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Our Work
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2024
69. Alfaro GF, Palombo V, D’Andrea MS, Cao W, Zhang Y, Beever J, Muntifering RB, Pacheco W, Rodning SP, Wang X, Moisá SJ (2024). Hepatic transcript profiling in beef cattle: effects of feeding endophyte-infected tall fescue seeds. PLoS ONE, 19 (7), e0306431. [link]
68. Wang H, Su B, Zhang Y, Mei S, Li S, Xing D, Wang J, Bern L, Johnson A, Al-Armanazi J, Hasin T, Hettiarachchi D, Paladines Parrales A, Dilawar H, Bruce T, Dunham RA, and Wang X* (2024). From heterosis to outbreeding depression: genotype-by-environment interaction shifts hybrid fitness in opposite directions. Genetics, 227(4), iyae090. [link]
67. Richter E, Patel P, Babu JR, Wang X, and Thangiah G (2024). The importance of sleep in overcoming childhood obesity and reshaping epigenetics. Biomedicines, 12(6), 1334. [link]
66. Ma X, Brinker E, Lea CR, Delmain D, Chamorro ED, Martin D, Graff EC, and Wang X* (2024). Evaluation of fecal sample collection methods for feline gut microbiome profiling: fecal loop vs. litter box. Frontiers in Microbiology, 15, 1337917. [link]
65. Ma X, Lazarowski L, Zhang Y, Krichbaum S, Smith JG, Zheng J, Cao W, Haney PS, Wilborn RR, Price SB, Singletary M, Waggoner LP, and Wang X* (2024). Metagenomic analysis reveals associations between memory performance and Bifidobacterium pseudolongum abundance in canine gut microbiome. iScience, 27(5), 109611. [link]
64. Wang H, Su B, Zhang Y, Mei S, Wang J, Johnson A, Dilawar H, Bruce T, Dunham RA, and Wang X* (2024). Transcriptome analysis revealed potential mechanisms of channel catfish growth advantage over blue catfish in tank culture environment. Frontiers in Genetics, 15, 1341555. [link]
2023
63. Zhang Y, Reynoso Y, Reznick D, Wang X* (2023). Whole genome assembly and annotation of blackstripe livebearer Poeciliopsis prolifica. Genome Biology and Evolution, in press. [link]
62. Nance RL, Wang X, Sandey M, Matz B, Thomas A and Smith BF (2023). Single-Nuclei Multiome (ATAC + Gene Expression) Sequencing of a Primary Canine Osteosarcoma Elucidates Intra-Tumoral Heterogeneity and Characterizes the Tumor Microenvironment. International Journal of Molecular Science, 24(22), 16365. [link]
61. Alfaro GF, Palombo V, D’Andrea MS, Cao W, Zhang Y, Beever J, Muntifering RB, Pacheco W, Rodning SP, Wang X, Moisá SJ (2023). Hepatic transcript profiling in beef cattle: effects of rumen-protected niacin supplementation. PLoS ONE, 18 (8), e0289409. [link]
60. Schrock MS, Zalenski A, Tallman M, Kollin L, Bratasz A, Weeks G, Miller MA, Sweeney CN, Pluhar EG, Olin MR, Kisseberth W, Bentley RT, Dickinson PJ, York D, Webb A, Wang X, Moore S, Venere M, and Summers MK (2023). Establishment and characterization of two novel patient-derived lines of canine high-grade glioma. Veterinary and Comparative Oncology, 21(3):492-502. [link] [cover image]
59. Patel P, Selvaraju V, Babu JR, Wang X, and Thangiah G (2023). Novel Differentially Methylated Regions Identified by Genome-Wide DNA Methylation Analyses Contribute to Racial Disparities in Childhood Obesity. Genes, 14(5), 1098. [link]
58. Xie Q, Zhan W, Shi Z, Liu F, Niu B, He X, Liu M, Liang Q, Xie Y, Xu P*, Wang X*, and Lou B* (2023). Whole-genome assembly and annotation of little yellow croaker (Larimichthys polyactis) provide insights into hermaphroditism and gonochorism evolution. Molecular Ecology Resources, 23 (3), 632-658. (*corresponding authors) [link]
57. Xiong X, Geden C, Bergstralh DT, White RL, Werren JH, and Wang X* (2023). New insights into the genome and transmission of the microsporidian pathogen Nosema muscidifuracis. Frontiers in Microbiology, 14, 1086. [link]
56. Luo Y, Woodie LN, Graff EC, Zhang J, Flowers S, Wang XZ, Wang X, O’Neill AM, and Greene MW (2023). Role of liquid fructose/sucrose in regulating the hepatic transcriptome in a high-fat Western diet model of NAFLD. Journal of Nutritional Biochemistry, 112, 109174. [link]
55. Cao W, Horzmann K, Schemera S, Petrofski M, Kendall T, Spooner J, Rynders PE, VandeBerg JL, Wang X (2023). Blood transcriptome responses to PFOA and GenX treatment in the marsupial biomedical model Monodelphis domestica. Frontiers in Genetics, fgene.2023.1073461. [link]
54. Cao W, Douglas KC, Samollow PB, VandeBerg JL, Wang X*, and Clark AG* (2023). Origin and evolution of marsupial-specific imprinting clusters through lineage-specific gene duplications and acquisition of promoter differential methylation. Molecular Biology and Evolution, msad022. (*corresponding authors) [link]
53. Brinker EJ, Towns TJ, Watanabe R, Ma X, Bashir A, Cole RC, Wang X, Graff EC (2023). Direct activation of the fibroblast growth factor-21 pathway in overweight and obese cats. Frontiers in Veterinary Sciences, 10:1072680. [link]
2022
52. Patel P, Selvaraju V, Babu JR, Wang X, and Thangiah G (2022). Racial Disparities in Methylation of NRF1, FTO, and LEPR gene in Childhood Obesity. Genes, 13(11):genes13112030. [link]
51. Ma X, Brinker E, Cao W, Graff EC, and Wang X (2022). Effect of mineral oil as a lubricant to collect feces from cats for microbiome studies. Journal of Veterinary Internal Medicine, 36(6):1974-1980. [link]
50. Wang H, Montague RH, Hess NH, Zhang Y, Dunham RA, Butts IAE*, and Wang X* (2022). Transcriptome analysis reveals key gene expression changes in blue catfish sperm in response to cryopreservation. International Journal of Molecular Science, 23(14):7618. (*corresponding authors) [link]
49. Wang H, Su B, Butts IAE, Dunham RA, and Wang X (2022). Chromosome-level assembly and annotation of the blue catfish Ictalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies. GigaScience, 11:giac070. [link]
48. Abass N, Simora RM, Wang J, Li S, Su B, Xing D, Coogan M, Johnson A, Creamer D, Wang X, and Dunham RA (2022). Response of cecropin transgenesis to challenge with Edwardsiella ictaluri in channel catfish Ictalurus punctatus. Fish and Shellfish Immunology, [link]
47. Ma X, Brinker E, Graff EC, Cao W, Gross AL, Johnson A, Zhang C, Martin D, and Wang X (2022). Whole-genome shotgun metagenomic sequencing revealed distinct gut microbiome signatures of obese cats. Microbiology Spectrum, e00837-22. [link]
46. Nance RL, Cooper S, Starenki D, Wang X, Matz B, Lindley S, Smith A, Smith A, Bergman N, Sandey M, Koehler J, Agarwal P, and Smith BF (2022). Transcriptomic Analysis of Canine Osteosarcoma from a Precision Medicine Perspective Reveals Limitations of Differential Gene Expression Studies. Genes, 13(4), 680. [link]
