Rong Fan
@RongFan8
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Harold Hodgkinson Professor of Biomedical Engineering and Pathology, Yale University https://t.co/kLH8WPg2c2 https://t.co/kbDKoBh9Ak https://t.co/MduFkomdDj
Connecticut, USA
Joined September 2017
Just picked up the beautiful offprint of our Patho-DBiT paper that was on the cover of @CellCellPress, highlighting its power to spatially explore molecular biology in human FFPE tissues 🤩🤩 . Congratulations to my phenomenal postdoc @Zhiliang_Bai and all amazing collaborators!!
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Spatial epigenome–transcriptome co-sequencing🤩🤩🤩Beyond excited to see it out today @Nature! Enjoyable collaboration between my lab @YaleBME @YaleSEAS @YaleMed and @GoCasteloBranco of @karolinskainst. The most informative tool for spatial multi-omics!!.
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Here comes "spatial-ATAC-seq"!!! A wonderful collaboration between my lab at @YaleSEAS and @GoCasteloBranco at @karolinskainst. #epigenetics #spatialomics #spatialbiology . Spatial profiling of chromatin accessibility in mouse and human tissues | Nature
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Thrilled to report Patho-DBiT, just published in Cell 😊. It allows us to directly “see” all kinds of RNA species on the same clinical FFPE tissue slide, including mRNA, miRNA, snRNA, snoRNA, tRNA, etc, and splicing isoforms, genetic alterations (SNV, CNV, etc). Really a fun,
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Spatial-CUT&Tag! @ScienceMagazine, unfolding a new chapter of #spatialomics 🤗 . From my phenomenal postdoc @DengYanxiang of @YaleSEAS.@YaleBME, @yalepathology @YaleMed @YaleCancer.Thanks to awesome collaborators @GoCasteloBranco @marekbartosovic @PKukanja
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Thrilled to see our new paper out in @NatureBiotech . Spatial-CITE-seq: spatially resolved co-indexing of transcriptome and epitopes for multi-omics sequencing. Big shoutout to Yang Liu, my former postdoc @YaleBME and now assistant professor of pathology and neurology @YaleMed !.
High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq
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Today is the day!!! Our DBiT-seq work is out in Cell. This is a fundamentally new approach in this space. It may unlock a wide range of spatial omics technologies. The limit is only our imagination ^_^.
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Today is the day 🤩. Thrilled to share our @Nature paper on Th2 function, CAR-T, & 8-year remission!! Huge team effort w/@GruppSteve @carlhjune @MelenhorstLab @Tang_Lab_EPFL, kudos to my postdoc @Zhiliang_Bai
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🤩🤩🤩 Spatial Omics fans, I am super excited to share our latest manuscript!!! 🤩🤩🤩 .#spatialomics #spatialbiology #singlecell . Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues .
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Spatial-ATAC-seq: spatially resolved chromatin accessibility profiling of tissues at genome scale and cellular level. #spatialomics #spatialbiology .Collaboration w/ @GoCasteloBranco @Halene_lab, Sai Ma, Joe Craft, and Mina Xu. Kudos to @DengYanxiang.
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Spatial Omics enthusiasts!! Spatial Proteomics is the Method of the Year 2024 .🤩🤩🤩.
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What an exciting week for CUT&Tag!!! After we published spatial-CUT&Tag in Science last week, Prof. Xiaowei Zhang lab demonstrated combining CUT&Tag and MERFISH to image, for example, 127 target H3K4me3 loci or 139 H3K27ac loci in mouse brain. Very cool!.
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Super-resolved single-cell atlas of a human lymphoma FFPE tissue slide profiled using our latest Patho-DBiT technology and the novel pipeline iStar developed by @DrMingyaoLi . Just too psyched to not share 🤩🤩
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Delighted to share our latest preprint "spatial-CITE-seq": spatially resolved high-plex protein and whole transcriptome co-mapping by NGS 😀😀😀. #spatialomics #spatialbiology.#singlecell.
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Thrilled to share Perturb-DBiT — spatial unbiased in vivo perturb-seq with genome-scale CRISPR libraries! Hope you enjoy reading it over the Thanksgiving week 🥰 Kudos to @AlevBaysoy, Xiaolong, Feifei, and Paul. & collaboration with @sidichen, Hongbo Chi.
