Ziv Bar-Joseph
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Explore the profile of Ziv Bar-Joseph including associated specialties, affiliations and a list of published articles.
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155
Citations
7101
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Recent Articles
1.
Kamel M, Song Y, Solbas A, Villordo S, Sarangi A, Senin P, et al.
Bioinformatics
. 2025 Mar;
PMID: 40053700
Motivation: Spatial transcriptomics (ST) enables the study of gene expression within its spatial context in histopathology samples. To date, a limiting factor has been the resolution of sequencing based ST...
2.
Li S, Noroozizadeh S, Moayedpour S, Kogler-Anele L, Xue Z, Zheng D, et al.
Nucleic Acids Res
. 2025 Feb;
53(3).
PMID: 39898548
The success of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) messenger RNA (mRNA) vaccine has led to increased interest in the design and use of mRNA for vaccines and therapeutics....
3.
Song Q, Singh A, McDonough J, Adams T, Vos R, De Man R, et al.
PLoS Comput Biol
. 2024 Dec;
20(12):e1012632.
PMID: 39700255
Age prediction based on single cell RNA-Sequencing data (scRNA-Seq) can provide information for patients' susceptibility to various diseases and conditions. In addition, such analysis can be used to identify aging...
4.
Nguyen N, Rosas L, Khaliullin T, Jiang P, Hasanaj E, Ovando-Ricardez J, et al.
Genome Biol
. 2024 Nov;
25(1):288.
PMID: 39516853
The low resolution of spatial transcriptomics data necessitates additional information for optimal use. We developed scDOT, which combines spatial transcriptomics and single cell RNA sequencing to improve the ability to...
5.
Adamek L, Padiasek G, Zhang C, ODwyer I, Capit N, Dormont F, et al.
Comput Biol Med
. 2024 Oct;
183:109158.
PMID: 39437603
Objective: Computational drug re-purposing has received a lot of attention in the past decade. However, methods developed to date focused on established compounds for which information on both, successfully treated...
6.
Teng H, Stoiber M, Bar-Joseph Z, Kingsford C
Genome Res
. 2024 Oct;
34(11):1987-1999.
PMID: 39406497
Direct nanopore-based RNA sequencing can be used to detect posttranscriptional base modifications, such as N6-methyladenosine (m6A) methylation, based on the electric current signals produced by the distinct chemical structures of...
7.
Chen H, Lee Y, Ovando-Ricardez J, Rosas L, Rojas M, Mora A, et al.
Cell Rep Methods
. 2024 Sep;
4(10):100864.
PMID: 39326411
Many popular spatial transcriptomics techniques lack single-cell resolution. Instead, these methods measure the collective gene expression for each location from a mixture of cells, potentially containing multiple cell types. Here,...
8.
Kryukov M, Moriarty K, Villamea M, ODwyer I, Chow O, Dormont F, et al.
J Biomed Inform
. 2024 Sep;
158:104723.
PMID: 39299565
Objective: Disease severity scores, or endpoints, are routinely measured during Randomized Controlled Trials (RCTs) to closely monitor the effect of treatment. In real-world clinical practice, although a larger set of...
9.
Kamel M, Sarangi A, Senin P, Villordo S, Sunaal M, Barot H, et al.
Bioinformatics
. 2024 Aug;
40(9).
PMID: 39152991
Motivation: Spatial transcriptomics allow to quantify mRNA expression within the spatial context. Nonetheless, in-depth analysis of spatial transcriptomics data remains challenging and difficult to scale due to the number of...
10.
Mathur S, Mattoo H, Bar-Joseph Z
IEEE/ACM Trans Comput Biol Bioinform
. 2024 Aug;
21(6):2076-2088.
PMID: 39137087
Time series RNASeq studies can enable understanding of the dynamics of disease progression and treatment response in patients. They also provide information on biomarkers, activated and repressed pathways, and more....