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Fast optimal leaf ordering for hierarchical clustering.
Automated constraint-based nucleotide sequence selection for DNA computation.
Negative information for motif discovery.
Lineage-based identification of cellular states and expression programs.
GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data.
Blazing pathways through genetic mountains.
Transcriptional regulatory networks in Saccharomyces cerevisiae.
Continuous representations of time-series gene expression data.
Rapid haplotype inference for nuclear families.
Design and implementation of computational systems based on programmed mutagenesis.
Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape.
An integrated model of multiple-condition ChIP-Seq data reveals predeterminants of Cdx2 binding.
Universal count correction for high-throughput sequencing.
Interactions between chromosomal and nonchromosomal elements reveal missing heritability.
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding.
Training Program in Computational Biology(RMI)
MIT EECS/Whitehead/Broad Training Program in Computational Biology(RMI)
Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding.
Predicting gene expression in massively parallel reporter assays: A comparative study.
Accurate eQTL prioritization with an ensemble-based framework.
Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.
Differential chromatin profiles partially determine transcription factor binding.
A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction.
High resolution discovery of chromatin interactions.
Molecular Biology Computational