Lydia Freddolino
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Explore the profile of Lydia Freddolino including associated specialties, affiliations and a list of published articles.
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9
Citations
6
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Recent Articles
1.
Majhi S, Roy P, Jo M, Liu J, Hurto R, Freddolino L, et al.
J Biol Chem
. 2025 Feb;
:108359.
PMID: 40015636
Increasing lines of evidence link the expression of the interferon-stimulated gene RSAD2, encoding the antiviral enzyme, viperin, to autoimmune disease. Autoimmune diseases are characterized by chronic over-production of cytokines such...
2.
Schroeder J, Wolfe M, Freddolino L
bioRxiv
. 2025 Feb;
PMID: 39975017
Determining where transcriptional regulators bind within a genome is paramount to understanding how gene expression is regulated. Historically, position weight matrices (PWMs) have been used to define the binding preferences...
3.
Guan J, Hurto R, Rai A, Azaldegui C, Ortiz-Rodriguez L, Biteen J, et al.
bioRxiv
. 2025 Feb;
PMID: 39975000
Uncovering what drives select biomolecules to form phase-separated condensates and identifying their physiological significance are topics of fundamental importance. Here we show that nitrogen-starved produce long-chain polyphosphates, which scaffold the...
4.
Racki L, Freddolino L
Mol Microbiol
. 2025 Feb;
123(3):279-293.
PMID: 39967274
Polyphosphate (polyP), broadly defined, consists of a chain of orthophosphate units connected by phosphoanhydride bonds. PolyP is the only universal inorganic biopolymer known to date and is present in all...
5.
Morgan W, Amemiya H, Freddolino L
bioRxiv
. 2025 Jan;
PMID: 39829790
The activity of DNA adenine methyltransferase (Dam) and DNA cytosine methyltransferase (Dcm) together account for nearly all methylated nucleotides in the K-12 MG1655 genome. Previous studies have shown that perturbation...
6.
Liu Q, Zhang C, Freddolino L
Bioinformatics
. 2024 Nov;
40(11).
PMID: 39499152
Motivation: Accurate protein function prediction is crucial for understanding biological processes and advancing biomedical research. However, the rapid growth of protein sequences far outpaces the experimental characterization of their functions,...
7.
Rangarajan A, Schroeder J, Hurto R, Severin G, Pell M, Hsieh M, et al.
bioRxiv
. 2024 Sep;
PMID: 39257796
The signaling molecule cyclic di-GMP (cdG) controls the switch between bacterial motility and biofilm production, and fluctuations in cellular levels of cdG have been implicated in pathogenesis. Intracellular concentrations of...
8.
Chen Z, Seman M, Fyodorova Y, Farhat A, Ames A, Levashkevich A, et al.
Nucleic Acids Res
. 2024 Aug;
52(18):10731-10746.
PMID: 39142658
Visualizing and measuring molecular-scale interactions in living cells represents a major challenge, but recent advances in single-molecule super-resolution microscopy are bringing us closer to achieving this goal. Single-molecule super-resolution microscopy...
9.
Zhang C, Freddolino L
PLoS Biol
. 2024 Jul;
22(7):e3002476.
PMID: 39074139
Despite the increasing number of 3D RNA structures in the Protein Data Bank, the majority of experimental RNA structures lack thorough functional annotations. As the significance of the functional roles...
10.
Zhang C, Freddolino L
Brief Bioinform
. 2024 Jul;
25(4).
PMID: 39038936
Sequence database searches followed by homology-based function transfer form one of the oldest and most popular approaches for predicting protein functions, such as Gene Ontology (GO) terms. These searches are...