Publications

2023

Lin YP, Chen HW, Yeh PM, Anand SS, Lin J, Li J, Noble T, Nair R, Schafleitner R, Samsonova M, Bishop-von-Wettberg E, Nuzhdin SV, Ting CT, Lawn RJ, Lee CR. Demographic history and distinct selection signatures of two domestication genes in mungbean: Plant Physiology. 2023. [PDF]
Igolkina AA, Noujdina NV, Vishnyakova M, Longcore T, von Wettberg E, Nuzhdin SV, Samsonova MG. Historical routes for diversification of domesticated chickpea inferred from landrace genomics: Molecular Biology and Evolution. 2023. [PDF]
Ong PW, Lin YP, Chen HW, Lo CY, Burlyaeva M, Noble T, Nair RM, Schafleitner R, Vishnyakova M, Bishop-von-Wettberg E, Samsonova MG, Nuzhdin SV, Ting CT, Lee CR. Environment as a limiting factor of the historical global spread of mungbean: eLife. 2023. [PDF]
Hua Z, Churches N, Nuzhdin SV. Balancing selection and candidate loci for survival and growth during larval development in the Mediterranean mussel, Mytilus galloprovincialis: G3: Genes, Genomes, Genetics. 2023. [PDF]
Nanni AV, Martinez N, Graze R, Morse A, Newman JR, Jain V, Vlaho S, Signor S, Nuzhdin SV, Renne R, McIntyre LM. Sex-Biased Expression Is Associated With Chromatin State in Drosophila melanogaster and Drosophila simulans: Molecular Biology and Evolution. 2023. [PDF]
Lin M, Simons AL, Harrigan RJ, Curd EE, Schneider FD, Ruiz‐Ramos DV, Gold Z, Osborne MG, Shirazi S, Schweizer TM, Moore TN. Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity in California: Ecological Applications. 2021. [PDF]
Osborne MG, Molano G, Simons AL, Dao V, Ong B, Vong B, Singh A, Montecinos Arismendi GJ, Alberto F, Nuzhdin SV. Natural variation of Macrocystis pyrifera gametophyte germplasm culture microbiomes and applications for improving yield in offshore farms. Journal of Phycology. 2023. [PDF]
Simons AL, Theroux S, Osborne M, Nuzhdin SV, Mazor R, Steele J. Zeta diversity patterns in metabarcoded lotic algal assemblages as a tool for bioassessment: Ecological Applications. 2023. [PDF]
Gretsova M, Surkova S, Kanapin A, Samsonova A, Logacheva M, Shcherbakov A, Logachev A, Bankin M, Nuzhdin SV, Samsonova M. Transcriptomic Analysis of Flowering Time Genes in Cultivated Chickpea and Wild Cicer: International Journal of Molecular Sciences. 2023. [PDF]

2022

Xu R, Martelossi J, Smits M, Iannello M, Peruzza L, Babbucci M, Milan M, Dunham JP, Breton S, Milani L, Nuzhdin SV. Multi-tissue RNA-Seq analysis and long-read-based genome assembly reveal complex sex-specific gene regulation and molecular evolution in the Manila clam: Genome Biology and Evolution. 2022. [PDF]
Bavykina M, Kostina N, Lee CR, Schafleitner R, Bishop-von Wettberg E, Nuzhdin SV, Samsonova M, Gursky V, Kozlov K. Modeling of Flowering Time in Vigna radiata with Artificial Image Objects, Convolutional Neural Network and Random Forest: Plants. 2022. [PDF]
Courcoubetis G, Xu C, Nuzhdin SV, Haas S. Avalanches during epithelial tissue growth; Uniform Growth and a drosophila eye disc model: PLoS Computational Biology. 2022. [PDF]
Molano G, Diesel J, Montecinos GJ, Alberto F, Nuzhdin SV. Sporophyte stage genes exhibit stronger selection than gametophyte stage genes in haplodiplontic giant kelp: Frontiers in Marine Science. 2022. [PDF]
Lin YP, Chen HW, Yeh PM, Lin J, Anand S, Li J, Noble T, Nair RM, Schafleitner R, Samsonova M, Bishop-von-Wettberg E, Nuzhdin SV, Ting CT, Lawn RJ, Lee CR. Distinct selection signatures during domestication and improvement in crops: a tale of two genes in mungbean: BioRxiv. 2022. [PDF]

