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Search life-sciences literature (45,103,589 articles, preprints and more)

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Noninvasive Lung Cancer Subtype Classification Using Tumor-Derived Signatures and cfDNA Methylome.
Li S, Li W, Liu B, Krysan K, Dubinett SM
Cancer Res Commun, 4(7):1738-1747, 01 Jul 2024
Cited by: 0 articles | PMID: 38856716 | PMCID: PMC11249519
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MAMS: matrix and analysis metadata standards to facilitate harmonization and reproducibility of single-cell data.
Sarfraz I, Wang Y, Shastry A, Teh WK, Sokolov A, Herb BR, Creasy HH, Virshup I, Dries R, Degatano K, Mahurkar A, Schnell DJ, Madrigal P, Hilton J, Gehlenborg N, Tickle T, Campbell JD
Genome Biol, 25(1):205, 01 Aug 2024
Cited by: 2 articles | PMID: 39090672 | PMCID: PMC11292877
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Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy.
Hickey JW, Agmon E, Horowitz N, Tan TK, Lamore M, Sunwoo JB, Covert MW, Nolan GP
Cell Syst, 15(4):322-338.e5, 01 Apr 2024
Cited by: 3 articles | PMID: 38636457 | PMCID: PMC11030795
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Graph Perceiver Network for Lung Tumor and Bronchial Premalignant Lesion Stratification from Histopathology.
Gindra RH, Zheng Y, Green EJ, Reid ME, Mazzilli SA, Merrick DT, Burks EJ, Kolachalama VB, Beane JE
Am J Pathol, 194(7):1285-1293, 06 Apr 2024
Cited by: 0 articles | PMID: 38588853
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An atlas of epithelial cell states and plasticity in lung adenocarcinoma.
Han G, Sinjab A, Rahal Z, Lynch AM, Treekitkarnmongkol W, Liu Y, Serrano AG, Feng J, Liang K, Khan K, Lu W, Hernandez SD, Liu Y, Cao X, Dai E, Pei G, Hu J, Abaya C, Gomez-Bolanos LI, [...] Kadara H
Nature, 627(8004):656-663, 28 Feb 2024
Cited by: 12 articles | PMID: 38418883 | PMCID: PMC10954546
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T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response.
Hickey JW, Haist M, Horowitz N, Caraccio C, Tan Y, Rech AJ, Baertsch MA, Rovira-Clavé X, Zhu B, Vazquez G, Barlow G, Agmon E, Goltsev Y, Sunwoo JB, Covert M, Nolan GP
Cell Rep, 42(12):113494, 11 Dec 2023
Cited by: 3 articles | PMID: 38085642 | PMCID: PMC10765317
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Single-Cell Characterization of Pulmonary Nodules Implicates Suppression of Immunosurveillance across Early Stages of Lung Adenocarcinoma.
Yanagawa J, Tran LM, Salehi-Rad R, Lim RJ, Dumitras C, Fung E, Wallace WD, Prosper AE, Fishbein G, Shea C, Hong R, Kahangi B, Deng JJ, Gower AC, Liu B, Campbell JD, Mazzilli SA, Beane JE, Kadara H, [...] Dubinett SM
Cancer Res, 83(19):3305-3319, 01 Oct 2023
Cited by: 5 articles | PMID: 37477508 | PMCID: PMC10544016
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Convergence of YAP/TAZ, TEAD and TP63 activity is associated with bronchial premalignant severity and progression.
Ning B, Tilston-Lunel AM, Simonetti J, Hicks-Berthet J, Matschulat A, Pfefferkorn R, Spira A, Edwards M, Mazzilli S, Lenburg ME, Beane JE, Varelas X
J Exp Clin Cancer Res, 42(1):116, 08 May 2023
Cited by: 6 articles | PMID: 37150829 | PMCID: PMC10165825
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A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy.
Mayer AT, Holman DR, Sood A, Tandon U, Bhate SS, Bodapati S, Barlow GL, Chang J, Black S, Crenshaw EC, Koron AN, Streett SE, Gambhir SS, Sandborn WJ, Boland BS, Hastie T, Tibshirani R, Chang JT, Nolan GP, [...] Rogalla S
Sci Adv, 9(3):eadd1166, 20 Jan 2023
Cited by: 13 articles | PMID: 36662860 | PMCID: PMC9858501
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Smoking modulates different secretory subpopulations expressing SARS-CoV-2 entry genes in the nasal and bronchial airways.
Xu K, Shi X, Husted C, Hong R, Wang Y, Ning B, Sullivan TB, Rieger-Christ KM, Duan F, Marques H, Gower AC, Xiao X, Liu H, Liu G, Duclos G, Platt M, Spira AE, Mazzilli SA, Billatos E, [...] Beane JE
Sci Rep, 12(1):18168, 28 Oct 2022
Cited by: 2 articles | PMID: 36307504 | PMCID: PMC9615627
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Spatial epitope barcoding reveals clonal tumor patch behaviors.
Rovira-Clavé X, Drainas AP, Jiang S, Bai Y, Baron M, Zhu B, Dallas AE, Lee MC, Chu TP, Holzem A, Ayyagari R, Bhattacharya D, McCaffrey EF, Greenwald NF, Markovic M, Coles GL, Angelo M, Bassik MC, Sage J, Nolan GP
Cancer Cell, 40(11):1423-1439.e11, 13 Oct 2022
Cited by: 16 articles | PMID: 36240778 | PMCID: PMC9673683
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Annotation of spatially resolved single-cell data with STELLAR.
