Publications

We broadcast research in scientific journals and GitHub.

Pre-prints

  1. Ahsan U, Liu Q, Wang K. NanoCaller for accurate detection of SNPs and small indels from long-read sequencing by deep neural networks. bioRxiv, 2019.
  2. Zhao M, Havrilla JM, Fang L, Chen Y, Peng J, Liu C, Wu C, Sarmady M, Botas P, Isla J, Lyon GJ, Weng C*, Wang K*. Phen2Gene: Rapid Phenotype-Driven Gene Prioritization for Rare Diseases. bioRxiv, 2019.
  3. Georgieva D, Liu Q, Wang K*, Egli D*. Detection of Base Analogs Incorporated During DNA Replication by Nanopore Sequencing. bioRxiv, 2019.
  4. Hu Y, Wang K, Li M. Detecting differential alternative splicing events in scRNA-seq with or without UMIs. bioRxiv, 2019.
  5. Evgrafov OV, Armoskus C, Wrobel BB, Spitsyna VN, Souaiaia T, Herstein JS, Walker CP, Nguyen JD, Camarena A, Weitz JR, Kim JM, Duarte EL, Wang K, Simpson GM, Sobell JL, Medeiros H, Pato MT, Pato CN, Knowles JA: Gene expression in patient-derived neural progenitors provide insights into neurodevelopmental aspects of schizophrenia. bioRxiv, 2017.
  6. Yang H, Chen G, Lima L, Fang H, Jimenez L, Li M, Lyon GJ, He M, Wang K: HadoopCNV: A dynamic programming imputation algorithm to detect copy number variants from sequencing data. bioRxiv, 2017.

