Single Cell Publications

Selected Scientific Peer-Reviewed Publications Authored by SCBL Service Members

Bozal SB, Sjogren G, Costa AP, Brown JS, Roberts S, Baker D, Gabriel P, Jr., Ristau BT, Samuels M, Flynn WF, Robson P, Courtois ET. Development of an automated 3D high content cell screening platform for organoid phenotyping. SLAS Discov. 2024 Sep; 29(7):100182.

Enkhmandakh B, Joshi P, Robson P, Vijaykumar A, Mina M, Shin DG, Bayarsaihan D. Single-cell Transcriptome Landscape of DNA Methylome Regulators Associated with Orofacial Clefts in the Mouse Dental Pulp. Cleft Palate Craniofac J. 2024 Sep; 61(9):1480-92.

Mukashyaka P, Kumar P, Mellert DJ, Nicholas S, Noorbakhsh J, Brugiolo M, Courtois ET, Anczukow O, Liu ET, Chuang JH. High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos. Nat Commun. 2023 Dec 18; 14(1):8406.

Wang L, Wang B, Gasek NS, Zhou Y, Cohn RL, Martin DE, Zuo W, Flynn WF, Guo C, Jellison ER, Kim T, Prata L, Palmer AK, Li M, Inman CL, Barber LS, Al-Naggar IMA, Zhou Y, Du W, Kshitiz, Kuchel GA, Meves A, Tchkonia T, Kirkland JL, Robson P, Xu M. Targeting p21(Cip1) highly expressing cells in adipose tissue alleviates insulin resistance in obesity. Cell Metab. 2022 Jan 4; 34(1):75-89.e8.

Varn FS, Johnson KC, Martinek J, Huse JT, Nasrallah MP, Wesseling P, Cooper LAD, Malta TM, Wade TE, Sabedot TS, Brat D, Gould PV, Wöehrer A, Aldape K, Ismail A, Sivajothi SK, Barthel FP, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon HE, Pollock S, Goldfarb C, Lee GH, Garofano L, Anderson KJ, Nehar-Belaid D, Barnholtz-Sloan JS, Bakas S, Byrne AT, D'Angelo F, Gan HK, Khasraw M, Migliozzi S, Ormond DR, Paek SH, Van Meir EG, Walenkamp AME, Watts C, Weiss T, Weller M, Palucka K, Stead LF, Poisson LM, Noushmehr H, Iavarone A, Verhaak RGW, The GLASS Consortium. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell. 2022 Jun 9; 185(12):2184-99.e16.

Tan Y, Flynn WF, Sivajothi S, Luo D, Bozal SB, Davé M, Luciano AA, Robson P, Luciano DE, Courtois ET. Single-cell analysis of endometriosis reveals a coordinated transcriptional programme driving immunotolerance and angiogenesis across eutopic and ectopic tissues. Nat Cell Biol. 2022 Aug; 24(8):1306-18. https://pubmed.ncbi.nlm.nih.gov/35864314

Johnson KC, Anderson KJ, Courtois ET, Gujar AD, Barthel FP, Varn FS, Luo D, Seignon M, Yi E, Kim H, Estecio MRH, Zhao D, Tang M, Navin NE, Maurya R, Ngan CY, Verburg N, de Witt Hamer PC, Bulsara K, Samuels ML, Das S, Robson P, Verhaak RGW. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. Nat Genet. 2021 Oct; 53(10):1456-68. https://pubmed.ncbi.nlm.nih.gov/34594038

Fujita A, Zhong L, Antony MS, Chamiec-Case E, Mickelsen LE, Kanoski SE, Flynn WF, Jackson AC. Neurokinin B-Expressing Neurons of the Central Extended Amygdala Mediate Inhibitory Synaptic Input onto Melanin-Concentrating Hormone Neuron Subpopulations. J Neurosci. 2021 Nov 17; 41(46):9539-60. https://pubmed.ncbi.nlm.nih.gov/34642212

Elyada E, Bolisetty M, Laise P, Flynn WF, Courtois ET, Burkhart RA, Teinor JA, Belleau P, Biffi G, Lucito MS, Sivajothi S, Armstrong TD, Engle DD, Yu KH, Hao Y, Wolfgang CL, Park Y, Preall J, Jaffee EM, Califano A, Robson P, Tuveson DA. Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts. Cancer Discov. 2019 Aug; 9(8):1102-23.

Li H, Courtois ET, Sengupta D, Tan Y, Chen KH, Goh JJL, Kong SL, Chua C, Hon LK, Tan WS, Wong M, Choi PJ, Wee LJK, Hillmer AM, Tan IB, Robson P, Prabhakar S. Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors. Nat Genet. 2017 May; 49(5):708-18.

Selected Scientific Technology Development Publications Authored by SCBL Service Members

Soja E, Sivajothi S, Flynn WF, Courtois ET. Hematoxylin and Eosin (H&E) Staining of Tissues following Multiplexed Imaging on Phenocycler-Fusion. protocols.io. 2024.

Sivajothi S, Soja E, Bhargava S, Flynn WF, Courtois ET. FFPE Tissue Processing for Multimodal Imaging Assays (Phenocycler-Fusion + H&E) following Xenium In Situ Gene Expression. protocols.io. 2024.

Sivajothi S, Ramasamy R, Robson P. 8-placenta-full-term-imc (v1.1) graph data. Human Reference Atlas Knowledge Graph. 2024.

Sivajothi S, Soja E, Flynn WF, Courtois E. Tissue Sectioning Guidelines (FFPE) - CODEX/PhenoCycler. protocols.io. 2023.

Tan Y, Luo D, Bozal S, Robson P, Courtois E. Human endometrium and endometriosis tissue dissociation for single-cell RNA sequencing. protocols.io. 2022.

Perry GA, Gabriel P, Luo D, Grassmann J, Flynn WF, Courtois ET, Robson P, Daigle SL. Nuclei Prep from Frozen Mouse Brain Tissues with Optional Sucrose Column for single nuclei RNA-seq. protocols.io. 2022.

Martinek J, Wu TC, Sun L, Lin J, Kim KI, Marches F, Robson P, George J, Palucka K. Multiplex immunofluorescence-guided laser capture microdissection for spatial transcriptomics of metastatic melanoma tissues. STAR Protoc. 2022 Dec 16; 3(4):101698.

Selected Consortium-Publications Authored by SCBL Service Members

Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, HuBMAP Consortium [Courtois ET, Flynn, W.], Börner K, Snyder MP. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol. 2023 Jul 19; 25(8):1089-100.

SenNet Consortium [Courtois ET ]. NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. Nat Aging. 2022 Dec; 2(12):1090-100.

Bose S, Barroso M, Chheda MG, Clevers H, Elez E, Kaochar S, Kopetz SE, Li XN, Meric-Bernstam F, Meyer CA, Mou H, Naegle KM, Pera MF, Perova Z, Politi KA, Raphael BJ, Robson P, Sears RC, Tabernero J, Tuveson DA, Welm AL, Welm BE, Willey CD, Salnikow K, Chuang JH, Shen X. A path to translation: How 3D patient tumor avatars enable next generation precision oncology. Cancer Cell. 2022 Dec 12; 40(12):1448-53.