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I am humbled to share this article @NatRevMCB 🎊🎊 Kudos to my phenomenal student @AlevBaysoy who put together this comprehensive & impressive review! Kudos to @Zhiliang_Bai, a super talented postdoc and rising star! Thanks a ton to @satijalab for the computational section!!!
Our newest & very comprehensive #NRMCBReview discusses both established and cutting-edge multi-omics technologies, and the optimization of throughput and resolution, modality integration, and accuracy. @AlevBaysoy, @Zhiliang_Bai, @RongFan8 & @satijalab .👉🏼
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We have multiple postdoc positions open. Should you be interested, please send a CV, a brief statement of research interests, and the names of 3 references to rong.fan@yale.edu. Thanks!!! .#spatialomics #spatialbiology #singlecell #cancer #immunology #postdocjobs #microfluidics
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Spatial Epigenome Sequencing.😀😀😀 Fantastic work from our team and kudos to super-talented postdoc @DengYanxiang.
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Honored and humbled to be inducted to NAI. Believe in technology innovation for science, humanity, inclusion and patients! @AcadofInventors #NAI2022
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So glad our single-cell multi-omics review article made the cover @NatRevMCB 🤩.Congrats @AlevBaysoy and @Zhiliang_Bai and thanks to @satijalab !!!
I am humbled to share this article @NatRevMCB 🎊🎊 Kudos to my phenomenal student @AlevBaysoy who put together this comprehensive & impressive review! Kudos to @Zhiliang_Bai, a super talented postdoc and rising star! Thanks a ton to @satijalab for the computational section!!!
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We are thrilled to receive the NCI Human Tumor Atlas Network (HTAN) center grant to map spatiotemporal dynamics of human lymphoma development, progression, transformation, and therapeutic response. 🤩🤩🤩. @MinaXu7 @Halene_lab @ZongmingMa @YaleCancer @YaleEngineering @YaleMed.
Congratulations to @RongFan8, Mina L. Xu, MD, Stephanie Halene, MD, Dr Med, @HaleneLab and @ZongmingMa, who received an @NIH #U01 award to create the Center for Human #Lymphoma Spatiotemporal Atlas (HuLymSTA). .@SmilowCancer @YaleMed @YNHH @yalepathology.
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Honored and humbled to be elected to National Academy of Inventors @AcadofInventors.Will continue my passion about innovation for science, humanity, diversity, and patients!!! Thx for the support from @YaleSEAS @YaleBME @YaleMed @YaleCancer @yalepathology.
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Thrilled to share two @biorxivpreprint papers from my lab and @StimulatedRaman, reporting on the SAME tissue section multi-modality spatial omics! 🤩🥳🙂
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Happy New Year!! Single-Cell Genomics 2024 Gordon Research Conference to be held in the breathtaking Swiss Alps! 🤩🤩🤩 We plan to finalize the program this month. If you are interested in presenting opportunities, please submit your abstracts ASAP! .
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Submitted 3 manuscripts, finished 1 NIH review panel, taught the most math-heavy part of my class (fluid mechanics, transport physics,. ), it's been a busy week but fulfiling 😀. Hope it is off to a great start of October and gonna do a lot of university services and traveling :)
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Making single-cell proteomics biologically relevant | Nature Methods.A great commentary, congrats Florian, Marvin and Matthias @labs_mann
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A call for spatial omics submissions | Nature Genetics 🤩🤩🤩 . So glad to see this Call for Submissions! The field is expanding & the impact is broad and far reaching! @NatureGenet
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Thrilled to see our Patho-DBiT paper is on the cover of Cell 🤩🤩🤩. Also truly honored to be included in this focus issue celebrating 50 years of Cell focusing on molecular biology. Patho-DBiT enables the exploration of rich molecular biology in clinical patient FFPE tissue.
For a perfect ending of our focus issues celebrating #50 years of Cell, we are diving into Molecular Biology!! .👉 Molecular biology is driven by curiosity about the details of life and has enabled dazzling achievements in virtually all areas of
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Thrilled to share this huge team work from @SU2C.Single CAR T Cell Multi-Omics Research Team @carlhjune @GruppSteve.@MelenhorstLab.@camara_pg. Big shout out and congratulations to my phenomenal postdoc Zhiliang!!!
