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Xiangmeng Kong

dblp:277/1062 · DBLP profile ↗
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1ranked-venue papers
0as first author
0since 2021 · last 2020
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Computational science and engineering · 61% Bioinformatics and computational biology · 30% Medical and health informatics · 9%

Topics — the 4 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › gene regulation › gene regulatory network
gene regulatory network analysis
0.412020
TopicNet: a framework for measuring transcriptional regulatory network change · Bioinform. 2020
Computational science and engineering › dynamical systems › network dynamics
network rewiring
0.412020
TopicNet: a framework for measuring transcriptional regulatory network change · Bioinform. 2020
Computational science and engineering
topic modeling
0.412020
TopicNet: a framework for measuring transcriptional regulatory network change · Bioinform. 2020
Medical and health informatics › clinical prediction
cancer survival analysis
0.112020
TopicNet: a framework for measuring transcriptional regulatory network change · Bioinform. 2020

Methods — techniques the papers use, named apart from their topics

latent dirichlet allocation · 0.4
YearPublicationVenuePosition
2020 TopicNet: a framework for measuring transcriptional regulatory network change
abstract
MOTIVATION: Recently, many chromatin immunoprecipitation sequencing experiments have been carried out for a diverse group of transcription factors (TFs) in many different types of human cells. These experiments manifest large-scale and dynamic changes in regulatory network connectivity (i.e. network 'rewiring'), highlighting the different regulatory programs operating in disparate cellular states. However, due to the dense and noisy nature of current regulatory networks, directly comparing the gains and losses of targets of key TFs across cell states is often not informative. Thus, here, we seek an abstracted, low-dimensional representation to understand the main features of network change. RESULTS: We propose a method called TopicNet that applies latent Dirichlet allocation to extract functional topics for a collection of genes regulated by a given TF. We then define a rewiring score to quantify regulatory-network changes in terms of the topic changes for this TF. Using this framework, we can pinpoint particular TFs that change greatly in network connectivity between different cellular states (such as observed in oncogenesis). Also, incorporating gene expression data, we define a topic activity score that measures the degree to which a given topic is active in a particular cellular state. And we show how activity differences can indicate differential survival in various cancers. AVAILABILITY AND IMPLEMENTATION: The TopicNet framework and related analysis were implemented using R and all codes are available at https://github.com/gersteinlab/topicnet. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Shaoke Lou, Tianxiao Li 0001, Xiangmeng Kong, Jing Zhang 0062, Jason Liu 0003, Donghoon Lee 0006, Mark Gerstein
Bioinform.3