Artificial intelligence-based multi-omics analysis fuels cancer precision medicine

Protein Sequencing, One Molecule at a Time

(2022) Brendan M. Floyd et al.   Annual Review of Biophysics

Metabolite discovery: Biochemistry’s scientific driver

(2022) Martin Giera et al.   Cell Metabolism

The contrast-enhanced MRI can be substituted by unenhanced MRI in identifying and automatically segmenting primary nasopharyngeal carcinoma with the aid of deep learning models: an exploratory study in large-scale population of endemic area

(2022) Yishu Deng et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Machine learning for multi-omics data integration in cancer

(2022) Zhaoxiang Cai et al.   iScience

Spatial analysis of tumor‐infiltrating lymphocytes in histological sections using deep learning techniques predicts survival in colorectal carcinoma

(2022) Hongming Xu et al.   Journal of Pathology Clinical Research

Spatial transcriptomics

(2022) Ana C. Anderson et al.   CANCER CELL

Artificial intelligence‐driven consensus gene signatures for improving bladder cancer clinical outcomes identified by multi‐center integration analysis

(2022) Hui Xu et al.   Molecular Oncology

Recent advances in microfluidic single-cell analysis and its applications in drug development

(2022) Yufeng Jiao et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Artificial Intelligence for Histology-Based Detection of Microsatellite Instability and Prediction of Response to Immunotherapy in Colorectal Cancer

(2021) Lindsey A. Hildebrand et al.   Cancers

Noninvasive Prediction of Occult Peritoneal Metastasis in Gastric Cancer Using Deep Learning

(2021) Yuming Jiang et al.   JAMA Network Open

Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion

(2021) Chris J. Frangieh et al.   NATURE GENETICS

Artificial intelligence for clinical oncology

(2021) Benjamin H. Kann et al.   CANCER CELL

Glioblastomas acquire myeloid-affiliated transcriptional programs via epigenetic immunoediting to elicit immune evasion

(2021) Ester Gangoso et al.   CELL

Artificial Intelligence in Bulk and Single-Cell RNA-Sequencing Data to Foster Precision Oncology

(2021) Marco Del Giudice et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Combination of MAPK inhibition with photothermal therapy synergistically augments the anti-tumor efficacy of immune checkpoint blockade

(2021) Xiaowei Liu et al.   JOURNAL OF CONTROLLED RELEASE

High-Resolution Single-Molecule FRET via DNA eXchange (FRET X)

(2021) Mike Filius et al.   NANO LETTERS

Ultra-high-performance liquid chromatography high-resolution mass spectrometry variants for metabolomics research

(2021) Leonardo Perez de Souza et al.   NATURE METHODS

Artificial Intelligence in Cancer Research and Precision Medicine

(2021) Bhavneet Bhinder et al.   Cancer Discovery

Current Challenges and Recent Developments in Mass Spectrometry–Based Metabolomics

(2021) Stephanie L. Collins et al.   Annual Review of Analytical Chemistry

Assessment of mitotic activity in breast cancer: revisited in the digital pathology era

(2021) Asmaa Ibrahim et al.   JOURNAL OF CLINICAL PATHOLOGY

Exploring tissue architecture using spatial transcriptomics

(2021) Anjali Rao et al.   NATURE

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

(2021) Saleh Alseekh et al.   NATURE METHODS

SpaceM reveals metabolic states of single cells

(2021) Luca Rappez et al.   NATURE METHODS

Artificial intelligence for proteomics and biomarker discovery

(2021) Matthias Mann et al.   Cell Systems

Proteomics, Personalized Medicine and Cancer

(2021) Miao Su et al.   Cancers

A roadmap for multi-omics data integration using deep learning

(2021) Mingon Kang et al.   BRIEFINGS IN BIOINFORMATICS

Machine learning meets omics: applications and perspectives

(2021) Rufeng Li et al.   BRIEFINGS IN BIOINFORMATICS

Artificial intelligence in oncology: current applications and future perspectives

(2021) Claudio Luchini et al.   BRITISH JOURNAL OF CANCER

Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer

(2021) Yuanyuan Zhang et al.   CANCER CELL

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC

(2021) Evgenij Fiskin et al.   NATURE BIOTECHNOLOGY

Transcriptomics paving the way for improved diagnostics and precision medicine of acute leukemia

(2021) Henrik Lilljebjörn et al.   SEMINARS IN CANCER BIOLOGY

From bulk, single-cell to spatial RNA sequencing

(2021) Xinmin Li et al.   International Journal of Oral Science

Epigenetic Therapeutic Strategies to Target Molecular and Cellular Heterogeneity in Pancreatic Cancer

