Integrated Omics of Metastatic Colorectal Cancer

Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries

Bray, F., Ferlay, J., Soerjomataram, I., Siegel, R. L., Torre, L. A., & Jemal, A. (2018) · CA: A Cancer Journal for Clinicians · doi:10.3322/caac.21492 · Cited by 84,109 · see citing works

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888 · see citing works

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855 · see citing works

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

Zhou, Y., Zhou, B., Pache, L., Chang, M., Khodabakhshi, A. H., Tanaseichuk, O., Benner, C., & Chanda, S. K. (2019) · Nature Communications · doi:10.1038/s41467-019-09234-6 · Cited by 14,611 · see citing works

An Introduction to Propensity Score Methods for Reducing the Effects of Confounding in Observational Studies

Austin, P. C. (2011) · Multivariate Behavioral Research · doi:10.1080/00273171.2011.568786 · Cited by 12,242 · see citing works

Gephi: An Open Source Software for Exploring and Manipulating Networks

Bastian, M., Heymann, S., & Jacomy, M. (2009) · Proceedings of the International AAAI Conference on Web and Social Media · doi:10.1609/icwsm.v3i1.13937 · Cited by 11,675 · see citing works

Comprehensive molecular characterization of human colon and rectal cancer

The Cancer Genome Atlas Network (2012) · Nature · doi:10.1038/nature11252 · Cited by 8,499 · see citing works

Universal sample preparation method for proteome analysis

Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352 · see citing works

The Ensembl Variant Effect Predictor

McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016) · Genome Biology · doi:10.1186/s13059-016-0974-4 · Cited by 8,099 · see citing works

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

Barretina, J., Caponigro, G., Stransky, N., Venkatesan, K., Margolin, A. A., Kim, S., Wilson, C. J., Lehár, J., Kryukov, G. V., Sonkin, D., et al. (2012) · Nature · doi:10.1038/nature11003 · Cited by 7,950 · see citing works

An automated method for finding molecular complexes in large protein interaction networks

Bader, G. D., & Hogue, C. W. V. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-2 · Cited by 6,112 · see citing works

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

Wilkerson, M. D., & Hayes, D. N. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq170 · Cited by 5,719 · see citing works

Mutational heterogeneity in cancer and the search for new cancer-associated genes

Lawrence, M. S., Stojanov, P., Polak, P., Kryukov, G. V., Cibulskis, K., Sivachenko, A., Carter, S. L., Stewart, C., Mermel, C. H., Roberts, S. A., et al. (2013) · Nature · doi:10.1038/nature12213 · Cited by 5,461 · see citing works

Colorectal cancer

Dekker, E., Tanis, P. J., Vleugels, J. L. A., Kasi, P. M., & Wallace, M. B. (2019) · The Lancet · doi:10.1016/s0140-6736(19)32319-0 · Cited by 5,189 · see citing works

The consensus molecular subtypes of colorectal cancer

Guinney, J., Dienstmann, R., Wang, X., de Reyniès, A., Schlicker, A., Soneson, C., Marisa, L., Roepman, P., Nyamundanda, G., Angelino, P., et al. (2015) · Nature Medicine · doi:10.1038/nm.3967 · Cited by 5,170 · see citing works

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

Tyanova, S., Temu, T., & Cox, J. (2016) · Nature Protocols · doi:10.1038/nprot.2016.136 · Cited by 4,691 · see citing works

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips

Rappsilber, J., Mann, M., & Ishihama, Y. (2007) · Nature Protocols · doi:10.1038/nprot.2007.261 · Cited by 4,641 · see citing works

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

Aryee, M. J., Jaffe, A. E., Bravo, H. C., Ladd‐Acosta, C., Feinberg, A. P., Hansen, K. D., & Irizarry, R. A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu049 · Cited by 4,423 · see citing works

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

Mermel, C. H., Schumacher, S. E., Hill, B., Meyerson, M. M., Beroukhim, R., & Getz, G. A. (2011) · Genome biology · doi:10.1186/gb-2011-12-4-r41 · Cited by 3,469 · see citing works

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

Hornbeck, P. V., Zhang, B., Murray, B., Kornhauser, J. M., Latham, V. M., & Skrzypek, E. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1267 · Cited by 3,243 · see citing works

Systematic identification of genomic markers of drug sensitivity in cancer cells

Garnett, M. J., Edelman, E. J., Heidorn, S. J., Greenman, C. D., Dastur, A., Lau, K. W., Greninger, P., Thompson, I. R., Luo, X., Soares, J., et al. (2012) · Nature · doi:10.1038/nature11005 · Cited by 2,456 · see citing works

COSMIC: somatic cancer genetics at high-resolution

Forbes, S. A., Beare, D., Boutselakis, H., Bamford, S., Bindal, N., Tate, J., Cole, C. G., Ward, S., Dawson, E., Ponting, L., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1121 · Cited by 1,922 · see citing works

Colorectal cancer

Kuipers, E. J., Grady, W. M., Lieberman, D. A., Seufferlein, T. T. W., Sung, J. J. �., Boelens, P. G., van de Velde, C. J. �., & Watanabe, T. (2015) · Nature Reviews Disease Primers · doi:10.1038/nrdp.2015.65 · Cited by 1,683 · see citing works

Proteogenomic characterization of human colon and rectal cancer

CPTAC, T. N., Zhang, B., Wang, J., Wang, X., Zhu, J., Liu, Q., Shi, Z., Chambers, M. C., Zimmerman, L. J., Shaddox, K. F., et al. (2014) · Nature · doi:10.1038/nature13438 · Cited by 1,462 · see citing works

Deciphering Signatures of Mutational Processes Operative in Human Cancer

Alexandrov, L. B., Nik‐Zainal, S., Wedge, D. C., Campbell, P. J., & Stratton, M. R. (2013) · Cell Reports · doi:10.1016/j.celrep.2012.12.008 · Cited by 1,277 · see citing works

Kinase-targeted cancer therapies: progress, challenges and future directions

Bhullar, K. S., Orrego-Lagarón, N., McGowan, E. M., Parmar, I., Jha, A., Hubbard, B. P., & Rupasinghe, H. P. V. (2018) · Molecular Cancer · doi:10.1186/s12943-018-0804-2 · Cited by 1,260 · see citing works

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

Bruderer, R., Bernhardt, O. M., Gandhi, T., Miladinović, S. M., Cheng, L.-Y., Messner, S., Ehrenberger, T., Zanotelli, V., Butscheid, Y., Escher, C., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.044305 · Cited by 1,238 · see citing works

Pan-cancer whole-genome analyses of metastatic solid tumours

Priestley, P., Baber, J., Lolkema, M. P., Steeghs, N., de Bruijn, E., Shale, C., Duyvesteyn, K., Haidari, S., van Hoeck, A., Onstenk, W., et al. (2019) · Nature · doi:10.1038/s41586-019-1689-y · Cited by 1,106 · see citing works

Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma

Gao, Q., Zhu, H., Dong, L., Shi, W., Chen, R., Song, Z., Huang, C., Li, J., Dong, X., Zhou, Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.08.052 · Cited by 1,096 · see citing works

Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma.

