Enhancing scientific discoveries in molecular biology with deep generative models

Computational methods for single-cell omics across modalities

(2020) Mirjana Efremova et al.   NATURE METHODS

Realistic in silico generation and augmentation of single-cell RNA-seq data using generative adversarial networks

(2020) Mohamed Marouf et al.   Nature Communications

Interpretable factor models of single-cell RNA-seq via variational autoencoders

(2020) Valentine Svensson et al.   BIOINFORMATICS

scVAE: Variational auto-encoders for single-cell gene expression data

(2020) Christopher Heje Grønbech et al.   BIOINFORMATICS

Single-cell RNA-seq denoising using a deep count autoencoder

(2019) Gökcen Eraslan et al.   Nature Communications

Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning

(2019) Yue Deng et al.   NATURE METHODS

De novo gene signature identification from single‐cell RNA‐seq with hierarchical Poisson factorization

(2019) Hanna Mendes Levitin et al.   Molecular Systems Biology

Dr.VAE: Improving drug response prediction via modeling of drug perturbation effects

(2019) Ladislav Rampášek et al.   BIOINFORMATICS

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq

(2019) Michael B. Cole et al.   Cell Systems

Recording development with single cell dynamic lineage tracing

(2019) Aaron McKenna et al.   DEVELOPMENT

Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders

(2019) Matteo Manica et al.   MOLECULAR PHARMACEUTICS

Exploring single-cell data with deep multitasking neural networks

(2019) Matthew Amodio et al.   NATURE METHODS

Functional interpretation of single cell similarity maps

(2019) David DeTomaso et al.   Nature Communications

Rethinking drug design in the artificial intelligence era

(2019) Petra Schneider et al.   NATURE REVIEWS DRUG DISCOVERY

OUP accepted manuscript

(2018)   BIOINFORMATICS

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

Exploring patterns enriched in a dataset with contrastive principal component analysis

(2018) Abubakar Abid et al.   Nature Communications

Structural absorption by barbule microstructures of super black bird of paradise feathers

(2018) Dakota E. McCoy et al.   Nature Communications

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

Deep learning in biomedicine

(2018) Michael Wainberg et al.   NATURE BIOTECHNOLOGY

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

Inverse molecular design using machine learning: Generative models for matter engineering

(2018) Benjamin Sanchez-Lengeling et al.   SCIENCE

Deep reinforcement learning for de novo drug design

(2018) Mariya Popova et al.   Science Advances

A primer on deep learning in genomics

(2018) James Zou et al.   NATURE GENETICS

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Double-slit photoelectron interference in strong-field ionization of the neon dimer

(2018) Maksim Kunitski et al.   Nature Communications

VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder

(2018) Dongfang Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Stan: A Probabilistic Programming Language

(2017) Bob Carpenter et al.   Journal of Statistical Software

Variational Inference: A Review for Statisticians

(2017) David M. Blei et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

druGAN: An Advanced Generative Adversarial Autoencoder Model for de Novo Generation of New Molecules with Desired Molecular Properties in Silico

(2017) Artur Kadurin et al.   MOLECULAR PHARMACEUTICS

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

Normalizing single-cell RNA sequencing data: challenges and opportunities

(2017) Catalina A Vallejos et al.   NATURE METHODS

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

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

(2016) Atray Dixit et al.   CELL

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

On the use of Bayesian decision theory for issuing natural hazard warnings

(2016) T. Economou et al.   PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

The cornucopia of meaningful leads: Applying deep adversarial autoencoders for new molecule development in oncology

(2016) Artur Kadurin et al.   Oncotarget

hmmSeq: A hidden Markov model for detecting differentially expressed genes from RNA-seq data

(2015) Shiqi Cui et al.   Annals of Applied Statistics

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

Human-level control through deep reinforcement learning

(2015) Volodymyr Mnih et al.   NATURE

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Build, Compute, Critique, Repeat: Data Analysis with Latent Variable Models

(2014) David M. Blei   Annual Review of Statistics and Its Application

The ChEMBL bioactivity database: an update

(2013) A. Patrícia Bento et al.   NUCLEIC ACIDS RESEARCH

Density-ratio matching under the Bregman divergence: a unified framework of density-ratio estimation

(2011) Masashi Sugiyama et al.   ANNALS OF THE INSTITUTE OF STATISTICAL MATHEMATICS

Genes mirror geography within Europe

(2008) John Novembre et al.   NATURE