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Items: 1 to 50 of 135

1.

Novel approach to quantitative spatial gene expression uncovers genetic stochasticity in the developing Drosophila eye.

Ali S, Signor SA, Kozlov K, Nuzhdin SV.

Evol Dev. 2019 Feb 12. doi: 10.1111/ede.12283. [Epub ahead of print]

PMID:
30756455
2.

Inference of Transcription Factor Regulation Patterns Using Gene Expression Covariation in Natural Populations of Drosophila melanogaster.

Osman NM, Kitapci TH, Vlaho S, Wunderlich Z, Nuzhdin SV.

Biophysics (Oxf). 2018 Jan;63(1):43-51. doi: 10.1134/S0006350918010128. Epub 2018 Apr 23.

3.

Threshold response to stochasticity in morphogenesis.

Courcoubetis G, Ali S, Nuzhdin SV, Marjoram P, Haas S.

PLoS One. 2019 Jan 30;14(1):e0210088. doi: 10.1371/journal.pone.0210088. eCollection 2019.

4.

Quantitative analysis reveals genotype- and domain- specific differences between mRNA and protein expression of segmentation genes in Drosophila.

Surkova S, Sokolkova A, Kozlov K, Nuzhdin SV, Samsonova M.

Dev Biol. 2019 Apr 1;448(1):48-58. doi: 10.1016/j.ydbio.2019.01.006. Epub 2019 Jan 7.

PMID:
30629954
5.

Prediction of deleterious mutations in coding regions of mammals with transfer learning.

Plekhanova E, Nuzhdin SV, Utkin LV, Samsonova MG.

Evol Appl. 2018 May 9;12(1):18-28. doi: 10.1111/eva.12607. eCollection 2019 Jan.

6.

A Pipeline for Classifying Deleterious Coding Mutations in Agricultural Plants.

Kovalev MS, Igolkina AA, Samsonova MG, Nuzhdin SV.

Front Plant Sci. 2018 Nov 28;9:1734. doi: 10.3389/fpls.2018.01734. eCollection 2018.

7.

Dynamical Modeling of the Core Gene Network Controlling Flowering Suggests Cumulative Activation From the FLOWERING LOCUS T Gene Homologs in Chickpea.

Gursky VV, Kozlov KN, Nuzhdin SV, Samsonova MG.

Front Genet. 2018 Nov 20;9:547. doi: 10.3389/fgene.2018.00547. eCollection 2018.

8.

Analysis of Gene Expression Variance in Schizophrenia Using Structural Equation Modeling.

Igolkina AA, Armoskus C, Newman JRB, Evgrafov OV, McIntyre LM, Nuzhdin SV, Samsonova MG.

Front Mol Neurosci. 2018 Jun 11;11:192. doi: 10.3389/fnmol.2018.00192. eCollection 2018.

9.

Comparative Transcriptomics in Two Bivalve Species Offers Different Perspectives on the Evolution of Sex-Biased Genes.

Ghiselli F, Iannello M, Puccio G, Chang PL, Plazzi F, Nuzhdin SV, Passamonti M.

Genome Biol Evol. 2018 Jun 1;10(6):1389-1402. doi: 10.1093/gbe/evy082.

10.

Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection.

Wang X, Zhou T, Wunderlich Z, Maurano MT, DePace AH, Nuzhdin SV, Rohs R.

Mol Biol Evol. 2018 Aug 1;35(8):1958-1967. doi: 10.1093/molbev/msy099.

11.

The Evolution of Gene Expression in cis and trans.

Signor SA, Nuzhdin SV.

Trends Genet. 2018 Jul;34(7):532-544. doi: 10.1016/j.tig.2018.03.007. Epub 2018 Apr 18. Review.

PMID:
29680748
12.

Genetic Diversity, Population Structure, and Genetic Correlation with Climatic Variation in Chickpea (Cicer arietinum) Landraces from Pakistan.

Sani SGAS, Chang PL, Zubair A, Carrasquilla-Garcia N, Cordeiro M, Penmetsa RV, Munis MFH, Nuzhdin SV, Cook DR, von Wettberg EJ.

Plant Genome. 2018 Mar;11(1). doi: 10.3835/plantgenome2017.08.0067.

13.

Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation.

von Wettberg EJB, Chang PL, Başdemir F, Carrasquila-Garcia N, Korbu LB, Moenga SM, Bedada G, Greenlon A, Moriuchi KS, Singh V, Cordeiro MA, Noujdina NV, Dinegde KN, Shah Sani SGA, Getahun T, Vance L, Bergmann E, Lindsay D, Mamo BE, Warschefsky EJ, Dacosta-Calheiros E, Marques E, Yilmaz MA, Cakmak A, Rose J, Migneault A, Krieg CP, Saylak S, Temel H, Friesen ML, Siler E, Akhmetov Z, Ozcelik H, Kholova J, Can C, Gaur P, Yildirim M, Sharma H, Vadez V, Tesfaye K, Woldemedhin AF, Tar'an B, Aydogan A, Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin SV, Cook DR.

Nat Commun. 2018 Feb 13;9(1):649. doi: 10.1038/s41467-018-02867-z.

14.

Conservation of social effects (Ψ) between two species of Drosophila despite reversal of sexual dimorphism.

Signor SA, Abbasi M, Marjoram P, Nuzhdin SV.

Ecol Evol. 2017 Oct 22;7(23):10031-10041. doi: 10.1002/ece3.3523. eCollection 2017 Dec.

15.

Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology.

Zhigunov AV, Ulianich PS, Lebedeva MV, Chang PL, Nuzhdin SV, Potokina EK.

BMC Plant Biol. 2017 Nov 14;17(Suppl 1):180. doi: 10.1186/s12870-017-1127-y.

16.

Mapping Quantitative Trait Loci Underlying Circadian Light Sensitivity in Drosophila.

Adewoye AB, Nuzhdin SV, Tauber E.

J Biol Rhythms. 2017 Oct;32(5):394-405. doi: 10.1177/0748730417731863. Epub 2017 Oct 8.

PMID:
28990443
17.

Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network.

Gursky VV, Kozlov KN, Kulakovskiy IV, Zubair A, Marjoram P, Lawrie DS, Nuzhdin SV, Samsonova MG.

PLoS One. 2017 Sep 12;12(9):e0184657. doi: 10.1371/journal.pone.0184657. eCollection 2017.

18.

The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae).

Ghiselli F, Milani L, Iannello M, Procopio E, Chang PL, Nuzhdin SV, Passamonti M.

PeerJ. 2017 Aug 22;5:e3692. doi: 10.7717/peerj.3692. eCollection 2017.

19.

Basic reversal-learning capacity in flies suggests rudiments of complex cognition.

Foley BR, Marjoram P, Nuzhdin SV.

PLoS One. 2017 Aug 16;12(8):e0181749. doi: 10.1371/journal.pone.0181749. eCollection 2017.

20.

Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits.

Plekhanova E, Vishnyakova MA, Bulyntsev S, Chang PL, Carrasquilla-Garcia N, Negash K, Wettberg EV, Noujdina N, Cook DR, Samsonova MG, Nuzhdin SV.

Sci Rep. 2017 Jul 6;7(1):4816. doi: 10.1038/s41598-017-05087-5.

21.

Genetic Correlations among Developmental and Contextual Behavioral Plasticity in Drosophila melanogaster.

Saltz JB, Lymer S, Gabrielian J, Nuzhdin SV.

Am Nat. 2017 Jul;190(1):61-72. doi: 10.1086/692010. Epub 2017 Apr 24.

PMID:
28617639
22.

Social effects for locomotion vary between environments in Drosophila melanogaster females.

Signor SA, Abbasi M, Marjoram P, Nuzhdin SV.

Evolution. 2017 Jul;71(7):1765-1775. doi: 10.1111/evo.13266. Epub 2017 May 24.

PMID:
28489252
23.

Genomic exaptation enables Lasius niger adaptation to urban environments.

Konorov EA, Nikitin MA, Mikhailov KV, Lysenkov SN, Belenky M, Chang PL, Nuzhdin SV, Scobeyeva VA.

BMC Evol Biol. 2017 Feb 7;17(Suppl 1):39. doi: 10.1186/s12862-016-0867-x.

24.

In silico evolution of the Drosophila gap gene regulatory sequence under elevated mutational pressure.

Chertkova AA, Schiffman JS, Nuzhdin SV, Kozlov KN, Samsonova MG, Gursky VV.

