Silvia

Silvia (Shuchang) Liu, Ph.D.

Assistant Professor

Organ Pathobiology and Therapeutics Institute

Department of Pharmacology and Chemical Biology

Pittsburgh Liver Research Center

School of Medicine

University of Pittsburgh


Contact Me:

Email: shl96@pitt.edu

Phone: 412-648-4288

Office: S-406 Biomedical Science Tower, 203 Lothrop Street, Pittsburgh, PA 15261


External Link:

My CV

Linkedin

Google Scholar

Publications


2024 Publications

  1. Tourkova IL, Larrouture QC, Liu S, Luo J, Schlesinger PH, Blair HC. The ecto-nucleotide pyrophosphatase/phosphodiesterase 2 promotes early osteoblast differentiation and mineralization in stromal stem cells. Am J Physiol Cell Physiol. 2024 Mar 1;326(3):C843-C849. doi: 10.1152/ajpcell.00692.2023. Epub 2024 Jan 15. PMID: 38223929; PMCID: PMC11193479. [Role: WES data analysis.]

  2. Liu S*, Yu YP, Ren BG, Ben-Yehezkel T, Obert C, Smith M, Wang W, Ostrowska A, Soto-Gutierrez A, Luo JH*. Long-read single-cell sequencing reveals expressions of hypermutation clusters of isoforms in human liver cancer cells. Elife. 2024 Jan 11;12:RP87607. doi: 10.7554/eLife.87607. PMID: 38206124; PMCID: PMC10945587.

  3. Yu YP, Liu S, Geller D, Luo JH. Serum Fusion Transcripts to Assess the Risk of Hepatocellular Carcinoma and the Impact of Cancer Treatment through Machine Learning. Am J Pathol. 2024 Jul;194(7):1262-1271. doi: 10.1016/j.ajpath.2024.02.017. Epub 2024 Mar 25. PMID: 38537933; PMCID: PMC11220925. [Role: Machine learning statistical data analysis]

  4. Kader M, Sun W, Ren BG, Yu YP, Tao J, Foley LM, Liu S, Monga SP, Luo JH. Therapeutic targeting at genome mutations of liver cancer by the insertion of HSV1 thymidine kinase through Cas9-mediated editing. Hepatol Commun. 2024 Mar 18;8(4):e0412. doi: 10.1097/HC9.0000000000000412. PMID: 38497929; PMCID: PMC10948134. [Role: Statistical data analysis]

  5. Gui Y, Yu Y, Wang W, Wang Y, Lu H, Mozdzierz S, Eskander K, Lin YH, Li H, Tian XJ, Liu S*, Zhou D*. Proteome characterization of liver-kidney comorbidity after microbial sepsis. FASEB J. 2024 Apr 15;38(7):e23597. doi: 10.1096/fj.202302520R. PMID: 38581235. [Role as second corresponding author: proteomics data analysis]

  6. Tourkova IL, Larrouture QC, Liu S, Luo J, Shipman KE, Onwuka KM, Weisz OA, Riazanski V, Nelson DJ, MacDonald ML, Schlesinger PH, Blair HC. Chloride/proton antiporters ClC3 and ClC5 support bone formation in mice. Bone Rep. 2024 Apr 16;21:101763. doi: 10.1016/j.bonr.2024.101763. PMID: 38666049; PMCID: PMC11043850.[Role: DNA-seq data analysis]

  7. Gupta B, Rai RP, Pal PB, Rossmiller D, Chaudhary S, Chiaro A, Seaman S, Singhi AD, Liu S, Monga SP, Iyer SS, Raeman R. Selective Targeting of α4β7/MAdCAM-1 Axis Suppresses Fibrosis Progression by Reducing Proinflammatory T Cell Recruitment to the Liver. Cells. 2024 Apr 27;13(9):756. doi: 10.3390/cells13090756. PMID: 38727292; PMCID: PMC11083209. [Role: RNA-seq data analysis]

  8. Mehta K, Daghsni M, Raeisossadati R, Xu Z, Davis E, Naidich A, Wang B, Tao S, Pi S, Chen W, Kostka D, Liu S, Gross JM, Kuwajima T, Aldiri I. A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis. Cell Rep. 2024 Jun 25;43(6):114291. doi: 10.1016/j.celrep.2024.114291. Epub 2024 May 31. PMID: 38823017. [Role: RNA-seq, ChIP-seq and ATAC-seq data analysis]

  9. Shivarudrappa A, John J, Vashisht M, Ge H, Liu S, Chen J, Siddoway K, Dong R, Chen Z, Wang JH*. Differential tumor immune microenvironment coupled with tumor progression or tumor eradication in HPV-antigen expressing squamous cell carcinoma (SCC) models. Frontiers in Immunology. 2024 Jul 11;15:1405318. doi: 10.3389/fimmu.2024.1405318. PMID: 39055715; PMCID: PMC11269233. [Role: DNA-seq data analysis]

  10. Balogun O, Shao D, Carson M, King T, Kosar K, Zhang R, Zeng G, Cornuet P, Goel C, Lee E, Patel G, Brooks E, Monga SP, Liu S, Nejak-Bowen K. Loss of β-catenin reveals a role for glutathione in regulating oxidative stress during cholestatic liver disease. Hepatol Commun. 2024 Jul 5;8(7):e0485. doi: 10.1097/HC9.0000000000000485. PMID: 38967587; PMCID: PMC11227358. [Role: Statistical data analysis]

