. 2020 Sep; 11:1177.
doi: 10.3389/fphar.2020.01177.

Artificial Intelligence to Decode Cancer Mechanism: Beyond Patient Stratification for Precision Oncology

Sandip Kumar Patel 1 Bhawana George 2 Vineeta Rai 3 
  • PMID: 32903628
  •     201 References
  •     2 citations


The multitude of multi-omics data generated cost-effectively using advanced high-throughput technologies has imposed challenging domain for research in Artificial Intelligence (AI). Data curation poses a significant challenge as different parameters, instruments, and sample preparations approaches are employed for generating these big data sets. AI could reduce the fuzziness and randomness in data handling and build a platform for the data ecosystem, and thus serve as the primary choice for data mining and big data analysis to make informed decisions. However, AI implication remains intricate for researchers/clinicians lacking specific training in computational tools and informatics. Cancer is a major cause of death worldwide, accounting for an estimated 9.6 million deaths in 2018. Certain cancers, such as pancreatic and gastric cancers, are detected only after they have reached their advanced stages with frequent relapses. Cancer is one of the most complex diseases affecting a range of organs with diverse disease progression mechanisms and the effectors ranging from gene-epigenetics to a wide array of metabolites. Hence a comprehensive study, including genomics, epi-genomics, transcriptomics, proteomics, and metabolomics, along with the medical/mass-spectrometry imaging, patient clinical history, treatments provided, genetics, and disease endemicity, is essential. Cancer Moonshot℠ Research Initiatives by NIH National Cancer Institute aims to collect as much information as possible from different regions of the world and make a cancer data repository. AI could play an immense role in (a) analysis of complex and heterogeneous data sets (multi-omics and/or inter-omics), (b) data integration to provide a holistic disease molecular mechanism, (c) identification of diagnostic and prognostic markers, and (d) monitor patient's response to drugs/treatments and recovery. AI enables precision disease management well beyond the prevalent disease stratification patterns, such as differential expression and supervised classification. This review highlights critical advances and challenges in omics data analysis, dealing with data variability from lab-to-lab, and data integration. We also describe methods used in data mining and AI methods to obtain robust results for precision medicine from "big" data. In the future, AI could be expanded to achieve ground-breaking progress in disease management.

Keywords: artificial intelligence (AI); cancer biomarkers; data integration; multi-omics; patient stratification.

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Maria Luisa Dória, James S McKenzie, +9 authors, Zoltan Takats.
Sci Rep, 2016 Dec 16; 6. PMID: 27976698    Free PMC article.
Current State and Future Challenges of Mass Spectrometry Imaging for Clinical Research.
Ruben D Addie, Benjamin Balluff, +2 authors, Liam A McDonnell.
Anal Chem, 2015 Mar 25; 87(13). PMID: 25803124
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.
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Cancer Discov, 2012 May 17; 2(5). PMID: 22588877    Free PMC article.
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The UCSC Cancer Genomics Browser: update 2013.
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Nucleic Acids Res, 2012 Oct 31; 41(Database issue). PMID: 23109555    Free PMC article.
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Significantly increased monounsaturated lipids relative to polyunsaturated lipids in six types of cancer microenvironment are observed by mass spectrometry imaging.
Shuai Guo, Yanmin Wang, Dan Zhou, Zhili Li.
Sci Rep, 2014 Aug 06; 4. PMID: 25091112    Free PMC article.
Identification of secretory gelsolin as a plasma biomarker associated with distant organ metastasis of colorectal cancer.
Ming-Hung Tsai, Chih-Ching Wu, +8 authors, Jau-Song Yu.
J Mol Med (Berl), 2011 Oct 15; 90(2). PMID: 21997591
Comprehensive Genomic Profiling of Metastatic Squamous Cell Carcinoma of the Anal Canal.
Van Morris, Xiayu Rao, +8 authors, Cathy Eng.
Mol Cancer Res, 2017 Aug 09; 15(11). PMID: 28784613    Free PMC article.
Artificial neural networks applied to outcome prediction for colorectal cancer patients in separate institutions.
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Lancet, 1997 Aug 16; 350(9076). PMID: 9274582
Ovarian cancer detection from metabolomic liquid chromatography/mass spectrometry data by support vector machines.
Wei Guan, Manshui Zhou, +5 authors, Facundo M Fernández.
BMC Bioinformatics, 2009 Aug 25; 10. PMID: 19698113    Free PMC article.
Automated classification of multiphoton microscopy images of ovarian tissue using deep learning.
Mikko J Huttunen, Abdurahman Hassan, +5 authors, Sangeeta Murugkar.
J Biomed Opt, 2018 Jun 15; 23(6). PMID: 29900705
Deep Learning-Based Multi-Omics Integration Robustly Predicts Survival in Liver Cancer.