(2021) Lennart Versemann et al.   Visceral Medicine

Monitoring Retinoblastoma by Machine Learning of Aqueous Humor Metabolic Fingerprinting

(2021) Wanshan Liu et al.   Small Methods

Deep learning for prediction of colorectal cancer outcome: a discovery and validation study

(2020) Ole-Johan Skrede et al.   LANCET

Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study

(2020) Peter Ström et al.   LANCET ONCOLOGY

International evaluation of an AI system for breast cancer screening

(2020) Scott Mayer McKinney et al.   NATURE

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes

(2020) Jared O. Kafader et al.   NATURE METHODS

Pan-genomics in the human genome era

(2020) Rachel M. Sherman et al.   NATURE REVIEWS GENETICS

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

(2020) Wei Jiao et al.   Nature Communications

Utilizing Automated Breast Cancer Detection to Identify Spatial Distributions of Tumor-Infiltrating Lymphocytes in Invasive Breast Cancer

(2020) Han Le et al.   AMERICAN JOURNAL OF PATHOLOGY

Advancing Cancer Research and Medicine with Single-Cell Genomics

(2020) Bora Lim et al.   CANCER CELL

Integrative analysis of DNA methylation and gene expression in papillary renal cell carcinoma

(2020) Noor Pratap Singh et al.   MOLECULAR GENETICS AND GENOMICS

Integrating genomic features for non-invasive early lung cancer detection

(2020) Jacob J. Chabon et al.   NATURE

Antibody-free enzyme-assisted chemical approach for detection of N6-methyladenosine

(2020) Ye Wang et al.   Nature Chemical Biology

Unraveling tumor–immune heterogeneity in advanced ovarian cancer uncovers immunogenic effect of chemotherapy

(2020) Alejandro Jiménez-Sánchez et al.   NATURE GENETICS

Predicting cancer origins with a DNA methylation-based deep neural network model

(2020) Chunlei Zheng et al.   PLoS One

Integrative Methods and Practical Challenges for Single-Cell Multi-omics

(2020) Anjun Ma et al.   TRENDS IN BIOTECHNOLOGY

Early Diagnosis of Hepatocellular Carcinoma Using Machine Learning Method

(2020) Zi-Mei Zhang et al.   Frontiers in Bioengineering and Biotechnology

Development and Validation of an Image-based Deep Learning Algorithm for Detection of Synchronous Peritoneal Carcinomatosis in Colorectal Cancer

(2020) Zixu Yuan et al.   ANNALS OF SURGERY

Transfer Learning for Drug Discovery

(2020) Chenjing Cai et al.   JOURNAL OF MEDICINAL CHEMISTRY

Accuracy and Efficiency of Deep-Learning–Based Automation of Dual Stain Cytology in Cervical Cancer Screening

(2020) Nicolas Wentzensen et al.   JNCI-Journal of the National Cancer Institute

The proteome landscape of the kingdoms of life

(2020) Johannes B. Müller et al.   NATURE

A single-cell landscape of high-grade serous ovarian cancer

(2020) Benjamin Izar et al.   NATURE MEDICINE

Gut microbiome, big data and machine learning to promote precision medicine for cancer

(2020) Giovanni Cammarota et al.   Nature Reviews Gastroenterology & Hepatology

Epigenetic Therapies for Cancer

(2020) Susan E. Bates   NEW ENGLAND JOURNAL OF MEDICINE

Strategies to enable large-scale proteomics for reproducible research

(2020) Rebecca C. Poulos et al.   Nature Communications

AI in Medical Imaging Informatics: Current Challenges and Future Directions

(2020) Andreas S. Panayides et al.   IEEE Journal of Biomedical and Health Informatics

Utility of Circulating Tumor DNA for Detection and Monitoring of Endometrial Cancer Recurrence and Progression

(2020) Esther L. Moss et al.   Cancers

Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches

(2020) Dohoon Lee et al.   BRIEFINGS IN BIOINFORMATICS

Predicting 3D genome folding from DNA sequence with Akita

(2020) Geoff Fudenberg et al.   NATURE METHODS

Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics

(2020) Anna S. Nam et al.   NATURE REVIEWS GENETICS

Histone modifications in epigenetic regulation of cancer: Perspectives and achieved progress

(2020) Margarita E. Neganova et al.   SEMINARS IN CANCER BIOLOGY

Non-invasive decision support for NSCLC treatment using PET/CT radiomics

(2020) Wei Mu et al.   Nature Communications

Clinically applicable histopathological diagnosis system for gastric cancer detection using deep learning

(2020) Zhigang Song et al.   Nature Communications

Deep learning to estimate RECIST in patients with NSCLC treated with PD-1 blockade