  11. Liu S*, Obert C, Yu YP, Zhao J, Ren BG, Liu JJ, Wiseman K, Krajacich BJ, Wang W, Metcalfe K, Smith M, Ben-Yehezkel T, Luo JH*. Utility analyses of AVITI sequencing chemistry. BMC Genomics. 2024 Aug 10;25(1):778. doi: 10.1186/s12864-024-10686-4. PMID: 39127634. [Role: first and corresponding author]

  12. Zhu B*, Liu S, David NL, Dion W, Doshi NK, Siegel LB, Amorim T, Andrews RE, Kumar GN, Li H, Irfan S, Pesaresi T, Sharma AX, Sun M, Fazeli PH, Steinhauser ML*. Evidence for ~12-hour ultradian gene programs in humans. npj Biological Timing and Sleep. 2024;1(1):4. doi: 10.1038/s44323-024-00005-1. Epub 2024 Aug 9. PMID: 39148626; PMCID: PMC11325440. [Role: RNA-seq and rhythm data analysis]

  13. Lehrich BM, Tao J, Liu S, Hirsch TZ, Yasaka TM, Cao C, Delgado ER, Guan X, Lu S, Pan L, Liu Y, Singh S, Poddar M, Bell A, Singhi AD, Zucman-Rossi J, Wang Y, Monga SP*. Development of Mutated β-catenin Gene Signature to identify CTNNB1 mutations from whole and spatial transcriptomic data in patients with HCC. JHEP Reports. 2024 [Role: RNA-seq data analysis]

  14. Park Y, Hu S, Kim M, Oertel M, Singhi A, Monga SP, Liu S, Ko S*. Context-Dependent Distinct Roles of SOX9 in Combined Hepatocellular Carcinoma-Cholangiocarcinoma. Cells. 2024 Aug 29;13(17):1451. doi: 10.3390/cells13171451. PMID: 39273023; PMCID: PMC11394107. [Role: RNA-seq data analysis and public data mining]

  15. Liu S, Zahorchak AF, Dobrowolski SF, Metes DM, Thomson AW, Abdelsamed HA. Epigenetic signature of human vitamin D3 and IL-10 conditioned regulatory DCs. Sci Rep. 2024 Nov 20;14(1):28748. doi: 10.1038/s41598-024-79299-x. PMID: 39567586; PMCID: PMC11579388.

  16. Liu P, Pan Y, Chang HC, Wang W, Fang Y, Xue X, Zou J, Toothaker JM, Olaloye O, Santiago EG, McCourt B, Mitsialis V, Presicce P, Kallapur SG, Snapper SB, Liu JJ, Tseng GC*, Konnikova L*, Liu S*. Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating. Brief Bioinform. 2024 Nov 22;26(1):bbae633. doi: 10.1093/bib/bbae633. PMID: 39656848.

  17. Rashidi HH, Hu B, Pantanowitz J, Tran N, Liu S, Chamanzar A, Gur M, Chang CH, Wang Y, Tafti A, Pantanowitz L, Hanna MG*. Statistics of Generative AI & Non-Generative Predictive Analytics Machine Learning in Medicine. Mod Pathol. 2024 Nov 21:100663. doi: 10.1016/j.modpat.2024.100663. Epub ahead of print. PMID: 39579984. [Role: review generative AI methods for pathology study]

  18. Zhang Y, David NL, Pesaresi T, Andrews RE, Kumar GVN, Chen H, Qiao W, Yang J, Patel K, Amorim T, Sharma AX, Liu S, Steinhauser ML*. Noncoding variation near UBE2E2 orchestrates cardiometabolic pathophenotypes through polygenic effectors. JCI Insight. 2024 Dec 10:e184140. doi: 10.1172/jci.insight.184140. Epub ahead of print. PMID: 39656538. [Role: gRNA screening sequencing analysis]


    19. 2023 Publications

  19. Du Q, Liu S, Dong K, Cui X, Luo J, Geller DA. Downregulation of iNOS/NO Promotes Epithelial-Mesenchymal Transition and Metastasis in Colorectal Cancer. Mol Cancer Res. 2023 Feb 1;21(2):102-114. doi: 10.1158/1541-7786.MCR-22-0509. PMID: 36306210; PMCID: PMC9890133. [Role: RNA-seq analysis]

  20. Hurley EH, Tao J, Liu S, Krutsenko Y, Singh S, Monga SP. Inhibition of Heat Shock Factor 1 Signaling Decreases Hepatoblastoma Growth via Induction of Apoptosis. Am J Pathol. 2023 Feb;193(2):148-160. doi: 10.1016/j.ajpath.2022.10.006. Epub 2022 Nov 3. PMID: 36336065; PMCID: PMC9887635. [Role: statistical data analysis]

  21. Zhang X, Xiang S, Zhang Y, Liu S, Lei G, Hines S, Wang N, Lin H. In vitro study to identify ligand-independent function of estrogen receptor-α in suppressing DNA damage-induced chondrocyte senescence. FASEB J. 2023 Feb;37(2):e22746. doi: 10.1096/fj.202201228R. PMID: 36622202; PMCID: PMC10369926. [Role: RNA-seq data analysis]

