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Xinan Yang

TitleResearch Associate Professor
InstitutionUniversity of Chicago
DepartmentPediatrics-Hematology and Oncology
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    I am a bioinformatics scientist with expertise in the design, analysis, and interpretation of the vast amounts of data being generated by biologists and translational researchers.

    My innovative work has contributed to advancing translational bioinformatics. I am currently working on topological significance analyses of complex regulatory networks in complex diseases to facilitate the generation of new hypotheses.

    Collapse Research 
    Collapse research activities and funding
    R21LM012619     (YANG, XINAN HOLLY)Sep 7, 2017 - Aug 31, 2019
    NIH
    Differential enhancer transcription identifies cis-regulatory elements for disease
    Role: Principal Investigator
    R21CA167305     (YANG, XINAN HOLLY)Jul 1, 2013 - Jun 30, 2016
    NIH
    Modeling MicroRNA-Target Functional Networks for Acute Myeloid Leukemia Prognosis
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Rowton M, Perez-Cervantes C, Hur S, Jacobs-Li J, Lu E, Deng N, Guzzetta A, Hoffmann AD, Stocker M, Steimle JD, Lazarevic S, Oubaha S, Yang XH, Kim C, Yu S, Eckart H, Koska M, Hanson E, Chan SSK, Garry DJ, Kyba M, Basu A, Ikegami K, Pott S, Moskowitz IP. Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages. Dev Cell. 2022 09 26; 57(18):2181-2203.e9. PMID: 36108627; PMCID: PMC10506397.
      Citations:    Fields:    Translation:AnimalsCells
    2. Goldstein A, Wei M, Yang XH, Sun Y, Wang Z, Moskowitz IP, Cunningham JM. Detecting critical transition signals from single-cell transcriptomes to infer lineage-determining transcription factors. Nucleic Acids Res. 2022 09 09; 50(16):e91. PMID: 35640613; PMCID: PMC9458468.
      Citations: 4     Fields:    Translation:AnimalsCells
    3. Burnicka-Turek O, Broman MT, Steimle JD, Boukens BJ, Petrenko NB, Ikegami K, Nadadur RD, Qiao Y, Arnolds DE, Yang XH, Patel VV, Nobrega MA, Efimov IR, Moskowitz IP. Transcriptional Patterning of the Ventricular Cardiac Conduction System. Circ Res. 2020 07 17; 127(3):e94-e106. PMID: 32290757; PMCID: PMC8328577.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    4. Sun X, Wang Z, Hall JM, Perez-Cervantes C, Ruthenburg AJ, Moskowitz IP, Gribskov M, Yang XH. Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq. PLoS Comput Biol. 2020 02; 16(2):e1007119. PMID: 32040509; PMCID: PMC7034927.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    5. Steimle JD, Rankin SA, Slagle CE, Bekeny J, Rydeen AB, Chan SS, Kweon J, Yang XH, Ikegami K, Nadadur RD, Rowton M, Hoffmann AD, Lazarevic S, Thomas W, Boyle Anderson EAT, Horb ME, Luna-Zurita L, Ho RK, Kyba M, Jensen B, Zorn AM, Conlon FL, Moskowitz IP. Evolutionarily conserved Tbx5-Wnt2/2b pathway orchestrates cardiopulmonary development. Proc Natl Acad Sci U S A. 2018 11 06; 115(45):E10615-E10624. PMID: 30352852; PMCID: PMC6233116.
      Citations: 27     Fields:    Translation:AnimalsCells
    6. Wang Z, Cunningham JM, Yang XH. CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs. Bioinformatics. 2018 09 01; 34(17):i664-i670. PMID: 30423099; PMCID: PMC6129262.
      Citations:    Fields:    Translation:HumansCells
    7. Yang XH, Nadadur RD, Hilvering CR, Bianchi V, Werner M, Mazurek SR, Gadek M, Shen KM, Goldman JA, Tyan L, Bekeny J, Hall JM, Lee N, Perez-Cervantes C, Burnicka-Turek O, Poss KD, Weber CR, de Laat W, Ruthenburg AJ, Moskowitz IP. Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm. Elife. 2017 12 27; 6. PMID: 29280435; PMCID: PMC5745077.
      Citations: 26     Fields:    Translation:AnimalsCells
    8. Yang XH, Tang F, Shin J, Cunningham JM. Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma. BMC Syst Biol. 2017 Oct 03; 11(Suppl 5):92. PMID: 28984200; PMCID: PMC5629556.
      Citations: 6     Fields:    Translation:HumansCells
    9. Yang XH, Tang F, Shin J, Cunningham JM. A c-Myc-regulated stem cell-like signature in high-risk neuroblastoma: A systematic discovery (Target neuroblastoma ESC-like signature). Sci Rep. 2017 03 03; 7(1):41. PMID: 28246384; PMCID: PMC5427913.
      Citations: 16     Fields:    Translation:HumansCells
    10. Hoffmann AD, Yang XH, Burnicka-Turek O, Bosman JD, Ren X, Xie L, Steimle JD, Vokes SA, McMahon AP, Kalinichenko VV, Moskowitz IP. Correction: Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation. PLoS Genet. 2016 Dec; 12(12):e1006533. PMID: 28033319; PMCID: PMC5199006.
