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Publications

*: equal contribution; †: equal contribution; #: corresponding author; underlined: lab members

2024

  1. Fan, Z., R. Zhang, A. Zhou, J. Hey, Y. Song, N. Osada, Y. Hamada, B. Yue, J. Xing, and J. Li (2024) Genomic Evidence for the Complex Evolutionary History of Macaques (Genus Macaca). Journal of Molecular Evolution
  2. Prem S., B. Dev, C. Peng, M. Mehta, R. Alibutud, R. J. Connacher, M. St Thomas, X. Zhou, P. Matteson, J. Xing, J. H. Millonig, and E. DiCicco-Bloom (2024) Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells. eLife 13:e82809 [bioRxiv] [Press Release]
  3. Sun S., T. Defosse, A. Boyd, J. Sop, F. Verderose, D. Surray, M. Aziz, M. Howland, S. Wu, N. Changela, J. Jang, K. Schindler, J. Xing#, and K. S. McKim# (2024) Whole transcriptome and functional analyses identify novel genes involved in meiosis and fertility in Drosophila melanogaster. Scientific Reports 14:3602 [bioRxiv]
  4. Cao, X., S. Sun, J. Xing# (2024) A massive proteogenomic screen identifies thousands of novel peptides from the human “dark” proteome. Molecular & Cellular Proteomics 23(2):100719  [Data] [Code] [Website]

2023

  1. Wang, S., B. Wang, V. Drury, S. Drake, N. Sun, H. Alkhairo, J. Arbelaez, C. Duhn, Tourette International Collaborative Genetics (TIC Genetics, including X. Cao), V. H. Bal, K. Langley, J. Martin, J. Xing, G. A. Heiman, J. A. Tischfield, T. V. Fernandez, M. J. Owen, M. C. O’Donovan, A. Thapar, M. W. State, and A. J. Willsey (2023) Rare maternally inherited coding variants on Chromosome X carry predominantly male risk in Autism, Tourette Syndrome, and Attention-deficit/Hyperactivity Disorder. Nature Communication 14:8077 [medRxiv]
  2. Sun, S., M. Aboelenain, D. Ariad, M. E. Haywood, C. R. Wageman, M. Duke, A. Bag, M. Viotti, M. Katz-Jaffe, R. C. McCoy, K. Schindler, and J. Xing# (2023) Identifying risk genes for embryo aneuploidy using ultra-low coverage whole-genome sequencing. American Journal of Human Genetics 110(12):2092-2102 [medRxiv]  [Code] [Summary Statistics] [Press Release]
  3. Rybacki, K., M. Xia, M. U. Ahsan, J. Xing#, and K. Wang #(2023) Assessing the expression of Long INterspersed Elements (LINEs) via long-read sequencing in diverse human tissues and cell lines. Genes 14(10):1893 [LINE-Expression-LRS]
  4. Alibutud, R.*, S. Hansali*, X. Cao, A. Zhou, V. Mahaganapathy, M. Azaro, C. Gwin, S. Wilson, S. Buyske, C. W. Bartlett, J. F. Flax, L. M. Brzustowicz, and J. Xing# (2023) Structural variations contribute to the genetic etiology of autism spectrum disorder and language impairments. International Journal of Molecular Sciences 24(17):13248
  5. Zhang, C., L. Wang, L. Dou, B. Yue, J. Xing#, and J. Li# (2023) Transposable elements shape the genome diversity and the evolution of Noctuidae species. Genes 14(6): 1244 [Preprints.org]
  6. Zhou, A., X. Cao, V. Mahaganapathy, M. Azaro, C. Gwin, S. Wilson, S. Buyske, C. W. Bartlett, J. F. Flax, L. M. Brzustowicz, and J. Xing# (2023) Common genetic risk factors in ASD and ADHD co-occurring families. Human Genetics 142:217–230 [medRxiv]

2022

  1. Shrestha D.*, A. Bag*, R. Wu, Y. Zhang, X. Tang, Q. Qi, J. Xing#, and Y. Cheng#(2022) Genomics and epigenetics guided identification of tissue-specific genomic safe harbors. Genome Biology 23:199  [GEG-SH mapper] [Press Release]
  2. Zhang, R.*, C. Zhou*, X. Jin, K. Liu, Z. Fan, J. Xing, and J. Li (2022) Chromosome-level genome assembly of Tibetan macaque (Macaca thibetana) and species-specific structural variations. Zoological Research 43(5):880-885 [authorea] 
  3. Paulat, N. S., E. McGuire, K. Subramanian, A. B. Osmanski, D. D. Moreno-Santillán, D. A. Ray#, and J. Xing# (2022) Transposable elements in bats show differential accumulation patterns determined by class and functionality. Life 12(8):1190 [Supplemental Data]
  4. Wong, A., A. Zhou, X. Cao, V. Mahaganapathy, M. Azaro, C. Gwin, S. Wilson, S. Buyske, C. W. Bartlett, J. F. Flax, L. M. Brzustowicz, and J. Xing# (2022) MicroRNA and MicroRNA-target variants associated with autism spectrum disorder and related disorders. Genes 13(8):1329
  5. Sun, S., M. Miller, Y. Wang, K. M. Tyc, X. Cao, R. T. Scott, Jr., X. Tao, Y. Bromberg, K. Schindler, and J. Xing# (2022) Predicting embryonic aneuploidy rate in IVF patients using whole-exome sequencing. Human Genetics 141:1615–1627 [Gene Scores] [News feature in Rutgers Today]
  6. Baxter, S. M., J. E. Posey, N. J. Lake, N. Sobreira, J. X. Chong, S. Buyske, E. E. Blue, L. H. Chadwick, Z. H. Coban-Akdemir, K. F. Doheny, C. P. Davis, M. Lek, C. Wellington, S. N. Jhangiani, M. Gerstein, R. A. Gibbs, R. P. Lifton, D. G. MacArthur, T. C. Matise, J. R. Lupski, D. Valle, M. J. Bamshad, A. Hamosh, S. Mane, D. A. Nickerson, Centers for Mendelian Genomics Consortium (including X. Cao, Y. Zhang, and J. Xing), H. L. Rehm, A. O’Donnell-Luria (2022) Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genetics in Medicine 24(4):784-797 [medRxiv] 

