ZHANDONG LIU

TitleAssociate Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Pediatrics
Address1250 MOURSUND STREET
Houston, TX 77030
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    R01GM120033     (MALETIC-SAVATIC, MIRJANA)Jan 1, 2017 - Dec 31, 2021
    NIH
    Advanced Computational Approaches for NMR Data-mining
    Role: Co-Principal Investigator

    R01AG057339     (BOTAS, JUAN)Sep 15, 2017 - May 31, 2022
    NIH
    Functional Dissection of Alzheimer's Disease Networks in Drosophila: from Association to Causal Modulators of Age-Dependent Neurodegeration
    Role: Co-Principal Investigator

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    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.
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    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. Yalamanchili HK, Elrod ND, Jensen MK, Ji P, Lin A, Wagner EJ, Liu Z. A computational pipeline to infer alternative poly-adenylation from 3' sequencing data. Methods Enzymol. 2021; 655:185-204. PMID: 34183121.
      Citations:    Fields:    Translation:Cells
    2. Onur TS, Laitman A, Zhao H, Keyho R, Kim H, Wang J, Mair M, Wang H, Li L, Perez A, de Haro M, Wan YW, Allen G, Lu B, Al-Ramahi I, Liu Z, Botas J. Downregulation of glial genes involved in synaptic function mitigates Huntington's disease pathogenesis. Elife. 2021 04 19; 10. PMID: 33871358.
      Citations:    Fields:    
    3. Zhang W, Bado IL, Hu J, Wan YW, Wu L, Wang H, Gao Y, Jeong HH, Xu Z, Hao X, Lege BM, Al-Ouran R, Li L, Li J, Yu L, Singh S, Lo HC, Niu M, Liu J, Jiang W, Li Y, Wong STC, Cheng C, Liu Z, Zhang XH. The bone microenvironment invigorates metastatic seeds for further dissemination. Cell. 2021 04 29; 184(9):2471-2486.e20. PMID: 33878291.
      Citations: 4     Fields:    
    4. Bado IL, Zhang W, Hu J, Xu Z, Wang H, Sarkar P, Li L, Wan YW, Liu J, Wu W, Lo HC, Kim IS, Singh S, Janghorban M, Muscarella AM, Goldstein A, Singh P, Jeong HH, Liu C, Schiff R, Huang S, Ellis MJ, Gaber MW, Gugala Z, Liu Z, Zhang XH. The bone microenvironment increases phenotypic plasticity of ER+ breast cancer cells. Dev Cell. 2021 04 19; 56(8):1100-1117.e9. PMID: 33878299.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    5. Jin H, Liu Z. A benchmark for RNA-seq deconvolution analysis under dynamic testing environments. Genome Biol. 2021 04 12; 22(1):102. PMID: 33845875.
      Citations: 2     Fields:    
    6. Lee WS, Lavery L, Rousseaux MWC, Rutledge EB, Jang Y, Wan YW, Wu SR, Kim W, Al-Ramahi I, Rath S, Adamski CJ, Bondar VV, Tewari A, Soleimani S, Mota S, Yalamanchili HK, Orr HT, Liu Z, Botas J, Zoghbi HY. Dual targeting of brain region-specific kinases potentiates neurological rescue in Spinocerebellar ataxia type 1. EMBO J. 2021 04 01; 40(7):e106106. PMID: 33709453.
      Citations: 1     Fields:    
    7. Shao Y, Sztainberg Y, Wang Q, Bajikar SS, Trostle AJ, Wan YW, Jafar-Nejad P, Rigo F, Liu Z, Tang J, Zoghbi HY. Antisense oligonucleotide therapy in a humanized mouse model of MECP2 duplication syndrome. Sci Transl Med. 2021 03 03; 13(583). PMID: 33658357.
      Citations: 2     Fields:    Translation:Animals
    8. Alfradique-Dunham I, Al-Ouran R, von Coelln R, Blauwendraat C, Hill E, Luo L, Stillwell A, Young E, Kaw A, Tan M, Liao C, Hernandez D, Pihlstrom L, Grosset D, Shulman LM, Liu Z, Rouleau GA, Nalls M, Singleton AB, Morris H, Jankovic J, Shulman JM. Genome-Wide Association Study Meta-Analysis for Parkinson Disease Motor Subtypes. Neurol Genet. 2021 Apr; 7(2):e557. PMID: 33987465.
      Citations:    
    9. Mangleburg CG, Wu T, Yalamanchili HK, Guo C, Hsieh YC, Duong DM, Dammer EB, De Jager PL, Seyfried NT, Liu Z, Shulman JM. Integrated analysis of the aging brain transcriptome and proteome in tauopathy. Mol Neurodegener. 2020 09 29; 15(1):56. PMID: 32993812.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    10. Wang X, Yi H, Wang J, Liu Z, Yin Y, Zhang H. GDASC: a GPU parallel-based web server for detecting hidden batch factors. Bioinformatics. 2020 08 15; 36(14):4211-4213. PMID: 32386292.
