|
1
|
Identifying functional modules in protein-protein interaction networks: an integrated exact approach.
|
Bioinformatics
|
2008
|
3.00
|
|
2
|
5.8S-28S rRNA interaction and HMM-based ITS2 annotation.
|
Gene
|
2008
|
2.51
|
|
3
|
4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing.
|
BMC Bioinformatics
|
2006
|
2.24
|
|
4
|
Metabolic interdependence of obligate intracellular bacteria and their insect hosts.
|
Microbiol Mol Biol Rev
|
2004
|
2.19
|
|
5
|
Carbon metabolism of intracellular bacterial pathogens and possible links to virulence.
|
Nat Rev Microbiol
|
2010
|
2.04
|
|
6
|
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures.
|
RNA
|
2005
|
1.94
|
|
7
|
BioNet: an R-Package for the functional analysis of biological networks.
|
Bioinformatics
|
2010
|
1.93
|
|
8
|
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses.
|
Nucleic Acids Res
|
2006
|
1.92
|
|
9
|
Distinguishing species.
|
RNA
|
2007
|
1.74
|
|
10
|
Platelet protein interactions: map, signaling components, and phosphorylation groundstate.
|
Arterioscler Thromb Vasc Biol
|
2008
|
1.71
|
|
11
|
Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges.
|
ISME J
|
2010
|
1.66
|
|
12
|
L1Base: from functional annotation to prediction of active LINE-1 elements.
|
Nucleic Acids Res
|
2005
|
1.57
|
|
13
|
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE.
|
BMC Res Notes
|
2008
|
1.54
|
|
14
|
Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta).
|
BMC Evol Biol
|
2004
|
1.51
|
|
15
|
Metabolites: a helping hand for pathway evolution?
|
Trends Biochem Sci
|
2003
|
1.50
|
|
16
|
Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: the replacement of the missing "household" nucleoside diphosphate kinase gene and activity by glycolytic kinases.
|
OMICS
|
2002
|
1.50
|
|
17
|
Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes.
|
J Bacteriol
|
2006
|
1.48
|
|
18
|
Riboswitch finder--a tool for identification of riboswitch RNAs.
|
Nucleic Acids Res
|
2004
|
1.47
|
|
19
|
Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees.
|
Biol Direct
|
2010
|
1.44
|
|
20
|
The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'.
|
BMC Genomics
|
2008
|
1.42
|
|
21
|
The ITS2 Database II: homology modelling RNA structure for molecular systematics.
|
Nucleic Acids Res
|
2007
|
1.41
|
|
22
|
CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures.
|
In Silico Biol
|
2005
|
1.39
|
|
23
|
An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach.
|
Plant Cell
|
2006
|
1.37
|
|
24
|
XML schemas for common bioinformatic data types and their application in workflow systems.
|
BMC Bioinformatics
|
2006
|
1.33
|
|
25
|
Integrated network reconstruction, visualization and analysis using YANAsquare.
|
BMC Bioinformatics
|
2007
|
1.32
|
|
26
|
Interactions of methylene blue with human disulfide reductases and their orthologues from Plasmodium falciparum.
|
Antimicrob Agents Chemother
|
2007
|
1.28
|
|
27
|
Genome-wide mapping of foamy virus vector integrations into a human cell line.
|
J Gen Virol
|
2006
|
1.28
|
|
28
|
Toward computer-based cleavage site prediction of cysteine endopeptidases.
|
Biol Chem
|
2003
|
1.27
|
|
29
|
ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments.
|
Bioinformatics
|
2008
|
1.25
|
|
30
|
Iron regulation and the cell cycle: identification of an iron-responsive element in the 3'-untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy.
|
J Biol Chem
|
2006
|
1.25
|
|
31
|
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.
|
BMC Bioinformatics
|
2005
|
1.24
|
|
32
|
13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA.
|
Proc Natl Acad Sci U S A
|
2006
|
1.21
|
|
33
|
The highly attenuated oncolytic recombinant vaccinia virus GLV-1h68: comparative genomic features and the contribution of F14.5L inactivation.
