Nuzhdin Lab Publications...

Submitted/In Review

Chang, P. L., W. Leong, P. Zhang, M. L. Friesen. Population genomics of pooled

        Arabidopsis lyrata genome data show gene network evolution patterns

        consistent with flies, worms and yeast. PLoS ONE.

Vu, W. T., P. L. Chang, K. S. Moriuchi, M. L. Friesen. Genetic variation of            

        transgenerational plasticity on seed transcriptome and offspring early    

        response to salinity. Current Biology.

Main, B. J., H. S. Jang, A. D. Smith, S. V. Nuzhdin. Transcription start site turnover

        in Drosophila using CAGE. PLoS Genetics.

Moriuchi, K. S., M. L. Friesen, W. T. Vu, B. J. Main, M. A. Cordeiro, M. Badri,

        S.V. Nuzhdin, D. R. Cook, S. Y. Strauss, E. von Wettberg. Parental

        environmental effects alter phenotypic integration. New Phytologist.

Marjoram P., A. Zubair, S. V. Nuzhdin. Post-GWAS: Where next? More samples,         

        more SNPs or more biology? Heredity.

Cordeiro, M. A., K. S. Moriuchi, T. D. Fotinos, K. E. Miller, S. Arraouadi, K. Zribi, M.

        Badri, M. L. Friesen, S. V. Nuzhdin, S. Y. Strauss, E. von Wettberg, D. R. Cook.           

        Germination and early seedling root growth reveal patterns for salinity    

        adaptation in the annual legume Medicago truncatula. New Phytologist.

Friesen, M. L., E. J. B. von Wettberg, M. Badri, K. S. Moriuchi, F. Barhoumi,  S.    

        Cuellar-Ortiz, P. L. Chang, M. A. Cordeiro, W. T. Vu, S. Arraouadi, N. Djébali, K.    

        Zribi, Y. Badri, S. S. Porter, M. E. Aouani, D. R. Cook, S. Y. Strauss, S. V.

        Nuzhdin. Adaptation to saline soils in Tunisian populations of Medicago    

        truncatula. Proc. Natl. Acad. Sci. USA.

Graze, R. M., L. M. McIntyre, A. M. Morse, S. V. Nuzhdin, M. L. Wayne. The role of

        chromosome in the evolution of gene regulation, cis and trans on the X. PLoS

        Genetics.

Campo D., C. Fjeldsted, T. Souaiaia, J. Kao, K. Lehmann, S. V. Nuzhdin.    

        Genome sequencing of two North American Drosophila melanogaster

        population reveals differentiation and positive selection. Molecular Ecology.

Longcore, T., D. Pentcheff, S. V. Nuzhdin, C. Rich. Artificial night lighting as global

        change: processes and prospects. TREE (pending revisions).

Moriuchi, K. S., M. A. Cordeiro, M. L. Friesen, M. Badri, W. T. Vu, B. J. Main, S.

        Arraouadi, M. E. Aouani, S. V. Nuzhdin, D. R. Cook, S. Y. Strauss, Eric von

        Wettberg. Parental environmental effects on local adaptation, phenotypic

        integration, and mechanisms of salinity tolerance.

Dunham J. P., M. L. Friesen. A cost-effective method for high-throughput

        construction of  Illumina sequencing libraries.

Sze S-H, J. P. Dunham, B. Carey, P. L. Chang, F. Li, R. M. Edman, C. Fjeldsted, M. J.

        Scott, S. V. Nuzhdin, A. M. Tarone. A de novo transcriptome assembly of

        Lucilia sericata (Diptera: Calliphoridae) with predicted alternative splices,

        single nucleotide polymorphisms and transcript expression extimates. Insect

        Molecular Biology 21(2): 205-21.

Winbush, A., D. Reed, P. L. Chang, S. V. Nuzhdin, L. C. Lyons, M. N. Arbeitman.

        Identification of gene expression changes associated with long-term memory

        of courtship rejection in Drosophila males. G3 (in press).

Ardekani, S., A. Biyani, J. Dalton, J. Saltz, M. Arbeitman, J. Tower, S. V. Nuzhdin, S.

        Tavare. Three dimensional tracking and behavior monitoring of multiple fruit

        flies. J. R. Soc. Lond. Interface (in press).

