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How to use RNA velocity to infer cell trajectories? Check out CellPath, where we "connect" RNA velocity and detect representative trajectory paths in a population of cells. CellPath can find multiple trajectories with different start points. biorxiv.org/content/10.110… #SingleCell

Preprint alert! By harnessing differential activity of a DNA deaminase towards 5mC and chemically protected 5hmC, we can teach an old dog like bisulfite sequencing a new trick: quantitative 5hmC sequencing in single cells. doi.org/10.1101/2021.0…

Congratulations to all of the authors, especially first authors Emily Fabyanic & Peng Hu. Grateful to our close collaborators from Kohli Lab, Zhou lab Penn Genetics Penn Epigenetics.

MQuad preprint is up. It effectively detects mitochondrial variations for clonality analysis. We saw mtDNA variants are often complementary to nuclear SNVs or CNVs. Check it out with your scRNA, scDNA or scATAC data. biorxiv.org/content/10.110…

FRAME-tags: genetically encoded fluorescent markers for multiplexed barcoding and time-resolved tracking of live cells biorxiv.org/content/10.110…

After >2000 commits, I am thrilled to announce the release of dynamo 1.0.0! In this release, we pushed the limits of our continuous vector field approaches to develop an awesome set of techniques to enable functional and predictive analyses of (time-resolved)scRNA-seq experiments

Happy to announce our new project funded by the IGVF consortium & National Human Genome Research Institute. I am fortunate to collaborate with colleagues at Penn Medicine (Song and Ming Labs, Sarah Tishkoff | MagicEden CS 🪄, Kiran Musunuru Junwei Shi, Ziyue Gao, Wenli Yang) & University of Washington (Sreeram Kannan). 1/2

Come work with us to lead new single-cell & functional genomics projects. More info here: jobrxiv.org/job/university…

Please apply if you are interested in single cell genomics technologies

After 3.5+ years of perseverance, our dynamo paper is finally online in Cell today! Dynamo is an innovative and powerful framework of reconstructing continuous vector fields for mechanistic and predictive modeling of single cell fate transitions. Link: cell.com/cell/fulltext/…

Thrilled to see our single-cell DNA (hydroxy)methylome sequencing method out (rdcu.be/dkAMG) ! Interdisciplinary efforts from talented first authors: Emily Fabyanic (Emily's thesis project), Peng - Peng Hu, and Qi - Qi Qiu | 邱琦 !

Beautiful view from DiShui Lake in Shanghai

Eccrine sweat gland development ft. @dingwallaby, Reiko Tomizawa, Adam Aharoni, Peng Hu, Qi Qiu | 邱琦, Blerina Kokalari, Serenity Martinez, Joan Donahue, Daniel Aldea, Meryl Mendoza, Hao Wu | 吴昊 & kamberovlab (Penn Genetics) @PennSbdrc Penn Epigenetics tinyurl.com/5n6ebh6z

Excited to share our latest work: Deletion of hepcidin disrupts iron homeostasis and hematopoiesis in zebrafish embryogenesis journals.biologists.com/dev/article-ab…

Deletion of hepcidin disrupts iron homeostasis and hematopoiesis in zebrafish embryogenesis Read this Research Article by Wenyi Yang, Mingjian Peng, Liangbiao Chen and colleagues from Shanghai Ocean University: journals.biologists.com/dev/article/15…

🔥 New paper out! Hot temp = hot science: Heat triggers an alternative splicing switch in Kdm6bb, driving its nuclear translocation and flipping the sex fate in Nile tilapia. 👇 journals.plos.org/plosgenetics/a… #SexReversal #Epigenetics #Tilapia #Kdm6bb #GeneRegulation #ClimateBiology

Excited to share our work in Nature Communications We benchmarked metabolic RNA labeling chemistries for time-resolved scRNA-seq, enhancing detection of new RNA during zebrafish embryogenesis. 👉 rdcu.be/eujFN Many thanks to Hao Wu | 吴昊 and Qi Qiu | 邱琦 for their unwavering support.

Finally out! Single‐Cell Transcriptome Profiling Reveals Conserved IFNγ‐IL8 Signaling‐Induced Antibacterial Neutrophil States during Bacterial Infection - Zhai - Advanced Science - Wiley Online Library advanced.onlinelibrary.wiley.com/doi/10.1002/ad…

Beautiful view from Bodensee