Rudolf T Pillich
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Explore the profile of Rudolf T Pillich including associated specialties, affiliations and a list of published articles.
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Articles
18
Citations
140
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Recent Articles
1.
Wright S, Colton S, Schaffer L, Pillich R, Churas C, Pratt D, et al.
Mol Syst Biol
. 2024 Dec;
21(1):1-29.
PMID: 39653848
Advancements in genomic and proteomic technologies have powered the creation of large gene and protein networks ("interactomes") for understanding biological systems. However, the proliferation of interactomes complicates the selection of...
2.
Hu M, Alkhairy S, Lee I, Pillich R, Fong D, Smith K, et al.
Nat Methods
. 2024 Nov;
22(1):82-91.
PMID: 39609565
Gene set enrichment is a mainstay of functional genomics, but it relies on gene function databases that are incomplete. Here we evaluate five large language models (LLMs) for their ability...
3.
Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing
Maier A, Hartung M, Abovsky M, Adamowicz K, Bader G, Baier S, et al.
Nucleic Acids Res
. 2024 May;
52(W1):W481-W488.
PMID: 38783119
In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network...
4.
Wright S, Colton S, Schaffer L, Pillich R, Churas C, Pratt D, et al.
bioRxiv
. 2024 May;
PMID: 38746239
Advancements in genomic and proteomic technologies have powered the use of gene and protein networks ("interactomes") for understanding genotype-phenotype translation. However, the proliferation of interactomes complicates the selection of networks...
5.
Hu M, Alkhairy S, Lee I, Pillich R, Bachelder R, Ideker T, et al.
Res Sq
. 2023 Oct;
PMID: 37790547
Gene set analysis is a mainstay of functional genomics, but it relies on manually curated databases of gene functions that are incomplete and unaware of biological context. Here we evaluate...
6.
Hu M, Alkhairy S, Lee I, Pillich R, Fong D, Smith K, et al.
ArXiv
. 2023 Sep;
PMID: 37731657
Gene set analysis is a mainstay of functional genomics, but it relies on curated databases of gene functions that are incomplete. Here we evaluate five Large Language Models (LLMs) for...
7.
Drugst.One - A plug-and-play solution for online systems medicine and network-based drug repurposing
Maier A, Hartung M, Abovsky M, Adamowicz K, Bader G, Baier S, et al.
ArXiv
. 2023 Jun;
PMID: 37332567
In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood. In response, computational systems and network...
8.
Kratz A, Kim M, Kelly M, Zheng F, Koczor C, Li J, et al.
Cell Syst
. 2023 May;
14(6):447-463.e8.
PMID: 37220749
The DNA damage response (DDR) ensures error-free DNA replication and transcription and is disrupted in numerous diseases. An ongoing challenge is to determine the proteins orchestrating DDR and their organization...
9.
Pratt D, Pillich R, Morris J
Front Bioinform
. 2023 Apr;
3:1125949.
PMID: 37035036
Cytoscape is an open-source bioinformatics environment for the analysis, integration, visualization, and query of biological networks. In this perspective piece, we describe our project to bring the Cytoscape desktop application...
10.
Ochsner S, Pedroza M, Pillich R, Krishnan V, Konicek B, Dow E, et al.
J Invest Dermatol
. 2023 Mar;
143(9):1689-1699.
PMID: 36967086
Unbiased informatics approaches have the potential to generate insights into uncharacterized signaling pathways in human disease. In this study, we generated longitudinal transcriptomic profiles of plaque psoriasis lesions from patients...