      Citations:    Fields:    
    11. Nitschke L, Tewari A, Coffin SL, Xhako E, Pang K, Gennarino VA, Johnson JL, Blanco FA, Liu Z, Zoghbi HY. miR760 regulates ATXN1 levels via interaction with its 5' untranslated region. Genes Dev. 2020 09 01; 34(17-18):1147-1160. PMID: 32763910.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    12. Wan YW, Al-Ouran R, Mangleburg CG, Perumal TM, Lee TV, Allison K, Swarup V, Funk CC, Gaiteri C, Allen M, Wang M, Neuner SM, Kaczorowski CC, Philip VM, Howell GR, Martini-Stoica H, Zheng H, Mei H, Zhong X, Kim JW, Dawson VL, Dawson TM, Pao PC, Tsai LH, Haure-Mirande JV, Ehrlich ME, Chakrabarty P, Levites Y, Wang X, Dammer EB, Srivastava G, Mukherjee S, Sieberts SK, Omberg L, Dang KD, Eddy JA, Snyder P, Chae Y, Amberkar S, Wei W, Hide W, Preuss C, Ergun A, Ebert PJ, Airey DC, Mostafavi S, Yu L, Klein HU, Carter GW, Collier DA, Golde TE, Levey AI, Bennett DA, Estrada K, Townsend TM, Zhang B, Schadt E, De Jager PL, Price ND, Ertekin-Taner N, Liu Z, Shulman JM, Mangravite LM, Logsdon BA. Meta-Analysis of the Alzheimer's Disease Human Brain Transcriptome and Functional Dissection in Mouse Models. Cell Rep. 2020 07 14; 32(2):107908. PMID: 32668255.
      Citations: 26     Fields:    Translation:HumansAnimalsCells
    13. Yalamanchili HK, Alcott CE, Ji P, Wagner EJ, Zoghbi HY, Liu Z. PolyA-miner: accurate assessment of differential alternative poly-adenylation from 3'Seq data using vector projections and non-negative matrix factorization. Nucleic Acids Res. 2020 07 09; 48(12):e69. PMID: 32463457.
      Citations: 1     Fields:    Translation:HumansAnimalsCells
    14. Jeong H, Liu Z. PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing. Bioinformatics. 2020 07 01; 36(13):4021-4029. PMID: 32348450.
      Citations: 3     Fields:    
    15. Pang K, Wang L, Wang W, Zhou J, Cheng C, Han K, Zoghbi HY, Liu Z. Coexpression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders. Genome Res. 2020 06; 30(6):835-848. PMID: 32554779.
      Citations: 4     Fields:    Translation:HumansCells
    16. Alcott CE, Yalamanchili HK, Ji P, van der Heijden ME, Saltzman A, Elrod N, Lin A, Leng M, Bhatt B, Hao S, Wang Q, Saliba A, Tang J, Malovannaya A, Wagner EJ, Liu Z, Zoghbi HY. Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylation. Elife. 2020 04 22; 9. PMID: 32319885.
      Citations: 4     Fields:    Translation:HumansAnimalsCells
    17. Roy ER, Wang B, Wan YW, Chiu G, Cole A, Yin Z, Propson NE, Xu Y, Jankowsky JL, Liu Z, Lee VM, Trojanowski JQ, Ginsberg SD, Butovsky O, Zheng H, Cao W. Type I interferon response drives neuroinflammation and synapse loss in Alzheimer disease. J Clin Invest. 2020 04 01; 130(4):1912-1930. PMID: 31917687.
      Citations: 46     Fields:    Translation:HumansAnimalsCells
    18. Chen CA, Wang W, Pedersen SE, Raman A, Seymour ML, Ruiz FR, Xia A, van der Heijden ME, Wang L, Yin J, Lopez J, Rech ME, Lewis RA, Wu SM, Liu Z, Pereira FA, Pautler RG, Zoghbi HY, Schaaf CP. Nr2f1 heterozygous knockout mice recapitulate neurological phenotypes of Bosch-Boonstra-Schaaf optic atrophy syndrome and show impaired hippocampal synaptic plasticity. Hum Mol Genet. 2020 03 27; 29(5):705-715. PMID: 31600777.
      Citations: 1     Fields:    Translation:Animals
    19. Lavery LA, Ure K, Wan YW, Luo C, Trostle AJ, Wang W, Jin H, Lopez J, Lucero J, Durham MA, Castanon R, Nery JR, Liu Z, Goodell M, Ecker JR, Behrens MM, Zoghbi HY. Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome. Elife. 2020 03 11; 9. PMID: 32159514.
