Publications

2026

• 89 scSurvival: single-cell survival analysis of clinical cancer cohort data at cellular resolution
  Ren T^†, Zhao F^†, Chen C, Zhou L, Wu LY, Mills GB, Coussens LM, Xia Z.
  Cancer Discovery (2026) DOI
  Featured in NIH News Release  ·  ASCO AI in Oncology
• 88 Cyclin-dependent kinase-9 and oxidative phosphorylation inhibition overcome ibrutinib resistance in mantle cell lymphoma
  Roleder C^†, Zhao X^†, Lam V, Shen H, Dominguez EC, Chen C, Rodriguez-Rodriguez S, Wang L, Phillips T, Xia Z*, Danilov AV*.
  Cancer Research Communications (2026) DOI

2025

• 87 OmicsTweezer: A distribution-independent cell deconvolution model for multi-omics data
  Yang X^†, Zhao F^†, Ren T, Chen C, Byrne KT, Danilov AV, Sears RC, Nelson PS, Coussens LM, Mills GB, Xia Z.
  Cell Genomics (2025) DOI
• 86 Elevated tumor-associated androgen receptor activity correlates with poor immune infiltration and immunotherapy response across cancer types
  Hu YM, Zhao F, Graff JN, Chen C, Zhang Y, Stommel JM, Lee J, Zangirolani GM, Rose J, Thomas GV, Wu H, Kardosh A, Mills GB, Alumkal JJ, Moran AE, Xia Z.
  Cancer Research Communications (2025) DOI
• 85 Transcriptional profiling clarifies a program of enzalutamide extreme non-response in lethal prostate cancer
  Kumaraswamy A^†, Hu YM^†, Yates JA^†, Zhang C, Rodansky E, Khokhani D, Flores D, Duan Z, Zhang Y, Tabatabaei S, Slottke R, Ye S, Lara P, Foye A, Ryan CJ, Quigley DA, Huang J, Aggarwal R, Reiter RE, Wicha MS, Beer TM, Rettig M, Gleave M, Evans CP, Witte ON, Stuart JM, Thomas GV, Feng FY, Small EJ, Xia Z*, Alumkal JJ*.
  npj Precision Oncology (2025) DOI
• 84 The muscle-specific MEF2Dα2 isoform promotes muscle ketolysis and running capacity in mice
  Kumar S, Ji X, Iqbal H, Guan X, Mis B, Dave D, Kumar S, Besler J, Dash R*, Xia Z*, Singh RK*.
  EMBO Reports (2025) DOI
• 83 Stromal KITL/SCF maintains pancreas tissue homeostasis and restrains tumor progression
  Oñate MK, Oon C, Bhattacharyya S, Low V, Chen C, Zhao X, Arnold F, Yan Z, Pramod S, Hang Y, Ho YJ, Lowe SW, Kim SK, Xia Z, Sherman MH.
  Cancer Discovery (2025) DOI
• 82 Reproductive state controls transcription in the murine liver, with implications for breast cancer liver metastasis
  Ozaki MK, Zhang Y, Bartlett AQ, Wilde ED, Guan X, Yang A, Xia Z, Schedin P.
  PNAS (2025) DOI
• 81 CD4+ T cells mediate MHC-deficient tumor rejection and endothelial cell reprogramming
  Kim SI, Haerr ME, Al-Ghezi M, Chen C, Zhang Y, Phipps JL, Arora C, Gribbin KP, Kim G, Markosyan N, Xia Z, Vonderheide RH, Byrne KT.
  Cancer Immunology Research (2025) DOI
• 80 Safety and efficacy of the combination of copanlisib and nivolumab in patients with Richter's transformation or transformed non-Hodgkin lymphoma: results from a phase I trial
  Shouse G, Chen C, Muir A, Popplewell L, Siddiqi T, Zain J, Herrera AF, Danilova O, Roleder C, Wang L, Spurgeon SEF, Kittai AS, Chen L, Xia Z, Davids MS, Danilov AV.
  Haematologica (2025) DOI
• 79 PROX1 is an early driver of lineage plasticity in prostate cancer
  Duan Z, Shi M, Kumaraswamy A, Lin D, Khokhani D, Wang Y, Zhang C, Flores D, Rodansky E, Swaim OA, Storck WK, Beck HN, Patel RA, Sayar E, Hanratty BP, Xue H, Dong X, Maylin ZR, Wan R, Quigley DA, Sjöström M, Hu YM, Zhao F, Xia Z, Cheng S, Yu X, Feng FY, Zhang L, Aggarwal R, Small EJ, Ravikumar V, Rao A, Bedi K, Lee JK, Morrissey C, Coleman I, Nelson PS, Corey E, Udager AM, Rebernick RJ, Cieslik MP, Chinnaiyan AM, Yates JA, Haffner MC, Wang Y, Alumkal JJ.
  Journal of Clinical Investigation (2025) DOI
• 78 HuR-regulated extracellular vesicles promote endothelial cell remodeling in pancreatic cancer
  Finan JM, Guo Y, Bartlett AQ, Hawthorne K, Reyer M, Haerr M, Lamikanra O, Halamish H, Calvert V, Chen C, Xia Z, Petricoin EF, Sears RC, Byrne KT, Brody JR.
  Cancer Res Commun (2025) DOI
• 77 MBNL loss of function in smooth muscle as a model for myotonic dystrophy gastrointestinal dysmotility
  Peterson JA, Frias JA, Miller AN, Soni KG, Zhang Y, Xia Z, Day JW, Preidis GA, Cooper TA.
  Proc Natl Acad Sci U S A. (2025) DOI
• 76 MBNL overexpression rescues cardiac phenotypes in a myotonic dystrophy type 1 heart mouse model
  Hu RC, Zhang Y, Nitschke L, Johnson SJ, Hurley AE, Lagor WR, Xia Z, Cooper TA.
  Journal of Clinical Investigation (2025) DOI