Gao, Q., Zhu, H.-W., Dong, L.-Q., Shi, W.-W., Chen, R., Song, Z.-J., Huang, C., Li, J., Dong, X., Zhou, Y.-T., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.038 · Cited by 895 · see citing works

Clinical Sequencing Defines the Genomic Landscape of Metastatic Colorectal Cancer

Yaeger, R., Chatila, W. K., Lipsyc, M. D., Hechtman, J. F., Cercek, A., Sanchez-Vega, F., Jayakumaran, G., Middha, S., Zehir, A., Donoghue, M. T. A., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2017.12.004 · Cited by 858 · see citing works

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

Niu, B., Ye, K., Zhang, Q., Lu, C., Xie, M., McLellan, M. D., Wendl, M. C., & Ding, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt755 · Cited by 822 · see citing works

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

Favero, F., Joshi, T., Marquard, A. M., Birkbak, N. J., Krzystanek, M., Li, Q., Szállási, Z., & Eklund, A. C. (2014) · Annals of Oncology · doi:10.1093/annonc/mdu479 · Cited by 804 · see citing works

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

Vasaikar, S., Huang, C., Wang, X., Petyuk, V. A., Savage, S. R., Wen, B., Dou, Y., Zhang, Y., Shi, Z., Arshad, O. A., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.030 · Cited by 799 · see citing works

From tumour heterogeneity to advances in precision treatment of colorectal cancer

Punt, C. J. A., Koopman, M., & Vermeulen, L. (2017) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2016.171 · Cited by 654 · see citing works

Using i RT , a normalized retention time for more targeted measurement of peptides

Escher, C., Reiter, L., MacLean, B., Ossola, R., Herzog, F., Chilton, J. M., MacCoss, M. J., & Rinner, O. (2012) · PROTEOMICS · doi:10.1002/pmic.201100463 · Cited by 586 · see citing works

Two‐dimensional separation of peptides using RP‐RP‐HPLC system with different pH in first and second separation dimensions

Gilár, M., Olivova, P., Daly, A. E., & Gebler, J. C. (2005) · Journal of Separation Science · doi:10.1002/jssc.200500116 · Cited by 427 · see citing works

Modification‐specific proteomics: Strategies for characterization of post‐translational modifications using enrichment techniques

Zhao, Y., & Jensen, O. N. (2009) · PROTEOMICS · doi:10.1002/pmic.200900398 · Cited by 384 · see citing works

A multicenter study benchmarks software tools for label-free proteome quantification

Navarro, P., Kuharev, J., Gillet, L. C., Bernhardt, O. M., MacLean, B., Röst, H. L., Tate, S. A., Tsou, C.-C., Reiter, L., Distler, U., et al. (2016) · Nature Biotechnology · doi:10.1038/nbt.3685 · Cited by 346 · see citing works

KinomeXplorer: an integrated platform for kinome biology studies

Horn, H., Schoof, E. M., Kim, J., Robin, X., Miller, M. L., Diella, F., Palma, A., Cesareni, G., Jensen, L. J., & Linding, R. (2014) · Nature Methods · doi:10.1038/nmeth.2968 · Cited by 338 · see citing works

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation

Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Fröhlich, F., Cox, J., & Mann, M. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.003699 · Cited by 335 · see citing works

The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics

Wiredja, D. D., Koyutürk, M., & Chance, M. R. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx415 · Cited by 319 · see citing works

Molecular Evolution of Early-Onset Prostate Cancer Identifies Molecular Risk Markers and Clinical Trajectories

Gerhäuser, C., Favero, F., Risch, T. S., Simon, R., Feuerbach, L., Assenov, Y., Heckmann, D., Sidiropoulos, N., Waszak, S. M., Hübschmann, D., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.10.016 · Cited by 289 · see citing works

Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver

Naba, A., Clauser, K. R., Whittaker, C. A., Carr, S. A., Tanabe, K. K., & Hynes, R. O. (2014) · BMC Cancer · doi:10.1186/1471-2407-14-518 · Cited by 238 · see citing works

Global Effects of Kinase Inhibitors on Signaling Networks Revealed by Quantitative Phosphoproteomics

Pan, C., Olsen, J. V., Daub, H., & Mann, M. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900285-mcp200 · Cited by 222 · see citing works

Cell-centred meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD

Gaujoux, R., Starosvetsky, E., Maimon, N., Vallania, F., Bar‐Yoseph, H., Pressman, S., Weisshof, R., Goren, I., Rabinowitz, K. M., Waterman, M., et al. (2018) · Gut · doi:10.1136/gutjnl-2017-315494 · Cited by 196 · see citing works

Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition

Barkovits, K., Pacharra, S., Pfeiffer, K., Steinbach, S., Eisenacher, M., Marcus, K., & Uszkoreit, J. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra119.001714 · Cited by 188 · see citing works

Increasing Trend in Young-Onset Colorectal Cancer in Asia: More Cancers in Men and More Rectal Cancers

Sung, J. J. �., Chiu, H., Jung, K., Jun, J. K., Sekiguchi, M., Matsuda, T., & Kyaw, M. H. (2019) · The American Journal of Gastroenterology · doi:10.14309/ajg.0000000000000133 · Cited by 171 · see citing works

Racial Disparities in Incidence of Young-Onset Colorectal Cancer and Patient Survival

Murphy, C. C., Wallace, K., Sandler, R. S., & Baron, J. A. (2018) · Gastroenterology · doi:10.1053/j.gastro.2018.11.060 · Cited by 163 · see citing works

Reversed-Phase-Reversed-Phase Liquid Chromatography Approach with High Orthogonality for Multidimensional Separation of Phosphopeptides

Song, C., Ye, M., Han, G., Jiang, X., Wang, F., Yu, Z., Chen, R., & Zou, H. (2009) · Analytical Chemistry · doi:10.1021/ac9023044 · Cited by 150 · see citing works

Heterogeneity and cancer.