BMC Evol Biol. 2017 Feb 7;17(Suppl 1):4. doi: 10.1186/s12862-016-0866-y.

25.

Molecular analysis of six Rhynchospio Hartman, 1936 species (Annelida: Spionidae) with comments on the evolution of brooding within the group.

Radashevsky VI, Malyar VV, Pankova VV, Nuzhdin SV.

Zootaxa. 2016 Jun 24;4127(3):579-90. doi: 10.11646/zootaxa.4127.3.10.

PMID:
27395642
26.

Buffering of Genetic Regulatory Networks in Drosophila melanogaster.

Fear JM, León-Novelo LG, Morse AM, Gerken AR, Van Lehmann K, Tower J, Nuzhdin SV, McIntyre LM.

Genetics. 2016 Jul;203(3):1177-90. doi: 10.1534/genetics.116.188797. Epub 2016 May 18.

27.

Gene networks and developmental context: the importance of understanding complex gene expression patterns in evolution.

Signor SA, Arbeitman MN, Nuzhdin SV.

Evol Dev. 2016 May;18(3):201-9. doi: 10.1111/ede.12187.

PMID:
27161950
28.

Salinity Adaptation and the Contribution of Parental Environmental Effects in Medicago truncatula.

Moriuchi KS, Friesen ML, Cordeiro MA, Badri M, Vu WT, Main BJ, Aouani ME, Nuzhdin SV, Strauss SY, von Wettberg EJ.

PLoS One. 2016 Mar 4;11(3):e0150350. doi: 10.1371/journal.pone.0150350. eCollection 2016.

29.

Genetic Determinants of RNA Editing Levels of ADAR Targets in Drosophila melanogaster.

Kurmangaliyev YZ, Ali S, Nuzhdin SV.

G3 (Bethesda). 2015 Dec 12;6(2):391-6. doi: 10.1534/g3.115.024471.

30.

Postmating reproductive barriers contribute to the incipient sexual isolation of the United States and Caribbean Drosophila melanogaster.

Kao JY, Lymer S, Hwang SH, Sung A, Nuzhdin SV.

Ecol Evol. 2015 Aug;5(15):3171-82. doi: 10.1002/ece3.1596. Epub 2015 Jul 14.

31.

The Wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in Drosophila melanogaster.

Fear JM, Arbeitman MN, Salomon MP, Dalton JE, Tower J, Nuzhdin SV, McIntyre LM.

BMC Syst Biol. 2015 Sep 4;9:53. doi: 10.1186/s12918-015-0200-0.

32.

Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors.

Asgharian H, Chang PL, Lysenkov S, Scobeyeva VA, Reisen WK, Nuzhdin SV.

Proc Biol Sci. 2015 Jul 7;282(1810). pii: 20150728. doi: 10.1098/rspb.2015.0728.

33.

A Bayesian Approach to Social Structure Uncovers Cryptic Regulation of Group Dynamics in Drosophila melanogaster.

Foley BR, Saltz JB, Nuzhdin SV, Marjoram P.

Am Nat. 2015 Jun;185(6):797-808. doi: 10.1086/681084. Epub 2015 Apr 16.

34.

Natural variation of gene models in Drosophila melanogaster.

Kurmangaliyev YZ, Favorov AV, Osman NM, Lehmann KV, Campo D, Salomon MP, Tower J, Gelfand MS, Nuzhdin SV.

BMC Genomics. 2015 Mar 17;16:198. doi: 10.1186/s12864-015-1415-6.

35.

Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the south-eastern United States and Caribbean Islands.

Kao JY, Zubair A, Salomon MP, Nuzhdin SV, Campo D.

Mol Ecol. 2015 Apr;24(7):1499-509. doi: 10.1111/mec.13137.

PMID:
25735402
36.

The ecological genomic basis of salinity adaptation in Tunisian Medicago truncatula.

Friesen ML, von Wettberg EJ, Badri M, Moriuchi KS, Barhoumi F, Chang PL, Cuellar-Ortiz S, Cordeiro MA, Vu WT, Arraouadi S, Djébali N, Zribi K, Badri Y, Porter SS, Aouani ME, Cook DR, Strauss SY, Nuzhdin SV.

BMC Genomics. 2014 Dec 22;15:1160. doi: 10.1186/1471-2164-15-1160.

37.

GBshape: a genome browser database for DNA shape annotations.