2021

DeWeese KJ, Osborne MG. Understanding the metabolome and metagenome as extended phenotypes: The next frontier in macroalgae domestication and improvement: Journal of the World Aquaculture Society. 2021. [PDF]
Sherbina K, León-Novelo LG, Nuzhdin SV, McIntyre LM, Marroni F. Power calculator for detecting allelic imbalance using hierarchical Bayesian model: BMC Research Notes. 2021. [PDF]
Ageev A, Lee CR, Ting CT, Schafleitner R, Bishop-von Wettberg E, Nuzhdin SV, Samsonova M, Kozlov K. Modeling of Flowering Time in Vigna radiata with Approximate Bayesian Computation: Agronomy. 2021. [PDF]
Shin MG, Nuzhdin SV. Interspecific Sample Prioritization Can Improve QTL Detection With Tree-Based Predictive Models: Frontiers in Genetics. 2021. [PDF]
Surkova S, Görne J, Nuzhdin SV, Samsonova M. Interplay between sex determination cascade and major signaling pathways during Drosophila eye development: Perspectives for future research: Developmental Biology. 2021. [PDF]
Ageev A, Aydogan A, Bishop-von Wettberg E, Nuzhdin SV, Samsonova M, Kozlov K. Simulation Model for Time to Flowering with Climatic and Genetic Inputs for Wild Chickpea: Agronomy. 2021. [PDF]
Gretsova M, Surkova S, Kanapin A, Samsonova A, Scherbakov A, Logacheva M, Nuzhdin SV, Samsonova M. Transcriptomic analysis of flowering-time genes in wild and cultivated chickpea: PlantGen2021. 2021. [PDF]
Churches N, Chancellor J, Chang P, Nuzhdin S. Pacific oysters (Crassostrea gigas) dramatically recalibrate the model for the upper limit of the eukaryotic mutation rate: The Society for Integrative and Comparative Biology 2021 Virtual Annual Meeting. 2021. [Abstract]
Ithnin M, Vu WT, Shin M, Suryawanshi V, Sherbina K, Zolkafli SH, Serdari NM, Amiruddin MD, Abdullah N, Mustaffa S, Marjuni M, Nookiah R, Kushairi A, Marjoram P, Nuzhdin SV, Chang PL, Singh R: Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm. Plant Science. 2021. [PDF]
Igolkina AA, Noujdina NV, Samsonova MG, von Wettberg E, Longcore T, Nuzhdin SV. Historical trade routes for diversification of domesticated chickpea inferred from landrace genomics: bioRxiv. 2021. [PDF]
Ageev AY, Bishop-von Wettberg EJ, Nuzhdin SV, Samsonova MG, Kozlov KN. Forecasting the Timing of Floral Initiation in Wild Chickpeas under Climate Change: Biophysics. 2021. [PDF]
Sokolkova AB, Bulyntsev SV, Chang PL, Carrasquila-Garcia N, Cook DR, von Wettberg E, Vishnyakova MA, Nuzhdin SV, Samsonova MG. A Genomic Analysis of Historic Chickpea Landraces: Biophysics. 2021. [PDF]
Shin M, Ithnin M, Vu WT, Kamaruddin K, Chin T, Yaakub Z, Chang PL, Sritharan K, Nuzhdin SV, Singh R: Association mapping analysis of oil palm interspecific hybrid populations and predicting phenotypic values via machine learning algorithms. Plant Breeding, 2021.
Sokolkova AB, Bulyntsev SV, Chang PL, Carrasquila-Garcia N, Cook DR, von Wettberg E, Vishnyakova MA, Nuzhdin SV, Samsonova M: The Search for Agroislands in the Chickpea Genome. Molecular Biophysics, 2021. [PDF] [NCBI BioProject]
Chernova A, Gubaev R, Singh A, Sherbina K, Goryunova S, Martynova E, Goryunov D, Boldyrev S, Vanyushkina A, Anikanov N, Stekolshchikova E, Yushina E, Demurin Y, Mukhina Z, Gavrilova V, Anisimova I, Karabitsina Y, Alpatieva N, Chang PL, Khaitovich P, Mazin P, Nuzhdin S: Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content. BMC Genomics in review. [PDF]