  22. Yu YP^, Liu S^, Ren BG, Nelson J, Jarrard D, Brooks JD, Michalopoulos G, Tseng G, Luo JH. Fusion Gene Detection in Prostate Cancer Samples Enhances the Prediction of Prostate Cancer Clinical Outcomes from Radical Prostatectomy through Machine Learning in a Multi-Institutional Analysis. Am J Pathol. 2023 Apr;193(4):392-403. doi: 10.1016/j.ajpath.2022.12.013. Epub 2023 Jan 18. PMID: 36681188; PMCID: PMC10123524. [Role: Statistical and machine learning data analysis]

  23. Sato T, Head KZ, Li J, Dolin CE, Wilkey D, Skirtich N, Smith K, McCreary DD, Liu S, Beier JI, Singhi AD, McEnaney RM, Merchant ML, Arteel GE. Fibrosis resolution in the mouse liver: Role of Mmp12 and potential role of calpain 1/2. Matrix Biol Plus. 2022 Dec 28;17:100127. doi: 10.1016/j.mbplus.2022.100127. PMID: 36632559; PMCID: PMC9826883. [Role: Statistical genomic data analysis]

  24. Gayden J, Hu S, Joseph PN, Delgado E, Liu S, Bell A, Puig S, Monga SP, Freyberg Z. A Spatial Atlas of Wnt Receptors in Adult Mouse Liver. Am J Pathol. 2023 May;193(5):558-566. doi: 10.1016/j.ajpath.2023.01.011. Epub 2023 Feb 10. PMID: 36773785; PMCID: PMC10155265. [Role: Statistical genomic data analysis]

  25. Gui Y, Liu S, Fu H, Zhou D. Editorial: Tissue microenvironment in kidney diseases. Front Med (Lausanne). 2023 Feb 6;10:1134043. doi: 10.3389/fmed.2023.1134043. PMID: 36814777; PMCID: PMC9939817. [Role: Statistical data analysis]

  26. Gui Y, Wang Y, Palanza Z, Wang JL, Gupta P, Tao J, Qiao Y, Hargis G, Kreutzer DL, Bastacky SI, Yu Y, Wang Y, Liu S, Fu H, Zhou D. Calponin 2 harnesses metabolic reprogramming to determine kidney fibrosis. Mol Metab. 2023 May;71:101712. doi: 10.1016/j.molmet.2023.101712. Epub 2023 Mar 22. PMID: 36963615; PMCID: PMC10090436. [Role: scRNA-seq data analysis]

  27. Liu S, He L, Bannister OB, Li J, Schnegelberger RD, Vanderpuye CM, Althouse AD, Schopfer FJ, Wahlang B, Cave MC, Monga SP, Zhang X, Arteel GE, Beier JI. Western diet unmasks transient low-level vinyl chloride-induced tumorigenesis; potential role of the (epi-)transcriptome. Toxicol Appl Pharmacol. 2023 Jun 1;468:116514. doi: 10.1016/j.taap.2023.116514. Epub 2023 Apr 14. PMID: 37061008; PMCID: PMC10164119.

  28. Valenzi E, Bahudhanapati H, Tan J, Tabib T, Sullivan DI, Nouraie M, Sembrat J, Fan L, Chen K, Liu S, Rojas M, Lafargue A, Felsher DW, Tran PT, Kass DJ, Lafyatis R. Single-nucleus chromatin accessibility identifies a critical role for TWIST1 in idiopathic pulmonary fibrosis myofibroblast activity. Eur Respir J. 2023 Jul 7;62(1):2200474. doi: 10.1183/13993003.00474-2022. PMID: 37142338; PMCID: PMC10411550. [Role: RNA-seq data analysis]

  29. Kulkarni S, Li Q, Singhi AD, Liu S, Monga SP, Feranchak AP. TMEM16A partners with mTOR to influence pathways of cell survival, proliferation, and migration in cholangiocarcinoma. Am J Physiol Gastrointest Liver Physiol. 2023 Aug 1;325(2):G122-G134. doi: 10.1152/ajpgi.00270.2022. Epub 2023 May 23. PMID: 37219012; PMCID: PMC10390053. [Role: Public data mining]

  30. Zhu B, Liu S. Preservation of ∼12-h ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock. Front Physiol. 2023 May 30;14:1195001. doi: 10.3389/fphys.2023.1195001. PMID: 37324401; PMCID: PMC10267751.. [Role: RNA-seq data analysis]

  31. Guo X, Liu S, Sheng Y, Zenati M, Billiar T, Herbert A, Wang Q. ADAR1 Zα domain P195A mutation activates the MDA5-dependent RNA-sensing signaling pathway in brain without decreasing overall RNA editing. Cell Rep. 2023 Jul 25;42(7):112733. doi: 10.1016/j.celrep.2023.112733. Epub 2023 Jul 6. PMID: 37421629; PMCID: PMC10691306. [Role: RNA-seq data analysis and RNA editing calling]

  32. Tourkova IL, Larrouture QC, Onwuka KM, Liu S, Luo J, Schlesinger PH, Blair HC. Age-related decline in bone mineral transport and bone matrix proteins in osteoblasts from stromal stem cells. Am J Physiol Cell Physiol. 2023 Sep 1;325(3):C613-C622. doi: 10.1152/ajpcell.00227.2023. Epub 2023 Jul 31. PMID: 37519232; PMCID: PMC10635645. [Role: WES data analysis]