|
Mol Genet Genomics
|
2009
|
1.20
|
|
34
|
Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data.
|
Int J Syst Evol Microbiol
|
2004
|
1.16
|
|
35
|
Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens.
|
Nat Commun
|
2013
|
1.15
|
|
36
|
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.
|
Bioinformatics
|
2005
|
1.13
|
|
37
|
Shared components of protein complexes--versatile building blocks or biochemical artefacts?
|
Bioessays
|
2004
|
1.13
|
|
38
|
Analysis of SAGE data in human platelets: features of the transcriptome in an anucleate cell.
|
Thromb Haemost
|
2006
|
1.10
|
|
39
|
Use of functional highly purified human platelets for the identification of new proteins of the IPP signaling pathway.
|
Thromb Res
|
2007
|
1.07
|
|
40
|
RIP death domain structural interactions implicated in TNF-mediated proliferation and survival.
|
Proteins
|
2006
|
1.06
|
|
41
|
Perforin-like protein PPLP2 permeabilizes the red blood cell membrane during egress of Plasmodium falciparum gametocytes.
|
Cell Microbiol
|
2014
|
1.02
|
|
42
|
Integrated systems view on networking by hormones in Arabidopsis immunity reveals multiple crosstalk for cytokinin.
|
Plant Cell
|
2012
|
1.01
|
|
43
|
ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales).
|
BMC Evol Biol
|
2008
|
1.00
|
|
44
|
Molecular mechanisms of tolerance in tardigrades: new perspectives for preservation and stabilization of biological material.
|
Biotechnol Adv
|
2009
|
0.99
|
|
45
|
A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation.
|
Mol Biosyst
|
2011
|
0.99
|
|
46
|
Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades.
|
BMC Genomics
|
2009
|
0.98
|
|
47
|
ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae).
|
J Mol Evol
|
2005
|
0.96
|
|
48
|
The ITS2 Database.
|
J Vis Exp
|
2012
|
0.96
|
|
49
|
The role of auxin-cytokinin antagonism in plant-pathogen interactions.
|
PLoS Pathog
|
2012
|
0.95
|
|
50
|
Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms.
|
PLoS One
|
2010
|
0.94
|
|
51
|
Toward a Systemic Understanding of Listeria monocytogenes Metabolism during Infection.
|
Front Microbiol
|
2012
|
0.94
|
|
52
|
Exonization of active mouse L1s: a driver of transcriptome evolution?
|
BMC Genomics
|
2007
|
0.94
|
|
53
|
Lysosomal, cytoskeletal, and metabolic alterations in cardiomyopathy of cathepsin L knockout mice.
|
FASEB J
|
2006
|
0.94
|
|
54
|
Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer.
|
BMC Genomics
|
2010
|
0.93
|
|
55
|
Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species.
|
Mol Ecol Resour
|
2008
|
0.93
|
|
56
|
Quantitative single-molecule localization microscopy combined with rule-based modeling reveals ligand-induced TNF-R1 reorganization toward higher-order oligomers.
|
Histochem Cell Biol
|
2014
|
0.93
|
|
57
|
Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor.
|
J Cell Biochem
|
2011
|
0.92
|
|
58
|
PlateletWeb: a systems biologic analysis of signaling networks in human platelets.
|
Blood
|
2011
|
0.91
|
|
59
|
Modelling interaction sites in protein domains with interaction profile hidden Markov models.
|
Bioinformatics
|
2006
|
0.91
|
|
60
|
A versatile structural domain analysis server using profile weight matrices.
|
J Chem Inf Comput Sci
|
2002
|
0.91
|
|
61
|
Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling.
|
BMC Genomics
|
2010
|
0.90
|
|
62
|
Identification of new therapeutic targets by genome-wide analysis of gene expression in the ipsilateral cortex of aged rats after stroke.
|
PLoS One
|
2012
|
0.89
|
|
63
|
Detecting species-site dependencies in large multiple sequence alignments.
|
Nucleic Acids Res
|
2009
|
0.89
|
|
64
|
Integration of Boolean models exemplified on hepatocyte signal transduction.