45. Zhou Y, Wang Y, Xiong X, Appel A, Zhang C, and Wang X (2022). Profiles of telomeric repeats in Insecta reveal diverse forms of telomeric motifs in Hymenopterans. Life Science Alliance, 5 (7). [link]
44. Wang H, Bruce T, Su B, Li S, Dunham RA, and Wang X (2022). Environment-dependent heterosis and transgressive gene expression in reciprocal hybrids between the channel catfish Ictalurus punctatus and the blue catfish Ictalurus furcatus. Biology, 11(1), 117. [link]
43. Patel P, Babu JR, Wang X, and Thangiah G (2022). Role of Macronutrient Intake in the Epigenetics of Obesity. Biochemical Society Transactions, BST20211069. [link]
42. Xiong X, Samollow PB, Cao W, Metz, R, Zhang C, Leandro AC, VandeBerg JL, and Wang X. (2022). Genetic and genomic architecture in eight strains of the laboratory opossum Monodelphis domestica. Genes, Genomes, Genetics, 12(1), jkab389. [link]
2021
41. Tan Y, Wang C, Schneider T, Li H, de Souza RF, Tang X, Hsieh TF, Wang X, Li X, Zhang D (2021). Comparative phylogenomic analysis reveals evolutionary genomic changes and novel toxin families in endophytic Liberibacter pathogens. Microbiology Spectrum, 9 (2), e00509-21. [link]
40. Xiong X, Kelkar YD, Geden CJ, Zhang C, Wang Y, Jongepier E, Martinson EO, Verhulst E, Gadau J, Werren JH, and Wang X (2021). Long-read assembly and annotation of the parasitoid wasp Muscidifurax raptorellus, a biological control agent for filth flies. Frontiers in Genetics, in press. [link]
39. Hicks K*, Tan Y, Cao W, Hathcock T, Boothe D, Kennis RA, Zhang D, Wang X* and White AG (2021). Genomic and in vitro pharmacodynamic analysis of rifampicin resistance in multidrug-resistant canine Staphylococcus pseudintermedius isolates. Veterinary Dermatology, 32(3), 219-e67. (*corresponding authors) [link]
38. Ma X, Su B, Bangs M, Alston V, Backenstose NJC, Simora RM, Wang W, Xing D, Li S, Ye Z, Moss A, Duong TY, Wang X* and Dunham RA* (2021). Comparative genomic and transcriptomic analyses revealed twenty-six candidate genes involved in the air-breathing development and function of the bighead catfish Clarias macrocephalus. Marine Biotechnology, 23(1), 90-105. (*co-corresponding authors) [link]
37. Lü BB, Wu GG, Sun Y, Zhang LS, Wu X, Jiang W, Li P, Huang YN, Wang JB, Zhao YC, Liu H, Song LL, Mo Q, Pan AH, Yang Y, Long XQ, Cui WD, Zhang C, Wang X and Tang X. (2021). Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SH. Frontiers in Microbiology, 12, 1821. [link]
36. Lin ZJ, Wang XZ, Wang J, Tan Y, Tang X, Werren JH, Zhang D, and Wang X (2021). Comparative analysis reveals the expansion of the mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis. International Journal of Biological macromolecules, 166, 1246-1257. [link]
35. Xie Q, Li B, Zhan W, Liu F, Tan P, Wang X, and Lou B (2021). A transient hermaphroditic stage in early male gonadal development in little yellow croaker, Larimichthys polyactis. Frontiers in Endocrinology, 11, 542942. [link]
2020
34. Ruan H, Zhou Y, Shen J, Zhai Y, Xu Y, Pi L, Huang R, Chen K, Li X, Ma W, Wu Z, Deng X, Wang X*, Zhang C* and Guan M* (2020). Circulating tumor cell characterization of lung cancer brain metastasis in the cerebrospinal fluid through single-cell transcriptome analysis. Clinical and Translational Medicine, 10(8), e246. (*co-corresponding authors) [link].
33. Ma X, Shang M, Su B, Wiley A, Bangs M, Alston V, Simora RM, Nguyen MT, Backenstose NJC, Moss A, Duong TY, Wang X* and Dunham RA* (2020). Comparative Transcriptome Analysis During the Seven developmental Stages of Channel Catfish (Ictalurus punctatus) and Tra Catfish (Pangasianodon hypophthalmus) Provides Novel Insights for the Terrestrial Adaptation. Frontiers in Genetics, 11, 608325. (*co-corresponding authors) [link]
32. Simora RM, Xing D, Bangs M, Wang W, Ma X, Su B, Khan MGQ, Qin Z, Lu C, Alston V, Hettiarachchi D, Johnson A, Li S, Coogan M, Gurbatow J, Terhune J, Wang X and Dunham RA (2020). CRISPR/Cas9-mediated Knock-in of Alligator Cathelicidin Gene in a Non-coding Region of Channel Catfish Genome. Scientific Reports, 10, 22271. [link]
31. Wang XZ, Xiong X, Cao W, Zhang C, Werren JH and Wang X (2020). Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination. Genome Biology and Evolution, 12(12), 2508-2520. [link].
30. Phillips M, Babu JR, Wang X and Thangiah G (2020). DNA Copy Number and Structural Variation (CNV): Contributions to Adult and Childhood Obesity. Biochemical Society Transactions, BST20200556. [link]
29. Ma X, Su B, Tian Y, Backenstose NJC, Ye Z, Moss A, Duong TY, Wang X* and Dunham RA* (2020). Deep transcriptomic analysis reveals the dynamic developmental progression during early development of channel catfish (Ictalurus punctatus). International Journal of Molecular Science, 21(15):5535. (*co-corresponding authors) [link]
28. Haney PS, Lazarowski L, Wang XZ, Wang X, Hathcock J, Lofton R, Wilborn R, and Waggoner LP (2020). Effectiveness of PennHIP® and Orthopedic Foundation for Animals hip quality scores for breeding selection to reduce hip dysplasia in a population of purpose-bred detection dogs. Journal of the American Veterinary Medical Association, 257:299-304. [link]
27. Cao W, Hicks K, White AG, Hathcock T, Kennis RA, Boothe D, Zhang D and Wang X (2020). Draft genome assembly of two Staphylococcus pseudintermedius strains isolated from canine skin biopsy. Microbiology Resource Announcements, 9(22). [link]
26. Wang XZ, Kelkar KD, Xiong X, Martinson EO, Lynch J, Zhang C, Werren JH and Wang X (2020). Whole genome sequence and annotation of the parasitoid jewel wasp Nasonia giraulti laboratory strain RV2X[u]. Genes, Genomes, Genetics, 10:2565-2572. [link]
25. Koehler J, Sandey M, Prasad N, Levy SA, Wang XZ and Wang X (2020). Differential expression of miRNAs in hypoxia ("hypoxamiRs") in three canine high-grade glioma cell lines. Frontiers in Veterinary Science, 7:104. [link]
24. Rosenfeld CS, Hekman JP, Johnson JL, Zhen L, Ortega MT, Joshi T, Mao J, Vladimirova AV, Gulevich RG, Kharlamova AV, Acland GM, Wang X, Clark AG, Trut LN, Behura SK, Kukekova AV (2020). Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions. Genes, Brain and Behavior, 19(1):e12614. [link]
2019
23. Hamilton M, Ma X, McCrea B, Carrisosa M, Macklin K, Zhang C, Wang X* and Hauck R* (2019). Influence of Eimeria spp. infection on chicken jejunal microbiota and the efficacy of two alternative products against the infection. Avian Diseases, 64(2), 123-129. (*co-corresponding authors) [link]