Allison, K. H., & Sledge, G. W. (2014) · PubMed · Cited by 113 · see citing works

Rectal Cancer in Asian vs. Western Countries: Why the Variation in Incidence?

Deng, Y. (2017) · Current Treatment Options in Oncology · doi:10.1007/s11864-017-0500-2 · Cited by 102 · see citing works

Characterization of drug responses of mini patient‐derived xenografts in mice for predicting cancer patient clinical therapeutic response

Zhang, F., Wang, W., Long, Y., Liu, H., Cheng, J., Guo, L., Li, R., Meng, C., Yu, S., Zhao, Q., et al. (2018) · 癌症：英文版 · doi:10.1186/s40880-018-0329-5 · Cited by 94 · see citing works

Diagnosing phenotypes of single-sample individuals by edge biomarkers

Zhang, W., Zeng, T., Liu, X., & Chen, L. (2015) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjv025 · Cited by 81 · see citing works

Differences in Colorectal Cancer Outcomes by Race and Insurance

Tawk, R. H., Abner, A., Ashford, A., & Brown, C. (2015) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph13010048 · Cited by 76 · see citing works

Influence of DNA copy number and mRNA levels on the expression of breast cancer related proteins

Myhre, S., Lingjærde, O. C., Hennessy, B. T., Aure, M. R. R., Carey, M. S., Alsner, J., Tramm, T., Overgaard, J., Mills, G. B., Børresen‐Dale, A., et al. (2013) · Molecular Oncology · doi:10.1016/j.molonc.2013.02.018 · Cited by 71 · see citing works

Temporal Profiling of Lapatinib-suppressed Phosphorylation Signals in EGFR/HER2 Pathways

Imami, K., Sugiyama, N., Imamura, H., Wakabayashi, M., Tomita, M., Taniguchi, M., Ueno, T., Toi, M., & Ishihama, Y. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.019919 · Cited by 52 · see citing works

Integrating phosphoproteomics into kinase-targeted cancer therapies in precision medicine

Wu, X., Xing, X., Dowlut, D., Zeng, Y., Liu, J., & Liu, X. (2018) · Journal of Proteomics · doi:10.1016/j.jprot.2018.03.033 · Cited by 49 · see citing works

New opportunities for kinase drug repurposing and target discovery

Knapp, S. (2018) · British Journal of Cancer · doi:10.1038/s41416-018-0045-6 · Cited by 46 · see citing works

Novel phosphorylation site markers of protein kinase C delta activation

Durgan, J., Michael, N., Totty, N., & Parker, P. J. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.06.035 · Cited by 41 · see citing works

Personalized treatment based on mini patient‐derived xenografts and WES/RNA sequencing in a patient with metastatic duodenal adenocarcinoma

Zhao, P., Chen, H., Wen, D., Mou, S., Zhang, F., & Zheng, S. (2018) · 癌症：英文版 · doi:10.1186/s40880-018-0323-y · Cited by 37 · see citing works

Whole-Exome Sequencing Identifies Novel Somatic Mutations in Chinese Breast Cancer Patients

Zhang, Y., & Cai, Q. (2015) · Journal of Molecular and Genetic Medicine · doi:10.4172/1747-0862.1000183 · Cited by 34 · see citing works

Identification of metastasis driver genes by massive parallel sequencing of successive steps of breast cancer progression

Krøigård, A. B., Larsen, M. J., Lænkholm, A., Knoop, A. S., Jensen, J. D., Bak, M., Mollenhauer, J., Thomassen, M., & Kruse, T. A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0189887 · Cited by 34 · see citing works

Racial Differences in Colorectal Cancer Incidence and Mortality in the Women's Health Initiative

Simon, M. S., Thomson, C. A., Pettijohn, E. M., Kato, I., Rodabough, R. J., Lane, D. S., Hubbell, F. A., O’Sullivan, M. J., Adams-Campbell, L. L., Mouton, C. P., et al. (2011) · Cancer Epidemiology Biomarkers & Prevention · doi:10.1158/1055-9965.epi-11-0027 · Cited by 33 · see citing works

Prevalence of Advanced, Precancerous Colorectal Neoplasms in Black and White Populations: A Systematic Review and Meta-analysis

Imperiale, T. F., Abhyankar, P. R., Stump, T. E., & Emmett, T. W. (2018) · Gastroenterology · doi:10.1053/j.gastro.2018.08.020 · Cited by 27 · see citing works

Feasibility study of large-scale production of iodine-125 at the high temperature engineering test reactor

Ho, H. Q., Honda, Y., Hamamoto, S., Ishii, T., Fujimoto, N., & Ishitsuka, E. (2018) · Applied Radiation and Isotopes · doi:10.1016/j.apradiso.2018.07.024 · Cited by 8 · see citing works

The inflammatory pathogenesis of colorectal cancer

Schmitt, M., & Greten, F. R. (2021) · Nature reviews. Immunology · doi:10.1038/s41577-021-00534-x · Cited by 796 · see citing works

Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications

Zhong, Q., Xiao, X., Qiu, Y., Xu, Z., Chen, C., Chong, B., Zhao, X., Hai, S., Li, S., An, Z., et al. (2023) · MedComm · doi:10.1002/mco2.261 · Cited by 442 · see citing works

Proteogenomic characterization identifies clinically relevant subgroups of intrahepatic cholangiocarcinoma

Dong, L., Lu, D., Chen, R., Lin, Y., Zhu, H., Zhang, Z., Cai, S., Cui, P., Song, G., Rao, D., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2021.12.006 · Cited by 400 · see citing works

Multi-omics approaches for biomarker discovery in early ovarian cancer diagnosis

Xiao, Y., Bi, M., Guo, H., & Li, M. (2022) · EBioMedicine · doi:10.1016/j.ebiom.2022.104001 · Cited by 256 · see citing works

Cancer proteogenomics: current impact and future prospects

Mani, D. R., Krug, K., Zhang, B., Satpathy, S., Clauser, K. R., Ding, L., Ellis, M., Gillette, M. A., & Carr, S. A. (2022) · Nature Reviews Cancer · doi:10.1038/s41568-022-00446-5 · Cited by 229 · see citing works

The updated role of exosomal proteins in the diagnosis, prognosis, and treatment of cancer

Wang, X., Huang, J., Chen, W., Li, G., Li, Z., & Lei, J. (2022) · Experimental & Molecular Medicine · doi:10.1038/s12276-022-00855-4 · Cited by 190 · see citing works

Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics

Lou, R., Cao, Y., Li, S., Lang, X., Li, Y., Zhang, Y., & Shui, W. (2023) · Nature Communications · doi:10.1038/s41467-022-35740-1 · Cited by 143 · see citing works

A proteogenomic analysis of clear cell renal cell carcinoma in a Chinese population

Qu, Y., Feng, J., Wu, X., Bai, L., Xu, W., Zhu, L., Liu, Y., Xu, F., Zhang, X., Yang, G., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29577-x · Cited by 139 · see citing works

Macrophage STING signaling promotes NK cell to suppress colorectal cancer liver metastasis via 4-1BBL/4-1BB co-stimulation

Sun, Y., Hu, H., Liu, Z., Xu, J., Gao, Y., Zhan, X., Zhou, S., Zhong, W., Wu, D., Wang, P., et al. (2023) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2022-006481 · Cited by 118 · see citing works

Integrated approaches for precision oncology in colorectal cancer: The more you know, the better

Andrei, P., Battuello, P., Grasso, G., Rovera, E., Tesio, N., & Bardelli, A. (2021) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2021.04.007 · Cited by 113 · see citing works

Global mapping of cancers: The Cancer Genome Atlas and beyond

Ganini, C., Amelio, I., Bertolo, R. G., Bove, P., Buonomo, O. C., Candi, E., Cipriani, C., Daniele, N. D., Juhl, H. H., Mauriello, A., et al. (2021) · Molecular Oncology · doi:10.1002/1878-0261.13056 · Cited by 108 · see citing works

Integrated Multi-Omics Landscape of Liver Metastases

Yang, S., Qian, L., Li, Z., Li, Y., Bai, J., Zheng, B. J., Chen, K., Qiu, X., Cai, G., Wang, S., et al. (2022) · Gastroenterology · doi:10.1053/j.gastro.2022.11.029 · Cited by 102 · see citing works

Molecular Profiling Provides Clinical Insights Into Targeted and Immunotherapies as Well as Colorectal Cancer Prognosis

Guo, L., Wang, Y., Yang, W., Wang, C., Guo, T., Yang, J., Shao, Z., Cai, G., Cai, S., Zhang, L., et al. (2023) · Gastroenterology · doi:10.1053/j.gastro.2023.04.029 · Cited by 84 · see citing works

Bioinformatics Analysis and Validation of Potential Markers Associated with Prediction and Prognosis of Gastric Cancer

Matsuoka, T., & Yashiro, M. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25115880 · Cited by 83 · see citing works

Applications of human organoids in the personalized treatment for digestive diseases

Wang, Q., Guo, F., Jin, Y., & Ma, Y. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01194-6 · Cited by 81 · see citing works

Integrated multi-omics approach to distinct molecular characterization and classification of early-onset colorectal cancer

Du, M., Gu, D., Xin, J., Peters, U., Song, M., Cai, G., Li, S., Ben, S., Meng, Y., Chu, H., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.100974 · Cited by 80 · see citing works

Liquid biopsies and cancer omics

Amelio, I., Bertolo, R. G., Bove, P., Buonomo, O. C., Candi, E., Chiocchi, M., Cipriani, C., Daniele, N. D., Ganini, C., Juhl, H. H., et al. (2020) · Cell Death Discovery · doi:10.1038/s41420-020-00373-0 · Cited by 78 · see citing works

circCAPRIN1 interacts with STAT2 to promote tumor progression and lipid synthesis via upregulating ACC1 expression in colorectal cancer

Yang, Y., Luo, D., Shao, Y. W., Shan, Z., Liu, Q., Weng, J., He, W., Zhang, R., Li, Q., Wang, Z., et al. (2022) · 癌症：英文版 · doi:10.1002/cac2.12380 · Cited by 77 · see citing works

DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation

Lou, R., Liu, W., Li, R., Li, S., He, X., & Shui, W. (2021) · Nature Communications · doi:10.1038/s41467-021-26979-1 · Cited by 67 · see citing works

Exosomes: Another intercellular lipometabolic communication mediators in digestive system neoplasms?

Li, S., Dong, R., 康振华, Li, H., Wu, X., & Li, T. X. (2023) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2023.06.005 · Cited by 70 · see citing works

Integrative proteogenomic characterization of early esophageal cancer

Li, L., Jiang, D., Zhang, Q., Liu, H., Xu, F., Guo, C., Qin, Z., Wang, H., Feng, J., Liu, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37440-w · Cited by 67 · see citing works

Copy number amplification of ENSA promotes the progression of triple-negative breast cancer via cholesterol biosynthesis

Chen, Y., Ge, J., Zhu, S., Shao, Z., & Yu, K. (2022) · Nature Communications · doi:10.1038/s41467-022-28452-z · Cited by 66 · see citing works

Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues

Abelin, J. G., Bergstrom, E. J., Rivera, K. D., Taylor, H. B., Klaeger, S., Xu, C., Verzani, E. K., White, C. J., Woldemichael, H. B., Virshup, M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37547-0 · Cited by 61 · see citing works

Proteomics of post-translational modifications in colorectal cancer: Discovery of new biomarkers

Zhu, G., Jin, L., Sun, W., Wang, S., & Liu, N. (2022) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2022.188735 · Cited by 62 · see citing works

<i>Meta</i> Cancer: A deep learning-based pan-cancer metastasis prediction model developed using multi-omics data

Albaradei, S., Napolitano, F., Thafar, M. A., Gojobori, T., Essack, M., & Gao, X. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.08.006 · Cited by 61 · see citing works

Integrated omics landscape of hepatocellular carcinoma suggests proteomic subtypes for precision therapy

Xing, X., Hu, E., Ouyang, J., Zhong, X., Wang, F., Liu, K., Cai, L., Zhou, Y., Wang, Y., Chen, G., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101315 · Cited by 55 · see citing works

Age-Associated Proteomic Signatures and Potential Clinically Actionable Targets of Colorectal Cancer

Gong, Y., Liu, Y., Wang, T., Li, Z., Gao, L. P., Chen, H., Shu, Y., Li, Y., Xu, H., Zhou, Z., et al. (2021) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2021.100115 · Cited by 54 · see citing works

Integrated multi-omics characterization of KRAS mutant colorectal cancer

Chong, W., Zhu, X., Ren, H., Ye, C., Xu, K., Wang, Z., Jia, S., Shang, L., Li, L., & Chen, H. (2022) · Theranostics · doi:10.7150/thno.73089 · Cited by 53 · see citing works

