6 Works

The transcriptomic landscape of normal and ineffective erythropoiesis at single cell resolution

Christopher Lausted, Raymond Doty, Adam Munday, Zhantao Yang, Xiaowei Yan, Changting Meng, Qiang Tian & Janis Abkowitz
Ineffective erythropoiesis, the death of maturing erythroid cells, is a common cause of anemia. To better understand why this occurs, we studied the fates and adaptations of single erythroid marrow cells from individuals with Diamond Blackfan anemia (DBA), del(5q) myelodysplastic syndrome (del(5q) MDS), and normal controls, and defined an unhealthy (vs. healthy) differentiation trajectory, using velocity pseudotime and cell surface protein assessment. The pseudotime trajectories diverge immediately after the cells upregulate transferrin receptor (CD71), import...

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki & Stephen A. Ramsey
Abstract Background Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can...

Additional file 1 of RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki & Stephen A. Ramsey
Additional file 1: Table S1. Ontologies from the OBO Foundry that are included in RTX-KG2

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki & Stephen A. Ramsey
Abstract Background Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can...

Additional file 1 of RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki & Stephen A. Ramsey
Additional file 1: Table S1. Ontologies from the OBO Foundry that are included in RTX-KG2

Colorectal cancer interleukin-10 blockade scRNA-seq

Christopher Lausted, Kevin Sulllivan, Xiuyun Jiang, Prajna Guha, Jason Carter, Cynthia Hsu, Kevin Labadie, Karen Kohli, Heidi Kenerson, Sara Daniel, Xiaowei Yan, Changting Meng, Stella Shin, Arezou Abbasi, David Seo, James Park, Nicholas Crispe, Taranjit Gujral, Raymond Yeung, Teresa Kim, Qiang Tian, Steven Katz & Venu Pillarisetty
Objective: PD-1 checkpoint inhibition and adoptive cellular therapy have limited success in patients with microsatellite stable colorectal cancer liver metastases (CRLM). We demonstrate that interleukin-10 (IL-10) blockade enhances endogenous T cell and chimeric antigen receptor T (CAR-T) cell anti-tumor function in CRLM slice cultures.Design: We created organotypic slice cultures from human CRLM (n = 38) and tested the anti-tumor effects of a neutralizing antibody against IL-10 (╬▒IL-10). We evaluated slice cultures with single and multiplex...

Registration Year

  • 2022
    6

Resource Types

  • Collection
    2
  • Dataset
    2
  • Text
    2

Affiliations

  • Institute for Systems Biology
    6
  • Oregon State University
    4
  • Radboud University Nijmegen
    4
  • King Mongkut's University of Technology North Bangkok
    4
  • Pennsylvania State University
    4
  • University of Washington
    2
  • Fred Hutchinson Cancer Research Center
    1
  • Ruijin Hospital
    1
  • Roger Williams Medical Center
    1
  • Hangzhou Medical College
    1