Jinchuan Xing

2024

A Massive Proteogenomic Screen Identifies Thousands of Novel Peptides From the Human “Dark” Proteome

Cao, X., Sun, S. & Xing, J., Feb 2024, In: Molecular and Cellular Proteomics. 23, 2, 100719.

Research output: Contribution to journal › Article › peer-review

Open Access

Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells

Prem, S., Dev, B., Peng, C., Mehta, M., Alibutud, R., Connacher, R. J., St Thomas, M., Zhou, X., Matteson, P., Xing, J., Millonig, J. H. & DiCicco-Bloom, E., Mar 25 2024, In: eLife. 13

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Genomic Evidence for the Complex Evolutionary History of Macaques (Genus Macaca)

Fan, Z., Zhang, R., Zhou, A., Hey, J., Song, Y., Osada, N., Hamada, Y., Yue, B., Xing, J. & Li, J., Jun 2024, In: Journal of Molecular Evolution. 92, 3, p. 286-299 14 p.

Research output: Contribution to journal › Article › peer-review

Whole transcriptome screening for novel genes involved in meiosis and fertility in Drosophila melanogaster

Sun, S., Defosse, T., Boyd, A., Sop, J., Verderose, F., Surray, D., Aziz, M., Howland, M., Wu, S., Changela, N., Jang, J., Schindler, K., Xing, J. & McKim, K. S., Dec 2024, In: Scientific reports. 14, 1, 3602.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

2023

Assessing the Expression of Long INterspersed Elements (LINEs) via Long-Read Sequencing in Diverse Human Tissues and Cell Lines

Rybacki, K., Xia, M., Ahsan, M. U., Xing, J. & Wang, K., Oct 2023, In: Genes. 14, 10, 1893.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Common genetic risk factors in ASD and ADHD co-occurring families

Zhou, A., Cao, X., Mahaganapathy, V., Azaro, M., Gwin, C., Wilson, S., Buyske, S., Bartlett, C. W., Flax, J. F., Brzustowicz, L. M. & Xing, J., Feb 2023, In: Human Genetics. 142, 2, p. 217-230 14 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Identifying risk variants for embryo aneuploidy using ultra-low coverage whole-genome sequencing from preimplantation genetic testing

Sun, S., Aboelenain, M., Ariad, D., Haywood, M. E., Wageman, C. R., Duke, M., Bag, A., Viotti, M., Katz-Jaffe, M., McCoy, R. C., Schindler, K. & Xing, J., Dec 7 2023, In: American Journal of Human Genetics. 110, 12, p. 2092-2102 11 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD

Wang, S., Wang, B., Drury, V., Drake, S., Sun, N., Alkhairo, H., Arbelaez, J., Duhn, C., Bromberg, Y., Brown, L. W., Cao, X., Cheon, K. A., Cheong, K., Choi, H., Coffey, B. J., Deng, L., Fremer, C., Garcia-Delgar, B., Gilbert, D. L. & Glover, D. & 47 others, Grice, D. E., Hagstrøm, J., Hedderly, T., Heyman, I., Hong, H. J., Huyser, C., Kim, H., Kim, Y. K., Kim, E., Kim, Y. S., King, R. A., Koh, Y. J., Kook, S., Kuperman, S., Lee, J., Leventhal, B. L., Madruga-Garrido, M., Mingbunjerdsuk, D., Mir, P., Morer, A., Murphy, T. L., Müller-Vahl, K., Münchau, A., Nasello, C., Oh, D. H., Plessen, K. J., Roessner, V., Shin, E. Y., Song, D. H., Song, J., Thackray, J. K., Visscher, F., Zinner, S. H., Bal, V. H., Langley, K., Martin, J., Hoekstra, P. J., Dietrich, A., Xing, J., Heiman, G. A., Tischfield, J. A., Fernandez, T. V., Owen, M. J., O’Donovan, M. C., Thapar, A., State, M. W. & Willsey, A. J., Dec 2023, In: Nature communications. 14, 1, 8077.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Structural Variations Contribute to the Genetic Etiology of Autism Spectrum Disorder and Language Impairments