2021

  1. Tong, K., O. A. Kothari, K. S. Haro, A. Panda, M. M. Bandari, J. N. Carrick, J. J. Hur, L. Zhang, C. S. Chan, J. Xing, M. L. Gatza, S. Ganesan, and M. P. Verzi (2021) SMAD4 is critical in suppression of BRAF-V600E serrated tumorigenesis. Oncogene 40(41):6034-6048
  2. Cao, X.*, Y. Zhang*, M. Abdulkadir, L. Deng, T. V. Fernandez, B. Garcia-Delgar, J. Hagstrøm, P. J. Hoekstra, R. A. King, J. Koesterich, S. Kuperman, A. Morer, C. Nasello, K. J. Plessen, J. K. Thackray, L. Zhou, Tourette International Collaborative Genetics Study (TIC Genetics), A. Dietrich, J. Tischfield, G. Heiman, and J. Xing# (2021) Whole exome sequencing identifies genes associated with Tourette’s Disorder in multiplex families. Molecular Psychiatry 26(11):6937-6951
  3. Cao, X. and J. Xing# (2021) PrecisionProDB: improving the proteomics performance for precision medicine. Bioinformatics 37(19):3361–3363
  4. Wartosch, L., K. Schindler, M. Schuh, J. R. Gruhn, E. R. Hoffmann, R. C. McCoy, and J. Xing (2021) Origins and Mechanisms Leading to Aneuploidy in Human Eggs. Prenatal Diagnosis 41:620–630
  5. Collantes J. C., V. M. Tan, H. Xu, M. Ruiz-Urigüen, A. Alasadi, J. Guo, H. Tao, C. Su, Tyc, K. M., T. Selmi, J. J. Lambourne, J. A. Harbottle, J. Stombaugh, J. Xing, C. M. Wiggins, and S. Jin (2021) Development and characterization of a modular CRISPR and RNA aptamer mediated base editing system. The CRISPR Journal 4(1):58–68 [News Release]
  6. Biswas, L., Tyc, K. M., W. E. Yakoubi, K. Morgan, J. Xing, and K. Schindler (2021) Meiosis interrupted: the genetics of female infertility via meiotic failure. Reproduction 161:R13-R35
  7. Tyc, K. M.*, A. Wong*, R. T. Scott, Jr., X. Tao, K. Schindler, and J. Xing# (2021) Analysis of DNA variants in miRNAs and miRNA 3’UTR binding sites in female infertility patients. Laboratory Investigation 101:503–512 [Code]
  8. Dyment, D. A.*, A. O’Donnell-Luria*, P. B. Agrawal, Z. Coban Akdemir, K. A. Aleck, D. Antaki, H. Al Sharhan, P. B. Au, H. Aydin, A. H. Beggs, K. Bilguvar, E. Boerwinkle, H. Brand, C. A. Brownstein, S. Buyske, B. Chodirker, J. Choi, A. E. Chudley, C. L. Clericuzio, G. F. Cox, C. Curry, E. de Boer, B. B. A. de Vries, K. Dunn, C. M. Dutmer, E. M. England, J. A. Fahrner, B. B. Geckinli, C. A. Genetti, A. Gezdirici, W. T. Gibson, J. G. Gleeson, C. R. Greenberg, A. Hall, A. Hamosh, T. Hartley, S. N. Jhangiani, E. Karaca, K. Kernohan, J. L. Lauzon, M. E. S. Lewis, R. B. Lowry, F. Lopez-Giraldez, T. C. Matise, J. McEvoy-Venneri, B. McInnes, A. Mhanni, S. Garcia Minaur, J. Moilanen, A. Nguyen, M. J. M. Nowaczyk, J. E. Posey, K. Ounap, D. Pehlivan, S. Pajusalu, L. S. Penney, T. Poterba, P. Prontera, M. J. R. Doriqui, S. L. Sawyer, N. Sobreira, V. Stanley, D. Torun, D. Wargowski, P. D. Witmer, I. Wong, J. Xing, M. S. Zaki, Y. Zhang, Care4Rare Consortium, Centers for Mendelian Genomics, K. M. Boycott, M. J. Bamshad, D. A. Nickerson, E. E. Blue# and A. M. Innes# (2021) Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome. American Journal of Medical Genetics Part A 185:119-133