Remolina, S., P. L. Chang, J. Leips,  S. V. Nuzhdin, K. A. Hughes. Genome evolution

        under selection for delayed reproduction. Evolution (in press).

Tarone, A. M., L. M. McIntyre, L. G. Harshman, S. V. Nuzhdin. Genetic variation in

        the Yolk protein expression network of Drosophila melanogaster: Sex biased

        negative correlations with longevity. Heredity 109: 226–234.

Nuzhdin, S. V., M. L. Friesen, L. M. McIntyre. Genotype-phenotype mapping in a

        post GWAS world. Trends in Genetics 28: 421-426.

Thomas, A., P.-J. Lee, J. Dalton, K. J. Nomie, L. Stoica, M. Costa-Mattioli, P. L. Chang,

        S. V. Nuzhdin, M. N. Arbeitman, H. A. Dierick. A versatile method for cell-

        specific profiling of translated mRNAs in Drosophila. PLoS One 7: e40276.

Graze, R. M., L. L. Novelo, J. M. Fear, G. Casella, S. V. Nuzhdin, L. M. McIntyre.

        Allelic imbalance in Drosophila hybrid heads: exons, isoforms and evolution.

        Mol. Biol. Evol 29: 1521–1532.

Saltz, J. B., E. T. Alicuben, J. Grubman, M. Harkenrider, N. Megowan and S. V.

        Nuzhdin. Complex effects of group genetic diversity on larval viability in

        Drosophila melanogaster imply key role of maternal decision-making.

        Molecular Ecology 9: 2270 -2281.

Ghiselli, F., L. Milani, P. L. Chang, D. Hedgecock, J. P. Davis, S. V. Nuzhdin, M.    

       Passamonti. De novo assembly of Venerupis philippinarum transcriptome

        provides new insights on expression-bias, mitochondrial Doubly Uniparental

        Inheritance and sex-determination. Mol. Bio. Evol 29: 771-786.

Chang, P. L., J. P. Dunham, S. V. Nuzhdin, M. N. Arbeitman. Somatic sex-specific

        transcriptome differences in Drosophila revealed by whole transcriptome

        sequencing. BMC Genomics 12: 364.

Yang, Y. Y., R. M. Graze, B. M. Wats, C. Lopez, H. V. Baker, M. L. Wayne, S. V.

        Nuzhdin, L. M. McIntyre. Deconstructing transcription using a custom

        microarray for Drosophila: abundance, isoforms and alleles. G3 1:427-436.

Saltz, J. B. Natural genetic variation in social environment choice: context

        dependent gene-environment correlation in Drosophila melanogaster.    

        Evolution 65: 2325-2334.

Friesen, M. L., S. S. Porter, S. C. Stark, E. J. von Wettberg, J. L. Sachs, E. Martinez-

        Romero. Annu. Rev. Ecol. Evol. Syst 42: 23-46.

McIntyre, L. M., K. K. Lopiano, A. M. Morse, V. Amin, L. A. Oberg, L. J. Young, S.

        V. Nuzhdin. RNA-seq: technical variability and samling. BMC Genomics 12:

        293.

Saltz, J. B., B. R. Foley. Natural genetic variation in social niche construction:

        social effects of aggression drive disruptive sexual selection in Drosophila

        melanogaster. American Naturalist 177: 645-654.

Foley, B. R., M. Telonis-Scott. Quantitative genetic analysis suggests causal    

        association between cuticular hydrocarbon composition and desiccation

        survival in Drosophila melanogaster. Heredity 106(1): 68-77.

Wayne, M. L., J. Pienaar, M. L. Telonis-Scott, L.-S. Sylvestre, S. V. Nuzhdin, L. M.

        McIntyre. Relaxed selection is consistent with expression evolution for many

       defense genes in Drosophila. Evolution 65: 1068–1078.

Bickel, R. D., A. Kopp, S. V. Nuzhdin. Large effect QTL alleles at the Drosophila    

        bric-a-brac locus are composed of cumulative polymorphisms in the

        promoter, tissue-specific enhancer, and Polycomb response element. PLoS

        Genetics 7: e1001275.