2024

• 75 Biologically informed machine learning modeling of immune cells to reveal physiological and pathological aging process
  Zhang C^†, Ren T^†, Zhao X^†, Su Y^†, Wang Q, Zhang T, He B, Chen Y, Wu L-Y, Sun L, Zhang B, Xia Z.
  Immunity & Ageing (2024) DOI Website
• 74 Androgen receptor inhibition increases MHC Class I expression and improves immune response in prostate cancer
  Chesner LN, Polesso F, Graff JN, Hawley JE, Smith A, Lundberg A, Das R, Shenoy T, Sjöström M, Zhao F, Hu YM, Linder S, Chen WS, Hawkins RM, Shrestha R, Zhu X, Foye A, Li H, Kim L, Bhalla M, O'loughlin T, Ozturk DK, Hua T, Badura M, Wilkinson S, Trostel SY, Bergman AM, Ruggero D, Drake CG, Sowalsky AG, Fong L, Cooperberg M, Zwart W, Guan X, Ashworth A, Xia Z, Quigley DA, Gilbert LA, Feng FY, Moran AE.
  Cancer Discovery (2024) DOI

2023

• 73 Supervised learning of high-confidence phenotypic subpopulations from single-cell data
  Ren T, Chen C, Danilov AV, Liu S, Guan X, Du S, Wu X, Sherman MH, Spellman PT, Coussens LM, Adey AC, Mills GB, Wu LY, Xia Z.
  Nature Machine Intelligence (2023) DOI
• 72 CDK9 inhibition induces epigenetic reprogramming revealing strategies to circumvent resistance in lymphoma
  Thieme E^†, Bruss N^†, Sun D^†, Dominguez EC, Coleman D, Liu T, Roleder C, Martinez M, Garcia-Mansfield K, Ball B, Pirrotte P, Wang L, Xia Z*, Danilov AV*.
  Molecular Cancer (2023) DOI
• 71 PathExpSurv: pathway expansion for explainable survival analysis and disease gene discovery
  Hou Z, Leng J, Yu J, Xia Z*, Wu LY*.
  BMC Bioinformatics (2023) DOI
• 70 Pharmacologic targeting of Nedd8-activating enzyme reinvigorates T cell responses in lymphoid neoplasia
  Wang X^†, Chen C^†, Vuong D, Rodriguez-Rodriguez S, Lam V, Roleder C, Wang J, Kambhampati S, Berger A, Pennock N, Torka P, Hernandez-Ilizaliturri F, Siddiqi T, Wang L, Xia Z, Danilov AV.
  Leukemia (2023) DOI
• 69 LSD1 Promotes Prostate Cancer Cell Reprogramming by Repressing TP53 Signaling Independently of Its Demethylase Function
  Kumaraswamy A, Duan Z, Flores D, Zhang C, Sehrawat A, Hu YM, Swaim OA, Rodansky E, Storck WK, Kuleape JA, Bedi K, Mannan R, Wang XM, Udager A, Ravikumar V, Bankhead A, Coleman I, Lee JK, Morrissey C, Nelson PS, Chinnaiyan AM, Rao A, Xia Z, Yates JA, Alumkal JJ.
  JCI Insight (2023) DOI
• 68 T helper 1 effector memory CD4+ T cells protect the skin from poxvirus infection
  Harbour JC, Abdelbary M, Schell JB, Fancher SP, McLean JJ, Nappi TJ, Liu S, Nice TJ, Xia Z, Früh K, Nolz JC.
  Cell Reports (2023) DOI