2020

  1. Li, J., Z. Fan, F. Shen, A. L. Pendleton, Y. Song, J. Xing, B. Yue, J. M. Kidd#, and J. Li# (2020) Genome-wide CNV study of nine Macaca species provides new insights into their genetic divergence, adaptation and biomedical application. Genome Biology and Evolution 12:2211–2230 [Cover artile]
  2. Tyc, K. M.*, W. El Yakoubi*, A. Bag, J. Landis, Y. Zhan, N. R. Treff, R. T. Scott, Jr., X. Tao, K. Schindler#, and J. Xing# (2020) Exome sequencing links CEP120 mutation to maternally-derived aneuploid conception risk. Human Reproduction 35:2134-2148 [Variant Calls]
  3. Yan, C, X. Zhang, L. Zhou, Q. Yang, M. Zhou, L. Zhang, J. Xing, Z. Yan, M. Price, J. Li, B. Yue, and Z. Fan (2020) Effects of aging on gene expression in the blood of captive Tibetan Macaques (Macaca thibetana) and comparisons with expressions in humans. Zoological Research 41:557-563  
  4. Cao, X.*, Y. Zhang*, L. M. Payer, H. Lords, J. P. Steranka, K. H. Burns, J. Xing# (2020) Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues. Genome Biology 21:185 [bioRxiv]  [pMEI genotypes]
  5. Qiu S., H. Liu, Z. Jian, Z. Fan, S. Liu, J. Xing, and J. Li (2020) Characterization of the primate TRIM gene family reveals the recent evolution in primates. Molecular Genetics and Genomics 295:1281-1294  
  6. Abel, H. J., D. E. Larson, A. A. Regier, C. Chiang, I. Das, K. L. Kanchi, R. M. Layer, B. M. Neale, W. J. Salerno, C. Reeves, S. Buyske, NHGRI Centers for Common Disease Genomics (including Y. Zhang and J. Xing), T. C. Matise, D. M. Muzny, M. C. Zody, E. S. Lander, S. K. Dutcher, N. O. Stitziel, and I. M. Hall (2020) Mapping and characterization of structural variation in 17,795 human genomes. Nature 583:83-89 [bioRxiv]  
  7. Du, L.*, T. Guo*, Q. Liu, J. Li, X. Zhang, J. Xing, B. Yue, J. Li#, and Z. Fan# (2020) MACSNVdb: a high-quality SNV database for interspecies genetic divergence investigation among macaques. Database (Oxford) 2020:baaa027  
  8. Tyc, K. M., R. C. McCoy, K. Schindler, and J. Xing# (2020) Mathematical modeling of human oocyte aneuploidy. Proceedings of the National Academy of Sciences, USA 19:10455-10464  [Code] [News feature in Rutgers Today] [Commentary in PNAS]
  9. Loh, J.*, H. Ha*, T. Lin, N. Sun, K. H. Burns, and J. Xing# (2020) Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions. Mobile DNA 11:12 [Sequence Data] [Code]
  10. Liu, S.*, M. Tian*, F. He*, J. Li*, H. Xie*, W. Liu, Y. Zhang, R. Zhang, M. Yi, F. Che, X. Ma, Y. Zheng, H. Deng, G. Wang, L. Chen, X. Sun, Y. Xu, J. Wang, Y. Zang, M. Han, X. Wang, H. Guan, Y. Ge, C. Wu, H. Wang, H. Liang, H. Li, N. Ran, Z. Yang, H. Huang, Y. Wei, X. Zheng, X. Sun, X. Feng, L. Zheng, T. Zhu, W. Luo, Q. Chen, Y. Yan, Z. Huang, Z. Jing, Y. Guo, X. Zhang, C. P. Schaaf, J. Xing, C. Wang, F. Yu, and J. Guan (2020) Mutations in ASH1L confer susceptibility to Tourette Syndrome. Molecular Psychiatry 25:476–490
  11. Oppenheim, S.*, X. Cao*, O. Rueppel, S. Krongdang, P. Phokasem, R. DeSalle, S. Goodwin, J. Xing, P. Chantawannakul, and J. Rosenfeld (2020) Whole genome sequencing and assembly of the Asian honey bee Apis dorsata. Genome Biology and Evolution 12:3677–3683 [bioRxiv]

2019

  1. Zhou, A., T. Lin, and J. Xing# (2019) Evaluating nanopore sequencing data processing pipelines for structural variation identification. Genome Biology 20:237
  2. Feusier, J., W. S. Watkins, J. Thomas, A. Farrell, D. J. Witherspoon, L. Baird, H. Ha, J. Xing, and L. B. Jorde (2019) Pedigree-based estimation of mobile element retrotransposition rates in humans. Genome Research 29:1567–1577 [bioRxiv] [Cover artile]
  3. Vazquez, B. N.*, J. K. Thackray*, N. G. Simonet, S. Chahar, N. Kane-Goldsmith, S. J. Newkirk, S. Lee, J. Xing, M. P. Verzi, W. An, A. Vaquero, J. A. Tischfield, and L. Serrano (2019) SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina. Nucleic Acids Research 47:7870-7885
  4. Kumar, N.*, Y. Tsai*, L. Chen*, A. Zhou, K. K. Banerjee, M. Saxena, S. Huang, N. H. Toke, J. Xing, R. A. Shivdasani, J. R. Spence, and M. P. Verzi (2019) The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development. Development 146:dev172189