Miller, P. M., J. B.  Saltz, V. A. Cochrane, C. M. Marcinkowski, R. Mobin, T. L. Turner

        Natural variation in decision-making behavior in Drosophila

        melanogaster. PloS one 6(1):e16436.

Conrad, L., K. L. Weinersmith, T. Brodin, J. B. Saltz, A. Sih. Behavioural syndromes

        in fishes: a review with implications for ecology and fisheries management.

        Journal of Fish Biology 78(2):395-435.

Jost, D., A. Zubair, R. Everaers. Bubble statistics and positioning in superhelically

        stressed DNA. Physics Review E 84(3).

Conow, C., D. Fielder, Y. Ovadia, R. Libeskind-Hadas. Jane: A New Tool for the        

        Cophylogeny Reconstruction Problem. Algorithms for Molecular Biology 5

        (16).

Adewoye, A., A. Genissel, S. V. Nuzhdin, E. Tauber. Quantitative trait loci mapping

        of circadian photosensitivity in Drosophila. Journal of Neuroscience 24: 25.

Friesen, M. L., E. J. von Wettberg. Adapting genomics to study the evolution and

        ecology of agricultural systems. Curr. Opp. Plant Biol 13: 119-125.

Chang, P. L., B. Dilkes, M. M. McMahon, L. Comai, S. V. Nuzhdin. Homeolog

        specific retention and use in allotetraploid Arabidopsis suecica depends on

        parent of origin and network partners. Genome Biology 11: R125.

Yukilevich, R., T. L. Turner, S. V. Nuzhdin, J. R. True. Genomic patterns and

        population genetics of high Fst sites between North American and African

        Drosophila melanogaster. Genetics 186: 219–239.

Friesen, M. L., M. A. Cordeiro, R. V. Penmetsa, M. Badri, T. Huguet, M. E. Aouani, D.

       R. Cook, S. V. Nuzhdin. Population genomic analyses in Tunisian Medicago

        truncatula reveals candidates for salinity adaptation. Plant Journal 63: 623-

        635.

Nuzhdin, S. V., Rychkova, A., M. and M. W. Hahn. Transcription factor binding

        strength modulates co-variation in genetic networks. Trends in Genetics 26:

        51-53.

Foley, B. R., A. Genissel, K. L. Harmon, S. V. Nuzhdin. Does segregating variation

        in sexual or microhabitat preferences lead to non-random mating in natural

        Drosophila melanogaster? Biology Letters 6: 102-105.

Turner, T. L., E. Bourne, E. J. Von Wettberg, T. T. Hu, S. V. Nuzhdin. Population

        resequencing reveals local adaptation of Arabidopsis lyrata to serpentine

        soils. Nature Genetics 42: 260-U42.

Burke, M. K, J. P. Dunham, P. Shahrestani, K. R. Thornton, M. R.  Rose, A. D. Long.

        Genome wide analysis of a long-term evolution experiment with Drosophila.

        Nature 467(7315): 587-590.

Pardiñas, A. F., D. Campo, I. G. Pola, L. Miralles, F. Juanes, E. Garcia-Vazquez.

        Climate change and oceanic barriers: genetic differentiation in Pomatomus

        saltatrix (Pisces: Pomatomidae) in the North Atlantic Ocean and the

        Mediterranean Sea. Journal of Fish Biology 77: 1993-1998.

Asgharian, H., H. H. Sahafi, A. Kalirad, E. Elahi. Sequence data on four genes

        suggest nominal Gerres filamentosus specimens from Nayband National Park

        in the Persian Gulf represent two distinct species. Iranian Journal of Animal

        Biosystematics 6(2): 1-11.

Cabral, L. G., B. R. Foley, S. V. Nuzhdin. Does sex trade with violence in

        Drosophila melanogaster? PLoS ONE 3(4) e1986:1-6.

Baer, C. F., J. Joyner-Matos, D. G. Ostrow, V. Grigaltchik, M. P. Salomon, A.

        Upadhyay. Rapid decline in fitness of mutation accumulation lines of

        gonochoristic (outcrossing) Caenorhabditis nematodes. Evolution 64: 3242

        -3253.

Salomon, M.P., D. G. Ostrow, G. Clark, J. Kneebone, J. Sulikowski, P. C. W. Tsang.