2020

Ithnin M, Vu WT, Shin M, Suryawanshi V, Sherbina K, Zolkafli SH, Serdari NM, Din M, Abdullah N, Mustaffa S, Marjuni M, Nookiah R, Kushairi A, Marjoram P, Nuzhdin S, Chang PL, Singh R: Genomic diversity of wild American oil palm and evidence of selection acting on yield traits. Plant Sciences. 2020. [PDF] [NCBI BioProject]
Ting N-C, Sherbina K, Khoo J-S, Kamaruddin K, Chan P-L, Chan K-L, Halim MAA, Sritharan K, Yaakub Z, Mayes S, Massawe F, Chang PL, Nuzhdin SV, Sambanthamurthi R, Singh R: Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm. Scientific Reports, 2020. [PDF] [NCBI BioProject]
Sokolkova AB, Chang PL, Carrasquila-Garcia N, Noujdina NV, Cook DR, Nuzhdin SV, Samsonova MG: The signatures of ecological adaptation in the genomes of chickpea landraces. Molecular Biophysics, 2020. [PDF] [NCBI BioProject]
Sokolkova A, Bulyntsev SV, Chang PL, Carrasquila-Garcia N, Igolkina A, Noujdina NV, von Wettberg E, Vishnyakova MA, Cook DR, Nuzhdin SV, Samsonova MG: Genomic Analysis of Vavilov’s Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection. International Journal of Molecular Sciences, 2020. [PDF] [NCBI BioProject]
Newell NR, Ray S, Dalton JE, Fortier JC, Kao JY, Chang PL, Nuzhdin SV, Arbeitman MN. The Drosophila Post-mating Response: Gene Expression and Behavioral Changes Reveal Perdurance and Variation in Cross-Tissue Interactions. G3. 2020. [PDF]

2019

Kozlov, K., Singh, A., Berger, J. et al. Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors. BMC Plant Biol 19, 94 (2019). [PDF]
Sivasakthi K, Marques E, Kalungwana N, Carrasquilla-Garcia N, Chang PL, Bergmann E, Bueno E, Bosch C, Cook D, Cordeiro M, Udupa S, Mohammad I, Rouf RM, Vadez V, Vandemark G, Gaur P, von Wettberg E, Kholova J, Penmetsa RV: Functional dissection of the chickpea (Cicer arietinum L.) stay-green phenotype associated with molecular variation at an ortholog of Mendel’s I gene for cotyledon color: implications for crop production and carotenoid biofortification. International Journal of Molecular Sciences, 2019, 20:5562, doi:10.3390/ijms20225562. [PDF]
Simons AL, Mazor R, Stein ED, Nuzhdin S. Using alpha, beta, and zeta diversity in describing the health of stream-based benthic macroinvertebrate communities. Ecological Applications. 2019. [PDF]
Greenlon A, Chang PL, Damtew ZM, Muleta A, Carrasquilla-Garcia N, Kim D, Nguyen HP, Suryawanshi V, Krieg CP, Yadav SK, Patel JS, Mukherjee A, Udupa S, Benjelloun I, Thami-Alami I, Yasin M, Patil B, Singh S, Sarma BK, von Wettberg EJB, Kahraman A, Bukun B, Assefa F, Tesfaye K, Fikre A, Cook DR. Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria. PNAS. 2019. [PDF] [NCBI BioProject]
Shin MG, Bulyntsev SV, Chang PL, Korbu LB, Carrasquila-Garcia N, Vishnyakova MA, Samsonova MG, Cook DR, Nuzhdin SV. Multi-trait analysis of domestication genes in Cicer arietinum – Cicer reticulatum hybrids with a multidimensional approach: Modeling wide crosses for crop improvement. Plant Sciences. 2019. [PDF] [NCBI BioProject]
Fu S, Chang PL, Friesen ML, Teakle NL, Tarone AM, Sze S-H. Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus. BMC Genomics. 2019. [PDF] [NCBI BioProject1] [NCBI BioProject2]
Zubair A, Rosen IG, Nuzhdin SV, Marjoram P. Bayesian model selection for the gap gene network. BMC Bioinformatics. 2019.