      Citations: 11     Fields:    Translation:AnimalsCells
    20. Scott TM, Guo H, Eichler EE, Rosenfeld JA, Pang K, Liu Z, Lalani S, Bi W, Yang Y, Bacino CA, Streff H, Lewis AM, Koenig MK, Thiffault I, Bellomo A, Everman DB, Jones JR, Stevenson RE, Bernier R, Gilissen C, Pfundt R, Hiatt SM, Cooper GM, Holder JL, Scott DA. BAZ2B haploinsufficiency as a cause of developmental delay, intellectual disability, and autism spectrum disorder. Hum Mutat. 2020 05; 41(5):921-925. PMID: 31999386.
      Citations: 3     Fields:    Translation:Humans
    21. Liu J, Ding G, Zou K, Jiang Z, Zhang J, Lu Y, Pignata A, Venner E, Liu P, Liu Z, Wangler MF, Sun Z. Genome sequencing analysis of a family with a child displaying severe abdominal distention and recurrent hypoglycemia. Mol Genet Genomic Med. 2020 03; 8(3):e1130. PMID: 31971667.
      Citations: 2     Fields:    Translation:Humans
    22. Jeong HH, Liu Z. Are HHV-6A and HHV-7 Really More Abundant in Alzheimer's Disease? Neuron. 2019 12 18; 104(6):1034-1035. PMID: 31855626.
      Citations: 7     Fields:    Translation:HumansCells
    23. Hsieh YC, Guo C, Yalamanchili HK, Abreha M, Al-Ouran R, Li Y, Dammer EB, Lah JJ, Levey AI, Bennett DA, De Jager PL, Seyfried NT, Liu Z, Shulman JM. Tau-Mediated Disruption of the Spliceosome Triggers Cryptic RNA Splicing and Neurodegeneration in Alzheimer's Disease. Cell Rep. 2019 10 08; 29(2):301-316.e10. PMID: 31597093.
      Citations: 27     Fields:    Translation:HumansAnimalsCells
    24. Patel AJ, Wan YW, Al-Ouran R, Revelli JP, Cardenas MF, Oneissi M, Xi L, Jalali A, Magnotti JF, Muzny DM, Doddapaneni H, Sebastian S, Heck KA, Goodman JC, Gopinath SP, Liu Z, Rao G, Plon SE, Yoshor D, Wheeler DA, Zoghbi HY, Klisch TJ. Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors. Proc Natl Acad Sci U S A. 2019 10 22; 116(43):21715-21726. PMID: 31591222.
      Citations: 21     Fields:    Translation:HumansCells
    25. Al-Ouran R, Wan YW, Mangleburg CG, Lee TV, Allison K, Shulman JM, Liu Z. A Portal to Visualize Transcriptome Profiles in Mouse Models of Neurological Disorders. Genes (Basel). 2019 09 26; 10(10). PMID: 31561642.
      Citations: 2     Fields:    Translation:AnimalsCells
    26. Wang J, Mao D, Fazal F, Kim SY, Yamamoto S, Bellen H, Liu Z. Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity. Curr Protoc Bioinformatics. 2019 09; 67(1):e85. PMID: 31524990.
      Citations: 4     Fields:    Translation:Humans
    27. Zhou W, He Y, Rehman AU, Kong Y, Hong S, Ding G, Yalamanchili HK, Wan YW, Paul B, Wang C, Gong Y, Zhou W, Liu H, Dean J, Scalais E, O'Driscoll M, Morton JEV, Hou X, Wu Q, Tong Q, Liu Z, Liu P, Xu Y, Sun Z. Author Correction: Loss of function of NCOR1 and NCOR2 impairs memory through a novel GABAergic hypothalamus-CA3 projection. Nat Neurosci. 2019 Sep; 22(9):1533. PMID: 31222187.
      Citations:    Fields:    
    28. Wang J, Liu Z, Bellen HJ, Yamamoto S. Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information. J Vis Exp. 2019 08 15; (150). PMID: 31475990.
      Citations: 6     Fields:    Translation:HumansAnimals
    29. Jeong HH, Kim SY, Rousseaux MWC, Zoghbi HY, Liu Z. Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives. Genome Res. 2019 06; 29(6):999-1008. PMID: 31015259.
      Citations: 7     Fields:    Translation:Cells
    30. Wang L, Adamski CJ, Bondar VV, Craigen E, Collette JR, Pang K, Han K, Jain A, Y Jung S, Liu Z, Sifers RN, Holder JL, Zoghbi HY. A kinome-wide RNAi screen identifies ERK2 as a druggable regulator of Shank3 stability. Mol Psychiatry. 2020 10; 25(10):2504-2516. PMID: 30696942.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    31. Zhou W, He Y, Rehman AU, Kong Y, Hong S, Ding G, Yalamanchili HK, Wan YW, Paul B, Wang C, Gong Y, Zhou W, Liu H, Dean J, Scalais E, O'Driscoll M, Morton JEV, Hou X, Wu Q, Tong Q, Liu Z, Liu P, Xu Y, Sun Z. Loss of function of NCOR1 and NCOR2 impairs memory through a novel GABAergic hypothalamus-CA3 projection. Nat Neurosci. 2019 02; 22(2):205-217. PMID: 30664766.
