NDLI: Image data mining of fruitfly gene expression patterns

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2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05)

2005 IEEE Computational Systems Bioinformatics Conference - Copyright

Table of contents [2005 IEEE Computational Systems Bioinformatics Conference]

Sequential classification for microarray and clinical data

Efficient image texture analysis and classification for prostate ultrasound diagnosis

Diagnosis and biomarker identification on SELDI proteomics data by ADTBoost

Inverse design of large molecules using linear diophantine equations

Reducing gene regulatory networks by decomposition

A diffusion model to estimate the inter-arrival time of charged molecules in stochastic event based modeling of complex biological networks

Operon prediction in cyanobacteria using comparative genomics

Patterns of gene deletion following genome duplication in yeast

PLATCOM: a platform for computational comparative genomics on the Web

Classification methods for HIV-1 medicated neuronal damage

Key features of the UCSC genome site

PROMOCO: a new program for prediction of cis regulatory elements: from high-information content analysis to clique identification

Data integration in the mouse genome informatics (MGI) database

HIV structural and biothermodynamics databases: a resource for the pharmaceutical and biotechnology industry

A new clustering strategy with stochastic merging and removing based on kernel functions

Head and neck cancer metastasis prediction via artificial neural networks

Cluster utility: a new metric for clustering biological sequences

Problem solving environment approach to integrating diverse biological data sources

Predicting functional gene-links from phylogenetic-statistical analyses of whole genomes

Whole genome phylogeny based on clustered signature string composition

A polynomial algorithm for the minimum quartet inconsistency problem with O(n) quartet errors

Phylogenetic postprocessing

A novel quartet-based method for phylogenetic inference

Consensus methods using phylogenetic databases

Bacterial whole genome phylogeny using proteome comparison and optimal reversal distance

Identifying orthologs: cycle splitting on the breakpoint graph

Improving operon prediction in E. coli

Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiae

Automatic protein function annotation through candidate ortholog clusters from incomplete genomes

EST-based analysis of gene expression in the human cochlea

Eigenphenotypes: towards an algorithmic framework for phenotype discovery

A novel approach for prediction of multi-labeled protein subcellular localization for prokaryotic bacteria

Incorporating life sciences applications in the architectural optimizations of next-generation petaflop-system

A generic algorithm to find all common intervals of two permutations

M@CBETH: optimizing clinical microarray classification

Similarity and cluster analysis algorithms for microarrays using R* trees

Maximum significance clustering of oligonucleotide microarrays

Gene-ontology-based analysis of gene expression changes in early development of Ceratopteris spores

Fractal clustering for microarray data analysis

Multivariate gene selection: does it help?

Considerations in making microarray cross-platform correlations

Two-way clustering of gene expression profiles by sparse matrix factorization

Novel hybrid hierarchical-K-means clustering method (H-K-means) for microarray analysis

A general methodology for integration of microarray data

K-means+ method for improving gene selection for classification of microarray data

Sequential diagonal linear discriminant analysis (SeqDLDA) for microarray classification and gene identification

A storage, processing, and retrieval system for microtubule tracking data

BioMap: discovering schema mapping using ontologies

Minimal marker sets to discriminate among seedlines

A fast shotgun assembly heuristic

Simulated pharmacogenomics exercises for the Cybertory/spl trade/ Virtual Molecular Biology Laboratory

Aligning peaks across multiple mass spectrometry data sets using a scale-space based approach

Lossless compression of DNA microarray images

Predicting continuous epitopes in proteins

Which normalization method is best? A platform-independent biologically inspired quantitative comparison of normalization methods

BioNavigation: using ontologies to express meaningful navigational queries over biological resources

RNAMute: RNA secondary structure mutation analysis tool

Data mining in situ gene expression patterns at cellular resolution

Adapting support vector machines to predict translation initiation sites in the human genome

Semantic similarity-based validation of human protein-protein interactions

A protein interaction verification system based on a neural network algorithm

Pathway logic helping biologists understand and organize pathway information

MassTRAQ: a fully automated tool for iTRAQ-labeled protein quantification

Biological pathway prediction from multiple data sources using iterative Bayesian updating

Functional modularity in a large-scale mammalian molecular interaction network

Oscillatory dynamics in the mitogen-activated protein kinase cascade

Predicting gene function by combining expression and interaction data

A symbolic approach to the simulation of biochemical models: application to circadian rhythms

iSimBioSys: an 'in silico' discrete event simulation framework for modeling biological systems

Unravelling the murine osteoblast differentiation pathway by network structure analysis using time-series microarray data

A parallel algorithm for clustering protein-protein interaction networks

Discovering functional transcription factor binding from superimposed gene networks

Identifying local gene expression patterns in biomolecular networks

Automated characterization of cellular migration phenomena

Artificial neural networks to predict daylily hybrids

Combinatorial method of splice sites prediction

Computational identification and characterization of Type III secretion substrates

Integration of RNA search methods for identifying novel riboswitch patterns in eukaryotes

Joint genomic and metabolomic analysis of toxic dose-response experiments

Predicting a transcription start site: case study with different genomes

On discriminating a TATA-box from putative TATA boxes: a case study using plant genome

cis-Regulatory element prediction in mammalian genomes

TPR packing analysis and 3D modeling for the HAT domain of human crooked neck protein

Extending the incorporation of superfamily structural information in the process of flexible fitting in 3D-EM