2018

  1. Peng, C., L. Niu, J. Deng, J. Yu, X. Zhang, C. Zhou, J. Xing#, and J. Li# (2018) Can-SINE dynamics in the giant panda and three other Caniformia genomes. Mobile DNA 9:32
  2. Regier, A. A. , Y. Farjoun, D. E. Larson, O. Krasheninina, H. M. Kang, D. P. Howrigan, B. Chen, M. Kher, E. Banks, D. C. Ames, A. C. English, H. Li , J. Xing, Y. Zhang, T. Matise, G. R. Abecasis, W. Salerno, M. C. Zody, B. M. Neale, and I. M. Hall (2018) Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects. Nature Communication 9:4038
  3. Wang S., J. D. Mandell, Y. Kumar, N. Sun, M. T. Morris, J. Arbelaez, C. Nasello, S. Dong, C. Duhn, X. Zhao, Z. Yang, S. S. Padmanabhuni, D. Yu, R. A. King, A. Dietrich, N. Khalifa, N. Dahl, A. Y. Huang, B. M. Neale, G. Coppola, C. A. Mathews, J. M. Scharf, Tourette International Collaborative Genetics Study (TIC Genetics) (including H. Poisner and Y. Zhang), Tourette Syndrome Genetics Southern and Eastern Europe Initiative (TSGENESEE), Tourette Association of America International Consortium for Genetics (TAAICG), T. V. Fernandez, J. D. Buxbaum, S. De Rubeis, D. E. Grice, J. Xing, G. A. Heiman, J. A. Tischfield, P. Paschou, A. J. Willsey, and M. W. State (2018) de novo sequence and copy number variants are strongly associated with Tourette Disorder and implicate cell polarity in pathogenesis. Cell Reports 24:3441–3454
  4. Perekatt, A. O., P. P. Shah, S. Cheung, N. Jariwala, A. Wu, V. Gandhi, N. Kumar, Q. Fang, N. Patel, L. Chen, S. Joshi, A. Zhou, M. M. Taketo, J. Xing, E. White, N. Gao, M. L. Gatza, and M. P. Verzi (2018) SMAD4 suppresses WNT-driven de-differentiation and oncogenesis in the differentiated gut epithelium. Cancer Research 78:4878-4890
  5. Fan Z, A. Zhou, N. Osada, J. Yu, J. Jiang, P. Li, L. Du, L. Niu, J. Deng, H. Xu, J. Xing, B. Yue, and J. Li (2018) Ancient hybridization and admixture in macaques (genus Macaca) inferred from whole genome sequences. Molecular Phylogenetics and Evolution 127:376-386
  6. Zhou, A., Y. Zhang, Y. Sun#, and J. Xing# (2018) PipelineDog: a simple and flexible graphic pipeline con-struction and maintenance tool. Bioinformatics 34(9):1603–5
  7. Sun, N., C. Nasello, L. Deng, N. Wang, Y. Zhang, Z. Xu, Z. Song, K. Kwan, R. A. King, Z. P. Pang, J. Xing, G. A. Heiman, and J. A. Tischfield (2018) The PNKD gene is associated with Tourette Disorder or Tic disorder in a multiplex family. Molecular Psychiatry 23:1487-1495

2017

  1. Tong K.*, O. Pellón-Cárdenas*, V. R. Sirihorachai, B. N. Warder, O. A. Kothari, A. O. Perekatt, E. E. Fokas, R. L. Fullem, A. Zhou, J. K. Thackray, H. Tran, L. Zhang, J. Xing, and M. P. Verzi (2017) Degree of tissue differentiation dictates susceptibility to BRAF-driven colorectal cancer. Cell Reports 21:3833–45
  2. Wang, N.*, Y. Zhang*, E. Gedvilaite, J. Loh, T. Lin, X. Liu, C. Liu, D. Kumar, R. Donnelly, K. Raymond, E. H. Schuchman, D. E. Sleat#, P. Lobel#, and J. Xing# (2017) Using whole-exome sequencing to investigate the genetic bases for lysosomal storage diseases of unknown etiology. Human Mutation 38(11):1491–9
  3. Rustagi, N., A. Zhou, W. S. Watkins, E. Gedvilaite, S. Wang, N. Ramesh, D. Muzny, R. A. Gibbs, L. B. Jorde#, F. Yu#, and J. Xing# (2017) Extremely low-coverage whole genome sequencing in South Asians captures population genomics information. BMC Genomics 18(1):396
  4. Willsey, A. J.*, T. V. Fernandez*, D. Yu†, R. A. King†, A. Dietrich†, J. Xing†, S. J. Sanders, J. D. Mandell, A. Y. Huang, P. Richer, L. Smith, S. Dong, K. E. Samocha, Tourette International Collaborative Genetics (TIC Genetics) (including E. Gedvilaite, S. Wang, Y. Zhang, A. Zhou), Tourette Syndrome Association International Consortium for Genetics (TSAICG), B. M. Neale, G. Coppola, C. A. Mathews, J. A. Tischfield, J. M. Scharf, M. W. State, and G. A. Heiman (2017) De novo coding variants are strongly associated with Tourette Disorder. Neuron 94(3):486–99.e9 [Cover artile] [Best of Neuron 2016-2017] [News release 1] [News release 2]
  5. Nguyen A. L.*, D. Marin*, A. Zhou, A. S. Gentilello, E. M. Smoak, Z. Cao, A. Fedick, Y. Wang, D. Taylor, R. T. Scott Jr., J. Xing, N. Treff, and K. Schindler (2017) Identification and characterization of Aurora Kinase B and C variants associated with maternal aneuploidy. Molecular Human Reproduction 23(6):406-16
  6. Viljetic B*, L. Diao*, J. Liu*, Z. Krsnik*, S. H. R. Wijeratne, R. Kristopovich, M. L. Kraushar, J. Song, J. Xing#, K. C. Chen#, M. R. Rasin# (2017) Multiple roles of PIWIL1 in mouse neocorticogenesis. bioRxiv doi: https://doi.org/10.1101/106070
  7. Ha, H., N. Wang, and J. Xing# (2017) Library Construction for High-Throughput Mobile Element Identification and Genotyping. Methods in Molecular Biology 1589:1-15
  8. Jadot, M., M. Boonen, J. Thirion, N. Wang, J. Xing, C. Zhao, M. Qian, H. Zheng, J. Everett, D. Moore, D. Sleat, and P. Lobel (2017) Accounting for protein subcellular localization Molecular and Cellular Proteomics. Molecular and Cellular Proteomics 16(2):194-212

