Single-Cell Techniques and Deep Learning in Predicting Drug Response

Network-based prediction of drug–target interactions using an arbitrary-order proximity embedded deep forest

(2020) Xiangxiang Zeng et al.   BIOINFORMATICS

Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma

(2020) Benjamin P. Fairfax et al.   NATURE MEDICINE

FB5P-seq: FACS-Based 5-Prime End Single-Cell RNA-seq for Integrative Analysis of Transcriptome and Antigen Receptor Repertoire in B and T Cells

(2020) Noudjoud Attaf et al.   Frontiers in Immunology

Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication

(2020) Tzong-Yi Lee et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

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

(2020) Anjun Ma et al.   TRENDS IN BIOTECHNOLOGY

Drug Resistance Prediction Using Deep Learning Techniques on HIV-1 Sequence Data

(2020) Margaret C. Steiner et al.   Viruses-Basel

Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis

(2020) Xiangjie Li et al.   Nature Communications

Dual Relief of T-lymphocyte Proliferation and Effector Function Underlies Response to PD-1 Blockade in Epithelial Malignancies

(2020) Camille-Charlotte Balança et al.   Cancer Immunology Research

Drug-Induced Resistance in Micrometastases: Analysis of Spatio-Temporal Cell Lineages

(2020) Judith Pérez-Velázquez et al.   Frontiers in Physiology

Sparsity-Penalized Stacked Denoising Autoencoders for Imputing Single-Cell RNA-seq Data

(2020) Weilai Chi et al.   Genes

Deep-AmPEP30: Improve Short Antimicrobial Peptides Prediction with Deep Learning

(2020) Jielu Yan et al.   Molecular Therapy-Nucleic Acids

Deep learning-based ovarian cancer subtypes identification using multi-omics data

(2020) Long-Yi Guo et al.   BioData Mining

Checkpoint Blockade Immunotherapy Induces Dynamic Changes in PD-1−CD8+ Tumor-Infiltrating T Cells

(2019) Sema Kurtulus et al.   IMMUNITY

A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications

(2019) He Peng et al.   PLoS Computational Biology

DeepAffinity: interpretable deep learning of compound–protein affinity through unified recurrent and convolutional neural networks

(2019) Mostafa Karimi et al.   BIOINFORMATICS

deepDR: A network-based deep learning approach to in silico drug repositioning

(2019) Xiangxiang Zeng et al.   BIOINFORMATICS

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Multiplexed single-cell RNA-seq via transient barcoding for simultaneous expression profiling of various drug perturbations

(2019) Dongju Shin et al.   Science Advances

Single-cell Analysis Reveals a Preexisting Drug-Resistant Subpopulation in the Luminal Breast Cancer Subtype

(2019) Marta Prieto-Vila et al.   CANCER RESEARCH

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Cell signaling and cancer: a mechanistic insight into drug resistance

(2019) Munmun Panda et al.   MOLECULAR BIOLOGY REPORTS

Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection

(2019) Chen Yao et al.   NATURE IMMUNOLOGY

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia

(2019) Charles C. Bell et al.   Nature Communications

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

(2019) Mandeep Singh et al.   Nature Communications

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences

(2019) Ingoo Lee et al.   PLoS Computational Biology

A dream of single-cell proteomics

(2019) Vivien Marx   NATURE METHODS

Data denoising with transfer learning in single-cell transcriptomics

(2019) Jingshu Wang et al.   NATURE METHODS

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

(2019) Thomas M. Norman et al.   SCIENCE

Macrophage-Derived CXCL9 and CXCL10 Are Required for Antitumor Immune Responses Following Immune Checkpoint Blockade

(2019) Imran G. House et al.   CLINICAL CANCER RESEARCH

Single-cell profiling guided combinatorial immunotherapy for fast-evolving CDK4/6 inhibitor-resistant HER2-positive breast cancer

(2019) Qingfei Wang et al.   Nature Communications

Mitochondrial Cholesterol in Alzheimer's Disease and Niemann–Pick Type C Disease

(2019) Sandra Torres et al.   Frontiers in Neurology

Deep Learning Reveals Cancer Metastasis and Therapeutic Antibody Targeting in the Entire Body

(2019) Chenchen Pan et al.   CELL

High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity

(2019) Ian Setliff et al.   CELL

Massively multiplex chemical transcriptomics at single-cell resolution

(2019) Sanjay R. Srivatsan et al.   SCIENCE

Using transfer learning from prior reference knowledge to improve the clustering of single-cell RNA-Seq data

(2019) Bettina Mieth et al.   Scientific Reports

B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

(2018) Simone Rizzetto et al.   BIOINFORMATICS

Modeling polypharmacy side effects with graph convolutional networks

(2018) Marinka Zitnik et al.   BIOINFORMATICS

A Convergence-Based Framework for Cancer Drug Resistance

(2018) David J. Konieczkowski et al.   CANCER CELL

The role of alternative splicing in cancer drug resistance

(2018) Zahava Siegfried et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Molecular targeted therapy: treating cancer with specificity

(2018) Yeuan Ting Lee et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR

(2018) David Zemmour et al.   NATURE IMMUNOLOGY

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

(2018) Amit A. Upadhyay et al.   Genome Medicine

KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance

(2018) Kunihiko Hinohara et al.   CANCER CELL

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

Single-cell Sequencing Reveals Variants in ARID1A, GPRC5A and MLL2 Driving Self-renewal of Human Bladder Cancer Stem Cells

(2017) Zhao Yang et al.   EUROPEAN UROLOGY

Deep-Learning-Based Drug–Target Interaction Prediction

(2017) Ming Wen et al.   JOURNAL OF PROTEOME RESEARCH

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Tumour heterogeneity and resistance to cancer therapies

(2017) Ibiayi Dagogo-Jack et al.   Nature Reviews Clinical Oncology

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network

(2017) Bülent Arman Aksoy et al.   Database-The Journal of Biological Databases and Curation

Low Data Drug Discovery with One-Shot Learning

(2017) Han Altae-Tran et al.   ACS Central Science

More Is Better: Recent Progress in Multi-Omics Data Integration Methods

(2017) Sijia Huang et al.   Frontiers in Genetics

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Construction of single-cell arrays and assay of cell drug resistance in an integrated microfluidic platform

(2016) Long Pang et al.   LAB ON A CHIP

Deep Learning Applications for Predicting Pharmacological Properties of Drugs and Drug Repurposing Using Transcriptomic Data

(2016) Alexander Aliper et al.   MOLECULAR PHARMACEUTICS

Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition

(2016) Aaron N Hata et al.   NATURE MEDICINE

Ultra-high-throughput sequencing of the immune receptor repertoire from millions of lymphocytes

(2016) Jonathan R McDaniel et al.   Nature Protocols

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Whole–genome characterization of chemoresistant ovarian cancer

(2015) Ann-Marie Patch et al.   NATURE

Deep learning

(2015) Yann LeCun et al.   NATURE

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

(2015) Kyu-Tae Kim et al.   GENOME BIOLOGY

Molecular profiling of single circulating tumor cells with diagnostic intention

(2014) B. Polzer et al.   EMBO Molecular Medicine

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

(2012) Jordi Barretina et al.   NATURE

Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells

(2012) Wanjuan Yang et al.   NUCLEIC ACIDS RESEARCH