        Characterization of 9 polymorphic microsatellite loci in the thorny skate,

        Amblyraja radiata, from micro-satellite-enriched libraries and EST

        sequences. Molecular Ecology Resources 10: 576-579.

Vu, W. T., S. V. Nuzhdin. Genetic Variation of Copia Suppression in Drosophila

        Melanogaster. Heredity 106: 201-217.

Cabral, L. G., B. R. Foley, S. V. Nuzhdin. Does sex trade with violence in

        Drosophila melanogaster? PLoS ONE 3(4) e1986:1-6.

Salomon, M. P., D. Ostrow, N. Phillips, D. Blanton, W. Bour, T. E. Keller, L. Levy, T.

        Sylvestre, A. Upadhyay, C. F. Baer. Comparing mutational and standing genetic

        variability for fitness and body size in Caenorhabditis briggsae and C. elegans.

        Genetics 183: 685–692. Issue Highlight October 2009.

Joyner-Matos, J., A. Upadhyay, M. P. Salomon, V. Grigaltchik, C. F. Baer. Genetic

        (co)variation for life span in rhabditid nematodes: Role of mutation, selection,

        and history. Journal of Gerontology Series A: Biological Sciences and Medical

        Sciences 64: 1134-1145.

Phillips, N., M. P. Salomon, A. Custer, D. Ostrow, C. F. Baer. Spontaneous

        mutational and standing genetic (co)variation at dinucleotide microsatellites

        in Caenorhabditis briggsae and Caenorhabditis elegans. Molecular Biology and

        Evolution 26: 659-669.

Graze, R. M., L. M. McIntyre, B. Main, M. L. Wayne, S. V. Nuzhdin. Regulatory

        divergence in Drosophila melanogaster and D. simulans, a genome-wide

        analysis of allele-specific expression. Genetics 183: 547-561.

Main, B., R. Bickel, R. Graze, P. Calabrese, S. V. Nuzhdin. Allele-specific expression

        assays using Solexa. BMC Genomics 10: 422. 

Bickel, R. D., L. Pennachio, S. V. Nuzhdin, A. Kopp. Contrast patterns of sequence

        evolution at functionally redundant bric a brac paralogs in Drosophila

        melanogaster. J. Mol. Evol. 69: 194-202.

Brisson, J. A., S. V. Nuzhdin, D. L. Stern. Similar patterns of linkage disequilibrium

        and nucleotide diversity in native and introduced populations of the pea

        aphid, Acuthosiphon pisum. BMC Genetics 10: 22.

Nuzhdin, S. V., A. Pickering, J. A. Brisson, L. Harshman, M. L. Wayne and L. M.

        McIntyre. Natural genetic variation in transcriptome reflects network

        structure inferred with major effect mutations: insulin / TOR and associated

        phenotypes in Drosophila melanogaster. BMC Genomics 10: 124.

Telonis-Scott, M., A. Kopp, S. V. Nuzhdin, M. L. Wayne and L. McIntyre.

        Evolutionary conservation of sex dimorphic alternative splicing in

        Drosophila. Genetics 181: 421-434.

Jovelin, R., J. P. Dunham, F. S. Sung, P. C. Phillips. High nucleotide divergence in

        developmental regulatory genes contrasts with the structural elements of

        olfactory pathways in caenorhabditis. Genetics 181 (4): 1387-97       

Foley, B.R., A. Genissel, K.L. Harmon, S.V. Nuzhdin. Does segregating variation in

        sexual or microhabitat preferences lead to non-random mating within a

        population of Drosophila melanogaster? Biology Letters 9(10): 102-105.

Nuzhdin, S. V., D. M. Tufts, M. W. Hahn. Abundant genetic variation in transcript

        level during early Drosophila development. Evol. Development 10: 683-689.

Turner, T. L., E. von Wettburg, S. V. Nuzhdin. The genomic basis of adaptation to

        serpentinic soils in Arabidopsis lyrata. PLoS One 3: e3182.

Bergland, A., A. Genissel, S. V. Nuzhdin, M. Tatar. Quantitative trait loci affecting

        phenotypic plasticity and the relationship of ovariole number and thorax

        length in Drosophila melanogaster. Genetics 180: 567-782.

