Author details

Full Name

Koon-Kiu Yan

Affiliation

ORCID

Career Start Year

2004

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36747870	scMINER: a mutual information-based framework for identifying hidden drivers from single-cell omics data.	bioRxiv	2023
37142594	NetBID2 provides comprehensive hidden driver analysis.	Nat Commun	2023
36747874	scMINER: a mutual information-based framework for identifying hidden drivers from single-cell omics data.	Res Sq	2023
35502723	Single-cell analysis reveals the Comma-1D cell line as a unique model for mammary gland development and breast cancer.	J Cell Sci	2022
34413129	SLFN11 is Widely Expressed in Pediatric Sarcoma and Induces Variable Sensitization to Replicative Stress Caused By DNA-Damaging Agents.	Mol Cancer Ther	2021
33910004	The miR-424(322)/503 gene cluster regulates pro- versus anti-inflammatory skin DC subset differentiation by modulating TGF-Î² signaling.	Cell Rep	2021
32733009	Cross-talk between GLI transcription factors and FOXC1 promotes T-cell acute lymphoblastic leukemia dissemination.	Leukemia	2021
34633138	miR-424/503 modulates Wnt/Î²-catenin signaling in the mammary epithelium by targeting LRP6.	EMBO Reports	2021
32717640	Network Approaches for Dissecting the Immune System.	iScience	2020
32213348	Comparing Technological Development and Biological Evolution from a Network Perspective.	Cell Syst	2020
32471347	The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data.	BMC Bioinformatics	2020
32737473	Supervised enhancer prediction with epigenetic pattern recognition and targeted validation.	Nat Methods	2020
32728046	An integrative ENCODE resource for cancer genomics.	Nat Commun	2020
30890172	Measuring the reproducibility and quality of Hi-C data.	Genome Biol	2019
29284660	The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of <i>Drosophila</i> and <i>Caenorhabditis elegans</i> Transcription Factors.	Genetics	2018
28742097	MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.	PLoS Comput Biol	2017
28369339	HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps.	Bioinformatics	2017
27005445	Temporal Dynamics of Collaborative Networks in Large Scientific Consortia.	Trends Genet	2016
27047991	Cross-Disciplinary Network Comparison: Matchmaking Between Hairballs.	Cell Syst	2016
25880651	An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome.	Genome Biol	2015
25884877	Loregic: a method to characterize the cooperative logic of regulatory factors.	PLoS Comput Biol	2015
25164755	Comparative analysis of the transcriptome across distant species.	Nature	2014
25249401	OrthoClust: an orthology-based network framework for clustering data across multiple species.	Genome Biol	2014
24811311	Cellular superspreaders: an epidemiological perspective on HIV infection inside the body.	PLoS Pathog	2014
25164757	Comparative analysis of regulatory information and circuits across distant species.	Nature	2014
22955619	Architecture of the human regulatory network derived from ENCODE data.	Nature	2012
22955978	Understanding transcriptional regulation by integrative analysis of transcription factor binding data.	Genome Res	2012
22125477	Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.	PLoS Comput Biol	2011
21253555	Measuring the evolutionary rewiring of biological networks.	PLoS Comput Biol	2011
21324173	A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets.	Genome Biol	2011
21603617	The spread of scientific information: insights from the web usage statistics in PLoS article-level metrics.	PLoS One	2011
20126643	Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data.	PLoS One	2010
21177976	Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.	Science	2010
20439753	Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.	Proc Natl Acad Sci U S A	2010
20351254	Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels.	Proc Natl Acad Sci U S A	2010
20523742	Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.	PLoS Comput Biol	2010
19437675	Fluctuations in mass-action equilibrium of protein binding networks.	Phys Rev Lett	2008
18039386	Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins.	Biol Direct	2007
15070432	Upstream plasticity and downstream robustness in evolution of molecular networks.	BMC Evol Biol	2004