2022

• 67 Androgen receptor activity in T cells limits checkpoint blockade efficacy
  Guan X^†, Polesso F^†, Wang C^†, Sehrawat A, Hawkins RM, Murray SE, Thomas GV, Caruso B, Thompson RF, Wood MA, Hipfinger C, Hammond SA, Graff JN, Xia Z*, Moran AE*.
  Nature (2022) DOI
• 66 Transcriptional Profiling of Matched Patient Biopsies Clarifies Molecular Determinants of Enzalutamide-Induced Lineage Plasticity
  Westbrook TC^†, Guan X^†, Rodansky E, Flores D, Liu CJ, Udager AM, Patel RA, Haffner MC, Hu YM, Sun D, Beer TM, Foye A, Aggarwal R, Quigley DA, Youngren JF, Ryan CJ, Gleave M, Wang Y, Huang J, Coleman I, Morrissey C, Nelson PS, Evans CP, Lara P, Reiter RE, Witte O, Rettig M, Wong CK, Weinstein AS, Uzunangelov V, Stuart JM, Thomas GV, Feng FY, Small EJ, Yates JA, Xia Z*, Alumkal JJ*.
  Nature Communications (2022) DOI
• 65 Pevonedistat, a Nedd8-activating enzyme inhibitor, in combination with ibrutinib in patients
  Torka P, Kambhampati S, Chen L, Wang X, Chen C, Vuong D, Qin H, Muir A, Orand K, Borja I, Smith L, Herrera AF, Spurgeon SEF, Park B, Lewis LD, Hernandez-Ilizaliturri F, Xia Z*, Danilov AV*.
  Blood Cancer Journal (2022) DOI
• 64 A cancer cell-intrinsic GOT2-PPARδ axis suppresses antitumor immunity
  Abrego J, Sanford-Crane H, Oon C, Xiao X, Betts CB, Sun D, Nagarajan S, Diaz L, Sandborg H, Bhattacharyya S, Xia Z, Coussens LM, Tontonoz P, Sherman MH.
  Cancer Discovery (2022) DOI

2021

• 63 Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data
  Sun D, Guan X, Moran AE, Wu LY, Qian DZ, Schedin P, Dai MS, Danilov AV, Alumkal JJ, Adey A, Spellman PT, Xia Z.
  Nature Biotechnology (2021) DOI
• 62 Postpartum breast cancer has a distinct molecular profile that predicts poor outcomes
  Jindal S^†, Pennock N^†, Sun D^†, Horton W, Ozaki M, Narasimhan J, Bartlett A, Weinmann S, Goss P, Borges V, Xia Z*, Schedin P*.
  Nature Communications (2021) DOI
• 61 BET Bromodomain Inhibition Blocks an AR-Repressed, E2F1-Activated Treatment-Emergent Neuroendocrine Prostate Cancer Lineage Plasticity Program
  Kim DH^†, Sun D^†, Storck WK, Leng KW, Jenkins C, Coleman DJ, Sampson D, Guan X, Kumaraswamy A, Rodansky ES, Urrutia JA, Schwartzman JA, Zhang C, Beltran H, Labrecque MP, Morrissey C, Lucas JM, Coleman IM, Nelson PS, Corey E, Handelman SK, Sexton JZ, Aggarwal R, Abida W, Feng FY, Small EJ, Spratt DE, Bankhead A, Rao A, Gesner EM, Attwell S, Lakhotia S, Campeau E, Yates JA, Xia Z*, Alumkal JJ*.
  Clinical Cancer Research (2021) DOI
• 60 Mesenchymal Lineage Heterogeneity Underlies Non-Redundant Functions of Pancreatic Cancer-Associated Fibroblasts
  Helms EJ, Berry MW, Chaw RC, DuFort CC, Sun D, Onate MK, Oon C, Bhattacharyya S, Sanford-Crane H, Horton W, Finan JM, Sattler A, Makar R, Dawson DW, Xia Z, Hingorani SR, Sherman MH.
  Cancer Discovery (2021) DOI
• 59 Pregnancy and weaning regulate human maternal liver size and function
  Bartlett AQ, Vesco KK, Purnell JQ, Francisco M, Goddard E, Guan X, DeBarber A, Leo MC, Baetscher E, Rooney W, Naugler W, Guimaraes A, Catalano P, Xia Z, Schedin P.
  Proc National Acad Sci (2021) DOI
• 58 Mammary collagen is under reproductive control with implications for breast cancer
  Guo Q, Sun D, Barrett AS, Jindal S, Pennock ND, Conklin MW, Xia Z, Mitchel E, Samatham R, Mirza N, Jacques S, Weinmann S, Borges VF, Hansen KC, Schedin P.
  Matrix Biology (2021) DOI
• 57 Pharmacologic targeting Mcl-1 induces mitochondrial dysfunction and apoptosis in B-cell lymphoma cells in TP53- and BAX-dependent manner
  Liu T, Lam V, Thieme E, Sun D, Wang X, Xu F, Wang L, Danilova OV, Xia Z, Tyner JW, Kurtz SE, Danilov AV.
  Clinical Cancer Research (2021) DOI
• 56 A Distinct Innate Immune Signature of Early Onset Colorectal Cancer
  Gardner IH, Siddharthan R, Watson K, Dewey E, Ruhl R, Khou S, Guan X, Xia Z, Tsikitis VL and Anand S.
  ImmunoHorizons (2021) DOI
• 55 Reversible cardiac disease features in an inducible CUG-repeat RNA expressing mouse model of myotonic dystrophy
  Rao AN, Campbell HM, Guan X, Word TA, Wehrens XHT, Xia Z, Cooper TA.
  JCI Insight (2021) DOI