Alibutud, R., Hansali, S., Cao, X., Zhou, A., Mahaganapathy, V., Azaro, M., Gwin, C., Wilson, S., Buyske, S., Bartlett, C. W., Flax, J. F., Brzustowicz, L. & Xing, J., Sep 2023, In: International journal of molecular sciences. 24, 17, 13248.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Transposable Elements Shape the Genome Diversity and the Evolution of Noctuidae Species

Zhang, C., Wang, L., Dou, L., Yue, B., Xing, J. & Li, J., Jun 2023, In: Genes. 14, 6, 1244.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

2022

Centers for Mendelian Genomics: A decade of facilitating gene discovery

Centers for Mendelian Genomics Consortium, Apr 2022, In: Genetics in Medicine. 24, 4, p. 784-797 14 p.

Rutgers, The State University

Research output: Contribution to journal › Review article › peer-review

Open Access

Chromosome-level genome assembly of Tibetan macaque (Macaca thibetana) and species-specific structural variations

Zhang, R. S., Zhou, C., Jin, X. L., Liu, K. H., Fan, Z. X., Xing, J. C. & Li, J., 2022, In: Zoological research. 43, 5, p. 880-885 6 p.

Rutgers, The State University

Research output: Contribution to journal › Letter › peer-review

Open Access

Genomics and epigenetics guided identification of tissue-specific genomic safe harbors

Shrestha, D., Bag, A., Wu, R., Zhang, Y., Tang, X., Qi, Q., Xing, J. & Cheng, Y., Dec 2022, In: Genome biology. 23, 1, 199.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

MicroRNA and MicroRNA-Target Variants Associated with Autism Spectrum Disorder and Related Disorders

Wong, A., Zhou, A., Cao, X., Mahaganapathy, V., Azaro, M., Gwin, C., Wilson, S., Buyske, S., Bartlett, C. W., Flax, J. F., Brzustowicz, L. M. & Xing, J., Aug 2022, In: Genes. 13, 8, 1329.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Predicting embryonic aneuploidy rate in IVF patients using whole-exome sequencing

Sun, S., Miller, M., Wang, Y., Tyc, K. M., Cao, X., Scott, R. T., Tao, X., Bromberg, Y., Schindler, K. & Xing, J., Oct 2022, In: Human Genetics. 141, 10, p. 1615-1627 13 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Transposable Elements in Bats Show Differential Accumulation Patterns Determined by Class and Functionality

Paulat, N. S., McGuire, E., Subramanian, K., Osmanski, A. B., Moreno-Santillán, D. D., Ray, D. A. & Xing, J., Aug 2022, In: Life. 12, 8, 1190.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

2021

Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome

Care4Rare Consortium & Centers for Mendelian Genomics, Jan 2021, In: American Journal of Medical Genetics, Part A. 185, 1, p. 119-133 15 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Analysis of DNA variants in miRNAs and miRNA 3ʼUTR binding sites in female infertility patients

Tyc, K. M., Wong, A., Scott, R. T., Tao, X., Schindler, K. & Xing, J., Apr 2021, In: Laboratory Investigation. 101, 4, p. 503-512 10 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Correction to: Whole exome sequencing identifies novel candidate genes that modify chronic obstructive pulmonary disease susceptibility (Human Genomics, (2016), 10, 1, (1), 10.1186/s40246-015-0058-7)

Bruse, S., Moreau, M., Bromberg, Y., Jang, J. H., Wang, N., Ha, H., Picchi, M., Lin, Y., Langley, R. J., Qualls, C., Klesney-Tait, J., Zabner, J., Leng, S., Mao, J., Belinsky, S. A., Xing, J. & Nyunoya, T., Dec 2021, In: Human genomics. 15, 1, 74.