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Awesome!!! The largest single-cell ATAC-seq dataset of 25 adult human tissues 👏.
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Immensely thrilled, honored, and humbled to receive the CMBE Momentum Award! Also, congratulations to @profmikeking and @NPeppas for the truly deserving recognitions! Looking forward to meeting you all at the CMBE annual meeting in January 2024!.
Congrats to the #CMBE2024 Award Winners! . @ CMBE_BMES is excited to announce the award-winning class for the 2024 Cellular and Molecular Bioengineering Conference. View the winners for each of the three award categories here:
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First “Spatial Omics” conference organized by a major academic/professional society! 🤩🤩 Terrific line up and beautiful place in Rome. Can’t wait to catch up with many friends there 🤗🤗🤗.@EMBO @embl #spatialomics
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SPATIAL PROTEOMICS is the Method of the Year 2024 🤩.
The wait is over!! We are thrilled to announce that we have chosen Spatial Proteomics as 2024’s Method of the Year! 🥳. For more on Spatial Proteomics and a road map to this special issue, please see this month’s Editorial or read on in this thread.
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Super excited about the 2024 Single-Cell Genomics Gordon Research Conference to be kicked off on Sunday, May 19!!! We are grateful to @StephenQuake, @JoakimLundeberg, Aviv Regev, and @JswLab for accepting our invite as the keynote speakers. It was
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To all my friends who are celebrating today, happy new year ( year of the dragon ) 🎉🎉🎉 !!!
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🤩🤩🤩 Spatial Multi-Omics for Cancer Systems Biology Workshop!! Organized by our NCI cancer systems biology center funded by @NCIsysbio. We will highlight talks by the leaders in the field as well as some hands-on computational data analyses 🤩🤩🤩
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Dr. Shu Chien just turned 93 and also just received a new R01. Extremely sharp and super kind! A true role model for generations 👏👏♥️♥️.
As we wrap up #NHLBI75, NHLBI wants to acknowledge Dr. Shu Chien, the longest active NHLBI-funded researcher. His studies on cell behavior related to blood flow have helped find new ways to prevent and treat certain types of heart disease. Learn more:
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🤩EXPANDING UNIVERSE OF #DBiT 🤩 .Now you can simultaneously map 9 or even more tissue sections in a single DBiT-seq #spatialomics run. Incredible work & beautiful data! Congrats .@Meier_Lab @celia4science @johwirth & team .@PioneerCampus @HelmholtzMunich
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Very humbled to share a bit of my own views about this beautiful work “spatial translatome mapping” from @WangXiaoLab and where the field is headed to in the future 😊. #spatialomics #spatialbiology #singlecell. Mapping RNA translation | Science
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we mapped alternative splicing over the entire hemisphere of mouse brain (FFPE) and discovered a lot of region-specific isoforms :)
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Terrific review article "unbiased spatial proteomics" from @labs_mann and colleagues!!! .#spatialomics #spatialbiology #proteomics #SingleCell.
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Congratulations @WangXiaoLab 🎉🎉🎉 Very elegant technology with unlimited potential!!! . Spatially resolved single-cell translatomics at molecular resolution | Science.
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Gonçalo @GoCasteloBranco and I are so excited to share our work on mapping spatial dynamics of brain development & neuroinflammation! 🤩🤩🤩Kudos to amazing postdocs Di Zhang and Leslie Kirby! 👍👍👍 @YaleEngineering @karolinskainst
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Looking forward to speaking at the Nature Conference Virtual Symposium on Spatial Biology! Thanks @rita_strack for the invitation 😊. @NaturePortfolio.@naturemethods @NatureGenet @NatureBiotech.@Nature.
Please join us for our free Technology Live Virtual Symposium on Spatial Biology this October 29th! Speakers include Rong Fan, Andrea Radtke, Long Cai, Sarah Teichmann and many more!
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Glad to see spatial multi-omics among "Seven technologies to watch in 2022" !!! Thanks Michael for the interview ☺️
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official debut of AtlasXomics -- the first and only company for spatial epigenomics! 🙂🙂🙂. Thanks @OGConferences. #spatialomics #spatialbiology #epigenomics #epigenetics #neuroscience #cancer #immunology #immunooncology
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Truly grateful to the @CMBE_BMES family!!!.