  33. Gabdulkhakova A, Krutsenko Y, Zhu J, Liu S, Poddar M, Singh S, Ma X, Nejak-Bowen K, Monga SPS, Molina LM. Loss of TAZ after YAP deletion severely impairs foregut development and worsens cholestatic hepatocellular injury. Hepatol Commun. 2023 Aug 9;7(9):e0220. doi: 10.1097/HC9.0000000000000220. PMID: 37556373; PMCID: PMC10412434. [Role: RNA-seq data analysis]

  34. Mooring M, Yeung GA, Luukkonen P, Liu S, Akbar MW, Zhang GJ, Balogun O, Yu X, Mo R, Nejak-Bowen K, Poyurovsky MV, Booth CJ, Konnikova L, Shulman GI, Yimlamai D. Hepatocyte CYR61 polarizes profibrotic macrophages to orchestrate NASH fibrosis. Sci Transl Med. 2023 Sep 27;15(715):eade3157. doi: 10.1126/scitranslmed.ade3157. Epub 2023 Sep 27. PMID: 37756381; PMCID: PMC10874639. [Role: bulk and single-cell RNA-seq data analysis]

  35. Singh-Varma A, Shah AM, Liu S, Zamora R, Monga SP, Vodovotz Y. Defining spatiotemporal gene modules in liver regeneration using Analytical Dynamic Visual Spatial Omics Representation (ADViSOR). Hepatol Commun. 2023 Oct 27;7(11):e0289. doi: 10.1097/HC9.0000000000000289. PMID: 37889540; PMCID: PMC10615476. [Role: Spatial transcriptomic analysis]

  36. Gui Y, Palanza Z, Gupta P, Li H, Pan Y, Wang Y, Hargis G, Kreutzer DL, Wang Y, Bastacky SI, Liu Y, Liu S, Zhou D. Calponin 2 regulates ketogenesis to mitigate acute kidney injury. JCI Insight. 2023 Nov 8;8(21):e170521. doi: 10.1172/jci.insight.170521. PMID: 37751293; PMCID: PMC10721266. [Role: Single-cell RNA-seq data analysis]

  37. Liu Z, Annarapu G, Yazdani HO, Wang Q, Liu S, Luo JH, Yu YP, Ren B, Neal MD, Monga SP, Mota Alvidrez RI. Restoring glucose balance: Conditional HMGB1 knockdown mitigates hyperglycemia in a Streptozotocin induced mouse model. Heliyon. 2023 Dec 12;10(1):e23561. doi: 10.1016/j.heliyon.2023.e23561. PMID: 38187339; PMCID: PMC10770459. [Role: RNA-seq data analysis]

  38. Ayers M, Kosar K, Xue Y, Goel C, Carson M, Lee E, Liu S, Brooks E, Cornuet P, Oertel M, Bhushan B, Nejak-Bowen K. Inhibiting Wnt Signaling Reduces Cholestatic Injury by Disrupting the Inflammatory Axis. Cell Mol Gastroenterol Hepatol. 2023;16(6):895-921. doi: 10.1016/j.jcmgh.2023.08.004. Epub 2023 Aug 12. PMID: 37579970; PMCID: PMC10616556. [Role: RNA-seq data analysis and public data mining.]


    39. 2022 Publications

  39. Ayers M, Liu S, Singhi AD, Kosar K, Cornuet P, Nejak-Bowen K. Changes in beta-catenin expression and activation during progression of primary sclerosing cholangitis predict disease recurrence. Sci Rep. 2022 Jan 7;12(1):206. doi: 10.1038/s41598-021-04358-6. PMID: 34997170; PMCID: PMC8741932. [Role: Statistical data analysis]

  40. Lee WP, Zhu Q, Yang X, Liu S, Cerveira E, Ryan M, Mil-Homens A, Bellfy L, Ye K, Lee C, Zhang C. JAX-CNV: A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level. Genomics Proteomics Bioinformatics. 2022 Dec;20(6):1197-1206. doi: 10.1016/j.gpb.2021.06.003. Epub 2022 Jan 25. PMID: 35085778; PMCID: PMC10225484. [Role: copy number variation analysis on DNA sequencing]

  41. Liu S, Nalesnik MA, Singhi A, Wood-Trageser MA, Randhawa P, Ren BG, Humar A, Liu P, Yu YP, Tseng GC, Michalopoulos G, Luo JH. Transcriptome and Exome Analyses of Hepatocellular Carcinoma Reveal Patterns to Predict Cancer Recurrence in Liver Transplant Patients. Hepatol Commun. 2022 Apr;6(4):710-727. doi: 10.1002/hep4.1846. Epub 2021 Nov 1. PMID: 34725972; PMCID: PMC8948579.

  42. Wang N, Zhang X, Rothrauff BB, Fritch MR, Chang A, He Y, Yeung M, Liu S, Lipa KE, Lei G, Alexander PG, Lin H. Novel role of estrogen receptor-α on regulating chondrocyte phenotype and response to mechanical loading. Osteoarthritis Cartilage. 2022 Feb;30(2):302-314. doi: 10.1016/j.joca.2021.11.002. Epub 2021 Nov 9. PMID: 34767957. [Role: RNA-seq data analysis.]

