Ivo L. Hofacker

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Ivo L. Hofacker is affiliated with the following schools: University of Copenhagen, University of Vienna

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Ivo L. Hofacker

Computer Science

#5896

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#6220

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Programming

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#78

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computer-science Degrees

Ivo L. Hofacker

Biology

#8846

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#11980

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Bioinformatics

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#101

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biology Degrees

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Computer Science
Biology

Ivo L. Hofacker's Degrees

PhD Bioinformatics University of Vienna
Masters Computer Science University of Vienna
Bachelors Computer Science University of Vienna

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Ivo L. Hofacker's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007) (5196)
ViennaRNA Package 2.0 (2011) (3343)
Fast folding and comparison of RNA secondary structures (1994) (2338)
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription (2007) (2327)
Vienna RNA secondary structure server (2003) (2224)
The Vienna RNA Websuite (2008) (1816)
From sequences to shapes and back: a case study in RNA secondary structures (1994) (850)
Fast and reliable prediction of noncoding RNAs (2005) (728)
Secondary structure prediction for aligned RNA sequences. (2002) (663)
Complete suboptimal folding of RNA and the stability of secondary structures. (1999) (616)
RNAalifold: improved consensus structure prediction for RNA alignments (2008) (540)
Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering (2007) (513)
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome (2005) (412)
Thermodynamics of RNA-RNA Binding (2006) (368)
The expansion of the metazoan microRNA repertoire (2006) (349)
RNAplex: a fast tool for RNA-RNA interaction search (2008) (333)
RNA folding at elementary step resolution. (1999) (323)
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. (2012) (299)
Partition function and base pairing probabilities of RNA heterodimers (2006) (288)
The impact of target site accessibility on the design of effective siRNAs (2008) (281)
Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams (2015) (280)
Alignment of RNA base pairing probability matrices (2004) (259)
RNAz 2.0: Improved Noncoding RNA Detection (2010) (253)
Local RNA base pairing probabilities in large sequences (2006) (234)
Conserved RNA secondary structures in Flaviviridae genomes. (2004) (215)
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes (2005) (207)
Barrier Trees of Degenerate Landscapes (2002) (207)
Structured RNAs in the ENCODE selected regions of the human genome. (2007) (201)
Combinatorics of RNA Secondary Structures (1998) (198)
Oxygen and proton pathways in cytochrome c oxidase (1998) (193)
Memory Efficient Folding Algorithms for Circular RNA Secondary Structures (2006) (185)
Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis (2008) (184)
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. (2011) (183)
Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks (1995) (180)
Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. (2004) (177)
AREsite: a database for the comprehensive investigation of AU-rich elements (2010) (176)
Analysis of RNA sequence structure maps by exhaustive enumeration II. Structures of neutral networks and shape space covering (1996) (171)
RNA Secondary Structure Analysis Using the Vienna RNA Package (2003) (165)
Automatic detection of conserved RNA structure elements in complete RNA virus genomes. (1998) (162)
Prediction of locally stable RNA secondary structures for genome-wide surveys (2004) (149)
SnoReport: computational identification of snoRNAs with unknown targets (2008) (143)
Design of multistable RNA molecules. (2001) (143)
RNApredator: fast accessibility-based prediction of sRNA targets (2011) (126)
Conserved RNA secondary structures in Picornaviridae genomes. (2001) (123)
RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs (2013) (120)
Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. (1997) (119)
Efficient computation of RNA folding dynamics (2004) (118)
The RNAsnp web server: predicting SNP effects on local RNA secondary structure (2013) (117)
RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction (2012) (113)
Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation (2011) (110)
Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering☆ (2011) (103)
AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements (2015) (102)
Algorithm independent properties of RNA secondary structure predictions (1996) (102)
The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures (2007) (97)
Folding kinetics of large RNAs. (2008) (94)
Variations on RNA folding and alignment: lessons from Benasque (2007) (90)