2016

  1. Kumar, N., M. Srivillibhuthur, S. Joshi, K. D. Walton, A. Zhou, W. J. Faller, A. O. Perekatt, O. J. Sansom, D. L. Gumucio, J. Xing, E. M. Bonder, N. Gao, E. White, and M. P. Verzi (2016) A YY1-dependent increase in aerobic metabolism is indispensable for intestinal organogenesis. Development 143(20):3711-22
  2. Sleat D.#, E. Gedvilaite, Y. Zhang, P. Lobel, and J. Xing# (2016) Analysis of large-scale whole exome sequencing data to determine the prevalence of genetically-distinct forms of neuronal ceroid lipofuscinosis. Gene 593(2):284–91
  3. Alexander, J., H. Potamianou, J. Xing, L. Deng, I. Karagiannidis, F. Tsetsos, P. Drineas, Z. Tarnok, R. Rizzo, T. Wolanczyk, L. Farkas, P. Nagy, U. Szymanska, C. Androutsos, V. Tsironi, A. Koumoula, C. Barta, TSGeneSEE, P. Sandor, C. L. Barr, J. Tischfield, P. Paschou, G. A. Heiman, and M. Georgitsi (2016) Targeted re-sequencing approach of candidate genes implicates rare potentially functional variants in Tourette Syndrome etiology. Frontiers in Neuroscience 10:428
  4. Ross J.#, E. Gedvilaite, J. A. Badner, C. Erdman, S. Barondes, L. Baird, N. Matsunami, M. Leppert, J. Xing#, and W. Byerley# (2016) A Rare Variant in CACNA1D segregates with 7 Bipolar I cases in a large pedigree. Molecular Neuropsychiatry 2(3):145-50
  5. H. Ha, J. Loh, and J. Xing# (2016) Identification of polymorphic SVA retrotransposons using a mobile element scanning method for SVA (ME-Scan-SVA). Mobile DNA 7:15
  6. Fan Z., P. Silva, I. Gronau, S. Wang, A. S. Armero, R. M. Schweizer, O. Ramirez, J. Pollinger, M. Galaverni, D. Ortega Del-Vecchyo, L. Du, W. Zhang, Z. Zhang, J. Xing, C. Vilá, T. Marques-Bonet, R. Godinho, B. Yue, and R. K. Wayne (2016) Worldwide patterns of genomic variation and admixture in gray wolves. Genome Research 26(2):163-73
  7. Bruse S.*, M. Moreau*, Y. Bromberg*, J. Jang, N. Wang, H. Ha, M. Picchi, Y. Lin, R. J. Langley, C. Qualls, J. Klensney-Tait, J. Zabner, S. Leng, J. Mao, S. A. Belinsky, J. Xing#, and T. Nyunoya# (2016) Whole exome sequencing in severe chronic obstructive pulmonary disease. Human Genomics 10:1

2015

  1. The 1000 Genomes Project Consortium (2015) A global reference for human genetic variation. Nature 526(7571):68-74
  2. Parrish N. F., K. Fujino, Y. Shiromoto, Y. W. Iwasaki, H. Ha, J. Xing, A. Makino, S. Kuramochi-Miyagawa, T. Nakano, H. Siomi, T. Honda, and K. Tomonaga (2015) piRNA derived from ancient viral processed pseudogenes suggests transgenerational sequence-specific immunity in mammals. RNA 21(10):1691-703
  3. Platt II R. N., Y. Zhang, D. J. Witherspoon, J. Xing, A. Suh, M. S. Keith, L. B. Jorde, R. D. Stevens, and D. A. Ray (2015) Targeted capture of phylogenetically-informative Ves SINE insertions in genus Myotis. Genome Biology and Evolution 7(6):1664-75
  4. Kwak, Y., Y. Kim, J. Xing, and K. Han (2015) Evolutionary fate of SVA2 elements in primate genomes. Genes & Genomics 37:153–9

2014

  1. Song, J., J. Liu, S. L. Schnakenberg, H. Ha, J. Xing, and K. C. Chen (2014) Variation in piRNA and transposable element content in strains of Drosophila melanogaster. Genome Biology and Evolution 6(10):2786-98 [Sequence Data]
  2. Lorenzo, F. R., C. Huff, M. Myllymäki, B. Olenchock, S. Swierczek, T. Tashi, V. Gordeuk, T. Wuren, R. L. Ge, D. A. McClain, T. M. Khan, P. A. Koul, P. Guchhait, M. E. Salama, J. Xing, G. L. Semenza, E. Liberzon, A. Wilson, T. S. Simonson, L. B. Jorde, W. G. Kaelin Jr., P. Koivunen, and J. T. Prchal (2014) A genetic mechanism for Tibetan high-altitude adaptation. Nature Genetics 46(9):951-6 [news feature in ScienceDaily]
  3. The Marmoset Genome Sequencing and Analysis Consortium (2014) The common marmoset genome provides insight into primate biology and evolution. Nature Genetics 46(8):850-7 [news feature in ScienceDaily]
  4. Ha H.*, J. Song*, S. Wang, A. Kapusta, C. Feschotte, K. C. Chen and J. Xing# (2014) A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements. BMC Genomics 15:545 [Sequence Data]
  5. Hu H., J. C. Roach, H. Coon, S. L. Guthery, K. V. Volkerding, R. L. Margraf, J. D. Durtschi, S. V. Tavtigian, Shankaracharya, W. Wu, P. Scheet, S. Wang, J. Xing, G. Glusman, R. Hubley, H. Li, V. Garg, B. Moore, L. Hood, D. J. Galas, D. Srivastava, M. G. Reese, L. B. Jorde, M. Yandell, and C. D. Huff (2014) A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nature Biotechnology 32(7):663-9 [news feature in Science Daily]
  6. Fan, Z., G. Zhao, P. Li, N. Osada, J. Xing, Y. Yi, L. Du, P. Silva, H. Wang, R. Sakate, X. Zhang, H. Xu, B. Yue, J. Li (2014) Whole genome sequencing of Tibetan macaque (Macaca thibetana) provides new insight into the macaque evolutionary history. Molecular Biology and Evolution 31(6):1475–89
  7. Wuren T., T. S. Simonson, G. Qin, J. Xing, C. D. Huff, D. J. Witherspoon, L. B. Jorde, and R. L. Ge (2014) Shared and unique signals of high-altitude adaptation in geographically distinct Tibetan populations. PLoS One 9(3):e88252

