PubRank

Ralf Zimmer

Author PubWeight™ 105.38‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 ProMiner: rule-based protein and gene entity recognition. BMC Bioinformatics 2005 6.12
2 RelEx--relation extraction using dependency parse trees. Bioinformatics 2006 4.81
3 High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 2008 3.13
4 A simple approach for protein name identification: prospects and limits. BMC Bioinformatics 2005 3.12
5 Playing biology's name game: identifying protein names in scientific text. Pac Symp Biocomput 2003 3.03
6 Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res 2009 2.26
7 Large-scale gene expression profiling reveals major pathogenetic pathways of cartilage degeneration in osteoarthritis. Arthritis Rheum 2006 2.13
8 Co-clustering of biological networks and gene expression data. Bioinformatics 2002 2.12
9 Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe 2010 1.91
10 Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer. Nucleic Acids Res 2010 1.80
11 Profile-profile alignment: a powerful tool for protein structure prediction. Pac Symp Biocomput 2003 1.76
12 Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog 2009 1.67
13 miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature. BMC Bioinformatics 2010 1.57
14 Reliable gene signatures for microarray classification: assessment of stability and performance. Bioinformatics 2006 1.54
15 Gene and protein nomenclature in public databases. BMC Bioinformatics 2006 1.52
16 Bootstrapping the interactome: unsupervised identification of protein complexes in yeast. J Comput Biol 2009 1.51
17 Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome. PLoS One 2007 1.42
18 Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo. PLoS Pathog 2012 1.40
19 Inferring gene regulatory networks by ANOVA. Bioinformatics 2012 1.39
20 Alternative splicing and protein structure evolution. Nucleic Acids Res 2007 1.35
21 BioWeka--extending the Weka framework for bioinformatics. Bioinformatics 2007 1.26
22 Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism. Mol Biosyst 2007 1.25
23 Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Res 2012 1.24
24 Microarrays: how many do you need? J Comput Biol 2003 1.19
25 New methods for joint analysis of biological networks and expression data. Bioinformatics 2004 1.17
26 Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics 2004 1.16
27 Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis. BMC Struct Biol 2009 1.16
28 From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. Bioinformatics 2011 1.15
29 Vorolign--fast structural alignment using Voronoi contacts. Bioinformatics 2007 1.14
30 The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors. PLoS Pathog 2011 1.14
31 SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles. Bioinformatics 2005 1.11
32 Protein structure alignment considering phenotypic plasticity. Bioinformatics 2008 1.09
33 Contextual analysis of RNAi-based functional screens using interaction networks. Bioinformatics 2011 1.07
34 Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays. PLoS One 2009 1.07
35 Microarray analyses of transdifferentiated mesenchymal stem cells. J Cell Biochem 2008 1.06
36 ProCope--protein complex prediction and evaluation. Bioinformatics 2008 1.05
37 Expert knowledge without the expert: integrated analysis of gene expression and literature to derive active functional contexts. Bioinformatics 2005 1.05
38 MIRTFnet: analysis of miRNA regulated transcription factors. PLoS One 2011 0.99
39 AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings. Bioinformatics 2007 0.99
40 Petri Nets with Fuzzy Logic (PNFL): reverse engineering and parametrization. PLoS One 2010 0.98
41 Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection. PLoS Pathog 2012 0.98
42 Gene expression profiling of serum- and interleukin-1 beta-stimulated primary human adult articular chondrocytes--a molecular analysis based on chondrocytes isolated from one donor. Cytokine 2005 0.98
43 A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication. PLoS Pathog 2013 0.98
44 Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics 2006 0.97
45 Identifying active transcription factors and kinases from expression data using pathway queries. Bioinformatics 2005 0.96
46 ToPNet--an application for interactive analysis of expression data and biological networks. Bioinformatics 2004 0.95
47 ProSAS: a database for analyzing alternative splicing in the context of protein structures. Nucleic Acids Res 2007 0.95