2018

Ghiselli F, Iannello M, Puccio G, Chang PL, Plazzi F, Nuzhdin SV, Passamonti M. Comparative transcriptomics in two bivalve species offers different perspectives on the evolution of sex-biased genes. Genome Biology Evolution. 2018. [PDF] [NCBI BioProject]
Simons A, Churches N, Nuzhdin S. High turnover of gut microbiome from algal feedstock experimental manipulations in the Pacific oyster (Crassostrea gigas). Microbial Biotechnology. 2018. [PDF] [NCBI BioProject]
von Wettberg EJB, Chang PL, Basdemir F, Carrasquilla-Garcia N, Balcha L, Moenga S, Sefara G, Greenlon A, Moriuchi K, Singh V, Cordeiro M, Noujdina N, Dinegde K, Sani S, Getahun T, Vance L, Bergmann E, Lindsay D, Mamo BE, Warschefsky E, Dacosta-Calheiros E, Marques E, Yilmaz M, Cakmak A, Rose J, Migneault A, Krieg C, Saylak S, Temel H, Friesen M, Siler E, Akhmetov Z, Ozelik H, Khalova J, Jan C, Gaur P, Yildirin M, Sharma H, Vadez V, Tesfaye K, Woldemedhin A, Bunyamin T, Aydogan A, Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin S, Cook DR. Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications. 2018. [PDF] [NCBI BioProject]

2017

Zhigunov AV, Ulianich PS, Lebedeva MV, Chang PL, Nuzhdin SV, Potokina EK. Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology. BMC Plant Biology. 2017. [PDF] [NCBI BioProject]
Kahraman A, Pandey A, Khan MK, Lindsay D, Moenga S, Vance L, Bergmann E, Carrasquilla-Garcia N, Shin M, Chang PL, von Wettberg E, Tar’an B, Cook DR, Penmetsa RV: Distinct subgroups of Cicer echinospermum, a crop wild relative from the secondary gene pool, are associated with hybrid sterility and hybrid breakdown in interspecific crosses with cultivated chickpea. Crop Science, 2017, 57:3101–3111, doi:10.2135/cropsci2017.06.0335. [PDF]
Sani SGAS, Chang PL, Zubair A, Munis MFH, Carrasquilla-Garcia N, Cordeiro M, Penmetsa RV, Nuzhdin SV, Cook DR, von Wettberg EJB. Genetic diversity, population structure, and genetic correlation with climatic variation in Chickpea (Cicer arietinum) landraces from Pakistan. The Plant Genome. 2017. [PDF] [NCBI BioProject]
Gursky VV, Kozlov KN, Kulakovskiy IV, Zubair A, Marjoram P, Lawrie DS, Nuzhdin SV, Samsonova MG. Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network. PLoS One. 2017.
Ghiselli F, Milani L, Iannello M, Procopio E, Chang PL, Nuzhdin SV, Passamonti M. The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae). PeerJ. 2017. [PDF] [NCBI BioProject]
Foley BR, Marjoram P, Nuzhdin SV. Basic reversal-learning capacity in flies suggests rudiments of complex cognition. PLoS One. 2017.
Colombo AR, Zubair A, Thiagarajan D, Nuzhdin S, Triche TJ, Ramsingh G. Suppression of Transposable Elements in Leukemic Stem Cells. Scientific Reports. 2017.
Plekhanova E, Vishnyakova MA, Bulyntsev S, Chang PL, Carrasquilla-Garcia N, Negash K, Wettberg EV, Noujdina N, Cook DR, Samsonova MG, Nuzhdin SV. Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits. Scientific Reports. 2017. [PDF] [NCBI BioProject]
Saltz JB, Lymer S, Gabrielian J, Nuzhdin SV. Genetic Correlations among Developmental and Contextual Behavioral Plasticity in Drosophila melanogaster. American Naturalist. 2017.
Konorov EA, Nikitin MA, Mikhailov KV, Lysenkov SN, Belenky M, Chang PL, Nuzhdin SV, Scobeyeva VA. (2017) Genomic exaptation enables Lasius niger adaptation to urban environments. BMC Evolutionary Biology. 2017. [PDF] [NCBI BioProject]
Chertkova AA, Schiffman JS, Nuzhdin SV, Kozlov KN, Samsonova MG, Gursky VV. In silico evolution of the Drosophila gap gene regulatory sequence under elevated mutational pressure. BMC Evolutionary Biology. 2017.
Porter SS, Chang PL, Conow CA, Dunham JP, Friesen ML. Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium. ISME J. 2017. [PDF] [NCBI BioProject]