22. Wang XZ, Xiong X, Cao W, Zhang C, Werren JH and Wang X (2019). Genome assembly of the A-group Wolbachia in Nasonia oneida using linked-reads technology. Genome Biology and Evolution, 10: 3008-3013. [link]
21. Chen L, Wang Y, Yao B, Mitra A, Wang X and Qin X (2018) TIVAN: Tissue-specific cis-eQTL single nucleotide variant annotation and prediction. Bioinformatics, 35 (9), 1573-1575. [link]
2018
20. Wang X*, Pipes L, Acland GM, Trut LN, Herbeck Y, Kharlamova AV, Gulevich RG, Vladimirova AV, Johnson JL, Kukekova AV*, Clark AG* (2018) Responses to selection for tame/aggressive behaviors in silver foxes (Vulpes vulpes). PNAS, 115 (41), 10398-10403. (*co-corresponding authors) [link]
19. Kukekova, AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli K, Gulevich RG, Vladimirova AV, Hekman JP, Perelman P, Graphodatsky AS, Brien SO, Wang X, Clark AG, Acland GM, Trut LN, Zhang G (2018). Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviors. Nature Ecology & Evolution, 2:1479-91. [link]
2017
18. Hillman PR, Christian SGB, Doan R, Cohen ND, Douglas KC, Konganti K, Wang X, Samollow PB and Dindot SV (2017). Genomic imprinting does not reduce UBE3A in neurons. Epigenetics & Chromatin, 10:27. [link]
23. Hamilton M, Ma X, McCrea B, Carrisosa M, Macklin K, Zhang C, Wang X* and Hauck R* (2019). Influence of Eimeria spp. infection on chicken jejunal microbiota and the efficacy of two alternative products against the infection. Avian Diseases, 64(2), 123-129. (*co-corresponding authors) [link]
22. Wang XZ, Xiong X, Cao W, Zhang C, Werren JH and Wang X (2019). Genome assembly of the A-group Wolbachia in Nasonia oneida using linked-reads technology. Genome Biology and Evolution, 10: 3008-3013. [link]
21. Chen L, Wang Y, Yao B, Mitra A, Wang X and Qin X (2018) TIVAN: Tissue-specific cis-eQTL single nucleotide variant annotation and prediction. Bioinformatics, 35 (9), 1573-1575. [link]
2018
20. Wang X*, Pipes L, Acland GM, Trut LN, Herbeck Y, Kharlamova AV, Gulevich RG, Vladimirova AV, Johnson JL, Kukekova AV*, Clark AG* (2018) Responses to selection for tame/aggressive behaviors in silver foxes (Vulpes vulpes). PNAS, 115 (41), 10398-10403. (*co-corresponding authors) [link]
19. Kukekova, AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli K, Gulevich RG, Vladimirova AV, Hekman JP, Perelman P, Graphodatsky AS, Brien SO, Wang X, Clark AG, Acland GM, Trut LN, Zhang G (2018). Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviors. Nature Ecology & Evolution, 2:1479-91. [link]
2017
18. Hillman PR, Christian SGB, Doan R, Cohen ND, Douglas KC, Konganti K, Wang X, Samollow PB and Dindot SV (2017). Genomic imprinting does not reduce UBE3A in neurons. Epigenetics & Chromatin, 10:27. [link]
2016
17. Rago A, Gilbert D, Choi JH, Sackton T, Wang X, Kelkar Y, Werren JH, Colbourne JK (2016) OGS2: Genome Re-Annotation of the Jewel Wasp Nasonia vitripennis. BMC Genomics, 17:678. [link]
16. Wang X*, Werren JH*, Clark AG* (2016) Allele-specific transcriptome and methylome analysis reveals stable transmission and cis-regulation of DNA methylation in Nasonia. PLoS Biology, 14(7):e1002500. (*co-corresponding authors) [link]
2015
15. Alexander KA, Wang X, Shibata M, Clark AG, Garcia-Garcia MJ (2015) Genomic imprinting is regulated by TRIM28 through a novel mechanism that is distinct from the maintenance of germline imprints. Cell Reports, 13(6):1194-1205. [link]
14. Wang X, Werren JH, Clark AG (2015) Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti. PNAS, 112(27): E3545-E3554. [link] Commented in Biology of Reproduction. [link]
13. Chow CY, Wang X, Riccardi D, Wolfner MF, Clark AG (2015) The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse. PLoS Genetics, 11(2):e1004924. [link]
2014
12. Douglas KC, Wang X, Jasti M, Wolff A, VandeBerg JL, Clark AG, Samollow PB (2014) Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene. BMC Genomics, 15:89. [link]
11. Wang X and Clark AG (2014). Using next-generation RNA sequencing to identify imprinted genes. Heredity, 113(2):156–166. [link]
10. Wang X, Douglas KC, VandeBerg JL, Clark AG, Samollow PB (2014). Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, monodelphis domestica. Genome Research, 24 (1):70-83. [link]
2013
9. Wang X, Wheeler D, Avery A, Rago A, Choi JH, Colbourne JK, Clark AG, Werren JH (2013). Function and evolution of DNA methylation of the genome of Nasonia vitripennis. PLoS Genetics, 9(10): e1003872. [link] [cover image]
8. Wang X, Miller DC, Harman R, Antczak DF, Clark AG (2013). Paternally expressed genes predominate in the placenta. PNAS, 110(26):10705-10710. [link] Commented in Biology of Reproduction [link] and Science Daily. [link]
17. Rago A, Gilbert D, Choi JH, Sackton T, Wang X, Kelkar Y, Werren JH, Colbourne JK (2016) OGS2: Genome Re-Annotation of the Jewel Wasp Nasonia vitripennis. BMC Genomics, 17:678. [link]
16. Wang X*, Werren JH*, Clark AG* (2016) Allele-specific transcriptome and methylome analysis reveals stable transmission and cis-regulation of DNA methylation in Nasonia. PLoS Biology, 14(7):e1002500. (*co-corresponding authors) [link]
2015
15. Alexander KA, Wang X, Shibata M, Clark AG, Garcia-Garcia MJ (2015) Genomic imprinting is regulated by TRIM28 through a novel mechanism that is distinct from the maintenance of germline imprints. Cell Reports, 13(6):1194-1205. [link]
14. Wang X, Werren JH, Clark AG (2015) Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti. PNAS, 112(27): E3545-E3554. [link] Commented in Biology of Reproduction. [link]
13. Chow CY, Wang X, Riccardi D, Wolfner MF, Clark AG (2015) The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse. PLoS Genetics, 11(2):e1004924. [link]
2014
12. Douglas KC, Wang X, Jasti M, Wolff A, VandeBerg JL, Clark AG, Samollow PB (2014) Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene. BMC Genomics, 15:89. [link]
11. Wang X and Clark AG (2014). Using next-generation RNA sequencing to identify imprinted genes. Heredity, 113(2):156–166. [link]
10. Wang X, Douglas KC, VandeBerg JL, Clark AG, Samollow PB (2014). Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, monodelphis domestica. Genome Research, 24 (1):70-83. [link]
2013
9. Wang X, Wheeler D, Avery A, Rago A, Choi JH, Colbourne JK, Clark AG, Werren JH (2013). Function and evolution of DNA methylation of the genome of Nasonia vitripennis. PLoS Genetics, 9(10): e1003872. [link] [cover image]
8. Wang X, Miller DC, Harman R, Antczak DF, Clark AG (2013). Paternally expressed genes predominate in the placenta. PNAS, 110(26):10705-10710. [link] Commented in Biology of Reproduction [link] and Science Daily. [link]
