Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Search Page

Filters

My Custom Filters

Edit custom filters

Results by year

Table representation of search results timeline featuring number of search results per year.

Year Number of Results
2006 1
2014 1
2016 3
2017 1
2018 3
2019 6
2020 2
2021 3
2022 5
2023 8
2024 8
2025 6
2026 4

Publication date

Text availability

Article attribute

Article type

Additional filters

Article Language

Species

Sex

Age

Other

Search Results

47 results

Results by year

Filters applied: . Clear all
Your search was processed without automatic term mapping because it retrieved zero results.
Page 1
The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma.
Steen CB, Luca BA, Esfahani MS, Azizi A, Sworder BJ, Nabet BY, Kurtz DM, Liu CL, Khameneh F, Advani RH, Natkunam Y, Myklebust JH, Diehn M, Gentles AJ, Newman AM, Alizadeh AA. Steen CB, et al. Cancer Cell. 2021 Oct 11;39(10):1422-1437.e10. doi: 10.1016/j.ccell.2021.08.011. Epub 2021 Sep 30. Cancer Cell. 2021. PMID: 34597589 Free PMC article.
However, dissecting these cell states and their clinical relevance at scale remains challenging. Here, we implemented EcoTyper, a machine-learning framework integrating transcriptome deconvolution and single-cell RNA sequencing, to characterize clinically relevant DLBCL ce …
However, dissecting these cell states and their clinical relevance at scale remains challenging. Here, we implemented EcoTyper, a mac …
Determining cell type abundance and expression from bulk tissues with digital cytometry.
Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, Khodadoust MS, Esfahani MS, Luca BA, Steiner D, Diehn M, Alizadeh AA. Newman AM, et al. Nat Biotechnol. 2019 Jul;37(7):773-782. doi: 10.1038/s41587-019-0114-2. Epub 2019 May 6. Nat Biotechnol. 2019. PMID: 31061481 Free PMC article.
Single-cell RNA-sequencing has emerged as a powerful technique for characterizing cellular heterogeneity, but it is currently impractical on large sample cohorts and cannot be applied to fixed specimens collected as part of routine clinical care. We previously developed an …
Single-cell RNA-sequencing has emerged as a powerful technique for characterizing cellular heterogeneity, but it is currently impract …
Atlas of clinically distinct cell states and ecosystems across human solid tumors.
Luca BA, Steen CB, Matusiak M, Azizi A, Varma S, Zhu C, Przybyl J, Espín-Pérez A, Diehn M, Alizadeh AA, van de Rijn M, Gentles AJ, Newman AM. Luca BA, et al. Cell. 2021 Oct 14;184(21):5482-5496.e28. doi: 10.1016/j.cell.2021.09.014. Epub 2021 Sep 30. Cell. 2021. PMID: 34597583 Free PMC article.
Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understanding processes as diverse as development, aging, and cancer. Here we introduce EcoTyper, a machine learning framework for large-scale …
Determining how cells vary with their local signaling environment and organize into distinct cellular communities is critical for understand …
A human lymphoma organoid model for evaluating and targeting the follicular lymphoma tumor immune microenvironment.
Kastenschmidt JM, Schroers-Martin JG, Sworder BJ, Sureshchandra S, Khodadoust MS, Liu CL, Olsen M, Kurtz DM, Diehn M, Wagar LE, Alizadeh AA. Kastenschmidt JM, et al. Cell Stem Cell. 2024 Mar 7;31(3):410-420.e4. doi: 10.1016/j.stem.2024.01.012. Epub 2024 Feb 22. Cell Stem Cell. 2024. PMID: 38402619 Free PMC article.
