Single Cell Biology Publications

Single Cell Biology Collaborations

Note there are numerous publications that have used our services, and given Acknowledgement, without listed authorship from a Single Cell Biology Laboratory team member. These are too challenging for us to track and thus are not listed here.

bold = Single Cell Biology team member

  1. Patience Mukashyaka, Pooja Kumar1, David J. Mellert, Shadae Nicholas, Javad Noorbakhsh, Mattia Brugiolo, Elise T. Courtois, Olga Anczukow, Edison T. Liu1, Jeffrey H. Chuang. Cellos: High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology Nature Communications (2023). In press
  2. Aaron MichaelTaylor, Patrick Kwok ShingNg, Jeffrey M.Harder, ParveenKumar, Alissa M.Dzis, Nathaniel L.Jillette,  AndrewGoodspeed, AveryBodlak, QianWu, Michael S.Isakoff, JoshyGeorge, Jessica D.S.Grassman, DianeLuo, William F.Flynn,  Elise T.Courtois, PaulRobson, MasanoriHayashi, Alini TrujilloPaulillo, Silvia Regina Caminadade Toledo, Fabiola SaraBalarezo, Adam D.Lindsay, BangHoang, Ching C.Lau. BioRxiv (2023) 2023.11.01.565008; doi: https://doi.org/10.1101/2023.11.01.565008
  3. Jain, S., Pei, L., Spraggins, J.M. … , Elise. T. Courtois, W.F. Flynn, S. Sivajothi,… , et al. 2023. “Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)”. Nat Cell Biol 25, 1089–1100 (2023). https://doi.org/10.1038/s41556-023-01194-w PMID: 37468756
  4. Paul Robson; Santhosh Sivajothi; Ramalakshmi Ramasamy. 2023. “OMAP-8: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Placenta with Imaging Mass Cytometry (IMC), v1.0.” DOI: 10.1038/nmeth.2869 PMID: 24584193 https://doi.org/10.48539/HBM375.WFJN.332
  5. Santhosh Sivajothi, Emily Soja, William F Flynn, Elise Courtois " Tissue Sectioning Guidelines (FFPE) - CODEX/PhenoCycler V.2" 2023 DOI:10.17504/protocols.io.eq2ly7xoqlx9/v2
  6. Enkhmandakh, B., P. Joshi, P. Robson, A. Vijaykumar, M. Mina, D. G. Shin, and D. Bayarsaihan. 2023. "Single-cell Transcriptome Landscape of DNA Methylome Regulators Associated with Orofacial Clefts in the Mouse Dental Pulp." Cleft Palate Craniofac J: 10556656231172296. DOI: 10.1177/10556656231172296 PMID: 37161276
  7. Olivier B Poirion, Wulin Zuo, Catrina Spruce, Sandra L Daigle, Ashley Olson, Daniel A Skelly, Elissa J Chesler, Christopher L Baker, Brian S White 2023. "Enhlink infers distal and context-specific enhancer-promoter linkages[SD1] DOI: 10.1101/2023.05.11.540453 PMCID: PMC10197707 PMID: 37214950
  8. Abdelfattah, N., P. Kumar, C. Wang, J. S. Leu, W. F. Flynn, R. Gao, D. S. Baskin, K. Pichumani, O. B. Ijare, S. L. Wood, S. Z. Powell, D. L. Haviland, B. C. Parker Kerrigan, F. F. Lang, S. S. Prabhu, K. M. Huntoon, W. Jiang, B. Y. S. Kim, J. George, and K. Yun. 2022. "Single-cell analysis of human glioma and immune cells identifies S100A4 as an immunotherapy target." Nat Commun 13 (1): 767. DOI:10.1038/s41467-022-28372-y PMID:35140215 PMCID: PMC8828877
