Project Websites

You can read more about our Research or go to the Publications page.


High-throughput genomics High-throughput genomics Biological networks Biological networks Transcription regulation Transcription regulation Human disease Human disease Genome rearrangements Genome rearrangements Evolution Evolution
 
recycler Recycler - detecting plasmids from de novo assembly graphs
High-throughput genomics
RichMind RichMind - Analysis of enrichment within neuroimaging findings
Docks DOCKS - A software for finding a compact set of k-mers that hits every L-long sequence
High-throughput genomics
Transcription regulation
Adeptus Adeptus - A database of annotated disease expression profiles transformed into a unified suite, and tools for multi-disease analysis
High-throughput genomics
Transcription regulation
Biological networks
ElemeNT ElemeNT - An interactive tool for rapid and convenient detection of core promoter elements within a given sequence
Transcription regulation
twigs TWIGS - Three-Way module Inference via Gibbs Sampling.
High-throughput genomics
Transcription regulation
Biological networks
barcode BARCODE - A fast lossless read compression tool based on Bloom filters.
High-throughput genomics
ModMap ModMap - Detecting maps of modules by simultaneous analysis of two biological networks.
Biological networks
High-throughput genomics
Transcription regulation
ShortCake ShortCAKE - A software for designing the shortest DNA sequence to cover all k-mers, exploiting reverse complementarity
High-throughput genomics
Transcription regulation
Fame FAME - A tool for Functional Assignment to MicroRNAs via Enrichment
High-throughput genomics
Transcription regulation
Dicer Dicer - A tool for advanced analysis of differential co-expression (DC) case-control gene expression data
High-throughput genomics
Transcription regulation
Biological networks
Morph Morph - A webtool and software for ranking candidate genes in pathways.
Biological networks
High-throughput genomics
RAP RAP (short for Rank, Align, PWM) is a software for inferring binding site motifs from protein binding microarrays (PBMs).
High-throughput genomics
Transcription regulation
HiDe HiDe - A software package for inferring highways of horizontal gene transfer in the evolutionary history of a set of species.
Evolution
ModEnt ModEnt - A tool that reconstructs gene regulatory networks from high throughput experimental data.
High-throughput genomics
Transcription regulation
Biological networks
Stack STACK - A website for analyzing statistical associations among cancer karyotypes. Associations between cancer types and aberrations can be studied, filtered and evaluated.
Human disease
Genome rearrangements
Expander EXPANDER - A Java-based tool for analysis of gene expression data, including a large scale of capabilities such as clustering, visualizing, biclustering and performing downstream analysis of clusters and biclusters such as functional enrichment and promoter analysis. In particular, Expander can analyze groups of genes for enrichment of transcription factor binding sites in their promoters.
High-throughput genomics
Transcription regulation
Biological networks
Allegro ALLEGRO - A user-friendly software tool for simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3' UTRs) and genome-wide expression dataset(s). Its output is the set of motifs found, and for each motif the set of genes it regulates and their shared expression pattern.
Transcription regulation
High-throughput genomics
Amadeus AMADEUS - A user-friendly Java software for finding known and novel motifs in DNA sequences. Given a set of co-regulated genes, Amadeus searches for short over-represented motifs in their promoter (or 3' UTR) sequences, which may represent binding sites of transcription factors (or microRNAs) that regulate the given genes.
Transcription regulation
High-throughput genomics
Samba SAMBA - A framework for dissection of complex biological systems using analysis of a highly diverse collection of genome-wide datasets, including gene expression, protein interactions, growth phenotype data and transcription factor binding.
High-throughput genomics
Biological networks
Transcription regulation
Prima PRIMA - PRomoter Integration in Microarray Analysis - a program for finding transcription factors (TFs) whose binding sites are enriched in a given set of promoters.
Transcription regulation
High-throughput genomics
Spike SPIKE - (previously SHARP) A signaling pathway knowledge engine. An interactive software environment that graphically displays biological interaction networks, allows dynamic layout and navigation through these networks, and enables the superposition of DNA microarray data on interaction maps.
Biological networks
Matisse MATISSE - A tool for joint analysis of interaction networks and gene expression data.
High-throughput genomics
Biological networks
Torque TORQUE - Given a complex (set of proteins) for a query species, Torque seeks a matching set of proteins of a target species that are sequence-similar to the query proteins and span a connected region of the target network. It allows both deletions (query proteins that have no match in the output) and insertions (proteins in the output that do not match any query input and are inserted to keep the output connected).
Biological networks
Gevalt GEVALT - GEnotype Visualization and ALgorithmic Tool - An integrated software for genotype analysis.
Human disease
Rat RAT - A software for rapid association tests.
Human disease
Psat PSAT - A software for evaluating the significance of association scores in whole-genome cohorts with stratification.
Human disease
MetaReg MetaReg - A tool for modeling of biological systems
Biological networks
High-throughput genomics
Transcription Regulation
cofactors Linking transcription factors and chromatin modifiers (Steinfeld et al., Nature Genetics 2007)
High-throughput genomics
Transcription Regulation
SIMBA SIMBA - Understanding genome-wide experiments at the system level using integrative analysis of large-scale biological compendia.
High-throughput genomics
Transcription Regulation
Biological networks
Cisprof Cisprof - Evolutionary mechanisms underlying conservation and evolvability in regulatory networks.
Evolution
Transcription Regulation
PREVO Promoter evolution (PREVO) - An analysis of the network of selection forces in the evolution of yeast cis-regulation
Evolution
Transcription Regulation
HYDEN HYDEN - A software for designing degenerate primers.
PIVOT PIVOT - Java-based protein interactions visualization tool.
Biological networks
GREAL GREAL - software for the graph realization Problem.
Human disease