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ZHANDONG LIU

TitleAssociate Professor
InstitutionBaylor College of Medicine
DepartmentDepartment of Pediatrics
Address1250 MOURSUND STREET
Houston, TX 77030
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    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
    R01GM120033     (MALETIC-SAVATIC, MIRJANA)Jan 1, 2017 - Dec 31, 2021
    NIH
    Advanced Computational Approaches for NMR Data-mining
    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. Liu C, Wang L, Liu Z. Correction: Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss. BMC Bioinformatics. 2023 Mar 29; 24(1):123. PMID: 36991331; PMCID: PMC10053718.
      Citations:    Fields:    
    2. Anvar Z, Chakchouk I, Sharif M, Mahadevan S, Nasiotis ET, Su L, Liu Z, Wan YW, Van den Veyver IB. Loss of the Maternal Effect Gene Nlrp2 Alters the Transcriptome of Ovulated Mouse Oocytes and Impacts Expression of Histone Demethylase KDM1B. Reprod Sci. 2023 Mar 28. PMID: 36976514.
      Citations:    Fields:    
    3. Trostle AJ, Li L, Kim SY, Wang J, Al-Ouran R, Yalamanchili HK, Liu Z, Wan YW. A Comprehensive and Integrative Approach to MeCP2 Disease Transcriptomics. Int J Mol Sci. 2023 Mar 07; 24(6). PMID: 36982190; PMCID: PMC10049497.
      Citations:    Fields:    Translation:AnimalsCells
    4. Bajikar SS, Anderson AG, Zhou J, Durham MA, Trostle AJ, Wan YW, Liu Z, Zoghbi HY. MeCP2 regulates Gdf11, a dosage-sensitive gene critical for neurological function. Elife. 2023 02 27; 12. PMID: 36848184; PMCID: PMC9977283.
      Citations:    Fields:    Translation:Animals
    5. Kim J, de Haro M, Al-Ramahi I, Garaicoechea LL, Jeong HH, Sonn JY, Tadros B, Liu Z, Botas J, Zoghbi HY. Evolutionarily conserved regulators of tau identify targets for new therapies. Neuron. 2023 03 15; 111(6):824-838.e7. PMID: 36610398.
      Citations:    Fields:    Translation:HumansAnimals
    6. Liu C, Wang L, Liu Z. Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss. BMC Bioinformatics. 2023 Jan 04; 24(1):5. PMID: 36600199.
      Citations:    Fields:    Translation:HumansCells
    7. Coffin SL, Durham MA, Nitschke L, Xhako E, Brown AM, Revelli JP, Villavicencio Gonzalez E, Lin T, Handler HP, Dai Y, Trostle AJ, Wan YW, Liu Z, Sillitoe RV, Orr HT, Zoghbi HY. Disruption of the ATXN1-CIC complex reveals the role of additional nuclear ATXN1 interactors in spinocerebellar ataxia type 1. Neuron. 2023 02 15; 111(4):481-492.e8. PMID: 36577402; PMCID: PMC9957872.
      Citations: 2     Fields:    Translation:AnimalsCells
    8. Wang L, Maletic-Savatic M, Liu Z. Region-specific denoising identifies spatial co-expression patterns and intra-tissue heterogeneity in spatially resolved transcriptomics data. Nat Commun. 2022 Nov 14; 13(1):6912. PMID: 36376296; PMCID: PMC9663444.
      Citations:    
    9. Singh S, Lee N, Pedroza DA, Bado IL, Hamor C, Zhang L, Aguirre S, Hu J, Shen Y, Xu Y, Gao Y, Zhao N, Chen SH, Wan YW, Liu Z, Chang JT, Hollern D, Perou CM, Zhang XHF, Rosen JM. Chemotherapy Coupled to Macrophage Inhibition Induces T-cell and B-cell Infiltration and Durable Regression in Triple-Negative Breast Cancer. Cancer Res. 2022 06 15; 82(12):2281-2297. PMID: 35442423; PMCID: PMC9219596.
      Citations:    Fields:    Translation:HumansAnimalsCells
    10. Hill EJ, Robak LA, Al-Ouran R, Deger J, Fong JC, Vandeventer PJ, Schulman E, Rao S, Saade H, Savitt JM, von Coelln R, Desai N, Doddapaneni H, Salvi S, Dugan-Perez S, Muzny DM, McGuire AL, Liu Z, Gibbs RA, Shaw C, Jankovic J, Shulman LM, Shulman JM. Genome Sequencing in the Parkinson Disease Clinic. Neurol Genet. 2022 Aug; 8(4):e200002. PMID: 35747619; PMCID: PMC9210549.
      Citations:    
    11. Harnish JM, Li L, Rogic S, Poirier-Morency G, Kim SY, Undiagnosed Diseases Network, Boycott KM, Wangler MF, Bellen HJ, Hieter P, Pavlidis P, Liu Z, Yamamoto S. ModelMatcher: A scientist-centric online platform to facilitate collaborations between stakeholders of rare and undiagnosed disease research. Hum Mutat. 2022 06; 43(6):743-759. PMID: 35224820; PMCID: PMC9133126.