2012
7. Wang X, Miller DC, Antczak DF, Clark AG (2012). Random X inactivation in the horse and mule placenta. Genome Research, 22 (10):1855-1863. [link]
2011
6. Wang X, Soloway PB, Clark AG (2011). A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq. Genetics, 189(1):1-14. [link]
2010
5. Clark AG, Wang X, Matise TC (2010). Contrasting methods of quantifying fine structure of human recombination. Annual Review of Genomics and Human Genetics, 11:45-64. [link]
4. Wang X, Soloway PD, Clark AG (2010). Paternally biased X inactivation in mouse neonatal brain. Genome Biology, 11(7):R79. [link]
2008
3. Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG (2008). Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE, 3(12):e3839. [link]
2. Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K (2008). A genome-wide approach to identifying novel-imprinted genes. Human Genetics, 122(6),625-634. [link]
1. Brideau NJ, Flores HA, Wang J, Maheshwari S, Wang X, Barbash, DA (2006). Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. Science, 314(5803):1292-1295. [link]
7. Wang X, Miller DC, Antczak DF, Clark AG (2012). Random X inactivation in the horse and mule placenta. Genome Research, 22 (10):1855-1863. [link]
2011
6. Wang X, Soloway PB, Clark AG (2011). A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq. Genetics, 189(1):1-14. [link]
2010
5. Clark AG, Wang X, Matise TC (2010). Contrasting methods of quantifying fine structure of human recombination. Annual Review of Genomics and Human Genetics, 11:45-64. [link]
4. Wang X, Soloway PD, Clark AG (2010). Paternally biased X inactivation in mouse neonatal brain. Genome Biology, 11(7):R79. [link]
2008
3. Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG (2008). Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE, 3(12):e3839. [link]
2. Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K (2008). A genome-wide approach to identifying novel-imprinted genes. Human Genetics, 122(6),625-634. [link]
1. Brideau NJ, Flores HA, Wang J, Maheshwari S, Wang X, Barbash, DA (2006). Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. Science, 314(5803):1292-1295. [link]
Opossum (Monodephis domestica, a marsupial species)
12. Douglas KC, Wang X, Jasti M, Wolff A, VandeBerg JL, Clark AG, Samollow PB (2014) Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene. BMC Genomics, 15:89. [link]
10. Wang X, Douglas KC, VandeBerg JL, Clark AG, Samollow PB (2014). Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, monodelphis domestica. Genome Research, 24 (1):70-83. [link]
Dogs, cats and foxes
28. Haney PS, Lazarowski L, Wang X, Wang X, Hathcock J, Lofton R, Wilborn R, and Waggoner LP (2020). Effectiveness of PennHIP® and Orthopedic Foundation for Animals hip quality scores for breeding selection to reduce hip dysplasia in a population of purpose-bred detection dogs. Journal of the American Veterinary Medical Association, 257:299-304. [link]
27. Cao W, Hicks K, White AG, Hathcock T, Kennis RA, Boothe D, Zhang D and Wang X (2020). Draft genome assembly of two Staphylococcus pseudintermedius strains isolated from canine skin biopsy. Microbiology Resource Announcements, 9(22). [link]
25. Koehler J, Sandey M, Prasad N, Levy SA, Wang X and Wang X (2020). Differential expression of miRNAs in hypoxia ("hypoxamiRs") in three canine high-grade glioma cell lines. Frontiers in Veterinary Science, 7:104. [link]
24. Rosenfeld CS, Hekman JP, Johnson JL, Zhen L, Ortega MT, Joshi T, Mao J, Vladimirova AV, Gulevich RG, Kharlamova AV, Acland GM, Wang X, Clark AG, Trut LN, Behura SK, Kukekova AV (2020). Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions. Genes, Brain and Behavior, 19(1):e12614. [link]
20. Wang X*, Pipes L, Acland GM, Trut LN, Herbeck Y, Kharlamova AV, Gulevich RG, Vladimirova AV, Johnson JL, Kukekova AV*, Clark AG* (2018) Responses to selection for tame/aggressive behaviors in silver foxes (Vulpes vulpes). PNAS, 115 (41), 10398-10403. [link]
19. Kukekova, AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli K, Gulevich RG, Vladimirova AV, Hekman JP, Perelman P, Graphodatsky AS, Brien SO, Wang X, Clark AG, Acland GM, Trut LN, Zhang G (2018). Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviors. Nature Ecology & Evolution, 2:1479-91. [link]
Parasitoids (jewel wasps) and biological control
33. Lin ZJ, Wang X, Wang J, Tan Y, Tang X, Werren JH, Zhang D and Wang X* (2020). Comparative analysis reveals the expansion of the mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis. International Journal of Biological macromolecules, in press. [link]
26. Wang X, Kelkar KD, Xiong X, Martinson EO, Lynch J, Zhang C, Werren JH and Wang X (2020). Whole genome sequence and annotation of the parasitoid jewel wasp Nasonia giraulti laboratory strain RV2X[u]. Genes, Genomes, Genetics, 10:2565-2572. [link]
17. Rago A, Gilbert D, Choi JH, Sackton T, Wang X, Kelkar Y, Werren JH, Colbourne JK (2016) OGS2: Genome Re-Annotation of the Jewel Wasp Nasonia vitripennis. BMC Genomics, 17:678. [link]
16. Wang X*, Werren JH*, Clark AG* (2016) Allele-specific transcriptome and methylome analysis reveals stable transmission and cis-regulation of DNA methylation in Nasonia. PLoS Biology, 14(7):e1002500. (*co-corresponding authors) [link]
14. Wang X, Werren JH, Clark AG (2015) Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti. PNAS, 112(27): E3545-E3554. [link] Commented in Biology of Reproduction. [link]
9. Wang X, Wheeler D, Avery A, Rago A, Choi JH, Colbourne JK, Clark AG, Werren JH (2013). Function and evolution of DNA methylation of the genome of Nasonia vitripennis. PLoS Genetics, 9(10): e1003872. [link] [cover image]
Wolbachia pipientis (intracellular symbiont)
31. Wang X, Xiong X, Cao W, Zhang C, Werren JH* and Wang X* (2020). Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination. Genome Biology and Evolution, in press, doi: 10.1093/gbe/evaa219.
22. Wang X, Xiong X, Cao W, Zhang C, Werren JH and Wang X (2019). Genome assembly of the A-group Wolbachia in Nasonia oneida using linked-reads technology. Genome Biology and Evolution, 10: 3008-3013. [link]
Catfish
34. Simora RM, Xing D, Bangs M, Wang W, Ma X, Su B, Khan MGQ, Qin Z, Lu C, Alston V, Hettiarachchi D, Johnson A, Li S, Coogan M, Gurbatow J, Terhune J, Wang X and Dunham RA (2020). CRISPR/Cas9-mediated Knock-in of Alligator Cathelicidin Gene in a Non-coding Region of Channel Catfish Genome. Scientific Reports, in press.
