https://danwagnerlab.org/resources daily 0.75 2025-03-13 https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1633459789169-KOQ4PXFUVOSF1IT4WSC7/25231.png Resources - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565292335357-BXRLDDANB81H56IMKNCX/Wagner2018.png Resources https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/b94d06ae-a4f2-44a9-96c1-d5831920ea75/StemCellParnassusSunset2.jpg Resources - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://danwagnerlab.org/contact daily 0.75 2022-12-13 https://danwagnerlab.org/publications daily 0.75 2021-06-23 https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1586201940462-2QYEMDS7701D4UIQKX2W/Screen+Shot+2020-04-06+at+12.38.41+PM.png Publications In this review, we discuss the differences between a gene expression trajectory and a cell lineage, and modern experimental methods for integrating these two complimentary aspects of cellular history. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565114968918-I780235OOAPK4FOCZDNL/May2011Cover.png Publications https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565158111860-EVCKTGD0KQ4NP78YBS2X/TSH_PCA.png Publications Genetic perturbations alter the positional identity of regenerating tissues (microfluidic transcriptional profiling + principal component analysis). D.Wagner, 2015. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565113365113-TJPOA5Y7TWB8G6100IDG/2018Cover.jpg Publications https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565290320867-4QKAJECJ5B6221MWH4PD/WagnerCellStemCell2012.jpg Publications Clones of planarian stem cells (red) generate precise numbers of (blue) epidermal progenitors. D.Wagner, 2012. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1586207241416-P4UEYDA1ZQ15JV3YC15E/Screen+Shot+2020-04-06+at+12.58.50+PM.png Publications Gene expression trajectories for somatosensory neurons, constructed using the STITCH algorithm. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565112850277-OA0RCYSVKTU2XCL88TMN/2018Breakthrough.jpg Publications https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1586206817480-T6HXAF95858TNB0PFWV4/Screen%2BShot%2B2020-04-06%2Bat%2B12.54.33%2BPM.jpg Publications Single-cell transcriptomics-based classification of cells differentiated in vitro, using reference states from the E9.5 mouse embryo. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565892604723-3RCICBQK58OT9SJ31ECM/GPSmix-R_collagen-G_DAPI.png Publications Patterning genes that drive regeneration polarity decisions (magenta) are expressed predominantly in muscle cell bodies (green). D.Wagner, 2013. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565370804331-XS0WXLKX1F43U2DYM9GE/Wagner2012_tFISH.jpg Publications Sequential early markers (green > yellow > magenta) of the epidermal lineage in planarians. D.Wagner, 2012. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565884916537-J5YGE97TK3P01W5GEQQC/6_d14_PI-BrdU_worm2-2_dorsalAnterior-ZOOM_Maximumintensityprojection-1.jpg Publications Recently born BrdU+ cells (magenta) in the planarian epidermis. D.Wagner, 2014. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565886234134-1PYFFT1IL9DLRHOXL32R/Screen_Merge.jpg Publications Two classes of mitotic stem cells (magenta & green) were identified in planarians using a first-generation single-cell transcriptomics method. D.Wagner, 2014. https://danwagnerlab.org/home-1 daily 1.0 2025-03-13 https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/41d778b8-6b12-455b-8302-b4e2a163b13b/IMG_6062.jpeg Home - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1592329138141-AK370IJITJJ3JCI4OAIC/GoldenGateParnassusArrow.jpg Home https://danwagnerlab.org/team daily 0.75 2023-12-27 https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1639950668461-YEIXDS91HR2UP497MX4F/Cambria+Chou-Freed.jpg Team - Make it stand out Cambria received her B.S. in Neurobiology at Brown University, where she worked in Prof. Gilad Barnea's lab on trans-Tango, a genetically-encoded system for tracing and manipulating neural circuits in flies. After graduating, she worked in Prof. Jesica Raingo's lab at the IMBICE in La Plata Argentina, studying GPCR regulation of voltage-gated calcium channel activity. Now a Biomedical Sciences Ph.D. student at UCSF, she