Defining the T cell transcriptional landscape in pediatric liver transplant rejection at single cell resolution.

Autor: Peters AL; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA., DePasquale EAK; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Begum G; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Roskin KM; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Woodle ES; Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA., Hildeman DA; Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.; Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Feb 29. Date of Electronic Publication: 2024 Feb 29.

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.

Autor: Miller TE; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA., Lareau CA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Pathology, Stanford University, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA.; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA., Verga JA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA., DePasquale EAK; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA., Liu V; Department of Pathology, Stanford University, Stanford, CA, USA.; Department of Genetics, Stanford University, Stanford, CA, USA., Ssozi D; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA., Sandor K; Department of Pathology, Stanford University, Stanford, CA, USA., Yin Y; Department of Pathology, Stanford University, Stanford, CA, USA., Ludwig LS; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany., El Farran CA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA., Morgan DM; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA., Satpathy AT; Department of Pathology, Stanford University, Stanford, CA, USA., Griffin GK; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA., Lane AA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.; Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA., Love JC; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA., Bernstein BE; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.; Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA.; Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA., Sankaran VG; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA., van Galen P; Broad Institute of MIT and Harvard, Cambridge, MA, USA. pvangalen@bwh.harvard.edu.; Division of Hematology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA. pvangalen@bwh.harvard.edu.; Ludwig Center at Harvard, Harvard Medical School, Boston, MA, USA. pvangalen@bwh.harvard.edu.

Publikováno v: Nature biotechnology [Nat Biotechnol] 2022 Jul; Vol. 40 (7), pp. 1030-1034. Date of Electronic Publication: 2022 Feb 24.

Single-Cell Multiomics Reveals Clonal T-Cell Expansions and Exhaustion in Blastic Plasmacytoid Dendritic Cell Neoplasm.

Autor: DePasquale EAK; Division of Hematology, Brigham and Women's Hospital, Boston, MA, United States.; Department of Medicine, Harvard Medical School, Boston, MA, United States.; Broad Institute of MIT and Harvard, Cambridge, MA, United States.; Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States., Ssozi D; Division of Hematology, Brigham and Women's Hospital, Boston, MA, United States.; Broad Institute of MIT and Harvard, Cambridge, MA, United States., Ainciburu M; Hemato-Oncology Program, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, Instituto de Investigación Sanitaria de Navarra (IDISNA), Pamplona, Spain., Good J; Division of Hematology, Brigham and Women's Hospital, Boston, MA, United States.; Department of Human Biology, Sattler College, Boston, MA, United States., Noel J; Division of Hematology, Brigham and Women's Hospital, Boston, MA, United States.; Broad Institute of MIT and Harvard, Cambridge, MA, United States., Villanueva MA; Broad Institute of MIT and Harvard, Cambridge, MA, United States.; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States.; Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, United States.; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, United States.; Ragon Institute, Harvard University, Massachusetts Institute of Technology, and Massachusetts General Hospital, Cambridge, MA, United States., Couturier CP; Broad Institute of MIT and Harvard, Cambridge, MA, United States.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States.; Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, United States., Shalek AK; Broad Institute of MIT and Harvard, Cambridge, MA, United States.; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States.; Division of Health Science & Technology, Harvard Medical School, Cambridge, MA, United States.; Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, United States.; Ragon Institute, Harvard University, Massachusetts Institute of Technology, and Massachusetts General Hospital, Cambridge, MA, United States.; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States., Aranki SF; Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, Boston, MA, United States., Mallidi HR; Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, Boston, MA, United States., Griffin GK; Broad Institute of MIT and Harvard, Cambridge, MA, United States.; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, United States.; Department of Pathology, Brigham and Women's Hospital, Boston, MA, United States., Lane AA; Department of Medicine, Harvard Medical School, Boston, MA, United States.; Broad Institute of MIT and Harvard, Cambridge, MA, United States.; Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States.; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States., van Galen P; Division of Hematology, Brigham and Women's Hospital, Boston, MA, United States.; Department of Medicine, Harvard Medical School, Boston, MA, United States.; Broad Institute of MIT and Harvard, Cambridge, MA, United States.; Ludwig Center at Harvard, Harvard Medical School, Boston, MA, United States.

Publikováno v: Frontiers in immunology [Front Immunol] 2022 Mar 10; Vol. 13, pp. 809414. Date of Electronic Publication: 2022 Mar 10 (Print Publication: 2022).

Corticostriatal dysfunction and social interaction deficits in mice lacking the cystine/glutamate antiporter.

Autor: Bentea E; Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium., Villers A; Department of Neurosciences, Research Institute for Biosciences, University of Mons, Mons, Belgium., Moore C; Research Services, Neurocytology Laboratory, Veterans Affairs Medical Center, Portland, OR, USA., Funk AJ; Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, USA., O'Donovan SM; Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, USA., Verbruggen L; Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium., Lara O; Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium., Janssen P; Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium., De Pauw L; Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium., Declerck NB; Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium., DePasquale EAK; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA., Churchill MJ; Research Services, Neurocytology Laboratory, Veterans Affairs Medical Center, Portland, OR, USA., Sato H; Department of Medical Technology, Faculty of Medicine, Laboratory of Biochemistry and Molecular Biology, Niigata University, Niigata, Japan., Hermans E; Institute of Neuroscience, Université Catholique de Louvain, Brussels, Belgium., Arckens L; Laboratory of Neuroplasticity and Neuroproteomics, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium., Meshul CK; Research Services, Neurocytology Laboratory, Veterans Affairs Medical Center, Portland, OR, USA.; Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA., Ris L; Department of Neurosciences, Research Institute for Biosciences, University of Mons, Mons, Belgium., McCullumsmith RE; Department of Neurosciences, University of Toledo College of Medicine, Toledo, OH, USA., Massie A; Neuro-Aging & Viro-Immunotherapy, Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium. Ann.Massie@vub.be.

Publikováno v: Molecular psychiatry [Mol Psychiatry] 2021 Sep; Vol. 26 (9), pp. 4754-4769. Date of Electronic Publication: 2020 May 04.

cellHarmony: cell-level matching and holistic comparison of single-cell transcriptomes.

Autor: DePasquale EAK; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA.; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Schnell D; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.; Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Dexheimer P; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA.; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Ferchen K; Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA.; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Hay S; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Chetal K; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Valiente-Alandí Í; Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Blaxall BC; Heart Institute and Center for Translational Fibrosis Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA., Grimes HL; Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA.; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA.; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA., Salomonis N; Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA.; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.; Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA.

Publikováno v: Nucleic acids research [Nucleic Acids Res] 2019 Dec 02; Vol. 47 (21), pp. e138.