32. Ma X, Su B, Bangs M, Alston V, Backenstose NJC, Simora RM, Wang W, Xing D, Li S, Ye Z, Moss A, Duong TY, Wang X* and Dunham RA* (2020). Comparative genomic and transcriptomic analyses revealed twenty-six candidate genes involved in the air-breathing development and function of the bighead catfish Clarias macrocephalus. Marine Biotechnology, in press. [link]
29. Ma X, Su B, Tian Y, Backenstose NJC, Ye Z, Moss A, Duong TY, Wang X* and Dunham RA* (2020). Deep transcriptomic analysis reveals the dynamic developmental progression during early development of channel catfish (Ictalurus punctatus). International Journal of Molecular Science, 21(15):5535. [link]
Little yellow croaker
36. Xie Q, Li B, Zhan W, Liu F, Tan P, Wang X and Lou B (2020). A transient hermaphroditic stage in early male gonadal development in little yellow croaker, Larimichthys polyactis. Frontiers of Endocrinology, in press. [link]
Chicken
23. Hamilton M, Ma X, McCrea B, Carrisosa M, Macklin K, Zhang C, Wang X* and Hauck R* (2019). Influence of Eimeria spp. infection on chicken jejunal microbiota and the efficacy of two alternative products against the infection. Avian Diseases, 64(2), 123-129. [link]
Mouse
18. Hillman PR, Christian SGB, Doan R, Cohen ND, Douglas KC, Konganti K, Wang X, Samollow PB and Dindot SV (2017). Genomic imprinting does not reduce UBE3A in neurons. Epigenetics & Chromatin, 10:27. [link]
15. Alexander KA, Wang X, Shibata M, Clark AG, Garcia-Garcia MJ (2015) Genomic imprinting is regulated by TRIM28 through a novel mechanism that is distinct from the maintenance of germline imprints. Cell Reports, 13(6):1194-1205. [link]
13. Chow CY, Wang X, Riccardi D, Wolfner MF, Clark AG (2015) The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse. PLoS Genetics, 11(2):e1004924. [link]
6. Wang X, Soloway PB, Clark AG (2011). A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq. Genetics, 189(1):1-14. [link]
4. Wang X, Soloway PD, Clark AG (2010). Paternally biased X inactivation in mouse neonatal brain. Genome Biology, 11(7):R79. [link]
3. Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG (2008). Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE, 3(12):e3839. [link]
Equids (horse, donkey, mule and hinny)
8. Wang X, Miller DC, Harman R, Antczak DF, Clark AG (2013). Paternally expressed genes predominate in the placenta. PNAS, 110(26):10705-10710. [link] Commented in Biology of Reproduction [link] and Science Daily. [link]
7. Wang X, Miller DC, Antczak DF, Clark AG (2012). Random X inactivation in the horse and mule placenta. Genome Research, 22 (10):1855-1863. [link]
Other insects (Drosophila, Apis, etc.)
1. Brideau NJ, Flores HA, Wang J, Maheshwari S, Wang X, Barbash, DA (2006). Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. Science, 314(5803):1292-1295. [link]
Human (population genetics, obesity, and cancer)
35. Ruan H, Zhou Y, Shen J, Zhai Y, Xu Y, Pi L, Huang R, Chen K, Li X, Ma W, Wu Z, Deng X, Wang X*, Zhang C* and Guan M* (2020). Circulating tumor cell characterization of lung cancer brain metastasis in the cerebrospinal fluid through single-cell transcriptome analysis. Clinical and Translational Medicine, in press, [link]
30. Phillips M, Babu JR, Wang X and Thangiah G (2020). DNA Copy Number and Structural Variation (CNV): Contributions to Adult and Childhood Obesity. Biochemical Society Transactions, BST20200556. [link]
5. Clark AG, Wang X, Matise TC (2010). Contrasting methods of quantifying fine structure of human recombination. Annual Review of Genomics and Human Genetics, 11:45-64. [link]
2. Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K (2008). A genome-wide approach to identifying novel-imprinted genes. Human Genetics, 122(6),625-634. [link]
Methods
21. Chen L, Wang Y, Yao B, Mitra A, Wang X and Qin X (2019) TIVAN: Tissue-specific cis-eQTL single nucleotide variant annotation and prediction. Bioinformatics, 35 (9), 1573-1575. [link]
11. Wang X and Clark AG (2014). Using next-generation RNA sequencing to identify imprinted genes. Heredity, 113(2):156–166. [link]
12. Douglas KC, Wang X, Jasti M, Wolff A, VandeBerg JL, Clark AG, Samollow PB (2014) Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene. BMC Genomics, 15:89. [link]
10. Wang X, Douglas KC, VandeBerg JL, Clark AG, Samollow PB (2014). Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, monodelphis domestica. Genome Research, 24 (1):70-83. [link]
Dogs, cats and foxes
28. Haney PS, Lazarowski L, Wang X, Wang X, Hathcock J, Lofton R, Wilborn R, and Waggoner LP (2020). Effectiveness of PennHIP® and Orthopedic Foundation for Animals hip quality scores for breeding selection to reduce hip dysplasia in a population of purpose-bred detection dogs. Journal of the American Veterinary Medical Association, 257:299-304. [link]
27. Cao W, Hicks K, White AG, Hathcock T, Kennis RA, Boothe D, Zhang D and Wang X (2020). Draft genome assembly of two Staphylococcus pseudintermedius strains isolated from canine skin biopsy. Microbiology Resource Announcements, 9(22). [link]
25. Koehler J, Sandey M, Prasad N, Levy SA, Wang X and Wang X (2020). Differential expression of miRNAs in hypoxia ("hypoxamiRs") in three canine high-grade glioma cell lines. Frontiers in Veterinary Science, 7:104. [link]
24. Rosenfeld CS, Hekman JP, Johnson JL, Zhen L, Ortega MT, Joshi T, Mao J, Vladimirova AV, Gulevich RG, Kharlamova AV, Acland GM, Wang X, Clark AG, Trut LN, Behura SK, Kukekova AV (2020). Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions. Genes, Brain and Behavior, 19(1):e12614. [link]
20. Wang X*, Pipes L, Acland GM, Trut LN, Herbeck Y, Kharlamova AV, Gulevich RG, Vladimirova AV, Johnson JL, Kukekova AV*, Clark AG* (2018) Responses to selection for tame/aggressive behaviors in silver foxes (Vulpes vulpes). PNAS, 115 (41), 10398-10403. [link]
19. Kukekova, AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli K, Gulevich RG, Vladimirova AV, Hekman JP, Perelman P, Graphodatsky AS, Brien SO, Wang X, Clark AG, Acland GM, Trut LN, Zhang G (2018). Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviors. Nature Ecology & Evolution, 2:1479-91. [link]
Parasitoids (jewel wasps) and biological control
33. Lin ZJ, Wang X, Wang J, Tan Y, Tang X, Werren JH, Zhang D and Wang X* (2020). Comparative analysis reveals the expansion of the mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis. International Journal of Biological macromolecules, in press. [link]
26. Wang X, Kelkar KD, Xiong X, Martinson EO, Lynch J, Zhang C, Werren JH and Wang X (2020). Whole genome sequence and annotation of the parasitoid jewel wasp Nasonia giraulti laboratory strain RV2X[u]. Genes, Genomes, Genetics, 10:2565-2572. [link]
17. Rago A, Gilbert D, Choi JH, Sackton T, Wang X, Kelkar Y, Werren JH, Colbourne JK (2016) OGS2: Genome Re-Annotation of the Jewel Wasp Nasonia vitripennis. BMC Genomics, 17:678. [link]
16. Wang X*, Werren JH*, Clark AG* (2016) Allele-specific transcriptome and methylome analysis reveals stable transmission and cis-regulation of DNA methylation in Nasonia. PLoS Biology, 14(7):e1002500. (*co-corresponding authors) [link]
14. Wang X, Werren JH, Clark AG (2015) Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti. PNAS, 112(27): E3545-E3554. [link] Commented in Biology of Reproduction. [link]
9. Wang X, Wheeler D, Avery A, Rago A, Choi JH, Colbourne JK, Clark AG, Werren JH (2013). Function and evolution of DNA methylation of the genome of Nasonia vitripennis. PLoS Genetics, 9(10): e1003872. [link] [cover image]
Wolbachia pipientis (intracellular symbiont)
31. Wang X, Xiong X, Cao W, Zhang C, Werren JH* and Wang X* (2020). Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination. Genome Biology and Evolution, in press, doi: 10.1093/gbe/evaa219.
