PubRank

Ivo L Hofacker

Author PubWeight™ 206.22‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007 75.09
2 RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007 18.59
3 ViennaRNA Package 2.0. Algorithms Mol Biol 2011 9.43
4 The Vienna RNA websuite. Nucleic Acids Res 2008 9.02
5 Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A 2005 8.15
6 Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol 2005 4.68
7 Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol 2007 4.28
8 miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res 2006 3.59
9 RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 2008 3.29
10 Thermodynamics of RNA-RNA binding. Bioinformatics 2006 3.10
11 The expansion of the metazoan microRNA repertoire. BMC Genomics 2006 2.80
12 Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol 2006 2.74
13 Structured RNAs in the ENCODE selected regions of the human genome. Genome Res 2007 2.69
14 The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol 2008 2.51
15 Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J Mol Biol 2004 2.49
16 Local RNA base pairing probabilities in large sequences. Bioinformatics 2005 2.17
17 Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis. Nucleic Acids Res 2008 2.10
18 Variations on RNA folding and alignment: lessons from Benasque. J Math Biol 2007 1.91
19 The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. Nucleic Acids Res 2007 1.88
20 RNAz 2.0: improved noncoding RNA detection. Pac Symp Biocomput 2010 1.87
21 Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol 2004 1.81
22 RNAplex: a fast tool for RNA-RNA interaction search. Bioinformatics 2008 1.80
23 AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res 2010 1.58
24 SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics 2007 1.51
25 LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA 2012 1.51
26 Evolutionary patterns of non-coding RNAs. Theory Biosci 2005 1.49
27 Visualization of barrier tree sequences. IEEE Trans Vis Comput Graph 2006 1.45
28 RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. RNA 2011 1.42
29 RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol 2007 1.38
30 De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol 2009 1.31
31 RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Res 2012 1.27
32 RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res 2011 1.25
33 Strategies for measuring evolutionary conservation of RNA secondary structures. BMC Bioinformatics 2008 1.21
34 RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles. Nucleic Acids Res 2010 1.13
35 Multiple sequence alignments of partially coding nucleic acid sequences. BMC Bioinformatics 2005 1.11
36 Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinformatics 2006 1.10
37 Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics 2011 1.09
38 Model-based probe set optimization for high-performance microarrays. Nucleic Acids Res 2008 1.08
39 Folding kinetics of large RNAs. J Mol Biol 2008 1.05
40 Arthropod 7SK RNA. Mol Biol Evol 2008 1.04
41 RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum Mutat 2013 1.03
42 A folding algorithm for extended RNA secondary structures. Bioinformatics 2011 1.03
43 Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. J Biotechnol 2011 1.01
44 RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics 2009 1.01
45 Prediction of consensus RNA secondary structures including pseudoknots. IEEE/ACM Trans Comput Biol Bioinform 2006 1.01
46 The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res 2013 1.00
47 From structure prediction to genomic screens for novel non-coding RNAs. PLoS Comput Biol 2011 0.99
48 How microRNAs choose their targets. Nat Genet 2007 0.95
49 Bcheck: a wrapper tool for detecting RNase P RNA genes. BMC Genomics 2010 0.95
50 TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinformatics 2014 0.94
51 From consensus structure prediction to RNA gene finding. Brief Funct Genomic Proteomic 2009 0.94
52 Discriminatory power of RNA family models. Bioinformatics 2010 0.92
53 Invertebrate 7SK snRNAs. J Mol Evol 2008 0.91
54 Computational design of RNAs with complex energy landscapes. Biopolymers 2013 0.88
55 RNA Accessibility in cubic time. Algorithms Mol Biol 2011 0.88
56 Detection of RNA structures in porcine EST data and related mammals. BMC Genomics 2007 0.86
57 Nematode sbRNAs: homologs of vertebrate Y RNAs. J Mol Evol 2010 0.85
58 Automated identification of RNA 3D modules with discriminative power in RNA structural alignments. Nucleic Acids Res 2013 0.85
59 Animal snoRNAs and scaRNAs with exceptional structures. RNA Biol 2011 0.84
60 Unorthodox mRNA start site to extend the highly structured leader of retrotransposon Tto1 mRNA increases transposition rate. RNA 2005 0.80
61 Identifying structural noncoding RNAs using RNAz. Curr Protoc Bioinformatics 2007 0.80
62 CMCompare webserver: comparing RNA families via covariance models. Nucleic Acids Res 2013 0.79
63 Product Grammars for Alignment and Folding. IEEE/ACM Trans Comput Biol Bioinform 2015 0.79
64 Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. J Proteomics 2013 0.79
65 Folding RNA/DNA hybrid duplexes. Bioinformatics 2012 0.78
66 Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon. Gene 2004 0.77
67 NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations. J Am Chem Soc 2017 0.76
68 Nucleic acid sequence and structure databases. Methods Mol Biol 2010 0.75
69 Concepts and introduction to RNA bioinformatics. Methods Mol Biol 2014 0.75
70 On the evolution of primitive genetic codes. Orig Life Evol Biosph 2003 0.75