Author details

Full Name

Ivo L Hofacker

Affiliation

ORCID

Career Start Year

1990

Papers

162

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37546804	MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS): a global mechanism for the regulation of alternative splicing.	Res Sq	2023
36357372	Avirulent phenotype promotes adaptation to the intramacrophage environment.	Emerging Microbes and Infections	2023
38071473	3D Feasibility of 2D RNA-RNA Interaction Paths by stepwise Folding Simulations.		2023
37971965	Modified RNAs and predictions with the ViennaRNA Package.		2023
36655786	DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model.		2023
36999609	Investigating RNA-RNA interactions through computational and biophysical analysis.		2023
37425843	MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS): a global mechanism for the regulation of alternative splicing.	bioRxiv	2023
37522173	Local RNA folding revisited.		2023
37516881	Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package.		2023
35380920	Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site.	RNA Biology	2022
36304289	Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction.		2022
34677509	Enhancing the Cell-Free Expression of Native Membrane Proteins by In Silico Optimization of the Coding Sequence-An Experimental Study of the Human Voltage-Dependent Anion Channel.	Membranes	2021
33538792	RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes.		2021
32657398	The locality dilemma of Sankoff-like RNA alignments.		2020
32070192	Transcriptional profiling of human macrophages during infection with .	RNA Biology	2020
31919376	Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution.	Nat Commun	2020
30909641	Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses.	Viruses	2019
31856671	IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction.	Journal of Bioinformatics and Computational Biology	2019
30385321	RNA modifications in structure prediction - Status quo and future challenges.	Methods	2019
31035717	Conserved Secondary Structures in Viral mRNAs.	Viruses	2019
30760640	Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.	Plant Physiol	2019
31470643	Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture.	Viruses	2019
29730250	Efficient computation of co-transcriptional RNA-ligand interaction dynamics.	Methods	2018
30071678	RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates.	Genes	2018
30184175	Comparative genomics of Czech vaccine strains of Bordetella pertussis.	Pathogens and Disease	2018
29660485	In silico design of ligand triggered RNA switches.	Methods	2018
29554223	CMV: visualization for RNA and protein family models and their comparisons.		2018
29277874	Comparative RNA Genomics.	Methods in Molecular Biology	2018
28108657	RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.	Nucleic Acids Research	2017
33525808	RNA structure prediction: from 2D to 3D.	Emerging topics in life sciences	2017
28449031	RNAblueprint: flexible multiple target nucleic acid sequence design.		2017
28074834	Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.	Sci Rep	2017
27677491	microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3' untranslated region: function in replication and influence of RNA secondary structure.	Cellular and Molecular Life Sciences	2017
28134517	NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations.	Journal of the American Chemical Society	2017
27713552	Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells.	Sci Rep	2016
27110276	RNA folding with hard and soft constraints.	Algorithms for Molecular Biology	2016
27064083	Predicting RNA secondary structures from sequence and probing data.	Methods	2016
26934089	Computational Design of a Circular RNA with Prionlike Behavior.	Artificial Life	2016
27330139	RNAlien - Unsupervised RNA family model construction.	Nucleic Acids Research	2016
27178967	Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammationÂ resolution.	Molecular Systems Biology	2016
26441429	Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks.	IEEE/ACM Transactions on Computational Biology and Bioinformatics	2016
26602692	AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.	Nucleic Acids Research	2016
26353838	SHAPE directed RNA folding.		2016
26428288	Pseudoknots in RNA folding landscapes.		2016
27782844	Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.		2016
26099263	Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams.		2015
25904133	Predicting RNA 3D structure using a coarse-grain helix-centered model.	RNA	2015
25726466	Thermodynamic and kinetic folding of riboswitches.	Methods in Enzymology	2015
26357262	Product Grammars for Alignment and Folding.	IEEE/ACM Transactions on Computational Biology and Bioinformatics	2015
25999318	Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM.	RNA	2015