Rutgers, The State University

Research output: Contribution to journal › Comment/debate › peer-review

Open Access

Development and Characterization of a Modular CRISPR and RNA Aptamer Mediated Base Editing System

Collantes, J. C., Tan, V. M., Xu, H., Ruiz-Uriguën, M., Alasadi, A., Guo, J., Tao, H., Su, C., Tyc, K. M., Selmi, T., Lambourne, J. J., Harbottle, J. A., Stombaugh, J., Xing, J., Wiggins, C. M. & Jin, S., Feb 2021, In: CRISPR Journal. 4, 1, p. 58-68 11 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Meiosis interrupted: The genetics of female infertility via meiotic failure

Biswas, L., Tyc, K., El Yakoubi, W., Morgan, K., Xing, J. & Schindler, K., Feb 2021, In: Reproduction. 161, 2, p. R13-R35

Rutgers, The State University

Research output: Contribution to journal › Review article › peer-review

Open Access

2 Scopus citations

Origins and mechanisms leading to aneuploidy in human eggs

Wartosch, L., Schindler, K., Schuh, M., Gruhn, J. R., Hoffmann, E. R., McCoy, R. C. & Xing, J., Apr 2021, In: Prenatal Diagnosis. 41, 5, p. 620-630 11 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

PrecisionProDB: improving the proteomics performance for precision medicine

Cao, X. & Xing, J., Oct 1 2021, In: Bioinformatics. 37, 19, p. 3361-3363 3 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

SMAD4 is critical in suppression of BRAF-V600E serrated tumorigenesis

Tong, K., Kothari, O. A., Haro, K. S., Panda, A., Bandari, M. M., Carrick, J. N., Hur, J. J., Zhang, L., Chan, C. S., Xing, J., Gatza, M. L., Ganesan, S. & Verzi, M. P., Oct 14 2021, In: Oncogene. 40, 41, p. 6034-6048 15 p.

Hackensack Meridian School of Medicine, Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Whole-exome sequencing identifies genes associated with Tourette’s disorder in multiplex families

Tourette International Collaborative Genetics Study (TIC Genetics), Nov 2021, In: Molecular psychiatry. 26, 11, p. 6937-6951 15 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

2020

Characterization of the primate TRIM gene family reveals the recent evolution in primates

Qiu, S., Liu, H., Jian, Z., Fan, Z., Liu, S., Xing, J. & Li, J., Sep 1 2020, In: Molecular Genetics and Genomics. 295, 5, p. 1281-1294 14 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Effects of aging on gene expression in blood of captive Tibetan macaques (Macaca thibetana) and comparisons with expression in humans

Yan, C. C., Zhang, X. S., Zhou, L., Yang, Q., Zhou, M., Zhang, L. W., Xing, J. C., Yan, Z. F., Price, M., Li, J., Yue, B. S. & Fan, Z. X., 2020, In: Zoological research. 41, 5, p. 557-563 7 p.

Rutgers, The State University

Research output: Contribution to journal › Review article › peer-review

Open Access

2 Scopus citations

Exome sequencing links CEP120 mutation to maternally derived aneuploid conception risk

Tyc, K. M., Yakoubi, W. E., Bag, A., Landis, J., Zhan, Y., Treff, N. R., Scott, R. T., Tao, X., Schindler, K. & Xing, J., Sep 1 2020, In: Human Reproduction. 35, 9, p. 2134-2148 15 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Genomic copy number variation study of ninemacaca species provides new insights into their genetic divergence, adaptation, and biomedical application

Li, J., Fan, Z., Shen, F., Pendleton, A. L., Song, Y., Xing, J., Yue, B., Kidd, J. M. & Li, J., 2020, In: Genome biology and evolution. 12, 12, p. 2211-2230 20 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions

Loh, J. W., Ha, H., Lin, T., Sun, N., Burns, K. H. & Xing, J., Feb 22 2020, In: Mobile DNA. 11, 1, 12.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

MACSNVdb: A high-quality SNV database for interspecies genetic divergence investigation among macaques

Du, L., Guo, T., Liu, Q., Li, J., Zhang, X., Xing, J., Yue, B. & Fan, Z., 2020, In: Database. 2020, baaa027.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

Mapping and characterization of structural variation in 17,795 human genomes

NHGRI Centers for Common Disease Genomics, Jul 2 2020, In: Nature. 583, 7814, p. 83-89 7 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