Molecular differences of angiogenic versus vessel co-opting colorectal cancer liver metastases at single-cell resolution

Fleischer, J. R., Schmitt, A. M., Haas, G., Xu, X., Zeisberg, E. M., Bohnenberger, H., Küffer, S., Teuwen, L.-A. M. N., Karras, P. J., Beißbarth, T., et al. (2023) · Molecular Cancer · doi:10.1186/s12943-023-01713-1 · Cited by 54 · see citing works

Stemness Refines the Classification of Colorectal Cancer With Stratified Prognosis, Multi-Omics Landscape, Potential Mechanisms, and Treatment Options

Liu, Z., Xu, H., Weng, S., Ren, Y., & Han, X. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.828330 · Cited by 52 · see citing works

m6A modification of lncRNA ABHD11-AS1 promotes colorectal cancer progression and inhibits ferroptosis through TRIM21/IGF2BP2/ FOXM1 positive feedback loop

Bian, Y., Xu, S., Gao, Z., Ding, J., Li, C., Cui, Z., Sun, H., Li, J., Pu, J., & Wang, K. (2024) · Cancer Letters · doi:10.1016/j.canlet.2024.217004 · Cited by 52 · see citing works

Baicalin triggers apoptosis, inhibits migration, and enhances anti‐tumor immunity in colorectal cancer via TLR4/NF‐κB signaling pathway

Song, L., Zhu, S., Liu, C., Zhang, Q., & Liang, X. (2022) · Journal of Food Biochemistry · doi:10.1111/jfbc.13703 · Cited by 51 · see citing works

Mitochondrial metabolic reprogramming in colorectal cancer: mechanisms of resistance and future clinical interventions

Qiu, X., Wang, A., Wang, J., Zhang, Z., & Tao, L. (2025) · Cell Death Discovery · doi:10.1038/s41420-025-02670-y · Cited by 56 · see citing works

Multilevel proteomic analyses reveal molecular diversity between diffuse-type and intestinal-type gastric cancer

Shi, W., Wang, Y., Xu, C., Li, Y., Ge, S., Bai, B., Zhang, K., Wang, Y., Zheng, N., Wang, J., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-35797-6 · Cited by 50 · see citing works

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., et al. (2022) · Communications Biology · doi:10.1038/s42003-022-03884-x · Cited by 48 · see citing works

Molecular biomarkers, network biomarkers, and dynamic network biomarkers for diagnosis and prediction of rare diseases

Tang, S., Yuan, K., & Chen, L. (2022) · Fundamental Research · doi:10.1016/j.fmre.2022.07.011 · Cited by 47 · see citing works

Integrative proteomic characterization of adenocarcinoma of esophagogastric junction

Li, S., Li, Y., Xu, Z., Xu, J., Chen, G., Guan, X., Pan, G.-Z., Hu, C., Dong, J., Du, Y., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36462-8 · Cited by 46 · see citing works

Proteogenomics refines the molecular classification of chronic lymphocytic leukemia

Herbst, S. A., Vesterlund, M., Helmboldt, A. J., Jafari, R., Siavelis, I., Stahl, M. M. S., Schitter, E. C., Liebers, N., Brinkmann, B. J., Czernilofsky, F., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33385-8 · Cited by 46 · see citing works

Proteomics of adjacent-to-tumor samples uncovers clinically relevant biological events in hepatocellular carcinoma

Zhu, H.-W., Lin, Y.-P., Lu, D.-Y., Wang, S., Liu, Y., Dong, L.-Q., Meng, Q., Gao, J., Wang, Y., Song, N., et al. (2023) · National Science Review · doi:10.1093/nsr/nwad167 · Cited by 40 · see citing works

Quartet protein reference materials and datasets for multi-platform assessment of label-free proteomics

Tian, S., Zhan, D., Yu, Y., Wang, Y., Liu, M., Tan, S., Li, Y., Song, L., Qin, Z., Li, X., et al. (2023) · Genome Biology · doi:10.1186/s13059-023-03048-y · Cited by 43 · see citing works

Genetic interactions reveal distinct biological and therapeutic implications in breast cancer

Lin, C., Jin, X., Ma, D., Chen, C., Ou-Yang, Y., Pei, Y., Zhou, C., Qu, F., Wang, Y., Liu, C., et al. (2024) · Cancer Cell · doi:10.1016/j.ccell.2024.03.006 · Cited by 42 · see citing works

Comprehensive characterization of tumor microenvironment in colorectal cancer via molecular analysis

Wu, X., Yan, H., Qiu, M., Qu, X., Wang, J., Xu, S., Zheng, Y., Ge, M., Yan, L., & Li, L. (2023) · eLife · doi:10.7554/elife.86032 · Cited by 42 · see citing works

Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypes

Gao, E., Li, W., Wu, C., Shao, W., Di, Y., & Liu, Y. (2021) · Molecular Omics · doi:10.1039/d0mo00188k · Cited by 41 · see citing works

TRIM21 is a druggable target for the treatment of metastatic colorectal cancer through ubiquitination and activation of MST2

Liu, Y.-X., Wan, S., Yang, X., Wang, Y., Gan, W.-J., Ye, W.-L., He, X., Chen, J.-J., Yang, Y., Yang, X., et al. (2023) · Cell chemical biology · doi:10.1016/j.chembiol.2023.05.009 · Cited by 40 · see citing works

Translation Potential and Challenges of In Vitro and Murine Models in Cancer Clinic

Long, Y., Xie, B., Shen, H. C., & Wen, D. (2022) · Cells · doi:10.3390/cells11233868 · Cited by 40 · see citing works

LncRNA NALT1 promotes colorectal cancer progression via targeting PEG10 by sponging microRNA-574-5p

Ye, M., Zhao, L., Zhang, L., Wu, S., Zhao, L., Qin, Y., Lin, F., & Pan, L. (2022) · Cell Death and Disease · doi:10.1038/s41419-022-05404-5 · Cited by 37 · see citing works

Phosphoproteomics of patient-derived xenografts identifies targets and markers associated with sensitivity and resistance to EGFR blockade in colorectal cancer

Beekhof, R., Bertotti, A., Böttger, F., Vurchio, V., Cottino, F., Zanella, E. R., Migliardi, G., Viviani, M., Grassi, E., Lupo, B., et al. (2023) · Science Translational Medicine · doi:10.1126/scitranslmed.abm3687 · Cited by 36 · see citing works

Medicinal chemistry perspectives on anticancer drug design based on clinical applications (2015–2025)

Al-Karmalawy, A. A., Eissa, M. E., Ashour, N. A., Yousef, T. A., Khatib, A. O. A., & Hawas, S. S. (2025) · RSC Advances · doi:10.1039/d5ra05472a · Cited by 38 · see citing works

Proteogenomic characterization of primary colorectal cancer and metastatic progression identifies proteome-based subtypes and signatures

Tanaka, A., Ogawa, M., Zhou, Y., Namba, K., Hendrickson, R. C., Miele, M. M., Li, Z., Klimstra, D. S., Buckley, P. G., Gulcher, J. R., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113810 · Cited by 33 · see citing works

Personalized Immunotherapy in Colorectal Cancers: Where Do We Stand?

