Liquid biopsies and cancer omics

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

(2020) Bernardo Rodriguez-Martin et al.   NATURE GENETICS

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

(2020) Wei Jiao et al.   Nature Communications

Liquid biopsy for breast cancer using extracellular vesicles and cell-free microRNAs as biomarkers

(2020) Patricia Midori Murobushi Ozawa et al.   Translational Research

Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking

(2020) George D. Cresswell et al.   Nature Communications

Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer

(2020) Marc Clos-Garcia et al.   Cancers

Computational identification and characterization of glioma candidate biomarkers through multi-omics integrative profiling

(2020) Lin Liu et al.   Biology Direct

Long non-coding RNA LINC00426 contributes to doxorubicin resistance by sponging miR-4319 in osteosarcoma

(2020) Lulin Wang et al.   Biology Direct

The Role of Circulating MicroRNA in Glioblastoma Liquid Biopsy

(2020) Catherine M. Garcia et al.   World Neurosurgery

Circulating Tumor Cells in Metastatic Breast Cancer: From Genome Instability to Metastasis

(2020) Ekaterina Ivanova et al.   Frontiers in Molecular Biosciences

Integrated Omics of Metastatic Colorectal Cancer

(2020) Chen Li et al.   CANCER CELL

The future is now? Clinical and translational aspects of “Omics” technologies

(2020) Gemma L D’Adamo et al.   IMMUNOLOGY AND CELL BIOLOGY

DNA methylation markers detected in blood, stool, urine, and tissue in colorectal cancer: a systematic review of paired samples

(2020) Eivor Alette Laugsand et al.   INTERNATIONAL JOURNAL OF COLORECTAL DISEASE

Liquid biopsy technologies for hematological diseases

(2020) Yatian Fu et al.   MEDICINAL RESEARCH REVIEWS

Microbiome Patterns in Matched Bile, Duodenal, Pancreatic Tumor Tissue, Drainage, and Stool Samples: Association with Preoperative Stenting and Postoperative Pancreatic Fistula Development

(2020) Melanie Langheinrich et al.   Journal of Clinical Medicine

Liquid Biopsy of Extracellular Vesicle-Derived miR-193a-5p in Colorectal Cancer and Discovery of Its Tumor-Suppressor Functions

(2020) Rui Wei et al.   Frontiers in Oncology

Liquid Biopsy as a Tool Exploring in Real-Time Both Genomic Perturbation and Resistance to EGFR Antagonists in Colorectal Cancer

(2020) Valeria Internò et al.   Frontiers in Oncology

Beyond EGFR, ALK and ROS1: Current evidence and future perspectives on newly targetable oncogenic drivers in lung adenocarcinoma

(2020) Giuseppe Lamberti et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

Genome and pan-genome analysis to classify emerging bacteria

(2019) Aurélia Caputo et al.   Biology Direct

Integrative analysis based on survival associated co-expression gene modules for predicting Neuroblastoma patients’ survival time

(2019) Yatong Han et al.   Biology Direct

From tumors to species: a SCANDAL hypothesis

(2019) A. Y. Panchin et al.   Biology Direct

Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies

(2019) So Yeon Kim et al.   Biology Direct

Personalized detection of circulating tumor DNA antedates breast cancer metastatic recurrence

(2019) R. Charles Coombes et al.   CLINICAL CANCER RESEARCH

Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data

(2019) Alejandro R. Walker et al.   Biology Direct

Novel secretome-to-transcriptome integrated or secreto-transcriptomic approach to reveal liquid biopsy biomarkers for predicting individualized prognosis of breast cancer patients

(2019) J. Astor Ankney et al.   BMC Medical Genomics

Integration of molecular features with clinical information for predicting outcomes for neuroblastoma patients

(2019) Yatong Han et al.   Biology Direct

Application of machine learning techniques for creating urban microbial fingerprints

(2019) Feargal Joseph Ryan   Biology Direct

Gene connectivity and enzyme evolution in the human metabolic network

(2019) Begoña Dobon et al.   Biology Direct

Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples

(2019) Carlos S. Casimiro-Soriguer et al.   Biology Direct

Tumor-derived extracellular vesicles in breast cancer: From bench to bedside

(2019) Hong-Xia Wang et al.   CANCER LETTERS

Non-blood sources of cell-free DNA for cancer molecular profiling in clinical pathology and oncology

(2019) Giovanni Ponti et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

Advances in the therapy of BRAFV600E metastatic colorectal cancer

(2019) Zhaohui Jin et al.   Expert Review of Anticancer Therapy

Environmental metagenome classification for constructing a microbiome fingerprint

(2019) Jolanta Kawulok et al.   Biology Direct

Fingerprinting cities: differentiating subway microbiome functionality

(2019) Chengsheng Zhu et al.   Biology Direct

A novel framework for horizontal and vertical data integration in cancer studies with application to survival time prediction models

(2019) Iliyan Mihaylov et al.   Biology Direct

Huge whole-genome study of human metastatic cancers

(2019) Jillian F. Wise et al.   NATURE

Clinical applications of the CellSearch platform in cancer patients

(2018) Sabine Riethdorf et al.   ADVANCED DRUG DELIVERY REVIEWS

Circulating tumor cell-derived organoids: Current challenges and promises in medical research and precision medicine

(2018) Prakash P. Praharaj et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles

(2018) Alejandro R. Walker et al.   Biology Direct

Predicting survival times for neuroblastoma patients using RNA-seq expression profiles

(2018) Tyler Grimes et al.   Biology Direct

Multi-omics integration for neuroblastoma clinical endpoint prediction

(2018) Margherita Francescatto et al.   Biology Direct

Profiling microbial strains in urban environments using metagenomic sequencing data

(2018) Moreno Zolfo et al.   Biology Direct

Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach

(2018) Léon-Charles Tranchevent et al.   Biology Direct

Accumulation of potential driver genes with genomic alterations predicts survival of high-risk neuroblastoma patients

(2018) Chen Suo et al.   Biology Direct

ZNF281 inhibits neuronal differentiation and is a prognostic marker for neuroblastoma

(2018) Marco Pieraccioli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integration of multiple types of genetic markers for neuroblastoma may contribute to improved prediction of the overall survival

(2018) Aneta Polewko-Klim et al.   Biology Direct

Predicting clinical outcomes in neuroblastoma with genomic data integration

(2018) Ilyes Baali et al.   Biology Direct

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome

(2018) Marta R. Hidalgo et al.   Biology Direct

Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole

(2018) Dino Osmanovic et al.   Biology Direct

Assessment of urban microbiome assemblies with the help of targeted in silico gold standards

(2018) Samuel M. Gerner et al.   Biology Direct

Molecular characterization of breast cancer CTCs associated with brain metastasis

(2017) Debasish Boral et al.   Nature Communications

Non-blood circulating tumor DNA detection in cancer

(2017) Muyun Peng et al.   Oncotarget

The dawn of the liquid biopsy in the fight against cancer

(2017) Irma G. Domínguez-Vigil et al.   Oncotarget

SynTarget: an online tool to test the synergetic effect of genes on survival outcome in cancer

(2016) I Amelio et al.   CELL DEATH AND DIFFERENTIATION

Metabolic reprogramming during neuronal differentiation

(2016) M Agostini et al.   CELL DEATH AND DIFFERENTIATION

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Promise and limits of the CellSearch platform for evaluating pharmacodynamics in circulating tumor cells

(2016) Lihua Wang et al.   SEMINARS IN ONCOLOGY

Phenotypic characterization of circulating tumor cells in triple negative breast cancer patients

(2016) Sofia Agelaki et al.   Oncotarget

Serum-Based Quantification of MYCN Gene Amplification in Young Patients with Neuroblastoma: Potential Utility as a Surrogate Biomarker for Neuroblastoma

(2016) Shigeki Yagyu et al.   PLoS One

The relevance of EMT in breast cancer metastasis: Correlation or causality?

(2015) Ruben Bill et al.   FEBS LETTERS

Precision Medicine — Personalized, Problematic, and Promising

(2015) J. Larry Jameson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Neuroblastoma: oncogenic mechanisms and therapeutic exploitation of necroptosis

(2015) S Nicolai et al.   Cell Death & Disease

Detection of tumorALKstatus in neuroblastoma patients using peripheral blood

(2015) Valérie Combaret et al.   Cancer Medicine

miR-34: from bench to bedside

(2015) Massimiliano Agostini et al.   Oncotarget

Dual VEGF/VEGFR inhibition in advanced solid malignancies

(2014) Kriti Mittal et al.   CANCER BIOLOGY & THERAPY

Circulating Breast Tumor Cells Exhibit Dynamic Changes in Epithelial and Mesenchymal Composition

(2013) M. Yu et al.   SCIENCE

Mass Spectrometry (LC–MS/MS) Identified Proteomic Biosignatures of Breast Cancer in Proximal Fluid

(2012) Stephen A. Whelan et al.   JOURNAL OF PROTEOME RESEARCH

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Preparing for Precision Medicine

(2012) Reza Mirnezami et al.   NEW ENGLAND JOURNAL OF MEDICINE

Intratumor Heterogeneity: Seeing the Wood for the Trees

(2012) T. A. Yap et al.   Science Translational Medicine

Primary anti-vascular endothelial growth factor (VEGF)-refractory metastatic renal cell carcinoma: clinical characteristics, risk factors, and subsequent therapy

(2011) D. Y. Heng et al.   ANNALS OF ONCOLOGY

Stool DNA testing for the detection of pancreatic cancer

(2011) John B. Kisiel et al.   CANCER

How Darwinian models inform therapeutic failure initiated by clonal heterogeneity in cancer medicine

(2010) M Gerlinger et al.   BRITISH JOURNAL OF CANCER

Isoform-specific p73 knockout mice reveal a novel role for  Np73 in the DNA damage response pathway

(2010) M. T. Wilhelm et al.   GENES & DEVELOPMENT

Molecular mechanisms of metastasis in breast cancer—clinical applications

(2010) Michal Mego et al.   Nature Reviews Clinical Oncology

Influence of neuroblastoma stage on serum-based detection ofMYCNamplification

(2009) Valerie Combaret et al.   PEDIATRIC BLOOD & CANCER

Non-invasive techniques for assessing postoperative recurrence in Crohn's disease

(2008) L. Biancone et al.   DIGESTIVE AND LIVER DISEASE

TAp73 knockout shows genomic instability with infertility and tumor suppressor functions

(2008) R. Tomasini et al.   GENES & DEVELOPMENT

Circulating mutant DNA to assess tumor dynamics

(2008) Frank Diehl et al.   NATURE MEDICINE