      Citations: 18     Fields:    Translation:AnimalsCells
    32. Wang L, Pang K, Han K, Adamski CJ, Wang W, He L, Lai JK, Bondar VV, Duman JG, Richman R, Tolias KF, Barth P, Palzkill T, Liu Z, Holder JL, Zoghbi HY. An autism-linked missense mutation in SHANK3 reveals the modularity of Shank3 function. Mol Psychiatry. 2020 10; 25(10):2534-2555. PMID: 30610205.
      Citations: 16     Fields:    Translation:HumansAnimalsCells
    33. Choi WT, Tosun M, Jeong HH, Karakas C, Semerci F, Liu Z, Maletic-Savatic M. Metabolomics of mammalian brain reveals regional differences. BMC Syst Biol. 2018 12 21; 12(Suppl 8):127. PMID: 30577853.
      Citations: 4     Fields:    Translation:Animals
    34. Litvinchuk A, Wan YW, Swartzlander DB, Chen F, Cole A, Propson NE, Wang Q, Zhang B, Liu Z, Zheng H. Complement C3aR Inactivation Attenuates Tau Pathology and Reverses an Immune Network Deregulated in Tauopathy Models and Alzheimer's Disease. Neuron. 2018 12 19; 100(6):1337-1353.e5. PMID: 30415998.
      Citations: 75     Fields:    Translation:HumansAnimalsCells
    35. De Maio A, Yalamanchili HK, Adamski CJ, Gennarino VA, Liu Z, Qin J, Jung SY, Richman R, Orr H, Zoghbi HY. RBM17 Interacts with U2SURP and CHERP to Regulate Expression and Splicing of RNA-Processing Proteins. Cell Rep. 2018 10 16; 25(3):726-736.e7. PMID: 30332651.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    36. Rousseaux MWC, Vázquez-Vélez GE, Al-Ramahi I, Jeong HH, Bajic A, Revelli JP, Ye H, Phan ET, Deger JM, Perez AM, Kim JY, Lavery LA, Xu Q, Li MZ, Kang H, Kim JJ, Shulman JM, Westbrook TF, Elledge SJ, Liu Z, Botas J, Zoghbi HY. A Druggable Genome Screen Identifies Modifiers of a-Synuclein Levels via a Tiered Cross-Species Validation Approach. J Neurosci. 2018 10 24; 38(43):9286-9301. PMID: 30249792.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    37. Martini-Stoica H, Cole AL, Swartzlander DB, Chen F, Wan YW, Bajaj L, Bader DA, Lee VMY, Trojanowski JQ, Liu Z, Sardiello M, Zheng H. TFEB enhances astroglial uptake of extracellular tau species and reduces tau spreading. J Exp Med. 2018 09 03; 215(9):2355-2377. PMID: 30108137.
      Citations: 47     Fields:    Translation:AnimalsCells
    38. Raman AT, Pohodich AE, Wan YW, Yalamanchili HK, Lowry WE, Zoghbi HY, Liu Z. Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations. Nat Commun. 2018 08 13; 9(1):3225. PMID: 30104565.
      Citations: 16     Fields:    Translation:HumansAnimalsCells
    39. Al-Ramahi I, Lu B, Di Paola S, Pang K, de Haro M, Peluso I, Gallego-Flores T, Malik NT, Erikson K, Bleiberg BA, Avalos M, Fan G, Rivers LE, Laitman AM, Diaz-García JR, Hild M, Palacino J, Liu Z, Medina DL, Botas J. High-Throughput Functional Analysis Distinguishes Pathogenic, Nonpathogenic, and Compensatory Transcriptional Changes in Neurodegeneration. Cell Syst. 2018 07 25; 7(1):28-40.e4. PMID: 29936182.
      Citations: 9     Fields:    Translation:HumansAnimalsCells
    40. Guo C, Jeong HH, Hsieh YC, Klein HU, Bennett DA, De Jager PL, Liu Z, Shulman JM. Tau Activates Transposable Elements in Alzheimer's Disease. Cell Rep. 2018 06 05; 23(10):2874-2880. PMID: 29874575.
      Citations: 54     Fields:    Translation:HumansAnimalsCells
    41. Ma Z, Wang H, Cai Y, Wang H, Niu K, Wu X, Ma H, Yang Y, Tong W, Liu F, Liu Z, Zhang Y, Liu R, Zhu ZJ, Liu N. Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila. Elife. 2018 05 29; 7. PMID: 29809154.
