AI-powered therapeutic target discovery

Chemistry42: An AI-Driven Platform for Molecular Design and Optimization

(2023) Yan A. Ivanenkov et al.   Journal of Chemical Information and Modeling

AlphaFold accelerates artificial intelligence powered drug discovery: efficient discovery of a novel CDK20 small molecule inhibitor

(2023) Feng Ren et al.   Chemical Science

In-depth quantitative proteomics analysis revealed C1GALT1 depletion in ECC-1 cells mimics an aggressive endometrial cancer phenotype observed in cancer patients with low C1GALT1 expression

(2023) Ana Montero-Calle et al.   CELLULAR ONCOLOGY

Improving clinical trial design using interpretable machine learning based prediction of early trial termination

(2023) Ece Kavalci et al.   Scientific Reports

Artificial intelligence for compound pharmacokinetics prediction

(2023) Olga Obrezanova   CURRENT OPINION IN STRUCTURAL BIOLOGY

SIRT3‐dependent delactylation of cyclin E2 prevents hepatocellular carcinoma growth

(2023) Jing Jin et al.   EMBO REPORTS

Deacetylation induced nuclear condensation of HP1γ promotes multiple myeloma drug resistance

(2023) Xin Li et al.   Nature Communications

BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2

(2022) Avi J. Samelson et al.   NATURE CELL BIOLOGY

Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis

(2022) Sai Zhang et al.   NEURON

Tissue-specific multi-omics analysis of atrial fibrillation

(2022) Ines Assum et al.   Nature Communications

Why 90% of clinical drug development fails and how to improve it?

(2022) Duxin Sun et al.   Acta Pharmaceutica Sinica B

Interleukin-23 in the Pathogenesis of Inflammatory Bowel Disease and Implications for Therapeutic Intervention

(2022) Gavin W Sewell et al.   Journal of Crohns & Colitis

Parallel‐reaction monitoring revealed altered expression of a number of epitranscriptomic reader, writer, and eraser proteins accompanied with colorectal cancer metastasis

(2022) Tianyu F. Qi et al.   PROTEOMICS

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Multiple causal variants underlie genetic associations in humans

(2022) Nathan S. Abell et al.   SCIENCE

Utility Metrics for Evaluating Synthetic Health Data Generation Methods: Validation Study

(2022) Khaled El Emam et al.   JMIR Medical Informatics

Treating Duchenne Muscular Dystrophy: The Promise of Stem Cells, Artificial Intelligence, and Multi-Omics

(2022) Carlos D. Vera et al.   Frontiers in Cardiovascular Medicine

Phenotypic screening with deep learning identifies HDAC6 inhibitors as cardioprotective in a BAG3 mouse model of dilated cardiomyopathy

(2022) Jin Yang et al.   Science Translational Medicine

Multiomics characterization implicates PTK7 in ovarian cancer EMT and cell plasticity and offers strategies for therapeutic intervention

(2022) Juuli Raivola et al.   Cell Death & Disease

Identification of Therapeutic Targets for Amyotrophic Lateral Sclerosis Using PandaOmics – An AI-Enabled Biological Target Discovery Platform

(2022) Frank W. Pun et al.   Frontiers in Aging Neuroscience

Integrating transcriptomics, metabolomics, and GWAS helps reveal molecular mechanisms for metabolite levels and disease risk

(2022) Xianyong Yin et al.   AMERICAN JOURNAL OF HUMAN GENETICS

BioGPT: generative pre-trained transformer for biomedical text generation and mining

(2022) Renqian Luo et al.   BRIEFINGS IN BIOINFORMATICS

Combinatorial treatment with statins and niclosamide prevents CRC dissemination by unhinging the MACC1-β-catenin-S100A4 axis of metastasis

(2022) Benedikt Kortüm et al.   ONCOGENE

Synthetic data as an enabler for machine learning applications in medicine

(2022) Jean-Francois Rajotte et al.   iScience

DUT enhances drug resistance to proteasome inhibitors via promoting mitochondrial function in multiple myeloma

(2022) Yafei Wang et al.   CARCINOGENESIS

Adversarial generation of gene expression data

(2021) Ramon Viñas et al.   BIOINFORMATICS

Extended-culture and culture-independent molecular analysis of the airway microbiota in cystic fibrosis following CFTR modulation with ivacaftor

(2021) Gisli G. Einarsson et al.   Journal of Cystic Fibrosis

Novel CRISPR–Cas Systems: An Updated Review of the Current Achievements, Applications, and Future Research Perspectives

(2021) Sweta Nidhi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Synthetic single cell RNA sequencing data from small pilot studies using deep generative models

(2021) Martin Treppner et al.   Scientific Reports

Modular Approaches to Synthesize Activity- and Affinity-Based Chemical Probes

(2021) Antonie J. van der Zouwen et al.   Frontiers in Chemistry

Patient-derived organoids as a predictive biomarker for treatment response in cancer patients