Selected Publications

  1. Ling C, Dai Y, Fang Li, Yao F, Liu Z, Qiu Z, Cui L, Xia F, Zhao C, Zhang S, Wang K*, Zhang X*. Exonic rearrangements in DMD in Chinese Han individuals affected with Duchenne and Becker muscular dystrophies. Human Mutation, doi: 10.1002/humu.23953, 2019.
  2. Fang L, Kao C, Gonzalez MV, Mafra FA, Pellegrino da Silva R, Li M, Wenzel S, Wimmer K, Hakonarson H, Wang K. LinkedSV: Detection of mosaic structural variants from linked-read exome and genome sequencing data. Nature Communications, 10:5585, 2019.
  3. Doostparast Torshizi A, Armoskus C, Zhang H, Forrest MP, Zhang S, Souaiaia T, Evgrafov OV, Knowles JA, Duan J*, Wang K*: Deconvolution of Transcriptional Networks Identified TCF4 as a Master Regulator in Schizophrenia. Science Advances, 5:eaau4139, 2019.
  4. Dai Y, Li P, Wang Z, Liang F, Yang F, Fang L, Huang Y, Huang S, Zhou J, Wang D, Cui L, Wang K: Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD). Journal of Medical Genetics, jmedgenet-2019-106078, 2019.
  5. Liu C, Peres Kury FS, Li Z, Ta C, Wang K*, Weng C*. Doc2Hpo: a web application for efficient and accurate HPO concept curation. Nucleic Acids Research, 47:W566-W570, 2019
  6. He MM, Li Q, Yan M, Cao H, Hu Y, He KY, Cao K, Li MM, Wang K. Variant Interpretation for Cancer (VIC): a computational tool for assessing clinical impacts of somatic variants. Genome Medicine, 11:53, 2019
  7. Liu Q, Fang L, Yu G, Wang D, Xiao CL*, Wang K*. Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data. Nature Communications, 10:2449, 2019
  8. Xie G, Dong C, Kong Y, Zhong JF, Li M, Wang K. GDP: Group lasso regularized Deep learning for cancer Prognosis from multi-omics and clinical features. Genes, 10:240, 2019.
  9. Khan A, Liu Q, Chen X, Zeng Y, Stucky A, Sedghizadeh PP, Adelpour D, Zhang X, Wang K*, Zhong JF*: Detection of human papillomavirus in cases of head and neck squamous cell carcinoma by RNA-seq and VirTect. Molecular Oncology, 13:829-839, 2019
  10. Zeng S, Zhang MY, Wang XJ, Hu ZM, Li JC, Li N, Wang JL, Liang F, Yang Q, Liu Q, Fang L, Hao JW, Shi FD, Ding XB, Teng JF, Yin XM, Jiang H, Liao WP, Liu JY, Wang K*, Xia K*, Tang BS*: Long-read sequencing identified intronic repeat expansions in SAMD12 from Chinese pedigrees affected with Familial Cortical Myoclonic Tremor with Epilepsy. Journal of Medical Genetics, 56:265-270, 2019
  11. Borgmann-Winter KE, Wang K, Bandyopadhyay S, Doostparast Torshizi A, Blair I, Hahn CY. The proteome and its dynamics: A missing piece for integrative multi-omics in schizophrenia. Schizophrenia Research, doi: 10.1016/j.schres.2019.07.025, 2019
  12. Liu Q, Shi L, Wang K. Ethnicity-Specific Reference Genome Assembly by Long-Read Sequencing. J Mol Genet Med, 12:385, 2018
  13. Liu Q, Georgieva DC, Egli DM, Wang K. NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data. BMC Genomics, 20:78, 2018
  14. Khan A, Liu Q, Wang K. iMEGES: integrated Mental-disorder GEnome score for prioritizing the susceptibility genes for mental disorders in personal genomes. BMC Bioinformatics, 19:501, 2018
  15. He Z, Liu L, Wang K, Ionita-Laza I. A semi-supervised approach for predicting cell type specific functional consequences of non-coding variation using MPRAs. Nature Communications, 9:5199, 2018
  16. Xiao CL, Zhu S, He M-H, Chen Y, Yu GL, Chen D, Xie SQ, Luo F, Liang Z, Wang DP, Bo XC*, Gu XF*, Wang K*, Yan GR*. N6-methyladenine DNA modification in human genome. Molecular Cell, 71:306-318, 2018
  17. Hoon Son J, Xie G, Yuan C, Ena L, Li Z, Goldstein A, Huang L, Wang L, Shen F, Liu H, Mehl K, Groopman EE, Marasa M, Kiryluk K, Gharavi AG, Chung WK, Hripcsak G, Friedman C, Weng C*, Wang K*. Deep phenotyping on electronic health records facilitates genetic diagnosis by clinical exomes. American Journal of Human Genetics, 103:58-73, 2018
  18. Doostparast Torshizi A, Wang K. Next-generation sequencing in drug development: target identification and genetically stratified clinical trials. Drug Discovery Today, 23:1776-1783, 2018
  19. Fang L, Hu J, Wang D, Wang K. NextSV: a computational pipeline for structural variation analysis from low-coverage long-read sequencing. BMC Bioinformatics, 19:180, 2018
  20. Miao H, Zhou J, Yang Q, Liang F, Wang D, Ma N, Gao B, Du J, Lin G, Wang K*, Zhang Q*. Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis. Heraditas, 115:32, 2018
