Publications

[ Group member;  * Equal contribution;  † Corresponding author ]

2018
  1. Highly scalable generation of DNA methylation profiles in single cells
    Ryan M, Pokholok D, Norberg S, Torkenczy KA, Fields AJ, Sun D, Sinnamon JR, Mandel G, Shendure J, Trapnell C, O’Roak BJ, Xia Z, Steemers FJ, Adey AC.
    Nature Biotechnology (2018)

  2. 3ʹ-UTR Shortening Represses Tumor Suppressor Genes in trans by Disrupting ceRNA Crosstalk
    Park HJ, Ji P, Kim S, Xia Z, Rodriguez B, Li L, Su J, Chen K, Masamha C, Baillat D, Fontes C, Shyu AB, Neilson J, Wagner E, Li W
    Nature Genetics (2018)

  3. miR-205 Regulates Basal Cell Identity and Stem Cell Regenerative Potential During Mammary Reconstitution
    Lu Y, Cao J, Napoli M, Xia Z, Zhao N, Creighton CJ, Li W, Chen X, Flores ER, McManus MT, Rosen JM
    Stem Cells (2018)

  4. 3′ UTR lengthening as a novel mechanism in regulating cellular senescence
    Chen M, Lyu Guoliang, Han M, Nie H, Shen T, Chen W, Niu Y, Song Y, Li X, Li H, Chen X, Wang Z, Xia Z, ..., Wei G, Tao W, Ni T
    Genome Research (2018)

2017
  1. Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions
    Brinegar AE, Xia Z, Loehr JA, Li W, Rodney GG, Cooper TA
    Elife (2017)

  2. Gleason Score 7 Prostate Cancers Emerge Through Branched Evolution of Clonal Gleason Pattern 3 and 4
    Sowalsky AG, Kissick H, Gerrin S, Schaefer R, Xia Z, Russo J, Arredouani M, Bubley GJ, Sanda MG, Li W, Ye H, Balk SP
    Clinical Cancer Research (2017)

  3. Poly (A)-ClickSeq: click-chemistry for next-generation 3'-end sequencing without RNA enrichment or fragmentation
    Routh A, Ji P, Jaworski E, Xia Z, Li W, Wagner EJ
    Nucleic Acids Research (2017)

  4. Human mutations in integrator complex subunits link transcriptome integrity to brain development
    Oegema R, Baillat D, Schot R, van Unen LM, Brooks A, Kia SK, Hoogeboom AJM, Xia Z, Li W, Cesaroni M, Lequin MH, ... , Wagner EJ, Fornerod M, Mancini GMS
    PLoS Genet (2017)-

  5. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma
    The Cancer Genome Atlas Research Network (including Xia Z as co-author)
    Cell (2017)

  6. Aberrant plasticity of peripheral sensory axons in a painful neuropathy
    Hirai T, Mulpuri Y, Cheng Y, Xia Z, Li W, Ruangsri S, Spigelman I , Nishimura I
    Scientific Reports (2017)
2016
  1. KDM5 lysine demethylases are involved in maintenance of 3' UTR length
    Blair LP, Liu Z, Labitigan RL, Wu L, Zheng D, Xia Z, Pearson EL, Nazeer FI, Cao J, Lang SM, Rines RJ, Mackintosh, SG, Moore CL, Li W, Tian B, Tackett AJ, Yan Q
    Science Advances (2016)-

  2. Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1
    Giudice J, Xia Z, Li W, Cooper TA
    Scientific Reports (2016)-

  3. CFIm25 Regulates Glutaminase Alternative Terminal Exon Definition to Modulate miR-23 Function
    Masamha CP, Xia Z, Colllum S, Peart N, Li W, Wagner EJ, Shyu A
    RNA (2016)-

  4. The overlooked fact: fundamental need of spike-in control for virtually all genome-wide analyses
    Chen K, Hu Z, Xia Z, Li W, Tyler J
    Molecular and Cellular Biology (2016)-
2015
  1. Broad H3K4me3 Reveals Increased Transcription Elongation and Enhancer Activity at Tumor Suppressors
    Chen K, Chen Z, Wu D, Zhang L, Lin X, Su J, Rodriguez B, Xi Y, Xia Z, Chen X, Shi X, Wang Q, Li W
    Nature Genetics (2015)-

  2. Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function
    Luo M, Jeong M, Sun D, Park HJ, Rodrigues B, Xia Z, Yang L, Zhang, X, Darlington GJ, Li W, Goodell MA
    Cell Stem Cell (2015)-

  3. Whole Transcriptome Sequencing Reveals Extensive Unspliced mRNA in Metastatic Castration-Resistant Prostate Cancer
    Sowalsky AG*, Xia Z*, Wang L, Zhao H, Chen S, Bubley GJ, Balk SP, Li W
    Molecular Cancer Research (2015)-

  4. PRMT9 is a Type II methyltransferase that methylates the splicing factor SAP145
    Yang Y, Hadjikyriacou A, Xia Z, Gayatri S, Kim D, Zurita-Lopez C, Kelly R, Guo A, Li W, Clarke SG, Bedford MT
    Nature Communications (2015)-

  5. Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming
    Hirsch CL, Coban Akdemir Z, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X, Xia Z, Salinger AP, ..., Dent SYR
    Genes & Development (2015)-
2014
  1. Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3’-UTR Landscape Across 7 Tumor Types
    Xia Z, Donehower, LA, Wheeler DA, Cooper TA, Neilson JR, Wagner EJ, Li W
    Nature Communications (2014) -