23 Scopus citations

Mathematical modeling of human oocyte aneuploidy

Tyc, K. M., McCoy, R. C., Schindler, K. & Xing, J., May 12 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 19, p. 10455-10464 10 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus citations

Mutations in ASH1L confer susceptibility to Tourette syndrome

Liu, S., Tian, M., He, F., Li, J., Xie, H., Liu, W., Zhang, Y., Zhang, R., Yi, M., Che, F., Ma, X., Zheng, Y., Deng, H., Wang, G., Chen, L., Sun, X., Xu, Y., Wang, J., Zang, Y. & Han, M. & 28 others, Wang, X., Guan, H., Ge, Y., Wu, C., Wang, H., Liang, H., Li, H., Ran, N., Yang, Z., Huang, H., Wei, Y., Zheng, X., Sun, X., Feng, X., Zheng, L., Zhu, T., Luo, W., Chen, Q., Yan, Y., Huang, Z., Jing, Z., Guo, Y., Zhang, X., Schaaf, C. P., Xing, J., Wang, C., Yu, F. & Guan, J. S., Feb 1 2020, In: Molecular psychiatry. 25, 2, p. 476-490 15 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues

Cao, X., Zhang, Y., Payer, L. M., Lords, H., Steranka, J. P., Burns, K. H. & Xing, J., Jul 27 2020, In: Genome biology. 21, 1, 185.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Spontaneous hyperactivity in Ash1l mutant mice, a new model for Tourette syndrome

Liu, S., Tian, M., He, F., Li, J., Xie, H., Liu, W., Zhang, Y., Zhang, R., Yi, M., Che, F., Ma, X., Zheng, Y., Deng, H., Wang, G., Chen, L., Sun, X., Xu, Y., Wang, J., Zang, Y. & Han, M. & 28 others, Wang, X., Guan, H., Ge, Y., Wu, C., Wang, H., Liang, H., Li, H., Ran, N., Yang, Z., Huang, H., Wei, Y., Zheng, X., Sun, X., Feng, X., Zheng, L., Zhu, T., Luo, W., Chen, Q., Yan, Y., Huang, Z., Jing, Z., Guo, Y., Zhang, X., Schaaf, C. P., Xing, J., Wang, C., Yu, F. & Guan, J. S., Feb 1 2020, In: Molecular psychiatry. 25, 2, p. 241-242 2 p.

Rutgers, The State University

Research output: Contribution to journal › Comment/debate › peer-review

2019

Evaluating nanopore sequencing data processing pipelines for structural variation identification

Zhou, A., Lin, T. & Xing, J., Nov 14 2019, In: Genome biology. 20, 1, 237.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Pedigree-based estimation of human mobile element retrotransposition rates

Feusier, J., Watkins, W. S., Thomas, J., Farrell, A., Witherspoon, D. J., Baird, L., Ha, H., Xing, J. & Jorde, L. B., 2019, In: Genome research. 29, 10, p. 1567-1577 11 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

16 Scopus citations

SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina

Thackray, J. K., Simonet, N. G., Chahar, S., Kane-Goldsmith, N., Newkirk, S. J., Lee, S., Xing, J., Verzi, M. P., An, W., Vaquero, A., Tischfield, J. A. & Serrano, L., Sep 1 2019, In: Nucleic acids research. 47, 15, p. 7870-7885 16 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

12 Scopus citations

The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development

Kumar, N., Tsai, Y. H., Chen, L., Zhou, A., Banerjee, K. K., Saxena, M., Huang, S., Toke, N. H., Xing, J., Shivdasani, R. A., Spence, J. R. & Verzi, M. P., Mar 1 2019, In: Development (Cambridge). 146, 5, dev172189.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

15 Scopus citations

Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata

Oppenheim, S., Cao, X., Rueppel, O., Krongdang, S., Phokasem, P., Desalle, R., Goodwin, S., Xing, J., Chantawannakul, P. & Rosenfeld, J. A., Dec 16 2019, In: Genome biology and evolution. 12, 1, p. 3677-3683 7 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

