Gherman Novakovsky
@gnovakovsky.bsky.social
📤 165
📥 140
📝 20
PhD, Illumina AI lab
pinned post!
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/)
7 months ago
1
60
22
reposted by
Gherman Novakovsky
Dariia Mykhailyshyna
about 2 months ago
❗️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
1
25
17
reposted by
Gherman Novakovsky
Wyeth Wasserman
5 months ago
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...
loading . . .
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...
https://ubc.wd10.myworkdayjobs.com/ubcfacultyjobs/job/UBC-Off-Campus-Hospital-Sites/Research-Associate_JR20120-1
0
6
7
reposted by
Gherman Novakovsky
Anshul Kundaje
7 months ago
@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/
1
55
43
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/)
7 months ago
1
60
22
reposted by
Gherman Novakovsky
Stein Aerts
8 months ago
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...
loading . . .
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...
https://www.biorxiv.org/content/10.1101/2025.05.13.653733v1
1
38
16
reposted by
Gherman Novakovsky
Manu Saraswat
8 months ago
🧠 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🧵👇
1
78
35
reposted by
Gherman Novakovsky
Haky Im
8 months ago
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.
loading . . .
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 ...
https://www.cell.com/cell-genomics/fulltext/S2666-979X(25)00131-4
0
15
7
reposted by
Gherman Novakovsky
8 months ago
So excited to see Yawei's manuscript on long-range MPRAs out! Some really great insights into distal enhancer regulation 🙂
add a skeleton here at some point
1
15
4
reposted by
Gherman Novakovsky
Milot Mirdita
8 months ago
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...
1
20
4
reposted by
Gherman Novakovsky
Jesse Engreitz
9 months ago
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 👇
add a skeleton here at some point
1
116
30
reposted by
Gherman Novakovsky
Anya Korsakova
9 months ago
⚡️ Our latest preprint is on bioRxiv! Shift augmentation improves DNA convolutional neural network indel effect predictions
www.biorxiv.org/content/10.1...
loading . . .
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...
https://www.biorxiv.org/content/10.1101/2025.04.07.647656v1
2
13
5
reposted by
Gherman Novakovsky
Niklas Kempynck
9 months ago
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...
1
75
43
reposted by
Gherman Novakovsky
Wyeth Wasserman
10 months ago
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
loading . . .
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...
https://tinyurl.com/bm4ptux3
0
28
32
reposted by
Gherman Novakovsky
Vikram Agarwal
12 months ago
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.
loading . . .
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.
https://www.nature.com/articles/s41586-024-08430-9
2
36
10
reposted by
Gherman Novakovsky
Nadav Ahituv
12 months ago
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...
loading . . .
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.
https://www.nature.com/articles/s41586-024-08430-9
1
95
42
reposted by
Gherman Novakovsky
Vikram Agarwal
12 months ago
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,
loading . . .
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.
https://www.nature.com/articles/s41588-024-02053-6
2
71
27
reposted by
Gherman Novakovsky
Anshul Kundaje
12 months ago
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...
add a skeleton here at some point
1
37
7
reposted by
Gherman Novakovsky
Hani Goodarzi
12 months ago
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...
loading . . .
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 ...
https://www.biorxiv.org/content/10.1101/2024.12.31.630783v1
1
81
43
reposted by
Gherman Novakovsky
Sung Kim
about 1 year ago
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...
loading . . .
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!
https://www.speechmatics.com/company/articles-and-news/timing-operations-in-pytorch
0
21
4
reposted by
Gherman Novakovsky
Sarah Marzi
about 1 year ago
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-...
loading . . .
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
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae1212/7921050
3
70
29
reposted by
Gherman Novakovsky
Austin Wang
about 1 year ago
(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
loading . . .
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...
https://arxiv.org/abs/2412.05430
1
70
30
reposted by
Gherman Novakovsky
Richard McElreath 🐈⬛
over 1 year ago
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...
loading . . .
28
841
253
reposted by
Gherman Novakovsky
Axel Visel
about 1 year ago
Transcription and Chromatin Parts 1 and 2 by
@jxhoffman.bsky.social
Part 1:
go.bsky.app/5zgpZfg
Part 2:
go.bsky.app/Q5sXc6E
add a skeleton here at some point
1
7
4
reposted by
Gherman Novakovsky
Michael Kevin Spencer
about 1 year ago
Computational Biology
go.bsky.app/QVPoZXp
add a skeleton here at some point
0
6
3
reposted by
Gherman Novakovsky
bioRxiv Genetics
about 1 year ago
Mapping enhancer-gene regulatory interactions from single-cell data https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1
loading . . .
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
https://www.biorxiv.org/content/10.1101/2024.11.23.624931v1
0
36
21
you reached the end!!
feeds!
log in