      Citations:    Fields:    
    11. Burnicka-Turek O, Steimle JD, Huang W, Felker L, Kamp A, Kweon J, Peterson M, Reeves RH, Maslen CL, Gruber PJ, Yang XH, Shendure J, Moskowitz IP. Cilia gene mutations cause atrioventricular septal defects by multiple mechanisms. Hum Mol Genet. 2016 07 15; 25(14):3011-3028. PMID: 27340223; PMCID: PMC5181596.
      Citations: 28     Fields:    Translation:HumansAnimalsCells
    12. Priest JR, Osoegawa K, Mohammed N, Nanda V, Kundu R, Schultz K, Lammer EJ, Girirajan S, Scheetz T, Waggott D, Haddad F, Reddy S, Bernstein D, Burns T, Steimle JD, Yang XH, Moskowitz IP, Hurles M, Lifton RP, Nickerson D, Bamshad M, Eichler EE, Mital S, Sheffield V, Quertermous T, Gelb BD, Portman M, Ashley EA. De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects. PLoS Genet. 2016 Apr; 12(4):e1005963. PMID: 27058611; PMCID: PMC4825975.
      Citations: 54     Fields:    Translation:HumansAnimals
    13. Waldron L, Steimle JD, Greco TM, Gomez NC, Dorr KM, Kweon J, Temple B, Yang XH, Wilczewski CM, Davis IJ, Cristea IM, Moskowitz IP, Conlon FL. The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation. Dev Cell. 2016 Feb 08; 36(3):262-75. PMID: 26859351; PMCID: PMC4920128.
      Citations: 46     Fields:    Translation:HumansAnimalsCells
    14. Yang XH, Wang B, Cunningham JM. Identification of epigenetic modifications that contribute to pathogenesis in therapy-related AML: Effective integration of genome-wide histone modification with transcriptional profiles. BMC Med Genomics. 2015; 8 Suppl 2:S6. PMID: 26043758; PMCID: PMC4460748.
      Citations: 2     Fields:    Translation:HumansCells
    15. Wang B, Cunningham JM, Yang XH. Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data. Bioinformatics. 2015 Sep 15; 31(18):3043-5. PMID: 25979472; PMCID: PMC4565027.
      Citations: 10     Fields:    Translation:HumansCells
    16. Yang XH, Li M, Wang B, Zhu W, Desgardin A, Onel K, de Jong J, Chen J, Chen L, Cunningham JM. Systematic computation with functional gene-sets among leukemic and hematopoietic stem cells reveals a favorable prognostic signature for acute myeloid leukemia. BMC Bioinformatics. 2015 Mar 24; 16:97. PMID: 25887548; PMCID: PMC4376348.
      Citations: 4     Fields:    Translation:HumansCells
    17. Hoffmann AD, Yang XH, Burnicka-Turek O, Bosman JD, Ren X, Steimle JD, Vokes SA, McMahon AP, Kalinichenko VV, Moskowitz IP. Foxf genes integrate tbx5 and hedgehog pathways in the second heart field for cardiac septation. PLoS Genet. 2014 Oct; 10(10):e1004604. PMID: 25356765; PMCID: PMC4214600.
      Citations: 50     Fields:    Translation:HumansAnimalsCells
    18. van den Boogaard M, Smemo S, Burnicka-Turek O, Arnolds DE, van de Werken HJ, Klous P, McKean D, Muehlschlegel JD, Moosmann J, Toka O, Yang XH, Koopmann TT, Adriaens ME, Bezzina CR, de Laat W, Seidman C, Seidman JG, Christoffels VM, Nobrega MA, Barnett P, Moskowitz IP. A common genetic variant within SCN10A modulates cardiac SCN5A expression. J Clin Invest. 2014 Apr; 124(4):1844-52. PMID: 24642470; PMCID: PMC3973109.
      Citations: 94     Fields:    Translation:HumansAnimalsCells
    19. Yang X, Vasudevan P, Parekh V, Penev A, Cunningham JM. Bridging cancer biology with the clinic: relative expression of a GRHL2-mediated gene-set pair predicts breast cancer metastasis. PLoS One. 2013; 8(2):e56195. PMID: 23441166; PMCID: PMC3575392.
      Citations: 30     Fields:    Translation:HumansAnimalsCells
    20. Lee Y, Li H, Li J, Rebman E, Achour I, Regan KE, Gamazon ER, Chen JL, Yang XH, Cox NJ, Lussier YA. Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. J Am Med Inform Assoc. 2013 Jul-Aug; 20(4):619-29. PMID: 23355459; PMCID: PMC3721168.
      Citations: 23     Fields:    Translation:Humans
    21. Yang X, Lee Y, Huang Y, Chen JL, Xing RH, Lussier YA. Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. BMC Bioinformatics. 2010 Oct 28; 11 Suppl 9:S11. PMID: 21044358; PMCID: PMC2967741.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    22. Yang X, Huang Y, Chen JL, Xie J, Sun X, Lussier YA. Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia. BMC Bioinformatics. 2009 Sep 17; 10 Suppl 9:S6. PMID: 19761576; PMCID: PMC2745693.
      Citations: 4     Fields:    
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