Computational network biology: data, models, and applications

C Liu, Y Ma, J Zhao, R Nussinov, YC Zhang, F Cheng… - Physics Reports, 2020 - Elsevier
Biological entities are involved in intricate and complex interactions, in which uncovering the
biological information from the network concepts are of great significance. Benefiting from …

Precision oncology: the road ahead

D Senft, MDM Leiserson, E Ruppin, AR Ze'ev - Trends in molecular …, 2017 - cell.com
Current efforts in precision oncology largely focus on the benefit of genomics-guided
therapy. Yet, advances in sequencing techniques provide an unprecedented view of the …

Cancer-associated mutation and beyond: The emerging biology of isocitrate dehydrogenases in human disease

S Tommasini-Ghelfi, K Murnan, FM Kouri… - Science …, 2019 - science.org
Isocitrate dehydrogenases (IDHs) are critical metabolic enzymes that catalyze the oxidative
decarboxylation of isocitrate to α-ketoglutarate (αKG), NAD (P) H, and CO2. IDHs …

Dysregulated lipid synthesis by oncogenic IDH1 mutation is a targetable synthetic lethal vulnerability

D Thomas, M Wu, Y Nakauchi, M Zheng… - Cancer discovery, 2023 - AACR
Abstract Isocitrate dehydrogenase 1 and 2 (IDH) are mutated in multiple cancers and drive
production of (R)-2-hydroxyglutarate (2HG). We identified a lipid synthesis enzyme [acetyl …

[HTML][HTML] Computer-aided drug repurposing for cancer therapy: approaches and opportunities to challenge anticancer targets

C Mottini, F Napolitano, Z Li, X Gao… - Seminars in cancer biology, 2021 - Elsevier
Despite huge efforts made in academic and pharmaceutical worldwide research, current
anticancer therapies achieve effective treatment in a limited number of neoplasia cases only …

The m6A RNA demethylase FTO is a HIF-independent synthetic lethal partner with the VHL tumor suppressor

Y Xiao, KN Thakkar, H Zhao… - Proceedings of the …, 2020 - National Acad Sciences
Loss of the von Hippel–Lindau (VHL) tumor suppressor is a hallmark feature of renal clear
cell carcinoma. VHL inactivation results in the constitutive activation of the hypoxia-inducible …

Harnessing synthetic lethality to predict the response to cancer treatment

JS Lee, A Das, L Jerby-Arnon, R Arafeh… - Nature …, 2018 - nature.com
While synthetic lethality (SL) holds promise in developing effective cancer therapies, SL
candidates found via experimental screens often have limited translational value. Here we …

Dual-dropout graph convolutional network for predicting synthetic lethality in human cancers

R Cai, X Chen, Y Fang, M Wu, Y Hao - Bioinformatics, 2020 - academic.oup.com
Motivation Synthetic lethality (SL) is a promising form of gene interaction for cancer therapy,
as it is able to identify specific genes to target at cancer cells without disrupting normal cells …

SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery

J Wang, M Wu, X Huang, L Wang, S Zhang, H Liu… - Database, 2022 - academic.oup.com
Two genes are synthetic lethal if mutations in both genes result in impaired cell viability,
while mutation of either gene does not affect the cell survival. The potential usage of …

RUNX1 loss renders hematopoietic and leukemic cells dependent on IL-3 and sensitive to JAK inhibition

AC Fan, Y Nakauchi, L Bai, A Azizi… - The Journal of …, 2023 - Am Soc Clin Investig
Disease-initiating mutations in the transcription factor RUNX1 occur as germline and
somatic events that cause leukemias with particularly poor prognosis. However, the role of …