I. Hofacker

发表

Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force.

P. Stadler, A. Babajide, I. Hofacker, 1997, Folding & design.

Conserved RNA secondary structures in Picornaviridae genomes.

P. Stadler, I. Hofacker, C. Witwer, 2001, Nucleic acids research.

RNA Secondary Structures: A Tractable Model of Biopolymer Folding

I. Hofacker, 1998 .

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

William Stafford Noble, Nancy R. Zhang, Stephen C. J. Parker, 2007, Nature.

Analysis of RNA sequence structure maps by exhaustive enumeration II. Structures of neutral networks and shape space covering

P. Schuster, P. Stadler, I. Hofacker, 1996 .

Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks

P. Schuster, P. Stadler, I. Hofacker, 1995 .

MODELING RNA FOLDING

P. Stadler, I. Hofacker, 2006 .

From sequences to shapes and back: a case study in RNA secondary structures

P. Schuster, P. Stadler, I. Hofacker, 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Conserved RNA secondary structures in Flaviviridae genomes.

P. Stadler, I. Hofacker, C. Witwer, 2004, The Journal of general virology.

RNA folding at elementary step resolution.

P. Schuster, I. Hofacker, W. Fontana, 1999, RNA.

Barrier Trees of Degenerate Landscapes

Michael T. Wolfinger, P. Stadler, I. Hofacker, 2002 .

Folding kinetics of large RNAs.

Michael T. Wolfinger, Andrea Tanzer, P. Stadler, 2008, Journal of molecular biology.

Complete suboptimal folding of RNA and the stability of secondary structures.

P. Schuster, I. Hofacker, W. Fontana, 1999, Biopolymers.

Vienna RNA secondary structure server

Ivo L. Hofacker, I. Hofacker, 2003, Nucleic Acids Res..

Secondary structure prediction for aligned RNA sequences.

P. Stadler, I. Hofacker, M. Fekete, 2002, Journal of molecular biology.

Automatic detection of conserved RNA structure elements in complete RNA virus genomes.

M. Huynen, P. Stadler, I. Hofacker, 1998, Nucleic acids research.

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome

P. Stadler, I. Hofacker, S. Washietl, 2005, Nature Biotechnology.

Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics.

I. Hofacker, S. Washietl, Stefan Washietl, 2004, Journal of molecular biology.

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

Manolis Kellis, P. Stadler, I. Hofacker, 2012, Nucleic acids research.

RNA Secondary Structure Analysis Using the Vienna RNA Package

I. Hofacker, 2003, Current protocols in bioinformatics.

Design of multistable RNA molecules.

P. Stadler, I. Hofacker, C. Flamm, 2001, RNA.

Efficient computation of RNA folding dynamics

Michael T. Wolfinger, Michael T. Wolfinger, P. Stadler, 2004 .

The RNAsnp web server: predicting SNP effects on local RNA secondary structure

Peter F. Stadler, Jan Gorodkin, Hakim Tafer, 2013, Nucleic Acids Res..

RNAs everywhere: genome-wide annotation of structured RNAs.

Sonja J. Prohaska, Andrea Tanzer, P. Stadler, 2007, Journal of experimental zoology. Part B, Molecular and developmental evolution.

Bcheck: a wrapper tool for detecting RNase P RNA genes

P. Stadler, I. Hofacker, M. Marz, 2010, BMC Genomics.

Predicting RNA secondary structures from sequence and probing data.

Michael T. Wolfinger, Andrea Tanzer, I. Hofacker, 2016, Methods.

RNA Secondary Structure Analysis Using the Vienna RNA Package

I. Hofacker, 2003, Current protocols in bioinformatics.

How microRNAs choose their targets

I. Hofacker, 2007, Nature Genetics.

Exploring protein sequence space using knowledge-based potentials.

A. Lapedes, R. Farber, P. Stadler, 2001, Journal of theoretical biology.

Predicting RNA 3D structure using a coarse-grain helix-centered model

I. Hofacker, Peter Kerpedjiev, Christian Höner Zu Siederdissen, 2015, RNA.

RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

P. Stadler, I. Hofacker, G. Helt, 2007, Science.

Structural parameters affecting the kinetics of RNA hairpin formation

I. Hofacker, C. Flamm, C. Pleij, 2006, Nucleic acids research.

RNA Secondary Structure Prediction

I. Hofacker, 2005 .

RNA Secondary Structure Prediction including Pseudoknots

I. Hofacker, Wolfgang Beyer, 2010 .

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs.

