GersteinLab.org Overview

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Presentation transcript:

GersteinLab.org Overview Biological Knowledge Representation, Literature Mining, Genomic Privacy Genome Structural Variation & Personal Genomics Human Genome Annotation & Disease Genomics Networks of Genes & Protein Pathways Macromolecular Structures & Motions Big Data Analysis & Mining Simul- ation & Modeling

Annotating the Human Genome: Comparative & Functional [Nat. Rev. Genet. (2010) 11: 559] [Science 330:6012] Annotating the Human Genome: Comparative & Functional

Recasting Genome Annotation as Networks: Comparing Proximal & Distal Networks [ Gerstein et al. Nature (in press, '12) ]

Methods to Find Variants (SVs) in Personal Genomes 1. Paired ends Deletion Reference Mapping Genome Reference Sequenced paired-ends 2. Split read 3. Read depth Deletion Deletion Reference Reference Genome Genome Read Reads Mapping Mapping Read count Reference Zero level [Snyder et al. Genes & Dev. ('10)]

Identification of non-coding candidate drivers amongst somatic variants, using genome annotation & patterns of natural variation [Khurana et al., Science (‘13)]

Biological Data Science: Protecting Genomic Privacy from linking attacks [Harmanciet al. Nat. Meth. (in revision)]

to characterize deleterious variants Predicting Allosterically-Important Residues at the Surface via simulation, to characterize deleterious variants PDB: 3PFK Adapted from Clarke*, Sethi*, et al (2016) Structure