Modeling the intact FL TME, with its native, syngeneic tumor-infiltrating leukocytes, is a major challenge. Here, we describe an organoid culture method for cultivating patient-derived lymphoma organoids (PDLOs), which include cells from the native FL TME. ...PDLOs treated …
Modeling the intact FL TME, with its native, syngeneic tumor-infiltrating leukocytes, is a major challenge. Here, we describe an orga …
Risk of Second Tumors and T-Cell Lymphoma after CAR T-Cell Therapy.
Hamilton MP, Sugio T, Noordenbos T, Shi S, Bulterys PL, Liu CL, Kang X, Olsen MN, Good Z, Dahiya S, Frank MJ, Sahaf B, Mackall CL, Gratzinger D, Diehn M, Alizadeh AA, Miklos DB. Hamilton MP, et al. N Engl J Med. 2024 Jun 13;390(22):2047-2060. doi: 10.1056/NEJMoa2401361. N Engl J Med. 2024. PMID: 38865660 Free PMC article.
RESULTS: A total of 724 patients who had received T-cell therapies at our center were included in the study. A lethal T-cell lymphoma was identified in a patient who had received axicabtagene ciloleucel therapy for diffuse large B-cell lymphoma, and both lymp …
RESULTS: A total of 724 patients who had received T-cell therapies at our center were included in the study. A lethal T-cell l …
An ultrasensitive method for detection of cell-free RNA.
Nesselbush MC, Luca BA, Jeon YJ, Jabara I, Meador CB, Garofalo A, Binkley MS, Hui AB, van 't Erve I, Xu N, Shi WY, Liu KJ, Sugio T, Kastelowitz N, Hamilton EG, Liu CL, Olsen M, Bonilla RF, Wang YP, Jiang A, Lau B, Eichholz J, Banwait M, Schroers-Martin J, Boegeholz J, King DA, Luikart H, Esfahani MS, Mehrmohamadi M, Stehr H, Raclin T, Tibshirani R, Khush K, Srinivas S, Yu H, Rogers AJ, Nair VS, Isbell JM, Li BT, Piotrowska Z, Sequist LV, Hata AN, Neal JW, Wakelee HA, Gentles AJ, Alizadeh AA, Diehn M. Nesselbush MC, et al. Nature. 2025 May;641(8063):759-768. doi: 10.1038/s41586-025-08834-1. Epub 2025 Apr 16. Nature. 2025. PMID: 40240612 Free PMC article.
Here we describe RARE-seq (random priming and affinity capture of cfRNA fragments for enrichment analysis by sequencing), a method optimized for cfRNA analysis. We demonstrate that platelet contamination can substantially confound cfRNA analyses and develop an approach to …
Here we describe RARE-seq (random priming and affinity capture of cfRNA fragments for enrichment analysis by sequencing), a method op …
Inferring gene expression from cell-free DNA fragmentation profiles.
Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, Steen CB, Macaulay CW, Schultz A, Nesselbush MC, Soo J, Schroers-Martin JG, Chen B, Binkley MS, Stehr H, Chabon JJ, Sworder BJ, Hui AB, Frank MJ, Moding EJ, Liu CL, Newman AM, Isbell JM, Rudin CM, Li BT, Kurtz DM, Diehn M, Alizadeh AA. Esfahani MS, et al. Nat Biotechnol. 2022 Apr;40(4):585-597. doi: 10.1038/s41587-022-01222-4. Epub 2022 Mar 31. Nat Biotechnol. 2022. PMID: 35361996 Free PMC article.
We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification …
We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of pr …
Field-effect-informed urine liquid biopsy for bladder cancer.
Shi WY, Liu KJ, Esfahani MS, Mach KE, Phillips NA, Almanza D, Bajpai RK, Schroers-Martin JG, Trabanino L, Lee TJ, La V, Rodriguez G, Holton G, Chen SB, Mullane P, Wu DJ, Nesselbush MC, Sugio T, Cheng JC, Jabara I, Hamilton EG, Alig SK, Liu CL, Peterson DJ, Prado K, Shkolyar E, Thong A, Shah JB, Gill H, Kunder CA, Chan E, Khaki AR, Skinner EC, Alizadeh AA, Liao JC, Diehn M. Shi WY, et al. Cell. 2026 Feb 19;189(4):1024-1038.e9. doi: 10.1016/j.cell.2025.12.054. Epub 2026 Jan 27. Cell. 2026. PMID: 41605210 Free PMC article.
47 results