2013

  1. Wang, S and J. Xing# (2013) A Primer for Disease Gene Prioritization Using Next-Generation Sequencing Data. Genomics & Informatics 11(4):191-9
  2. Wang, S., J. Lachance, S. Tishkoff, J. Hey, and J. Xing# (2013) Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from non-African Populations. Genome Biology and Evolution 5(11):2075-81
  3. Xing, J.*, T. Wuren*, T. S. Simonson*, W. S. Watkins, D. J. Witherspoon, W. Wu, G. Qin, C. D. Huff, L. B. Jorde, and R. L. Ge (2013) Genomic analysis of nature selection and phenotypic variation in high-altitude Mongolians. PLOS Genetics 9(7):e1003634 [news feature in ChinaDaily]
  4. Ge, R. L., Q. Cai, Y. Y. Shen, A. San, L. Ma, Y. Zhang, X. Yi, Y. Chen, L. Yang, Y. Huang, R. He, Y. Hui, M. Hao, Y. Li, B. Wang, X. Ou, J. Xu, Y. Zhang, K. Wu, C. Geng, W. Zhou, T. Zhou, D. M. Irwin, Y. Yang, L. Ying, H. Bao, J. Kim, D. M. Larkin, J. Ma, H. A. Lewin, J. Xing, R. N. Platt II, D. A. Ray, L. Auvil, B. Capitanu, X. Zhang, G. Zhang, R. W. Murphy, J. Wang, Y. P. Zhang, J. Wang (2013) Draft genome sequence of the Tibetan antelope. Nature Communications 4:1858 [news feature in ScienceDaily]
  5. Wu, W., E. A. Clark, G. J. Stoddard, W. S. Watkins, M. S. Esplin, T. A. Manuck, J. Xing, M. W. Varner, and L. B. Jorde (2013) Effect of interleukin-6 polymorphism on risk of preterm birth within population strata: a meta-analysis. BMC Genetics 14:30
  6. Witherspoon, D. J., Y. Zhang, J. Xing, W. S. Watkins, H. Ha, M. A. Batzer and L. B. Jorde (2013) Mobile Element Scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations. Genome Research 23(7):1170-81 [news feature in Nature Reviews Genetics]
  7. Xing, J., D. J. Witherspoon, and L. B. Jorde (2013) Mobile element biology – new possibilities with high-throughput sequencing. Trends in Genetics 29(5):280-9

2012

  1. Kim, W. , D. Londono, L. Zhou, J. Xing, A. Nato, A. Musolf, T. C. Matise, S. J. Finch, and D. Gordon (2012) Single variant and multi-variant trend tests for genetic association with next generation sequencing that are robust to sequencing error. Human Heredity 74(3-4):172-183
  2. The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56–65 [news feature in ScienceDaily]
  3. Watkins W. S., J. Xing, C. Huff, D. J. Witherspoon, Y. Zhang, U. A. Perego, S. R. Woodward and L. B. Jorde (2012) Genetic analysis of ancestry, admixture and selection in Bolivian and Totonac populations of the New World. BMC Genetics 13:39
  4. Ge, R. L., T. S. Simonson, R. C. Cooksey, U. Tanna, G. Qin, C. D. Huff, D. J. Witherspoon, J. Xing, B. Zhengzhong, J. T. Prchal, L. B. Jorde, and D. A. McClain (2012) Metabolic insight into mechanisms of high-altitude adaptation in Tibetans. Molecular Genetics and Metabolism 106(2):244-7
  5. Stringham, S. A., E. E. Mulroy, J. Xing, D. Record, M. W. Guernsey, J. T. Aldenhoven, E. J. Osborne, and M. D. Shapiro (2012) Divergence, Convergence, and the Ancestry of Feral Populations in the Domestic Rock Pigeon. Current Biology 22(4):302–8 [cover article] [news feature in ScienceDaily]
  6. Huff, C. D., D. Witherspoon, Y. Zhang, C. Gatenbee, L. A. Denson, S. Kugathasan, H. Hakonarson, A. Whiting, C. Davis, W. Wu, J. Xing, W. S. Watkins, M. Bamshad, J. P. Bradfield, K. Bulayeva, T. S. Simonson, L. B. Jorde, and S. L. Guthery (2012) Crohn’s disease and genetic hitchhiking at IBD5. Molecular Biology and Evolution 29(1):101-11

