Biomedical Research
Cellular Multicellular Systems
Comparative Genomics
Data Mining
Evolution and Phylogenetics
Functional Genomics
High Content Analysis
High Performance Computing
Microarray Analysis
Other
Pathways Networks Systems Biology
Pattern Recognition
Promoter Analysis
Protein Structure Analysis
RNAi Analysis
Sequence Alignment
SNPs and Haplotyping
Synthetic Biological Systems
Visualization

High-throughput Computational and Experimental Biology Strategies for Identifying Tumor Expressing CAMs

State-Space Model with Time Delays for Genetic Regulatory Networks

Nonlinear Modeling on Protein Kinase C(PKC)-ε Negative Regulation of Stress Fibers in Oncogenically Transformed Cells

Analysis of Population Dynamics in Beta-cell Destruction Lead to Identification of Novel Candidate Genes for Type 1 Diabetes

Exploring Genomic Context Patterns for Rhodobacter sphaeroides in the HERBE Knowledge Discovery Environment

RepeatAssembler: A Package for Annotation of Full-length Repetitive DNA Sequences in Fungal Genomes

Search-space Reduction of a Non-redundant Peptide Database Using De novo Sequencing

Automated and Rapid Bacterial Identification Using LC-Mass Spectrometry with a Relational Database Management System

Development of a Knowledge-based Multi-scheme Cancer Microarray Data Analysis System

FigSearch: A Figure Legend Indexing and Classification System

GeneTIDE: Terra Incognita Discovery Endeavor - Mining ESTs and Expression Data to Elucidate Known and De Novo GeneCards Genes

ProtExt, a Web-based Protein-protein Interaction Extraction System for PubMed Abstracts

Biclustering Gene-feature Matrices for Statistically Significant Patterns

Recognition of Exon/Intron Boundaries Using Dynamic Ensembles

Probabilistic Consistency Analysis for Gene Selection

Automating the Biological Data Collection Process with Agents

An Intelligent Digital Library System for Biologists

A New Approach to Clustering Biological Data Using Message Passing

Ontology Specific Data Mining Based on Dynamic Grammars

Application of Relief-F Feature Filtering Algorithm to Application of Relief-F Feature Filtering Algorithm to Selecting Informative Genes for Cancer Classification Using Microarray Data

Probability Profile Method - New Road for Data Analysis in Tandem Mass Spectrometry

Assigning Gene Ontology (GO) Categories to Yeast Genes Using Text-based Supervised Learning Methods

PPM-chain Efficient and Precise Tool for De Novo Peptide Identification in Tandem Mass Spectrometry

Comparative Genomic Analysis of Cyclin-Dependent Kinases and the Evolution of the RNAP II CTD Kinases

Embedded Computation of Maximum-Likelihood Phylogeny Inference Using Platform FPGA

Gene Lengths and Alternative Transcription of Fruit Fly

Protein Classification into Domains of Life Using Markov Chain Models

EcMLST: an Online Database for Multilocus Sequence Typing of Pathogenic Escherichia coli

On Complexity Measures for Biological Sequences

A Markov Model Based Gene Discrimination Approach in Trypanosomes

Predicting Gene Ontology Annotations from Sequence Data using Kernel-based Machine Learning Algorithms

Deriving a Novel Codon Index by Combining Period-3 and Fractal Features of DNA Sequences

Using Stem-loop Characteristics as Means to Locate Structural RNA Genes

RNA Gene Prediction via Positive Sample Only Learning (PSOL)

Quantitative Analysis of Membrane Protein Localization and Signaling

The SSAHA Trace Server

Agent-oriented Approach to DNA Computing

Accelerating the Kernels of BLAST with an Efficient PIM (Processor-In-Memory) Architecture

Qvalue Method May Not Always Control False Discovery Rate in Genomics Applications

Application of a Genetic Algorithm to the Classification of Renal Cell Carcinoma

Mining Estrogen Microarray Data: An approach Using Contrast Data Analysis

A Comprehensive Genomics and Proteomics Data Analysis and Biological Function Interpretation System

A Java Program to Create Simulated Microarray Images

Inferring Genetic Networks from Microarray Data

ChipQC: A Microarray Chip Quality Control Tool

Extracting Characteristic Patterns from Genome Wide Expression Data by Non-negative Matrix Factorization

Imputation of Missing Values in DNA Microarray Gene Expression Data

Disease Gene Explorer: Displaying Disease Gene Dependency by Combining Bayesian Networks with Clustering

DNA Microarray Image Analysis Using Active Contour Model

Meanshift Clustering for DNA Microarray Analysis

The Dynamic Range of Gene Expressions Depend on Their Ontology

Subspace Clustering for Microarray Data Analysis: Multiple Criteria and Significance Assessment

Comparative Analysis of Gene Expression and DNA Copy Number Data for Pancreatic and Breast Cancers Using an Orthogonal Decomposition

High-throughput Microarray-based Genotyping

Computational Methods for Predicting Intramolecular G-quadruplexes in Nucleotide Sequences