      Citations: 25     Fields:    Translation:AnimalsCells
    42. Ito-Ishida A, Yamalanchili HK, Shao Y, Baker SA, Heckman LD, Lavery LA, Kim JY, Lombardi LM, Sun Y, Liu Z, Zoghbi HY. Genome-wide distribution of linker histone H1.0 is independent of MeCP2. Nat Neurosci. 2018 06; 21(6):794-798. PMID: 29802390.
      Citations: 6     Fields:    Translation:AnimalsCells
    43. Pohodich AE, Yalamanchili H, Raman AT, Wan YW, Gundry M, Hao S, Jin H, Tang J, Liu Z, Zoghbi HY. Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity. Elife. 2018 03 23; 7. PMID: 29570050.
      Citations: 20     Fields:    Translation:AnimalsCells
    44. Rousseaux MWC, Tschumperlin T, Lu HC, Lackey EP, Bondar VV, Wan YW, Tan Q, Adamski CJ, Friedrich J, Twaroski K, Chen W, Tolar J, Henzler C, Sharma A, Bajic A, Lin T, Duvick L, Liu Z, Sillitoe RV, Zoghbi HY, Orr HT. ATXN1-CIC Complex Is the Primary Driver of Cerebellar Pathology in Spinocerebellar Ataxia Type 1 through a Gain-of-Function Mechanism. Neuron. 2018 03 21; 97(6):1235-1243.e5. PMID: 29526553.
      Citations: 25     Fields:    Translation:HumansAnimalsCells
    45. Yin J, Chen W, Chao ES, Soriano S, Wang L, Wang W, Cummock SE, Tao H, Pang K, Liu Z, Pereira FA, Samaco RC, Zoghbi HY, Xue M, Schaaf CP. Otud7a Knockout Mice Recapitulate Many Neurological Features of 15q13.3 Microdeletion Syndrome. Am J Hum Genet. 2018 02 01; 102(2):296-308. PMID: 29395075.
      Citations: 16     Fields:    Translation:AnimalsCells
    46. Tan Q, Brunetti L, Rousseaux MWC, Lu HC, Wan YW, Revelli JP, Liu Z, Goodell MA, Zoghbi HY. Loss of Capicua alters early T cell development and predisposes mice to T cell lymphoblastic leukemia/lymphoma. Proc Natl Acad Sci U S A. 2018 02 13; 115(7):E1511-E1519. PMID: 29382756.
      Citations: 13     Fields:    Translation:AnimalsCells
    47. Jeong HH, Yalamanchili HK, Guo C, Shulman JM, Liu Z. An ultra-fast and scalable quantification pipeline for transposable elements from next generation sequencing data. Pac Symp Biocomput. 2018; 23:168-179. PMID: 29218879.
      Citations: 21     Fields:    Translation:HumansAnimalsCells
    48. Liu Z, Zheng WJ, Allen GI, Liu Y, Ruan J, Zhao Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools. BMC Bioinformatics. 2017 Oct 03; 18(Suppl 11):405. PMID: 28984189.
      Citations:    Fields:    Translation:HumansCells
    49. Zhao Z, Liu Z, Chen K, Guo Y, Allen GI, Zhang J, Jim Zheng W, Ruan J. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics. BMC Genomics. 2017 Oct 03; 18(Suppl 6):703. PMID: 28984207.
      Citations: 1     Fields:    
    50. Jeong HH, Kim SY, Rousseaux MWC, Zoghbi HY, Liu Z. CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution. Bioinformatics. 2017 Sep 15; 33(18):2963-2965. PMID: 28541456.
      Citations: 8     Fields:    Translation:Cells
    51. Yalamanchili HK, Wan YW, Liu Z. Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing. Curr Protoc Bioinformatics. 2017 09 13; 59:11.15.1-11.15.21. PMID: 28902396.
      Citations: 8     Fields:    Translation:Cells
    52. Delaney MA, Wan YW, Kim GE, Creighton CJ, Taylor MG, Masand R, Park A, Valdes C, Gibbons W, Liu Z, Anderson ML. A Role for Progesterone-Regulated sFRP4 Expression in Uterine Leiomyomas. J Clin Endocrinol Metab. 2017 09 01; 102(9):3316-3326. PMID: 28637297.
      Citations:    Fields:    Translation:HumansCells
    53. Jiang X, Zhang H, Quan X, Liu Z, Yin Y. Disease-related gene module detection based on a multi-label propagation clustering algorithm. PLoS One. 2017; 12(5):e0178006. PMID: 28542379.
      Citations: 3     Fields:    Translation:HumansAnimals
    54. Wang J, Al-Ouran R, Hu Y, Kim SY, Wan YW, Wangler MF, Yamamoto S, Chao HT, Comjean A, Mohr SE, Perrimon N, Liu Z, Bellen HJ. MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome. Am J Hum Genet. 2017 Jun 01; 100(6):843-853. PMID: 28502612.