SHAPE directed RNA folding (2015) (85)
Evolutionary patterns of non-coding RNAs (2005) (85)
Predicting RNA secondary structures from sequence and probing data. (2016) (78)
Strategies for measuring evolutionary conservation of RNA secondary structures (2008) (77)
Comments on the alpha -peak shapes for relaxation in supercooled liquids (1991) (77)
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes (1998) (76)
Stochastic pairwise alignments (2002) (76)
RNA folding with hard and soft constraints (2016) (75)
RIsearch2: suffix array-based large-scale prediction of RNA–RNA interactions and siRNA off-targets (2017) (73)
Exploring protein sequence space using knowledge-based potentials. (2001) (69)
Prediction of consensus RNA secondary structures including pseudoknots (2004) (67)
A folding algorithm for extended RNA secondary structures (2011) (67)
Predicting RNA 3D structure using a coarse-grain helix-centered model (2015) (66)
Conserved RNA secondary structures in viral genomes: A survey (2004) (64)
De novo prediction of structured RNAs from genomic sequences. (2010) (64)
RNAs everywhere: genome-wide annotation of structured RNAs. (2006) (62)
Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution (2016) (60)
RNAs everywhere: genome-wide annotation of structured RNAs. (2007) (60)
RNA consensus structure prediction with RNAalifold. (2007) (60)
How microRNAs choose their targets (2007) (59)
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation (2006) (58)
Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics (2008) (58)
RNAsnoop: efficient target prediction for H/ACA snoRNAs (2010) (58)
BarMap: RNA folding on dynamic energy landscapes. (2010) (57)
TSSAR: TSS annotation regime for dRNA-seq data (2014) (57)
Beyond energy minimization: approaches to the kinetic folding of RNA (2008) (56)
Fast accessibility-based prediction of RNA-RNA interactions (2011) (52)
RNA Accessibility in cubic time (2011) (51)
Challenges in RNA virus bioinformatics (2014) (51)
Arthropod 7SK RNA. (2008) (50)
RNPomics: Defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles (2010) (49)
RNA Secondary Structure Analysis Using the Vienna RNA Package (2003) (49)
Invertebrate 7SK snRNAs (2008) (48)
RNAsnp: Efficient Detection of Local RNA Secondary Structure Changes Induced by SNPs (2013) (46)
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells (2016) (45)
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes (2014) (43)
From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs (2011) (43)
Nematode sbRNAs: Homologs of Vertebrate Y RNAs (2010) (42)
2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction (2013) (41)
Impact of Hfq on the Bacillus subtilis Transcriptome (2014) (41)
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution (2020) (40)
Animal snoRNAs and scaRNAs with exceptional structures (2011) (40)
Prediction of RNA Base Pairing Probabilities on Massively Parallel Computers (2000) (40)
Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA (2015) (39)
Functional RNA Structures in the 3′UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses (2019) (38)
Dynamic Programming Algorithm for the Density of States of RNA Secondary Structures (1996) (38)
From consensus structure prediction to RNA gene finding. (2009) (35)
RNA In Silico The Computational Biology of RNA Secondary Structures (1999) (35)
Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. (2013) (35)
NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations. (2017) (35)
Design of Multi-Stable RNA Molecules (2000) (34)
Computational design of RNAs with complex energy landscapes (2013) (34)
Exact Folding Dynamics of RNA Secondary Structures (2003) (33)
Bcheck: a wrapper tool for detecting RNase P RNA genes (2010) (31)
Multiple sequence alignments of partially coding nucleic acid sequences (2005) (30)
Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs (2006) (30)
Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers (1996) (30)
2D Projections of RNA Folding Landscapes (2009) (30)
Energy-directed RNA structure prediction. (2014) (29)
Exploring the lower part of discrete polymer model energy landscapes (2006) (29)
Interactions in Oligonucleotide Hybrid Duplexes on Microarrays (2004) (29)
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 (2017) (28)
Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture (2019) (27)
Pseudoknots in RNA folding landscapes (2015) (27)
On the Evolution of Primitive Genetic Codes (2003) (26)
RNAlien – Unsupervised RNA family model construction (2016) (26)
Model-based probe set optimization for high-performance microarrays (2008) (26)
Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs1[OPEN] (2019) (26)
RNA modifications in structure prediction - Status quo and future challenges. (2019) (25)
The Hepatitis B Virus Pregenome: Prediction of RNA Structure and Implications for the Emergence of Deletions (2000) (25)
Evolutionary Genomics of microRNAs and Their Relatives (2010) (25)
Hybridization thermodynamics of NimbleGen Microarrays (2010) (25)
RNA Secondary Structures (2006) (24)
Product Grammars for Alignment and Folding (2015) (24)