(2020) Kathryn C. Arbour et al.   Cancer Discovery

Ensemble transfer learning for the prediction of anti-cancer drug response

(2020) Yitan Zhu et al.   Scientific Reports

Deep learning in cancer pathology: a new generation of clinical biomarkers

(2020) Amelie Echle et al.   BRITISH JOURNAL OF CANCER

Using Machine Learning Algorithms to Predict Immunotherapy Response in Patients with Advanced Melanoma

(2020) Paul Johannet et al.   CLINICAL CANCER RESEARCH

Artificial intelligence-based pathology for gastrointestinal and hepatobiliary cancers

(2020) Julien Calderaro et al.   GUT

Deep learning model for the prediction of microsatellite instability in colorectal cancer: a diagnostic study

(2020) Rikiya Yamashita et al.   LANCET ONCOLOGY

Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy

(2020) Satyen H. Gohil et al.   Nature Reviews Clinical Oncology

Integrating genome sequence and structural data for statistical learning to predict transcription factor binding sites

(2020) Pengpeng Long et al.   NUCLEIC ACIDS RESEARCH

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Group Lasso Regularized Deep Learning for Cancer Prognosis from Multi-Omics and Clinical Features

(2019) Gangcai Xie et al.   Genes

Machine Learning and Integrative Analysis of Biomedical Big Data

(2019) Bilal Mirza et al.   Genes

Personalization of Logical Models With Multi-Omics Data Allows Clinical Stratification of Patients

(2019) Jonas Béal et al.   Frontiers in Physiology

Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes

(2019) Zhou Fang et al.   Cell Reports

Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma

(2019) Luc-Matthieu Fornecker et al.   Scientific Reports

Unravelling Intratumoral Heterogeneity through High-Sensitivity Single-Cell Mutational Analysis and Parallel RNA Sequencing

(2019) Alba Rodriguez-Meira et al.   MOLECULAR CELL

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

Applications of machine learning in drug discovery and development

(2019) Jessica Vamathevan et al.   NATURE REVIEWS DRUG DISCOVERY

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Spatial transcriptomics coming of age

(2019) Darren J. Burgess   NATURE REVIEWS GENETICS

Multi-label transfer learning for the early diagnosis of breast cancer

(2019) Hiba Chougrad et al.   NEUROCOMPUTING

A Practical Guide to the Measurement and Analysis of DNA Methylation

(2019) Benjamin D Singer   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer

(2019) Jakob Nikolas Kather et al.   NATURE MEDICINE

Addressing the challenges of high‐throughput cancer tissue proteomics for clinical application: ProCan ®

(2019) Brett Tully et al.   PROTEOMICS

Single-base mapping of m6A by an antibody-independent method

(2019) Zhang Zhang et al.   Science Advances

A 23 gene–based molecular prognostic score precisely predicts overall survival of breast cancer patients

(2019) Hideyuki Shimizu et al.   EBioMedicine

Deep Neural Networks for Classification of LC-MS Spectral Peaks

(2019) Edward D. Kantz et al.   ANALYTICAL CHEMISTRY

DART-seq: an antibody-free method for global m6A detection

(2019) Kate D. Meyer   NATURE METHODS

Artificial intelligence in digital pathology — new tools for diagnosis and precision oncology

(2019) Kaustav Bera et al.   Nature Reviews Clinical Oncology

Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification

(2019) Gabriel E Hoffman et al.   NUCLEIC ACIDS RESEARCH

Metabolomics for Investigating Physiological and Pathophysiological Processes

(2019) David S. Wishart   PHYSIOLOGICAL REVIEWS

A hierarchical integration deep flexible neural forest framework for cancer subtype classification by integrating multi-omics data

(2019) Jing Xu et al.   BMC BIOINFORMATICS

Extension of the CONSORT and SPIRIT statements

(2019) Xiaoxuan Liu et al.   LANCET

Deep learning-based classification of mesothelioma improves prediction of patient outcome

(2019) Pierre Courtiol et al.   NATURE MEDICINE

Identification of 12 cancer types through genome deep learning

(2019) Yingshuai Sun et al.   Scientific Reports

Practical implementation of DNA methylation and copy-number-based CNS tumor diagnostics: the Heidelberg experience

(2018) David Capper et al.   ACTA NEUROPATHOLOGICA

OUP accepted manuscript

(2018)   BIOINFORMATICS

Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing

(2018) Ahmed Alfares et al.   GENETICS IN MEDICINE

Are whole-exome and whole-genome sequencing approaches cost-effective? A systematic review of the literature

(2018) Katharina Schwarze et al.   GENETICS IN MEDICINE

Transfer Learning for Molecular Cancer classification using Deep Neural Networks

(2018) Rahul Kumar Sevakula et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The emerging clinical relevance of genomics in cancer medicine