  9. Barroso, M., M. G. Chheda, H. Clevers, E. Elez, S. Kaochar, S. E. Kopetz, X. N. Li, F. Meric-Bernstam, C. A. Meyer, H. Mou, K. M. Naegle, M. F. Pera, Z. Perova, K. A. Politi, B. J. Raphael, P. Robson, R. C. Sears, J. Tabernero, D. A. Tuveson, A. L. Welm, B. E. Welm, C. D. Willey, K. Salnikow, J. H. Chuang, X. Shen, and Shree Bose. 2022. "A path to translation: How 3D patient tumor avatars enable next generation precision oncology." Cancer Cell 40 (12): 1448-1453. DOI:10.1016/j.ccell.2022.09.017 PMCID: PMC10576652 PMID: 36270276
  10. Yuliana Tan, Diane Luo, Suleyman Bozal, Paul Robson, Elise Courtois "Human endometrium and endometriosis tissue dissociation for single-cell RNA sequencing" DOI: 10.17504/protocols.io.bvy8n7zw
  11. SenNet Consortium … , Elise. T. Courtois,… , P. Robson, et al., 2022. "NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health." Nat Aging 2 (12): 1090-1100. DOI: 10.1038/s43587-022-00326-5 PMCID: PMC10019484 PMID: 36936385
  12. Martinek, J., J. Lin, K. I. Kim, V. G. Wang, T. C. Wu, M. Chiorazzi, H. Boruchov, A. Gulati, S. Seeniraj, L. Sun, F. Marches, P. Robson, A. Rongvaux, R. A. Flavell, J. George, J. H. Chuang, J. Banchereau, and K. Palucka. 2022. "Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization-dependent phenotypes and function." Cell Rep Med 3 (5): 100621. DOI:10.1016/j.xcrm.2022.100621 PMCID:PMC9133468 PMID: 35584631
  13. Martinek, J., T. C. Wu, L. Sun, J. Lin, K. I. Kim, F. Marches, P. Robson, J. George, and K. Palucka. 2022. "Multiplex immunofluorescence-guided laser capture microdissection for spatial transcriptomics of metastatic melanoma tissues." STAR Protoc 3 (4): 101698. DOI:10.1016/j.xpro.2022.101698 PMCID: PMC9519630 PMID: 36149794
  14. Pandey, R. S., M. P. Krebs, M. T. Bolisetty, J. R. Charette, J. K. Naggert, P. Robson, P. M. Nishina, and G. W. Carter. 2022. "Single-Cell RNA Sequencing Reveals Molecular Features of Heterogeneity in the Murine Retinal Pigment Epithelium." Int J Mol Sci 23 (18). DOI:10.3390/ijms231810419 PMCID:PMC9499471 PMID:36142331
  15. Tan, Y., W. F. Flynn, S. Sivajothi, D. Luo, S. B. Bozal, M. Davé, A. A. Luciano, P. Robson*, D. E. Luciano*, and E. T. Courtois*. 2022. "Single-cell analysis of endometriosis reveals a coordinated transcriptional programme driving immunotolerance and angiogenesis across eutopic and ectopic tissues." Nat Cell Biol 24 (8): 1306-1318. *corresponding authors DOI: 10.1038/s41556-022-00961-5 PMCID: PMC9901845 PMID: 35864314
  16. Yuliana Tan, D. Luo, S. B. Bozal, P. Robson, and E. T. Courtois. 2022. "Human endometrium and endometriosis tissue dissociation for single-cell RNA sequencing." Protocols.io. DOi: 10.17504/protocols.io.bvy8n7zw
  17. Varn, F. S., K. C. Johnson, J. Martinek, J. T. Huse, M. P. Nasrallah, P. Wesseling, L. A. D. Cooper, T. M. Malta, T. E. Wade, T. S. Sabedot, D. Brat, P. V. Gould, A. Wöehrer, K. Aldape, A. Ismail, S. K. Sivajothi, F. P. Barthel, H. Kim, E. Kocakavuk, N. Ahmed, K. White, I. Datta, H. E. Moon, S. Pollock, C. Goldfarb, G. H. Lee, L. Garofano, K. J. Anderson, D. Nehar-Belaid, J. S. Barnholtz-Sloan, S. Bakas, A. T. Byrne, F. D'Angelo, H. K. Gan, M. Khasraw, S. Migliozzi, D. R. Ormond, S. H. Paek, E. G. Van Meir, A. M. E. Walenkamp, C. Watts, T. Weiss, M. Weller, K. Palucka, L. F. Stead, L. M. Poisson, H. Noushmehr, A. Iavarone, R. G. W. Verhaak, and GLASS Consortium. 2022. "Glioma progression is shaped by genetic evolution and microenvironment interactions." Cell 185 (12): 2184-2199.e16. DOI:10.1016/j.cell.2022.04.038 PMCID: PMC9189056 PMID: 35649412