  43. Dion W, Ballance H, Lee J, Pan Y, Irfan S, Edwards C, Sun M, Zhang J, Zhang X, Liu S, Zhu B. Four-dimensional nuclear speckle phase separation dynamics regulate proteostasis. Sci Adv. 2022 Jan 7;8(1):eabl4150. doi: 10.1126/sciadv.abl4150. Epub 2022 Jan 5. PMID: 34985945; PMCID: PMC8730402. [Role: statistical data analysis]

  44. Guo X^, Liu S^, Yan R, Nguyen V, Zenati M, Billiar TR, Wang Q. ADAR1 RNA editing regulates endothelial cell functions via the MDA-5 RNA sensing signaling pathway. Life Sci Alliance. 2021 Dec 30;5(3):e202101191. doi: 10.26508/lsa.202101191. PMID: 34969816; PMCID: PMC8739526. [Role as co-first author: RNA editing detection and statistical analysis on RNA-seq data.]

  45. Yao K, Tarabra E, Sia D, Morotti R, Fawaz R, Valentino P, Santoro N, Caprio S, Liu S*, Yimlamai D*. Transcriptomic profiling of a multiethnic pediatric NAFLD cohort reveals genes and pathways associated with disease. Hepatol Commun. 2022 Jul;6(7):1598-1610. doi: 10.1002/hep4.1940. Epub 2022 Mar 21. PMID: 35312185; PMCID: PMC9234638. [Role as co-corresponding author: RNA-seq and statistical data analysis, manuscript writing and project overall design.]

  46. Chen SMY, Popolizio V, Woolaver RA, Ge H, Krinsky AL, John J, Danis E, Ke Y, Kramer Y, Bian L, Nicklawsky AG, Gao D, Liu S, Chen Z, Wang XJ, Wang JH. Differential responses to immune checkpoint inhibitor dictated by pre-existing differential immune profiles in squamous cell carcinomas caused by same initial oncogenic drivers. J Exp Clin Cancer Res. 2022 Apr 2;41(1):123. doi: 10.1186/s13046-022-02337-x. PMID: 35366939; PMCID: PMC8976353. [Role as co-author: whole exome sequencing data analysis for mutation calling.]

  47. Li Z, Lin Z, Liu S, Yagi H, Zhang X, Yocum L, Romero-Lopez M, Rhee C, Makarcyzk MJ, Yu I, Li EN, Fritch MR, Gao Q, Goh KB, O'Donnell B, Hao T, Alexander PG, Mahadik B, Fisher JP, Goodman SB, Bunnell BA, Tuan RS, Lin H. Human Mesenchymal Stem Cell-Derived Miniature Joint System for Disease Modeling and Drug Testing. Adv Sci (Weinh). 2022 Jul;9(21):e2105909. doi: 10.1002/advs.202105909. Epub 2022 Apr 18. PMID: 35436042; PMCID: PMC9313499. [Role: RNA-seq and statistical data analysis.]

  48. Sasaki K, Moussawy MA, Abou-Daya KI, Macedo C, Hosni-Ahmed A, Liu S, Juya M, Zahorchak AF, Metes DM, Thomson AW, Lakkis FG, Abdelsamed HA. Activated-memory T cells influence naïve T cell fate: a noncytotoxic function of human CD8 T cells. Commun Biol. 2022 Jun 29;5(1):634. doi: 10.1038/s42003-022-03596-2. PMID: 35768564; PMCID: PMC9243096. [Role: Statistical data analysis]

  49. Bian F, Daghsni M, Lu F, Liu S, Gross JM, Aldiri I. Functional analysis of the Vsx2 super-enhancer uncovers distinct cis-regulatory circuits controlling Vsx2 expression during retinogenesis. Development. 2022 Aug 1;149(15):dev200642. doi: 10.1242/dev.200642. Epub 2022 Aug 8. PMID: 35831950; PMCID: PMC9440754. [Role: RNA-seq, ChIP-seq and ATAC-seq data analysis]

  50. Hu S, Molina L, Tao J, Liu S, Hassan M, Singh S, Poddar M, Bell A, Sia D, Oertel M, Raeman R, Nejak-Bowen K, Singhi A, Luo J, Monga SP, Ko S. NOTCH-YAP1/TEAD-DNMT1 Axis Drives Hepatocyte Reprogramming Into Intrahepatic Cholangiocarcinoma. Gastroenterology. 2022 Aug;163(2):449-465. doi: 10.1053/j.gastro.2022.05.007. Epub 2022 May 10. PMID: 35550144; PMCID: PMC9329208. [Role: RNA-seq, ChIP-seq data analysis, and public data mining.]

  51. Hu S, Liu S, Bian Y, Poddar M, Singh S, Cao C, McGaughey J, Bell A, Blazer LL, Adams JJ, Sidhu SS, Angers S, Monga SP. Single-cell spatial transcriptomics reveals a dynamic control of metabolic zonation and liver regeneration by endothelial cell Wnt2 and Wnt9b. Cell Rep Med. 2022 Oct 18;3(10):100754. doi: 10.1016/j.xcrm.2022.100754. Epub 2022 Oct 10. PMID: 36220068; PMCID: PMC9588996. [Role: Spatial single-cell transcriptome data analysis]

