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Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization.
Peixoto C, Lopes MB, Martins M, Casimiro S, Sobral D, Grosso AR, Abreu C, Macedo D, Costa AL, Pais H, Alvim C, Mansinho A, Filipe P, Costa PMD, Fernandes A, Borralho P, Ferreira C, Malaquias J, Quintela A, Kaplan S, Golkaram M, Salmans M, Khan N, Vijayaraghavan R, Zhang S, Pawlowski T, Godsey J, So A, Liu L, Costa L, Vinga S. Peixoto C, et al. Among authors: zhang s. BMC Bioinformatics. 2023 Jan 16;24(1):17. doi: 10.1186/s12859-022-05104-z. BMC Bioinformatics. 2023. PMID: 36647008 Free PMC article.
Genetic and microenvironmental intra-tumor heterogeneity impacts colorectal cancer evolution and metastatic development.
Sobral D, Martins M, Kaplan S, Golkaram M, Salmans M, Khan N, Vijayaraghavan R, Casimiro S, Fernandes A, Borralho P, Ferreira C, Pinto R, Abreu C, Costa AL, Zhang S, Pawlowski T, Godsey J, Mansinho A, Macedo D, Lobo-Martins S, Filipe P, Esteves R, Coutinho J, Costa PM, Ramires A, Aldeia F, Quintela A, So A, Liu L, Grosso AR, Costa L. Sobral D, et al. Among authors: zhang s. Commun Biol. 2022 Sep 9;5(1):937. doi: 10.1038/s42003-022-03884-x. Commun Biol. 2022. PMID: 36085309 Free PMC article.
HERVs establish a distinct molecular subtype in stage II/III colorectal cancer with poor outcome.
Golkaram M, Salmans ML, Kaplan S, Vijayaraghavan R, Martins M, Khan N, Garbutt C, Wise A, Yao J, Casimiro S, Abreu C, Macedo D, Costa AL, Alvim C, Mansinho A, Filipe P, Marques da Costa P, Fernandes A, Borralho P, Ferreira C, Aldeia F, Malaquias J, Godsey J, So A, Pawlowski T, Costa L, Zhang S, Liu L. Golkaram M, et al. Among authors: zhang s. NPJ Genom Med. 2021 Feb 15;6(1):13. doi: 10.1038/s41525-021-00177-w. NPJ Genom Med. 2021. PMID: 33589643 Free PMC article.
Comprehensive Genomic Profiling of Cell-Free Circulating Tumor DNA Detects Response to Ribociclib Plus Letrozole in a Patient with Metastatic Breast Cancer.
Silveira C, Sousa AC, Corredeira P, Martins M, Sousa AR, Da Cruz Paula A, Selenica P, Brown DN, Golkaram M, Kaplan S, Zhang S, Liu L, Weigelt B, Reis-Filho JS, Costa L, Carmo-Fonseca M. Silveira C, et al. Among authors: zhang s. Biomolecules. 2022 Dec 6;12(12):1818. doi: 10.3390/biom12121818. Biomolecules. 2022. PMID: 36551247 Free PMC article.
Spatiotemporal evolution of the clear cell renal cell carcinoma microenvironment links intra-tumoral heterogeneity to immune escape.
Golkaram M, Kuo F, Gupta S, Carlo MI, Salmans ML, Vijayaraghavan R, Tang C, Makarov V, Rappold P, Blum KA, Zhao C, Mehio R, Zhang S, Godsey J, Pawlowski T, DiNatale RG, Morris LGT, Durack J, Russo P, Kotecha RR, Coleman J, Chen YB, Reuter VE, Motzer RJ, Voss MH, Liu L, Reznik E, Chan TA, Hakimi AA. Golkaram M, et al. Among authors: zhang s. Genome Med. 2022 Dec 19;14(1):143. doi: 10.1186/s13073-022-01146-3. Genome Med. 2022. PMID: 36536472 Free PMC article.
Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy.
Krishna C, DiNatale RG, Kuo F, Srivastava RM, Vuong L, Chowell D, Gupta S, Vanderbilt C, Purohit TA, Liu M, Kansler E, Nixon BG, Chen YB, Makarov V, Blum KA, Attalla K, Weng S, Salmans ML, Golkaram M, Liu L, Zhang S, Vijayaraghavan R, Pawlowski T, Reuter V, Carlo MI, Voss MH, Coleman J, Russo P, Motzer RJ, Li MO, Leslie CS, Chan TA, Hakimi AA. Krishna C, et al. Among authors: zhang s. Cancer Cell. 2021 May 10;39(5):662-677.e6. doi: 10.1016/j.ccell.2021.03.007. Epub 2021 Apr 15. Cancer Cell. 2021. PMID: 33861994 Free PMC article.
Development and Validation of an Ultradeep Next-Generation Sequencing Assay for Testing of Plasma Cell-Free DNA from Patients with Advanced Cancer.
Janku F, Zhang S, Waters J, Liu L, Huang HJ, Subbiah V, Hong DS, Karp DD, Fu S, Cai X, Ramzanali NM, Madwani K, Cabrilo G, Andrews DL, Zhao Y, Javle M, Kopetz ES, Luthra R, Kim HJ, Gnerre S, Satya RV, Chuang HY, Kruglyak KM, Toung J, Zhao C, Shen R, Heymach JV, Meric-Bernstam F, Mills GB, Fan JB, Salathia NS. Janku F, et al. Among authors: zhang s. Clin Cancer Res. 2017 Sep 15;23(18):5648-5656. doi: 10.1158/1078-0432.CCR-17-0291. Epub 2017 May 23. Clin Cancer Res. 2017. PMID: 28536309 Free PMC article.
Feasibility of monitoring advanced melanoma patients using cell-free DNA from plasma.
Gangadhar TC, Savitch SL, Yee SS, Xu W, Huang AC, Harmon S, Lieberman DB, Soucier D, Fan R, Black TA, Morrissette JJD, Salathia N, Waters J, Zhang S, Toung J, van Hummelen P, Fan JB, Xu X, Amaravadi RK, Schuchter LM, Karakousis GC, Hwang WT, Carpenter EL. Gangadhar TC, et al. Among authors: zhang s. Pigment Cell Melanoma Res. 2018 Jan;31(1):73-81. doi: 10.1111/pcmr.12623. Epub 2017 Oct 23. Pigment Cell Melanoma Res. 2018. PMID: 28786531 Free PMC article. Clinical Trial.
MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma.
Zhang S, Wei JS, Li SQ, Badgett TC, Song YK, Agarwal S, Coarfa C, Tolman C, Hurd L, Liao H, He J, Wen X, Liu Z, Thiele CJ, Westermann F, Asgharzadeh S, Seeger RC, Maris JM, Guidry Auvil JM, Smith MA, Kolaczyk ED, Shohet J, Khan J. Zhang S, et al. Cancer Lett. 2016 Feb 28;371(2):214-24. doi: 10.1016/j.canlet.2015.11.045. Epub 2015 Dec 10. Cancer Lett. 2016. PMID: 26683771 Free PMC article.
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