Chiu TP, Yang L, Zhou T, Main BJ, Parker SC, Nuzhdin SV, Tullius TD, Rohs R.

Nucleic Acids Res. 2015 Jan;43(Database issue):D103-9. doi: 10.1093/nar/gku977. Epub 2014 Oct 17.

38.

Genetic variation in niche construction and its implications: response to Shuker.

Saltz JB, Nuzhdin SV.

Trends Ecol Evol. 2014 Jun;29(6):304-5. doi: 10.1016/j.tree.2014.03.009. Epub 2014 Apr 13. No abstract available.

PMID:
24735777
39.

What the X has to do with it: differences in regulatory variability between the sexes in Drosophila simulans.

Graze RM, McIntyre LM, Morse AM, Boyd BM, Nuzhdin SV, Wayne ML.

Genome Biol Evol. 2014 Apr;6(4):818-29. doi: 10.1093/gbe/evu060.

40.

Population differentiation for germination and early seedling root growth traits under saline conditions in the annual legume Medicago truncatula (Fabaceae).

Cordeiro MA, Moriuchi KS, Fotinos TD, Miller KE, Nuzhdin SV, von Wettberg EJ, Cook DR.

Am J Bot. 2014 Mar;101(3):488-98. doi: 10.3732/ajb.1300285. Epub 2014 Mar 17.

41.

Paternally transmitted mitochondria express a new gene of potential viral origin.

Milani L, Ghiselli F, Maurizii MG, Nuzhdin SV, Passamonti M.

Genome Biol Evol. 2014 Feb;6(2):391-405. doi: 10.1093/gbe/evu021.

42.

Genomic changes under rapid evolution: selection for parasitoid resistance.

Jalvingh KM, Chang PL, Nuzhdin SV, Wertheim B.

Proc Biol Sci. 2014 Feb 5;281(1779):20132303. doi: 10.1098/rspb.2013.2303. Print 2014 Mar 22.

43.

Promises and limitations of hitchhiking mapping.

Nuzhdin SV, Turner TL.

Curr Opin Genet Dev. 2013 Dec;23(6):694-9. doi: 10.1016/j.gde.2013.10.002. Epub 2013 Nov 12. Review.

44.

Genetic variation in niche construction: implications for development and evolutionary genetics.

Saltz JB, Nuzhdin SV.

Trends Ecol Evol. 2014 Jan;29(1):8-14. doi: 10.1016/j.tree.2013.09.011. Epub 2013 Oct 11.

45.

Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection.

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

Mol Ecol. 2013 Oct;22(20):5084-97. doi: 10.1111/mec.12468. Epub 2013 Sep 19.

46.

Structure, transcription, and variability of metazoan mitochondrial genome: perspectives from an unusual mitochondrial inheritance system.

Ghiselli F, Milani L, Guerra D, Chang PL, Breton S, Nuzhdin SV, Passamonti M.

Genome Biol Evol. 2013;5(8):1535-54. doi: 10.1093/gbe/evt112.

47.

Nuclear genes with sex bias in Ruditapes philippinarum (Bivalvia, veneridae): Mitochondrial inheritance and sex determination in DUI species.

Milani L, Ghiselli F, Nuzhdin SV, Passamonti M.

J Exp Zool B Mol Dev Evol. 2013 Nov;320(7):442-54. doi: 10.1002/jez.b.22520. Epub 2013 Jul 19.

PMID:
23873694
48.

Post-GWAS: where next? More samples, more SNPs or more biology?

Marjoram P, Zubair A, Nuzhdin SV.

Heredity (Edinb). 2014 Jan;112(1):79-88. doi: 10.1038/hdy.2013.52. Epub 2013 Jun 12. Review.

49.

Transcription start site evolution in Drosophila.

Main BJ, Smith AD, Jang H, Nuzhdin SV.

Mol Biol Evol. 2013 Aug;30(8):1966-74. doi: 10.1093/molbev/mst085. Epub 2013 May 6.

50.

Identification of gene expression changes associated with long-term memory of courtship rejection in Drosophila males.

Winbush A, Reed D, Chang PL, Nuzhdin SV, Lyons LC, Arbeitman MN.

G3 (Bethesda). 2012 Nov;2(11):1437-45. doi: 10.1534/g3.112.004119. Epub 2012 Nov 1.

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