      Citations: 63     Fields:    Translation:Humans
    55. Jin H, Wan YW, Liu Z. Comprehensive evaluation of RNA-seq quantification methods for linearity. BMC Bioinformatics. 2017 Mar 22; 18(Suppl 4):117. PMID: 28361706.
      Citations: 15     Fields:    Translation:HumansCells
    56. Lu HC, Tan Q, Rousseaux MW, Wang W, Kim JY, Richman R, Wan YW, Yeh SY, Patel JM, Liu X, Lin T, Lee Y, Fryer JD, Han J, Chahrour M, Finnell RH, Lei Y, Zurita-Jimenez ME, Ahimaz P, Anyane-Yeboa K, Van Maldergem L, Lehalle D, Jean-Marcais N, Mosca-Boidron AL, Thevenon J, Cousin MA, Bro DE, Lanpher BC, Klee EW, Alexander N, Bainbridge MN, Orr HT, Sillitoe RV, Ljungberg MC, Liu Z, Schaaf CP, Zoghbi HY. Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans. Nat Genet. 2017 Apr; 49(4):527-536. PMID: 28288114.
      Citations: 43     Fields:    Translation:HumansAnimals
    57. Maass JC, Gu R, Cai T, Wan YW, Cantellano SC, Asprer JS, Zhang H, Jen HI, Edlund RK, Liu Z, Groves AK. Transcriptomic Analysis of Mouse Cochlear Supporting Cell Maturation Reveals Large-Scale Changes in Notch Responsiveness Prior to the Onset of Hearing. PLoS One. 2016; 11(12):e0167286. PMID: 27918591.
      Citations: 15     Fields:    Translation:AnimalsCells
    58. Tan Q, Yalamanchili HK, Park J, De Maio A, Lu HC, Wan YW, White JJ, Bondar VV, Sayegh LS, Liu X, Gao Y, Sillitoe RV, Orr HT, Liu Z, Zoghbi HY. Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models. Hum Mol Genet. 2016 12 01; 25(23):5083-5093. PMID: 28007900.
      Citations: 33     Fields:    Translation:HumansAnimalsCells
    59. Lo YH, Chung E, Li Z, Wan YW, Mahe MM, Chen MS, Noah TK, Bell KN, Yalamanchili HK, Klisch TJ, Liu Z, Park JS, Shroyer NF. Transcriptional Regulation by ATOH1 and its Target SPDEF in the Intestine. Cell Mol Gastroenterol Hepatol. 2017 Jan; 3(1):51-71. PMID: 28174757.
      Citations: 18     Fields:    
    60. Wan YW, Allen GI, Baker Y, Yang E, Ravikumar P, Anderson M, Liu Z. XMRF: an R package to fit Markov Networks to high-throughput genetics data. BMC Syst Biol. 2016 08 26; 10 Suppl 3:69. PMID: 27586041.
      Citations: 5     Fields:    
    61. Veeraragavan S, Wan YW, Connolly DR, Hamilton SM, Ward CS, Soriano S, Pitcher MR, McGraw CM, Huang SG, Green JR, Yuva LA, Liang AJ, Neul JL, Yasui DH, LaSalle JM, Liu Z, Paylor R, Samaco RC. Loss of MeCP2 in the rat models regression, impaired sociability and transcriptional deficits of Rett syndrome. Hum Mol Genet. 2016 08 01; 25(15):3284-3302. PMID: 27365498.
      Citations: 22     Fields:    Translation:HumansAnimals
    62. Allen GI, Amoroso N, Anghel C, Balagurusamy V, Bare CJ, Beaton D, Bellotti R, Bennett DA, Boehme KL, Boutros PC, Caberlotto L, Caloian C, Campbell F, Chaibub Neto E, Chang YC, Chen B, Chen CY, Chien TY, Clark T, Das S, Davatzikos C, Deng J, Dillenberger D, Dobson RJ, Dong Q, Doshi J, Duma D, Errico R, Erus G, Everett E, Fardo DW, Friend SH, Fröhlich H, Gan J, St George-Hyslop P, Ghosh SS, Glaab E, Green RC, Guan Y, Hong MY, Huang C, Hwang J, Ibrahim J, Inglese P, Iyappan A, Jiang Q, Katsumata Y, Kauwe JS, Klein A, Kong D, Krause R, Lalonde E, Lauria M, Lee E, Lin X, Liu Z, Livingstone J, Logsdon BA, Lovestone S, Ma TW, Malhotra A, Mangravite LM, Maxwell TJ, Merrill E, Nagorski J, Namasivayam A, Narayan M, Naz M, Newhouse SJ, Norman TC, Nurtdinov RN, Oyang YJ, Pawitan Y, Peng S, Peters MA, Piccolo SR, Praveen P, Priami C, Sabelnykova VY, Senger P, Shen X, Simmons A, Sotiras A, Stolovitzky G, Tangaro S, Tateo A, Tung YA, Tustison NJ, Varol E, Vradenburg G, Weiner MW, Xiao G, Xie L, Xie Y, Xu J, Yang H, Zhan X, Zhou Y, Zhu F, Zhu H, Zhu S. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease. Alzheimers Dement. 2016 06; 12(6):645-53. PMID: 27079753.
