Maria Mircea

PostDoc - trying to understand biology through mathematics.

[Mo Lotfollahi @mo_lotfollahi]

(1/2) scTranslator: Training on large-scale RNA data to impute protein abundance.

- pretrain on paired RNA+ protein in sc and bulk and predict on single-cell RNA-only data
- Genes are encoded by raw expression embedding combined with gene embedding

[Maria Mircea @Siliegia]

Received my PhD today! Many thanks to my supervisor @SemrauLab. Thanks to @ItaiYanai for being part of my committee. And also thanks to my paranymphs @JuliaEckert10 and @GeorgeDadu_!

[SemrauLab @SemrauLab]

Happy to share that our study of co-differentiation of cardiomyocytes and endothelial cells from human iPSCs was published in Stem Cells https://t.co/RA7aTT8roA Excellent work by @Xu_Cao_PhD and @Siliegia and a great collaboration with the Orlova lab.

[Maria Mircea @Siliegia]

Our new preprint on the influence of tissue microenvironment on endothelial cell development is out!
https://t.co/jntYCQkq6t

[SemrauLab @SemrauLab]

Thrilled to announce that our paper on XEN-enhanced gastruloids is now online https://t.co/BzVpcsduM3 . We hope you'll find it interesting. Thanks to everybody involved for all of the hard work!

[Portland Press @PPPublishing]

How does a cell decide its own fate? Read more into this fascinating review by @SemrauLab and @Siliegia where they delve into a single-cell view of cell-type specification #BiochemSocTrans #openaccess https://t.co/PG8b5OdtaI

[Maria Mircea @Siliegia]

The paper can be found here: https://t.co/frHAUSiC3L

[Maria Mircea @Siliegia]

Our new paper from @SemrauLab on clusterability of scRNA-seq data is now published in Genome Biology! The new name is phiclust and the code is available at Github https://t.co/AqtH0CGshb.

[Maria Mircea @Siliegia]

Are you interested in the decision-making of single cells? Check out our new review paper from @SemrauLab. We review the important molecular players and single-cell methods to measure them!
https://t.co/67B2zO1hWg

[Maria Mircea @Siliegia]

@CasualVariant @razoralign (6) Please do let me know if you have any more questions!

[Maria Mircea @Siliegia]

@CasualVariant @razoralign (5) It is not possible to recover the full signal matrix (without random noise) which is why we only calculate the distance from the measured expression matrix to the real (unobservable) signal.

[Maria Mircea @Siliegia]

@CasualVariant @razoralign (4) On the other hand, the low-rank approximation is not necessarily noise-free by the conventional definition of noise (random effects) but merely non-sparse.

[Maria Mircea @Siliegia]

@CasualVariant @razoralign (3) The definition of a purely sparse population can still have non-random correlations.

[Maria Mircea @Siliegia]

@CasualVariant @razoralign (2) From that point of view the low-rank signal is also permitted to be sparse. We rather define a pure cell population by having only fluctuations in gene expression space that can be explained by randomness.

[Maria Mircea @Siliegia]

@CasualVariant @razoralign (1) Great question! There are two main differences:
We do not assume the noise matrix to be sparse, but only to be random. So, we disentangle random variations from deterministic ones, rather than sparse signals from low-rank signals.

[antisense. @razoralign]

SIGMA: A clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations https://t.co/pIN2GCsdda

[Maria Mircea @Siliegia]

Is a scRNA-seq cluster worth sub-clustering or are the fluctuations consistent with random noise? Check out SIGMA, our new clusterability measure for scRNA-seq data, purely based on first principles! By @SemrauLab https://t.co/ok08vbqtZT

[single-cell network Netherlands @scNL4]

Tomorrow, April 20 from 15.00h to 17.00h, scNL will be hosting our first meeting online! Join us to brainstorm about what scNL should become here: https://t.co/5gbaNSybbV

[Maria Mircea @Siliegia]

Enhanced maturation in 3D microtissue! Nice work from the LUMC!
https://t.co/1oGWJWJnuw

[Cell Mentor @CellMentor]

.@SemrauLab at @UniLeiden adopted #scrum for their latest research project. Here's why they think you should do the same.

https://t.co/6EVHqcE2Ao