Sequencing Informatics

Next Generation sequencing technology offers unparalleled opportunities for biological discoveries, translational discoveries, and personalized medicine.

NYULMC has recently acquired Illumina GA (Solexa) and Rosche 454 instruments and several research groups utilize this technology at NYU for a variety of studies that include:

• De novo genome assembly and re-sequencing
• RNA seq (digital gene expression)
• miRNA studies
• CNV studies
• Splice variation studies
• Epigenetics
• Microbiomics
• Chip seq studies

Several of the above projects address fundamental biological questions, others are translational, and others clinical.
The Genome Technology Center is handling the assay part of these studies, while CHIBI faculty and staff are handling both low-level (instrument-specific, or “upstream”) informatics as well as higher-level (hypothesis testing and generation oriented, or “downstream informatics”). CHIBI also has the scientific responsibility for the high-end computing needed to process the genomic data.

Contacts per specialty area:

Upstream:

• De novo genome assembly and re-sequencing : Alexander Alekseyenko and Jinhua Wang
• RNA seq and miRNA studies: Jinhua Wang, Stuart Brown, Yuval Kluger; external consultant: Chris Mason Ph.D
• CNV studies & Splice variation studies: Jinhua Wang, Stuart Brown
• Epigenetics & Chip seq studies: Stuart Brown
• Microbiomics: Alexander Alekseyenko

Downstream:

• Phenotype-genotype predictive and diagnostic modeling, biomarker discovery, personalized medicine high dimensional analysis: Yuval Kluger, Alexander Aleksyeneko, Jinhua Wang, Constantin Aliferis, Alexander Statnikov