Prof. Rong Fan @RongFan8 from @YaleBme receiving the #CMBE2024 Momentum Award (sponsored by @aplbioeng). Congratulations!
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Truly grateful for the support from @YaleSEAS, @YaleOCR, @YaleCancer, @YaleMed . Will continue our commitment in technology innovation to advance science and help patients!!.
Best wishes to BME professor Rong Fan (@RongFan8) and his company Isoplexis on their IPO today (ISO - Nasdaq). The School is incredibly proud of how much you have accomplished and excited about your future developments!.
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Many thanks again to @CellCellPress for publishing DBiT-seq. Indeed, it is not another spatial transcriptome technology, but an enabling platform to unlock numerous "possibilities"!.
A #microfluidic-based method to deliver #barcodes to the surface of a #tissue slide that allows for #spatial-omics #sequencing @Yale @RongFan8 #bps2021
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Thanks so much Bill @YaleSEAS for highlighting our spatial-ATAC-RNA-seq paper out today in @nature . Love this picture ☺️. Have been collaborating with @GoCasteloBranco for over a year in two papers. We finally met in person last month in Stockholm :) .
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Spatial transcriptome sequencing of FFPE tissues at the cellular level! . This work was done before the lockdown. So glad we finally write it up to share with the spatial omics & spatial biology community ^_^ . #spatialomics #singlecell #NGS #Genomics .
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Dear Spatial Omics fans, so excited to announce Spatial Omics Seminar series 7 with a terrific lineup of speakers! @slinnarsson @ChenLabNeuro .@zhou_tianming @10xGenomics @WangXiaoLab @miltenyibiotec @lunaphore @fabian_theis @KC_DC_01 @Danidiin @Fiona_Ginty @dana_peer @AskaryLab
Dear Spatial Omics Community, .Kicking off the "Spatial Omics Seminar Series 7".Thrilled for our first speaker on 3/11/2022 (Prof @slinnarsson) at 2-pm EST. Excited to present the pioneers from Academia&Industry at the nexus of technology and computation. Co-hosted w/ @RongFan8
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Happy holidays from Fan Lab @ Yale BME 🥳🎉🥳. Picture of our group's holiday dinner last week. Also, a farewell party for @DengYanxiang who is gonna start soon as Assistant Professor at @Penn. Congrats🎉🎉! Yanxiang gave me this precious gift 🤩. I was truly touched! Thank you!
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Mind blowing development in single cell mass spec proteomics!!! Impressive talk by Matthias @labs_mann at @VIBConferences #SpatialOmics conference!
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Spatial Omics fans, please check out the full schedule of seminar series 4 with an impressive lineup of speakers in this field. Co-organized with @ahmetfcoskun . Join the seminar at (PWD: 109379). #spatialomics #spatialbiology #genomics #transcriptomcis
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Dear Spatial Omics fans, our seminar series 6 is kicking off next week. See the terrific lineup of speakers @ResolveBioSci, @vizgen_inc, @ACDbio, @spatialgenomics, @ABoettiger, @JeffSpraggins, @NanoPOTS_SCP, @MichaelYGerner, @ColeTrapnell, @IoaVlachos, @Lu_Wei8, @KellyStevensLab.
After a summer break, Spatial Omics Seminar Series- 6 is kicking off next Friday (9/3)!. A unique mix of industry leaders and pioneers in Academia. Registration is at Co-organized with @RongFan8
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Enjoyed so much the visit to Basel 🇨🇭 to speak at @Roche Institute of Human Biology (IHB). So glad to catch up with @TheLutolfLab @GrayCampLab and meet new friends! An old Chinese saying is “auspicious snow heralds a year of good harvests”. 😊 🥳 wishing you all a prosperous and
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Fan Lab warmly wishes you a joyful holiday season! We truly appreciate the continued support and trust of our friends and collaborators. May the new year be filled with limitless energy, inspiration, and even greater success! ☀️🥰🎊
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Thrilled to receive this NIH SenNet U54 grant and thanks so much Yale Cancer Center and School of Medicine for the support!!!.