48 Factors influencing the efficiency of generating genetically engineered pigs by nuclear transfer: multi-factorial analysis of a large data set. BMC Biotechnol 2013 0.93
49 Mining RNA-seq data for infections and contaminations. PLoS One 2013 0.93
50 Gene expression in chondrocytes assessed with use of microarrays. J Bone Joint Surg Am 2003 0.92
51 Experiment and mathematical modeling of gene expression dynamics in a cell-free system. Integr Biol (Camb) 2012 0.92
52 Systems analysis of bioenergetics and growth of the extreme halophile Halobacterium salinarum. PLoS Comput Biol 2009 0.91
53 Colored Petri net modeling and simulation of signal transduction pathways. Metab Eng 2005 0.91
54 Rigorous assessment of gene set enrichment tests. Bioinformatics 2012 0.91
55 Inactivation of intergenic enhancers by EBNA3A initiates and maintains polycomb signatures across a chromatin domain encoding CXCL10 and CXCL9. PLoS Pathog 2013 0.90
56 Classification of ncRNAs using position and size information in deep sequencing data. Bioinformatics 2010 0.89
57 A context-based approach to identify the most likely mapping for RNA-seq experiments. BMC Bioinformatics 2012 0.88
58 Functional genomics of osteoarthritis: on the way to evaluate disease hypotheses. Clin Orthop Relat Res 2004 0.88
59 PARma: identification of microRNA target sites in AGO-PAR-CLIP data. Genome Biol 2013 0.88
60 Influence of degree correlations on network structure and stability in protein-protein interaction networks. BMC Bioinformatics 2007 0.87
61 Toward the complete interactome. Nat Biotechnol 2006 0.87
62 Identifying the topology of protein complexes from affinity purification assays. Bioinformatics 2009 0.87
63 FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics 2008 0.86
64 ProML--the protein markup language for specification of protein sequences, structures and families. In Silico Biol 2002 0.85
65 Comprehensive analysis of varicella-zoster virus proteins using a new monoclonal antibody collection. J Virol 2013 0.85
66 Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis. PLoS Comput Biol 2010 0.85
67 Assigning functional linkages to proteins using phylogenetic profiles and continuous phenotypes. Bioinformatics 2008 0.82
68 Analysis of differential gene expression in healthy and osteoarthritic cartilage and isolated chondrocytes by microarray analysis. Methods Mol Med 2004 0.82
69 A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae. Nucleic Acids Res 2013 0.82
70 Improving fold recognition of protein threading by experimental distance constraints. In Silico Biol 2002 0.81
71 Complementing the Eukaryotic Protein Interactome. PLoS One 2013 0.81
72 HALO--a Java framework for precise transcript half-life determination. Bioinformatics 2010 0.81
73 Detecting outlier peptides in quantitative high-throughput mass spectrometry data. J Proteomics 2012 0.81
74 Normalization and gene p-value estimation: issues in microarray data processing. Bioinform Biol Insights 2008 0.80
75 Knowledge representation model for systems-level analysis of signal transduction networks. Genome Inform 2004 0.80
76 Web servicing the biological office. Bioinformatics 2005 0.80
77 RIP-chip enrichment analysis. Bioinformatics 2012 0.79
78 Detection and correction of probe-level artefacts on microarrays. BMC Bioinformatics 2012 0.79
79 A Turing test for artificial expression data. Bioinformatics 2013 0.78
80 Functional genomics of osteoarthritis. Pharmacogenomics 2002 0.78
81 Confidence measures for protein fold recognition. Bioinformatics 2002 0.76
82 A commonly used rumen-protected conjugated linoleic acid supplement marginally affects fatty acid distribution of body tissues and gene expression of mammary gland in heifers during early lactation. Lipids Health Dis 2013 0.75
83 AutoPSI: a database for automatic structural classification of protein sequences and structures. Nucleic Acids Res 2007 0.75
84 The promise and limitations of DNA microarray analysis: comment on the editorial by Firestein and Pisetsky. Arthritis Rheum 2003 0.75
85 Vorescore--fold recognition improved by rescoring of protein structure models. Bioinformatics 2010 0.75
86 Functional genomics, evo-devo and systems biology: a chance to overcome complexity? Curr Opin Rheumatol 2007 0.75
87 A hypergraph-based method for unification of existing protein structure- and sequence-families. In Silico Biol 2002 0.75
88 Experiment specific expression patterns. J Comput Biol 2011 0.75
89 QUASAR--scoring and ranking of sequence-structure alignments. Bioinformatics 2005 0.75