SemrauLab (@SemrauLab) profile picture

SemrauLab

@SemrauLab

The Semrau Lab is interested in quantitative stem cell biology. We use molecular profiling and machine learning to study iPSC-derived disease models.

 New York Stem Cell Foundation
semraulab.com
Joined September 2015
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Check out our new publication in PLOS Computational Biology on morphogenesis in gastruloids (journals.plos.org/ploscompbi…)
The shapes of elongating gastruloids are consistent with convergent extension driven by a combina...

The shapes of elongating gastruloids are consistent with convergent extension driven by a combina...

Author summary During embryonic development, a mammalian embryo develops from a single cell to a complete organism with a complex body plan. To ensure that tissues and organs are formed exactly in...

journals.plos.org
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Using Cellular Potts Model simulations and accurate shape quantification we show that gastruloids are shaped by a combination of active cell crawling and differential adhesion.
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Our multi-omics study of stem cell differentiation dynamics is out in PLOS Genetics (journals.plos.org/plosgeneti…). We show how a dynamical model of gene expression can be used to explain the discordance between mRNA and protein abundance and …
Integration of a multi-omics stem cell differentiation dataset using a dynamical model

Integration of a multi-omics stem cell differentiation dataset using a dynamical model

Author summary Pluripotent stem cells, which can be derived from an adult individual, can be grown indefinitely in a dish and turned into each cell type of the body. These abilities enable applicat...

journals.plos.org
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identify post-transcriptional regulatory mechanisms. Thanks to @slavov_n for a great collaboration!
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Thank you @Siliegia for being an amazing PhD student! It was a pleasure to be your supervisor.
Maria Mircea (@Siliegia) profile pictureMaria Mircea@Siliegia20 Dec 2022
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_!
Image from Maria Mircea (@Siliegia)
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Happy to share that our study of co-differentiation of cardiomyocytes and endothelial cells from human iPSCs was published in Stem Cells academic.oup.com/stmcls/adva… Excellent work by @Xu_Cao_PhD and @Siliegia and a great collaboration with the Orlova lab.
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Big news: The Semrau lab has moved to @nyscf, the New York Stem Cell Foundation! We are excited to help realize the amazing medical potential of stem cells and look forward to collaborations with many excellent colleagues. If you like our research at the intersection of
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developmental biology, bioinformatics, deep learning and systems biology, join us! We have an opening for a postdoctoral fellow in computational biology jobs.lever.co/nyscf-2/740379… Please share with anybody who might be interested!
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Enjoying great discussions at #CLD2022 in beautiful Alleppey.
Living Machines-NCBS (@NCBStheory) profile pictureLiving Machines-NCBS@NCBStheory2 Nov 2022
Replying to @NCBStheory
The next two sessions for Day 2 of #CLD2022 included some excellent talks by: - @ArjunGuha1 - @semrau_stefan - @shaon_chak - #PhilippThomas On a variety of topics ranging from cellular #lineages, #differentiation, plasticity, single cell molecules & stochastic #gene expression!
Image from Living Machines-NCBS (@NCBStheory)
Image from Living Machines-NCBS (@NCBStheory)
Image from Living Machines-NCBS (@NCBStheory)
Image from Living Machines-NCBS (@NCBStheory)
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A while ago @arjunrajlab asked: What are open conceptual questions in the single-cell field? My suggestion: How can we explain the scaling relationship between the number of cell types and the number of cells in an organism? 1/2
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Here's my answer: frontiersin.org/articles/10.… I hope you will find it interesting. Thanks a lot @arjunrajlab for getting me to think about this! I am also really grateful for encouragement and feedback from @ItaiYanai, @LaanLiedewij and Günter P. Wagner. 2/2
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Thrilled to announce that our paper on XEN-enhanced gastruloids is now online journals.sagepub.com/doi/10.… . We hope you'll find it interesting. Thanks to everybody involved for all of the hard work!
A gastruloid model of the interaction between embryonic and extra-embryonic cell types - Noémie MLP...

A gastruloid model of the interaction between embryonic and extra-embryonic cell types - Noémie MLP...

Stem-cell derived in vitro systems, such as organoids or embryoids, hold great potential for modeling in vivo development. Full control over their initial compo...

journals.sagepub.com
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Thanks a lot to all participants of our @lorentzcenter workshop on Integrative Developmental Biology lorentzcenter.nl/integrative… for a fantastic week! Big shout-out to the co-organizers Jeroen van Zon,@AKicheva ,@NRivron,@TimonIdema and @lorentzcenter
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We are excited to present a new clusterability measure for single-cell transcriptomics: biorxiv.org/content/10.1101/… . Great work by Maria @Siliegia ! You can find the R implementation here github.com/Siliegia/SIGMA . We hope you find the method useful!
A clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations

A clusterability measure for single-cell transcriptomics reveals phenotypic subpopulations

The ability to discover new cell populations by unsupervised clustering of single-cell transcriptomics data has revolutionized biology. Currently, there is no principled way to decide, whether a...

biorxiv.org
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Dynamic enhancer methylation drives cell-to-cell heterogeneity in ESCs cell.com/molecular-cell/full… Thanks to the labs of Rudolf Jaenisch, Yonatan Stelzer and Rick Young for a great collaboration! Great work, @LuckyYSong and @pvdb90 !
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Looking forward to learn about single-cell proteomics. #SCP2019 @slavovLab
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Our single-cell transcriptomics study of human fetal kidney development is now online @PLOSBiology journals.plos.org/plosbiolog…. Find the data here: semraulab.com/kidney . Shout-out to the Chuva Sousa Lopes lab @LUMC_Leiden for a great collaboration!
Image from SemrauLab (@SemrauLab)
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We are looking for a new outreach officer for the physics department @UniLeiden (fluency in Dutch required) universiteitleiden.nl/vacatu… . Thanks for spreading the word!
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Great time to be in #devbio with exciting papers from @AMartinezArias (go.nature.com/2BZn9Ny), @_CellySally_ (bit.ly/2OOm3fe) - both featuring cool in vitro models of development - and P. Keller @HHMIJanelia (bit.ly/2qbkqth) - amazing images of mouse dev. !
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Looking forward to some great stem cell research at #NYSCF18
Image from SemrauLab (@SemrauLab)
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Excited to have been awarded an @NWONieuws Vidi grant for research on bioelectricity in embryonic development and regenerative medicine!
Image from SemrauLab (@SemrauLab)
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Just learned about this cool method for smoothing single-cell RNA-seq data by Wagner et al. @ItaiYanai's lab biorxiv.org/content/early/20…
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Glad to have contributed to the Mikkers lab's study of repression of Sox2 through the lncRNA Sox2ot, now published @SciReports nature.com/articles/s41598-0…
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Congratulations! nitter.gq/stormkees/status/93005…
Kees Storm (@stormkees) profile pictureKees Storm@stormkees13 Nov 2017
Prof. dr. Kees Storm appointed as full-time professor in 'Theoretical Biophysics' and group leader Theory of Polymers and Soft Matter (TPS) tue.nl/en/university/departm… via @TUeindhoven
Image from Kees Storm (@stormkees)
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