  21. Khan A, Wang K. A deep learning based scoring system for prioritizing susceptibility variants for mental disorders. IEEE International Conference on Bioinformatics and Biomedicine. Page: 1698-1705, DOI: 10.1109/BIBM.2017.8217916, 2017
  22. Li Q, Wang K. InterVar: Clinical interpretation of genetic variants by ACMG/AMP 2015 guidelines, American Journal of Human Genetics, 100:267-280, 2017
  23. Liu Q, Zhang P, Wang D, Gu W, Wang K. Interrogating the "unsequenceable" genomic trinucleotide repeat disorders by long-read sequencing. Genome Medicine, 9:65, 2017
  24. Li J, Zhang W, Yang H, Howrigan DP, Wilkinson B, Souaiaia T, Evgrafov OV, Genovese G, Clementel VA, Tudor JC, Abel T, Knowles JA, Neale BM, Wang K, Sun F, Coba MP: Spatiotemporal profile of postsynaptic interactomes integrates components of complex brain disorders. Nature Neuroscience, 20:1150-1161, 2017
  25. de Araújo Lima LA, Wang K: PennCNV in whole-genome sequencing data. BMC Bioinformatics, 18:383, 2017
  26. Dong C, Guo Y, Yang H, He Z, Liu X, Wang K. iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes, Genome Medicine, 8:135, 2016
  27. Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, Lintner KE, Ding Q, Wang Z, Hu J, Wang D, Wang F, Wang L, Lyon GJ, Guan Y, Shen Y, Evgrafov OV, Knowles JA, Thibaud-Nissen F, Schneider V, Yu CY, Zhou L, Eichler EE, So KF, Wang K. Long read sequencing and de novo assembly of a Chinese genome. Nature Communications, 7:12065, 2016
  28. Cai M, Gao F, Lu W, Wang K. w4CSeq: software and web application to analyze 4C-Seq data, Bioinformatics, 32:3333-3335, 2016
  29. Song X, Zhang N, Han P, Lai RK*, Wang K*, Lu W*. Circular RNA Profile in Gliomas Revealed by Identification Tool UROBORUS. Nucleic Acids Research, 44:e87, 2016
  30. He KY, Zhao Y, McPherson EW, Li Q, Xia F, Weng C, Wang K*, He MM*. Pathogenic Mutations in Cancer-Predisposing Genes: A Survey of 300 Patients with Whole-Genome Sequencing and Lifetime Electronic Health Records. PLoS One, 11:e0167847, 2016
  31. Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, et al. The PsychENCODE Project, Nature Neuroscience, 18:1707-1712, 2015
  32. Guo Y, Ding X, Shen Y, Lyon GJ, Wang K. SeqMule: automated analysis pipeline for analysis of human exome/genome sequencing data. Scientific Reports, 5:14283, 2015
  33. Yang H, Wang K. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nature Protocols, 10:1556-1566, 2015
  34. Yang H., Robinson PN, Wang K. Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. Nature Methods, 12:841-843, 2015
  35. He M, Person TN, Hebbring SJ, Heinzen E, Ye Z, Schrodi SJ, McPherson EW, Lin SM, Peissig PL, Brilliant MH, O'Rawe J, Robison RJ, Lyon GJ, Wang K. SeqHBase: a big data toolset for family-based sequencing data analysis. Journal of Medical Genetics, 52:282-288, 2015
  36. Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K*, Liu X*. Comparison and integration of deleteriousness prediction methods of nonsynonymous SNPs in whole exome sequencing studies. Human Molecular Genetics, 24:2125-2137, 2015
  37. Guo Y, Conti DV, Wang K. Enlight: web-based integration of GWAS results with biological annotations. Bioinformatics, 31:275-276, 2015
  38. Gao F, Wang K. Ligation-anchored PCR unveils immune repertoire of TCR-beta from whole blood. BMC Biotechnology, 15:39, 2015
  39. Jia H, Guo Y, Zhao W, Wang K. Long-range PCR in next-generation sequencing: comparison of six enzymes and evaluation on the MiSeq sequencer. Scientific Reports, 4:5737, 2014
  40. Shi L, Li B, Huang YL, Ling XY, Liu T, Lyon GJ, Xu A, Wang K. "Genotype-first" approaches on a curious case of idiopathic progressive cognitive decline. BMC Medical Genomics, 7:66, 2014
  41. Gao F, Wei Z, Lu W, Wang K. Comparative analysis of 4C-Seq data generated from enzyme-based and sonication-based methods. BMC Genomics, 14:345, 2013
  42. Wei Z, Gao F, Kim S, Yang H, Wang K, Lu W. Klf4 Organizes Long-Range Chromosomal Interactions with the Oct4 Locus in Reprogramming and Pluripotency. Cell Stem Cell, 13:36-47, 2013
  43. Chen G, Chang X, Curtis C, Wang K. Precise inference of copy number alterations from SNP arrays. Bioinformatics, 29:2964-2970, 2013
