Sergey Nuzhdin

Summary

Affiliation: University of Southern California
Country: USA

Publications

  1. pmc Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin/TOR and associated phenotypes in Drosophila melanogaster
    Sergey V Nuzhdin
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    BMC Genomics 10:124. 2009
  2. pmc Promises and limitations of hitchhiking mapping
    Sergey V Nuzhdin
    Program in Molecular and Computation Biology, University of Southern California, Los Angeles 90089, United States Electronic address
    Curr Opin Genet Dev 23:694-9. 2013
  3. pmc Genotype-phenotype mapping in a post-GWAS world
    Sergey V Nuzhdin
    University of Southern California, Program in Molecular and Computational Biology, Department of Biology, Los Angeles, CA 90089, USA
    Trends Genet 28:421-6. 2012
  4. pmc Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners
    Peter L Chang
    Molecular and Computational Biology, University of Southern California, 1050 Childs Way, RRI 201, Los Angeles, CA 90089 2910, USA
    Genome Biol 11:R125. 2010
  5. pmc Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing
    Peter L Chang
    Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    BMC Genomics 12:364. 2011
  6. pmc RNA-seq: technical variability and sampling
    Lauren M McIntyre
    Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
    BMC Genomics 12:293. 2011
  7. pmc Allele-specific expression assays using Solexa
    Bradley J Main
    Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    BMC Genomics 10:422. 2009
  8. pmc Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum
    Jennifer A Brisson
    Section of Ecology and Evolution, University of California at Davis, Davis, CA, USA
    BMC Genet 10:22. 2009
  9. pmc Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome
    Jason G Mezey
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    BMC Evol Biol 8:2. 2008
  10. pmc The strength of transcription-factor binding modulates co-variation in transcriptional networks
    Sergey V Nuzhdin
    University of Southern California, Program in Molecular and Computational Biology, Los Angeles, CA 90089, USA
    Trends Genet 26:51-3. 2010

Detail Information

Publications14

  1. pmc Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin/TOR and associated phenotypes in Drosophila melanogaster
    Sergey V Nuzhdin
    Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
    BMC Genomics 10:124. 2009
    ..We focus on the latter problem by describing genetic variation in transcript levels of genes in the InR/TOR pathway among 72 Drosophila melanogaster genotypes...
  2. pmc Promises and limitations of hitchhiking mapping
    Sergey V Nuzhdin
    Program in Molecular and Computation Biology, University of Southern California, Los Angeles 90089, United States Electronic address
    Curr Opin Genet Dev 23:694-9. 2013
    ..We propose several developments required for sensible data analyses that will fully realize the great power of the HH technique, and outline ways of moving forward...
  3. pmc Genotype-phenotype mapping in a post-GWAS world
    Sergey V Nuzhdin
    University of Southern California, Program in Molecular and Computational Biology, Department of Biology, Los Angeles, CA 90089, USA
    Trends Genet 28:421-6. 2012
    ..The SEM framework can be used to quantitate a GRN, evaluate its consistency across environments or sexes, identify the differences in GRNs between species, and annotate GRNs de novo in non-model organisms...
  4. pmc Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners
    Peter L Chang
    Molecular and Computational Biology, University of Southern California, 1050 Childs Way, RRI 201, Los Angeles, CA 90089 2910, USA
    Genome Biol 11:R125. 2010
    ..Three stages of the allopolyploidization process--parental species divergence, hybridization, and genome duplication--have been well analyzed. The last stage of evolutionary adjustments remains mysterious...
  5. pmc Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing
    Peter L Chang
    Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    BMC Genomics 12:364. 2011
    ..We have used deep RNA sequencing to gain insight into how the Drosophila sex hierarchy generates somatic sex differences, by examining gene and transcript isoform expression differences between the sexes in adult head tissues...
  6. pmc RNA-seq: technical variability and sampling
    Lauren M McIntyre
    Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
    BMC Genomics 12:293. 2011
    ..However, strategies for dealing with technical variation will differ depending on the magnitude. The size of technical variance, and the role of sampling are examined in this manuscript...
  7. pmc Allele-specific expression assays using Solexa
    Bradley J Main
    Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
    BMC Genomics 10:422. 2009
    ..While ASE is commonly measured via relative fluorescence at a SNP, next generation sequencing provides an opportunity to measure ASE in an accurate and high-throughput manner using read counts...
  8. pmc Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum
    Jennifer A Brisson
    Section of Ecology and Evolution, University of California at Davis, Davis, CA, USA
    BMC Genet 10:22. 2009
    ..Because introductions can cause population bottlenecks, we hypothesized that U.S. populations harbor lower levels of nucleotide diversity and higher levels of LD than native populations...
  9. pmc Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome
    Jason G Mezey
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
    BMC Evol Biol 8:2. 2008
    ..Clusters where expression evolution of each gene is not independent of their neighbors are important units for understanding transcriptome evolution...
  10. pmc The strength of transcription-factor binding modulates co-variation in transcriptional networks
    Sergey V Nuzhdin
    University of Southern California, Program in Molecular and Computational Biology, Los Angeles, CA 90089, USA
    Trends Genet 26:51-3. 2010
    ..Here we integrate two publicly available data sets in Drosophila melanogaster, as well as conduct novel analyses, to address these questions...
  11. doi request reprint Population genomic analysis of Tunisian Medicago truncatula reveals candidates for local adaptation
    Maren L Friesen
    Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
    Plant J 63:623-35. 2010
    ..These populations provide a strong resource for genome-wide association studies...
  12. pmc Does segregating variation in sexual or microhabitat preferences lead to non-random mating within a population of Drosophila melanogaster?
    Brad R Foley
    Department of Molecular and Computational Biology, University of Southern California, CA 90089, USA
    Biol Lett 6:102-5. 2010
    ..We detected directional selection at loci across the genome, but are unable to provide support for differential male success because of variation in female genotype...
  13. pmc Contrasting patterns of sequence evolution at the functionally redundant bric à brac paralogs in Drosophila melanogaster
    Ryan D Bickel
    Department of Biological Sciences, University of Southern California, Los Angeles, 90089, USA
    J Mol Evol 69:194-202. 2009
    ..Thus, the two paralogs are evolving under different selective regimes in the same natural population, illuminating the different evolutionary trajectories of partially redundant duplicate genes...
  14. doi request reprint Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils
    Thomas L Turner
    Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA
    Nat Genet 42:260-3. 2010
    ..lyrata indicates parallel differentiation of the same polymorphism at one locus, confirming ecological adaptation, and different polymorphisms at two other loci, which may indicate convergent evolution...

Research Grants2

  1. Nucleotide polymorphisms responsible for expression variation in Drosophila
    Sergey Nuzhdin; Fiscal Year: 2009
    ..These studies will contribute to building a pathway-minded description of complex character variation. They will shed light on the genetic architecture of transcript level variation in nature. ..
  2. QUANTITATIVE TRAIT LOCI RELATED TO DROSOPHILA SPECIATION
    Sergey Nuzhdin; Fiscal Year: 2004
    ..This comprehensive assessment of the genetics of several traits will further our understanding of the genetics of speciation. ..