      Citations: 24     Fields:    Translation:Humans
    63. Yang E, Ravikumar P, Allen GI, Liu Z. Graphical Models via Univariate Exponential Family Distributions. J Mach Learn Res. 2015 Dec; 16:3813-3847. PMID: 27570498.
      Citations: 14     
    64. Sztainberg Y, Chen HM, Swann JW, Hao S, Tang B, Wu Z, Tang J, Wan YW, Liu Z, Rigo F, Zoghbi HY. Reversal of phenotypes in MECP2 duplication mice using genetic rescue or antisense oligonucleotides. Nature. 2015 Dec 03; 528(7580):123-6. PMID: 26605526.
      Citations: 59     Fields:    Translation:HumansAnimalsCells
    65. Choi SY, Pang K, Kim JY, Ryu JR, Kang H, Liu Z, Kim WK, Sun W, Kim H, Han K. Post-transcriptional regulation of SHANK3 expression by microRNAs related to multiple neuropsychiatric disorders. Mol Brain. 2015 Nov 16; 8(1):74. PMID: 26572867.
      Citations: 28     Fields:    Translation:HumansAnimalsCells
    66. Wan YW, Allen GI, Liu Z. TCGA2STAT: simple TCGA data access for integrated statistical analysis in R. Bioinformatics. 2016 03 15; 32(6):952-4. PMID: 26568634.
      Citations: 40     Fields:    Translation:Humans
    67. Adesina AM, Veo BL, Courteau G, Mehta V, Wu X, Pang K, Liu Z, Li XN, Peters L. FOXG1 expression shows correlation with neuronal differentiation in cerebellar development, aggressive phenotype in medulloblastomas, and survival in a xenograft model of medulloblastoma. Hum Pathol. 2015 Dec; 46(12):1859-71. PMID: 26433703.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    68. Yamamoto S, Jaiswal M, Charng WL, Gambin T, Karaca E, Mirzaa G, Wiszniewski W, Sandoval H, Haelterman NA, Xiong B, Zhang K, Bayat V, David G, Li T, Chen K, Gala U, Harel T, Pehlivan D, Penney S, Vissers LELM, de Ligt J, Jhangiani SN, Xie Y, Tsang SH, Parman Y, Sivaci M, Battaloglu E, Muzny D, Wan YW, Liu Z, Lin-Moore AT, Clark RD, Curry CJ, Link N, Schulze KL, Boerwinkle E, Dobyns WB, Allikmets R, Gibbs RA, Chen R, Lupski JR, Wangler MF, Bellen HJ. A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. Cell. 2014 Sep 25; 159(1):200-214. PMID: 25259927.
      Citations: 137     Fields:    Translation:HumansAnimalsCells
    69. Ye J, Fan J, Venneti S, Wan YW, Pawel BR, Zhang J, Finley LW, Lu C, Lindsten T, Cross JR, Qing G, Liu Z, Simon MC, Rabinowitz JD, Thompson CB. Serine catabolism regulates mitochondrial redox control during hypoxia. Cancer Discov. 2014 Dec; 4(12):1406-17. PMID: 25186948.
      Citations: 159     Fields:    Translation:HumansAnimalsCells
    70. Wan YW, Mach CM, Allen GI, Anderson ML, Liu Z. On the reproducibility of TCGA ovarian cancer microRNA profiles. PLoS One. 2014; 9(1):e87782. PMID: 24489963.
      Citations: 13     Fields:    Translation:HumansCells
    71. Pang K, Wan YW, Choi WT, Donehower LA, Sun J, Pant D, Liu Z. Combinatorial therapy discovery using mixed integer linear programming. Bioinformatics. 2014 May 15; 30(10):1456-63. PMID: 24463180.
      Citations: 12     Fields:    Translation:Humans
    72. Zhang W, Wan YW, Allen GI, Pang K, Anderson ML, Liu Z. Molecular pathway identification using biological network-regularized logistic models. BMC Genomics. 2013; 14 Suppl 8:S7. PMID: 24564637.
      Citations: 23     Fields:    Translation:Humans
    73. Mahadevan S, Wen S, Wan YW, Peng HH, Otta S, Liu Z, Iacovino M, Mahen EM, Kyba M, Sadikovic B, Van den Veyver IB. NLRP7 affects trophoblast lineage differentiation, binds to overexpressed YY1 and alters CpG methylation. Hum Mol Genet. 2014 Feb 01; 23(3):706-16. PMID: 24105472.