  18. Wang, L., B. Wang, N. S. Gasek, Y. Zhou, R. L. Cohn, D. E. Martin, W. Zuo, W. F. Flynn, C. Guo, E. R. Jellison, T. Kim, L. G. P. Langhi Prata, A. K. Palmer, M. Li, C. L. Inman, L. S. Barber, I. M. A. Al-Naggar, W. Du, Kshitiz, G. A. Kuchel, A. Meves, T. Tchkonia, J. L. Kirkland, P. Robson, and M. Xu. 2022. "Targeting p21CIP1 highly expressing cells in adipose tissue alleviates insulin resistance in obesity." Cell Metab 34 (1): 186. DOI:10.1016/j.cmet.2021.11.002 PMCID: PMC8732323 PMID:34813734
  19. G. A. Perry, S. L. Daigle, P. Gabriel, D. Luo, J. Grassmann, W. F. Flynn, and E. T. Courtois. 2022. “Nuclei Prep from Frozen Mouse Brain Tissues with Optional Sucrose Column for single nuclei RNA‑seq”. Procotols.io. DOi:10.17504/protocols.io.81wgb657ylpk/v1
  20. Elvira Forte Is a corresponding authorMirana RamialisonHieu T NimMadison MaraJacky Y LiRachel Cohn Sandra L Daigle Sarah BoydEdouard G StanleyAndrew G ElefantyJohn Travis HinsonMauro W CostaNadia A RosenthalMilena B Furtado "Adult mouse fibroblasts retain organ-specific transcriptomic identity" 2022 DOI:10.7554/elife.71008 PMCID: PMC8959603 PMID:35293863
  21. C.M.Cleary, B.M.Milla, F.-S.Kuo, S.James, W.F.Flynn, P.Robson, D.K.Mulkey (2021) Somatostatin-expressing parafacial neurons are CO2/H+sensitive and regulate baseline breathing. eLife, DOI: 10.7554/elife.60317 PMCID: PMC8169115 PMID: 34013884
  22. K.C.Johnson, K.J.Anderson, E.T. Courtois, A.D.Gujar, F.P.Barthel, F.S.Varn, D.Luo, M.Seignon, E.Yi, H.Kim, M.R.H.Estecio, D.Zhao, M.Tang, N.E.Navin, R.Maurya, C.Y.Ngan, N.Verburg, P.C.De Witt Hamer, K.Bulsara, M.L.Samuels, S.Das, P.Robson, R.G.W.Verhaak (2021) Single-cell multimodal glioma analyses reveal epigenetic regulators of cellular plasticity and environmental stress response. Nat Genet 53 (10): 1456-1468 DOI:10.1038/s41588-021-00926-8 PMCID:PMC8570135 PMID:34594038
  23. A.M.Pettinato, D.Yoo, J.Van Oudenhove, Y-S.Chen, R.Cohn, F.A.Ladha, X.Yang, K.Thakar, R.Romano, N.Legere, E.Meredith, P.Robson, M.Regnier, J.L.Cotney, C.E.Murry, J.T.Hinson (2021) Sarcomere function activates a p53-dependent DNA damage response that promotes polyploidization and limits in vivo cell engraftment. Cell Reports 35 DOI:10.1016/j.celrep.2021.109088 PMCID:PMC8161465 PMID:33951429
  24. C.Yu, J.Martinek, T-C.Wu, K.I.Kim, J.George, E.Ahmadzadeh, R.Maser, F.Marches, P.Metang, P.Authie, V.Oliveira, V.Wang, J.Chuang, P.Robson, J.Banchereau, K.Palucka (2021) Human KIT+ myeloid cells facilitate visceral metastasis by melanoma. Journal of Experimental Medicine 218 (6): DOI:10.1084/jem.20182163 PMCID: PMC8056753 PMID:33857287