      Citations: 3     Fields:    Translation:Humans
    12. Zhou J, Hamdan H, Yalamanchili HK, Pang K, Pohodich AE, Lopez J, Shao Y, Oses-Prieto JA, Li L, Kim W, Durham MA, Bajikar SS, Palmer DJ, Ng P, Thompson ML, Bebin EM, Burlingame AL, Liu Z, Rasband MN, Zoghbi HY, M?ller AJ, Kuechler A, Kampmeier A, Haack TB. Disruption of MeCP2-TCF20 complex underlies distinct neurodevelopmental disorders. Proc Natl Acad Sci U S A. 2022 01 25; 119(4). PMID: 35074918; PMCID: PMC8794850.
      Citations:    Fields:    Translation:AnimalsCells
    13. 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
    14. 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; PMCID: PMC8087656.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    15. 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; PMCID: PMC8062036.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    16. 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; PMCID: PMC8149125.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    17. 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; PMCID: PMC8042713.
      Citations: 12     Fields:    
    18. 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; PMCID: PMC8013850.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    19. 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; PMCID: PMC8976688.
      Citations: 5     Fields:    Translation:Animals
    20. 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; PMCID: PMC8112852.
      Citations: 3     
    21. 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; PMCID: PMC7526226.
      Citations: 7     Fields:    Translation:HumansAnimalsCells
    22. 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:    
    23. 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; PMCID: PMC7462065.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
    24. 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, Liu Z, Shulman JM, Mangravite LM, Logsdon BA, Accelerating Medicines Partnership-Alzheimer?s Disease Consortium, Ertekin-Taner N. 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; PMCID: PMC7428328.
      Citations: 53     Fields:    Translation:HumansAnimalsCells
    25. 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; PMCID: PMC7337927.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    26. 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: 6     Fields:    
    27. 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; PMCID: PMC7370880.
      Citations: 5     Fields:    Translation:HumansCells
    28. 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; PMCID: PMC7176433.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    29. 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; PMCID: PMC7108898.
      Citations: 75     Fields:    Translation:HumansAnimalsCells
    30. 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; PMCID: PMC7104670.
      Citations: 3     Fields:    Translation:Animals
    31. 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; PMCID: PMC7065908.
      Citations: 17     Fields:    Translation:AnimalsCells
    32. 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; PMCID: PMC7262739.
      Citations: 6     Fields:    Translation:Humans
    33. 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; PMCID: PMC7057095.
      Citations: 3     Fields:    Translation:Humans
    34. 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: 9     Fields:    Translation:HumansCells
    35. 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; PMCID: PMC6919331.
      Citations: 34     Fields:    Translation:HumansAnimalsCells
    36. 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; PMCID: PMC6815170.
      Citations: 35     Fields:    Translation:HumansCells
    37. 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; PMCID: PMC6826490.
      Citations: 3     Fields:    Translation:AnimalsCells
    38. 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; PMCID: PMC6750039.
      Citations: 6     Fields:    Translation:Humans
    39. 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, DDD study, 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:    
    40. 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; PMCID: PMC7401700.
      Citations: 8     Fields:    Translation:HumansAnimals
    41. 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; PMCID: PMC6581060.
      Citations: 13     Fields:    Translation:Cells
    42. 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; PMCID: PMC6663662.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    43. 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, DDD study, 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; PMCID: PMC6361549.
      Citations: 24     Fields:    Translation:AnimalsCells
    44. 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; PMCID: PMC6609509.
      Citations: 25     Fields:    Translation:HumansAnimalsCells
    45. 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; PMCID: PMC6302375.
      Citations: 11     Fields:    Translation:Animals
    46. 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; PMCID: PMC6309202.
      Citations: 114     Fields:    Translation:HumansAnimalsCells
    47. 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; PMCID: PMC6292215.
      Citations: 18     Fields:    Translation:HumansAnimalsCells
    48. Rousseaux MWC, 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, V?zquez-V?lez GE. 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; PMCID: PMC6199406.
      Citations: 15     Fields:    Translation:HumansAnimalsCells
    49. 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; PMCID: PMC6122971.
      Citations: 70     Fields:    Translation:AnimalsCells
    50. 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; PMCID: PMC6089998.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    51. 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, Hild M, Palacino J, Liu Z, Medina DL, Botas J, Diaz-Garc?a JR. 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; PMCID: PMC6082401.
      Citations: 13     Fields:    Translation:HumansAnimalsCells
    52. 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; PMCID: PMC6181645.
      Citations: 91     Fields:    Translation:HumansAnimalsCells
    53. 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; PMCID: PMC5991832.
      Citations: 41     Fields:    Translation:AnimalsCells
    54. 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; PMCID: PMC6099063.
      Citations: 9     Fields:    Translation:AnimalsCells
    55. 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; PMCID: PMC5906096.