      Citations: 22     Fields:    Translation:HumansCells
    74. Allen GI, Liu Z. A Local Poisson Graphical Model for inferring networks from sequencing data. IEEE Trans Nanobioscience. 2013 Sep; 12(3):189-98. PMID: 23955777.
      Citations: 22     Fields:    Translation:Humans
    75. Hawkins SM, Loomans HA, Wan YW, Ghosh-Choudhury T, Coffey D, Xiao W, Liu Z, Sangi-Haghpeykar H, Anderson ML. Expression and functional pathway analysis of nuclear receptor NR2F2 in ovarian cancer. J Clin Endocrinol Metab. 2013 Jul; 98(7):E1152-62. PMID: 23690307.
      Citations: 21     Fields:    Translation:HumansCells
    76. Zhong Y, Wan YW, Pang K, Chow LM, Liu Z. Digital sorting of complex tissues for cell type-specific gene expression profiles. BMC Bioinformatics. 2013 Mar 07; 14:89. PMID: 23497278.
      Citations: 71     Fields:    
    77. Han K, Gennarino VA, Lee Y, Pang K, Hashimoto-Torii K, Choufani S, Raju CS, Oldham MC, Weksberg R, Rakic P, Liu Z, Zoghbi HY. Human-specific regulation of MeCP2 levels in fetal brains by microRNA miR-483-5p. Genes Dev. 2013 Mar 01; 27(5):485-90. PMID: 23431031.
      Citations: 50     Fields:    Translation:HumansCells
    78. Zhong Y, Liu Z. Gene expression deconvolution in linear space. Nat Methods. 2011 Dec 28; 9(1):8-9; author reply 9. PMID: 22205510.
      Citations: 24     Fields:    Translation:HumansAnimals
    79. Ivanova AV, Ivanov SV, Prudkin L, Nonaka D, Liu Z, Tsao A, Wistuba I, Roth J, Pass HI. Mechanisms of FUS1/TUSC2 deficiency in mesothelioma and its tumorigenic transcriptional effects. Mol Cancer. 2009 Oct 24; 8:91. PMID: 19852844.
      Citations: 18     Fields:    Translation:HumansCells
    80. Wertheim GB, Yang TW, Pan TC, Ramne A, Liu Z, Gardner HP, Dugan KD, Kristel P, Kreike B, van de Vijver MJ, Cardiff RD, Reynolds C, Chodosh LA. The Snf1-related kinase, Hunk, is essential for mammary tumor metastasis. Proc Natl Acad Sci U S A. 2009 Sep 15; 106(37):15855-60. PMID: 19717424.
      Citations: 23     Fields:    Translation:HumansAnimals
    81. Liu Z, Wang M, Alvarez JV, Bonney ME, Chen CC, D'Cruz C, Pan TC, Tadesse MG, Chodosh LA. Singular value decomposition-based regression identifies activation of endogenous signaling pathways in vivo. Genome Biol. 2008; 9(12):R180. PMID: 19094238.
      Citations: 9     Fields:    Translation:AnimalsCells
    82. Liu Z, Venkatesh SS, Maley CC. Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples. BMC Genomics. 2008 Oct 30; 9:509. PMID: 18973670.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    83. Pass HI, Lott D, Lonardo F, Harbut M, Liu Z, Tang N, Carbone M, Webb C, Wali A. Asbestos exposure, pleural mesothelioma, and serum osteopontin levels. N Engl J Med. 2005 Oct 13; 353(15):1564-73. PMID: 16221779.
      Citations: 106     Fields:    Translation:HumansPHPublic Health
    84. Krawetz SA, Draghici S, Goodrich R, Liu Z, Ostermeier GC. In silico and wet-bench identification of nuclear matrix attachment regions. Methods Mol Med. 2005; 108:439-58. PMID: 16028699.
      Citations: 7     Fields:    Translation:HumansCells
    85. Pass HI, Liu Z, Wali A, Bueno R, Land S, Lott D, Siddiq F, Lonardo F, Carbone M, Draghici S. Gene expression profiles predict survival and progression of pleural mesothelioma. Clin Cancer Res. 2004 Feb 01; 10(3):849-59. PMID: 14871960.
      Citations: 42     Fields:    Translation:Humans
    86. Ostermeier GC, Liu Z, Martins RP, Bharadwaj RR, Ellis J, Draghici S, Krawetz SA. Nuclear matrix association of the human beta-globin locus utilizing a novel approach to quantitative real-time PCR. Nucleic Acids Res. 2003 Jun 15; 31(12):3257-66. PMID: 12799453.
      Citations: 23     Fields:    Translation:HumansCells
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