Evolution of metabolic networks: a computational frame-work (2010) (24)
Visualization of Barrier Tree Sequences (2006) (22)
Thermodynamic and kinetic folding of riboswitches. (2015) (21)
Alterations of the Transcriptome of Sulfolobus acidocaldarius by Exoribonuclease aCPSF2 (2013) (21)
Discriminatory power of RNA family models (2010) (20)
Structural parameters affecting the kinetics of RNA hairpin formation (2006) (20)
Saddles and barrier in landscapes of generalized search operators (2007) (19)
Concurrent Neutral Evolution of mRNA Secondary Structures and Encoded Proteins (2000) (19)
Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity (2016) (18)
Folding RNA/DNA hybrid duplexes (2012) (17)
AREsite 2 : an enhanced database for the comprehensive investigation of AU / GU / Urich elements (2015) (17)
Neutral Networks in Protein Space (1996) (17)
Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM (2015) (16)
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments (2013) (16)
Detection of RNA structures in porcine EST data and related mammals (2007) (16)
Predicting RNA structure: advances and limitations. (2014) (16)
In silico design of ligand triggered RNA switches. (2018) (15)
RNAblueprint: flexible multiple target nucleic acid sequence design (2017) (15)
Designing optimal siRNA based on target site accessibility. (2010) (14)
How to Multiply Dynamic Programming Algorithms (2013) (14)
RNA Folding Algorithms with G-Quadruplexes (2012) (14)
The Trouble with Long-Range Base Pairs in RNA Folding (2013) (14)
Conserved secondary structures in hepatitis B virus DNA (1999) (13)
An efficient potential for protein sequence design (1999) (13)
RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure (2015) (13)
Efficient computation of co-transcriptional RNA-ligand interaction dynamics. (2018) (13)
RNA Folding on Parallel Computers: The Minimum Free Energy Structures of Complete HIV Genomes (1995) (13)
RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates (2018) (13)
The Partition Function Variant of Sankoff's Algorithm (2004) (12)
Transcriptional profiling of human macrophages during infection with Bordetella pertussis (2020) (11)
CMCompare webserver: comparing RNA families via covariance models (2013) (11)
Comparative RNA Genomics. (2018) (11)
RNA structure prediction: from 2D to 3D. (2017) (11)
Symmetric circular matchings and RNA folding (2012) (10)
RNA Secondary Structures: A Tractable Model of Biopolymer Folding (1998) (10)
Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate. (2005) (10)
Modelling Translation Initiation under the Influence of sRNA (2012) (9)
Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses (2019) (9)
www.rnaworkbench.com: A new program for analyzing RNA interference (2008) (9)
Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon. (2004) (9)
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. (2019) (8)
RNALfoldz: Efficient Prediction of Thermodynamically Stable, Local Secondary Structures (2010) (7)
Computational Chemistry with RNA Secondary Structures (2004) (7)
Comparative genomics of Czech vaccine strains of Bordetella pertussis. (2018) (6)
Processed Small RNAs in Archaea and BHB Elements (2015) (6)
An ESS-analysis for ensembles of prisoner's dilemma strategies. (1990) (6)
Optimizing RNA structures by sequence extensions using RNAcop (2015) (5)
CMV: visualization for RNA and protein family models and their comparisons (2018) (5)
IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction (2019) (5)
Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure (2019) (5)
Nucleic acid sequence and structure databases. (2010) (4)
Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction (2021) (4)
RNA Secondary Structure Prediction (2005) (3)
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. (2019) (3)
Functional RNA Structures in the 3′ UTR of Mosquito-Borne Flaviviruses (2021) (3)
The Rules of the Evolutionary Game for RNA: A Statistical Characterization of the Sequence to Struct (1994) (3)
MODELING RNA FOLDING (2006) (3)
Arthropod 7 SK RNA (2008) (3)
Computational Design of a Circular RNA with Prionlike Behavior (2016) (3)
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 (2018) (3)
COMPUTATIONAL STUDIES OF NON-CODING RNAS – Session Introduction (2009) (3)
Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks (2016) (3)
Functional RNA Structures in the 3’UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses (2019) (2)
RNA Secondary Structure Prediction including Pseudoknots (2010) (2)
Conserved RNA Pseudoknots (2004) (2)
RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes (2021) (2)
Concepts and introduction to RNA bioinformatics. (2014) (2)
Efficient Algorithms for Co-folding of Multiple RNAs (2020) (2)
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding (2020) (2)
RNA Folding in silico (2005) (2)
Cyclization studies of Japanese encephalitis virus non-coding RNA terminal regions (2022) (1)
Visualization of Barrier Tree Sequences Revisited (2008) (1)
Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site (2021) (1)