Hu, L., Lan, H., Huang, D., Li, X., & Jin, K. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.769305 · Cited by 34 · see citing works

A tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes

Trip, D. S. L., van Oostrum, M., Memon, D., Frommelt, F., Baptista, D., Panneerselvam, K., Bradley, G., Licata, L., Hermjakob, H., Orchard, S. E., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02659-z · Cited by 39 · see citing works

Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4–pRB Axis in Fibroblasts at the Invasive Tumor Edge

Bouchard, G., Garcia-Marques, F. J., Karacosta, L. G., Zhang, W., Bermudez, A., Riley, N. M., Varma, S., Mehl, L. C., Benson, J. A., Shrager, J. B., et al. (2021) · Cancer Research · doi:10.1158/0008-5472.can-21-1705 · Cited by 31 · see citing works

Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors unravels clinically relevant subgroups

Ji, S., Cao, L., Gao, J., Du, Y., Zeng, Y., Lou, X., Liu, F., Zhang, Y., Xu, J., Shi, X., et al. (2025) · Cancer Cell · doi:10.1016/j.ccell.2025.03.016 · Cited by 30 · see citing works

Targeting the NOTCH2/ADAM10/TCF7L2 Axis‐Mediated Transcriptional Regulation of Wnt Pathway Suppresses Tumor Growth and Enhances Chemosensitivity in Colorectal Cancer

Xiang, Z., Wang, Y., Ma, X., Song, S., He, Y., Zhou, J., Feng, L.-H., Yang, S., Wu, Y., Yu, B., et al. (2024) · Advanced Science · doi:10.1002/advs.202405758 · Cited by 27 · see citing works

Proteomics of Colorectal Cancer: Tumors, Organoids, and Cell Cultures—A Minireview

Lindhorst, P. H., & Hummon, A. B. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.604492 · Cited by 27 · see citing works

Inferring kinase activity from phosphoproteomic data: Tool comparison and recent applications

Piersma, S. R., Vallés‐Martí, A., Rolfs, F., Pham, T. V., Henneman, A. A., & Jiménez, C. R. (2022) · Mass Spectrometry Reviews · doi:10.1002/mas.21808 · Cited by 27 · see citing works

PRDM15 interacts with DNA-PK-Ku complex to promote radioresistance in rectal cancer by facilitating DNA damage repair

Yu, Y., Liu, T., Yu, G., Wang, H., Du, Z., Chen, Y., Yang, N., Cao, K., Liu, C., Wan, Z., et al. (2022) · Cell Death and Disease · doi:10.1038/s41419-022-05402-7 · Cited by 26 · see citing works

LncRNA SNHG1 facilitates colorectal cancer cells metastasis by recruiting HNRNPD protein to stabilize SERPINA3 mRNA

Yang, H., Gong, C., Wu, Y., Xie, X., Chen, Y., Li, Z., Shi, Q., Liu, J., Gao, N., He, B., et al. (2024) · Cancer Letters · doi:10.1016/j.canlet.2024.217217 · Cited by 24 · see citing works

Immune dynamics shaping pre-metastatic and metastatic niches in liver metastases: from molecular mechanisms to therapeutic strategies

Zhu, C., Liao, J.-Y., Liu, Y., Chen, Z., Chang, R.-Z., Chen, X., Zhang, B., & Liang, J.-N. (2024) · Molecular Cancer · doi:10.1186/s12943-024-02171-z · Cited by 26 · see citing works

The liver metastatic niche: modelling the extracellular matrix in metastasis

Drew, J., & Machesky, L. M. (2021) · Disease Models & Mechanisms · doi:10.1242/dmm.048801 · Cited by 24 · see citing works

Integrated Analysis of a Ferroptosis-Related LncRNA Signature for Evaluating the Prognosis of Patients with Colorectal Cancer

Xu, S., Zhou, Y., Luo, J., Chen, S., Xie, J., Liu, H., Wang, Y., & Li, Z. (2022) · Genes · doi:10.3390/genes13061094 · Cited by 24 · see citing works

PDGFA‐associated protein 1 is a novel target of c‐Myc and contributes to colorectal cancer initiation and progression

Cui, H., Wei, W., Qian, M., Tian, R., Fu, X., Li, H., Nan, G., Yang, T., Lin, P., Chen, X., et al. (2022) · 癌症：英文版 · doi:10.1002/cac2.12322 · Cited by 22 · see citing works

Colorectal cancer liver metastasis: genomic evolution and crosstalk with the liver microenvironment

Liu, Q.-L., Zhou, H., Zhou, Z., & Chen, H. (2023) · Cancer and Metastasis Reviews · doi:10.1007/s10555-023-10107-0 · Cited by 22 · see citing works

Proteomic characterization of the colorectal cancer response to chemoradiation and targeted therapies reveals potential therapeutic strategies

Li, Y., Wang, B., Ma, F., Jiang, D., Wang, Y., Li, K., Tan, S., Feng, J., Wang, Y., Qin, Z., et al. (2023) · Cell Reports Medicine · doi:10.1016/j.xcrm.2023.101311 · Cited by 21 · see citing works

Mitochondrial DNA-boosted dendritic cell-based nanovaccination triggers antitumor immunity in lung and pancreatic cancers

Shang, L., Jiang, X., Zhao, X., Huang, X., Wang, X., Jiang, X., Kong, X., Yao, M., Jiang, S., & Wong, P. (2024) · Cell Reports Medicine · doi:10.1016/j.xcrm.2024.101648 · Cited by 21 · see citing works

Molecular subtyping in colorectal cancer: A bridge to personalized therapy (Review)

