Joshua S Bloom
Affiliation: Princeton University
- 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...
- 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...
- 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....
- 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...
- Quantitative proteomics reveals direct and indirect alterations in the histone code following methyltransferase knockdownMariana D Plazas-Mayorca
Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
Mol Biosyst 6:1719-29. 2010..Our results provide new insights into the intra- and inter- histone cross-regulation of histone K9 methylation and its potential downstream gene targets...
- Finding the sources of missing heritability in a yeast crossJoshua S Bloom
Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08540, USA
Nature 494:234-7. 2013..These results substantially advance our understanding of the missing heritability problem and have important implications for future studies of complex and quantitative traits...
- Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversityErik C Andersen
Lewis Sigler Institute for Integrative Genomics, Princeton University, New Jersey, USA
Nat Genet 44:285-90. 2012..These sweeps, which we hypothesize to be a result of human activity, have drastically reshaped the global C. elegans population in the recent past...