Kumardeep Chaudhary, Olivier B Poirion, Liangqun Lu, Lana X Garmire.
Clin Cancer Res, 2017 Oct 07; 24(6). PMID: 28982688    Free PMC article.
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Application of a two-stage fuzzy neural network to a prostate cancer prognosis system.
Ren-Jieh Kuo, Man-Hsin Huang, +2 authors, Yung-Hung Wu.
Artif Intell Med, 2015 Jan 13; 63(2). PMID: 25576196
Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues.
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Nat Med, 2001 Apr 03; 7(4). PMID: 11283679
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A multimodal deep neural network for human breast cancer prognosis prediction by integrating multi-dimensional data.
Dongdong Sun, Minghui Wang, Ao Li.
IEEE/ACM Trans Comput Biol Bioinform, 2018 Jul 12;. PMID: 29994639
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Takanori Hiraide, Koji Ikegami, +14 authors, Hiroyuki Konno.
Sci Rep, 2016 Jul 21; 6. PMID: 27435310    Free PMC article.
Locality Sensitive Deep Learning for Detection and Classification of Nuclei in Routine Colon Cancer Histology Images.
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IEEE Trans Med Imaging, 2016 Feb 11; 35(5). PMID: 26863654
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Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma.
Kun-Hsing Yu, Gerald J Berry, +3 authors, Michael Snyder.
Cell Syst, 2017 Nov 21; 5(6). PMID: 29153840    Free PMC article.
Quantitative Mass Spectrometry Imaging Reveals Mutation Status-independent Lack of Imatinib in Liver Metastases of Gastrointestinal Stromal Tumors.
Denis Abu Sammour, Christian Marsching, +8 authors, Carsten Hopf.
Sci Rep, 2019 Jul 25; 9(1). PMID: 31337874    Free PMC article.
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Nat Biotechnol, 2016 Aug 10; 34(8). PMID: 27504778    Free PMC article.
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Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks.
Dylan Z Kelley, Emily L Flam, +19 authors, Daria A Gaykalova.
Cancer Res, 2017 Sep 28; 77(23). PMID: 28947419    Free PMC article.
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A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action.
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PLoS Comput Biol, 2017 Oct 17; 13(10). PMID: 29036168    Free PMC article.
Proteomics Analysis of FLT3-ITD Mutation in Acute Myeloid Leukemia Using Deep Learning Neural Network.
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Prospective evaluation of serum sarcosine and risk of prostate cancer in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial.
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Carcinogenesis, 2013 May 24; 34(10). PMID: 23698636    Free PMC article.
Plasma metabolomics in adults with cystic fibrosis during a pulmonary exacerbation: A pilot randomized study of high-dose vitamin D3 administration.
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Metabolism, 2017 Apr 14; 70. PMID: 28403943    Free PMC article.
Identification of Metastatic Lymph Nodes in MR Imaging with Faster Region-Based Convolutional Neural Networks.
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Cancer Res, 2018 Jul 22; 78(17). PMID: 30026330
Joint learning improves protein abundance prediction in cancers.
Hongyang Li, Omer Siddiqui, Hongjiu Zhang, Yuanfang Guan.
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A novel histology-directed strategy for MALDI-MS tissue profiling that improves throughput and cellular specificity in human breast cancer.
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Deep Learning Applications for Predicting Pharmacological Properties of Drugs and Drug Repurposing Using Transcriptomic Data.
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Improvement in prediction of prostate cancer prognosis with somatic mutational signatures.
Shengping Zhang, Yafei Xu, +5 authors, Yejun Wang.
J Cancer, 2017 Nov 22; 8(16). PMID: 29158798    Free PMC article.
Reliable Entity Subtyping in Non-small Cell Lung Cancer by Matrix-assisted Laser Desorption/Ionization Imaging Mass Spectrometry on Formalin-fixed Paraffin-embedded Tissue Specimens.
Mark Kriegsmann, Rita Casadonte, +7 authors, Wilko Weichert.
Mol Cell Proteomics, 2016 Jul 31; 15(10). PMID: 27473201    Free PMC article.
Deep learning and 3D-DESI imaging reveal the hidden metabolic heterogeneity of cancer.
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Nat Methods, 2018 Dec 24; 16(1). PMID: 30573843
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Machine learning models for predicting post-cystectomy recurrence and survival in bladder cancer patients.
Zaki Hasnain, Jeremy Mason, +4 authors, Paul K Newton.
PLoS One, 2019 Feb 21; 14(2). PMID: 30785915    Free PMC article.
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Proc Natl Acad Sci U S A, 2018 Dec 19; 116(1). PMID: 30559182    Free PMC article.
Efficient identification of nationally mandated reportable cancer cases using natural language processing and machine learning.
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J Am Med Inform Assoc, 2016 Mar 31; 23(6). PMID: 27026618    Free PMC article.