2016

Hall M, Foley B, Cheung E, Abbasi M, Churches ND. A new behavioral phenotyping strategy for Pacific oyster (Crassostrea gigas) larvae reveals cohort-level effects on copper toxicity swimming response. Annals of Aquaculture and Research. 2016.
Fear JM, León-Novelo LG, Morse AM, Gerken AR, Van Lehmann K, Tower J, Nuzhdin SV, McIntyre LM. Buffering of Genetic Regulatory Networks in Drosophila melanogaster. Genetics. 2016. [NCBI BioProject]
Moriuchi KS, Friesen ML, Cordeiro MA, Badri M, Vu WT, Main BJ, Aouani ME, Nuzhdin SV, Strauss SY, von Wettberg EJ. Salinity Adaptation and the Contribution of Parental Environmental Effects in Medicago truncatula. PLoS One. 2016. [NCBI BioProject]

2015

Vu WT, Chang PL, Moriuchi KS, Friesen ML: Genetic variation of transgenerational plasticity on seed transcriptome and offspring early response to salinity. BMC Plant, 2015 15(59):1186. [PDF] [NCBI BioProject]
Kurmangaliyev YZ, Ali S, Nuzhdin SV. Genetic Determinants of RNA editing levels of ADAR Targets in Drosophila melanogaster. G3. 2015. [NCBI BioProject]
Kao JY, Lymer S, Hwang SH, Sung A, Nuzhdin SV. Postmating reproductive barriers contribute to the incipient sexual isolation of the United States and Caribbean Drosophila melanogaster. Ecology and Evolution. 2015. [PDF] [NCBI BioProject]
Fear JM, Arbeitman MN, Salomon MP, Dalton JE, Tower J, Nuzhdin SV, McIntyre LM. The Wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in Drosophila melanogaster. BMC Systems Biology. 2015. [NCBI BioProject]
Asgharian H, Chang PL, Lysenkov S, Scobeyeva VA, Reisen WK, Nuzhdin SV. Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors. Proceedings Biological Sciences. 2015. [PDF] [NCBI BioProject]
Foley BR, Saltz JB, Nuzhdin SV, Marjoram P. Bayesian approach to social structure uncovers cryptic tegulation of group dynamics in Drosophila melanogaster. American Naturalist. 2015.
Kurmangaliyev YZ, Favorov AV, Osman NM, Lehmann KV, Campo D, Salomon MP, Tower J, Gelfand MS, Nuzhdin SV. Natural variation of gene models in Drosophila melanogaster. BMC Genomics. 2015. [PDF] [NCBI BioProject]
Kao JY, Zubair A, Salomon MP, Nuzhdin SV, Campo D. Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the south-eastern United States and Caribbean Islands. Molecular Ecology. 2015. [PDF] [NCBI BioProject]