P. Stadler, I. Hofacker, R. Backofen, 2012, RNA.

A Toy Model of Chemical Reaction Networks

Michael T. Wolfinger, Ingrid G. Abfalter, P. Schuster, 2002 .

Evolutionary Genomics of microRNAs and Their Relatives

Peter F. Stadler, Jan Gorodkin, Ivo L. Hofacker, 2010 .

CHAPTER 1 EVOLUTIONARY GENOMICS OF microRNAs AND THEIR RELATIVES

Andrea Tanzer, P. Stadler, I. Hofacker, 2008 .

The Rules of the Evolutionary Game for RNA: A Statistical Characterization of the Sequence to Struct

I. Hofacker, Christian Forst Organisiert, 1994 .

Model-based probe set optimization for high-performance microarrays

David P. Kreil, I. Hofacker, P. Sykacek, 2008, Nucleic acids research.

From consensus structure prediction to RNA gene finding.

I. Hofacker, S. Bernhart, 2009, Briefings in functional genomics & proteomics.

RNA consensus structure prediction with RNAalifold.

I. Hofacker, 2007, Methods in molecular biology.

De novo prediction of structured RNAs from genomic sequences.

W. L. Ruzzo, I. Hofacker, Zizhen Yao, 2010, Trends in biotechnology.

Structured Rnas in the Encode Selected Regions of the Human Genome

M. Gerstein, Andrea Tanzer, A. Reymond, 2022 .

Beyond energy minimization: approaches to the kinetic folding of RNA

I. Hofacker, C. Flamm, 2008 .

BarMap: RNA folding on dynamic energy landscapes.

Michael T. Wolfinger, P. Stadler, I. Hofacker, 2010, RNA.

Nucleic acid sequence and structure databases.

I. Hofacker, S. Washietl, Stefan Washietl, 2010, Methods in molecular biology.

structural RNAs LocARNA-P : Accurate boundary prediction and improved detection of Material Supplemental

P. Stadler, I. Hofacker, R. Backofen, 2012 .

Arthropod 7SK RNA.

P. Stadler, I. Hofacker, A. Mosig, 2008, Molecular biology and evolution.

Incongruences Between Sequence and Secondary Structure Alignments of Nucleic Acids

Michael T. Wolfinger, P. Stadler, I. Hofacker, 2020 .

Design of Multi-Stable RNA Molecules

P. Stadler, I. Hofacker, C. Flamm, 2000 .

Computational design of RNAs with complex energy landscapes

Ingrid G. Abfalter, P. Stadler, I. Hofacker, 2013, Biopolymers.

Computational Chemistry with RNA Secondary Structures

P. Stadler, I. Hofacker, C. Flamm, 2004 .

Recombination and the Structure of Globular Proteins

Michael T. Wolfinger, Ingrid G. Abfalter, P. Schuster, 2001 .

Processed Small RNAs in Archaea and BHB Elements

Sonja J. Prohaska, Sarah J. Berkemer, P. Stadler, 2015 .

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.

I. Hofacker, Peter Kerpedjiev, Bernhard C Thiel, 2019, F1000Research.

Dynamics of small autocatalytic reaction network IV : Inhomogeneous replicator equations

P. Schuster, P. Stadler, I. Hofacker, 2016 .

A Variation on Algorithms for Pairwise Global Alignments

Ingrid G. Abfalter, P. Schuster, P. Stadler, 2001 .

Comparative RNA Genomics.

P. Stadler, I. Hofacker, J. Gorodkin, 2018, Methods in molecular biology.

AREsite: a database for the comprehensive investigation of AU-rich elements

Ivo L. Hofacker, Jörg Fallmann, Andreas R. Gruber, 2010, Nucleic Acids Res..

Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution

Andrea Tanzer, I. Hofacker, F. Ebner, 2016, Molecular systems biology.

Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation

I. Hofacker, T. Rülicke, Mathias Müller, 2011, Molecular systems biology.

The impact of target site accessibility on the design of effective siRNAs

Stefan L Ameres, I. Hofacker, G. Obernosterer, 2008, Nature Biotechnology.

RIsearch2: suffix array-based large-scale prediction of RNA–RNA interactions and siRNA off-targets

Peter F. Stadler, Jan Gorodkin, Ivo L. Hofacker, 2017, Nucleic acids research.

RNAs everywhere: genome-wide annotation of structured RNAs.

Ivo L Hofacker, I. Hofacker, 2006, Genome informatics. International Conference on Genome Informatics.

On the Evolution of Primitive Genetic Codes

Peter F. Stadler, Ivo L. Hofacker, P. Stadler, 2003, Origins of life and evolution of the biosphere.