22. Wang X, Xiong X, Cao W, Zhang C, Werren JH and Wang X (2019). Genome assembly of the A-group Wolbachia in Nasonia oneida using linked-reads technology. Genome Biology and Evolution, 10: 3008-3013. [link]
Catfish
34. Simora RM, Xing D, Bangs M, Wang W, Ma X, Su B, Khan MGQ, Qin Z, Lu C, Alston V, Hettiarachchi D, Johnson A, Li S, Coogan M, Gurbatow J, Terhune J, Wang X and Dunham RA (2020). CRISPR/Cas9-mediated Knock-in of Alligator Cathelicidin Gene in a Non-coding Region of Channel Catfish Genome. Scientific Reports, in press.
32. Ma X, Su B, Bangs M, Alston V, Backenstose NJC, Simora RM, Wang W, Xing D, Li S, Ye Z, Moss A, Duong TY, Wang X* and Dunham RA* (2020). Comparative genomic and transcriptomic analyses revealed twenty-six candidate genes involved in the air-breathing development and function of the bighead catfish Clarias macrocephalus. Marine Biotechnology, in press. [link]
29. Ma X, Su B, Tian Y, Backenstose NJC, Ye Z, Moss A, Duong TY, Wang X* and Dunham RA* (2020). Deep transcriptomic analysis reveals the dynamic developmental progression during early development of channel catfish (Ictalurus punctatus). International Journal of Molecular Science, 21(15):5535. [link]
Little yellow croaker
36. Xie Q, Li B, Zhan W, Liu F, Tan P, Wang X and Lou B (2020). A transient hermaphroditic stage in early male gonadal development in little yellow croaker, Larimichthys polyactis. Frontiers of Endocrinology, in press. [link]
Chicken
23. Hamilton M, Ma X, McCrea B, Carrisosa M, Macklin K, Zhang C, Wang X* and Hauck R* (2019). Influence of Eimeria spp. infection on chicken jejunal microbiota and the efficacy of two alternative products against the infection. Avian Diseases, 64(2), 123-129. [link]
Mouse
18. Hillman PR, Christian SGB, Doan R, Cohen ND, Douglas KC, Konganti K, Wang X, Samollow PB and Dindot SV (2017). Genomic imprinting does not reduce UBE3A in neurons. Epigenetics & Chromatin, 10:27. [link]
15. Alexander KA, Wang X, Shibata M, Clark AG, Garcia-Garcia MJ (2015) Genomic imprinting is regulated by TRIM28 through a novel mechanism that is distinct from the maintenance of germline imprints. Cell Reports, 13(6):1194-1205. [link]
13. Chow CY, Wang X, Riccardi D, Wolfner MF, Clark AG (2015) The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse. PLoS Genetics, 11(2):e1004924. [link]
6. Wang X, Soloway PB, Clark AG (2011). A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq. Genetics, 189(1):1-14. [link]
4. Wang X, Soloway PD, Clark AG (2010). Paternally biased X inactivation in mouse neonatal brain. Genome Biology, 11(7):R79. [link]
3. Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG (2008). Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE, 3(12):e3839. [link]
Equids (horse, donkey, mule and hinny)
8. Wang X, Miller DC, Harman R, Antczak DF, Clark AG (2013). Paternally expressed genes predominate in the placenta. PNAS, 110(26):10705-10710. [link] Commented in Biology of Reproduction [link] and Science Daily. [link]
7. Wang X, Miller DC, Antczak DF, Clark AG (2012). Random X inactivation in the horse and mule placenta. Genome Research, 22 (10):1855-1863. [link]
Other insects (Drosophila, Apis, etc.)
1. Brideau NJ, Flores HA, Wang J, Maheshwari S, Wang X, Barbash, DA (2006). Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. Science, 314(5803):1292-1295. [link]
Human (population genetics, obesity, and cancer)
35. Ruan H, Zhou Y, Shen J, Zhai Y, Xu Y, Pi L, Huang R, Chen K, Li X, Ma W, Wu Z, Deng X, Wang X*, Zhang C* and Guan M* (2020). Circulating tumor cell characterization of lung cancer brain metastasis in the cerebrospinal fluid through single-cell transcriptome analysis. Clinical and Translational Medicine, in press, [link]
30. Phillips M, Babu JR, Wang X and Thangiah G (2020). DNA Copy Number and Structural Variation (CNV): Contributions to Adult and Childhood Obesity. Biochemical Society Transactions, BST20200556. [link]
5. Clark AG, Wang X, Matise TC (2010). Contrasting methods of quantifying fine structure of human recombination. Annual Review of Genomics and Human Genetics, 11:45-64. [link]
2. Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K (2008). A genome-wide approach to identifying novel-imprinted genes. Human Genetics, 122(6),625-634. [link]
Methods
21. Chen L, Wang Y, Yao B, Mitra A, Wang X and Qin X (2019) TIVAN: Tissue-specific cis-eQTL single nucleotide variant annotation and prediction. Bioinformatics, 35 (9), 1573-1575. [link]
11. Wang X and Clark AG (2014). Using next-generation RNA sequencing to identify imprinted genes. Heredity, 113(2):156–166. [link]
Agricultural Genomics and Metagenomics
34. Simora RM, Xing D, Bangs M, Wang W, Ma X, Su B, Khan MGQ, Qin Z, Lu C, Alston V, Hettiarachchi D, Johnson A, Li S, Coogan M, Gurbatow J, Terhune J, Wang X and Dunham RA (2020). CRISPR/Cas9-mediated Knock-in of Alligator Cathelicidin Gene in a Non-coding Region of Channel Catfish Genome. Scientific Reports, in press.
32. Ma X, Su B, Bangs M, Alston V, Backenstose NJC, Simora RM, Wang W, Xing D, Li S, Ye Z, Moss A, Duong TY, Wang X* and Dunham RA* (2020). Comparative genomic and transcriptomic analyses revealed twenty-six candidate genes involved in the air-breathing development and function of the bighead catfish Clarias macrocephalus. Marine Biotechnology, in press. [link]
29. Ma X, Su B, Tian Y, Backenstose NJC, Ye Z, Moss A, Duong TY, Wang X* and Dunham RA* (2020). Deep transcriptomic analysis reveals the dynamic developmental progression during early development of channel catfish (Ictalurus punctatus). International Journal of Molecular Science, 21(15):5535. [link]
23. Hamilton M, Ma X, McCrea B, Carrisosa M, Macklin K, Zhang C, Wang X* and Hauck R* (2019). Influence of Eimeria spp. infection on chicken jejunal microbiota and the efficacy of two alternative products against the infection. Avian Diseases, 64(2), 123-129. [link]
Detection dogs and behavioral genomics
28. Haney PS, Lazarowski L, Wang X, Wang X, Hathcock J, Lofton R, Wilborn R, and Waggoner LP (2020). Effectiveness of PennHIP® and Orthopedic Foundation for Animals hip quality scores for breeding selection to reduce hip dysplasia in a population of purpose-bred detection dogs. Journal of the American Veterinary Medical Association, 257:299-304. [link]
24. Rosenfeld CS, Hekman JP, Johnson JL, Zhen L, Ortega MT, Joshi T, Mao J, Vladimirova AV, Gulevich RG, Kharlamova AV, Acland GM, Wang X, Clark AG, Trut LN, Behura SK, Kukekova AV (2020). Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions. Genes, Brain and Behavior, 19(1):e12614. [link]