Wang, C., Zhang, H., Liu, Y., Wang, Y., Hu, H., & Wang, G. (2023) · Oncology Letters · doi:10.3892/ol.2023.13816 · Cited by 20 · see citing works

Predictive value of intratumoral-metabolic heterogeneity derived from 18F-FDG PET/CT in distinguishing microsatellite instability status of colorectal carcinoma

Zhang, L., Liu, Y., Ding, Y., Deng, Y., Chen, H., Hu, F., Fan, J., Lan, X., & Cao, W. W. (2023) · Frontiers in Oncology · doi:10.3389/fonc.2023.1065744 · Cited by 20 · see citing works

Investigating the modulatory effects of Moringa oleifera on the gut microbiota of chicken model through metagenomic approach

Soundararajan, S., Selvakumar, J., Joseph, Z. M. M., Gopinath, Y., Saravanan, V., & Santhanam, R. K. (2023) · Frontiers in Veterinary Science · doi:10.3389/fvets.2023.1153769 · Cited by 20 · see citing works

Biological and Clinical Characteristics of Proximal Colon Cancer: Far from Its Anatomical Subsite

Yang, Q. Z., Qu, R., Lu, S., Zhang, Y., Zhang, Z., & Fu, W. (2024) · International Journal of Medical Sciences · doi:10.7150/ijms.97574 · Cited by 20 · see citing works

Integrated Profiling Identifies PLOD3 as a Potential Prognostic and Immunotherapy Relevant Biomarker in Colorectal Cancer

Shi, J., Bao, M., Wang, W.-F., Wu, X., Li, Y., Changdong, Z., & Liu, W. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.722807 · Cited by 20 · see citing works

Spatial multi-omics reveals the potential involvement of SPP1+ fibroblasts in determining metabolic heterogeneity and promoting metastatic growth of colorectal cancer liver metastasis

Gao, Y., Zhang, X., Xia, S., Chen, Q., Tong, Q., Yu, S., An, R., Cheng, C., Zou, W., Liang, L., et al. (2025) · Molecular Therapy · doi:10.1016/j.ymthe.2025.05.004 · Cited by 19 · see citing works

Phenotypic Heterogeneity Analysis of APC-Mutant Colon Cancer by Proteomics and Phosphoproteomics Identifies RAI14 as a Key Prognostic Determinant in East Asians and Westerners

Zhang, R., Hu, M. X., Chen, H., Wang, X., Xia, Z., Liu, Y., Wang, R., Xia, X., Yang, S., Du, D., et al. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100532 · Cited by 19 · see citing works

PRPF19 facilitates colorectal cancer liver metastasis through activation of the Src-YAP1 pathway via K63-linked ubiquitination of MYL9

Zhou, R., Chen, J., Jia, J., Ye, Y., Ye, Y., 钟国平, Chen, T., & Qiu, L. (2023) · Cell Death and Disease · doi:10.1038/s41419-023-05776-2 · Cited by 19 · see citing works

Multiomics of HER2-low triple-negative breast cancer identifies a receptor tyrosine kinase–relevant subgroup with therapeutic prospects

Chen, L., Liu, C., Zhu, S., Ge, J., Chen, Y., Ma, D., Shao, Z., & Yu, K. (2023) · JCI Insight · doi:10.1172/jci.insight.172366 · Cited by 19 · see citing works

Lipid metabolism in metastasis and therapy

Martín‐Pérez, M., Urdiroz-Urricelqui, U., Bigas, C., & Benitah, S. A. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.100401 · Cited by 19 · see citing works

Recent Advances in Our Knowledge of mCRC Tumor Biology and Genetics: A Focus on Targeted Therapy Development

Gmeiner, W. H. (2021) · OncoTargets and Therapy · doi:10.2147/ott.s242224 · Cited by 18 · see citing works

Multi-omics characterization of esophageal squamous cell carcinoma identifies molecular subtypes and therapeutic targets

Zhao, D., Guo, Y., Wei, H., Jia, X., Zhi, Y., He, G., Nie, W., Huang, L., Wang, P., Laster, K. V., et al. (2024) · JCI Insight · doi:10.1172/jci.insight.171916 · Cited by 18 · see citing works

Multi-omics synergy in oncology: Unraveling the complex interplay of radiomic, genoproteomic, and pathological data

Luo, Y., Li, Y., Fang, M., Wang, S., Shao, L., Zou, R., Dong, D., Liu, Z., Wei, J., & Tian, J. (2024) · Intelligent Oncology · doi:10.1016/j.intonc.2024.10.003 · Cited by 17 · see citing works

Chromatin accessibility dynamics in colorectal cancer liver metastasis: Uncovering the liver tropism at single cell resolution

Li, S., Yang, M. J., Teng, S., Lin, K., Wang, Y., Zhang, Y., Guo, W., & Wang, D. (2023) · Pharmacological Research · doi:10.1016/j.phrs.2023.106896 · Cited by 17 · see citing works

An interpretable deep learning framework for predicting liver metastases in postoperative colorectal cancer patients using natural language processing and clinical data integration

Li, J., Wang, X., Cai, L., Sun, J., Yang, Z., Liu, W., Wang, Z., & Lv, H. (2023) · Cancer Medicine · doi:10.1002/cam4.6523 · Cited by 18 · see citing works

Integration of proteomics in the molecular tumor board

Thiery, J., & Fahrner, M. (2023) · PROTEOMICS · doi:10.1002/pmic.202300002 · Cited by 18 · see citing works

High-Coverage Serum Metabolomics Reveals Metabolic Pathway Dysregulation in Diabetic Retinopathy: A Propensity Score-Matched Study

Guo, C., Jiang, D., Xu, Y., Peng, F., Zhao, S., Li, H., Jin, D., Xu, X., Xia, Z., Che, M., et al. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.822647 · Cited by 18 · see citing works

Proteomic Stratification of Prognosis and Treatment Options for Small Cell Lung Cancer

Huo, Z., Duan, Y., Zhan, D., Xu, X., Zheng, N., Cai, J., Sun, R., Wang, J., Cheng, F., Gao, Z. C., et al. (2024) · Genomics Proteomics & Bioinformatics · doi:10.1093/gpbjnl/qzae033 · Cited by 17 · see citing works

Cytogenetic signatures favoring metastatic organotropism in colorectal cancer

Golas, M. M., Gunawan, B., Gutenberg, A., Danner, B. C., Gerdes, J. S., Stadelmann, C., FÜZESI, L., Liersch, T., & Sander, B. O. (2025) · Nature Communications · doi:10.1038/s41467-025-58413-1 · Cited by 17 · see citing works