Detection of RNA structures in porcine EST data and related mammals

Jan Gorodkin, Peter F Stadler, Ivo L Hofacker, 2007, BMC Genomics.

Genome-wide mapping of conserved RNA Secondary Structures Reveals Evidence for Thousands of functional Non-Coding RNAs in Human

Peter F. Stadler, Ivo L. Hofacker, Stefan Washietl, 2022 .

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

I. Hofacker, F. Amman, S. Damiati, 2021, Membranes.

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

I. Hofacker, F. Amman, S. Damiati, 2018, bioRxiv.

Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

Doo Nam Kim, Trushar R. Patel, I. Hofacker, 2020, Nature Communications.

Transcriptional profiling of human macrophages during infection with Bordetella pertussis

Mariam R Farman, I. Hofacker, M. E. Rodriguez, 2020, RNA biology.

Chapter 1 MODELING RNA FOLDING

I. Hofacker, 2022 .

Arthropod 7 SK RNA

P. Stadler, I. Hofacker, A. Mosig, 2008 .

PSB 2010 Tutorial : Computational Studies of Non-coding RNAs

P. Stadler, I. Hofacker, H. Chitsaz, 2009 .

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

Craig L. Zirbel, Christian Höner zu Siederdissen, I. Hofacker, 2015, PloS one.

Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs1[OPEN]

Andrea Tanzer, I. Hofacker, I. Xenarios, 2019, Plant Physiology.

Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells

Sita J. Saunders, Michael T. Wolfinger, Andrea Tanzer, 2016, Scientific Reports.

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.

P. Stadler, I. Hofacker, Sven Findeiß, 2013, Journal of proteomics.

Pseudoknots in RNA folding landscapes SUPPLEMENTAL MATERIAL

P. Stadler, I. Hofacker, 2015 .

Nematode sbRNAs: Homologs of Vertebrate Y RNAs

Andrea Tanzer, P. Stadler, I. Hofacker, 2010, Journal of Molecular Evolution.

An ESS-analysis for ensembles of prisoner's dilemma strategies.

G. L. Hofacker, I. Hofacker, B. Borštnik, 1990, Journal of theoretical biology.

3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.

I. Hofacker, Peter Kerpedjiev, Bernhard C Thiel, 2019, F1000Research.

Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

Michael T. Wolfinger, I. Hofacker, Roman Ochsenreiter, 2019, bioRxiv.

Functional RNA Structures in the 3’UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

Michael T. Wolfinger, I. Hofacker, Roman Ochsenreiter, 2019, bioRxiv.

Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering

Renate Kunert, Alexander Goesmann, Stephan H. Bernhart, 2011, Journal of biotechnology.

Impact of Hfq on the Bacillus subtilis Transcriptome

I. Hofacker, B. Večerek, U. Bläsi, 2014, PloS one.

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

I. Hofacker, M. Marz, Christian Höner Zu Siederdissen, 2017, Cellular and Molecular Life Sciences.

Animal snoRNAs and scaRNAs with exceptional structures

Andrea Tanzer, P. Stadler, I. Hofacker, 2011, RNA biology.

The Hepatitis B Virus Pregenome: Prediction of RNA Structure and Implications for the Emergence of Deletions

Michael Zuker, Ivo L. Hofacker, I. Hofacker, 2000, Intervirology.

Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding

Peter F. Stadler, Ronny Lorenz, Christoph Flamm, 2020, BIOINFORMATICS.

RNA Secondary Structures

Peter F. Stadler, Ivo L. Hofacker, P. Stadler, 2006 .

Conserved secondary structures in hepatitis B virus DNA

Peter F. Stadler, Ivo L. Hofacker, Roman R. Stocsits, 1999, German Conference on Bioinformatics.

NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations.

Michael T. Wolfinger, I. Hofacker, H. Schwalbe, 2017, Journal of the American Chemical Society.

COMPUTATIONAL STUDIES OF NON-CODING RNAS – Session Introduction

P. Stadler, I. Hofacker, H. Chitsaz, 2009 .

RNA Folding in silico

P. Stadler, I. Hofacker, C. Flamm, 2005 .

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

Craig L. Zirbel, Christian Höner zu Siederdissen, I. Hofacker, 2015, PloS one.

Control of cognate sense mRNA translation by cis -natural antisense RNAs 3

Andrea Tanzer, I. Hofacker, I. Xenarios, 2019 .

RNA Folding Algorithms with G-Quadruplexes

Peter F. Stadler, Ronny Lorenz, Stephan H. Bernhart, 2012, BSB.

