Deep learning for computational biology

C Angermueller, T Pärnamaa, L Parts… - Molecular systems …, 2016 - embopress.org
Technological advances in genomics and imaging have led to an explosion of molecular
and cellular profiling data from large numbers of samples. This rapid increase in biological …

Toxicity testing in the 21st century: progress in the past decade and future perspectives

D Krewski, ME Andersen, MG Tyshenko… - Archives of …, 2020 - Springer
Advances in the biological sciences have led to an ongoing paradigm shift in toxicity testing
based on expanded application of high-throughput in vitro screening and in silico methods …

DeepTox: toxicity prediction using deep learning

A Mayr, G Klambauer, T Unterthiner… - Frontiers in …, 2016 - frontiersin.org
The Tox21 Data Challenge has been the largest effort of the scientific community to compare
computational methods for toxicity prediction. This challenge comprised 12,000 …

Deep learning for drug response prediction in cancer

D Baptista, PG Ferreira, M Rocha - Briefings in bioinformatics, 2021 - academic.oup.com
Predicting the sensitivity of tumors to specific anti-cancer treatments is a challenge of
paramount importance for precision medicine. Machine learning (ML) algorithms can be …

A microfluidics platform for combinatorial drug screening on cancer biopsies

F Eduati, R Utharala, D Madhavan… - Nature …, 2018 - nature.com
Screening drugs on patient biopsies from solid tumours has immense potential, but is
challenging due to the small amount of available material. To address this, we present here …

[HTML][HTML] The US Federal Tox21 Program: A strategic and operational plan for continued leadership

RS Thomas, RS Paules, A Simeonov, SC Fitzpatrick… - Altex, 2018 - ncbi.nlm.nih.gov
Background The traditional approaches to toxicity testing have posed multiple challenges for
evaluating the safety of industrial and environmental chemicals, pesticides, food additives …

Big data in basic and translational cancer research

P Jiang, S Sinha, K Aldape, S Hannenhalli… - Nature Reviews …, 2022 - nature.com
Historically, the primary focus of cancer research has been molecular and clinical studies of
a few essential pathways and genes. Recent years have seen the rapid accumulation of …

A data-driven approach to predicting successes and failures of clinical trials

KM Gayvert, NS Madhukar, O Elemento - Cell chemical biology, 2016 - cell.com
Over the past decade, the rate of drug attrition due to clinical trial failures has risen
substantially. Unfortunately it is difficult to identify compounds that have unfavorable toxicity …

Map** the functional landscape of T cell receptor repertoires by single-T cell transcriptomics

Z Zhang, D **ong, X Wang, H Liu, T Wang - Nature methods, 2021 - nature.com
Many experimental and bioinformatics approaches have been developed to characterize the
human T cell receptor (TCR) repertoire. However, the unknown functional relevance of TCR …

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

R Huang, M **a, S Sakamuru, J Zhao… - Nature …, 2016 - nature.com
Target-specific, mechanism-oriented in vitro assays post a promising alternative to
traditional animal toxicology studies. Here we report the first comprehensive analysis of the …