphg @markrobinsonca @stephaniehicks , and the @Bioconductor core team and community. Thank you everyone! 🎉🧬
Lukas Weber retweeted
Orchestrating Spatial Transcriptomics Analysis with Bioconductor
(including interoperability with Python)
Paper: biorxiv.org/content/10.1101/…
Book: bioconductor.org/books/OSTA/
#Rstats
Lukas Weber retweeted
so excited to share that our preprint characterizing the dorsal anterior cingulate cortex in post-mortem human brain from @LieberInstitute is out! we integrated matched SRT and snRNA-seq data to investigate agranularity and von Economo neurons
Lukas Weber retweeted
This a really exciting leap forward for genomic sequence to activity gene regulation models. It is a genuine improvement over pretty much all SOTA models spanning a wide range of regulatory, transcriptional and post-transcriptional processes. 1/
Happy to introduce AlphaGenome, @GoogleDeepMind's new AI model for genomics.
AlphaGenome offers a comprehensive view of the human non-coding genome by predicting the impact of DNA variations. It will deepen our understanding of disease biology and open new avenues of research.
Lukas Weber retweeted
Happy to introduce AlphaGenome, @GoogleDeepMind's new AI model for genomics.
AlphaGenome offers a comprehensive view of the human non-coding genome by predicting the impact of DNA variations. It will deepen our understanding of disease biology and open new avenues of research.
Lukas Weber retweeted
🚨 New paper published in @naturemethods!
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
💻 Code: github.com/MicTott/SpotSweep…
📈 Website: mictott.github.io/SpotSweepe…
📰 Paper : nature.com/articles/s41592-0…
🧵👇
Lukas Weber retweeted
🤔Could quality control create more harm than good? We explore this question in the context of #SRT.
SpotSweeper is here to combat implicit selection bias.
Led by rising star @MicTott and mentor @stephaniehicks
Tweetorial:
xitter.cf/MicTott/status/1930957…
Quality control matters in spatial transcriptomics. Check out this paper from Guo and colleagues on SpotSweeper that corrects for both local and regional artifacts, across diverse technologies. nature.com/articles/s41592-0…
Lukas Weber retweeted
🚨 New paper published in @naturemethods!
We introduce SpotSweeper, the first spatially-aware QC methods for spatial transcriptomics.
💻 Code: github.com/MicTott/SpotSweep…
📈 Website: mictott.github.io/SpotSweepe…
📰 Paper : nature.com/articles/s41592-0…
🧵👇
Lukas Weber retweeted
my work with @stephaniehicks and @BoyiGuo has been published in Biostatistics! tldr: the mean-variance bias exists in SRT data & impacts SVG detection. we propose #spoon, available on @Bioconductor, to address this! pmc.ncbi.nlm.nih.gov/article… 🤩
Fascinating week of Nobel Prizes related to computational biology and machine learning 🙂 nobelprize.org/
Lukas Weber retweeted
We are thrilled to announce two open rank faculty searches @UofUGenetics: a broad search for all areas of genetics research (utah.peopleadmin.com/posting…)
& one focused on computational genomics faculty (utah.peopleadmin.com/posting…).
This launches a multi-year recruiting initiative!
(1/4)
Lukas Weber retweeted
Exciting opportunity! I am hiring a postdoc to join the group and to develop computational methods for the analysis of biomedical data including imaging and genomics data at a single-cell or spatial resolution 🧬
stephaniehicks.com/join
Lukas Weber retweeted
huge momentum for mRNA personalized cancer vaccines, with clinical trials ongoing for most cancers
after decades of setback & improper use against metastatic disease, now technology, science, funding & trust are coming together to unlock their potential
nature.com/articles/d41586-0…
Lukas Weber retweeted
Excited to share that my undergrad work is now out in @GenomeBiology!
There are thousands of tools for analyzing single-cell RNA-seq data: could supervised learning help recommend the best?
We ran 24,768 dataset-pipeline combinations and trained models to help answer this question, out now in @GenomeBiology
📰 genomebiology.biomedcentral.…
1/4
Lukas Weber retweeted
🚨preprint & career milestone🚨
My 1️⃣ SENIOR-author manuscript, led by 🌟🧑🔬@MicTott - 🧹SpotSweeper🧹
We introduce novel spatially-aware QC for #SRT, including the popular @10xGenomics #Visium.
👇Tweetorial👇
P.S.: 🤔wonder why we named SpotSweeper
I'm very excited to share my first postdoc preprint with
@BoyiGuo and @stephaniehicks!
Here we preset SpotSweeper - the first spatially-aware quality control methods developed for spatial transcriptomics. 🧵
biorxiv.org/content/10.1101/…