Protein structure prediction using physical-based global optimization and knowledge-guided fragment packing

Protein secondary structure prediction using support vector machine with a PSSM profile and an advanced tertiary classifier

Mining protein sequence motifs representing common 3D structures

Structural genomics analysis of alternative splicing and its application in modeling structures of alternatively spliced variants

GANA-a genetic algorithm for NMR backbone resonance assignment

Creating a protein ontology resource

Efficient sampling of protein folding pathways using HMMSTR and probabilistic roadmaps

Rule clustering and super-rule generation for transmembrane segments prediction

Analysis of four different sets of predictive features for metalloproteins

Maximum sequence alignment fails to predict off-targeted gene regulation by RNAi

Temperature and mutation switches in the secondary structure of small RNAs

Using parallel algorithms for searching molecular sequence databases

Massive multiple sequence alignment of 16S bacterial ribosomal RNAs using ClustalW-Message Passing Interface (MPI) Based on Beowulf Linux system

Improved pairwise alignment of proteins in the Twilight Zone using local structure predictions

Classification method for prediction of multifactorial disease development using interaction between genetic and environmental factors

Mapping SNP association results into type 2 DM pathways-metabolic syndrome as a robust system

ssahaSNP - a polymorphism detection tool on a whole genome scale

Noise propagation in transcriptional cascades

Non-occurring and rare quads in PDB and translated introns from XPro with possible applications in nanostructure design

The synthetic gene designer: a flexible Web platform to explore sequence space of synthetic genes for heterologous expression

ECOME: a simple model for an evolving consumption web

Engineering a 1:2 bio-multiplexer for controlled stem cell differentiation

Engineering multi-signal systems for complex pattern formation

Chemical structure-activity relationship visualization using structure-activity maps

SinicView: an interactive visualization tool for comparison of multiple sequence alignment results

DockingShop: a tool for interactive protein docking

ProteinShop and POSE: bringing robotics and intelligent systems into the field of molecular modeling

Visualization of logic analysis of phylogenetic profiles (LAPP)

The significance of linearity of quantities in electrophoresed and blotted materials demonstrated by BandScan/spl copy/ - an analytical program

Autonomicity - an antidote for complexity?

An approach to distributed interactive simulation and visualization of complex systems using cluster computing

An information fusion approach to controlling complexity in bioinformatics research

An approach to generating and verifying complex scripts and procedures

Clustering gene expression data using continuous Markov models

A comparison of particle swarms techniques for the development of quantitative structure-activity relationship models for drug design

Computing MEG signal sources

Electron microscope tomography of cells and tissues: studying the 3D structure of molecular machines at molecular resolution

PET imaging of tumor integrin expression

Volume measurements in the embryonic zebrafish heart using 4D confocal microscopy

Multispectral multidimensional multiplexed data: the more, the merrier

Image data mining of fruitfly gene expression patterns

Toward automatic annotation of in situ mRNA expression patterns of drosophila embryos

Registering Drosophila embryos at cellular resolution to build a quantitative 3D atlas of gene expression patterns and morphology

Data Mining in situ gene expression patterns at cellular resolution

Content-based tissue image mining

Efficient 3D binary image skeletonization

Digital pathological image analysis and cell segmentation

Cell phenotype classification based on 3D cell image analysis

Current challenges in bioimage database design

Open microscopy environment

Towards interactive exploration of images, meta-data, and analytic results in the open microscopy environment

Structure elucidation and visualization of reconstructed 3D maps of macromolecular complexes

Large-scale drug function prediction by integrating QIS D/sup 2/ and biospice

Drug characteristics prediction

Image data mining of fruitfly gene expression patterns

Content Provider	IEEE Xplore Digital Library
Author	Peng, H.
Copyright Year	2005
Description	Author affiliation: Lawrence Berkeley Nat. Lab., California Univ., Berkeley, CA, USA (Peng, H.)
Abstract	Understanding the spatio-temporal gene expression patterns is critical in studying genes roles and their complicated relationships. With the availability of high-resolution digital images of in situ mRNA hybridization expression pattern of Drosophila embryos collected through both the Berkeley Drosophila Transcriptional Network Project (BDTNP) and the Berkeley Drosophila Genome Project (BDGP), we will be able to answer a series of interesting questions, e.g., what are the variations of gene expression patterns, what are the patterning process of gene expression, etc. To achieve these goals at a large scale, it is extremely important to automate the image mining and informatics processes of embryogenesis expression patterns. We developed computer programs to register, compare and analyze these spatio-temporal pattern images. In this talk, I will review four projects on image mining of fruitfly embryo gene expression patterns: (a) Gaussian mixture model based embryonic expression pattern extraction and comparison, (b) Gene expression pattern clustering using novel MSTCUT and probabilistic ensemble clustering techniques, (c) Surface/volume models for 3D modeling and registration of early embryos, and (d) A manifold learning method for spatio-temporal registration of 3D gene expression patterns and reconstruction of the embryonic developmental time series.
Sponsorship	IEEE Comput. Soc. Tech. Comm. on Bioinformatics
File Size	69870
File Format	PDF
ISBN	0769524427
DOI	10.1109/CSBW.2005.74
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2005-08-08
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Embryo Image analysis Digital images Genomics Large-scale systems Registers Data mining Gene expression Bioinformatics Informatics
Content Type	Text
Resource Type	Article

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