Cabral, L. G., B. R. Foley, S. V. Nuzhdin. Does sex trade with violence among

        genotypes in Drosophila melanogaster? PLoS One 3: e1986.

Wang, H.-I., Y. Fu, M. S. McPeek, X. Lu, S. V. Nuzhdin, M.-L. Wu, C.-I. Wu.

        Genetic architecture of gene expression within and between Drosophila races

        –  a whole-genome analysis. Proc. Natl. Acad. Sci. USA 105: 6362-6367.

Genissel, A., L. M. Bono, L. M. McIntyre, S. V. Nuzhdin. Cis and trans regulatory

        effects contribute to the natural variation of gene expression profile in

        Drosophila melanogaster. Mol. Biol. Evol. 25: 101-110.

Mezey, J. G., S. V. Nuzhdin, Y. Fangfei, C. Jones. Coordinated evolution of co

        expressed gene clusters in the Drosophila transcriptome. BMC Evolutionary

        Biology 8: 2.

Brisson, J. A., S. V. Nuzhdin. Rarity of males in pea aphids causes their mutational

        decay. Science: 319: 58.

Kochzius, M., M. Nölte, H. Weber, N. Silkenbeumer, S. Hjörleifsdottir, G. O.

        Hreggvidsson, V. Marteinsson, K. Kappel, S. Planes, F. Tinti, A. Magoulas, E.

*McBride, C. S., J. R. Arguello, B. C. O'Meara. Five Drosophila genomes reveal

        nonneutral evolution and the signature of host specialization in the

        chemoreceptor superfamily. Genetics 177: 1395-1416.

Wayne, M. L., M. Telonis-Scott, L. Bono, L. Harshman, A. Kopp, S. V. Nuzhdin, L. M.

        McIntyre. Simpler mode of inheritance of transcriptional variation in male

        Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 104: 18577-18582.

Proulx, S. R., S. V. Nuzhdin, D. E. L. Promislow. Direct selection on genetic

        robustness revelaed in the yeast transcriptome. PLoS One 9: e911.

*Turner, T. L., M. W. Hahn. Locus specific selection against gene flow between

        incipient species of Anopheles gambiae. Mol. Biol. Evol. 24: 2132-2138.

Khazaeli, A. A., S. V. Nuzhdin, J. W. Curtsinger. Genetic variation for life span,

        resistance to paraquat, and spontaneous activity in unselected populations of

        Drosophila melanogaster: Implications for transgenic rescue of life span.

        Mech. Ageing Development 124: 486-493. 

Graze, R. M., O. Barmina, D. Tufts, E. Naderi, K. Harmon, M. Persianova, S. V.

        Nuzhdin. Candidate genes for sex comb divergence between Drosophila

        mauritiana and D.  simulans. Genetics 176: 2561-2576.

Nuzhdin, S. V., L. Harshman, M. Zhou, K. Harmon. Genome-enabled hitch hiking

        mapping identifies QTLs for stress resistance in natural Drosophila. Heredity

        99: 313 - 321

*McBride, C. S. Rapid evolution of smell and taste receptors during host

        specialization in Drosophila sechellia. Proc. Natl. Acad. Sci. USA 104: 4996

        -5001. 

Foley, B. R., S. F. Chenoweth, S. V. Nuzhdin, M. W. Blows. First evidence for

        natural genetic variation in cuticular hydrocarbon expression in male and

        female Drosophila melanogaster. Genetics 175: 1465-1477.

Miller, M.R., J. P. Dunham, A. Amores, W. A. Cresko, E. A. Johnson. Rapid and cost

        effective polymorphism identification and genotyping using restriction site

        associated (RAD) markers. Genome Research 17:240-248.

McIntyre, L. M., L. M. Bono, A. Genisse, M. Telonis, R. Westerman, D. Junk, L.

        Harshman, M. L. Wayne, A. Kopp , S. V. Nuzhdin. Sex specific gene expression

        and alternative splicing in Drosophila. Genome Biology 7:R79.

