Publications

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

Manuscripts Under Review
  • Copy Number Loss of 17q22 is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer
    Guan X, Sun D, Lu E, Urrutia JA, Reiter RE, Rettig M, Evans CP, Lara JP, Gleave M, Beer TM, Thomas GV, Huang J, Aggarwal RR, Quigley DA, Foye A, Chen WS, Youngren J, Weinstein AS, Stuart JM, Feng FY*, Small EJ*, Xia Z*, Alumkal JJ*
    Submitted


  • 2020
    1. TGFβ signaling is critical for maintenance of the tendon cell fate
      Tan GK, Pryce BA, Stabio A, Brigande JV, Wang C, Xia Z, Tufa SF, Keene DR, Schweitzer R.
      eLIFE (2020)

    2019
    1. RNA-seq from archival FFPE Breast Cancer samples: Molecular Pathway Fidelity and Novel Discovery
      Pennock N, Jindal S, Horton W, Sun D, Narasimhan J, Carbone L, Fei SS, Searles R, Harrington CA, Burchard J, Weinmann S, Schedin P*, Xia Z*
      BMC Medical Genomics (2019)

    2. Genomic Drivers of Poor Prognosis and Enzalutamide Resistance in Metastatic Castration-resistant Prostate Cancer
      Chen W, Aggarwal R, Zhang L, Zhao SG, Thomas GV, Beer TM, Quigley D, Foye A, Playdle D, Huang J, Lloyd P, Lu E, Sun D, Guan X, Rettig M, Gleave M, Evans CP, Youngren J, True L, Lara P, Kothari V, Xia Z, Chi KN, Reiter RE, Maher CA, Feng FY, Small EJ, Alumkal JJ.
      European Urology (2019)

    3. BET Bromodomain Inhibition Blocks the Function of a Critical AR-Independent Master Regulator Network in Lethal Prostate Cancer
      Coleman D, Gao L, Schwartzman J, Urrutia J, Sehrawat A, Tayou J, Balter A, Burchard J, Chiotti KE, Derrick DS, Sun D, Xia Z, Heiser LM, Alumkal JJ
      Oncogene (2019)

    4. MEK-ERK signaling is a therapeutic target in metastatic castration resistant prostate cancer
      Nickols NG, Nazarian R, Zhao S, Tan V, Uzunangelov V, Xia Z , Baertsch R, Neeman E, ..., Alumkal JJ, Reiter RE, Rettig MB
      Prostate Cancer and Prostatic Diseases (2019)

    5. The Genomic Landscape of Estrogen Receptor α Binding Sites in Mouse Mammary Gland
      Palaniappan M, Nguyen L, Grimm SL, Xi Y, Xia Z, Li W and Coarfa C
      PLoS One (2019)

    6. Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation
      Weng T, Ko J, Masamha C, Xia Z, Xiang Y, Chen NY, Molina JG, ..., Wagner J, Blackburn MR.
      Journal of Clinical Investigation (2019)

    7. Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients
      Chu Y, Elrod N, Wang C, Li L, Chen T, Routh A, Xia Z, Li W, Wagner E, Ji P
      Oncogene (2019)

    2018
    1. Highly scalable generation of DNA methylation profiles in single cells
      Mulqueen RM, 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)