Computational biologist. PI at Altos Labs. Formerly from the wonderful DBMI at the Harvard Medical School. Expressed thoughts and opinions are my own.
Joined October 2017
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30 Photos and videos
May 14
Lineage tracing with cell state readouts (scRNA-seq, etc.) offers a wealth of information! Navigating such data and extracting biological insights can be tricky, especially with sparse clonal sampling. Sergey's thread and our preprint describe a new analysis tool for such data:
May 5
(2) Meet (again) clone2vec – a method for building clonal embeddings. In short: it measures similarity between clones based on their distributions in gene expression space. Sounds simple, but apparently it's not.
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Ever stare at your spatial DE results and wonder if something's off? Segmentation errors might be the culprit. Our new paper shows how pervasive this problem is - and introduces a fix using matrix factorization of local molecular neighborhoods.
nature.com/articles/s41588-0…
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11 Dec 2024
As part of our embryo clonal tracing and perturbation efforts with @adameykolab, a quick twittorial from Sergey on generating stable and informative representations of clonal fate variations from sparse and noisy barcode-based lineage tracing data.
26 Nov 2024
(1) Hi, X!
Don't miss Igor's thread about our recent preprint, it’s a very cool reading! Here I will try to go a bit deeper into the computational part of the study — our new method clone2vec, how we developed it, what it does, and what it doesn't do. Grab a drink, and let's go!
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11 Dec 2024
Our pre-print with @adameykolab on continuous spectra of progenitor fates during mammalian development. Using multiplexed clonal tracing, mosaic perturbations, and robust computational representations, we look at spatial and temporal modulation of cell fates in mouse embryos.
21 Nov 2024
(1) How can we build complex structures from a limited set of progenitors and cell types? In our new preprint, we describe patterns of cell fate decisions during early development and (in some cases) identify molecular correlates of different behaviors. biorxiv.org/content/10.1101/…
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Great to be part of this collaboration with @baryawno and @KharchenkoLab among others!
Joint single-cell WGS/mRNA seq is an important tool to understand evolutionary processes in tumors!
4 Sep 2024
Transformation of fetal Schwann cell precursors (SCPs) may represent one possible mechanism of tumour initiation in #neuroblastoma with chromosome 17 aberrations as a characteristic element. New KI study published in Molecular Cancer @BioMedCentral. doi.org/10.1186/s12943-024-0…
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24 Sep 2024
Happy to see our work with Jimmie Ye's lab on coordinated variation of different cell types in healthy and diseased individuals published! At the core of it is the scITD tool for tensor decomposition, rotation and interpretation strategy. Great effort by @J_E_Mitchel et al.!
23 Sep 2024
Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition go.nature.com/47ARizC
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PeterK retweeted
11 Apr 2024
How to pick a problem. Today in @CellCellPress. 1/53
cell.com/cell/fulltext/S0092…
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10 Apr 2024
New preprint 🎉 led by @AervaI 👇! We introduce an approach to prioritize biological driver genes by recalibrating differential expression fold changes with population variance. This extracts new meaning out of DE analysis, which is a cornerstone of computational biology!
10 Apr 2024
Very happy to share our latest work from my postdoc with @tuuliel_lab on recalibrating gene expression changes relative to natural dosage variance: biorxiv.org/content/10.1101/…
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PeterK retweeted
2 Apr 2024
Just finished teaching another semester of genomic #datavisualization 🥳
Discover the awesome #dataviz made by students in the class for various #singlecell #spatialtranscriptomics data
Check out the course notes #Rstats code to explore for yourself: jef.works/genomic-data-visua…
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PeterK retweeted
14 Feb 2024
Our latest out today in @Nature. We profiled 12 million single cells from mouse embryos spanning gastrulation to birth, defined cell type tree from zygote to birth, and unexpectedly found crazy fast changes within first hour of extrauterine life. OA PDF: rdcu.be/dyDAg
6 Apr 2023
Excited to share our lab's latest preprint, led by @CXchengxiangQIU, @bethkarenmartin & Ian Welsh of @jacksonlab.
We set out to build a single cell roadmap for all of mouse prenatal development, from single cell zygote to free-living pup.