(2021) G. Emerens Wensink et al.   npj Precision Oncology

Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite

(2021) Océane Cassan et al.   BMC GENOMICS

The Problem of Fairness in Synthetic Healthcare Data

(2021) Karan Bhanot et al.   Entropy

Applications of Brain Organoids for Infectious Diseases

(2021) Wenqiang Fan et al.   JOURNAL OF MOLECULAR BIOLOGY

Systems biomarkers for papillary thyroid cancer prognosis and treatment through multi-omics networks

(2021) Gizem Gulfidan et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

The Discovery of New Drug-Target Interactions for Breast Cancer Treatment

(2021) Jiali Song et al.   MOLECULES

An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci

(2021) Edward Mountjoy et al.   NATURE GENETICS

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

(2021) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents

(2021) Ying Zhou et al.   NUCLEIC ACIDS RESEARCH

Network pharmacology: curing causal mechanisms instead of treating symptoms

(2021) Cristian Nogales et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Network analysis reveals rare disease signatures across multiple levels of biological organization

(2021) Pisanu Buphamalai et al.   Nature Communications

A unified drug–target interaction prediction framework based on knowledge graph and recommendation system

(2021) Qing Ye et al.   Nature Communications

Multi-Omics Analysis of Fatty Acid Metabolism in Thyroid Carcinoma

(2021) Jinghui Lu et al.   Frontiers in Oncology

Brain organoids: an ensemble of bioassays to investigate human neurodevelopment and disease

(2020) Jaydeep Sidhaye et al.   CELL DEATH AND DIFFERENTIATION

Molecular Generation for Desired Transcriptome Changes With Adversarial Autoencoders

(2020) Rim Shayakhmetov et al.   Frontiers in Pharmacology

A mobile robotic chemist

(2020) Benjamin Burger et al.   NATURE

Accelerating Therapeutics for Opportunities in Medicine: A Paradigm Shift in Drug Discovery

(2020) Izumi V. Hinkson et al.   Frontiers in Pharmacology

COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning

(2020) Edison Ong et al.   Frontiers in Immunology

CRISPR-based screens uncover determinants of immunotherapy response in multiple myeloma

(2020) Poornima Ramkumar et al.   Blood Advances

A role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics

(2020) Michael A. Crone et al.   Nature Communications

GuiltyTargets: Prioritization of Novel Therapeutic Targets With Network Representation Learning

(2020) Ozlem Muslu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Rectal Organoids Enable Personalized Treatment of Cystic Fibrosis

(2019) Gitte Berkers et al.   Cell Reports

Elucidating the druggability of the human proteome with eFindSite

(2019) Omar Kana et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

3D model for CAR‐mediated cytotoxicity using patient‐derived colorectal cancer organoids

(2019) Theresa E Schnalzger et al.   EMBO JOURNAL

Applications of machine learning in drug discovery and development

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

Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing

(2019) Brett K. Beaulieu-Jones et al.  

Deep learning enables rapid identification of potent DDR1 kinase inhibitors

(2019) Alex Zhavoronkov et al.   NATURE BIOTECHNOLOGY

Deep biomarkers of aging and longevity: from research to applications

(2019) Alex Zhavoronkov et al.   Aging-US

A meta-analysis of genome-wide association studies identifies multiple longevity genes

(2019) Joris Deelen et al.   Nature Communications

Using deep learning to associate human genes with age-related diseases

(2019) Fabio Fabris et al.   BIOINFORMATICS

Machine Learning on Human Muscle Transcriptomic Data for Biomarker Discovery and Tissue-Specific Drug Target Identification

(2018) Polina Mamoshina et al.   Frontiers in Genetics

Machine Learning for Drug-Target Interaction Prediction

(2018) Ruolan Chen et al.   MOLECULES

Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response

(2018) Janet Piñero et al.   Frontiers in Genetics

Artificial intelligence for aging and longevity research: Recent advances and perspectives

(2018) Alex Zhavoronkov et al.   AGEING RESEARCH REVIEWS

Drug repurposing: progress, challenges and recommendations

(2018) Sudeep Pushpakom et al.   NATURE REVIEWS DRUG DISCOVERY

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Onco-Multi-OMICS Approach: A New Frontier in Cancer Research

(2018) Sajib Chakraborty et al.   Biomed Research International

The druggable genome and support for target identification and validation in drug development

(2017) Chris Finan et al.   Science Translational Medicine

Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of COX7A1 in embryonic and cancer cells

(2017) Michael D. West et al.   Oncotarget

3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping

(2016) Yu-Chen Lo et al.   ACS Chemical Biology

Using reverse docking for target identification and its applications for drug discovery

(2016) Aeri Lee et al.   Expert Opinion on Drug Discovery

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

(2016) Alexander Aliper et al.   MOLECULAR PHARMACEUTICS

A comprehensive map of molecular drug targets

(2016) Rita Santos et al.   NATURE REVIEWS DRUG DISCOVERY

CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks

(2014) Zeeshan Gillani et al.   BMC BIOINFORMATICS

Molecule-pharmacophore superpositioning and pattern matching in computational drug design

(2007) G WOLBER   DRUG DISCOVERY TODAY