Gherman Novakovsky
@gnovakovsky.bsky.social
PhD, Illumina AI lab
Pinned
Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)
Reposted by Gherman Novakovsky
❗️Our next workshop will be on Dec 11 6 pm CET titled A Gentle Introduction to Mathematical Simulation in R by
@damiepak.bsky.social
Register or sponsor a student by donating to support Ukraine!
Details: bit.ly/3wBeY4S
Please share!
#AcademicSky #EconSky #RStats
@damiepak.bsky.social
Register or sponsor a student by donating to support Ukraine!
Details: bit.ly/3wBeY4S
Please share!
#AcademicSky #EconSky #RStats
November 14, 2025 at 10:09 AM
❗️Our next workshop will be on Dec 11 6 pm CET titled A Gentle Introduction to Mathematical Simulation in R by
@damiepak.bsky.social
Register or sponsor a student by donating to support Ukraine!
Details: bit.ly/3wBeY4S
Please share!
#AcademicSky #EconSky #RStats
@damiepak.bsky.social
Register or sponsor a student by donating to support Ukraine!
Details: bit.ly/3wBeY4S
Please share!
#AcademicSky #EconSky #RStats
Reposted by Gherman Novakovsky
I'm hiring a Bioinformatics Research Associate for the Silent Genomes Project. PhD required, restricted to Canadians, work must be performed in British Columbia.
Great for those who love pipelines, whole genome data and work with a social purpose.
ubc.wd10.myworkdayjobs.com/ubcfacultyjo...
Great for those who love pipelines, whole genome data and work with a social purpose.
ubc.wd10.myworkdayjobs.com/ubcfacultyjo...
Research Associate
Academic Job Category Faculty Non Bargaining Job Title Research Associate Department Wasserman Laboratory | Department of Medical Genetics | Faculty of Medicine (Wyeth Wasserman) Posting End Date Augu...
ubc.wd10.myworkdayjobs.com
July 22, 2025 at 8:42 PM
I'm hiring a Bioinformatics Research Associate for the Silent Genomes Project. PhD required, restricted to Canadians, work must be performed in British Columbia.
Great for those who love pipelines, whole genome data and work with a social purpose.
ubc.wd10.myworkdayjobs.com/ubcfacultyjo...
Great for those who love pipelines, whole genome data and work with a social purpose.
ubc.wd10.myworkdayjobs.com/ubcfacultyjo...
Reposted by Gherman Novakovsky
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
June 19, 2025 at 8:55 PM
@saramostafavi.bsky.social (@Genentech) & I (@Stanford) r excited to announce co-advised postdoc positions for candidates with deep expertise in ML for bio (especially sequence to function models, causal perturbational models & single cell models). See details below. Pls RT 1/
Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)
May 29, 2025 at 11:57 PM
Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)
Reposted by Gherman Novakovsky
Two massive glioblastoma papers, datasets, trajectories, insights, and.. a very cool new method for GRN inference - scDORI -from @steglelab.bsky.social @oliverstegle.bsky.social @bayraktarlab.bsky.social & Moritz Mall www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...
Decoding Plasticity Regulators and Transition Trajectories in Glioblastoma with Single-cell Multiomics
Glioblastoma (GB) is one of the most lethal human cancers, marked by profound intratumoral heterogeneity and near-universal treatment resistance. Cellular plasticity, the capacity of cancer cells to t...
www.biorxiv.org
May 16, 2025 at 7:31 AM
Two massive glioblastoma papers, datasets, trajectories, insights, and.. a very cool new method for GRN inference - scDORI -from @steglelab.bsky.social @oliverstegle.bsky.social @bayraktarlab.bsky.social & Moritz Mall www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...