2020

• 54 Transcriptional profiling identifies an androgen receptor activity-low, stemness program associated with enzalutamide resistance
  Alumkal JJ, Sun D, Lu E, Beer TM, Thomas GV, Latour E, Aggarwal R, Cetnar J, Ryan CJ, Tabatabaei S, Bailey S, Turina CB, Quigley DA, Guan X, Foye A, Youngren JF, Urrutia J, Huang J, Weinstein AS, Friedl V, Rettig M, Reiter RE, Spratt DE, Gleave M, Evans CP, Stuart JM, Chen Y, Feng FY, Small EJ, Witte O, Xia Z.
  Proc National Acad Sci (2020) DOI
• 53 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*.
  Clinical Cancer Research (2020) DOI
• 52 Increased nuclear but not cytoplasmic activities of CELF1 protein contribute to muscle wasting
  Cox DC, Guan X, Xia Z, Cooper TA.
  Human Molecular Genetics (2020) DOI
• 51 Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4
  Coleman DJ, Sampson DA, Sehrawat A, Kumaraswamy A, Sun D, Wang Y, Schwartzman J, Urrutia J, Lee AR, Coleman IM, Nelson PS, Dong X, Morrissey C, Corey E, Xia Z, Yates JA, Alumkal JJ.
  Neoplasia (2020) DOI
• 50 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) DOI

2019

• 49 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) DOI
• 48 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) DOI
• 47 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) DOI
• 46 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) DOI
• 45 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) DOI
• 44 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) DOI
• 43 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) DOI

2018

• 42 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) DOI
• 41 3′-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) DOI
• 40 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) DOI
• 39 3′ UTR lengthening as a novel mechanism in regulating cellular senescence
  Chen M, Lyu G, 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) DOI

2017

• 38 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) DOI
• 37 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) DOI
• 36 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) DOI
• 35 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 Genetics (2017) DOI
• 34 Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma
  The Cancer Genome Atlas Research Network (including Xia Z as co-author).
  Cell (2017) DOI
• 33 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) DOI

2016

• 32 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) DOI
• 31 Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1
  Giudice J, Xia Z, Li W, Cooper TA.
  Scientific Reports (2016) DOI
• 30 CFIm25 Regulates Glutaminase Alternative Terminal Exon Definition to Modulate miR-23 Function
  Masamha CP, Xia Z, Collum S, Peart N, Li W, Wagner EJ, Shyu A.
  RNA (2016) DOI
• 29 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) DOI

2015

• 28 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) DOI
• 27 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) DOI
• 26 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) DOI
• 25 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) DOI
• 24 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) DOI

2014

• 23 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) DOI
• 22 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) DOI
• 21 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) DOI
• 20 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) DOI
• 19 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) DOI
• 18 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) DOI
• 17 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) DOI
• 16 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) DOI
• 15 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) DOI
• 14 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) DOI

2013

• 13 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) DOI
• 12 The Cancer Genome Atlas Pan-Cancer analysis project
  The Cancer Genome Atlas Research Network (including Xia Z as co-author).
  Nature Genetics (2013) DOI

2012

• 11 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) DOI

2011

• 10 NSMAP: A Method for Spliced Isoforms Identification and Quantification from RNA-Seq
  Xia Z, Wen J, Chang C, Zhou X.
  BMC Bioinformatics (2011) DOI Website

2010

• 9 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 (2010) DOI
• 8 Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces
  Xia Z, Wu L, Zhou X, Wong STC.
  BMC Systems Biology (2010) DOI

2009

• 7 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.
  IEEE/NIH Life Science Systems and Applications Workshop (2009) DOI

2008

• 6 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) DOI
• 5 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

• 4 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) DOI
• 3 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)
• 2 Registration of 3D FMT and CT images of mouse via affine transformation using sequential Monte Carlo
  Xia Z, Zhou X, Sun Y, Wong STC.
  International Symposium on Computational Models of Life Sciences, AIP Conference Proceedings (2007) DOI
• 1 A Survey for Study of Feature Selection Algorithms
  Mao Y, Zhou X, Xia Z, Yin Z, Sun Y.
  Pattern Recognition and Artificial Intelligence (2007)