Dmitry Kobak
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Explore the profile of Dmitry Kobak including associated specialties, affiliations and a list of published articles.
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26
Citations
1419
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Recent Articles
1.
Stanley J, Stanley 3rd J, Yang J, Li R, Lindenbaum O, Kobak D, et al.
bioRxiv
. 2025 Feb;
PMID: 39975320
Principal component analysis (PCA) is indispensable for processing high-throughput omics datasets, as it can extract meaningful biological variability while minimizing the influence of noise. However, the suitability of PCA is...
2.
Bernaerts Y, Deistler M, Goncalves P, Beck J, Stimberg M, Scala F, et al.
bioRxiv
. 2025 Jan;
PMID: 39803528
Neural cell types have classically been characterized by their anatomy and electrophysiology. More recently, single-cell transcriptomics has enabled an increasingly fine genetically defined taxonomy of cortical cell types, but the...
3.
Lause J, Berens P, Kobak D
PLoS Comput Biol
. 2024 Oct;
20(10):e1012403.
PMID: 39356722
A recent paper claimed that t-SNE and UMAP embeddings of single-cell datasets are "specious" and fail to capture true biological structure. The authors argued that such embeddings are as arbitrary...
4.
Gonzalez-Marquez R, Schmidt L, Schmidt B, Berens P, Kobak D
Patterns (N Y)
. 2024 Jul;
5(6):100968.
PMID: 39005482
The number of publications in biomedicine and life sciences has grown so much that it is difficult to keep track of new scientific works and to have an overview of...
5.
Damrich S, Klockow M, Berens P, Hamprecht F, Kobak D
bioRxiv
. 2024 May;
PMID: 38746298
The two-dimensional embedding methods t-SNE and UMAP are ubiquitously used for visualizing single-cell data. Recent theoretical research in machine learning has shown that, despite their very different formulation and implementation,...
6.
Lause J, Kobak D, Berens P
bioRxiv
. 2024 Apr;
PMID: 38585748
A recent paper in (Chari and Pachter, 2023) claimed that -SNE and UMAP embeddings of single-cell datasets fail to capture true biological structure. The authors argued that such embeddings are...
7.
Lause J, Ziegenhain C, Hartmanis L, Berens P, Kobak D
bioRxiv
. 2023 Aug;
PMID: 37577688
Recent work employed Pearson residuals from Poisson or negative binomial models to normalize UMI data. To extend this approach to non-UMI data, we model the additional amplification step with a...
8.
Scholey J, Karlinsky A, Kobak D, Tallack C
Lancet
. 2023 Feb;
401(10375):431-432.
PMID: 36774147
No abstract available.
9.
Shen S, Jiang X, Scala F, Fu J, Fahey P, Kobak D, et al.
Nat Commun
. 2022 Oct;
13(1):6389.
PMID: 36302912
Neocortical feedback is critical for attention, prediction, and learning. To mechanically understand its function requires deciphering its cell-type wiring. Recent studies revealed that feedback between primary motor to primary somatosensory...
10.
Kobak D
Signif (Oxf)
. 2022 May;
19(2):10-13.
PMID: 35601695
Throughout the Covid-19 pandemic, we have become used to seeing daily numbers of cases and deaths go up and down. But in some countries, the reported numbers show very little...