  2. CFIm25 links Alternative Polyadenylation to Glioblastoma Tumor Suppression
    Masamha CP*, Xia Z*, Yang J, Albrecht TR, Li M, Shyu A, Li W, Wagner EJ
    Nature (2014)-

  3. Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis
    Singh RK*, Xia Z*, Bland CS, Kalsotra A, Ruddy M, Curk T, Ule J, Li W, Cooper TA
    Molecular Cell (2014)-

  4. Nucleosome loss leads to global transcriptional upregulation and genomic instability during yeast aging
    Zheng H, Chen K, Xia Z, Chavez M, Pal S, Seol J, Chen C, Li W, Tyler JK
    Genes & Development (2014)-

  5. Alternative splicing regulates vesicular trafficking genes in cardiomyocytes during postnatal heart development
    Giudice J, Xia Z, Wang ET, Scavuzzo MA, Ward AJ, Kalsotra A, Wei W, Wehrens XHT, Burge CB, Li W, Cooper TA
    Nature Communications (2014)-

  6. ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression
    Wen H, Li Y, Xi Y, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W, Li H, Shi X
    Nature (2014)-

  7. Epigenomic profiling of young and aged HSCs reveals concerted changes during aging that reinforce self-renewal
    Sun D, Luo M, Jeong M, Rodriguez B, Xia Z, Hannah R, Wang H, Le T, Faull KF, Chen R, Gu H, Bock C, Meissner A, Gottgens B, Darlington GJ, Li W, Goodell MA
    Cell Stem Cell (2014)-

  8. Dnmt3a and Dnmt3b have Overlapping and Distinct Functions in Hematopoietic Stem Cells
    Challen GA, Sun D, Mayle A, Jeong M, Luo M, Rodrigues B, Mallaney C, Celik H, Yang L, Xia Z, Culleng S, Berg JS, Zheng Y, Darlington GJ, Li W, Goodell MA
    Cell Stem Cell (2014) -

  9. Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin
    Hoadley et al. and The Cancer Genome Atlas Research Network (including Xia Z as co-author)
    Cell (2014)-

  10. The Histone-H3K4-Specific Demethylase KDM5B Binds to Its Substrate and Product through Distinct PHD Fingers
    Klein, BJ, Piao L, Xi Y, Rincon-Arano H, Rothbart SB, Peng D, Wen H, Larson C, Zhang X, Xia Z, Cortazar MA, Pena PV, Mangan A, Bentley DL, Strahl BD, Groudine M, Li W, Shi X, Kutateladze TG
    Cell Reports (2014)
2013
  1. A novel network and sparsity constraint regression model for functional module identification in genomic data analysis
    Xia Z, Chen W, Chang C, Zhou X
    International Journal of Data Mining and Bioinformatics (2013) -

  2. The Cancer Genome Atlas Pan-Cancer analysis project
    The Cancer Genome Atlas Research Network (including Xia Z as co-author)
    Nature Genetics (2013)
2012
  1. Computer-assisted lip diagnosis on traditional Chinese medicine using multi-class support vector machines
    Li F, Zhao C, Xia Z, Wang Y, Zhou X, Li GC
    BMC Complementary and Alternative Medicine (2012)
2011
  1. NSMAP: A Method for Spliced Isoforms Identification and Quantification from RNA-Seq
    Xia Z, Wen J, Chang C, Zhou X
    BMC Bioinformatics (2011), (Highly accessed paper).
2010
  1. A Graph-based Elastic Net for Variable Selection and Module Identification for Genomic Data Analysis
    Xia Z, Zhou X, Chen W, Chang C
    IEEE International Conference on Bioinformatics & Biomedicine Dec 2010 Hong Kong. -

  2. Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces
    Xia Z, Wu L, Zhou X, Wong STC
    BMC Syst Biol (2010)_
2009
  1. A Novel Image Based System Biology Approach for Alzheimer’s Disease Study
    Huang Y, Zhou X, Miao B, Lipinski M, Xia Z, Hu G, Degterev A, Yuan Y, Wong STC
    The IEEE/NIH 2009 Life Science Systems and Applications Workshop (2009) -
2008
  1. Registration of 3-D CT and 2-D Flat Images of Mouse via Affine Transformation
    Xia Z, Huang X, Zhou X, Sun Y, Ntziachristos V, Wong STC
    IEEE Transactions on Information Technology in Biomedicine (2008)-

  2. Graph Kernel by Spectral Transform in Kernel Fisher Discriminant Analysis
    Xia Z, Wang C, Hu C, Sun Y
    Journal of Computational Information Systems (2008)
2007
  1. Automated Recognition of Cellular Phenotypes by Support Vector Machines with feature reduction
    Xia Z, Zhou X, Sun Y, Wong STC, Mao Y
    International Journal of Knowledge-Based and Intelligent Engineering Systems (2007)-

  2. Fault diagnosis based on fuzzy support vector machine with parameter tuning and feature selection
    Mao Y, Xia Z, Yin Z, Sun Y
    Chinese Journal of Chemical Engineering (2007)-

  3. Registration of 3D FMT and CT images of mouse via affine transformation using sequential Monte Carlo
    Xia Z, Zhou, X, Sun Y, Wong STC
    2007 International Symposium on Computational Models of Life Sciences AIP Conference Proceedings-

  4. A Survey for Study of Feature Selection Algorithms
    Mao Y, Zhou X, Xia Z, Yin Z, Sun Y
    Pattern Recognition and Artificial Intelligence (2007)