Congratulations to .@RongFan8 & @Halene_lab awarded a 5-year @NIH_CommonFund grant to launch a Tissue Mapping Center for Cellular Senescence to study human lymphoid organs. @SmilowCancer @YaleMed @YNHH @YaleSEAS @yalepathology @oncoalert
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Spatial Omics Seminar Series 1 -- dear friends, if you are interested in this emerging field, please check out our online seminar series scheduled for every Friday at 3pm. . Also see schedule attached. Today, Jon Patsenker of Yale discussing IMC!
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Our latest work (although have been working on it for two years😜) to use single-cell sequencing to understand the immune function modules of CAR-T cells essential for achieving long term remission in ALL patients.
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Truly thrilled to receive this award! I am so grateful for the Class '61 alum and their support of cancer research!.
We are proud to announce @RongFan8 and Dr. Shangqin Guo @GuoLabatYale as recipients of the 2021 Class of '61 Cancer Research Awards in recognition of their accomplishments in #cancerresearch. @SmilowCancer @YaleMed @YNHH.
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Life is like the tide, always changing. Embrace the inevitable waves and navigate through them with grace, confidence, and joy😊
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Dear friends, please check out the Spatial Omics Seminar series 2 schedule filled with a panel of terrific speakers and exciting talks. Join the seminar using the Zoom link (Password: 109379). Looking forward to seeing you this Friday at 3pm! -Rong
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DBiT-seq protocol. Hope this is gonna be very helpful for anyone interested in adopting this technology 😀.
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Thanks so much to the Lasker Foundation for a shout-out about our work on spatial histone modification sequencing!.
Scientists have been able to profile #epigenetic modifications in individual cells, but not within their tissue—until now. Using a new method, they discovered epigenetic control of spatial patterning in the mouse brain. @RongFan8 @DengYanxiang .
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Congratulations again Dr. Jun Hee Lee! Ultra-high resolution spatial transcriptome sequencing!!.
New resource now online! Seq-Scope achieves sub-micron resolution spatial transcriptomics, enabling the visualization of transcriptomic heterogeneity at cellular and subcellular levels.
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Immensely enjoyable visit to Johns Hopkins Biomedical Engineering!!! Thank you Josh and Jean for inviting me, and my greatest pleasure to see many friends and get to know new ones! 😍🤩🥳.
Amazing hosting Single cell and Spatial Omics Guru Extraordinaire @YaleMed @YaleBme Prof. Rong Fan for our @JHUBME Seminar Series today!. Thanks for taking me up on the invite. It was an amazing talk and visit! @HopkinsMedicine @HopkinsEngineer
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3D tumor genomics!!!.
CODA day!.The CODA team at @JohnsHopkins maps pancreatic precursor lesions in 3D and at single-cell level. First 3D spatial genomic maps of large tissue samples. A human pancreas contains a staggering ~1000 lesions, some showing multifocality. Here:
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Congratulations Goncalo and team! Single cell sequencing enables patient stratification and precision medicine!.
An snRNA-seq atlas of #MultipleSclerosis brains is presented in @NeuroCellPress today by KI professor @GoCasteloBranco and colleagues. Patient-specific glial gene expression patterns stratify MS patients, supporting precision medicine approaches for #MS.
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beautiful data and excellent quality!! Seems like we need to update our own lab’s spatial-ATAC-seq protocol now 😊.
🚀 Unveiling the power of spatial genomics! Our cutting-edge spatial ATAC-seq platform sets new benchmarks in quality with insight into unique spatial regulatory elements in the spleen. Start exploring here: #SpatialGenomics #ResearchInnovation
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Impressive computational pipeline for spatial transcriptomics -- ClusterMap, which "precisely clusters RNAs into subcellular structures, cell bodies, and tissue regions in both two- and three-dimensional space" demonstrated in diverse tissue types .
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Single cell transcriptomes of ∼17,000 cells from 18 primary or early-relapse HCC cases. Early-relapse tumors have reduced levels of regulatory T cells, increased dendritic cells (DCs), and increased infiltrated CD8+ T cells, compared with primary tumors.
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Wow!! Amazing keynote talk by Prof. Xiaowei Zhuang! Glad to be in this picture chatting with Xiaowei 😊.