Reposted by Gherman Novakovsky
🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇
May 16, 2025 at 10:05 AM
🧠 Excited to share my main PhD project! We mapped the regulatory rules governing Glioblastoma plasticity using single-cell multi-omics and deep learning. This work is part of a two-paper series with @bayraktarlab.bsky.social @oliverstegle.bsky.social and @moritzmall.bsky.social, Preprint at end🧵👇
Reposted by Gherman Novakovsky
Check out our scPrediXcan paper
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
scPrediXcan integrates deep learning methods and single-cell data into a cell-type-specific transcriptome-wide association study framework
Zhou et al. introduce scPrediXcan, a novel transcriptome-wide association study framework
that integrates the deep learning-based model ctPred for cell-type-specific expression
prediction. Applied to ...
www.cell.com
May 14, 2025 at 10:41 PM
Check out our scPrediXcan paper
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
www.cell.com/cell-genomic...
Led by the talented @Charles_Zhou12 and supervised by @MengjieChen6
and me, with thanks to many contributors.
scPrediXcan integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework.
Reposted by Gherman Novakovsky
So excited to see Yawei's manuscript on long-range MPRAs out! Some really great insights into distal enhancer regulation 🙂
🚨PRE-PRINT 🧪🧬🖥️👩🔬
Long-range massively parallel reporter assay reveals rules of distal enhancer-promoter interactions
From Barak Cohen's lab at @washu.bsky.social
Read the pre-print 👇
doi.org/10.1101/2025...
Learn more about the research from the Cohen lab: bclab.wustl.edu
Long-range massively parallel reporter assay reveals rules of distal enhancer-promoter interactions
From Barak Cohen's lab at @washu.bsky.social
Read the pre-print 👇
doi.org/10.1101/2025...
Learn more about the research from the Cohen lab: bclab.wustl.edu
April 23, 2025 at 9:10 PM
So excited to see Yawei's manuscript on long-range MPRAs out! Some really great insights into distal enhancer regulation 🙂
Reposted by Gherman Novakovsky
Day 1 of #RECOMB2025-SEQ starts with @rayanchikhi.bsky.social and an introduction to Logan, a planetary-scale effort to assemble everything.
Currently cataloguing about 700k virus species!
📄 www.biorxiv.org/content/10.1...
Currently cataloguing about 700k virus species!
📄 www.biorxiv.org/content/10.1...
April 24, 2025 at 1:12 AM
Day 1 of #RECOMB2025-SEQ starts with @rayanchikhi.bsky.social and an introduction to Logan, a planetary-scale effort to assemble everything.
Currently cataloguing about 700k virus species!
📄 www.biorxiv.org/content/10.1...
Currently cataloguing about 700k virus species!
📄 www.biorxiv.org/content/10.1...
Reposted by Gherman Novakovsky
Our latest work now online in Cell:
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
April 17, 2025 at 6:26 PM
Our latest work now online in Cell:
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Rewriting regulatory DNA to dissect and reprogram gene expression
Our new method (Variant-EFFECTS) uses high-throughput prime editing + flow sorting + sequencing to precisely measure effects of noncoding variants on gene expression
Thread 👇
Reposted by Gherman Novakovsky
⚡️ Our latest preprint is on bioRxiv!
Shift augmentation improves DNA convolutional neural network indel effect predictions
www.biorxiv.org/content/10.1...
Shift augmentation improves DNA convolutional neural network indel effect predictions
www.biorxiv.org/content/10.1...
Shift augmentation improves DNA convolutional neural network indel effect predictions
Determining genetic variant effects on molecular phenotypes like gene expression is a task of paramount importance to medical genetics. DNA convolutional neural networks (CNNs) attain state-of-the-art...
www.biorxiv.org
April 16, 2025 at 9:13 PM
⚡️ Our latest preprint is on bioRxiv!
Shift augmentation improves DNA convolutional neural network indel effect predictions
www.biorxiv.org/content/10.1...
Shift augmentation improves DNA convolutional neural network indel effect predictions
www.biorxiv.org/content/10.1...
Reposted by Gherman Novakovsky
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
April 3, 2025 at 2:30 PM
We released our preprint on the CREsted package. CREsted allows for complete modeling of cell type-specific enhancer codes from scATAC-seq data. We demonstrate CREsted’s robust functionality in various species and tissues, and in vivo validate our findings: www.biorxiv.org/content/10.1...
Reposted by Gherman Novakovsky
Bioinformatics Job Opportunity
Research Associate / Staff Scientist
Vancouver Canada
Join the Silent Genomes Project to provide an outstanding genetic variation database for Indigenous peoples of Canada to improve rare disease diagnosis
tinyurl.com/bm4ptux3
Priority to Canadians
Please repost
Research Associate / Staff Scientist
Vancouver Canada
Join the Silent Genomes Project to provide an outstanding genetic variation database for Indigenous peoples of Canada to improve rare disease diagnosis
tinyurl.com/bm4ptux3
Priority to Canadians
Please repost
Research Associate
Academic Job Category Faculty Non Bargaining Job Title Research Associate Department Wasserman Laboratory | Department of Medical Genetics | Faculty of Medicine (Wyeth Wasserman) Posting End Date Febr...
tinyurl.com
February 27, 2025 at 11:59 PM
Bioinformatics Job Opportunity
Research Associate / Staff Scientist
Vancouver Canada
Join the Silent Genomes Project to provide an outstanding genetic variation database for Indigenous peoples of Canada to improve rare disease diagnosis
tinyurl.com/bm4ptux3
Priority to Canadians
Please repost
Research Associate / Staff Scientist
Vancouver Canada
Join the Silent Genomes Project to provide an outstanding genetic variation database for Indigenous peoples of Canada to improve rare disease diagnosis
tinyurl.com/bm4ptux3
Priority to Canadians
Please repost
Reposted by Gherman Novakovsky
Super excited to announce our latest work. On a personal note, it's not an exaggeration to say that blood, sweat, and tears got us to the finish line on this: working w/ an outstanding global team of scientists in Germany, Japan, Russia, and USA responding in >100 pages of complex reviewer comments.
Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
www.nature.com
January 15, 2025 at 5:39 PM
Super excited to announce our latest work. On a personal note, it's not an exaggeration to say that blood, sweat, and tears got us to the finish line on this: working w/ an outstanding global team of scientists in Germany, Japan, Russia, and USA responding in >100 pages of complex reviewer comments.
Reposted by Gherman Novakovsky
Massively parallel reporter assays (MPRAs) testing >680,000 sequences combined with machine learning to improve regulatory element & variant effect prediction. Amazing work by @vagar.bsky.social, Fumitaka Inoue, @jshendure.bsky.social and many others as part of ENCODE.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
www.nature.com
January 15, 2025 at 5:05 PM
Massively parallel reporter assays (MPRAs) testing >680,000 sequences combined with machine learning to improve regulatory element & variant effect prediction. Amazing work by @vagar.bsky.social, Fumitaka Inoue, @jshendure.bsky.social and many others as part of ENCODE.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Gherman Novakovsky
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 Gherman Novakovsky
Our original biorxiv submission of the ChromBPNet preprint had issues with supp. methods & file links not working (even though we they were uploaded). This updated version has fixed those issues. Everything shud be available now. Thanks for your patience.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
January 9, 2025 at 7:50 PM
Our original biorxiv submission of the ChromBPNet preprint had issues with supp. methods & file links not working (even though we they were uploaded). This updated version has fixed those issues. Everything shud be available now. Thanks for your patience.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Gherman Novakovsky
The first preprint of 2025! Together with Matvei, @halfacrocodile.bsky.social, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. www.biorxiv.org/content/10.1...
A generative framework for enhanced cell-type specificity in rationally designed mRNAs
mRNA delivery offers new opportunities for disease treatment by directing cells to produce therapeutic proteins. However, designing highly stable mRNAs with programmable cell type-specificity remains ...
www.biorxiv.org
January 2, 2025 at 1:10 PM
The first preprint of 2025! Together with Matvei, @halfacrocodile.bsky.social, & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. www.biorxiv.org/content/10.1...
