(Q31043070)

28 June 2017

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title

Transforming omics data into context: bioinformatics on genomics and proteomics raw data (English)

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28 June 2017

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Paul Perco

1

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Gert Mayer

object named as

Gert Mayer

6

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author name string

Ronald Rapberger

2

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28 June 2017

Christian Siehs

3

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28 June 2017

Arno Lukas

4

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28 June 2017

Rainer Oberbauer

5

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28 June 2017

Bernd Mayer

7

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28 June 2017

publication date

1 July 2006

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28 June 2017

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28 June 2017

volume

27

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28 June 2017

issue

13

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28 June 2017

page(s)

2659-2675

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Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

28 June 2017

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Design and implementation of microarray gene expression markup language (MAGE-ML)

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A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

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A Bayesian missing value estimation method for gene expression profile data

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7 January 2021

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7 January 2021

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7 January 2021

Analysis of large-scale gene expression data

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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7 January 2021

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Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

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Gibbs Recursive Sampler: finding transcription factor binding sites

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7 January 2021

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7 January 2021

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7 January 2021

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Discrete simulation of regulatory homo- and heterodimerization in the apoptosis effector phase.

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7 January 2021

Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico

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Automated Gene Ontology annotation for anonymous sequence data

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7 January 2021

GOblet: a platform for Gene Ontology annotation of anonymous sequence data

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7 January 2021

SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data

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7 January 2021

Profiling Gene Expression Using Onto-Express

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7 January 2021

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GeneMerge—post-genomic analysis, data mining, and hypothesis testing

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7 January 2021

GOToolBox: functional analysis of gene datasets based on Gene Ontology

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7 January 2021

GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

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7 January 2021

OntologyTraverser: an R package for GO analysis.

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7 January 2021

Ontological analysis of gene expression data: current tools, limitations, and open problems

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7 January 2021

The KEGG databases at GenomeNet

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Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary

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An architecture for biological information extraction and representation.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Cytoscape: a software environment for integrated models of biomolecular interaction networks

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Osprey: a network visualization system

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

VisANT: data-integrating visual framework for biological networks and modules

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Linking the genes: inferring quantitative gene networks from microarray data

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Intervention in context-sensitive probabilistic Boolean networks

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

External control in Markovian genetic regulatory networks: the imperfect information case.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

An empirical Bayes approach to inferring large-scale gene association networks.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Identifying periodically expressed transcripts in microarray time series data

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Reverse engineering of genetic networks with Bayesian networks

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Discovery of meaningful associations in genomic data using partial correlation coefficients

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

New methods for joint analysis of biological networks and expression data

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

ToPNet--an application for interactive analysis of expression data and biological networks

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Reverse engineering of regulatory networks: simulation studies on a genetic algorithm approach for ranking hypotheses.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Outer membranes of gram-negative bacteria. XIX. Isolation from Pseudomonas aeruginosa PAO1 and use in reconstitution and definition of the permeability barrier

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Use of fluorescent-protein tagging to determine the subcellular localization of mycoplasma pneumoniae proteins encoded by the cytadherence regulatory locus.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Subcellular localization of the Agrobacterium tumefaciens T-DNA transport pore proteins: VirB8 is essential for the assembly of the transport pore

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Correlation of the amino acid composition of a protein to its structural and biological characters

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Predicting protein subcellular localization: past, present, and future.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Using neural networks for prediction of the subcellular location of proteins

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Using neural networks for prediction of subcellular location of prokaryotic and eukaryotic proteins.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Support vector machine approach for protein subcellular localization prediction

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Prediction of protein subcellular locations using Markov chain models

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Prediction of protein subcellular locations using fuzzy k-NN method

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Relation between amino acid composition and cellular location of proteins.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Predicting subcellular localization of proteins based on their N-terminal amino acid sequence

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Computational method to predict mitochondrially imported proteins and their targeting sequences

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Predotar: A tool for rapidly screening proteomes for N-terminal targeting sequences

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Extensive feature detection of N-terminal protein sorting signals

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Finding nuclear localization signals

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Predicting protein cellular localization using a domain projection method

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

SMART: a web-based tool for the study of genetically mobile domains

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Predicting subcellular localization of proteins using machine-learned classifiers

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Sequence conserved for subcellular localization

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Predicting subcellular localization via protein motif co-occurrence

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

A knowledge base for predicting protein localization sites in eukaryotic cells

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

PSLpred: prediction of subcellular localization of bacterial proteins

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

LOCSVMPSI: a web server for subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

The Universal Protein Resource (UniProt): an expanding universe of protein information

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Human housekeeping genes are compact

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Housekeeping genes as internal standards in cancer research

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Housekeeping proteins: a preliminary study illustrating some limitations as useful references in protein expression studies.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

dbEST--database for "expressed sequence tags"

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

GeneNote: whole genome expression profiles in normal human tissues

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Database of mRNA gene expression profiles of multiple human organs

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Proteomic research: potential opportunities for clinical and physiological investigators.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Reg1p targets protein phosphatase 1 to dephosphorylate hexokinase II in Saccharomyces cerevisiae: characterizing the effects of a phosphatase subunit on the yeast proteome

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Sequence and structure-based prediction of eukaryotic protein phosphorylation sites

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Prediction of Human Protein Function from Post-translational Modifications and Localization Features

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Prediction of solvent accessibility and sites of deleterious mutations from protein sequence.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Accurate prediction of solvent accessibility using neural networks-based regression.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

NETASA: neural network based prediction of solvent accessibility.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Real value prediction of solvent accessibility from amino acid sequence.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Predicting surface exposure of amino acids from protein sequence

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Prediction of coordination number and relative solvent accessibility in proteins.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Conservation and prediction of solvent accessibility in protein families

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Predicting solvent accessibility: higher accuracy using Bayesian statistics and optimized residue substitution classes.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

New method for accurate prediction of solvent accessibility from protein sequence.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Prediction of protein surface accessibility with information theory.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Prediction of protein relative solvent accessibility with support vector machines and long-range interaction 3D local descriptor

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Prediction of protein solvent accessibility using support vector machines.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

The bottom line for prediction of residue solvent accessibility.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Real value prediction of solvent accessibility in proteins using multiple sequence alignment and secondary structure.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Protein conformational prediction

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

A critical evaluation of methods for prediction of protein secondary structures

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Protein secondary structure prediction based on position-specific scoring matrices

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Review: protein secondary structure prediction continues to rise.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

JPred: a consensus secondary structure prediction server

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Molecular dynamics simulations in biology

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Knowledge-based potentials for proteins

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Assessment of the CASP4 fold recognition category

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

LiveBench-1: continuous benchmarking of protein structure prediction servers

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

EVA: continuous automatic evaluation of protein structure prediction servers.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Discovery of promiscuous HLA-II-restricted T cell epitopes with TEPITOPE.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

BEPITOPE: predicting the location of continuous epitopes and patterns in proteins

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

EMBOSS: the European Molecular Biology Open Software Suite

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

T-cell epitope prediction with combinatorial peptide libraries

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

A data integration methodology for systems biology

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

A data integration methodology for systems biology: experimental verification

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Integrative analysis of the cancer transcriptome

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

A molecular signature of metastasis in primary solid tumors

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

A comprehensive transcript index of the human genome generated using microarrays and computational approaches

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Distribution of NF-kappaB-binding sites across human chromosome 22

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Detection and measurement of alternative splicing using splicing-sensitive microarrays.

1 reference

https://api.crossref.org/works/10.1002%2FELPS.200600064

7 January 2021

Identifiers

DOI

10.1002/ELPS.200600064

1 reference

28 June 2017

1 reference