Publications (2016 - present)

Preprints:

R. G. Aubin, J. Montelongo, R. Hu, P. G. Camara. Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data. (2023). DOI: 10.1101/2023.02.06.527318 (bioRxiv). [GitHub]

K. W. Govek, P. Nicodemus, Y. Lin, J. Crawford, A. B. Saturnino, H. Cui, K. Zoga, M. P. Hart, P. G. Camara. CAJAL enables analysis and integration of single-cell morphological data using metric geometry. Nature Communications 14 (2023) 3672. DOI: 10.1038/s41467-023-39424-2 [GitHub].

K. W. Govek*, S. Chen*, P. Sgourdou, Y. Yao, S. Woodhouse, T. Chen, M. V. Fuccillo, D. J. Epstein^#, P. G. Camara^#. Developmental trajectories of thalamic progenitors revealed by single-cell transcriptome profiling and Shh perturbation. Cell Reports 41 (2022) 111768. DOI: 10.1016/j.celrep.2022.111768 [*authors contributed equally]. [^#corresponding authors].
R. Aubin*, E. C. Troisi*, J. Montelongo, A. N. Alghalith, M. P. Nasrallah, M. Santi, and P. G. Cámara. Pro-Inflammatory Cytokines Mediate the Epithelial-to-Mesenchymal-Like Transition of Pediatric Posterior Fossa Ependymoma. Nature Communications 13 (2022) 3936. DOI: 10.1038/s41467-022-31683-9. [*authors contributed equally]. [GitHub]
Z. Bai*, S. Woodhouse*, Z. Zhao, R. Arya, K. Govek, D. Kim, S. Lundh, A. Baysoy, H. Sun, Y. Deng, Y. Xiao, D. M. Barrett, R. M. Myers, S. A. Grupp, C. H. June, R. Fan^#, P. G. Camara^#, J. J. Melenhorst^#. Single-cell antigen-specific activation landscape of CAR T infusion product identifies determinants of CD19-positive relapse in patients with ALL. Science Advances 8 (2022) eabj2820. DOI: 10.1126/sciadv.abj2820. [*authors contributed equally]. [^#corresponding authors].

M. Haniffa, D. Taylor, S. Linnarsson, B. J. Aronow, G. D. Bader, R. A. Barker, P. G. Cámara, J. G. Camp, A. Chédotal, A. Copp, H. C. Etchevers, P. Giacobini, B. Gottgens, G. Guo, A. Hupalowska, K. R. James, E. Kirby, A. Kriegstein, J. Lundeberg, J. Marioni, K. B. Meyer, K. K. Niakan, M. Nilsson, B. Olabi, D. Pe'er, A. Regev, J. Rood, O. Rozenblatt-Rosen, R. Satija, S. A. Teichmann, B. Treutlein, R. Vento-Tormo, S. Webb, and the Human Cell Atlas Developmental Biological Network. A roadmap for the Human Developmental Cell Atlas. Nature 597 (2021) 196-205. DOI: 10.1038/s41586-021-03620-1.
K. W. Govek*, E. C. Troisi*, Z. Miao, R. G. Aubin, S. Woodhouse, and P. G. Cámara. Single-Cell Transcriptomic Analysis of mIHC Images via Antigen Mapping. Science Advances 7 (2021) eabc5464. DOI: 10.1126/sciadv.abc5464. [*authors contributed equally]. [GitHub] [Website] [Video Poster].
Z. Bai, S. Lundh, D. Kim, S. Woodhouse, D. M. Barrett, R. M. Myers, S. A. Grupp, M. V. Maus, C. H. June, P. G. Cámara, J. J. Melenhorst*, R. Fan*. Single-cell multiomics dissection of basal and antigen-specific activation states of CD19-targeted CAR T cells. Journal for ImmunoTherapy of Cancer 9 (2021) e002328. DOI: 10.1136/jitc-2020-002328. [*authors contributed equally]