Wang, Y., D. Pot, S. Kachman, S. V. Nuzhdin, L. G. Harshman. A quantitative trait

        locus analysis of natural genetic variation for oxidative stress survival of

        Drosophila melanogaster. Journal of Heredity 97:355-366

Wang, M. H., L. G. Harshman, S. V. Nuzhdin. Quantitative trait loci for lipid content

        in Drosophila melanogaster. Obesity Res. 13: 1891-1897.

Lanzaro, G. C., S. V. Nuzhdin, F. Tripet. Tools for monitoring the genetic structure

        and stability of mosquito populations. Proc. WHO/TDR, NIAID, IAEA and

        Frontis “Bridging Laboratory and Field Research for Genetic Control of Disease

        Vectors”, Nairobi, Kenya, http:// library.wur.nl/frontis/disease_ vectorstocdisease

        _vectors.html.

Turner, T. L., M. Hahn, S. V. Nuzhdin. Genomic islands of speciation in Anopheles

        gambiae. PLoS Biology 3: 1572-1578.

Tarone, A. M., Y. M. Nasser, S. V. Nuzhdin. Genetic variation for expression of

        the sex determination pathway genes in D. melanogaster. Genet. Res. 86:

        31-40.

Coffman, C., M. L. Wayne, S. V. Nuzhdin, L. Higgins and L. M. McIntyre.

        Identification of coregulated transcripts controlling male body size in

        Drosophila. Genome Biology 6: R53.

Nuzhdin, S. V., A. A. Khazaeli, J. W. Curtsinger. Survival analysis of life span

        QTL in Drosophila melanogaster. Genetics 170: 719-731.

Mezey, J. G., D. Houle, S. V. Nuzhdin. Quantiative trait loci affecting wing shape in

        Drosophila melanogaster. Genetics 169: 2101-2113. 

Wayne, M. L., Y.-J. Pan , S. V. Nuzhdin, L. M. McIntyre. Additivity and epistasis for

        expression in male Drosophila simulans. Genetics 168: 1413-1420.

Kern, A. D., F. A. Kondrashov. Mechanisms and convergence of compensatory

        evolution in mammalian mitochondrial tRNAs. Nature Genet. 36: 1207-1212.

Gibson, G., R. Riley-Berger, L. Harshman, A. Kopp, S. Vacha, S. V. Nuzhdin, M.

        Wayne. Extensive sex-specific non-additivity of gene expression in Drosophila

        melanogaster. Genetics 167: 1791-1799.

Pasyukova, E. G., S. V. Nuzhdin, T. V. Morozova and T. F. C. Mackay. Accumulation

        of transposable elements in the genome of Drosophila melanogaster is

        associated with a decrease in fitness. J. Hered. 95: 284-290.

Nuzhdin, S. V., M. L. Wayne, K. L. Harmon, L. McIntyre. Common pattern of

        evolution of gene expression level and protein sequence in Drosophila. Mol.

        Biol. Evol. 21: 1308-1317.

*Leonardo, T. E. Removal of a specialization-associated symbiont does not affect

        aphid fitness. Ecology Letters 7: 461-463.

Wang, M. H., O. Lazebny, L. G. Harshman, S. V. Nuzhdin. Environment dependent

        survival of Drosophila melanogaster: a quantitative genetic analysis. Aging

        Cell 3: 133-141.

Hahn, M. W., S. V. Nuzhdin. The fixation of malaria refractoriness in mosquito.

        Current Biology 14: R264-R265.

Houle, D., S. V. Nuzhdin. Mutation accumulation and the effect of copia insertions

        in Drosophila melanogaster. Genet. Res. 83: 7-18.

Stocker, A.J., B. R. Foley, A.A. Hoffmann. 2004. “Inversion frequencies in

        Drosophila serrata along an eastern Australian transect." Genome 47(6): 1144

        -1153

 

McIntyre, L. M. M. Wayne, S. V. Nuzhdin, M. Popp, X. Yan.  Exploiting the null to

        reduce false positives in microarray experimentation. Proc. Joint Statistics

        Meetings, 946.

*Leonardo, T., G. T. Muiru. Symbionts are associated with host plant specialization

        in pea aphid populations. Proc. R. Soc. Lond. B BIO 270: S209-S212.

Fry, J. D., S. V. Nuzhdin. Dominance of mutations affecting viability in Drosophila

        melanogaster. Genetics 163: 1357-1364.