Automating Quality Measures for Heart Failure Using Natural Language Processing: A Descriptive Study in the Department of Veterans Affairs.
Jennifer Hornung Garvin, Youngjun Kim, +11 authors, Stephane M Meystre.
JMIR Med Inform, 2018 Jan 18; 6(1). PMID: 29335238    Free PMC article.
Three-Dimensional Mass Spectrometry Imaging Identifies Lipid Markers of Medulloblastoma Metastasis.
Martin R L Paine, Jingbo Liu, +6 authors, Tobey J MacDonald.
Sci Rep, 2019 Feb 20; 9(1). PMID: 30778099    Free PMC article.
Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer.
Venkatrao Vantaku, Jianrong Dong, +22 authors, Nagireddy Putluri.
Clin Cancer Res, 2019 Mar 09; 25(12). PMID: 30846479    Free PMC article.
Connecting Histopathology Imaging and Proteomics in Kidney Cancer through Machine Learning.
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J Clin Med, 2019 Sep 29; 8(10). PMID: 31557788    Free PMC article.
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A Deep Learning Framework for Predicting Response to Therapy in Cancer.
Theodore Sakellaropoulos, Konstantinos Vougas, +20 authors, Vassilis G Gorgoulis.
Cell Rep, 2019 Dec 12; 29(11). PMID: 31825821
The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space.
Johanna Klughammer, Barbara Kiesel, +51 authors, Christoph Bock.
Nat Med, 2018 Aug 29; 24(10). PMID: 30150718    Free PMC article.
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Rapid discrimination of pediatric brain tumors by mass spectrometry imaging.
Amanda R Clark, David Calligaris, +9 authors, Soma Sengupta.
J Neurooncol, 2018 Aug 22; 140(2). PMID: 30128689    Free PMC article.
Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.
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Cancer Subtype Discovery Using Prognosis-Enhanced Neural Network Classifier in Multigenomic Data.
Prasanna Vasudevan, Thangamani Murugesan.
Technol Cancer Res Treat, 2018 Aug 11; 17. PMID: 30092720    Free PMC article.
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Visualizing Energy Charge in Breast Carcinoma Tissues by MALDI Mass-spectrometry Imaging Profiles of Low-molecular-weight Metabolites.
Nobuhiro Torata, Makoto Kubo, +9 authors, Masafumi Nakamura.
Anticancer Res, 2018 Jul 05; 38(7). PMID: 29970560
Tissue and plasma proteomics for early stage cancer detection.
Liyuan Peng, David I Cantor, +3 authors, Edouard C Nice.
Mol Omics, 2018 Sep 27; 14(6). PMID: 30251724
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Imaging mass spectrometry distinguished the cancer and stromal regions of oral squamous cell carcinoma by visualizing phosphatidylcholine (16:0/16:1) and phosphatidylcholine (18:1/20:4).
Yoshiyuki Uchiyama, Takahiro Hayasaka, +5 authors, Mitsutoshi Setou.
Anal Bioanal Chem, 2013 Jun 04; 406(5). PMID: 23728729
Serum metabolomics as a novel diagnostic approach for gastrointestinal cancer.
Atsuki Ikeda, Shin Nishiumi, +8 authors, Masaru Yoshida.
Biomed Chromatogr, 2011 Jul 21; 26(5). PMID: 21773981
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.
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Sci Signal, 2013 Apr 04; 6(269). PMID: 23550210    Free PMC article.
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In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities.
Carlota Rubio-Perez, David Tamborero, +6 authors, Nuria Lopez-Bigas.
Cancer Cell, 2015 Mar 12; 27(3). PMID: 25759023
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Machine Learning-Based Radiomics for Molecular Subtyping of Gliomas.
Chia-Feng Lu, Fei-Ting Hsu, +8 authors, Cheng-Yu Chen.
Clin Cancer Res, 2018 May 24; 24(18). PMID: 29789422
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Metabolomic profiling of prostate cancer by matrix assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry imaging using Matrix Coating Assisted by an Electric Field (MCAEF).
Xiaodong Wang, Jun Han, +3 authors, Christoph H Borchers.
Biochim Biophys Acta Proteins Proteom, 2016 Dec 27; 1865(7). PMID: 28017863
Lipid Heterogeneity Resulting from Fatty Acid Processing in the Human Breast Cancer Microenvironment Identified by GCIB-ToF-SIMS Imaging.
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Anal Chem, 2016 Oct 27; 88(23). PMID: 27783898
Multisensor Imaging-From Sample Preparation to Integrated Multimodal Interpretation of LA-ICPMS and MALDI MS Imaging Data.
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Anal Chem, 2018 Jul 03; 90(15). PMID: 29961333
Man against machine: diagnostic performance of a deep learning convolutional neural network for dermoscopic melanoma recognition in comparison to 58 dermatologists.