|
Brief Bioinform
|
2011
|
0.89
|
|
65
|
A software tool-box for analysis of regulatory RNA elements.
|
Nucleic Acids Res
|
2003
|
0.88
|
|
66
|
Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus.
|
BMC Microbiol
|
2006
|
0.88
|
|
67
|
Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling.
|
BMC Bioinformatics
|
2013
|
0.88
|
|
68
|
Robustness and accuracy of functional modules in integrated network analysis.
|
Bioinformatics
|
2012
|
0.87
|
|
69
|
Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysis.
|
BMC Cancer
|
2008
|
0.87
|
|
70
|
GoSynthetic database tool to analyse natural and engineered molecular processes.
|
Database (Oxford)
|
2013
|
0.86
|
|
71
|
Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.
|
Gene
|
2007
|
0.86
|
|
72
|
Host insulin stimulates Echinococcus multilocularis insulin signalling pathways and larval development.
|
BMC Biol
|
2014
|
0.86
|
|
73
|
Modeling system states in liver cells: survival, apoptosis and their modifications in response to viral infection.
|
BMC Syst Biol
|
2009
|
0.85
|
|
74
|
Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations.
|
Bioinform Biol Insights
|
2012
|
0.85
|
|
75
|
Stress response in tardigrades: differential gene expression of molecular chaperones.
|
Cell Stress Chaperones
|
2009
|
0.85
|
|
76
|
Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data.
|
Proteomics
|
2011
|
0.85
|
|
77
|
Developmental profiling by mass spectrometry of phosphocholine containing phospholipids in the rat nervous system reveals temporo-spatial gradients.
|
J Neurochem
|
2010
|
0.84
|
|
78
|
Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells.
|
Genome Biol
|
2011
|
0.84
|
|
79
|
NO-bound myoglobin: structural diversity and dynamics of the NO ligand.
|
J Am Chem Soc
|
2004
|
0.83
|
|
80
|
Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation.
|
BMC Syst Biol
|
2011
|
0.83
|
|
81
|
A novel conserved family of nitric oxide synthase?
|
Trends Biochem Sci
|
2004
|
0.83
|
|
82
|
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.
|
BMC Bioinformatics
|
2009
|
0.82
|
|
83
|
Immune response of the ant Camponotus floridanus against pathogens and its obligate mutualistic endosymbiont.
|
Insect Biochem Mol Biol
|
2011
|
0.82
|
|
84
|
Analysing molecular polar surface descriptors to predict blood-brain barrier permeation.
|
Int J Comput Biol Drug Des
|
2013
|
0.81
|
|
85
|
High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis.
|
BMC Genomics
|
2010
|
0.81
|
|
86
|
inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons.
|
BMC Bioinformatics
|
2006
|
0.81
|
|
87
|
Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum.
|
BMC Syst Biol
|
2012
|
0.81
|
|
88
|
Molecular characterization of antimicrobial peptide genes of the carpenter ant Camponotus floridanus.
|
PLoS One
|
2012
|
0.80
|
|
89
|
Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function.
|
Bioinformation
|
2010
|
0.80
|
|
90
|
Pharmacogenomic strategies against resistance development in microbial infections.
|
Pharmacogenomics
|
2004
|
0.80
|
|
91
|
Jimena: efficient computing and system state identification for genetic regulatory networks.
|
BMC Bioinformatics
|
2013
|
0.80
|
|
92
|
Understanding platelets. Lessons from proteomics, genomics and promises from network analysis.
|
Thromb Haemost
|
2005
|
0.80
|
|
93
|
Exogenous administration of a recombinant variant of TWEAK impairs healing after myocardial infarction by aggravation of inflammation.
|
PLoS One
|
2013
|
0.80
|
|
94
|
LONELY-GUY Knocks Every Door: Crosskingdom Microbial Pathogenesis.
|
Trends Plant Sci
|
2015
|
0.80
|
|
95
|
Deep metazoan phylogeny.
|
In Silico Biol
|
2007
|
0.79
|
|
96
|
Characterization of a novel interaction between vasodilator-stimulated phosphoprotein and Abelson interactor 1 in human platelets: a concerted computational and experimental approach.