Brbić M, Cao K, Hickey JW, Tan Y, Snyder MP, Nolan GP, Leskovec J
Nat Methods, 19(11):1411-1418, 24 Oct 2022
Cited by: 41 articles | PMID: 36280720
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The Single-Cell Immunogenomic Landscape of B and Plasma Cells in Early-Stage Lung Adenocarcinoma.
Hao D, Han G, Sinjab A, Gomez-Bolanos LI, Lazcano R, Serrano A, Hernandez SD, Dai E, Cao X, Hu J, Dang M, Wang R, Chu Y, Song X, Zhang J, Parra ER, Wargo JA, Swisher SG, Cascone T, [...] Wang L
Cancer Discov, 12(11):2626-2645, 01 Nov 2022
Cited by: 36 articles | PMID: 36098652 | PMCID: PMC9633381
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Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data.
Hong R, Koga Y, Bandyadka S, Leshchyk A, Wang Y, Akavoor V, Cao X, Sarfraz I, Wang Z, Alabdullatif S, Jansen F, Yajima M, Johnson WE, Campbell JD
Nat Commun, 13(1):1688, 30 Mar 2022
Cited by: 24 articles | PMID: 35354805 | PMCID: PMC8967915
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MITI minimum information guidelines for highly multiplexed tissue images.
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA, Human Tumor Atlas Network, Chang YH, Farhi SL, Thorsson V, [...] Sorger PK
Nat Methods, 19(3):262-267, 01 Mar 2022
Cited by: 31 articles | PMID: 35277708 | PMCID: PMC9009186
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Multicellular modules as clinical diagnostic and therapeutic targets.
Baertsch MA, Nolan GP, Hickey JW
Trends Cancer, 8(3):164-173, 03 Dec 2021
Cited by: 6 articles | PMID: 34872889 | PMCID: PMC8854341
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Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma.
Phillips D, Matusiak M, Gutierrez BR, Bhate SS, Barlow GL, Jiang S, Demeter J, Smythe KS, Pierce RH, Fling SP, Ramchurren N, Cheever MA, Goltsev Y, West RB, Khodadoust MS, Kim YH, Schürch CM, Nolan GP
Nat Commun, 12(1):6726, 18 Nov 2021
Cited by: 85 articles | PMID: 34795254 | PMCID: PMC8602403
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CODEX multiplexed tissue imaging with DNA-conjugated antibodies.
Black S, Phillips D, Hickey JW, Kennedy-Darling J, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP
Nat Protoc, 16(8):3802-3835, 02 Jul 2021
Cited by: 202 articles | PMID: 34215862 | PMCID: PMC8647621
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Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data.
Hickey JW, Tan Y, Nolan GP, Goltsev Y
Front Immunol, 12:727626, 13 Aug 2021
Cited by: 51 articles | PMID: 34484237 | PMCID: PMC8415085
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Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing.
Sinjab A, Han G, Treekitkarnmongkol W, Hara K, Brennan PM, Dang M, Hao D, Wang R, Dai E, Dejima H, Zhang J, Bogatenkova E, Sanchez-Espiridion B, Chang K, Little DR, Bazzi S, Tran LM, Krysan K, Behrens C, [...] Kadara H
Cancer Discov, 11(10):2506-2523, 10 May 2021
Cited by: 58 articles | PMID: 33972311 | PMCID: PMC8487926
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Highly Multiplexed Phenotyping of Immunoregulatory Proteins in the Tumor Microenvironment by CODEX Tissue Imaging.
Phillips D, Schürch CM, Khodadoust MS, Kim YH, Nolan GP, Jiang S
Front Immunol, 12:687673, 19 May 2021
Cited by: 54 articles | PMID: 34093591 | PMCID: PMC8170307
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Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction.
Kennedy-Darling J, Bhate SS, Hickey JW, Black S, Barlow GL, Vazquez G, Vazquez G, Venkataraaman VG, Samusik N, Goltsev Y, Schürch CM, Nolan GP
Eur J Immunol, 51(5):1262-1277, 10 Mar 2021
Cited by: 43 articles | PMID: 33548142 | PMCID: PMC8251877
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Biomarkers for Lung Cancer Screening and Detection.
Ostrin EJ, Sidransky D, Spira A, Hanash SM
Cancer Epidemiol Biomarkers Prev, 29(12):2411-2415, 22 Oct 2020
Cited by: 24 articles | PMID: 33093160 | PMCID: PMC7710615
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Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front.
Schürch CM, Bhate SS, Barlow GL, Phillips DJ, Noti L, Zlobec I, Chu P, Black S, Demeter J, McIlwain DR, Kinoshita S, Samusik N, Goltsev Y, Nolan GP
Cell, 182(5):1341-1359.e19, 06 Aug 2020
Cited by: 340 articles | PMID: 32763154 | PMCID: PMC7479520
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Landscape of coordinated immune responses to H1N1 challenge in humans.
Rahil Z, Leylek R, Schürch CM, Chen H, Bjornson-Hooper Z, Christensen SR, Gherardini PF, Bhate SS, Spitzer MH, Fragiadakis GK, Mukherjee N, Kim N, Jiang S, Yo J, Gaudilliere B, Affrime M, Bock B, Hensley SE, Idoyaga J, [...] McIlwain DR
J Clin Invest, 130(11):5800-5816, 01 Nov 2020
Cited by: 20 articles | PMID: 33044226 | PMCID: PMC7598057
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