Nature Search

DeepTarget predicts anti-cancer mechanisms of action of small molecules by integrating drug and genetic screens

Sanju Sinha
Neelam Sinha
Eytan Ruppin
ResearchOpen Access05 Nov 2025
npj Precision Oncology

Volume: 9, P: 1-14
Author Correction: A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing

Sanju Sinha
Karina Barbosa
Eytan Ruppin
Amendments and CorrectionsOpen Access16 May 2022
Nature Communications

Volume: 13, P: 1
A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing

CRISPR-Cas9 gene editing can induce a p53 mediated damage response. Here the authors investigate the possibility of selection of pre-existing cancer driver mutations during CRISPR-Cas9 knockout based gene editing and identify KRAS mutants that may confer a selected advantage to edited cells.

Sanju Sinha
Karina Barbosa
Eytan Ruppin
ResearchOpen Access11 Nov 2021
Nature Communications

Volume: 12, P: 1-13
Higher prevalence of homologous recombination deficiency in tumors from African Americans versus European Americans

Ryan and colleagues analyze genomic features in tumors from African Americans and European Americans and find that homologous recombination deficiency is more prevalent in African Americans.

Sanju Sinha
Khadijah A. Mitchell
Bríd M. Ryan
Research13 Jan 2020
Nature Cancer

Volume: 1, P: 112-121
The 2023 generation

Twelve early-career investigators share their thoughts on the experiences they had starting their laboratories in 2023 and reflect on the opportunities they seized and the challenges they faced.

Joanna Achinger-Kawecka
Santiago Correa
Caroline J. Watson
Reviews15 Dec 2023
Nature Cancer

Volume: 4, P: 1630-1635
A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics

Hoang et al. developed a deep-learning framework called ENLIGHT–DeepPT that predicts therapy response based on imputed transcriptomics and shows predictive power across patient cohorts and cancer types.

Danh-Tai Hoang
Gal Dinstag
Eytan Ruppin
Research03 Jul 2024
Nature Cancer

Volume: 5, P: 1305-1317
PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors

Sinha and colleagues present PERCEPTION, a precision oncology computational pipeline that can predict the response and resistance of patients by analyzing single-cell transcriptomic data from their tumor samples.

Sanju Sinha
Rahulsimham Vegesna
Eytan Ruppin
Research18 Apr 2024
Nature Cancer

Volume: 5, P: 938-952
Author Correction: Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans

Khadijah A. Mitchell
Noah Nichols
Bríd M. Ryan
Amendments and CorrectionsOpen Access30 Jan 2020
Nature Communications

Volume: 11, P: 1
The synthetic lethal interaction between CDS1 and CDS2 is a vulnerability in uveal melanoma and across multiple tumor types

This study employs a functional genomic approach to identify a synthetic lethal interaction between CDS1 and CDS2 in uveal melanoma and other cancers, which may represent a potential therapeutic target.

Pui Ying Chan
Diana Alexander
David J. Adams
ResearchOpen Access04 Jul 2025
Nature Genetics

Volume: 57, P: 1672-1683
A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients

Alternative polyadenylation (APA) regulates the length of the 3′UTR of mRNA. Here, the authors describe a method to accurately measure APA in tumours and apply this method to investigate the differences in APA in African American and European American lung cancer samples.

Adriana Zingone
Sanju Sinha
Bríd M. Ryan
ResearchOpen Access23 Sept 2021
Nature Communications

Volume: 12, P: 1-12
The GPCR–Gα_s–PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure

Here, the authors use computational screening and a chemogenetic analysis of transgenic mice to show that Gα_s-coupled G-protein-coupled receptors on exhausted CD8⁺ T cells are involved in suppression of effector functions and inhibition of the protective effects of immune checkpoint immunotherapy.

Victoria H. Wu
Bryan S. Yung
J. Silvio Gutkind
Research12 Jun 2023
Nature Immunology

Volume: 24, P: 1318-1330
The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective

Intra-tumor heterogeneity is often associated with resistance to targeted therapy, requiring the design of combinatorial therapies. Here, based on tumor single-cell transcriptomic datasets, the authors develop a computational approach to identify optimal combinatorial treatments targeting membrane receptors for cancer therapy.

Saba Ahmadi
Pattara Sukprasert
Eytan Ruppin
ResearchOpen Access25 Mar 2022
Nature Communications

Volume: 13, P: 1-17
Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans

Lung cancer etiology has largely been studied in homogenous populations of European descent. Here, targeted sequencing in African American lung adenocarcinomas finds significantly higher prevalence of PTPRTand JAK2 mutations, validated independently by whole exome sequencing, highlighting potentially clinically actionable mutations in this population.

Khadijah A. Mitchell
Noah Nichols
Bríd M. Ryan
ResearchOpen Access16 Dec 2019
Nature Communications

Volume: 10, P: 1-7
Big data in basic and translational cancer research

The increasing size of cancer datasets requires new ways of thinking for analysing and integrating these data. In this Review, Jiang et al. discuss considerations and strategies for wielding ‘big data’ ― large, information-rich datasets ― in basic research and for translational applications such as identifying biomarkers, informing clinical trials and developing new assays and treatments.

Peng Jiang
Sanju Sinha
Eytan Ruppin
Reviews05 Sept 2022
Nature Reviews Cancer

Volume: 22, P: 625-639

Search

DeepTarget predicts anti-cancer mechanisms of action of small molecules by integrating drug and genetic screens

Author Correction: A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing

A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing

Higher prevalence of homologous recombination deficiency in tumors from African Americans versus European Americans

The 2023 generation

A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics

PERCEPTION predicts patient response and resistance to treatment using single-cell transcriptomics of their tumors

Author Correction: Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans

The synthetic lethal interaction between CDS1 and CDS2 is a vulnerability in uveal melanoma and across multiple tumor types

A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients

The GPCR–Gα_s–PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure

The landscape of receptor-mediated precision cancer combination therapy via a single-cell perspective

Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans

Big data in basic and translational cancer research

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