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 …

Network orientation via shortest paths

D Silverbush, R Sharan - Bioinformatics, 2014 - academic.oup.com
The graph orientation problem calls for orienting the edges of a graph so as to maximize the
number of pre-specified source–target vertex pairs that admit a directed path from the source …

Uncovering Hidden Connections and Functional Modules via pyPARAGON: a Hybrid Approach for Network Contextualization

MK ARICI - 2024 - open.metu.edu.tr
State-of-the-art omics technologies provide molecular insights into various biological
contexts, such as disease states, patients, and drug perturbations. Network inference and …

An optimization framework for network annotation

S Patkar, R Sharan - Bioinformatics, 2018 - academic.oup.com
Motivation A chief goal of systems biology is the reconstruction of large-scale executable
models of cellular processes of interest. While accurate continuous models are still beyond …

In silico tools to study diseases and polypharmacology through the lens of network medicine

J Aguirre Plans - 2021 - repositori.upf.edu
El funcionament intern de les cèl· lules pot entendre's com un conjunt d'interaccions entre
biomolècules, formant una xarxa que coneixem amb el nom d'interactoma. Els fàrmacs i …

Fantastic Sources of Tumor Heterogeneity and How to Characterize Them

S Patkar - 2021 - search.proquest.com
Cancer constantly evolves to evade the host immune system and resist different treatments.
As a consequence, we see a wide range of inter and intra-tumor heterogeneity. In this PhD …

2 Principles of Molecular Representations

T Engel - Chemoinformatics: Basic Concepts and Methods, 2018 - books.google.com
Chemical compounds are the daily working environment of a chemist. Therefore, a typical
workflow of an experimentally working chemist might be to perform a synthesis under certain …

[图书][B] Improving the interpretability of integer linear programming methods for biological subnetwork inference

DA Chasman - 2014 - search.proquest.com
Biologists often screen an entire genome for involvement in a cellular phenotype of interest.
To analyze the resulting data, computational methods have been developed to infer …

Assembling biological boolean networks using manually curated databases and prediction algorithms

A Calderone - arXiv preprint arXiv:1412.1013, 2014 - arxiv.org
Despite the large quantity of information available, thorough researches in various biological
databases are still needed in order to reconstruct and understand the steps that lead to …

[引用][C] Deciphering Cellular Signaling Pathways and Their Perturbations in Disease Using Network-Based Strategies

D Silverbush - 2017 - Tel Aviv University