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

Jan Gorodkin, Peter F Stadler, Radhakrishnan Sabarinathan, 2013, Human mutation.

The expansion of the metazoan microRNA repertoire

Christoph Flamm, Peter F Stadler, Jana Hertel, 2006, BMC Genomics.

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates

Ivo L Hofacker, Andrea Tanzer, Andrea Tanzer, 2018, Genes.

Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA

Ge Zhang, Ronny Lorenz, Ivo L. Hofacker, 2015, PLoS Comput. Biol..

Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses

Michael T. Wolfinger, I. Hofacker, Roman Ochsenreiter, 2019 .

Exact Folding Dynamics of RNA Secondary Structures

Peter F. Stadler, Christoph Flamm, Ivo L. Hofacker, 2003 .

FRETtranslator: translating FRET traces into RNA structural pathways

P. Stadler, I. Hofacker, J. Gorodkin, 2016, 1610.00340.

Session Introduction

Hamidreza Chitsaz, Rolf Backofen, Süleyman Cenk Sahinalp, 2003, Pacific Symposium on Biocomputing.

ViennaRNA Package 2.0

Peter F. Stadler, Ronny Lorenz, Stephan H. Bernhart, 2011, Algorithms for Molecular Biology.

RNAplex: a fast tool for RNA-RNA interaction search

Hakim Tafer, Ivo L. Hofacker, I. Hofacker, 2008, Bioinform..

The Vienna RNA Websuite

Ronny Lorenz, Stephan H. Bernhart, Ivo L. Hofacker, 2008, Nucleic Acids Res..

Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM

Christoph Flamm, Sabine Müller, Stefan Badelt, 2015, RNA.

Modelling Translation Initiation under the Influence of sRNA

I. Hofacker, C. Flamm, F. Amman, 2012, International journal of molecular sciences.

Evolutionary patterns of non-coding RNAs

Sonja J. Prohaska, Peter F. Stadler, Christoph Flamm, 2005, Theory in Biosciences.

www.rnaworkbench.com: A new program for analyzing RNA interference

Radka Svobodová Vareková, Hakim Tafer, Ivo L. Hofacker, 2008, Comput. Methods Programs Biomed..

SnoReport: computational identification of snoRNAs with unknown targets

Peter F. Stadler, Ivo L. Hofacker, Jana Hertel, 2008, Bioinform..

Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution

Doo Nam Kim, Trushar R. Patel, I. Hofacker, 2020, Nature Communications.

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

Nick Goldman, Peter F Stadler, Stefan Washietl, 2011, RNA.

From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs

Jan Gorodkin, Ivo L. Hofacker, I. Hofacker, 2011, PLoS Comput. Biol..

Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis

Peter F. Stadler, Ivo L. Hofacker, Jana Hertel, 2008, Nucleic acids research.

Strategies for measuring evolutionary conservation of RNA secondary structures

Stephan H. Bernhart, Ivo L. Hofacker, Andreas R. Gruber, 2008, BMC Bioinformatics.

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures

Ivo L. Hofacker, Andreas R. Gruber, Stefan Washietl, 2007, Nucleic Acids Res..

genome Structured RNAs in the ENCODE selected regions of the human Related Content

M. Gerstein, Andrea Tanzer, A. Reymond, 2007 .

Partition function and base pairing probabilities of RNA heterodimers

Peter F. Stadler, Stephan H. Bernhart, Hakim Tafer, 2006, Algorithms for Molecular Biology.

Fast and reliable prediction of noncoding RNAs

Peter F Stadler, Stefan Washietl, Ivo L Hofacker, 2005, Proc. Natl. Acad. Sci. USA.

Alignment of RNA base pairing probability matrices

Peter F. Stadler, Stephan H. Bernhart, Ivo L. Hofacker, 2004, Bioinform..

Conserved RNA secondary structures in viral genomes: A survey

Peter F. Stadler, Ivo L. Hofacker, Roman R. Stocsits, 2004, German Conference on Bioinformatics.

Concurrent Neutral Evolution of mRNA Secondary Structures and Encoded Proteins

Marc-Denis Weitze, G. L. Hofacker, G. Ludwig Hofacker, 2000, Journal of Molecular Evolution.

Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes

Peter F. Stadler, Ivo L. Hofacker, P. Stadler, 1998, Comput. Chem..

RNAlien – Unsupervised RNA family model construction

Florian Eggenhofer, Ivo L Hofacker, I. Hofacker, 2016, Nucleic acids research.

