Computer Science, Machine Learning, Language Technologies, Computational Biology | School of Computer Science | Carnegie Mellon

GenAMap : An integrated visualization and analytic platform for structured eQTL and GWAS Analysis.
Baycis : a generalized, hierarchical HMM for transcription factor binding site discovery in Metazoan genomes

CSMET : a multi-resolution mixture of evolutionary tree approach to transcription factor binding site detection for aligned genomes in eukaryotes

DISCOVER : a discriminative, conditional random field model for factor binding site discovery in Metazoan genomes

IMM-PGE : IMM-PGE focuses on the development of accurate and automatic image analysis systems to facilitate efficient mining of complex temporal-spatial mRNA patterns, essential for functional genomics and regulatory network inference in higher organisms.

mStruct : A New Admixture Model for Inference of Population Structure in Light of Both Genetic Admixing and Allele Mutations

N/w modelling : Developing new statistical formalisms and computational methodologies for modeling and inference the semantic underpinnings of network entities, and investigating how these aspects influence the network topology and its temporal evolution during biological and sociological processes. It also studies a number of yet unexplored topics such as discriminative learning of network structures, recovering temporally evolving network sequences, and related theoretical issues.

SPECTRUM : SPECTRUM is a program for jointly inferring population structure and recombination events using multi-locus SNP haplotypes.

KELLER : A kernel-reweighted logistic regression method (KELLER) for reverse engineering the dynamic interactions between genes based on their time series of expression values.

TESLA:TESLA is software for estimating time-varying network from time-series of nodal attributes using the l1-regularized total-variation penality. It is appropriate for estimating the structure of networks with sharp structual changes.

GFlasso : A regularized-regression method for discovering genotypes (inputs) influencing multiple correlated traits (outputs) in an association analysis of a quantitative trait network.
Haploi : A haplotype inference program for multi-population data.
Structured Input-output Lasso : Detecting SNPs associated with traits considering both genome (input) and transcriptome (output) structures
Treegl : Estimates multiple gene networks corresponding to cell types related by a tree-genealogy based on only a few samples from each cell type.

SPEX2

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TVNViewer : An interactive visualization tool for exploring networks that change over time or space.
StructHDP : automatically inferr the population structure and number of clusters from a sample of admixed genotype data.
MMTM : scalable mixed-membership network community detection algorithm, based on a triangular representation of the network.
SPHINX : Detecting non-linear/linear SNP-SNP interactions with piecewise linear model
Dynamic Traits : Nonparametric autoregressive model for dynamic trait association analysis

(C) SAILING Lab, 2008 Copyright of published papers held by publishing bodies in question