  25. C.M.Gay, C.A.Stewart, E.M.Park, L.Diao, S.M.Groves, S.Heeke, B.Y.Nabet, J.Fujimoto, L.M.Solis, W.Lu, Y.Xi, R.J.Cardnell, Q.Wang, G.Fabbri, K.R.Cargill, N.I.Vokes, K.Ramkumar, B.Zhang, C.M. Della Corte, P.Robson, S.G.Swisher, J.A.Roth, B.S.Glisson, D.S.Shames, I.I.Wistuba, J.Wang, V.Quaranta, J.D.Minna, J.V.Heymach, L.A.Byers (2021) Patterns of transcription factor programs and immune pathway activation define four major subtypes of SCLC with distinct therapeutic vulnerabilities. Cancer Cell, 39:346-360.e7 DOI: 10.1016/j.ccell.2020.12.014 PMCID: PMC8143037 PMID: 33482121
  26. P.Bargagna-Mohan, G.Schultz, B.Rheaume, E.Trakhtenberg, P.Robson, S.Pal-Ghosh, M.A.Stepp, K.S.Given, W.B.Macklin, R.Mohan (2020) Corneal nonmyelinating Schwann cells illuminated by single cell transcriptomics and visualized by protein biomarkers. Journal of Neuroscience Research, 99:731-749 DOI:10.1002/jnr.24757 PMCID: PMC7894186 PMID: 33197966
  27. E.Forte, D.A.Skelly, M.Chen, S.Daigle, K.A.Morelli, O.Hon, V.M.Philip, M.W.Costa, N.A.Rosenthal, M.B.Furtado (2020) Dynamic Interstitial Cell Response during Myocardial Infarction Predicts Resilience to Rupture in Genetically Diverse Mice. Cell Reports. 30:3149-3163 DOI: 10.1016/j.celrep.2020.02.008 PMCID: PMC7059115 PMID:32130914
  28. E.Forte, S.Daigle, N.A.Rosenthal (2020) Protocol for Isolation of Cardiac Interstitial Cells from Adult Murine Hearts for Unbiased Single Cell Profiling. STAR Protocols. DOI: 10.1016/j.xpro.2020.100077 PMCID: PMC7501728 PMID:33000003
  29. L.E.Mickelsen, W.F.Flynn, K.Springer, L.Wilson, E.J.Beltrami, M.Bolisetty, P.Robson*, A.C.Jackson* (2020) Cellular taxonomy and spatial organization of the murine ventral posterior hypothalamus. *corresponding authors eLife, DOI:10.7554/elife.58901 PMCID: PMC7595735 PMID:33119507
  30. D.Nehar-Belaid, S.Hong, R.Marches, G.Chen, M.Bolisetty, J.Baisch, L.Walters, M.Punaro, R.Rossi, C-H.Chung, R.Huynh, P.Singh, W.F.Flynn, J-A.Tabanor, N.Kuchipudi, A.Mejias, M.Collet, A.L.Lucido, K.Palucka, P.Robson, S.Lakshminarayanan, O.Ramilo, T.Wright, V.Pascual, J.Banchereau (2020) Mapping SLE heterogeneity at the single cell level. Nature Immunology, 21:1094–1106 DOI:10.1038/s41590-020-0743-0 PMCID: PMC7442743 PMID:32747814
  31. B.Wang, Z.Liu, V.P.Chen , L.Wang, C.L.Inman, C.Guo, Y.Zhou, T.Tchkonia, D.W.Rowe, G.A.Kuchel, P.Robson, J.L.Kirkland, M.Xu (2020) Transplanting cells from old but not young donors causes physical dysfunction in older recipients. Aging Cell, 19(3): DOI:10.1111/acel.13106 PMCID: PMC7059132 PMID:31971661
  32. C.A.Stewart, C.M.Gay, Y.Xi, S.Sivajothi, V.Sivakamasundari, J.Fujimoto, M.Bolisetty, P.M.Hartsfield, V.Balasubramaniyan, M.D.Chalishazar, C.Moran, N.Kalhor, J.Stewart, H.Tran, S.G.Swisher, J.A.Roth, J.Zhang, J.de.Groot, B.Glisson, T.G.Oliver, J.V.Heymach, I.Wistuba, P.Robson, J.Wang, L.A.Byers (2020) Single-cell analyses reveal increases in intratumoral heterogeneity following the onset of treatment resistance in small cell lung cancer. NatureCancer,1 :423–436 DOI:10.1038/s43018-019-0020-z PMCID: PMC7842382 PMID: 33521652
  33. J.Podojil, A.P.Glaser, D.Baker, E.T.Courtois, D.Fantini, Y.Yu, V.Eaton, S.Sivajothi, M.Chiang, A.Das, K.A.McLaughlin, P.Robson, S.Miller, J.Meeks (2020) Antibody Targeting of B7-H4 Enhances the Immune Response in Urothelial Carcinoma. OncoImmunology, 9(1), 1744897 DOI:10.1080/2162402x.2020.1744897 PMCID: PMC7185218 PMID:32363111