RNAalifold: improved consensus structure prediction for RNA alignments

Sebastian Will, Peter F. Stadler, Stephan H. Bernhart, 2008, BMC Bioinformatics.

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes

Hsien-Da Huang, Peter F. Stadler, Ivo L. Hofacker, 2005, Nucleic Acids Res..

Invertebrate 7SK snRNAs

P. Stadler, I. Hofacker, G. Obernosterer, 2008, Journal of Molecular Evolution.

RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes

Ronny Lorenz, Ivo L. Hofacker, Andrea Tanzer, 2021, Bioinform..

RNAxplorer: Harnessing the Power of Guiding Potentials for Sampling of RNA Landscapes

Andrea Tanzer, I. Hofacker, Y. Ponty, 2020, bioRxiv.

Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams

Ivo L. Hofacker, Peter Kerpedjiev, Stefan Hammer, 2015, Bioinform..

Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering

Rolf Backofen, Sebastian Will, Kristin Reiche, 2007, PLoS Comput. Biol..

RNAz 2.0: Improved Noncoding RNA Detection

Peter F. Stadler, Ivo L. Hofacker, Sven Findeiß, 2010, Pacific Symposium on Biocomputing.

Thermodynamics of RNA-RNA Binding

Peter F. Stadler, Stephan H. Bernhart, Hakim Tafer, 2006, German Conference on Bioinformatics.

Local RNA base pairing probabilities in large sequences

Peter F. Stadler, Stephan H. Bernhart, Ivo L. Hofacker, 2006, Bioinform..

Designing optimal siRNA based on target site accessibility.

Hakim Tafer, Ivo L Hofacker, I. Hofacker, 2010, Methods in molecular biology.

Hybridization thermodynamics of NimbleGen Microarrays

Ivo L. Hofacker, David P. Kreil, Ulrike Mückstein, 2010, BMC Bioinformatics.

RNPomics: Defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles

Stephan H. Bernhart, Ivo L. Hofacker, Andrea Tanzer, 2010, Nucleic acids research.

Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity

Michael T. Wolfinger, Michael T. Wolfinger, Andrea Tanzer, 2016, Genome Biology.

Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site

Michael T. Wolfinger, I. Hofacker, J. Wower, 2021, bioRxiv.

Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture

Michael T. Wolfinger, I. Hofacker, D. Janies, 2019, bioRxiv.

Investigating RNA–RNA interactions through computational and biophysical analysis

Michael T. Wolfinger, Trushar R. Patel, I. Hofacker, 2022, bioRxiv.

Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon.

P. Stadler, I. Hofacker, P. Brindley, 2004, Gene.

Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment

Mariam R Farman, I. Hofacker, B. Večerek, 2022, Emerging microbes & infections.

Challenges in RNA virus bioinformatics

Christian Drosten, Dmitrij Frishman, Martin Middendorf, 2014, Bioinform..

RNA folding with hard and soft constraints

P. Stadler, I. Hofacker, R. Lorenz, 2016, Algorithms for Molecular Biology.

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation

Christian V. Forst, Peter F. Stadler, Christoph Flamm, 2006, BMC Bioinformatics.

2D Projections of RNA Folding Landscapes

Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, 2009, GCB.

RNAsnoop: efficient target prediction for H/ACA snoRNAs

Peter F. Stadler, Hakim Tafer, Ivo L. Hofacker, 2010, Bioinform..

An efficient potential for protein sequence design

Peter F. Stadler, Ivo L. Hofacker, G. Weberndorfer, 1999, German Conference on Bioinformatics.

DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model

I. Hofacker, R. Lorenz, Stefan Badelt, 2022, bioRxiv.

Efficient computation of co-transcriptional RNA-ligand interaction dynamics

Christoph Flamm, Michael T. Wolfinger, Ivo L Hofacker, 2018, bioRxiv.

Variations on RNA folding and alignment: lessons from Benasque

Rolf Backofen, Peter F Stadler, Sebastian Will, 2007, Journal of mathematical biology.

Folding RNA/DNA hybrid duplexes

Ronny Lorenz, Stephan H. Bernhart, Ivo L. Hofacker, 2012, Bioinform..

Fast accessibility-based prediction of RNA-RNA interactions

Peter F. Stadler, Hakim Tafer, Ivo L. Hofacker, 2011, Bioinform..

CMV: visualization for RNA and protein family models and their comparisons

Rolf Backofen, Christian Höner zu Siederdissen, Ivo L. Hofacker, 2018, Bioinform..

AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements

Ivo L. Hofacker, Jörg Fallmann, Andrea Tanzer, 2015, Nucleic Acids Res..

AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements

Ivo L. Hofacker, Jörg Fallmann, Andrea Tanzer, 2015, Nucleic Acids Res..

Saddles and barrier in landscapes of generalized search operators

Peter F. Stadler, Christoph Flamm, Ivo L. Hofacker, 2007, FOGA'07.

Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures

Peter F. Stadler, Ivo L. Hofacker, Jan Cupal, 1996, German Conference on Bioinformatics.

RNA Accessibility in cubic time

Stephan H. Bernhart, Ivo L. Hofacker, Ulrike Mückstein, 2011, Algorithms for Molecular Biology.

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics

Peter F. Stadler, Stephan H. Bernhart, Hakim Tafer, 2008, BIRD.

Algorithm independent properties of RNA secondary structure predictions

P. Schuster, P. Stadler, I. Hofacker, 1996, European Biophysics Journal.

IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction

I. Hofacker, R. Backofen, S. Will, 2019, J. Bioinform. Comput. Biol..

Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction

Rolf Backofen, Sebastian Will, Ivo L. Hofacker, 2019, BIOINFORMATICS.

TSSAR: TSS annotation regime for dRNA-seq data

Peter F. Stadler, Ronny Lorenz, Ivo L. Hofacker, 2014, BMC Bioinformatics.

A folding algorithm for extended RNA secondary structures

Peter F. Stadler, Stephan H. Bernhart, Christian Höner zu Siederdissen, 2011, Bioinform..

RNApredator: fast accessibility-based prediction of sRNA targets

Peter F. Stadler, Hakim Tafer, Ivo L. Hofacker, 2011, Nucleic Acids Res..

Automated identification of RNA 3D modules with discriminative power in RNA structural alignments

Jan Gorodkin, Ivo L. Hofacker, Corinna Theis, 2013, Nucleic acids research.

2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction

Peter F. Stadler, Ronny Lorenz, Stephan H. Bernhart, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Prediction of locally stable RNA secondary structures for genome-wide surveys

Peter F. Stadler, Ivo L. Hofacker, Barbara Priwitzer, 2004, Bioinform..

CMCompare webserver: comparing RNA families via covariance models

Christian Höner zu Siederdissen, Ivo L. Hofacker, Florian Eggenhofer, 2013, Nucleic Acids Res..

Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate.

P. Stadler, I. Hofacker, Gudrun Böhmdorfer, 2005, RNA.

Multiple sequence alignments of partially coding nucleic acid sequences

Peter F. Stadler, Ivo L. Hofacker, Claudia Fried, 2005, BMC Bioinformatics.

Conserved RNA Pseudoknots

Peter F. Stadler, Ivo L. Hofacker, C. Thurner, 2004, German Conference on Bioinformatics.

SHAPE directed RNA folding

Peter F. Stadler, Ronny Lorenz, Ivo L. Hofacker, 2015, bioRxiv.

Optimizing RNA structures by sequence extensions using RNAcop

Peter F. Stadler, Jan Gorodkin, Ivo L. Hofacker, 2015, Nucleic acids research.

Combinatorics of RNA Secondary Structures

Peter F. Stadler, Ivo L. Hofacker, Peter Schuster, 1998, Discret. Appl. Math..

RNA Folding on Parallel Computers: The Minimum Free Energy Structures of Complete HIV Genomes

M. Huynen, P. Stadler, I. Hofacker, 1995 .

RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs

Peter F. Stadler, Jan Gorodkin, Ivo L. Hofacker, 2013, Human Mutation.

RNA In Silico The Computational Biology of RNA Secondary Structures

Peter F. Stadler, Christoph Flamm, Ivo L. Hofacker, 1999, Adv. Complex Syst..

Pseudoknots in RNA folding landscapes

Peter F. Stadler, Ivo L. Hofacker, Jing Qin, 2015, Bioinform..

Basin Hopping Graph: a computational framework to characterize RNA folding landscapes

Peter F. Stadler, Ivo L. Hofacker, Jing Qin, 2014, Bioinform..

RNA modifications in structure prediction - Status quo and future challenges.

Ronny Lorenz, Ivo L Hofacker, Andrea Tanzer, 2019, Methods.

Energy-directed RNA structure prediction.

Ivo L Hofacker, I. Hofacker, 2014, Methods in molecular biology.

Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs

Peter F. Stadler, Ivo L. Hofacker, Axel Mosig, 2006, German Conference on Bioinformatics.