      Citations: 22     Fields:    Translation:AnimalsCells
    56. 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; PMCID: PMC6422678.
      Citations: 34     Fields:    Translation:HumansAnimalsCells
    57. 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; PMCID: PMC5985472.
      Citations: 19     Fields:    Translation:AnimalsCells
    58. 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; PMCID: PMC5816173.
      Citations: 17     Fields:    Translation:AnimalsCells
    59. Yalamanchili HK, Guo C, Shulman JM, Liu Z, Jeong HH. 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: 30     Fields:    Translation:HumansAnimalsCells
    60. 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; PMCID: PMC5629550.
      Citations: 1     Fields:    Translation:HumansCells
    61. 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; PMCID: PMC5629612.
      Citations: 4     Fields:    
    62. 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; PMCID: PMC5870715.
      Citations: 10     Fields:    Translation:Cells
    63. 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; PMCID: PMC6373869.
      Citations: 14     Fields:    Translation:Cells
    64. 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; PMCID: PMC5587057.
      Citations: 1     Fields:    Translation:HumansCells
    65. 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; PMCID: PMC5438150.
      Citations: 3     Fields:    Translation:HumansAnimals
    66. Wang J, Al-Ouran R, Hu Y, Kim SY, Wan YW, Wangler MF, Yamamoto S, Chao HT, Comjean A, Mohr SE, UDN, 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; PMCID: PMC5670038.
      Citations: 82     Fields:    Translation:Humans
    67. 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; PMCID: PMC5374695.
      Citations: 25     Fields:    Translation:HumansCells
    68. 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, 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, Van Maldergem L. 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; PMCID: PMC5374026.
      Citations: 49     Fields:    Translation:HumansAnimals
    69. Gu R, Cai T, Wan YW, Asprer JS, Zhang H, Jen HI, Liu Z, Groves AK, Maass JC, Cantellano SC, Edlund RK. 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; PMCID: PMC5137903.
      Citations: 23     Fields:    Translation:AnimalsCells
    70. 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; PMCID: PMC5968355.
      Citations: 42     Fields:    Translation:HumansAnimalsCells
    71. 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; PMCID: PMC5247424.
      Citations: 29     Fields:    
    72. 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; PMCID: PMC5009817.
      Citations: 7     Fields:    
    73. 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; PMCID: PMC5179927.
      Citations: 29     Fields:    Translation:HumansAnimals
    74. Allen GI, Anghel C, Balagurusamy V, Bare CJ, Beaton D, 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, Erus G, Everett E, Fardo DW, Friend SH, 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, 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, Alzheimer's Disease Neuroimaging Initiative, Amoroso N, Bellotti R, Errico R, Fr?hlich H, Tateo A. Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease. Alzheimers Dement. 2016 06; 12(6):645-53. PMID: 27079753; PMCID: PMC5474755.
      Citations: 28     Fields:    Translation:Humans
    75. 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; PMCID: PMC4998206.
      Citations: 15     
    76. 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; PMCID: PMC4839300.
      Citations: 74     Fields:    Translation:HumansAnimalsCells
    77. 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; PMCID: PMC4647645.
      Citations: 35     Fields:    Translation:HumansAnimalsCells
    78. 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: 55     Fields:    Translation:Humans
    79. 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: 10     Fields:    Translation:HumansAnimalsCells
    80. 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; PMCID: PMC4298142.
      Citations: 168     Fields:    Translation:HumansAnimalsCells
    81. 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; PMCID: PMC4258153.
      Citations: 191     Fields:    Translation:HumansAnimalsCells
    82. 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; PMCID: PMC3906208.
      Citations: 14     Fields:    Translation:HumansCells
    83. 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; PMCID: PMC4016706.
      Citations: 18     Fields:    Translation:Humans
    84. 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; PMCID: PMC4046566.
      Citations: 27     Fields:    Translation:Humans
    85. 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; PMCID: PMC3888260.
      Citations: 24     Fields:    Translation:HumansCells
    86. 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: 24     Fields:    Translation:Humans
    87. 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; PMCID: PMC3701283.
      Citations: 26     Fields:    Translation:HumansCells
    88. 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; PMCID: PMC3626856.
      Citations: 84     Fields:    
    89. 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; PMCID: PMC3605462.
      Citations: 59     Fields:    Translation:HumansCells
    90. 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: 28     Fields:    Translation:HumansAnimals
    91. 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; PMCID: PMC2776015.
      Citations: 20     Fields:    Translation:HumansCells
    92. 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; PMCID: PMC2734880.
      Citations: 24     Fields:    Translation:HumansAnimals
    93. 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; PMCID: PMC2646284.
      Citations: 9     Fields:    Translation:AnimalsCells
    94. 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; PMCID: PMC2628393.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    95. 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: 110     Fields:    Translation:HumansPHPublic Health
    96. 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
    97. 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
    98. 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; PMCID: PMC162328.
      Citations: 24     Fields:    Translation:HumansCells
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