(2018) Michael F. Berger et al.   Nature Reviews Clinical Oncology

Linking imaging to omics utilizing image-guided tissue extraction

(2018) Jonathan A. Disselhorst et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting cancer outcomes from histology and genomics using convolutional networks

(2018) Pooya Mobadersany et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and localization of surgically resectable cancers with a multi-analyte blood test

(2018) Joshua D. Cohen et al.   SCIENCE

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

(2018) Joel Saltz et al.   Cell Reports

Serum exosomal microRNAs combined with alpha-fetoprotein as diagnostic markers of hepatocellular carcinoma

(2018) Yurong Wang et al.   Cancer Medicine

Module Analysis Captures Pancancer Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response

(2018) Magali Champion et al.   EBioMedicine

Improving the prediction of protein–nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods

(2018) Hong Su et al.   BIOINFORMATICS

Min-redundancy and max-relevance multi-view feature selection for predicting ovarian cancer survival using multi-omics data

(2018) Yasser EL-Manzalawy et al.   BMC Medical Genomics

Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning

(2018) Nicolas Coudray et al.   NATURE MEDICINE

Paving the way to single-molecule protein sequencing

(2018) Laura Restrepo-Pérez et al.   Nature Nanotechnology

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

Recurrent Neural Network for Predicting Transcription Factor Binding Sites

(2018) Zhen Shen et al.   Scientific Reports

Predicting the mutations generated by repair of Cas9-induced double-strand breaks

(2018) Felicity Allen et al.   NATURE BIOTECHNOLOGY

Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures

(2018) Jagannath Swaminathan et al.   NATURE BIOTECHNOLOGY

Metabolism as a guiding force for immunity

(2018) Jonathan Jung et al.   NATURE CELL BIOLOGY

A guide to deep learning in healthcare

(2018) Andre Esteva et al.   NATURE MEDICINE

Multi-Omics Profiling of the Tumor Microenvironment: Paving the Way to Precision Immuno-Oncology

(2018) Francesca Finotello et al.   Frontiers in Oncology

SIDR: simultaneous isolation and parallel sequencing of genomic DNA and total RNA from single cells

(2017) Kyung Yeon Han et al.   GENOME RESEARCH

Metabolic Regulation of the Immune Humoral Response

(2017) Mark Boothby et al.   IMMUNITY

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

De novo peptide sequencing by deep learning

(2017) Ngoc Hieu Tran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers

(2017) Akram Mohammed et al.   Oncotarget

Transcriptomics technologies

(2017) Rohan Lowe et al.   PLoS Computational Biology

Searching for prostate cancer by fully automated magnetic resonance imaging classification: deep learning versus non-deep learning

(2017) Xinggang Wang et al.   Scientific Reports

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

The US Cancer Moonshot initiative

(2016) C Marjorie Aelion et al.   LANCET ONCOLOGY

m6A-LAIC-seq reveals the census and complexity of the m6A epitranscriptome

(2016) Benoit Molinie et al.   NATURE METHODS

Radiomics: Images Are More than Pictures, They Are Data

(2016) Robert J. Gillies et al.   RADIOLOGY

Nongenetic functions of the genome

(2016) M. Bustin et al.   SCIENCE

Nutrients and the microenvironment to feed a T cell army

(2016) Marc O. Johnson et al.   SEMINARS IN IMMUNOLOGY

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

(2015) Bastian Linder et al.   NATURE METHODS

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Modelling the spatial heterogeneity and molecular correlates of lymphocytic infiltration in triple-negative breast cancer

(2014) Y. Yuan   Journal of the Royal Society Interface

A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Single-molecule spectroscopy of amino acids and peptides by recognition tunnelling

(2014) Yanan Zhao et al.   Nature Nanotechnology

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease

(2014) Adil Mardinoglu et al.   Nature Communications

Radiogenomics: Using Genetics to Identify Cancer Patients at Risk for Development of Adverse Effects Following Radiotherapy

(2014) S. L. Kerns et al.   Cancer Discovery

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Discovery and Validation of a Prostate Cancer Genomic Classifier that Predicts Early Metastasis Following Radical Prostatectomy

(2013) Nicholas Erho et al.   PLoS One

Proteomics in evolutionary ecology: linking the genotype with the phenotype

(2012) ANGEL P. DIZ et al.   MOLECULAR ECOLOGY

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

Semi-supervised learning improves gene expression-based prediction of cancer recurrence

(2011) Mingguang Shi et al.   BIOINFORMATICS

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

(2009) John R. Yates et al.   Annual Review of Biomedical Engineering

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL