Affiliation: Princeton University
- A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arraysZia Khan
Department of Computer Science, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
Bioinformatics 25:1609-16. 2009....
- Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MSZia Khan
Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
Mol Syst Biol 8:602. 2012..Our results provide the first analysis of the relative contribution of cis-acting and trans-acting regulatory differences to protein expression divergence between yeast species...
- Accurate proteome-wide protein quantification from high-resolution 15N mass spectraZia Khan
Lewis Sigler Institute for Integrative Genomics, Princeton University, Washington Rd, Princeton, NJ 08544, USA
Genome Biol 12:R122. 2011..Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods...
- Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarraysJoshua S Bloom
Lewis Sigler Institute of Integrative Genomics, Princeton University, New Jersey, USA
BMC Genomics 10:221. 2009..High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression...
- Protein quantification across hundreds of experimental conditionsZia Khan
Department of Computer Science, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
Proc Natl Acad Sci U S A 106:15544-8. 2009..We demonstrate the scalability of these techniques by applying them to a large dataset that comprises a total of 472 experimental conditions and replicates...
- Global secretome analysis identifies novel mediators of bone metastasisMario Andres Blanco
Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
Cell Res 22:1339-55. 2012..Overall, our study has uncovered several new secreted mediators of bone metastasis and therefore demonstrated that secretome analysis is a powerful method for identification of novel biomarkers and candidate therapeutic targets...
- Stable Isotope Labeling of Phosphoproteins for Large-scale Phosphorylation Rate DeterminationRosalynn C Molden
Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
Mol Cell Proteomics 13:1106-18. 2014..The data have been deposited to the ProteomeXchange with the identifier PXD000680. ..
- Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonizationManav Korpal
Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
Nat Med 17:1101-8. 2011..Overall, these findings suggest a pleiotropic role of miR-200s in promoting metastatic colonization by influencing E-cadherin-dependent epithelial traits and Sec23a-mediated tumor cell secretome...