Publications
[ Group member; † Equal contribution; * Corresponding/Senior authors ] Google Scholar2023
- 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) - 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) - PathExpSurv: pathway expansion for explainable survival analysis and disease gene discovery
Hou Z, Leng J, Yu J, Xia Z*, Wu LY*
BMC Bioinformatics (2023) - 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) - 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) - 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)
- 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) - 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) - Pevonedistat, a Nedd8-activating enzyme inhibitor, in combination with ibrutinib in patients
Torka P, RKambhampati 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) - A cancer cell-intrinsic GOT2-PPARd 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)
- 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) - 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) - 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) - 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, SanfordCrane H, Horton W, Finan JM, Sattler A,Makar R, Dawson DW, Xia Z, Hingorani SR, Sherman MH.
Cancer Discovery (2021) - 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) - 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) - 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) - 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) - 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)
- 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) - 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) - 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) - 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) - 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)
- 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) - 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) - 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) - 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) -
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) - 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) - 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)
- 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) - 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) - 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) - 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)
- 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) - 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) - 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) - 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)- - Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma
The Cancer Genome Atlas Research Network (including Xia Z as co-author)
Cell (2017) - 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)
- 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)- - Neonatal cardiac dysfunction and transcriptome changes caused by the absence of Celf1
Giudice J, Xia Z, Li W, Cooper TA
Scientific Reports (2016)- - 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)- - 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)-
- 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)- - 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)- - 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)- - 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)- - 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)-
- 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) - - 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)- - 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)- - 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)- - 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)- - 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)- - 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)- - 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) - - 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)- - 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)
- 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) - - The Cancer Genome Atlas Pan-Cancer analysis project
The Cancer Genome Atlas Research Network (including Xia Z as co-author)
Nature Genetics (2013)
- 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)
- 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).
- 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. - - Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces
Xia Z, Wu L, Zhou X, Wong STC
BMC Syst Biol (2010)_
- 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) -
- 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)- - Graph Kernel by Spectral Transform in Kernel Fisher Discriminant Analysis
Xia Z, Wang C, Hu C, Sun Y
Journal of Computational Information Systems (2008)
- 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)- - 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)- - 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- - A Survey for Study of Feature Selection Algorithms
Mao Y, Zhou X, Xia Z, Yin Z, Sun Y
Pattern Recognition and Artificial Intelligence (2007)