2014

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. The ecological genomic basis of salinity adaptation in Tunisian Medicago truncatula. BMC Genomics. 2014. [PDF] [NCBI BioProject]
Asgharian H, Chang PL, Mazzoglio PJ, Negri I: Wolbachia is not all about sex: Male-feminizing Wolbachia alters the leafhopper Zyginidia pullula transcriptome in a mainly sex-independent manner. Frontiers in Microbiology, 2014, 5(430). [PDF] [NCBI BioProject]
Marjoram P, Zubair A, Nuzhdin SV. Post-GWAS: where next? More samples, more SNPs or more biology? Heredity. 2014. [PDF]
Saltz JB, Nuzhdin SV. Genetic variation in niche construction and its implications: response to Shuker. Trends Ecology and Evolution. 2014.
Graze RM, McIntyre LM, Morse AM, Boyd BM, Nuzhdin SV, Wayne ML. What the X has to do with it: differences in regulatory variability between the sexes in Drosophila simulans. Genome Biology and Evolution. 2014.
Cordeiro MA, Moriuchi KS, Fotinos TD, Miller KE, Nuzhdin SV, von Wettberg EJ, Cook DR. Population differentiation for germination and early seedling root growth traits under saline conditions in the annual legume Medicago truncatula (Fabaceae). Am J Botany. 2014. [NCBI BioProject]
Jalvingh KM, Chang PL, Nuzhdin SV, Wertheim B. Genomic changes under rapid evolution: selection for parasitoid resistance. Proceedings Biological Sciences. 2014. [PDF] [NCBI BioProject]

2013

Campo D, Lehmann K, Fjeldsted C, Souaiaia, Kao J, Nuzhdin SV. Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection. Molecular Ecology. 2013. [PDF] [NCBI BioProject]
Nuzhdin SV, Turner TL. Promises and limitations of hitchhiking mapping. Curr Opin Genet Dev. 2013.
Saltz JB, Nuzhdin SV. Genetic variation in niche construction: implications for development and evolutionary genetics. Trends Ecol Evol. 2014.
Ghiselli F, Milani L, Guerra D, Chang PL, Breton S, Nuzhdin SV, Passamonti M. Structure, transcription, and variability of metazoan mitochondrial genome: perspectives from an unusual mitochondrial inheritance system. Genome Biol Evol. 2013. [PDF] [NCBI BioProject]
Main BJ, Smith AD, Jang H, Nuzhdin SV. Transcription start site evolution in Drosophila. Mol Biol Evol. 2013.
Ardekani R, Biyani A, Dalton JE, Saltz JB, Arbeitman MN, Tower J, Nuzhdin S, Tavaré S. Three-dimensional tracking and behaviour monitoring of multiple fruit flies. J R Soc Interface. 2013.

2012

Winbush A, Reed D, Chang PL, Nuzhdin SV, Lyons LC, Arbeitman MN. Identification of gene expression changes associated with long-term memory of courtship rejection in Drosophila males. G3. 2012. [PDF] [NCBI BioProject]
Remolina SC, Chang PL, Leips J, Nuzhdin SV, Hughes KA. Genomic basis of aging and life-history evolution in Drosophila melanogaster. Evolution. 2012. [PDF] [NCBI BioProject]
Sze S-H, Dunham JP, Carey B, Chang PL, Li F, Edman RM, Fjeldsted C, Scott MJ, Nuzhdin SV, Tarone AM: A de novo transcriptome assembly of Lucilia sericata (Diptera: Calliphoridae) with predicted alternative splices, single nucleotide polymorphisms and transcript expression estimates. Insect Molecular Biology, 2012, 21(2):205-21.
Nuzhdin SV, Friesen ML, McIntyre LM. Genotype-phenotype mapping in a post-GWAS world. Trends Genet. 2012.
Thomas A, Lee PJ, Dalton JE, Nomie KJ, Stoica L, Costa-Mattioli M, Chang PL, Nuzhdin S, Arbeitman MN, Dierick HA. A versatile method for cell-specific profiling of translated mRNAs in Drosophila. PLoS One. 2012. [PDF]
Saltz JB, Alicuben ET, Grubman J, Harkenrider M, Megowan N, Nuzhdin SV. Nonadditive indirect effects of group genetic diversity on larval viability in Drosophila melanogaster imply key role of maternal decision-making. Mol Ecol. 2012.
Ghiselli F, Milani L, Chang PL, Hedgecock D, Davis JP, Nuzhdin SV, Passamonti M. De Novo assembly of the Manila clam Ruditapes philippinarum transcriptome provides new insights into expression bias, mitochondrial doubly uniparental inheritance and sex determination. Mol Biol Evol. 2012. [PDF] [NCBI BioProject]

