Laura Martens (@lauradmartens.bsky.social)
@lauradmartens
PhD Student at Theis and Gagneur lab - Interested in ML, gene regulation and epigenetics. - Join me on BlueSky
Excited to present “scooby”, which models multi-omic profiles (scRNA-seq coverage & scATAC-seq insertions) directly from 500 kb DNA sequence at single-cell resolution. This was a fantastic collaboration co-led with @thisisjohahi. biorxiv.org/content/10.110…
I am really happy and excited to see CellRank 2 out in Nature Methods (nature.com/articles/s4159…)! @naturemethods @HelmholtzMunich @CompHealthMuc @TU_Muenchen @MariusLange8 @fabian_theis @dana_peer (1/16)
Introducing Flashzoi⚡! We’ve upgraded the Borzoi model with rotary pos. encodings and FlashAttention, resulting in a 3x speedup with similar or better accuracy for faster variant effect prediction or model development, and more efficient genomic analysis biorxiv.org/content/10.110…
Join us for our next Kipoi Seminar with with Dmitry Penzar, @dmitrypenzar @ autosome.org! 👉LegNet: parameter-efficient modeling of gene regulatory regions using modern convolutional neural network 📅Wed Dec 4, 5:30pm CET 🧬 kipoi.org/seminar/ 🦋@kipoizoo.bsky
Join us for the next Kipoi Seminar with with Abdul Muntakim Rafi (Rafi) @muntakim_rafi @CarldeBoerPhD @UBC! 👉Detecting and avoiding homology-based data leakage in genome-trained sequence models 📅Wed Nov 6, 5:30pm CET 🧬tum-conf.zoom.us/meeting/regist…
7 years ago, I met a junior fellow named @JD_Buenrostro who blew me away with a vision of futuristic genomic technologies Today, we (@ajaylabade31, @carolinecomenho) are excited to share our first steps into that future: Expansion in situ genome sequencing 1/
Want to aggregate rare variants into a single gene score while capturing diverse functional effects → Check out DeepRVAT, my first paper lead with @brianfclarke now out in @NatureGenet. DeepRVAT scores can be plugged into any testing framework to discover new disease genes.
🧵 1/9 Delighted to announce that #DeepRVAT is out today in Nature Genetics! Here's a recap of our tweetorial from the preprint, with updates for some exciting new results. It's been a joy to work with @Holtkamp_Eva, as well as @gagneurlab and @OliverStegle.
Have you ever wondered what the genome looks like through the eyes of a DNA language model? In our newest preprint we use DNA LMs to study nucleotide dependencies in the genome, revealing functional elements, characterizing variants and evaluating DNA LMs tinyurl.com/6wbwjaf4
Don't miss our next Kipoi Seminar with Sara Mostafavi @sara_mostafavi @UW! The meeting will not be recorded! 👉Machine learning models of differential gene expression 📆Wed June 5, 5:30pm CET 🧬tum-conf.zoom.us/meeting/regist…
Join us for our next Kipoi Seminar with Thomas Pierrot @thomas_pierrot @instadeepai! 👉The Nucleotide Transformer initiative: building and evaluating robust foundation models for genomics 📆Wed May 8, 5:30pm CET 🧬tum-conf.zoom.us/meeting/regist…
More DNA language modeling at the Kipoi seminar: This Wednesday @thomas_pierrot will tell us about the nucleotide transformer and its applications. Looking forward!
Join us for our next Kipoi Seminar with Thomas Pierrot @thomas_pierrot @instadeepai! 👉The Nucleotide Transformer initiative: building and evaluating robust foundation models for genomics 📆Wed May 8, 5:30pm CET 🧬tum-conf.zoom.us/meeting/regist…
Excited to share Nicheformer! Led by @Alejandro__TL & @AnnaCSchaar, Nicheformer is a foundation model for single-cell & spatial omics. Its innovation is going beyond disassociated analysis to capture & predict local tissue context at single-cell level. biorxiv.org/content/10.110…
Our paper with @pelechanolab “Cellular energy regulates mRNA degradation in a codon-specific manner” now out at Mol Syst Biol! 1/n embopress.org/doi/full/10.10…
Join us for our next Kipoi Seminar with Eric Nguyen from Chris Ré's lab @Stanford 👉HyenaDNA: Long-range Genomic Sequence Modeling at Single Nucleotide Resolution 📆Wed Feb 7, 5:30pm CET 🧬tum-conf.zoom.us/meeting/regist…