Q. Qiu*, P. Hu*, X. Qiu, K. W. Govek, P. G. Cámara, and H. Wu. Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq. Nature Methods 17 (2020) 991-1001. DOI: 10.1038/s41592-020-0935-4. [*authors contributed equally].
R. Rabadán, Y. Mohamedi, U. Rubin, T. Chu, A. N. Alghalith, O. Elliott, L. Arnés, S. Cal, Á. J. Obaya, A. J. Levine, and P. G. Cámara. Identification of Relevant Genetic Alterations in Cancer using Topological Data Analysis. Nature Communications 11 (2020) 3808. DOI: 10.1038/s41467-020-17659-7. [GitHub].
Y. Ho, P. Hu, M. T. Peel, S. Chen, P. G. Cámara, D. J. Epstein, H. Wu, and S. A. Liebhaber. Single-cell transcriptomic analysis of adult mouse pituitary reveals sexual dimorphism and physiologic demand-induced cellular plasticity. Protein Cell 11 (2020) 565-583. DOI: 10.1007/s13238-020-00705-x.

K. W. Govek*, V. S. Yamajala*, and P. G. Cámara. Clustering-Independent Analysis of Genomic Data using Spectral Simplicial Theory. PLOS Computational Biology 15 (2019) 11. DOI: 10.1371/journal.pcbi.1007509. [*authors contributed equally]. [GitHub].
J. H. Moore, M. R. Boland, P. G. Cámara, H. Chervitz, G. Gonzalez, B. E. Himes, D. Kim, D. L. Mowery, M. D. Ritchie, L. Shen, R. J. Urbanowicz, and J. H. Holmes. Preparing next-generation scientists for biomedical big data: artificial intelligence approaches. Personalized Medicine 16 (2019) 247-257. DOI:10.2217/pme-2018-0145.

P. G. Cámara. Methods and challenges in the analysis of single-cell RNA-sequencing data. Current Opinion in Systems Biology 7 (2018) 47 - 53. DOI: 10.1016/j.coisb.2017.12.007.

A.H. Rizvi*, P. G. Cámara*, E. K. Kandror, T. J. Roberts, I. Scheiren, T. Maniatis, and R. Rabadán. Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development. Nature Biotechnology 35 (2017) 551-560. DOI: 10.1038/nbt.3854. [*authors contributed equally]. [GitHub].
J.-K. Lee, J. Wang, J. K. Sa, E. Ladewig, H.-O. Lee, I.-H. Lee, H.-J. Kang, D. S. Rosenbloom, P. G. Cámara, Z. Liu, P. van Nieuwenhuizen, S. W. Jung, S. W. Choi, J. Kim, A. Chen, K.-T. Kim, S. Shin, Y. J. Seo, J. M. Oh, Y. J. Shin, D.-S. Kong, H. J. Seol, A. Blumberg, J.-I. Lee, A. Iavarone, W.-Y. Park, R. Rabadán, and D.-H. Nam. Spatiotemporal genomic architecture informs precision oncology in glioblastoma. Nature Genetics 49 (2017) 594 - 599. DOI: 10.1038/ng.3806.
P. G. Cámara. Topological methods for genomics: present and future directions. Current Opinion in Systems Biology 1 (2017) 95 - 101. DOI: 10.1016/j.coisb.2016.12.007.
D. S. Rosenbloom, P. G. Cámara, T. Chu, and R. Rabadán. Evolutionary scalpels for dissecting tumor ecosystems. Biochim. Biophys. Acta Rev. Cancer. 1867 (2017) 69 - 83. DOI: 10.1016/j.bbcan.2016.11.005.

P. G. Cámara, D. I. S. Rosenbloom, K. J. Emmett, A. J. Levine, and R. Rabadán. Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination. Cell Systems 3 (2016) 83-94. DOI: 10.1016/j.cels.2016.05.008.
P. G. Cámara, A. J. Levine, and R. Rabadán. Inference of ancestral recombination graphs through topological data analysis. PLOS Computational Biology 12 (2016) 8. DOI: 10.1371/journal.pcbi.1005071. [GitHub].