Reposted by Gherman Novakovsky
How to Accurately Time CUDA Kernels in Pytorch
In a world of increasingly costly machine learning model deployments, ensuring accurate GPU operation timing is key to resource optimization. In this blog post, we explore best practices to achieve this in PyTorch.
www.speechmatics.com/company/arti...
In a world of increasingly costly machine learning model deployments, ensuring accurate GPU operation timing is key to resource optimization. In this blog post, we explore best practices to achieve this in PyTorch.
www.speechmatics.com/company/arti...
How to Accurately Time CUDA Kernels in Pytorch
In a world of increasingly costly machine learning model deployments, ensuring accurate GPU operation timing is key to resource optimization. Read more!
www.speechmatics.com
December 23, 2024 at 4:41 AM
How to Accurately Time CUDA Kernels in Pytorch
In a world of increasingly costly machine learning model deployments, ensuring accurate GPU operation timing is key to resource optimization. In this blog post, we explore best practices to achieve this in PyTorch.
www.speechmatics.com/company/arti...
In a world of increasingly costly machine learning model deployments, ensuring accurate GPU operation timing is key to resource optimization. In this blog post, we explore best practices to achieve this in PyTorch.
www.speechmatics.com/company/arti...
Reposted by Gherman Novakovsky
So excited that our work on predicting gene expression from histone modifications using deep learning is out in NAR today. Brilliant to work with lead author @al-murphy.bsky.social and collaborators Aydan Askarova, @borislenhard.bsky.social and Nathan Skene 🧬⭐️🙏
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Predicting gene expression from histone marks using chromatin deep learning models depends on histone mark function, regulatory distance and cellular states
Abstract. To understand the complex relationship between histone mark activity and gene expression, recent advances have used in silico predictions based o
academic.oup.com
December 11, 2024 at 5:02 PM
So excited that our work on predicting gene expression from histone modifications using deep learning is out in NAR today. Brilliant to work with lead author @al-murphy.bsky.social and collaborators Aydan Askarova, @borislenhard.bsky.social and Nathan Skene 🧬⭐️🙏
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Gherman Novakovsky
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA
Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn gen...
arxiv.org
December 11, 2024 at 2:30 AM
(1/10) Excited to announce our latest work! @arpita-s.bsky.social, @amanpatel100.bsky.social , and I will be presenting DART-Eval, a rigorous suite of evals for DNA Language Models on transcriptional regulatory DNA at #NeurIPS2024. Check it out! arxiv.org/abs/2412.05430
Reposted by Gherman Novakovsky
If you hate statistics like I do, then you'll love my free lectures. Putting science before statistics, 20 lectures from basics of inference & causal modeling to multilevel models & dynamic state space models. It's all free, made with love and sympathy. 🧪 #stats www.youtube.com/playlist?lis...
September 19, 2024 at 10:56 AM
If you hate statistics like I do, then you'll love my free lectures. Putting science before statistics, 20 lectures from basics of inference & causal modeling to multilevel models & dynamic state space models. It's all free, made with love and sympathy. 🧪 #stats www.youtube.com/playlist?lis...
Reposted by Gherman Novakovsky
Transcription and Chromatin Parts 1 and 2 by @jxhoffman.bsky.social
Part 1: go.bsky.app/5zgpZfg
Part 2: go.bsky.app/Q5sXc6E
Part 1: go.bsky.app/5zgpZfg
Part 2: go.bsky.app/Q5sXc6E
December 2, 2024 at 7:51 PM
Transcription and Chromatin Parts 1 and 2 by @jxhoffman.bsky.social
Part 1: go.bsky.app/5zgpZfg
Part 2: go.bsky.app/Q5sXc6E
Part 1: go.bsky.app/5zgpZfg
Part 2: go.bsky.app/Q5sXc6E
Reposted by Gherman Novakovsky
December 2, 2024 at 6:31 AM
Reposted by Gherman Novakovsky
Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1
Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1
Mapping enhancers and their target genes in specific cell types is crucial for understanding gene re
www.biorxiv.org
November 24, 2024 at 10:32 AM
Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1