20. Wang X*, Pipes L, Acland GM, Trut LN, Herbeck Y, Kharlamova AV, Gulevich RG, Vladimirova AV, Johnson JL, Kukekova AV*, Clark AG* (2018) Responses to selection for tame/aggressive behaviors in silver foxes (Vulpes vulpes). PNAS, 115 (41), 10398-10403. [link]
19. Kukekova, AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli K, Gulevich RG, Vladimirova AV, Hekman JP, Perelman P, Graphodatsky AS, Brien SO, Wang X, Clark AG, Acland GM, Trut LN, Zhang G (2018). Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviors. Nature Ecology & Evolution, 2:1479-91. [link]
Veterinary Genomics and Animal Health
27. Cao W, Hicks K, White AG, Hathcock T, Kennis RA, Boothe D, Zhang D and Wang X (2020). Draft genome assembly of two Staphylococcus pseudintermedius strains isolated from canine skin biopsy. Microbiology Resource Announcements, 9(22). [link]
25. Koehler J, Sandey M, Prasad N, Levy SA, Wang X and Wang X (2020). Differential expression of miRNAs in hypoxia ("hypoxamiRs") in three canine high-grade glioma cell lines. Frontiers in Veterinary Science, 7:104. [link]
Repeat evolution in animal genomes
33. Lin ZJ, Wang X, Wang J, Tan Y, Tang X, Werren JH, Zhang D and Wang X* (2020). Comparative analysis reveals the expansion of the mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis. International Journal of Biological macromolecules, in press. [link]
Sex determination, sex-biased expression, and hermaphroditism
36. Xie Q, Li B, Zhan W, Liu F, Tan P, Wang X and Lou B (2020). A transient hermaphroditic stage in early male gonadal development in little yellow croaker, Larimichthys polyactis. Frontiers of Endocrinology, in press. [link]
14. Wang X, Werren JH, Clark AG (2015) Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti. PNAS, 112(27): E3545-E3554. [link] Commented in Biology of Reproduction. [link]
Allelic imbalance - genomics imprinting
18. Hillman PR, Christian SGB, Doan R, Cohen ND, Douglas KC, Konganti K, Wang X, Samollow PB and Dindot SV (2017). Genomic imprinting does not reduce UBE3A in neurons. Epigenetics & Chromatin, 10:27. [link]
15. Alexander KA, Wang X, Shibata M, Clark AG, Garcia-Garcia MJ (2015) Genomic imprinting is regulated by TRIM28 through a novel mechanism that is distinct from the maintenance of germline imprints. Cell Reports, 13(6):1194-1205. [link]
12. Douglas KC, Wang X, Jasti M, Wolff A, VandeBerg JL, Clark AG, Samollow PB (2014) Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene. BMC Genomics, 15:89. [link]
11. Wang X and Clark AG (2014). Using next-generation RNA sequencing to identify imprinted genes. Heredity, 113(2):156–166. [link]
8. Wang X, Miller DC, Harman R, Antczak DF, Clark AG (2013). Paternally expressed genes predominate in the placenta. PNAS, 110(26):10705-10710. [link] Commented in Biology of Reproduction [link] and Science Daily. [link]
6. Wang X, Soloway PB, Clark AG (2011). A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq. Genetics, 189(1):1-14. [link]
3. Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG (2008). Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE, 3(12):e3839. [link]
2. Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K (2008). A genome-wide approach to identifying novel-imprinted genes. Human Genetics, 122(6),625-634. [link]
Allelic imbalance - X chromosome inactivation
10. Wang X, Douglas KC, VandeBerg JL, Clark AG, Samollow PB (2014). Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, monodelphis domestica. Genome Research, 24 (1):70-83. [link]
7. Wang X, Miller DC, Antczak DF, Clark AG (2012). Random X inactivation in the horse and mule placenta. Genome Research, 22 (10):1855-1863. [link]
4. Wang X, Soloway PD, Clark AG (2010). Paternally biased X inactivation in mouse neonatal brain. Genome Biology, 11(7):R79. [link]
Epigenetics and gene expression regulation
21. Chen L, Wang Y, Yao B, Mitra A, Wang X and Qin X (2018) TIVAN: Tissue-specific cis-eQTL single nucleotide variant annotation and prediction. Bioinformatics, 35 (9), 1573-1575. [link]
13. Chow CY, Wang X, Riccardi D, Wolfner MF, Clark AG (2015) The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse. PLoS Genetics, 11(2):e1004924. [link]
Parasitoids and Wolbachia genomics and epigenomics
31. Wang X, Xiong X, Cao W, Zhang C, Werren JH* and Wang X* (2020). Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination. Genome Biology and Evolution, in press, doi: 10.1093/gbe/evaa219.
26. Wang X, Kelkar KD, Xiong X, Martinson EO, Lynch J, Zhang C, Werren JH and Wang X (2020). Whole genome sequence and annotation of the parasitoid jewel wasp Nasonia giraulti laboratory strain RV2X[u]. Genes, Genomes, Genetics, 10:2565-2572. [link]
22. Wang X, Xiong X, Cao W, Zhang C, Werren JH and Wang X (2019). Genome assembly of the A-group Wolbachia in Nasonia oneida using linked-reads technology. Genome Biology and Evolution, 10: 3008-3013. [link]
17. Rago A, Gilbert D, Choi JH, Sackton T, Wang X, Kelkar Y, Werren JH, Colbourne JK (2016) OGS2: Genome Re-Annotation of the Jewel Wasp Nasonia vitripennis. BMC Genomics, 17:678. [link]
16. Wang X*, Werren JH*, Clark AG* (2016) Allele-specific transcriptome and methylome analysis reveals stable transmission and cis-regulation of DNA methylation in Nasonia. PLoS Biology, 14(7):e1002500. (*co-corresponding authors) [link]
9. Wang X, Wheeler D, Avery A, Rago A, Choi JH, Colbourne JK, Clark AG, Werren JH (2013). Function and evolution of DNA methylation of the genome of Nasonia vitripennis. PLoS Genetics, 9(10): e1003872. [link] [cover image]
Population genetics, genomics & evolution
30. Phillips M, Babu JR, Wang X and Thangiah G (2020). DNA Copy Number and Structural Variation (CNV): Contributions to Adult and Childhood Obesity. Biochemical Society Transactions, BST20200556. [link]
5. Clark AG, Wang X, Matise TC (2010). Contrasting methods of quantifying fine structure of human recombination. Annual Review of Genomics and Human Genetics, 11:45-64. [link]
1. Brideau NJ, Flores HA, Wang J, Maheshwari S, Wang X, Barbash, DA (2006). Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila. Science, 314(5803):1292-1295. [link]
34. Simora RM, Xing D, Bangs M, Wang W, Ma X, Su B, Khan MGQ, Qin Z, Lu C, Alston V, Hettiarachchi D, Johnson A, Li S, Coogan M, Gurbatow J, Terhune J, Wang X and Dunham RA (2020). CRISPR/Cas9-mediated Knock-in of Alligator Cathelicidin Gene in a Non-coding Region of Channel Catfish Genome. Scientific Reports, in press.