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Ann Oncol, 2018 May 31; 29(8). PMID: 29846502
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Biomarkers of coordinate metabolic reprogramming in colorectal tumors in mice and humans.
Soumen K Manna, Naoki Tanaka, +8 authors, Frank J Gonzalez.
Gastroenterology, 2014 Jan 21; 146(5). PMID: 24440673    Free PMC article.
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More Is Better: Recent Progress in Multi-Omics Data Integration Methods.
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Front Genet, 2017 Jul 04; 8. PMID: 28670325    Free PMC article.
Highly Cited. Review.
Prognostic Metabolite Biomarkers for Soft Tissue Sarcomas Discovered by Mass Spectrometry Imaging.
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J Am Soc Mass Spectrom, 2016 Nov 23; 28(2). PMID: 27873216    Free PMC article.
Transfer Learning for Molecular Cancer Classification Using Deep Neural Networks.
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IEEE/ACM Trans Comput Biol Bioinform, 2018 Jul 12; 16(6). PMID: 29993662
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Genome Biol, 2014 Mar 04; 15(3). PMID: 24580837    Free PMC article.
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Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.
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Ting Wu, Yun Dai.
Cancer Lett, 2016 Feb 05; 387. PMID: 26845449
Highly Cited. Review.
Onco-Multi-OMICS Approach: A New Frontier in Cancer Research.
Sajib Chakraborty, Md Ismail Hosen, Musaddeque Ahmed, Hossain Uddin Shekhar.
Biomed Res Int, 2018 Nov 08; 2018. PMID: 30402498    Free PMC article.
A deep learning based strategy for identifying and associating mitotic activity with gene expression derived risk categories in estrogen receptor positive breast cancers.
David Romo-Bucheli, Andrew Janowczyk, +2 authors, Anant Madabhushi.
Cytometry A, 2017 Feb 14; 91(6). PMID: 28192639    Free PMC article.
A review on machine learning principles for multi-view biological data integration.
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Brief Bioinform, 2016 Dec 25; 19(2). PMID: 28011753
Highly Cited. Review.
IntOGen-mutations identifies cancer drivers across tumor types.
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Nat Methods, 2013 Sep 17; 10(11). PMID: 24037244    Free PMC article.
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Associations of cord blood metabolites with perinatal characteristics, newborn anthropometry, and cord blood hormones in project viva.
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Metabolism, 2017 Oct 11; 76. PMID: 28987236    Free PMC article.
TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.
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Bioinformatics, 2016 Sep 03; 32(17). PMID: 27587657
Pathway-based deep clustering for molecular subtyping of cancer.
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J Mol Histol, 2018 Nov 06; 50(1). PMID: 30390197    Free PMC article.
Deep neural networks are superior to dermatologists in melanoma image classification.
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A community effort to assess and improve drug sensitivity prediction algorithms.
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Nat Biotechnol, 2014 Jun 02; 32(12). PMID: 24880487    Free PMC article.
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Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.
Cancer Genome Atlas Research Network, Daniel J Brat, +305 authors, Jianan Zhang.
N Engl J Med, 2015 Jun 11; 372(26). PMID: 26061751    Free PMC article.
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Developing a Prognostic Gene Panel of Epithelial Ovarian Cancer Patients by a Machine Learning Model.
Tzu-Pin Lu, Kuan-Ting Kuo, +6 authors, Chi-An Chen.
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Differential Lipid Profiles of Normal Human Brain Matter and Gliomas by Positive and Negative Mode Desorption Electrospray Ionization - Mass Spectrometry Imaging.
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PLoS One, 2016 Sep 23; 11(9). PMID: 27658243    Free PMC article.
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Genome Biol, 2013 Nov 02; 14(10). PMID: 24176112    Free PMC article.
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Pregnancy to postpartum transition of serum metabolites in women with gestational diabetes.
Elin Chorell, Ulrika Andersson Hall, +5 authors, Agneta Holmäng.
Metabolism, 2017 Jun 24; 72. PMID: 28641781
The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data.
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The metabonomic signature of celiac disease.
Ivano Bertini, Antonio Calabrò, +6 authors, Leonardo Tenori.
J Proteome Res, 2008 Dec 17; 8(1). PMID: 19072164
Automated analysis of free speech predicts psychosis onset in high-risk youths.
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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.
Christina Curtis, Sohrab P Shah, +29 authors, Samuel Aparicio.
Nature, 2012 Apr 24; 486(7403). PMID: 22522925    Free PMC article.
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Matrix-assisted laser desorption/ionization mass spectrometry imaging of cell cultures for the lipidomic analysis of potential lipid markers in human breast cancer invasion.
Shujuan Wang, Xiaowu Chen, +6 authors, Yuyang Jiang.
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Proteomic Profiling and Artificial Intelligence for Hepatocellular Carcinoma Translational Medicine.
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