Current progress and open challenges for applying deep learning across the biosciences

N Sapoval, A Aghazadeh, MG Nute… - Nature …, 2022 - nature.com
Deep Learning (DL) has recently enabled unprecedented advances in one of the grand
challenges in computational biology: the half-century-old problem of protein structure …

Phenotypic drug discovery: recent successes, lessons learned and new directions

F Vincent, A Nueda, J Lee, M Schenone… - Nature Reviews Drug …, 2022 - nature.com
Many drugs, or their antecedents, were discovered through observation of their effects on
normal or disease physiology. For the past generation, this phenotypic drug discovery …

Next-generation cancer organoids

BL LeSavage, RA Suhar, N Broguiere, MP Lutolf… - Nature materials, 2022 - nature.com
Organotypic models of patient-specific tumours are revolutionizing our understanding of
cancer heterogeneity and its implications for personalized medicine. These advancements …

Oncogenic collagen I homotrimers from cancer cells bind to α3β1 integrin and impact tumor microbiome and immunity to promote pancreatic cancer

Y Chen, S Yang, J Tavormina, D Tampe, M Zeisberg… - Cancer cell, 2022 - cell.com
In contrast to normal type I collagen (Col1) heterotrimer (α1/α2/α1) produced by fibroblasts,
pancreatic cancer cells specifically produce unique Col1 homotrimer (α1/α1/α1). Col1 …

Understanding and overcoming resistance to PARP inhibitors in cancer therapy

MP Dias, SC Moser, S Ganesan… - Nature reviews Clinical …, 2021 - nature.com
Develo** novel targeted anticancer therapies is a major goal of current research. The use
of poly (ADP-ribose) polymerase (PARP) inhibitors in patients with homologous …

Artificial intelligence in cancer research and precision medicine

B Bhinder, C Gilvary, NS Madhukar, O Elemento - Cancer discovery, 2021 - AACR
Artificial intelligence (AI) is rapidly resha** cancer research and personalized clinical
care. Availability of high-dimensionality datasets coupled with advances in high …

[HTML][HTML] Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer

JM Chan, A Quintanal-Villalonga, VR Gao, Y **e… - Cancer cell, 2021 - cell.com
Small cell lung cancer (SCLC) is an aggressive malignancy that includes subtypes defined
by differential expression of ASCL1, NEUROD1, and POU2F3 (SCLC-A,-N, and-P …

Comprehensive metabolomics expands precision medicine for triple-negative breast cancer

Y **ao, D Ma, YS Yang, F Yang, JH Ding, Y Gong… - Cell research, 2022 - nature.com
Metabolic reprogramming is a hallmark of cancer. However, systematic characterizations of
metabolites in triple-negative breast cancer (TNBC) are still lacking. Our study profiled the …

Proteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma

MA Gillette, S Satpathy, S Cao, SM Dhanasekaran… - Cell, 2020 - cell.com
To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic
opportunities, we performed comprehensive proteogenomic characterization of 110 tumors …

Multi-omics data integration, interpretation, and its application

I Subramanian, S Verma, S Kumar… - … and biology insights, 2020 - journals.sagepub.com
To study complex biological processes holistically, it is imperative to take an integrative
approach that combines multi-omics data to highlight the interrelationships of the involved …