  52. Xiang S, Lin Z, Makarcyzk MJ, Riewruja K, Zhang Y, Zhang X, Li Z, Clark KL, Li E, Liu S, Hao T, Fritch MR, Alexander PG, Lin H. Differences in the intrinsic chondrogenic potential of human mesenchymal stromal cells and iPSC-derived multipotent cells. Clin Transl Med. 2022 Dec;12(12):e1112. doi: 10.1002/ctm2.1112. PMID: 36536500; PMCID: PMC9763539. [Role: RNA-seq analysis]


    53. 2021 Publications

  53. Velazquez JJ, LeGraw R, Moghadam F, Tan Y, Kilbourne J, Maggiore JC, Hislop J, Liu S, Cats D, Chuva de Sousa Lopes SM, Plaisier C, Cahan P, Kiani S, Ebrahimkhani MR. Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids. Cell Syst. 2021 Jan 20;12(1):41-55.e11. doi: 10.1016/j.cels.2020.11.002. Epub 2020 Dec 7. PMID: 33290741; PMCID: PMC8164844. [Role: ATAC-seq and RNA-seq analysis]

  54. Tao J, Krutsenko Y, Moghe A, Singh S, Poddar M, Bell A, Oertel M, Singhi AD, Geller D, Chen X, Lujambio A, Liu S*, Monga SP*. Nuclear factor erythroid 2-related factor 2 and β-Catenin Coactivation in Hepatocellular Cancer: Biological and Therapeutic Implications. Hepatology. 2021 Aug;74(2):741-759. doi: 10.1002/hep.31730. Epub 2021 Jun 21. PMID: 33529367; PMCID: PMC8326305. [Role as second corresponding author: RNA-seq and statistical data mining, overview of the bioinformatics analysis]

  55. Pantalone JM, Liu S, Olaloye OO, Prochaska EC, Yanowitz T, Riley MM, Buland JR, Brozanski BS, Good M, Konnikova L. Gestational Age-Specific Complete Blood Count Signatures in Necrotizing Enterocolitis. Front Pediatr. 2021 Feb 26;9:604899. doi: 10.3389/fped.2021.604899. PMID: 33718296; PMCID: PMC7952609. [Role: machine learning statistical data analysis]

  56. Pradhan-Sundd T, Liu S, Singh S, Poddar M, Ko S, Bell A, Franks J, Huck I, Stolz D, Apte U, Ranganathan S, Nejak-Bowen K, Monga SP. Dual β-Catenin and γ-Catenin Loss in Hepatocytes Impacts Their Polarity through Altered Transforming Growth Factor-β and Hepatocyte Nuclear Factor 4α Signaling. Am J Pathol. 2021 May;191(5):885-901. doi: 10.1016/j.ajpath.2021.02.008. Epub 2021 Mar 1. PMID: 33662348; PMCID: PMC8132180. [Role: RNA-seq and statistical data mining]

  57. Liu S, Wu I, Yu YP, Balamotis M, Ren B, Ben Yehezkel T, Luo JH. Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer. Commun Biol. 2021 Apr 27;4(1):506. doi: 10.1038/s42003-021-02024-1. PMID: 33907296; PMCID: PMC8079361.

  58. Zuo ZH, Yu YP, Ren BG, Liu S, Nelson J, Wang Z, Tao J, Pradhan-Sundd T, Bhargava R, Michalopoulos G, Chen Q, Zhang J, Ma D, Pennathur A, Luketich J, Satdarshan Monga P, Nalesnik M, Luo JH. Oncogenic Activity of Solute Carrier Family 45 Member 2 and Alpha-Methylacyl-Coenzyme A Racemase Gene Fusion Is Mediated by Mitogen-Activated Protein Kinase. Hepatol Commun. 2022 Jan;6(1):209-222. doi: 10.1002/hep4.1724. Epub 2021 Sep 10. PMID: 34505419; PMCID: PMC8710797. [Role: Statistical data mining]

  59. Kosar K, Cornuet P, Singh S, Lee E, Liu S, Gayden J, Sato T, Freyberg Z, Arteel G, Nejak-Bowen K. WNT7B Regulates Cholangiocyte Proliferation and Function During Murine Cholestasis. Hepatol Commun. 2021 Dec;5(12):2019-2034. doi: 10.1002/hep4.1784. Epub 2021 Aug 25. PMID: 34558852; PMCID: PMC8631094. [Role: Statistical data mining]

  60. Yu YP, Liu S, Nelson J, Luo JH. Detection of fusion gene transcripts in the blood samples of prostate cancer patients. Sci Rep. 2021 Aug 20;11(1):16995. doi: 10.1038/s41598-021-96528-9. PMID: 34417538; PMCID: PMC8379170. [Role: Statistical data analysis]

  61. Fu H, Gui Y, Liu S, Wang Y, Bastacky SI, Qiao Y, Zhang R, Bonin C, Hargis G, Yu Y, Kreutzer DL, Biswas PS, Zhou Y, Wang Y, Tian XJ, Liu Y, Zhou D. The hepatocyte growth factor/c-met pathway is a key determinant of the fibrotic kidney local microenvironment. iScience. 2021 Sep 9;24(10):103112. doi: 10.1016/j.isci.2021.103112. PMID: 34622165; PMCID: PMC8479790. [Role: single-cell RNA-seq and statiscal data analysis.]

