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

Results by year

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

Year Number of Results
2014 1
2015 1
2016 4
2017 5
2018 4
2019 13
2020 8
2021 7
2022 4
2023 8
2024 7
2025 0

Publication date

Text availability

Article attribute

Article type

Additional filters

Article Language

Species

Sex

Age

Other

Search Results

57 results

Results by year

Filters applied: . Clear all
Page 1
Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N. Thomas AM, et al. Nat Med. 2019 Apr;25(4):667-678. doi: 10.1038/s41591-019-0405-7. Epub 2019 Apr 1. Nat Med. 2019. PMID: 30936548 Free PMC article.
Defining and benchmarking open problems in single-cell analysis.
Luecken MD, Gigante S, Burkhardt DB, Cannoodt R, Strobl DC, Markov NS, Zappia L, Palla G, Lewis W, Dimitrov D, Vinyard ME, Magruder DS, Andersson A, Dann E, Qin Q, Otto DJ, Klein M, Botvinnik OB, Deconinck L, Waldrant K; Open Problems Jamboree Members; Bloom JM, Pisco AO, Saez-Rodriguez J, Wulsin D, Pinello L, Saeys Y, Theis FJ, Krishnaswamy S. Luecken MD, et al. Res Sq [Preprint]. 2024 Apr 4:rs.3.rs-4181617. doi: 10.21203/rs.3.rs-4181617/v1. Res Sq. 2024. PMID: 38645152 Free PMC article. Preprint.
SIMON: Open-Source Knowledge Discovery Platform.
Tomic A, Tomic I, Waldron L, Geistlinger L, Kuhn M, Spreng RL, Dahora LC, Seaton KE, Tomaras G, Hill J, Duggal NA, Pollock RD, Lazarus NR, Harridge SDR, Lord JM, Khatri P, Pollard AJ, Davis MM. Tomic A, et al. Patterns (N Y). 2021 Jan 8;2(1):100178. doi: 10.1016/j.patter.2020.100178. eCollection 2021 Jan 8. Patterns (N Y). 2021. PMID: 33511368 Free PMC article.
Curated single cell multimodal landmark datasets for R/Bioconductor.
Eckenrode KB, Righelli D, Ramos M, Argelaguet R, Vanderaa C, Geistlinger L, Culhane AC, Gatto L, Carey V, Morgan M, Risso D, Waldron L. Eckenrode KB, et al. PLoS Comput Biol. 2023 Aug 25;19(8):e1011324. doi: 10.1371/journal.pcbi.1011324. eCollection 2023 Aug. PLoS Comput Biol. 2023. PMID: 37624866 Free PMC article.
Orchestrating single-cell analysis with Bioconductor.
Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC. Amezquita RA, et al. Nat Methods. 2020 Feb;17(2):137-145. doi: 10.1038/s41592-019-0654-x. Epub 2019 Dec 2. Nat Methods. 2020. PMID: 31792435 Free PMC article. Review.
Sociodemographic variation in the oral microbiome.
Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L, Dowd JB. Renson A, et al. Ann Epidemiol. 2019 Jul;35:73-80.e2. doi: 10.1016/j.annepidem.2019.03.006. Epub 2019 May 8. Ann Epidemiol. 2019. PMID: 31151886 Free PMC article.
signifinder enables the identification of tumor cell states and cancer expression signatures in bulk, single-cell and spatial transcriptomic data.
Pirrotta S, Masatti L, Corrà A, Pedrini F, Esposito G, Martini P, Risso D, Romualdi C, Calura E. Pirrotta S, et al. bioRxiv [Preprint]. 2023 Mar 10:2023.03.07.530940. doi: 10.1101/2023.03.07.530940. bioRxiv. 2023. Update in: NAR Genom Bioinform. 2024 Oct 03;6(4):lqae138. doi: 10.1093/nargab/lqae138. PMID: 36945491 Free PMC article. Updated. Preprint.
Public data and open source tools for multi-assay genomic investigation of disease.
Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L. Kannan L, et al. Brief Bioinform. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12. Brief Bioinform. 2016. PMID: 26463000 Free PMC article. Review.
57 results