  44. Wang K*, Kim C, Bradfield J, Guo Y, Toskala E, Otieno FG, Hou C, Thomas K, Cardinale C, Lyon GL, Golhar R, Hakonarson H*. Whole-genome DNA/RNA sequencing on a novel Mendelian disease with neuromuscular and cardiac involvement. Genome Medicine, 5:67, 2013
  45. Shi L, Chang X, Zhang P, Coba M, Lu W, Wang K. The functional genetic link of NLGN4X knockdown and neurodevelopment in neural stem cells. Human Molecular Genetics, 22:3749:3760, 2013
  46. Gao F, Ling C, Shi L, Commins D, Zada G, Mack W, Wang K. Inversion-mediated gene fusion involving NAB2-STAT6 in an unusual malignant meningioma. British Journal of Cancer, 109:1051-1055, 2013
  47. Chang X, Xu T, Li Y, Wang K. Dynamic modular architecture of protein-protein interaction networks beyond the dichotomy of 'date' and 'party' hubs. Scientific Reports, 3:1691, 2013
  48. Qiu S, Luo S, Evgrafov O, Li R, Schroth GP, Levitt P, Knowles JA*, Wang K*. Single-neuron RNA-Seq: technical feasibility and reproducibility. Frontiers in Genetics, 3:124, 2012
  49. Lyon GJ, Wang K. Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome Medicine, 4:58, 2012
  50. Chang X, Wang K. wANNOVAR: annotating genetic variants for personal genomes via the web. Journal of Medical Genetics. 49:433-436, 2012
  51. Lyon GJ, Jiang T, Van Wijk R, Wang W, Bodily P, Xing J, Tian L, Robison R, Clement M, Yang L, Zhang P, Liu Y, Moore B, Glessner J, Elia J, Reimherr F, van Solinge W, Yandell M, Hakonarson H, Wang J, Johnson WE, Wei Z, Wang K. Exome Sequencing and Unrelated Findings in the context of Complex Disease Research: Ethical and Clinical Implications. Discovery Medicine, 12:41-55, 2011
  52. Wang K*, Diskin SJ*, Zhang H*, Attiyeh EF, Winter C, Hou C, Schnepp RW, Diamond M, Bosse K, Mayes PA, Glessner J, Kim C, Frackelton E, Garris M, Wang Q, Glaberson W, Chiavacci R, Nguyen L, Jagannathan J, Saeki N, Sasaki H, Grant SF, Iolascon A, Mosse YP, Cole KA, Li H, Devoto M, McGrady PW, London WB, Capasso M, Rahman N, Hakonarson H, Maris JM. Integrative genomics identifies LMO1 as a neuroblastoma oncogene. Nature, 469:216-220, 2011
  53. Wang K, Zhang H, Bloss CT, Duvvuri V, Kaye W, Schork NJ, Berrettini W, Hakonarson H, the Price Foundation Collaborative Group. A genome-wide association study on common SNPs and rare CNVs in anorexia nervosa. Molecular Psychiatry, 16:949-959, 2011
  54. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38:e164 2010
  55. Wang K, Li M, Hakonarson H. Analysing biological pathways from genome-wide association studies. Nature Reviews Genetics, 11:843-854, 2010
  56. Wang K, Bucan M, Grant SF, Schellenberg G, Hakonarson H. Strategies for genetic studies of complex diseases. Cell, 142:351-353, 2010
  57. Wang K*, Zhang H*, Ma D*, Bucan M, Glessner JT, Abrahams BS, Salyakina D, Imielinski M, Bradfield JP, Sleiman PM, Kim CE, Hou C, Frackelton E, Chiavacci R, Takahashi N, Sakurai T, Rappaport E, Lajonchere CM, Munson J, Estes A, Korvatska O, Piven J, Sonnenblick LI, Alvarez Retuerto AI, Herman EI, Dong H, Hutman T, Sigman M, Ozonoff S, Klin A, Owley T, Sweeney JA, Brune CW, Cantor RM, Bernier R, Gilbert JR, Cuccaro ML, McMahon WM, Miller J, State MW, Wassink TH, Coon H, Levy SE, Schultz RT, Nurnberger JI, Haines JL, Sutcliffe JS, Cook EH, Minshew NJ, Buxbaum JD, Dawson G, Grant SF, Geschwind DH, Pericak-Vance MA, Schellenberg GD, Hakonarson H. Common genetic variants on 5p14.1 associate with autism spectrum disorders. Nature, 459:528-533, 2009
  58. Wang K, Li M, Hadley D, Liu R, Glessner J, Grant S, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Research, 17:1665-1674, 2007
  59. Wang K, Li M, Bucan M. Pathway-based approaches for analysis of genome-wide association studies. American Journal of Human Genetics, 81:1278-1283, 2007

Book Chapters

  1. Guan Y, Wang K. Whole-genome multi-SNP analysis. In: Statistical Bioinformatics. Edited by Do KA, Qin Z, Vannucci M. Cambridge University Press, 2013
  2. Wang K. Epistasis. In: Encyclopedia of Autism Spectrum Disorders. Edited by Volkmar FR. Springer, 2013
  3. Fang L, Wang K. Identification of Copy Number Variants from SNP Arrays Using PennCNV. In: Methods in Molecular Biology. Edited by Derek Bickhart. Springer, vol. 1833, 2018

Software tools

We developed a number of software tools for genomic data analysis. Check them out at WGLab GitHub.

Other links

  • The Google Citation report for the PI can be accessed here (Total citation: >30,000; H-index: 66).