Our keynote speaker Xiaowei Zhuang delivered an outstanding presentation-“Spatially resolved single-cell genomics & cell atlas of the brain” at #CSSingleCells23. @Harvard #icon #spatialtranscriptomics #MERFISH
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Wow, a jaw-dropping spatial transcriptomics technology! Still based on the solid phase barcoded RNA capture method, but with the "nominal" spot size as small as 220nm. I thought the race to ultra high spatial resolution transcriptomics has started, but seems it is almost over 🤗.
Large field of view-spatially resolved transcriptomics at nanoscale resolution #bioRxiv.
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Must read -- a comprehensive review of spatial profiling technologies, by three awesome friends and our previous #spatialomics seminar speakers @Prof_Lundberg, @hoheyn and Jeff Moffitt!
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DBiT-seq - in-tissue barcoding for spatially revolved whole transcriptome sequencing at cellular level - .so much love this overlay of FFPE tissue image and spatial clustering map :)
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The best birthday 🥳 fun: enjoying the fantastic talk by an amazing scientist I truly admire Steve Henikoff at the #EMBLchromatin conference in the beautiful city Heidelberg! .@embl @EMBLHeidelberg
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Our efforts to understand the immune signaling programs in CAR engineered T cells and what we can learn from that to better engineering CAR-T therapy in the future. Thanks for all the wonderful collaborators @carlhjune @GruppSteve @MarcelaMaus @camara_pg and Jos Melenhorst.
New #JITC article: Single-cell multiomics dissection of basal and antigen-specific activation states of CD19-targeted CAR T cells @GruppSteve @RongFan8 @MarcelaMaus @carlhjune
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Extremely excited to join the @NCIHTAN consortium!!! Here is how we started our first Yale HTAN HuLymSTA center meeting 🥰. with @MinaXu7 @Halene_lab @ZongmingMa . @YaleCancer @YaleEngineering @YaleMed
The @Yale #HTAN Center, with a team led by @RongFan8, @Halene_lab, @ZongmingMa, & @MinaXu7, is constructing a comprehensive spatiotemporal molecular and cellular atlas of human #lymphomas as a resource for mechanistic discovery.
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So glad to see my former postdoc @DengYanxiang, Assistant professor at UPenn, coming back for the @YaleBME 20th anniversary reunion. Picture with Yanxiang and some of current Fan lab students @FarzadNegin, Jungmin Nam, @archie_enninful, @AlevBaysoy . 🙂
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Our lab has long-standing interest in GBM. It is such a complex, heterogenous, and deadly disease despite the huge breakthroughs in cancer research over the past 50 years. Much more to do for our patients!.
Dr. Rong Fan (@RongFan8) et al. @Yale #CancerTEC are developing a #TissueEngineered 3D microvascular niche-on-a-chip model to investigate #BrainTumor cell invasion and response to therapy. #BTSM
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Enjoying 2024 CMBE conference in San Juan PR is an unbelievable way to start the new year 🤩😊🎊.Amazing science and stunning view! You can see how psyched I am :) thanks to this amazing @BMES_CMBE SIG community!!
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Huge congratulations Carl 🍾️🎉👏. Penn Medicine’s Carl June to receive 2024 Breakthrough Prize in Life Sciences | Penn Today
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Thrilled to be back here again @sangerinstitute, talk about science with @bayraktar_lab, and then enjoy a cup of cappuccino 😋 at my favorite coffee shop.
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Deeply honored & humbled to be selected for the 2023 Benjamin Highman Lectureship at UC Davis Health Department of Pathology🥰. Looking forward to catching up with old friends and meeting new fields there next week #singlecell #sptialomics #spatialbiology
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Another ultra high resolution Spatial Transcriptomics approach! In 2021, we have Stereo-seq, Seq-scope, and now PIXEL-seq !.
New preprint from @GuLiangcai introducing PIXEL-Seq, which creates high-res oligo arrays from polony gels. Performs spatial transcriptomics at 1um resolution with impressive sensitivity:
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Fan lab @YaleBME had a lot of fun at #BMES2023 in Seattle 😀😀😀. Thanks to conference chairs @USCSysBio_Lab @kellystevenslab and @Prof_Harley, and my track co-chair @veiseho! Also, @profmikeking and @creinhartking for your leadership @BMESociety ! See you all 2024 in Baltimore!
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