Yang L, Chen R, Goodison S, Sun Y
Brief Bioinform. 2024; 26(1).
PMID: 39737568
PMC: 11684898.
DOI: 10.1093/bib/bbae692.
Fischer J, Shutta K, Chen C, Fanfani V, Saha E, Mandros P
bioRxiv. 2024; .
PMID: 39345481
PMC: 11430018.
DOI: 10.1101/2024.09.19.613876.
Hamlin R, Pienkos S, Chan L, Stabile M, Pinedo K, Rao M
bioRxiv. 2024; .
PMID: 38948732
PMC: 11212991.
DOI: 10.1101/2024.06.18.599612.
Odongo R, Demiroglu-Zergeroglu A, Cakir T
BioData Min. 2024; 17(1):5.
PMID: 38378612
PMC: 10880212.
DOI: 10.1186/s13040-024-00357-1.
Yang L, Chen R, Melendy T, Goodison S, Sun Y
Cancers (Basel). 2023; 15(16).
PMID: 37627118
PMC: 10452419.
DOI: 10.3390/cancers15164090.
AMEND: active module identification using experimental data and network diffusion.
Boyd S, Slawson C, Thompson J
BMC Bioinformatics. 2023; 24(1):277.
PMID: 37415126
PMC: 10324253.
DOI: 10.1186/s12859-023-05376-z.
Characterizing alternative splicing effects on protein interaction networks with LINDA.
Gjerga E, Naarmann-de Vries I, Dieterich C
Bioinformatics. 2023; 39(39 Suppl 1):i458-i464.
PMID: 37387163
PMC: 10311343.
DOI: 10.1093/bioinformatics/btad224.
An efficient and effective method to identify significantly perturbed subnetworks in cancer.
Yang L, Chen R, Goodison S, Sun Y
Nat Comput Sci. 2023; 1(1):79-88.
PMID: 37346964
PMC: 10284573.
DOI: 10.1038/s43588-020-00009-4.
A network embedding approach to identify active modules in biological interaction networks.
Pasquier C, Guerlais V, Pallez D, Rapetti-Mauss R, Soriani O
Life Sci Alliance. 2023; 6(9).
PMID: 37339804
PMC: 10282331.
DOI: 10.26508/lsa.202201550.
SEMtree: tree-based structure learning methods with structural equation models.
Grassi M, Tarantino B
Bioinformatics. 2023; 39(6).
PMID: 37294820
PMC: 10287946.
DOI: 10.1093/bioinformatics/btad377.
RNC: Uncovering the dynamic and condition-specific RBP-ncRNA circuits from multi-omics data.
Jiang L, Hao S, Lin L, Gao X, Xu J
Comput Struct Biotechnol J. 2023; 21:2276-2285.
PMID: 37035550
PMC: 10073992.
DOI: 10.1016/j.csbj.2023.03.035.
Mena regulates nesprin-2 to control actin-nuclear lamina associations, trans-nuclear membrane signalling and gene expression.
Li Mow Chee F, Beernaert B, Griffith B, Loftus A, Kumar Y, Wills J
Nat Commun. 2023; 14(1):1602.
PMID: 36959177
PMC: 10036544.
DOI: 10.1038/s41467-023-37021-x.
Time-Varying Gene Expression Network Analysis Reveals Conserved Transition States in Hematopoietic Differentiation between Human and Mouse.
Gao S, Chen Y, Wu Z, Kajigaya S, Wang X, Young N
Genes (Basel). 2022; 13(10).
PMID: 36292775
PMC: 9601530.
DOI: 10.3390/genes13101890.
Gaussian graphical models with applications to omics analyses.
Shutta K, De Vito R, Scholtens D, Balasubramanian R
Stat Med. 2022; 41(25):5150-5187.
PMID: 36161666
PMC: 9672860.
DOI: 10.1002/sim.9546.
The 22q11.2 region regulates presynaptic gene-products linked to schizophrenia.
Nehme R, Pietilainen O, Artomov M, Tegtmeyer M, Valakh V, Lehtonen L
Nat Commun. 2022; 13(1):3690.
PMID: 35760976
PMC: 9237031.
DOI: 10.1038/s41467-022-31436-8.
KeyPathwayMineR: Pathway Enrichment in the R Ecosystem.
Mechteridis K, Lauber M, Baumbach J, List M
Front Genet. 2022; 12:812853.
PMID: 35173764
PMC: 8842393.
DOI: 10.3389/fgene.2021.812853.
Temporal and sequential order of nonoverlapping gene networks unraveled in mated female Drosophila.
Pasquier C, Robichon A
Life Sci Alliance. 2021; 5(2).
PMID: 34844981
PMC: 8645335.
DOI: 10.26508/lsa.202101119.
Hierarchy of TGFβ/SMAD, Hippo/YAP/TAZ, and Wnt/β-catenin signaling in melanoma phenotype switching.
Luond F, Pirkl M, Hisano M, Prestigiacomo V, Kalathur R, Beerenwinkel N
Life Sci Alliance. 2021; 5(2).
PMID: 34819356
PMC: 8616544.
DOI: 10.26508/lsa.202101010.
KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism.
Ruberto A, Grechez-Cassiau A, Guerin S, Martin L, Revel J, Mehiri M
Elife. 2021; 10.
PMID: 34402428
PMC: 8410083.
DOI: 10.7554/eLife.65574.
Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer.
Uzuner D, Akkoc Y, Peker N, Pir P, Gozuacik D, Cakir T
Sci Rep. 2021; 11(1):15806.
PMID: 34349126
PMC: 8339123.
DOI: 10.1038/s41598-021-94005-x.