Proteomic Profiling and Biomarker Discovery in Colorectal Liver Metastases

Wong, G. Y. M., Diakos, C., Hugh, T., & Molloy, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23116091 · Cited by 16 · see citing works

3D matrix promotes cell dedifferentiation into colorectal cancer stem cells via integrin/cytoskeleton/glycolysis signaling

Han, T., Jiang, Y., Wang, X., Deng, S., Hu, Y., Jin, Q., Long, D., & Liu, K. (2022) · Cancer Science · doi:10.1111/cas.15548 · Cited by 17 · see citing works

Biological factors driving colorectal cancer metastasis

An, S.-X., Yu, Z., Fu, C., Wei, M., & Shen, L.-H. (2024) · World Journal of Gastrointestinal Oncology · doi:10.4251/wjgo.v16.i2.259 · Cited by 17 · see citing works

Standard operating procedure combined with comprehensive quality control system for multiple LC-MS platforms urinary proteomics

Liu, X., Sun, H., Hou, X., Sun, J., Tang, M., Zhang, Y., Zhang, Y., Sun, W., Liu, C., Urine Test Sample Working Group, et al. (2025) · Nature Communications · doi:10.1038/s41467-025-56337-4 · Cited by 15 · see citing works

The interplay between tissue‐resident microbiome and host proteins by integrated multi‐omics during progression of colorectal adenoma to carcinoma

Wu, D., Wang, A., Bu, D., Sun, Y., Li, C., Hong, Y.-M., Zhang, S., Chen, S., Zhou, J., Zhang, T., et al. (2025) · iMeta · doi:10.1002/imt2.70090 · Cited by 16 · see citing works

MEK-mediated CHPF2 phosphorylation promotes colorectal cancer cell proliferation and metastasis by activating NF-κB signaling

Wen, X., Qin, J., Zhang, X., Ye, L., Wang, Y., Yang, R., Di, Y., He, W., & Wang, Z. (2024) · Cancer Letters · doi:10.1016/j.canlet.2024.216644 · Cited by 16 · see citing works

Characterisation of Colorectal Cancer Cell Lines through Proteomic Profiling of Their Extracellular Vesicles

Heck, K. A., Lindholm, H. T., Niederdorfer, B., Tsirvouli, E., Kuiper, M. T. R., Flobak, Å., Lægreid, A., & Thommesen, L. (2023) · Proteomes · doi:10.3390/proteomes11010003 · Cited by 15 · see citing works

Network pharmacology and bioinformatics were used to construct a prognostic model and immunoassay of core target genes in the combination of quercetin and kaempferol in the treatment of colorectal cancer

Gu, C., Tang, L., Hao, Y., Dong, S., Shen, J., Xie, F., Han, Z., Luo, W., He, J., & Li, Y. (2023) · Journal of Cancer · doi:10.7150/jca.85517 · Cited by 15 · see citing works

Quantitative Proteomics of Tissue-Infiltrating T Cells From CRC Patients Identified Lipocalin-2 Induces T-Cell Apoptosis and Promotes Tumor Cell Proliferation by Iron Efflux

Che, R., Wang, Q., Li, M., Shen, J. H., & Ji, J. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100691 · Cited by 15 · see citing works

NUP43 promotes PD-L1/nPD-L1/PD-L1 feedback loop via TM4SF1/JAK/STAT3 pathway in colorectal cancer progression and metastatsis

Wu, F., Sun, G., Nai, Y., Shi, X., Ma, Y., & Cao, H. (2024) · Cell Death Discovery · doi:10.1038/s41420-024-02025-z · Cited by 16 · see citing works

Beyond ribosomal function: RPS6 deficiency suppresses cholangiocarcinoma cell growth by disrupting alternative splicing

Fu, W., Lin, Y., Bai, M., Yao, J., Huang, C., Gao, L., Mi, N., Ma, H., Tian, L., Yue, P., et al. (2024) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2024.06.028 · Cited by 15 · see citing works

Proteogenomics offers a novel avenue in neoantigen identification for cancer immunotherapy

Ren, Y., Yue, Y., Li, X., Weng, S., Xu, H., Liu, L., Cheng, Q., Luo, P., Zhang, T., Liu, Z., et al. (2024) · International Immunopharmacology · doi:10.1016/j.intimp.2024.113147 · Cited by 16 · see citing works

Genetic and microenvironmental evolution of colorectal liver metastases under chemotherapy

Shi, M., Yang, Y., Huang, N., Zeng, D., Mo, Z., Wang, J., Zhang, X., Liu, R., Wang, C., Rong, X., et al. (2024) · Cell Reports Medicine · doi:10.1016/j.xcrm.2024.101838 · Cited by 15 · see citing works

Integral-Omics: Serial Extraction and Profiling of Metabolome, Lipidome, Genome, Transcriptome, Whole Proteome and Phosphoproteome Using Biopsy Tissue

Li, W., Sun, J. P., Sun, R., Wei, Y., Zheng, J., Zhu, Y., & Guo, T. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.4c04421 · Cited by 15 · see citing works

Overlap of Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Matched Tissues for Proteomics and Phosphoproteomics

Humphries, E. M., Hains, P. G., & Robinson, P. J. (2025) · ACS Omega · doi:10.1021/acsomega.4c09289 · Cited by 15 · see citing works

Comprehensive bioinformatics analysis of functional molecules in colorectal cancer

Meng, T., Lan, Z., Zhao, X., Niu, L. N., Chen, C., & Zhang, W. (2022) · Journal of Gastrointestinal Oncology · doi:10.21037/jgo-21-921 · Cited by 15 · see citing works

Kinase substrate protein microarray analysis of human colon cancer and hepatic metastasis

Belluco, C., Mammano, E., Petricoin, E. F., Prevedello, L., Calvert, V. S., Liotta, L. A., Nitti, D., & Lise, M. (2005) · Clinica Chimica Acta · doi:10.1016/j.cccn.2005.03.024 · Cited by 40 · see citing works

Proteogenomic Characterization Reveals Metabolic Vulnerabilities and Aberrant Phosphorylation in Colorectal Metastasis to Liver

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Proteogenomic characterization of primary colorectal cancer and metastatic progression identifies proteome-based subtypes and signatures

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Alterations in molecular networks of metastatic colorectal carcinoma reveal organ-specific signatures: Implications for targeted therapy of metastatic disease

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Proteomic profiling and network biology of colorectal cancer liver metastasis

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