2018

Ancient hybridization and admixture in macaques (genus Macaca) inferred from whole genome sequences

Fan, Z., Zhou, A., Osada, N., Yu, J., Jiang, J., Li, P., Du, L., Niu, L., Deng, J., Xu, H., Xing, J., Yue, B. & Li, J., Oct 2018, In: Molecular Phylogenetics and Evolution. 127, p. 376-386 11 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Can-SINE dynamics in the giant panda and three other Caniformia genomes 06 Biological Sciences 0604 Genetics

Peng, C., Niu, L., Deng, J., Yu, J., Zhang, X., Zhou, C., Xing, J. & Li, J., Nov 10 2018, In: Mobile DNA. 9, 1, 32.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis

Tourette International Collaborative Genetics Study (TIC Genetics), Tourette Syndrome Genetics Southern and Eastern Europe Initiative (TSGENESEE), Tourette Association of America International Consortium for Genetics (TAAICG), Sep 25 2018, In: Cell Reports. 24, 13, p. 3441-3454.e12

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

27 Scopus citations

Erratum: De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis (Cell Reports (2018) 24(13) (3441–3454.e12), (S221112471831386X), (10.1016/j.celrep.2018.08.082))

Tourette International Collaborative Genetics Study (TIC Genetics), Tourette Syndrome Genetics Southern and Eastern Europe Initiative (TSGENESEE) & Tourette Association of America International Consortium for Genetics (TAAICG), Dec 18 2018, In: Cell Reports. 25, 12, p. 3544 1 p.

Rutgers, The State University

Research output: Contribution to journal › Comment/debate › peer-review

Open Access

6 Scopus citations

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

Regier, A. A., Farjoun, Y., Larson, D. E., Krasheninina, O., Kang, H. M., Howrigan, D. P., Chen, B. J., Kher, M., Banks, E., Ames, D. C., English, A. C., Li, H., Xing, J., Zhang, Y., Matise, T., Abecasis, G. R., Salerno, W., Zody, M. C., Neale, B. M. & Hall, I. M., Dec 1 2018, In: Nature communications. 9, 1, 4038.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

40 Scopus citations

PipelineDog: A simple and flexible graphic pipeline construction and maintenance tool

Zhou, A., Zhang, Y., Sun, Y. & Xing, J., May 1 2018, In: Bioinformatics. 34, 9, p. 1603-1605 3 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

SMAD4 suppresses WNt-driven dedifferentiation and oncogenesis in the differentiated gut epithelium

Perekatt, A. O., Shah, P. P., Cheung, S., Jariwala, N., Wu, A., Gandhi, V., Kumar, N., Feng, Q., Patel, N., Chen, L., Joshi, S., Zhou, A., Taketo, M. M., Xing, J., White, E., Gao, N., Gatza, M. L. & Verzi, M. P., Sep 1 2018, In: Cancer Research. 78, 17, p. 4878-4890 13 p.

Stevens Institute of Technology, Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

The PNKD gene is associated with Tourette Disorder or Tic disorder in a multiplex family

Sun, N., Nasello, C., Deng, L., Wang, N., Zhang, Y., Xu, Z., Song, Z., Kwan, K., King, R. A., Pang, Z. P., Xing, J., Heiman, G. A. & Tischfield, J. A., Jun 1 2018, In: Molecular psychiatry. 23, 6, p. 1487-1495 9 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

13 Scopus citations

2017

Accounting for protein subcellular localization: A compartmental map of the rat liver proteome

Jadot, M., Boonen, M., Thirion, J., Wang, N., Xing, J., Zhao, C., Tannous, A., Qian, M., Zheng, H., Everett, J. K., Moore, D. F., Sleat, D. & Lobel, P., Feb 2017, In: Molecular and Cellular Proteomics. 16, 2, p. 194-212 19 p.

Rutgers, The State University

Research output: Contribution to journal › Article › peer-review

Open Access

30 Scopus citations

Jinchuan Xing

Research output

Search results