Memory Efficient Folding Algorithms for Circular RNA Secondary Structures

Peter F. Stadler, Ivo L. Hofacker, P. Stadler, 2006, German Conference on Bioinformatics.

Prediction of consensus RNA secondary structures including pseudoknots

Peter F. Stadler, Ivo L. Hofacker, Christina Witwer, 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

The Trouble with Long-Range Base Pairs in RNA Folding

Sebastian Will, Peter F. Stadler, Stephan H. Bernhart, 2013, BSB.

In silico design of ligand triggered RNA switches

Christoph Flamm, Felix Kühnl, Sven Findeiß, 2018, bioRxiv.

In silico design of ligand triggered RNA switches

Christoph Flamm, Ivo L. Hofacker, Felix Kühnl, 2018, bioRxiv.

RNAblueprint: flexible multiple target nucleic acid sequence design

Christoph Flamm, Ivo L. Hofacker, Sven Findeiß, 2017, Bioinform..

Computational Design of a Circular RNA with Prionlike Behavior

Christoph Flamm, Ivo L. Hofacker, Stefan Badelt, 2016, Artificial Life.

Discriminatory power of RNA family models

Christian Höner zu Siederdissen, Ivo L. Hofacker, I. Hofacker, 2010, Bioinform..

Product Grammars for Alignment and Folding

Peter F. Stadler, Christian Höner zu Siederdissen, Ivo L. Hofacker, 2015, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

How to Multiply Dynamic Programming Algorithms

Peter F. Stadler, Christian Höner zu Siederdissen, Ivo L. Hofacker, 2013, BSB.

Alterations of the Transcriptome of Sulfolobus acidocaldarius by Exoribonuclease aCPSF2

Udo Bläsi, Fabian Amman, Ivo Hofacker, 2013, PloS one.

The locality dilemma of Sankoff-like RNA alignments

Rolf Backofen, Frank Hutter, Milad Miladi, 2020, Bioinform..

TSSAR: TSS annotation regime for dRNA-seq

Peter F. Stadler, Ronny Lorenz, Ivo L. Hofacker, 2014 .

Thermodynamic and kinetic folding of riboswitches.

Christoph Flamm, Stefan Hammer, Ivo L Hofacker, 2015, Methods in enzymology.

Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure

Peter F. Stadler, Ivo L. Hofacker, Sebastian Will, 2019, bioRxiv.

Evolution of metabolic networks: a computational frame-work

Gerik Scheuermann, Christoph Flamm, Martin Mann, 2010 .

Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers

Peter F. Stadler, Ivo L. Hofacker, Martijn A. Huynen, 1996, KDD.

Predicting RNA structure: advances and limitations.

Ronny Lorenz, Ivo L Hofacker, I. Hofacker, 2014, Methods in molecular biology.

Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers

Peter F. Stadler, Ivo L. Hofacker, Martin Fekete, 2000, J. Comput. Biol..

Fast folding and comparison of RNA secondary structures

Walter Fontana, Peter F. Stadler, Ivo L. Hofacker, 1994 .

RNA structure prediction: from 2D to 3D.

Christoph Flamm, Ivo L. Hofacker, I. Hofacker, 2017, Emerging topics in life sciences.

Exploring the lower part of discrete polymer model energy landscapes

Rolf Backofen, Peter F. Stadler, Ivo L. Hofacker, 2006 .

Comparative genomics of Czech vaccine strains of Bordetella pertussis.

I. Hofacker, J. Parkhill, M. Wildung, 2018, Pathogens and disease.

Comments on the alpha -peak shapes for relaxation in supercooled liquids

I. Hofacker, A. Latz, M. Fuchs, 1991 .

Oxygen and proton pathways in cytochrome c oxidase

K Schulten, I. Hofacker, K. Schulten, 1998, Proteins.

Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction

Michael T. Wolfinger, I. Hofacker, C. Flamm, 2021, bioRxiv.

Cyclization studies of Japanese encephalitis virus non-coding RNA terminal regions

Michael T. Wolfinger, Trushar R. Patel, I. Hofacker, 2022 .

Stochastic pairwise alignments

Peter F. Stadler, Ivo L. Hofacker, Ulrike Mückstein, 2002, ECCB.

ViennaRNA Package 2.0

P. Stadler, I. Hofacker, C. Flamm, 2011, Algorithms for Molecular Biology : AMB.

Interactions in Oligonucleotide Hybrid Duplexes on Microarrays

Toralf Kirsten, Peter F. Stadler, Ivo L. Hofacker, 2004 .