Before 2012

  1. Stewart, C.*, D. Kural*, M. P. Stromberg*, J. A. Walker, M. K. Konkel, A. M. Stutz, A. E. Urban, F. Grubert, H. Y. K. Lam, W. P. Lee, M. Busby, A. R. Indap, E. Garrison, C. Huff, J. Xing, M. P. Snyder, L. B. Jorde, M. A. Batzer, J. O. Korbe, G. T. Marth, and the 1000 Genomes Project (2011) A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genetics 7(8):e1002236
  2. Lyon, G. J. , T. Jiang, R. Van Wijk, W. Wang, P. M. Bodily, J. Xing, L. Tian, R. J. Robison, M. Clement, Y. Lin, P. Zhang, Y. Liu, B. Moore, J. T. Glessner, J. Elia, F. Reimherr, W. W. van Solinge, M. Yandell, H. Hakonarson, J. Wang, W. E. Johnson, Z. Wei, and K. Wang (2011) Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Discovery Medicine 12(62):41-55
  3. Rope, A. F., K. Wang, R. Evjenth, J. Xing, J. J. Johnston, J. J. Swensen, W. E. Johnson, B. Moore, C. D. Huff, L. M. Bird, J. C. Carey, J. M. Opitz, C. A. Stevens, T. Jiang, C. Schank, H. D. Fain, R. Robison, B. Dalley, S. Chin, S. T. South, T. J. Pysher, L. B. Jorde, H. Hakonarson, J. R. Lillehaug, L. G. Biesecker, M. Yandell, T. Arnesen, and G. J. Lyon (2011) Using VAAST to identify an X-Linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. American Journal of Human Genetics 89(1):28-43 [news feature in Nature]
  4. Yandell, M., C. D. Huff, H. Hu, M. Singleton, B. Moore, J. Xing, L. B. Jorde, and M. G. Reese (2011) A probabilistic disease-gene finder for personal genomes. Genome Research 21(9):1529-42 [news feature in Nature]
  5. Roos, C., D. Zinner, L. S. Kubatko, C. Schwarz, M. Yang, D. Meyer, S. D. Nash, J. Xing, M. A. Batzer, M. Brameier, F. H. Leendertz, T. Ziegler, D. Perwitasari-Farajallah, T. Nadler, L. Walter and M. Osterholz (2011) Nuclear versus mitochondrial DNA: Evidence for hybridization in colobine monkeys. BMC Evolutionary Biology 11:77
  6. Huff, C. D.*, Witherspoon, D. J.*, Simonson, T. S., J. Xing, W. S. Watkins, Y. Zhang, T. M. Tuohy, D. W. Neklason, R. W. Burt, S. L. Guthery, S. R. Woodward, and L. B. Jorde (2011) Maximum-likelihood estimation of recent shared ancestry (ERSA) using shared genome segments. Genome Research 21(5):768-74
  7. Simonson, T. S., J. Xing, R. Barrett, E. Jerah, P. Loa, Y. Zhang, W. S. Watkins, D. J. Witherspoon, C. D. Huff, S. Woodward, B. Mowry, and L. B. Jorde (2011) Ancestry of the Iban is predominantly Southeast Asian: genetic evidence from autosomal, mitochondrial, and Y chromosomes. PLoS One 6(1):e16338
  8. Xing, J., W. S. Watkins, Y. Hu, C. D. Huff, A. Sabo, D. M. Muzny, M. J. Bamshad, R. A. Gibbs, L. B. Jorde, and F. Yu (2010) Inference of human expansion in Eurasia and genetic diversity in India. Genome Biology 11:R113
  9. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population scale sequencing. Nature 467:1061-1073 [cover article] [news feature in Nature]
  10. Xing, J., W. S. Watkins, A. Shlien, E. Walker, C. D. Huff, D. J. Witherspoon, Y. Zhang, T. S. Simonson, R. B. Weiss, J. D. Schiffman, D. Malkin, S. R. Woodward and L. B. Jorde (2010) Toward a more Uniform Sampling of Human Genetic Diversity: A Survey of Worldwide Populations by High-density Genotyping. Genomics 96:199-210
  11. Witherspoon, D. J., J. Xing, Y. Zhang, W. S. Watkins, M. A. Batzer and L. B. Jorde (2010) Mobile element scanning (ME-Scan) by targeted high-throughput sequencing. BMC Genomics 11(1):410
  12. Simonson, T. S., Y. Yang, C. D. Huff, H. Yun, G. Qin, D. J. Witherspoon, Z. Bai, F. R. Lorenzo, J. Xing, L. B. Jorde, J. T. Prchal, and R. Ge (2010) Genetic Evidence for High-Altitude Adaptation in Tibet. Science 329(5987):72-5 [comment in Science]
  13. Simonson, T. S., Y. Zhang, C. D. Huff, J. Xing, W. S. Watkins, D. J. Witherspoon, S. R. Woodward and L. B. Jorde (2010) Limited Distribution of a Cardiomyopathy-Associated Variant in India. Annals of Human Genetics 74(2):184-8
  14. Huff, C. D., J. Xing, A. R. Rogers, D. J. Witherspoon, and L. B. Jorde (2010) Mobile elements reveal small population size in the ancient ancestors of Homo sapiens. Proceedings of the National Academy of Sciences, USA 107:2147-2152
  15. Witherspoon, D. J., W. S. Watkins, Y. Zhang, J. Xing, W. L. Tolpinrud, D. J. Hedges, M. A. Batzer and L. B. Jorde (2009) Alu repeats increase local recombination rates. BMC Genomics 10:530
  16. Damert, A., J. Raiz, A. V. Horn, J. Löwer, H. Wang, J. Xing, M. A. Batzer, R. Löwer and G. G. Schumann (2009) 5′-transduced SVA retrotransposon groups spread efficiently throughout the human genome. Genome Research 19(11):1992-2008
  17. Li, J., K. Han, J. Xing, H.-S. Kim, J. Rogers, O. A. Ryder, T. Disotell, B. Yue and M. A. Batzer (2009) Phylogeny of the macaques (Cercopithecidae: Macaca) based on Alu elements. Gene 448(2):242-9
  18. Xing, J., Y. Zhang, K. Han, A. H. Salem, S. K. Sen, C. D. Huff, Q. Zhou, E. F. Kirkness, S. Levy, M.A. Batzer, and L. B. Jorde (2009) Mobile elements create structural variation: analysis of a complete human genome. Genome Research 19(9):1516-26 Supplemental Data
