D. Zheng
@zhengdy
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Think more, talk less. Bioinformatics Genomics scientist, professor. Love life, brain & people.
New York City
Joined April 2009
😀announce a new release (v1.5) of our software for #scRNA-seq data integration. Yang has made quite a few changes to make #RISC/RPCI more memory efficient and faster. It can now handle > 1 million cells, to catch up where the field is moving 😀. More at
github.com
A R package for integrated scRNA-seq data analysis using the RPCI algorithm - bioinfoDZ/RISC
Thrilled and relieved this work, led by a talented postdoc Dr. Yang Liu, is finally out. We propose a new approach for integrating #scRNA-seq data from multiple samples. It is simply linear algebra, nothing as complicated as machine or deep learning. 1/3.
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Get new single cell data? Want to know which part of your pretty UMAP is “stable” and which part is more affected by hyper parameters? This little tool built by @RohanMisra may be handy.
shinyUMAP: an online tool for promoting understanding of single cell omics data visualization #biorxiv_bioinfo.
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Congrats @RohanMisra and @ferrenabio and thanks all reviewer’s excellent suggestions.
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Since reading the first scATACseq paper, I had been wondering if the reported difference from scRNAseq results is due to bioinformatic algorithms or biology. Finally we got a chance to look into this, by applying the same algorithm to both data types and their direct integration.
Binarized gene expression data can be concatenated with chromatin accessibility data for effective and integrated cell clustering @zhengdy @rohanmisra @EinsteinMed #BiotechNatureComms .
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RT @Claudia_Sahm: “Fifty years from now, you will want to be able to look in the mirror and know that you did what you thought was right, i….
federalreserve.gov
Thank you, President Eisgruber, for the opportunity to speak here today. Congratulations to the Princeton University class of 2025 on the tremendous achievemen
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RT @EinsteinMed: Yesterday, @EinsteinPHD honored the special connection between graduating Ph.D. students and their mentors during the 6th….
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Congratulations Tuomas, Xueqian for a fantastic work 🎉🎊 very grateful for the opportunity to contribute with former @EinsteinPhD student @ferrenabio.
Several years in the making (and aging), @Xueqian_Zhuang 's study on aging is out today @Nature. She finds, surprisingly, that aging suppresses tumorigenesis and stemness in the lung by promoting a functional iron insufficiency in the alveolar epithelium.
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RT @jsantoyo: scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison. #SingleCell #Tran….
academic.oup.com
Abstract. Single-cell transcriptomics profiling has increasingly been used to evaluate cross-group (or condition) differences in cell population and cell-t
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Congratulations to the 46 Ph.D. and M.D.-Ph.D. students who completed their qualifying exams this year and were awarded the M.S. degree from @EinsteinPhD. The students received their diplomas last week at the Qualification Jubilation ceremony held in Robbins Auditorium. #phdlife
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Despite how complex our brain is wired, we still believe or prefer simple stories or reasoning.
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RT @AnisHanna7: As Nick Frangogiannis has taught me, fibroblasts are often the cells that didn’t fit any other classification. A question t….
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Very happy to see this, congrats former PhD student Dr. Mingyan Lin and colleagues!! @EinsteinPhD
science.org
Despite continuous expansion of the RNA binding protein (RBP) world, there is a lack of systematic understanding of RBPs in the mammalian testis, which harbors one of the most complex tissue transc...
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Our latest contribution to a collaborative publication — Macrophages in the infarcted heart acquire a fibrogenic phenotype, expressing matricellular proteins, but do not undergo fibroblast conversion -
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RT @greally: Hiring in The Bronx, join our team:.Senior Bioinformatics Analyst. @EinsteinMed.
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RT @TuomasTammela: Thanks @NatureNV for covering our latest preprint on aging and lung cancer development alongside complementary findings….
nature.com
Nature - New research identifies some of the genes that could help to explain why lung cancer incidence rises with age but declines after the age of 75.
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RT @TuomasTammela: Excited to share our newest pre-print by Xueqian Zhuang on how aging suppresses tumorigenesis and stemness in the lung b….
biorxiv.org
Aging is associated with a decline in the number and fitness of adult stem cells[1][1]–[4][2]. Aging-associated loss of stemness is posited to suppress tumorigenesis[5][3],[6][4], but this hypothesis...
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Wonder if this bumblebee is thinking geez 🙄 I have to clean all these by myself, or 🤩 these food are all for me
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Biggest congratulations to Dr. Ferrena @ferrenabio for an outstanding thesis seminar and a very successful defense yesterday. It went so high and triggered 🔥 alarms that we had to move the defense outside the building
Monday, May 13, 2024 - Thesis Seminar: Alexander Ferrena, PhD Candidate, Clinical Investigation in the laboratories of Drs. Deyou Zheng and Bang Hoang,."Molecular and Clinical Implications of Skp2 Inhibition in Osteosarcoma".
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RT @MadsCapital: RIP Jim Simons."I did a lot of math. I made a lot of money, and I gave almost all of it away. That's the story of my life.….
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Happy to share an analysis pipeline that is developed in our group led by resident expert in the area @ferrenabio We have been using it for many projects and it saves a lot of time and guesswork when multi group comparisons are needed.
scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison #biorxiv_bioinfo.
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