Yang, H. P., S. V. Nuzhdin. Fitness costs of Doc expression are insufficient to

        stabilize its copy number in Drosophila melanogaster. Mol. Biol. Evol. 20: 800

        -804.

Nuzhdin, S. V., D. Petrov. Transposable elements in clonal population: lethal

        hangover from sex. Biol. J. Linnean. Soc. 79: 33-41.

Kopp, A., R. M. Graze, S. Xu, S. B. Carroll, S. V. Nuzhdin. Quantitative trait loci

        responsible for variation in sexually dimorphic traits in Drosophila

        melanogaster. Genetics 163: 771-787.

Leonardo, T. E., S. V. Nuzhdin. Intracellular battlegrounds: conflict and

        cooperation between transposable elements. Genet. Res. 80: 155-161.

Reiwitch, S. G., S. V. Nuzhdin. Quantitative trait loci for lifespan of mated

        Drosophila melanogaster affect both sexes. Genet. Res. 80: 1-6.

Gleason, J. M., S. V. Nuzhdin, M. G. Ritchie. Quantitative trait loci affecting a

        courtship signal in Drosophila melanogaster. Heredity 89: 1-6.

Nuzhdin, S. V., S. G. Reiwitch. Heterosis of quantitative trait loci affecting the life

        span in Drosophila melanogaster. Genetika (Russ) 38: 766-770.

Wayne, M. L., J. B. Hackett, C. L. Dilda, S. V. Nuzhdin, E. G. Pasyukova, T. F. C.

        Mackay. Quantitative trait locus mapping of fitness-related traits in Drosophila

        melanogaster: ovariole number, body size, early fecundity, and reproductive

        success. Genet. Res. 77: 107-116.

*Bolnick, D. I. Intraspecific competition favours niche width expansion in

        Drosophila melanogaster. Nature 410: 463-466.

*Yang H. P., A. Y. Tanikawa, A. S.  Kondrashov. Molecular nature of 11

        spontaneous de novo mutations in Drosophila melanogaster. Genetics 157:

        1285-1292.

Perdue, S., S. V. Nuzhdin. Master copy is not responsible for high rate of copia

        transposition in Drosophila. Mol. Biol. Evol. 17: 984-986.

Nuzhdin, S. V., S. G. Reiwitch. Are the same genes responsible for intra- and

        interspecific variability for sex comb tooth number in Drosophila? Heredity

        84:97-102.

Nuzhdin, S. V., C. L. Dilda, T. F. C. Mackay. The genetic architecture of selection

        response: inferences from fine-scale mapping of bristle number quantitative

        trait loci in Drosophila melanogaster. Genetics 153:1317-1331.

Gurganis, M., S. V. Nuzhdin, J. W. Leips, T. F. C. Mackay. High resolution mapping of

        quantitative trait loci for sternopleural bristle number in Drosophila

        melanogaster. Genetics 152: 1585-1604.

Fry, J. D., P. D. Keightley, S. L. Heinsohn, S. V. Nuzhdin. New estimates of the rates

        and effects of mildly deleterious mutations in Drosophila melanogaster. Proc.

        Natl. Acad. Sci., USA 96: 574-579.

Nuzhdin, S. V. Sure facts, speculations, and open questions about the evolution of

        transposable element copy number. Genetica 107: 129-137.

Pasyukova, E. G., S. V. Nuzhdin, D. A. Filatov, V. A. Gvozdev. Retrotransposon-host

        genome interaction: Mechanisms and effects. Mol. Biol. (Russ) 33: 20-29.

Filatov, D. A., S. V. Nuzhdin, E. G. Pasyukova. Enhanced transcription of the copia

        retrotransposon in Drosophila melanogaster testes. Mol. Biol. (Russ)

        32: 821-824.

Nuzhdin, S. V., P. D. Keightley, E. G. Pasyukova, E. A. Marozova. Quantitative trait

        loci mapping in the course of divergent selection for sternopleural bristle

        number of Drosophila melanogaster. Genet. Res. 72: 79-91.

Nuzhdin, S. V., Pasyukova, E. G., Morozova, E. A. and A. J. Flavell. Quantitative

        genetic analysis of copia retrotransposon activity in inbred Drosophila

        melanogaster lines. Genetics 150: 755-766.