  62. Hu S, Russell JO, Liu S, Cao C, McGaughey J, Rai R, Kosar K, Tao J, Hurley E, Poddar M, Singh S, Bell A, Shin D, Raeman R, Singhi AD, Nejak-Bowen K, Ko S, Monga SP. β-Catenin-NF-κB-CFTR interactions in cholangiocytes regulate inflammation and fibrosis during ductular reaction. Elife. 2021 Oct 5;10:e71310. doi: 10.7554/eLife.71310. PMID: 34609282; PMCID: PMC8555990.. [Role: RNA-seq and statistical data analysis.]

  63. Liu S, Gui Y, Wang MS, Zhang L, Xu T, Pan Y, Zhang K, Yu Y, Xiao L, Qiao Y, Bonin C, Hargis G, Huan T, Yu Y, Tao J, Zhang R, Kreutzer DL, Zhou Y, Tian XJ, Wang Y, Fu H, An X, Liu S*, Zhou D*. Serum integrative omics reveals the landscape of human diabetic kidney disease. Mol Metab. 2021 Dec;54:101367. doi: 10.1016/j.molmet.2021.101367. Epub 2021 Nov 1. PMID: 34737094; PMCID: PMC8609166. [Role as second corresponding author: Statistical data analysis and manuscript writing.]


    64. 2020 Publications

  64. Pan Y, Ballance H, Meng H, Gonzalez N, Kim SM, Abdurehman L, York B, Chen X, Schnytzer Y, Levy O, Dacso CC, McClung CA, O'Malley BW, Liu S*, Zhu B*. 12-h clock regulation of genetic information flow by XBP1s. PLoS Biol. 2020 Jan 14;18(1):e3000580. doi: 10.1371/journal.pbio.3000580. PMID: 31935211; PMCID: PMC6959563. [Role: RNA-seq data analysis and statistical analysis for 12hr and 24hr rhythm detection]

  65. Jiang L, Mu H, Xu F, Xie D, Su W, Xu J, Sun Z, Liu S, Luo J, Shi Y, Leak RK, Wechsler LR, Chen J, Hu X. Transcriptomic and functional studies reveal undermined chemotactic and angiostimulatory properties of aged microglia during stroke recovery. J Cereb Blood Flow Metab. 2020 Dec;40(1_suppl):S81-S97. doi: 10.1177/0271678X20902542. Epub 2020 Feb 16. PMID: 32065074; PMCID: PMC7687033. [Role: RNA sequencing and statistical analysis]

  66. Kosar K, Cornuet P, Singh S, Liu S, Nejak-Bowen K. The Thyromimetic Sobetirome (GC-1) Alters Bile Acid Metabolism in a Mouse Model of Hepatic Cholestasis. Am J Pathol. 2020 May;190(5):1006-1017. doi: 10.1016/j.ajpath.2020.01.015. Epub 2020 Mar 20. PMID: 32205094; PMCID: PMC7221298. [Role: Microarray statistical analysis]

  67. Vats R, Liu S, Zhu J, Mukhi D, Tutuncuoglu E, Cardenes N, Singh S, Brzoska T, Kosar K, Bamne M, Jonassaint J, Adebayo Michael A, Watkins SC, Hillery C, Ma X, Nejak-Bowen K, Rojas M, Gladwin MT, Kato GJ, Ramakrishnan S, Sundd P, Monga SP, Pradhan-Sundd T. Impaired Bile Secretion Promotes Hepatobiliary Injury in Sickle Cell Disease. Hepatology. 2020 Dec;72(6):2165-2181. doi: 10.1002/hep.31239. Epub 2020 Nov 13. PMID: 32190913; PMCID: PMC7923682. [Role: RNA-seq and statistical data analysis]

  68. Liu P^, Liu S^, Fang Y, Xue X, Zou J, Tseng G, Konnikova L. Recent Advances in Computer-Assisted Algorithms for Cell Subtype Identification of Cytometry Data. Front Cell Dev Biol. 2020 Apr 28;8:234. doi: 10.3389/fcell.2020.00234. PMID: 32411698; PMCID: PMC7198724.

  69. Silva Barbosa AC, Zhou D, Xie Y, Choi YJ, Tung HC, Chen X, Xu M, Gibbs RB, Poloyac SM, Liu S, Yu Y, Luo J, Liu Y, Xie W. Inhibition of Estrogen Sulfotransferase (SULT1E1/EST) Ameliorates Ischemic Acute Kidney Injury in Mice. J Am Soc Nephrol. 2020 Jul;31(7):1496-1508. doi: 10.1681/ASN.2019080767. Epub 2020 May 18. PMID: 32424001; PMCID: PMC7351010. [Role: statistical data analysis]

  70. Rai RP, Liu Y, Iyer SS, Liu S, Gupta B, Desai C, Kumar P, Smith T, Singhi AD, Nusrat A, Parkos CA, Monga SP, Czaja MJ, Anania FA, Raeman R. Blocking integrin α4β7-mediated CD4 T cell recruitment to the intestine and liver protects mice from western diet-induced non-alcoholic steatohepatitis. J Hepatol. 2020 Nov;73(5):1013-1022. doi: 10.1016/j.jhep.2020.05.047. Epub 2020 Jun 12. PMID: 32540177; PMCID: PMC7839272. [Role: RNA-seq analysis]