32. Ma X, Su B, Bangs M, Alston V, Backenstose NJC, Simora RM, Wang W, Xing D, Li S, Ye Z, Moss A, Duong TY, Wang X* and Dunham RA* (2020). Comparative genomic and transcriptomic analyses revealed twenty-six candidate genes involved in the air-breathing development and function of the bighead catfish Clarias macrocephalus. Marine Biotechnology, in press. [link]
29. Ma X, Su B, Tian Y, Backenstose NJC, Ye Z, Moss A, Duong TY, Wang X* and Dunham RA* (2020). Deep transcriptomic analysis reveals the dynamic developmental progression during early development of channel catfish (Ictalurus punctatus). International Journal of Molecular Science, 21(15):5535. [link]
23. Hamilton M, Ma X, McCrea B, Carrisosa M, Macklin K, Zhang C, Wang X* and Hauck R* (2019). Influence of Eimeria spp. infection on chicken jejunal microbiota and the efficacy of two alternative products against the infection. Avian Diseases, 64(2), 123-129. [link]
Detection dogs and behavioral genomics
28. Haney PS, Lazarowski L, Wang X, Wang X, Hathcock J, Lofton R, Wilborn R, and Waggoner LP (2020). Effectiveness of PennHIP® and Orthopedic Foundation for Animals hip quality scores for breeding selection to reduce hip dysplasia in a population of purpose-bred detection dogs. Journal of the American Veterinary Medical Association, 257:299-304. [link]
24. Rosenfeld CS, Hekman JP, Johnson JL, Zhen L, Ortega MT, Joshi T, Mao J, Vladimirova AV, Gulevich RG, Kharlamova AV, Acland GM, Wang X, Clark AG, Trut LN, Behura SK, Kukekova AV (2020). Hypothalamic transcriptome of tame and aggressive silver foxes (Vulpes vulpes) identifies gene expression differences shared across brain regions. Genes, Brain and Behavior, 19(1):e12614. [link]
20. Wang X*, Pipes L, Acland GM, Trut LN, Herbeck Y, Kharlamova AV, Gulevich RG, Vladimirova AV, Johnson JL, Kukekova AV*, Clark AG* (2018) Responses to selection for tame/aggressive behaviors in silver foxes (Vulpes vulpes). PNAS, 115 (41), 10398-10403. [link]
19. Kukekova, AV, Johnson JL, Xiang X, Feng S, Liu S, Rando HM, Kharlamova AV, Herbeck Y, Serdyukova NA, Xiong Z, Beklemischeva V, Koepfli K, Gulevich RG, Vladimirova AV, Hekman JP, Perelman P, Graphodatsky AS, Brien SO, Wang X, Clark AG, Acland GM, Trut LN, Zhang G (2018). Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviors. Nature Ecology & Evolution, 2:1479-91. [link]
Veterinary Genomics and Animal Health
27. Cao W, Hicks K, White AG, Hathcock T, Kennis RA, Boothe D, Zhang D and Wang X (2020). Draft genome assembly of two Staphylococcus pseudintermedius strains isolated from canine skin biopsy. Microbiology Resource Announcements, 9(22). [link]
25. Koehler J, Sandey M, Prasad N, Levy SA, Wang X and Wang X (2020). Differential expression of miRNAs in hypoxia ("hypoxamiRs") in three canine high-grade glioma cell lines. Frontiers in Veterinary Science, 7:104. [link]
Repeat evolution in animal genomes
33. Lin ZJ, Wang X, Wang J, Tan Y, Tang X, Werren JH, Zhang D and Wang X* (2020). Comparative analysis reveals the expansion of the mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis. International Journal of Biological macromolecules, in press. [link]
Sex determination, sex-biased expression, and hermaphroditism
36. Xie Q, Li B, Zhan W, Liu F, Tan P, Wang X and Lou B (2020). A transient hermaphroditic stage in early male gonadal development in little yellow croaker, Larimichthys polyactis. Frontiers of Endocrinology, in press. [link]
14. Wang X, Werren JH, Clark AG (2015) Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti. PNAS, 112(27): E3545-E3554. [link] Commented in Biology of Reproduction. [link]
Allelic imbalance - genomics imprinting
18. Hillman PR, Christian SGB, Doan R, Cohen ND, Douglas KC, Konganti K, Wang X, Samollow PB and Dindot SV (2017). Genomic imprinting does not reduce UBE3A in neurons. Epigenetics & Chromatin, 10:27. [link]
15. Alexander KA, Wang X, Shibata M, Clark AG, Garcia-Garcia MJ (2015) Genomic imprinting is regulated by TRIM28 through a novel mechanism that is distinct from the maintenance of germline imprints. Cell Reports, 13(6):1194-1205. [link]
12. Douglas KC, Wang X, Jasti M, Wolff A, VandeBerg JL, Clark AG, Samollow PB (2014) Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene. BMC Genomics, 15:89. [link]
11. Wang X and Clark AG (2014). Using next-generation RNA sequencing to identify imprinted genes. Heredity, 113(2):156–166. [link]
8. Wang X, Miller DC, Harman R, Antczak DF, Clark AG (2013). Paternally expressed genes predominate in the placenta. PNAS, 110(26):10705-10710. [link] Commented in Biology of Reproduction [link] and Science Daily. [link]
6. Wang X, Soloway PB, Clark AG (2011). A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq. Genetics, 189(1):1-14. [link]
3. Wang X, Sun Q, McGrath SD, Mardis ER, Soloway PD, Clark AG (2008). Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE, 3(12):e3839. [link]
2. Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K (2008). A genome-wide approach to identifying novel-imprinted genes. Human Genetics, 122(6),625-634. [link]
Allelic imbalance - X chromosome inactivation
10. Wang X, Douglas KC, VandeBerg JL, Clark AG, Samollow PB (2014). Chromosome-wide profiling of X-chromosome inactivation and epigenetic states in fetal brain and placenta of the opossum, monodelphis domestica. Genome Research, 24 (1):70-83. [link]
7. Wang X, Miller DC, Antczak DF, Clark AG (2012). Random X inactivation in the horse and mule placenta. Genome Research, 22 (10):1855-1863. [link]
4. Wang X, Soloway PD, Clark AG (2010). Paternally biased X inactivation in mouse neonatal brain. Genome Biology, 11(7):R79. [link]
Epigenetics and gene expression regulation
21. Chen L, Wang Y, Yao B, Mitra A, Wang X and Qin X (2018) TIVAN: Tissue-specific cis-eQTL single nucleotide variant annotation and prediction. Bioinformatics, 35 (9), 1573-1575. [link]
13. Chow CY, Wang X, Riccardi D, Wolfner MF, Clark AG (2015) The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse. PLoS Genetics, 11(2):e1004924. [link]
Parasitoids and Wolbachia genomics and epigenomics
31. Wang X, Xiong X, Cao W, Zhang C, Werren JH* and Wang X* (2020). Phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and recombination. Genome Biology and Evolution, in press, doi: 10.1093/gbe/evaa219.
26. Wang X, Kelkar KD, Xiong X, Martinson EO, Lynch J, Zhang C, Werren JH and Wang X (2020). Whole genome sequence and annotation of the parasitoid jewel wasp Nasonia giraulti laboratory strain RV2X[u]. Genes, Genomes, Genetics, 10:2565-2572. [link]
22. Wang X, Xiong X, Cao W, Zhang C, Werren JH and Wang X (2019). Genome assembly of the A-group Wolbachia in Nasonia oneida using linked-reads technology. Genome Biology and Evolution, 10: 3008-3013. [link]
17. Rago A, Gilbert D, Choi JH, Sackton T, Wang X, Kelkar Y, Werren JH, Colbourne JK (2016) OGS2: Genome Re-Annotation of the Jewel Wasp Nasonia vitripennis. BMC Genomics, 17:678. [link]
16. Wang X*, Werren JH*, Clark AG* (2016) Allele-specific transcriptome and methylome analysis reveals stable transmission and cis-regulation of DNA methylation in Nasonia. PLoS Biology, 14(7):e1002500. (*co-corresponding authors) [link]
9. Wang X, Wheeler D, Avery A, Rago A, Choi JH, Colbourne JK, Clark AG, Werren JH (2013). Function and evolution of DNA methylation of the genome of Nasonia vitripennis. PLoS Genetics, 9(10): e1003872. [link] [cover image]
Population genetics, genomics & evolution
30. Phillips M, Babu JR, Wang X and Thangiah G (2020). DNA Copy Number and Structural Variation (CNV): Contributions to Adult and Childhood Obesity. Biochemical Society Transactions, BST20200556. [link]
5. Clark AG, Wang X, Matise TC (2010). Contrasting methods of quantifying fine structure of human recombination. Annual Review of Genomics and Human Genetics, 11:45-64. [link]
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