Published in BMC Bioinformatics on May 17, 2011
Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics (2012) 1.69
Modeling formalisms in Systems Biology. AMB Express (2011) 1.61
PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). Bioinformatics (2011) 1.01
PathVisio-Validator: a rule-based validation plugin for graphical pathway notations. Bioinformatics (2011) 0.89
SIRT1/PARP1 crosstalk: connecting DNA damage and metabolism. Genome Integr (2013) 0.82
PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways. Bioinformatics (2013) 0.82
Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response. PLoS Comput Biol (2015) 0.78
NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules. BMC Syst Biol (2014) 0.78
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
LibSBML: an API library for SBML. Bioinformatics (2008) 5.61
VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics (2006) 4.38
Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics (2008) 4.34
Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping. Cancer Res (2003) 3.52
Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol Biol Cell (1999) 3.41
Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell (2005) 2.82
Cancer chemoprevention mechanisms mediated through the Keap1-Nrf2 pathway. Antioxid Redox Signal (2010) 2.45
Apoptosis defects and chemotherapy resistance: molecular interaction maps and networks. Oncogene (2004) 2.36
An overview of the CellML API and its implementation. BMC Bioinformatics (2010) 1.55
Molecular interaction map of the p53 and Mdm2 logic elements, which control the Off-On switch of p53 in response to DNA damage. Biochem Biophys Res Commun (2005) 1.33
Chk2 molecular interaction map and rationale for Chk2 inhibitors. Clin Cancer Res (2006) 1.28
Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks. Sci STKE (2004) 1.27
Properties of switch-like bioregulatory networks studied by simulation of the hypoxia response control system. Mol Biol Cell (2004) 1.27
Depicting combinatorial complexity with the molecular interaction map notation. Mol Syst Biol (2006) 1.17
Targeting chk2 kinase: molecular interaction maps and therapeutic rationale. Curr Pharm Des (2005) 1.17
Challenges for automatically extracting molecular interactions from full-text articles. BMC Bioinformatics (2009) 1.11
Circuit diagrams for biological networks. Mol Syst Biol (2006) 1.06
Chromatin challenges during DNA replication: a systems representation. Mol Biol Cell (2007) 1.04
PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). Bioinformatics (2011) 1.01
Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis. Nucleic Acids Res (2008) 0.86
Predicted functions of MdmX in fine-tuning the response of p53 to DNA damage. PLoS Comput Biol (2010) 0.83
Dynamic simulations of pathways downstream of ERBB-family, including mutations and treatments: concordance with experimental results. Curr Cancer Drug Targets (2010) 0.80
GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol (2003) 22.63
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics (2005) 14.02
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol (2003) 8.66
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res (2005) 7.66
The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol (2009) 7.36
Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins (2002) 5.79
Is allostery an intrinsic property of all dynamic proteins? Proteins (2004) 4.99
Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping. Cancer Res (2003) 3.52
Phosphorylation of histone H2AX and activation of Mre11, Rad50, and Nbs1 in response to replication-dependent DNA double-strand breaks induced by mammalian DNA topoisomerase I cleavage complexes. J Biol Chem (2003) 3.45
A method for simultaneous alignment of multiple protein structures. Proteins (2004) 3.45
Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc Natl Acad Sci U S A (2003) 3.42
Allostery: absence of a change in shape does not imply that allostery is not at play. J Mol Biol (2008) 3.24
Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. J Mol Biol (2004) 3.10
Stabilities and conformations of Alzheimer's beta -amyloid peptide oligomers (Abeta 16-22, Abeta 16-35, and Abeta 10-35): Sequence effects. Proc Natl Acad Sci U S A (2002) 3.06
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci (2002) 3.01
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci (2010) 2.97
Principles of protein-protein interactions: what are the preferred ways for proteins to interact? Chem Rev (2008) 2.96
FireDock: fast interaction refinement in molecular docking. Proteins (2007) 2.90
Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell (2005) 2.82
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther (2013) 2.64
CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set. Cancer Res (2012) 2.57
Repair of and checkpoint response to topoisomerase I-mediated DNA damage. Mutat Res (2003) 2.50
Close-range electrostatic interactions in proteins. Chembiochem (2002) 2.42
The intra-S-phase checkpoint affects both DNA replication initiation and elongation: single-cell and -DNA fiber analyses. Mol Cell Biol (2007) 2.41
FireDock: a web server for fast interaction refinement in molecular docking. Nucleic Acids Res (2008) 2.39
Apoptosis defects and chemotherapy resistance: molecular interaction maps and networks. Oncogene (2004) 2.36
The origin of allosteric functional modulation: multiple pre-existing pathways. Structure (2009) 2.33
Recognition of functional sites in protein structures. J Mol Biol (2004) 2.32
The human beta-globin locus control region can silence as well as activate gene expression. Mol Cell Biol (2005) 2.19
Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Mol Biosyst (2009) 2.18
Extended disordered proteins: targeting function with less scaffold. Trends Biochem Sci (2003) 2.12
A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci (2004) 2.11
PRISM: protein interactions by structural matching. Nucleic Acids Res (2005) 2.11
Protein-protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking. Structure (2004) 2.06
mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities. Mol Cancer Ther (2010) 2.00
Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol (2006) 1.98
Taking geometry to its edge: fast unbound rigid (and hinge-bent) docking. Proteins (2003) 1.95
Geometry-based flexible and symmetric protein docking. Proteins (2005) 1.95
Flexible protein alignment and hinge detection. Proteins (2002) 1.93
Relationship between ion pair geometries and electrostatic strengths in proteins. Biophys J (2002) 1.91
HingeProt: automated prediction of hinges in protein structures. Proteins (2008) 1.86
Preventing gene silencing with human replicators. Nat Biotechnol (2006) 1.84
Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc (2011) 1.84
Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol (2008) 1.80
Principles of flexible protein-protein docking. Proteins (2008) 1.71
Simulations as analytical tools to understand protein aggregation and predict amyloid conformation. Curr Opin Chem Biol (2006) 1.70
Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics (2012) 1.69
Ataxia telangiectasia mutated activation by transcription- and topoisomerase I-induced DNA double-strand breaks. EMBO Rep (2009) 1.69
ARTS: alignment of RNA tertiary structures. Bioinformatics (2005) 1.67
Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J Mol Biol (2004) 1.64
Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev (2010) 1.62
Enzyme dynamics point to stepwise conformational selection in catalysis. Curr Opin Chem Biol (2010) 1.61
Similar binding sites and different partners: implications to shared proteins in cellular pathways. Structure (2007) 1.60
Molecular dynamics simulations of alanine rich beta-sheet oligomers: Insight into amyloid formation. Protein Sci (2002) 1.59
Dynamic allostery: linkers are not merely flexible. Structure (2011) 1.58
Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. Proteins (2006) 1.58
CellMiner: a relational database and query tool for the NCI-60 cancer cell lines. BMC Genomics (2009) 1.58
Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. J Mol Biol (2004) 1.54
Inhibition of histone deacetylase in cancer cells slows down replication forks, activates dormant origins, and induces DNA damage. Cancer Res (2010) 1.53
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res (2008) 1.52
Nonclassic functions of human topoisomerase I: genome-wide and pharmacologic analyses. Cancer Res (2007) 1.51
Architectures and functional coverage of protein-protein interfaces. J Mol Biol (2008) 1.51
Bloom's syndrome helicase and Mus81 are required to induce transient double-strand DNA breaks in response to DNA replication stress. J Mol Biol (2007) 1.50
Truncated beta-amyloid peptide channels provide an alternative mechanism for Alzheimer's Disease and Down syndrome. Proc Natl Acad Sci U S A (2010) 1.48
FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins (2010) 1.47
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47
Hereditary ataxia SCAN1 cells are defective for the repair of transcription-dependent topoisomerase I cleavage complexes. DNA Repair (Amst) (2006) 1.45
Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res (2011) 1.44
Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities. Biophys J (2007) 1.44
Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process. Biophys J (2007) 1.44
New structures help the modeling of toxic amyloidbeta ion channels. Trends Biochem Sci (2008) 1.43
Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder. Proc Natl Acad Sci U S A (2005) 1.43
Atomic-level description of amyloid beta-dimer formation. J Am Chem Soc (2006) 1.41
Death receptor-induced activation of the Chk2- and histone H2AX-associated DNA damage response pathways. Mol Cell Biol (2008) 1.39
The ARTS web server for aligning RNA tertiary structures. Nucleic Acids Res (2006) 1.37
A novel norindenoisoquinoline structure reveals a common interfacial inhibitor paradigm for ternary trapping of the topoisomerase I-DNA covalent complex. Mol Cancer Ther (2006) 1.36
Mus81-mediated DNA cleavage resolves replication forks stalled by topoisomerase I-DNA complexes. J Cell Biol (2011) 1.36
Mechanisms of transcription factor selectivity. Trends Genet (2010) 1.35
Transcriptional regulation of mitotic genes by camptothecin-induced DNA damage: microarray analysis of dose- and time-dependent effects. Cancer Res (2002) 1.34
Short peptide amyloid organization: stabilities and conformations of the islet amyloid peptide NFGAIL. Biophys J (2003) 1.33
Structural stability and dynamics of an amyloid-forming peptide GNNQQNY from the yeast prion sup-35. Biophys J (2006) 1.33
Multiple structural alignment by secondary structures: algorithm and applications. Protein Sci (2003) 1.32
Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states. Proc Natl Acad Sci U S A (2010) 1.32
Allostery and population shift in drug discovery. Curr Opin Pharmacol (2010) 1.32
UCN-01 inhibits p53 up-regulation and abrogates gamma-radiation-induced G(2)-M checkpoint independently of p53 by targeting both of the checkpoint kinases, Chk2 and Chk1. Cancer Res (2002) 1.32
Apoptosis induced by topoisomerase inhibitors. Curr Med Chem Anticancer Agents (2003) 1.31
Models of toxic beta-sheet channels of protegrin-1 suggest a common subunit organization motif shared with toxic alzheimer beta-amyloid ion channels. Biophys J (2008) 1.30
MolAxis: efficient and accurate identification of channels in macromolecules. Proteins (2008) 1.30
The cyclin-dependent kinase inhibitor Dacapo promotes replication licensing during Drosophila endocycles. EMBO J (2007) 1.30
Nanoparticle-induced vascular blockade in human prostate cancer. Blood (2010) 1.30
Chk2 molecular interaction map and rationale for Chk2 inhibitors. Clin Cancer Res (2006) 1.28
Topological properties of protein interaction networks from a structural perspective. Biochem Soc Trans (2008) 1.28
The multiple common point set problem and its application to molecule binding pattern detection. J Comput Biol (2006) 1.28
The human beta-globin replication initiation region consists of two modular independent replicators. Mol Cell Biol (2004) 1.28
Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks. Sci STKE (2004) 1.27