Marta Lemanczyk
@mlemanczyk.bsky.social
Visiting Grad Student at Koo Lab (Cold Spring Harbor Laboratory) | PhD Student @renardlab.bsky.social (Hasso-Plattner-Institute) | XAI in Genomics 🧬
Reposted by Marta Lemanczyk
Science doesn’t need to be pretty and go according to plan; it just needs to lead to a discovery. If doesn’t have to be done alone or together with someone else; there just needs to be a discovery. It doesn’t need to happen fast or slow; just as long as there’s a discovery, then everybody is happy.
August 9, 2025 at 2:13 AM
Science doesn’t need to be pretty and go according to plan; it just needs to lead to a discovery. If doesn’t have to be done alone or together with someone else; there just needs to be a discovery. It doesn’t need to happen fast or slow; just as long as there’s a discovery, then everybody is happy.
Reposted by Marta Lemanczyk
german elections are up. i buy into many points on the ballot (inequality, fair migration reform incl repatriation of criminals). but i particularly disagree on lumping foreigners together as a motor of crime. this group has steadily become less criminal since '93. peace and love
February 13, 2025 at 12:19 PM
german elections are up. i buy into many points on the ballot (inequality, fair migration reform incl repatriation of criminals). but i particularly disagree on lumping foreigners together as a motor of crime. this group has steadily become less criminal since '93. peace and love
Reposted by Marta Lemanczyk
Super excited to announce our latest flagship model Borzoi: major props to Johannes & David Kelley et al for advancing it. It's been a long journey from our prior Enformer model into this one. A few innovations: i) longer DNA context, ii) adaptation to predict RNA-seq abundance and splice isoforms,
Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation - Nature Genetics
Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.
www.nature.com
January 9, 2025 at 3:08 AM
Super excited to announce our latest flagship model Borzoi: major props to Johannes & David Kelley et al for advancing it. It's been a long journey from our prior Enformer model into this one. A few innovations: i) longer DNA context, ii) adaptation to predict RNA-seq abundance and splice isoforms,
Reposted by Marta Lemanczyk
Reminder #jobalert for a starting postdoc or PhD position (for someone with strong ML background)!
Joint project with Gregoire Montavon’s lab at #BIFOLD @xtraexer.bsky.social -
explainable AI for self supervised LLMs in gene regulation. Apply until Dec 13!
www.bifold.berlin/about-us/opp...
Joint project with Gregoire Montavon’s lab at #BIFOLD @xtraexer.bsky.social -
explainable AI for self supervised LLMs in gene regulation. Apply until Dec 13!
www.bifold.berlin/about-us/opp...
BIFOLD is a Research Assistant (salary grade E 13 TV-L Berliner Hochschulen)
www.bifold.berlin
December 7, 2024 at 8:56 AM
Reminder #jobalert for a starting postdoc or PhD position (for someone with strong ML background)!
Joint project with Gregoire Montavon’s lab at #BIFOLD @xtraexer.bsky.social -
explainable AI for self supervised LLMs in gene regulation. Apply until Dec 13!
www.bifold.berlin/about-us/opp...
Joint project with Gregoire Montavon’s lab at #BIFOLD @xtraexer.bsky.social -
explainable AI for self supervised LLMs in gene regulation. Apply until Dec 13!
www.bifold.berlin/about-us/opp...
Reposted by Marta Lemanczyk
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 4:13 AM
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Marta Lemanczyk
Jessica Zhou (@zrcjessica) is a talented postdoc now on the job market looking for ML/data science industry positions in the NY area! If you have an open position reach out!
Please Repost to spread the word! 🙏🏻
Please Repost to spread the word! 🙏🏻
DEGU distills an ensemble of models into a single model, retaining the ensemble’s predictive performance while providing uncertainty estimates - ie both epistemic (or model) and aleatoric (or data) uncertainty.
Led by @zrcjessica
Paper: www.biorxiv.org/content/10.1...
2/n
Led by @zrcjessica
Paper: www.biorxiv.org/content/10.1...
2/n
Uncertainty-aware genomic deep learning with knowledge distillation
Deep neural networks (DNNs) have advanced predictive modeling for regulatory genomics, but challenges remain in ensuring the reliability of their predictions and understanding the key factors behind t...
www.biorxiv.org
November 16, 2024 at 10:07 PM
Jessica Zhou (@zrcjessica) is a talented postdoc now on the job market looking for ML/data science industry positions in the NY area! If you have an open position reach out!
Please Repost to spread the word! 🙏🏻
Please Repost to spread the word! 🙏🏻