Pasyukova, E. G., S. V. Nuzhdin, D. A. Filatov. The relationship between the rate of

        transposition and transposable element copy number for copia and Doc

        retrotransposons of Drosophila melanogaster. Genet. Res. 72: 1-11.

Gurganus, M. C., J. D. Fry, S. V. Nuzhdin, E. G. Pasyukova, R. F. Lyman and T. F. C.

        Mackay. Genotype-environment interaction for quantitative trait loci affecting

        sensory bristle number in Drosophila melanogaster. Genetics 149: 1883-1898.

Fry, J. D., S. V. Nuzhdin, E. G. Pasyukova, T. F. C. Mackay. QTL mapping of

        genotype-environment interaction for fitness in Drosophila melanogaster.

        Genet. Res. 71: 133-141.

Nuzhdin, S. V., E. G. Pasyukova, C. A. Dilda, Z.-B. Zeng, T. F. C. Mackay. Sex-

        specific quantitative trait loci affecting longevity in Drosophila melanogaster.

        Proc. Natl. Acad. Sci. USA 94: 9734-9739.

Nuzhdin, S. V., E. G. Pasyukova, T. F. C. Mackay. Accumulation of transposable

        elements in laboratory lines of Drosophila melanogaster. Genetica

        100: 167-175.

Pasyukova, E. G., S. V. Nuzhdin, W. Li, A. J. Flavell. Germ line transposition of the

        copia mobile element in Drosophila melanogaster is restricted to males by sex-

        specific control of copia RNA level. Mol. Gen. Genet. 255: 115-124.

Nuzhdin, S. V., E. G. Pasyukova, T. F. C. Mackay. Positive association between copia

        transposition rate and copy number in Drosophila melanogaster. Proc. R. Soc.

        Lond. B 263: 823-831.

Lyman, R. F., F. Sherrill, S. V. Nuzhdin, T. F. C. Mackay. Effects of single P element

        insertions on bristle number and viability in Drosophila melanogaster. Genetics

        143: 277-292.

Nuzhdin, S. V., T. F. C. Mackay. The genomic rate of transposable element

        movement in Drosophila melanogaster. Mol. Biol. Evol. 12: 180-181.

Nuzhdin, S. V., J. D. Fry, T. F. C. Mackay. Polygenic mutation in Drosophila   

        melanogaster: The causal relationship of bristle number and fitness. Genetics

        139: 861-872.

Nuzhdin, S. V. The distribution of transposable elements on X chromosomes from

        a natural population of Drosophila simulans. Genet. Res. 66: 159-166.

Mackay, T. F. C., J. D. Fry, R. F. Lyman, S. V. Nuzhdin. Polygenic mutation in

        Drosophila melanogaster: Estimates from response to selection of inbred

        strains. Genetics 136: 937-951.

Nuzhdin, S. V., T. F. C. Mackay. Direct determination of retrotransposon

        transposition rates in Drosophila melanogaster. Genet. Res. 63: 139-144.

Nurminski, D. I., Yu. Ya. Schevelyov, S. V. Nuzhdin, V. A. Gvozdev. Structure,

        molecular evolution and maintenance of copy number of extended repeated

        structures in the heterochromatin of Drosophila melanogaster. Chromosoma

        103: 277-285.

Pasyukova, E. G., S. V. Nuzhdin. Doc and copia instability in an isogenic Drosophila

        melanogaster stock. Mol. Gen. Genet. 240: 302-306.

Nuzhdin, S. V., P. D. Keightley, E. G. Pasyukova. The use of retrotransposons as

        markers for mapping genes responsible for fitness differences between related

        Drosophila melanogaster strains. Genet. Res. 62: 125-133.

Pasyukova, E. G., S. V. Nuzhdin. Mobilization of retrotransposon copia in

        Drosophila melanogaster genome. Genetika (Russ) 28: 5-18.

Nuzhdin, S. V., E. G. Pasyukova. New approach to polygene mapping. Location of

        genes controlling fitness level in related Drosophila melanogaster stocks.

        Genetika (Russ) 27: 849-859.

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*by trainees from their independent projects fulfilled in Nuzhdin lab.