Preprint: tinyurl.com/2nhe4mm9 1/n
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PeterK retweeted
30 Jan 2024
Our latest collaboration on metastatic renal cell carcinoma to the bone is published @GenomeMedicine. the bone metastatic environment is not well-defined, hindering progress towards therapeutic targets. Our group developed a unique translational research model.
Congrats to our talented diverse team across @karolinskainst @harvardmed, @MGHCancerCenter led by @baryawno 👏
link.springer.com/10.1186/s1…
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PeterK retweeted
13 Dec 2023
Excited to share two new papers, published today in @Nature!
Check them out here:
(1) Slide-tags, a new method to unite single-cell and spatial profiling:
nature.com/articles/s41586-0…
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PeterK retweeted
13 Dec 2023
6 papers for ligand-receptor interaction for single-cell data 👇
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PeterK retweeted
12 Dec 2023
We are very excited to present a major breakthrough achievement – the de novo design of synthetic enhancers for selected tissues in fruit fly embryos in vivo using deep- and transfer learning, @deAlmeida_BPet al published today in @Nature nature.com/articles/s41586-0…. Thread 👇(1/N)
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PeterK retweeted
7 Dec 2023
Very excited to share two papers published today in @CellCellPress describing stem cell plasticity in CRC. (1/22)
cell.com/cell/fulltext/S0092…
cell.com/cell/fulltext/S0092…
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PeterK retweeted
7 Dec 2023
✨#ImmuneDictionary✨is out today in @Nature!
Paper nature.com/articles/s41586-0…
Software immune-dictionary.org
We created scRNA-seq dictionary of 17 immune cell types responding to 86 cytokines in vivo, discovered the immune system is far more complex than previously known 1/
ALT The Immune Dictionary is a large-scale compendium of single-cell transcriptomic profiles of more than 17 immune cell types in response to each of 86 cytokines in vivo, a reference for understanding the complex immune system. The image lists the 86 cytokines, representing almost all major cytokines in the immune system, studied in the dictionary. For more information, see our Nature (2023) publication "Dictionary of immune responses to cytokines at single-cell resolution": https://www.nature.com/articles/s41586-023-06816-9
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PeterK retweeted
7 Dec 2023
We profiled #scRNAseq of 386,703 cells and uncovered 17 immune cell types in lymph nodes.
Well-known cytokine-responsive genes, such as Il4i1 in response to IL-4, Tnfaip3 in response to TNF, are robustly upregulated in our dictionary.
#ImmuneDictionary 6/
ALT We profiled 386,703 single cells using scRNA-seq, identified more than 17 immune cell types in lymph nodes, and found well established cytokine-responsive genes are robustly upregulated in the dictionary. Fig 1b, c in Nature (2023) https://www.nature.com/articles/s41586-023-06816-9
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PeterK retweeted
23 Nov 2023
BARtab & bartools: an integrated Nextflow pipeline and R package for the analysis of synthetic cellular barcodes in the genome and transcriptome biorxiv.org/content/10.1101/…
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30 Oct 2023
Congrats to Teng on this outstanding effort to push the limits of allele-based CNV detection in order to characterize somatic variation in healthy tissues!
Aneuploidy is a defining feature of cancer cells, but is it also present in healthy normal tissues? In our paper out today on @NatureGenet, we report hundreds of mosaic chromosomal alterations (mCAs) found in diverse tissues from #GTEx. A thread (1/7)
nature.com/articles/s41588-0…
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PeterK retweeted
12 Oct 2023
Human brain atlas papers by @kimsiletti @MossiAlejandro @ka_wai_rine
@ErnestArenasSWE @EmelieBraun1 @MiriDanan Rebecca Hodge Trygve Bakken Ed Lein @LarsBorm Elin Vinsland Erik Sundström and many others. With a stunning double cover illustration by @IKapustova
12 Oct 2023
In 21 papers across Science, @ScienceAdvances, and @ScienceTM, researchers with the #BICCN consortium present an atlas of the human and nonhuman primate brain in unprecedented detail.
The results uncover the genetic organization of the human brain. scim.ag/4ro
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