|
Arterioscler Thromb Vasc Biol
|
2010
|
0.79
|
|
97
|
Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state.
|
PLoS One
|
2012
|
0.79
|
|
98
|
Antigen profiling analysis of vaccinia virus injected canine tumors: oncolytic virus efficiency predicted by boolean models.
|
Bioengineered
|
2014
|
0.78
|
|
99
|
Current efforts in the analysis of RNAi and RNAi target genes.
|
Brief Bioinform
|
2005
|
0.77
|
|
100
|
Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL.
|
Proteomics
|
2010
|
0.77
|
|
101
|
New trends in pharmacogenomic strategies against resistance development in microbial infections.
|
Pharmacogenomics
|
2008
|
0.77
|
|
102
|
A semi-quantitative model of Quorum-Sensing in Staphylococcus aureus, approved by microarray meta-analyses and tested by mutation studies.
|
Mol Biosyst
|
2013
|
0.76
|
|
103
|
Diagnostic value of preoperative CT scan to stratify colon cancer for neoadjuvant therapy.
|
Int J Colorectal Dis
|
2015
|
0.76
|
|
104
|
PlanktoVision--an automated analysis system for the identification of phytoplankton.
|
BMC Bioinformatics
|
2013
|
0.76
|
|
105
|
Unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation.
|
Bioinform Biol Insights
|
2008
|
0.76
|
|
106
|
Modelling phagosomal lipid networks that regulate actin assembly.
|
BMC Syst Biol
|
2008
|
0.76
|
|
107
|
A Boolean view separates platelet activatory and inhibitory signalling as verified by phosphorylation monitoring including threshold behaviour and integrin modulation.
|
Mol Biosyst
|
2013
|
0.76
|
|
108
|
Different evolutionary modifications as a guide to rewire two-component systems.
|
Bioinform Biol Insights
|
2012
|
0.76
|
|
109
|
Dynamical modelling of prostaglandin signalling in platelets reveals individual receptor contributions and feedback properties.
|
Mol Biosyst
|
2013
|
0.76
|
|
110
|
In search of the prototype of nitric oxide synthase.
|
FEBS Lett
|
2003
|
0.76
|
|
111
|
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.
|
BMC Bioinformatics
|
2010
|
0.75
|
|
112
|
CA/C1 peptidases of the malaria parasites Plasmodium falciparum and P. berghei and their mammalian hosts--a bioinformatical analysis.
|
Biol Chem
|
2009
|
0.75
|
|
113
|
A comparative analysis of the bistability switch for platelet aggregation by logic ODE based dynamical modeling.
|
Mol Biosyst
|
2014
|
0.75
|
|
114
|
Integration of boolean models on hormonal interactions and prospects of cytokinin-auxin crosstalk in plant immunity.
|
Plant Signal Behav
|
2013
|
0.75
|
|
115
|
B-Raf and C-Raf signaling investigated in a simplified model of the mitogenic kinase cascade.
|
Biol Chem
|
2005
|
0.75
|
|
116
|
The impact of cytokinin on jasmonate-salicylate antagonism in Arabidopsis immunity against infection with Pst DC3000.
|
Plant Signal Behav
|
2013
|
0.75
|
|
117
|
Bioinformatical approaches to detect and analyze protein interactions.
|
Methods Mol Biol
|
2009
|
0.75
|
|
118
|
Oxime Ethers of (E)-11-Isonitrosostrychnine as Highly Potent Glycine Receptor Antagonists.
|
J Nat Prod
|
2016
|
0.75
|
|
119
|
An open source protein gel documentation system for proteome analyses.
|
J Chem Inf Comput Sci
|
2004
|
0.75
|
|
120
|
Mining biomedical images towards valuable information retrieval in biomedical and life sciences.
|
Database (Oxford)
|
2016
|
0.75
|
|
121
|
A java applet for exploring the new higher level classification of eukaryotes with emphasis on the taxonomy of protists.
|
J Eukaryot Microbiol
|
2006
|
0.75
|