ViennaRNA Package 2.0

P. Stadler, I. Hofacker, C. Flamm, 2011, Algorithms for Molecular Biology : AMB.

Hybridization thermodynamics of NimbleGen Microarrays

David P. Kreil, I. Hofacker, G. Leparc, 2010, BMC Bioinformatics.

The expansion of the metazoan microRNA repertoire.

Andrea Tanzer, P. Stadler, I. Hofacker, 2006, BMC genomics.

Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture

Michael T. Wolfinger, I. Hofacker, D. Janies, 2019, bioRxiv.

Conserved Secondary Structures in Viral mRNAs

D. Frishman, I. Hofacker, M. Kiening, 2019, Viruses.

Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks

Wei Yang, Christoph Flamm, Ivo L. Hofacker, 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package

P. Stadler, I. Hofacker, R. Lorenz, 2023, Algorithms for Molecular Biology.

A Folding Algorithm for Extended Rna Secondary Structures Received on *****; Revised on *****; Accepted on *****

I. Hofacker, S. Bernhart, P. F. Stadler, 2022 .

MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS): a global mechanism for the regulation of alternative splicing

I. Hofacker, S. Wuchty, Kai Ruan, 2023, Research Square.

MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS): a global mechanism for the regulation of alternative splicing

I. Hofacker, S. Wuchty, R. Zhai, 2023, bioRxiv.

MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing is a global mechanism for the regulation of alternative splicing

I. Hofacker, R. Zhai, Kai Ruan, 2023 .

A folding algorithm for extended RNA secondary structures

I. Hofacker, S. Bernhart, C. H. Z. Siederdissen, 2011, Bioinform..

LocARNA-P: Accurate Boundary Prediction and Improved Detection of Structured RNAs

I. Hofacker, R. Backofen, Peter F. Stadler, 2011 .

Of Structural Rnas Locarna-p: Accurate Boundary Prediction and Improved Detection Material Supplemental Open Access Locarna-p: Accurate Boundary Prediction and Improved Detection of Structural Rnas

I. Hofacker, Sebastian Will, Tejal Joshi, 2011 .

Evolutionary patterns of non-coding RNAs

Sonja J. Prohaska, Athanasius F. Bompfünewerer, Andrea Tanzer, 2005, Theory in Biosciences.

Structured RNAs in the ENCODE selected regions of the human genome.

M. Gerstein, Andrea Tanzer, A. Reymond, 2007, Genome research.

Invertebrate 7SK snRNAs

P. Stadler, I. Hofacker, G. Obernosterer, 2008, Journal of Molecular Evolution.

Arthropod 7sk Rna

I. Hofacker, Andreas R. Gruber, Carsten Kilgus, 2022 .

Folding kinetics of large RNAs.

Michael T. Wolfinger, Andrea Tanzer, P. Stadler, 2008, Journal of molecular biology.

RNA folding and combinatory landscapes.

Weinberger, E. D. Weinberger, Schuster, 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

Alignment of RNA base pairing probability matrices

I. Hofacker, S. Bernhart, Peter F. Stadler, 2004, Bioinform..

LocARNA-P: accurate boundary prediction and improved detection of structural RNAs.

P. Stadler, I. Hofacker, R. Backofen, 2012, RNA.

New Approach to Combat Glioblastoma Shows Promise in Preclinical Studies

P. Stadler, I. Hofacker, R. Backofen, 2005, PLoS Medicine.

The Partition Function Variant of Sankoff's Algorithm

Peter F. Stadler, Ivo L. Hofacker, P. Stadler, 2004, International Conference on Computational Science.

Partition function and base pairing probabilities of RNA heterodimers

I. Hofacker, Hakim Tafer, S. Bernhart, 2006, Algorithms for Molecular Biology.

Detection of RNA structures in porcine EST data and related mammals

P. Stadler, I. Hofacker, J. Gorodkin, 2007, BMC Genomics.

Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate.

P. Stadler, I. Hofacker, Gudrun Böhmdorfer, 2005, RNA.

The Rules of the Evolutionary Game for RNA: A Statistical Characterization of the Sequence to Struct

I. Hofacker, Christian Forst Organisiert, 1994 .

tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development

I. Hofacker, A. Pauli, Maria Waldl, 2024, bioRxiv.

IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction

I. Hofacker, R. Backofen, S. Will, 2019, J. Bioinform. Comput. Biol..

RNA folding with hard and soft constraints

P. Stadler, I. Hofacker, Ronny Lorenz, 2016, Algorithms for Molecular Biology.

SHAPE directed RNA folding

Michael T. Wolfinger, P. Stadler, I. Hofacker, 2015, bioRxiv.