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 …

Network-based machine learning approach to predict immunotherapy response in cancer patients

JH Kong, D Ha, J Lee, I Kim, M Park, SH Im… - Nature …, 2022 - nature.com
Immune checkpoint inhibitors (ICIs) have substantially improved the survival of cancer
patients over the past several years. However, only a minority of patients respond to ICI …

Tertiary lymphoid structures improve immunotherapy and survival in melanoma

R Cabrita, M Lauss, A Sanna, M Donia… - Nature, 2020 - nature.com
Checkpoint blockade therapies that reactivate tumour-associated T cells can induce durable
tumour control and result in the long-term survival of patients with advanced cancers …

Determining cell type abundance and expression from bulk tissues with digital cytometry

AM Newman, CB Steen, CL Liu, AJ Gentles… - Nature …, 2019 - nature.com
Single-cell RNA-sequencing has emerged as a powerful technique for characterizing
cellular heterogeneity, but it is currently impractical on large sample cohorts and cannot be …

The journey from melanocytes to melanoma

PP Centeno, V Pavet, R Marais - Nature Reviews Cancer, 2023 - nature.com
Over the past decade, melanoma has led the field in new cancer treatments, with impressive
gains in on-treatment survival but more modest improvements in overall survival. Melanoma …

The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy

JJ Havel, D Chowell, TA Chan - Nature Reviews Cancer, 2019 - nature.com
Checkpoint inhibitor-based immunotherapies that target cytotoxic T lymphocyte antigen 4
(CTLA4) or the programmed cell death 1 (PD1) pathway have achieved impressive success …

The PI3K-AKT-mTOR pathway and prostate cancer: at the crossroads of AR, MAPK, and WNT signaling

BY Shorning, MS Dass, MJ Smalley… - International journal of …, 2020 - mdpi.com
Oncogenic activation of the phosphatidylinositol-3-kinase (PI3K), protein kinase B
(PKB/AKT), and mammalian target of rapamycin (mTOR) pathway is a frequent event in …

TYRO3 induces anti–PD-1/PD-L1 therapy resistance by limiting innate immunity and tumoral ferroptosis

Z Jiang, SO Lim, M Yan, JL Hsu, J Yao… - The Journal of …, 2021 - Am Soc Clin Investig
Immune checkpoint blockade therapy has demonstrated promising clinical outcomes for
multiple cancer types. However, the emergence of resistance as well as inadequate …

Deep learning-based prediction of the T cell receptor–antigen binding specificity

T Lu, Z Zhang, J Zhu, Y Wang, P Jiang, X Xiao… - Nature machine …, 2021 - nature.com
Neoantigens play a key role in the recognition of tumour cells by T cells; however, only a
small proportion of neoantigens truly elicit T-cell responses, and few clues exist as to which …

Tumor microenvironment characterization in gastric cancer identifies prognostic and immunotherapeutically relevant gene signatures

D Zeng, M Li, R Zhou, J Zhang, H Sun, M Shi… - Cancer immunology …, 2019 - AACR
Tumor microenvironment (TME) cells constitute a vital element of tumor tissue. Increasing
evidence has elucidated their clinicopathologic significance in predicting outcomes and …