works in the Barber and Wagner Labs studying intracellular pH dynamics in zebrafish neural crest development. Outside of lab, she enjoys dancing, hiking, reading, traveling, and hanging out at the park! https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1660351196661-5E8RCDL0W5NVXNH6YWMW/IMG_3983.jpg Team - Make it stand out Kevin is a DSCB graduate student at UCSF. He received his M.S. in Cell & Molecular Biology at SFSU in 2022 through the CIRM Bridges program and his B.S./B.A. in Molecular Biology/ Theoretical Mathematics at UCSC in 2019. For his Masters in the lab of Dr. Robert Blelloch, he screened for proteins essential for de novo enhancer activation. In his undergrad, he studied how transcription factor and nucleosome kinetics impact gene activation specificity under Dr. Hinrich Boeger. Now, he is broadly excited to learn/combine systems-level biology methods with his experience in molecular biology to study embryonic development. Outside the lab, Kevin enjoys cooking, hiking/camping, traveling, and listening to Frank Ocean! https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1593642903151-GCCBQROKQJK9G0QCZX4O/IMG_5887.jpg Team Nicole received her B.S. in Molecular Biology at the University of Puerto Rico, Río Piedras, and a Ph.D. in Biology at Massachusetts Institute of Technology. As a Ph.D. student, she studied synapse plasticity due to changes in the activity of two neurons with one post-synaptic target in the fruit fly. Now, she is working on zebrafish brain development, focusing on neuronal activation and maturation. Nicole is also passionate about science education and an advocate for diversity in science. Outside the lab, she loves salsa dancing, creating exciting cocktails, and enjoying the sun. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1611007116847-TM63DOPBQZ7FNW1ZX6JJ/18489811_1510322652345809_2770457434653625649_ocrop.jpg Team Chris earned his bachelor’s in Biochemistry and Molecular Biology at the University of California, Davis. During his undergrad, he investigated how herpesviruses usurp control over the host cell nucleus by altering nuclear architecture. He then did his gap years at UCSF where he worked on understanding how tissues are built in the embryo and how failures in this process can lead to birth defects such as cleft palate. Now as a first year PhD student in the program for Developmental and Stem Cell Biology, he is interested in uncovering unifying mechanisms that cells implement to make decisions that ultimately result in developmental processes that are both robust and precise. In his free time, Chris enjoys being outdoors whether that is hiking in the Marin Headlands, skiing in Lake Tahoe, or playing soccer in Golden Gate Park. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1660351083811-GEWIUXRECY7A2HBA5FVD/8C4D5F1C-7E73-4BA5-A0B9-90BA292DE05A.jpg Team - Make it stand out Jay earned their bachelor’s in Biophysics and Gender, Sexuality, and Feminist Studies from Duke University in 2020. There, they investigated mechanisms of germline stem cell niche exit and mechanical properties of the gonadal basement membrane during ovulation in C. elegans. They began their MD-PhD at UCSF in 2020 and developed evidence-based guidelines for gender- and sex-inclusivity in clinical documentation and medical education during their preclinical years. As a graduate student in Developmental and Stem Cell Biology, Jay is co-advised by Dan Wagner and Diana Laird; they aim to leverage single cell transcriptomics and developmental lineage tracing to understand clonal dynamics in the developing germline in vitro and in vivo. Outside the lab, Jay loves cooking diverse cuisines and birding and hiking around the Bay Area with their partner. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1660350672902-3O1A6YJ1E1C3FX87V2ML/IMG_8805.jpg Team - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1603214141493-8MFUTNSFWXUHK5XEZXP9/Fake%2BIrena.jpg Team Irena earned her B.S. in Molecular, Cell, and Developmental Biology at UCLA in 2019 and is now a DSCB graduate student at UCSF. Previously, she studied stem cell metabolism and worked to understand how nutrient sources like glutamine drive early germ layer development. Broadly, she hopes to continue to understand the intrinsic and extrinsic signals that govern development. Outside the lab, Irena is an avid moviegoer and food enthusiast. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/5b88acee-71fa-4c52-9afa-0f4f45c4eeff/yingxin_headshot.jpg Team - Make it stand out Yingxin earned her B.S. in Animal Science in 2019 and her Ph.D. in Animal Biology at the University of California, Davis, in 2023. During her Ph.D. career at the Genomic Variation Laboratory, she applied RAD sequencing to designate the taxonomy and conserve the genetic diversity of wild fish populations. She is currently committed to advancing aquaculture and husbandry practices for zebrafish and is enthusiastic about exploring the intricacies of single-cell sequencing technology. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1664923588089-JO7D0GNC0XYIRWX7ODE5/Hannah-Greenfeld-5397_reduced.jpg Team - Make it stand out Hannah received her B.S. from the University of Wisconsin – Madison and completed her PhD at the University of Pennsylvania. As a PhD student in Mary Mullins’ lab, she studied how BMP signaling was interpreted to pattern the dorsal-ventral body axis during gastrulation. Now in the Wagner lab, Hannah is investigating how morphogen signaling is decoded to pattern the neural tube. When outside the lab, she enjoys playing racket sports and terrible television. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1633386696162-X30TMHRLHP0O5IVLFNY8/DEW_210822_1_edit_reduced.jpg Team https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1603214201930-A7BNBQA5UALTRS0ZSLHJ/Photo%2Bof%2BHaley.jpg Team Haley received her B.S. from the University of Pittsburgh in 2018 and is now a first year DSCB graduate student at UCSF. She’s broadly interested in using single cell genomics tools to study embryonic development. Outside the lab, she can be found running in the Marin headlands or cycling around San Fran. https://danwagnerlab.org/research daily 0.75 2020-04-06 https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565133823492-26D67Q6QU1V2TZPZKIYE/ezgif-4-380900bbc84f.gif Research - Collection https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1582253662782-AYYQEQI74ZEBIRC9TXJY/20x_191217-HCR3_DAPI_488-neurog1_546-cdh2_647-elavl3_zstack2_DAPIgrey_labels600bright.gif Research Triple-FISH labeling of transcripts defining stages of neural differentiation in the zebrafish CNS. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565133533097-K89F97POILWK34YY059Z/ezgif-4-9e4c9114c9cc.gif Research - Cell CAPTURE https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565276325577-AW7MF1POXQ620DRDQBN6/TracerSeq3.png Research 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https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565274890269-EEA9JKU68N5PBERV2V3E/ZebrafishStateManifold2.png Research https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565131715189-76HYE5HROIMWUREDLQ2X/DeviceDiagram.png Research https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1565281989496-LIPYBD4ZEFP2M4BULI44/PerturbMap1.jpg Research https://danwagnerlab.org/opportunities daily 0.75 2024-09-05 https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/8a63f093-9fec-4f7b-b570-6196db1cdbab/ezgif.com-crop.gif Opportunities - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1588715048441-ZWPTPBGZ49SJU3QKOEVS/ParnassusRMB_Feb2020-cropped.jpg Opportunities https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1588715096818-WHVL7QALG985YEE1A1PK/ParnassusRMB_October2019+%28daniel.wagner%40ucsf.edu%29.jpg Opportunities https://danwagnerlab.org/lab-events daily 0.75 2025-03-13 https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1634763897777-1H7KNR9TS8K6GJYQHX5N/IMG_3269.jpg Lab Events https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1634763897472-RO9BYTSKQCN041MAFMS7/IMG_3266.jpg Lab Events https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1634763898774-4KC45RCNM67JTXH8MDJE/IMG_3263.jpg Lab Events https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1634763901811-C1EM8G7OOJXF8F1BNKQG/IMG_3256.jpg Lab Events https://images.squarespace-cdn.com/content/v1/5d06fa45ff19610001852d21/1634763901552-C1YOTSGP8OYIXAEYEL17/IMG_3254.jpg Lab Events 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