Sampling globally and locally correct RNA 3D structures using ERNWIN, SPQR and experimental SAXS data (2022) (1)
Genome-wide mapping of conserved RNA Secondary Structures Reveals Evidence for Thousands of functional Non-Coding RNAs in Human (1)
TSSAR: transcription start site annotation regime for dRNA-seq data (2014) (1)
structural RNAs LocARNA-P : Accurate boundary prediction and improved detection of Material Supplemental (2012) (1)
TSSAR: TSS annotation regime for dRNA-seq data (2014) (1)
A Variation on Algorithms for Pairwise Global Alignments (2001) (1)
A Toy Model of Chemical Reaction Networks (2002) (1)
Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction (2019) (1)
Incongruences Between Sequence and Secondary Structure Alignments of Nucleic Acids (2020) (1)
Algorithm Independence Properties and RNA Secondary Structure Predicions (1)
MSF: Modulated Sub-graph Finder (2019) (1)
CHAPTER 1 EVOLUTIONARY GENOMICS OF microRNAs AND THEIR RELATIVES (2008) (1)
RNA Folding with Hard and Soft Constraints-Supplementary Material (2016) (0)
Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution (2020) (0)
The locality dilemma of Sankoff-like RNA alignments (2020) (0)
Chapter 1 MODELING RNA FOLDING (0)
The Double α‐Peak Phenomenon in Polymers (1991) (0)
Structural bioinformatics SHAPE directed RNA folding (2015) (0)
Corrigendum: Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells (2017) (0)
BIOINFORMATICS Discriminatory power of RNA family models (2010) (0)
Enhancing the Cell-Free Expression of Native Membrane Proteins by in-Silico Optimisation of the Coding Sequence - An Experimental Study of the Human Voltage-Dependent Anion Channel (2021) (0)
Control of cognate sense mRNA translation by cis -natural antisense RNAs 3 (2019) (0)
Procede de configuration de procedes d'analyse d'acides nucleiques paralleles destines a la classification par quantites de sequences (2002) (0)
Updated Phylogeny of Chikungunya Virus Reveals Lineage-Specific RNA Architecture (2019) (0)
Second Year Report, Bioinformatics Integration Network III (2008) (0)
A method for configuring parallel nucleic acid analysis method to sequence set of classification (2002) (0)
Salt corrections for RNA secondary structures in the ViennaRNA package (2023) (0)
RNAxplorer: Harnessing the Power of Guiding Potentials for Sampling of RNA Landscapes (2020) (0)
Recombination and the Structure of Globular Proteins (2001) (0)
FRETtranslator: translating FRET traces into RNA structural pathways (2016) (0)
MSF: Modulated Sub-graph Finder. (2019) (0)
genome Structured RNAs in the ENCODE selected regions of the human Related Content (2007) (0)
Genome analysis Challenges in RNA virus bioinformatics (2014) (0)
DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model (2022) (0)
RIsearch 2 : suffix array-based large-scale prediction of RNA – RNA interactions and siRNA off-targets ( Supplementary Document ) (2017) (0)
RNA Secondary Structures: Thermodynamics and Folding (2010) (0)
Session Introduction (2003) (0)
The inverse folding problem for RNA secondary structures (1994) (0)
RNA folding with hard and soft constraints (2016) (0)
MSF: Modulated Sub-graph Finder. (2018) (0)
MOESM1 of RNA folding with hard and soft constraints (2016) (0)
Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity (2016) (0)
Investigating RNA-RNA interactions through computational and biophysical analysis (2022) (0)
Final Report, Bioinformatics Integration Network III (2012) (0)
MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing is a global mechanism for the regulation of alternative splicing (2023) (0)
Supporting Material Mammalian Genomes Contain Thousands of Non-Coding RNAs with Conserved Secondary Structure (0)
TSSAR: TSS annotation regime for dRNA-seq (2014) (0)
New Approach to Combat Glioblastoma Shows Promise in Preclinical Studies (2005) (0)
In silico design of ligand triggered RNA switches (2018) (0)
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 (2021) (0)
Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment (2022) (0)
PSB 2010 Tutorial : Computational Studies of Non-coding RNAs (2009) (0)
Faculty Opinions recommendation of Geometric deep learning of RNA structure. (2021) (0)
Faculty Opinions recommendation of Genome-wide discovery of structured noncoding RNAs in bacteria. (2019) (0)
Pseudoknots in RNA folding landscapes SUPPLEMENTAL MATERIAL (2015) (0)
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 (2016) (0)
Title Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics Authors (2012) (0)
Theoretical Biochemistry Group (2006) (0)
Dynamics of small autocatalytic reaction network IV : Inhomogeneous replicator equations (2016) (0)

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What Schools Are Affiliated With Ivo L. Hofacker?

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Ivo L. Hofacker's Academic­Influence.com Rankings

Ivo L. Hofacker's Degrees

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Why Is Ivo L. Hofacker Influential?

Ivo L. Hofacker's Published Works

Published Works

What Schools Are Affiliated With Ivo L. Hofacker?

Ivo L. Hofacker's AcademicInfluence.com Rankings