  34. E.Elyada, M.Bolisetty, P.Laise, W.F.Flynn, E.T.Courtois, R.A.Burkhart, J.A.Teinor, P.Belleau, G.Biffi, M.S.Lucito, S.Sivajothi, T.D.Armstrong, D.D.Engle, K.H.Yu, Y.Hao, C.L.Wolfgang, Y.Park, J.Preall, E.M.Jaffee, A.Califano, P.Robson*, D.A.Tuveson* (2019) Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts. Cancer Discovery, 9:1102-1123 *corresponding authors DOI:10.1158/2159-8290.cd-19-0094 PMCID:PMC6727976 PMID:31197017
  35. Gowthaman U, Chen JS, Zhang B, Flynn WF, Lu Y, Song W, Joseph J, Gertie JA, Xu L, Collet MA, Grassmann JDS, Simoneau T, Chiang D, Berin MC, Craft JE, Weinstein JS, Williams A, Eisenbarth SC. (2019) Identification of a T follicular helper cell subset that drives anaphylactic IgE. Science. 2019-08-01. DOI:10.1126/science.aaw6433 PMCID: PMC6901029 PMID:31371561
  36. Sharma M, Srivastava A, Fairfield HE, Bergstrom D, Flynn WF, Braun RE (2019) Identification of EOMES-expression spermatogonial stem cells and their regulation by PLZF. eLife. 2019-05-31. DOI:10.7554/elife.43352 PMCID: PMC6544432 PMID: 31149899
  37. L.E.Mickelsen, M.Bolisetty, B.R.Chimileski, A.Fujita, E.Beltrami, J.T.Constanzo, J.R.Naparstek, P.Robson*, A.C.Jackson* (2019) Single cell transcriptomic analysis of the lateral hypothalamic area reveals molecularly distinct populations of inhibitory and excitatory neurons. Nature Neuroscience, 22:642-656 *corresponding authors DOI:10.1038/s41593-019-0349-8 PMCID: PMC7043322 PMID: 30858605
  38. D.Zhu, Z.Zhao, G.Cui, S.Chang, L.Hu, Y.X.See, M.G.L.Lim, D.Guo, X.Chen, P.Robson, Y.Luo, E.Cheung (2018) Single-cell transcriptome analysis reveals estrogen signaling coordinately augments one-carbon, polyamine, and purine synthesis in breast cancer. Cell Reports, 25:2285-2298 DOI: 10.1016/j.celrep.2018.10.093 PMID: 30463022
  39. B.Rheaume, J.Amyeo, M.Bolisetty, M.Sajid, Y.Yang, K.Renna, L.Sun, P.Robson, E.Trakhtenberg (2018) Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes. Nature Communications, 9:2759 DOI:10.1038/s41467-018-05134-3 PMCID: PMC6050223PMID: 30018341
  40. D.A.Skelly, G.T.Squiers, M.A.McLellan, M.T.Bolisetty, P.Robson, N.A.Rosenthal, A.R.Pinto (2018). Single-cell transcriptional profiling reveals cellular diversity and intercommunication in the mouse heart. Cell Reports, 22:600-610. DOI: 10.1016/j.celrep.2017.12.072 PMID: 29346760
  41. N.Lawlor, J.George, M.Bolisetty, R.Kursawe, L.Sun, Siva.V, I.Kycia, P.Robson, M.L.Stitzel (2017) Single cell transcriptomes identify human islet cell signatures and reveal cell type-specific expression changes in type 2 diabetes. Genome Research, 27:208-222 DOI:10.1101/gr.212720.116 PMCID: PMC5287227 PMID: 27864352
  42. H.Li, E.T.Courtois, D.Sengupta, Y.Tan, S.L.Kong, W.S.Tan, M.H.Chew, K.H.Lim, L.Wee, A.Hillmer, I.B.Tan*, P.Robson*, S.Prabhakar* (2017) Reference component analysis of single cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nature Genetics, 49:708–718 *corresponding authors DOI:10.1038/ng.3818 PMID: 28319088