  19. Marchani E. E., J. Xing, D. J. Witherspoon, L. B. Jorde, and A. R. Rogers (2009) Estimating the age of retrotransposon subfamilies using maximum likelihood. Genomics 94(1):78-82.
  20. Xing, J.,W. S. Watkins, D. J. Witherspoon, Y. Zhang, S. L. Guthery, R. Thara, B. J. Mowry, K. Bulayeva, R. B. Weiss, and L. B. Jorde (2009) Fine-Scaled Human Genetic Structure Revealed by SNP Microarrays. Genome Research 19(5):815-25. Supplemental Data
  21. Xing, J., W. S. Watkins, Y. Zhang, D. J. Witherspoon, and L. B. Jorde (2008) High Fidelity of Whole-Genome Amplified DNA on High-Density Single Nucleotide Polymorphism Arrays. Genomics 92(6):452-6 Supplemental Data
  22. Xing, J., D. J. Witherspoon, W. S. Watkins, Y. Zhang, W. Tolpinrud and L. B. Jorde (2008) HapMap tagSNP transferability in multiple populations:general guidelines. Genomics 92:41-51
  23. Xing, J., D. J. Witherspoon, D. A. Ray, M. A. Batzer and L. B. Jorde (2007) Mobile elements and primate evolution. Yearbook of Physical Anthropology 50:2-19
  24. Rhesus Macaque Genome Sequencing and Analysis Consortium (2007) Evolutionary and Biomedical Insights from the Rhesus Macaque Genome. Science 316:222-234 [cover article]
  25. Han K.*, M. K. Konkel*, J. Xing*, H. Wang*, J. Lee, T. J. Meyer, C. T. Huang, E. Sandifer, K. Hebert, E. W. Barnes, R. Hubley, W. Miller, A. F. A. Smit, B. Ullmer and M. A. Batzer (2007) Old World monkey mobile DNA: a glimpse through the rhesus macaque genome. Science 316:238-240
  26. Herke S. W., J. Xing, D. A. Ray, J. W. Zimmerman, R. Cordaux and M. A. Batzer (2007) A SINE-based dichotomous key for primate identification. Gene 390:39-51
  27. Xing, J., H. Wang, Y. Zhang, D. A. Ray, A. J. Tosi, T. R. Disotell and M. A. Batzer (2007) A mobile element based evolutionary history of guenons (Tribe Cercopithecini). BMC Biology 5:5
  28. Ray, D. A., J. Xing, A.-H. Salem and M. A. Batzer (2006) SINEs of a nearly perfect character. Systematic Biology 55(6):928-935
  29. Xing, J.*, H. Wang*, V. P. Belancio, R. Cordaux, P. L. Deininger and M. A. Batzer (2006) Emergence of new primate genes by retrotransposon-mediated sequence transduction. Proceedings of the National Academy of Sciences, USA 103(47):17608-13. [cover article]
  30. Wang, H.*, J. Xing*, D. Grover*, D. J. Hedges, K. Han, J. A. Walker and M. A. Batzer (2005) SVA elements: a hominid specific retroposon family. Journal of Molecular Biology 354:994-1007 [cover article]
  31. Xing, J., H. Wang, K. Han, D. A. Ray, C. H. Huang, L. G. Chemnick, C.-B. Stewart, T. Disotell, O. A. Ryder and M. A. Batzer (2005) A mobile element based phylogeny of Old World monkeys. Molecular Phylogenetics and Evolution 37:872-880
  32. Hedges, D. J., R. Cordaux, J. Xing, D. J. Witherspoon, A. R. Rogers, L. B. Jorde and M. A. Batzer (2005) Modeling the amplification dynamics of human Alu retrotransposons. PLOS Computational Biology 1:e44
  33. Han, K.*, J. Xing*, H. Wang, D. J. Hedges, R. K. Garber, R. Cordaux and M. A. Batzer (2005) Under the Genomic Radar: The Stealth Model of Alu Amplification. Genome Research 15:655-664 [cover article]
  34. Ray, D. A., J. Xing, D. J. Hedges, M. Hall, M. E. Laborde, B. A. Anders, B. R. White, J. D. Fowlkes, L. Chemnick, O. A. Ryder, and M. A. Batzer (2005) Alu insertion loci and platyrrhine phylogeny. Molecular Phylogenetics and Evolution 35:117-126
  35. Xing J., D. J. Hedges, K.D. Han, H. Wang, R. Cordaux and M.A. Batzer (2004) Alu elements mutation spectra: Molecular clocks and the effect of DNA methylation. Journal of Molecular Biology 344:657-682
  36. Hedges, D. J., P. A. Callinan, R. Cordaux, J. Xing, E. Barnes and M. A. Batzer. (2004) Differential Alu mobilization and polymorphism among the human and chimpanzee lineages. Genome Research 14:1068-1075
  37. Walker, J. A., R. K. Garber, D. J. Hedges, G. E. Kilroy, J. Xing and M. A. Batzer (2004) Resolution of mixed human DNA samples using mtDNA sequence variants. Analytical Biochemistry 325:171-173
  38. Salem, A.-H., D. A. Ray, J. Xing, P. A. Callinan, J. S. Myers, D. J. Hedges, R. K. Garber, D. J. Witherspoon, L. B. Jorde and M. A. Batzer (2003) Alu elements and Hominid phylogenetics. Proceedings of the National Academy of Sciences, USA. 22:12787-12791
  39. Xing, J., A.-H. Salem, D. J. Hedges, G. E. Kilroy, W. S. Watkins, J. E. Schienman, C.-B. Stewart, J. Jurka, L. B. Jorde and M. A. Batzer (2003) Comprehensive analysis of two Alu Yd subfamilies. Journal of Molecular Evolution 57:S76-S89
  40. Callinan, P. A., D. J. Hedges, A.-H. Salem, J. Xing, J. A. Walker, R. K. Garber, W. S. Watkins, M. J. Bamshad, L. B. Jorde and M. A. Batzer (2003) Comprehensive analysis of Alu associated diversity on the human sex chromosomes. Gene 317:103-110
  41. Walker, J. A., G. E. Kilroy, J. Xing, J. Shewale, S. Sinha, and M. A. Batzer (2003) Human DNA quantitation using Alu element based PCR. Analytical Biochemistry 315:122-128
  42. Gao Y, J. Xing, M Streuli, TL Leto and Y Zheng (2001) Trp(56) of Rac1 specifies interaction with a subset of guanine nucleotide exchange factors. Journal of Biological Chemistry 276:47530-47541