2011

Chang PL, Dunham JP, Nuzhdin SV, Arbeitman MN. Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing. BMC Genomics. 2011. [PDF] [NCBI BioProject]
Bickel RD, Kopp A, Nuzhdin SV. Composite effects of polymorphisms near multiple regulatory elements create a major-effect QTL. PLoS Genet. 2011

2010

Chang PL, Dilkes BP, McMahon M, Comai L, Nuzhdin SV. Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biol. 2010. [PDF]
Yukilevich R, Turner TL, Aoki F, Nuzhdin SV, True JR. Patterns and processes of genome-wide divergence between North American and African Drosophila melanogaster. Genetics. 2010.
Friesen ML, Cordeiro MA, Penmetsa RV, Badri M, Huguet T, Aouani ME, Cook DR, Nuzhdin SV. Population genomic analysis of Tunisian Medicago truncatula reveals candidates for local adaptation. Plant J. 2010. [NCBI BioProject]
Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nature Genetics. 2010.
Foley BR, Genissel A, Kristy HL, Nuzhdin SV. Does segregating variation in sexual or microhabitat preferences lead to non-random mating within a population of Drosophila melanogaster? Biol Lett. 2010.

2009

Main BJ, Bickel RD, McIntyre LM, Graze RM, Calabrese PP, Nuzhdin SV. Allele-specific expression assays using Solexa. BMC Genomics. 2009.
Graze RM, McIntyre LM, Main BJ, Wayne ML, Nuzhdin SV. Regulatory divergence in Drosophila melanogaster and D. simulans, a genomewide analysis of allele-specific expression. Genetics. 2009.
Bickel RD, Schackwitz WS, Pennacchio LA, Nuzhdin SV, Kopp A. Contrasting patterns of sequence evolution at the functionally redundant bric à brac paralogs in Drosophila melanogaster. J Mol Evol. 2009.
Brisson JA, Nuzhdin SV, Stern DL. Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum. BMC Genet. 2009.
Nuzhdin SV, Brisson JA, Pickering A, Wayne ML, Harshman LG, McIntyre LM. Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin/TOR and associated phenotypes in Drosophila melanogaster. BMC Genomics. 2009.
Telonis-Scott M, Kopp A, Wayne ML, Nuzhdin SV, McIntyre LM. Sex-specific splicing in Drosophila: widespread occurrence, tissue specificity and evolutionary conservation. Genetics. 2009.

2008

Turner TL, von Wettberg EJ, Nuzhdin SV. Genomic analysis of differentiation between soil types reveals candidate genes for local adaptation in Arabidopsis lyrata. PLoS One. 2008.
Cabral LG, Foley BR, Nuzhdin SV. Does sex trade with violence among genotypes in Drosophila melanogaster? PLoS One. 2008.
Mezey JG, Nuzhdin SV, Ye F, Jones CD. Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome. BMC Evol Biol. 2008.
Brisson JA, Nuzhdin SV. Rarity of males in pea aphids results in mutational decay. Science. 2008.

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Sergey Nuzhdin

USC Laboratory (MBIO)

USC Aquaculture Facility (AltaSea)