An Investigation of Gene Recovery and Biases Observed in Two Reduced Representation Sequencing Techniques when Applied to the Genome of Zea mays

Sequences Meet Biology: Integration of Sequences as Database Objects in Mouse Genome Informatics

Navigating through the Biological Maze

How Biological Source Capabilities May Affect Data Collection

Labeling and Enhancing Life Sciences Links

A New Hierarchical Method for Identification of Dynamic Regulatory Pathways from Time-series DNA Microarray Data

Boosted PRIM with Application to Searching for Oncogenic Pathways of Cancer

Genetic Algorithm for Inferring Time Delays in Gene Regulatory Networks

A Knowledge Base for Computational Pathway Reconstruction

In Silico Construction of the Carbon Fixation Pathway in Synechococcus sp. WH8102

A Finite Model Theory for Biological Hypotheses

Functional Modules from Protein Networks of Kinome and Cell Cycle in Saccharomyces cerevisiae

Bacillus subtilis Protein Interaction Network Analysis

Dynamical Robustness in Gene Regulatory Networks

An Algorithm for Reconstruction of Markov Blankets in Bayesian Networks of Gene Expression Datasets

Synchronized Oscillations and Chaos in Coupled Genetic Repressilators

Inference of Gene Regulatory Network Based on Module Network Model with Gene Functional Classifications

A Graph Analysis Method to Detect Metabolic Sub-networks Based on Phylogenetic Profile

Parallel Extreme Pathway Computation for Metabolic Networks

Computational Construction of Nitrogen Assimilation Pathway in Cyanobacteria Synechococcus sp. WH8102

Pathway Mapping With Operon Information, an Integer-programming Method

Analysis of Signaling Pathways in Human T-Cells Using Bayesian Network Modeling of Single Cell Data

An Efficient Bayesian Method for Biological Pathway Discovery from High-throughput Experimental Data

Applying Two-level Simulated Annealing on Bayesian Structure Learning to Infer Genetic Networks

An Efficient Algorithm for Unique Signature Discovery on Whole-genome EST Databases

VirusFinder: A Web-based Virus Identification System Using Viral Nucleotide Signatures

Finding Cancer Biomarkers from Mass Spectrometry Data by Decision Lists

Incremental and Decremental Least Squares Support Vector Machine and Its Application to Drug Design

A Prediction Model for the Drug Efficacy of Interferon in CHC Patients Based on SNPs

RNA Motif Search Using the Structure to String (STR2) Method

PRUNER: Algorithms for Finding Monad Patterns in DNA Sequences

CUBIC: A Program for Binding Sites Prediction

BioSPRINT: Classification of Intron and Exon Sequences Using the SPRINT Algorithm

A Hidden Markov Model for Gene Function Prediction from Sequential Expression Data

Using Enhancing Signals to Improve Specificity of Ab Initio Splice Site Sensors

SPVS: A Similar Parikh Vector Searching Algorithm for Protein Sequence Analysis

A Liner-time Algorithm for Locating All Tandem Repeat

Selection of Putative Cis-regulatory Motifs through Regional and Global Conservation

Computational Analysis and Classification of p53 Mutants According to Primary Structure

In Silico Prediction of Surface Residue Clusters for Enzyme-substrate Specificity

Comparing 3D Protein Structures Similarity by Using Fractal Features

Structural Analysis of FGFR1 Kinase Activation through Molecular Dynamics Simulation

Automatic Prediction of Functional Site Regions in Low Resolution Protein Structures

BPAP: A Computational Tool for Whole Genome Annotation and Analysis

Secondary Structure Assignment Based on the Delaunay Tessellation of Protein Structures

Molecular Modeling of Full-length OxyR from Shewanella oneidensis MR-1 and Molecular Dynamics Studies of the Activation Domain

A Combinatorial Method for Protein Loop Prediction

Prediction of Functional Sites by Analysis of Sequence and Structure Conservation

A Novel Computational Framework for Structural Classification of Proteins Using Local Geometric Parameter Matching

Large-scale Testing of Chemical Shift Prediction Algorithms and Improved Machine Learning-based Approaches to Shift Prediction

Contraction Graphs: A Unified Representation and Analysis of RNA Secondary Structure

Identifying MicroRNAs in Plant Genomes

Fine-grain Matrix Graph Representation for Predicting Mutations Leading to Conformational Rearrangements in Small RNAs

MUSCLE

A New Hardware Architecture for Genomic Sequence Alignment

DASHfaster: Accurate Sequence Alignment

SUPERCONTIGS: A Contig Scaffolding Tool

Multiple Alignment of Rearranged Genomes

A Novel Genome Assembler: Using K-mers to Indirectly Perform N-Squared Comparisons in O(N)

Association tests and estimation of haplotype frequencies and of penetrance-related parameters in a case-control study

Designing Synthetic Biological Systems by Multiple Time Scale Networks

Molecular Level Data Interpretation and Interaction Pathway Modeling Using 3-D Visualization

LigPro: Rapid Inspection of Protein-ligand Interactions

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