  71. Luo JH, Liu S, Tao J, Ren BG, Luo K, Chen ZH, Nalesnik M, Cieply K, Ma T, Cheng SY, Chen Q, Michalopoulos GK, Nelson JB, Bhargava R, Zhang J, Ma D, Jarrard D, Pennathur A, Luketich JD, DeFranco DB, Monga SP, Tseng G, Yu YP. Pten-NOLC1 fusion promotes cancers involving MET and EGFR signalings. Oncogene. 2021 Feb;40(6):1064-1076. doi: 10.1038/s41388-020-01582-8. Epub 2020 Dec 15. PMID: 33323972; PMCID: PMC7880894. [Role: RNA-seq, ChIP-seq and statistical analysis]


    72. Previous Publications

  72. Yu YP, Ding Y, Chen Z, Liu S, Michalopoulos A, Chen R, Gulzar ZG, Yang B, Cieply KM, Luvison A, Ren BG, Brooks JD, Jarrard D, Nelson JB, Michalopoulos GK, Tseng GC, Luo JH. Novel fusion transcripts associate with progressive prostate cancer. Am J Pathol. 2014 Oct;184(10):2840-9. doi: 10.1016/j.ajpath.2014.06.025. PMID: 25238935; PMCID: PMC4188871. [Role: perform machine learning analysis to predict prostate cancer status.]

  73. Zuo ZH, Yu YP, Ding Y, Liu S, Martin A, Tseng G, Luo JH. Oncogenic Activity of miR-650 in Prostate Cancer Is Mediated by Suppression of CSR1 Expression. Am J Pathol. 2015 Jul;185(7):1991-9. doi: 10.1016/j.ajpath.2015.03.015. Epub 2015 May 5. PMID: 25956032; PMCID: PMC4484220. [Role: perform statistical data analysis.]

  74. Yu YP^, Liu S^, Huo Z, Martin A, Nelson JB, Tseng GC, Luo JH. Genomic Copy Number Variations in the Genomes of Leukocytes Predict Prostate Cancer Clinical Outcomes. PLoS One. 2015 Aug 21;10(8):e0135982. doi: 10.1371/journal.pone.0135982. PMID: 26295840; PMCID: PMC4546524.

  75. Luo JH, Liu S, Zuo ZH, Chen R, Tseng GC, Yu YP. Discovery and Classification of Fusion Transcripts in Prostate Cancer and Normal Prostate Tissue. Am J Pathol. 2015 Jul;185(7):1834-45. doi: 10.1016/j.ajpath.2015.03.008. Epub 2015 May 9. PMID: 25963990; PMCID: PMC4483459. [Role: summarize fusion transcripts detected from in-house RNA-sequencing data.]

  76. Qi YB, Wang XL, Shi T, Liu S, Xu ZH, Li X, Shi X, Xu P, Zhao YL. Multicomponent kinetic analysis and theoretical studies on the phenolic intermediates in the oxidation of eugenol and isoeugenol catalyzed by laccase. Phys Chem Chem Phys. 2015 Nov 28;17(44):29597-607. doi: 10.1039/c5cp03475b. Epub 2015 Oct 19. PMID: 26477512. [Role: Pilot data generation and analysis for enzyme kinetic properties.]

  77. Huo Z, Ding Y, Liu S, Oesterreich S, Tseng G. Meta-analytic framework for sparse K-means to identify disease subtypes in multiple transcriptomic studies. J Am Stat Assoc. 2016;111(513):27-42. doi: 10.1080/01621459.2015.1086354. Epub 2016 May 5. PMID: 27330233; PMCID: PMC4908837. [Role: Algorithm development.]

  78. Liu S, Tsai WH, Ding Y, Chen R, Fang Z, Huo Z, Kim S, Ma T, Chang TY, Priedigkeit NM, Lee AV, Luo J, Wang HW, Chung IF, Tseng GC. Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic Acids Res. 2016 Mar 18;44(5):e47. doi: 10.1093/nar/gkv1234. Epub 2015 Nov 17. PMID: 26582927; PMCID: PMC4797269.

  79. Paranjpe S, Bowen WC, Mars WM, Orr A, Haynes MM, DeFrances MC, Liu S, Tseng GC, Tsagianni A, Michalopoulos GK. Combined systemic elimination of MET and epidermal growth factor receptor signaling completely abolishes liver regeneration and leads to liver decompensation. Hepatology. 2016 Nov;64(5):1711-1724. doi: 10.1002/hep.28721. Epub 2016 Oct 1. PMID: 27397846; PMCID: PMC5074871. [Role: microarray data analysis.]

  80. Wang L^, Liu S^, Ding Y, Yuan SS, Ho YY, Tseng GC. Meta-analytic framework for liquid association. Bioinformatics. 2017 Jul 15;33(14):2140-2147. doi: 10.1093/bioinformatics/btx138. PMID: 28334340; PMCID: PMC6044323.

  81. Chen ZH, Yu YP, Tao J, Liu S, Tseng G, Nalesnik M, Hamilton R, Bhargava R, Nelson JB, Pennathur A, Monga SP, Luketich JD, Michalopoulos GK, Luo JH. MAN2A1-FER Fusion Gene Is Expressed by Human Liver and Other Tumor Types and Has Oncogenic Activity in Mice. Gastroenterology. 2017 Oct;153(4):1120-1132.e15. doi: 10.1053/j.gastro.2016.12.036. Epub 2017 Feb 27. PMID: 28245430; PMCID: PMC5572118. [Role: fusion transcript analysis and data mining.]

  82. He DM, Ren BG, Liu S, Tan LZ, Cieply K, Tseng G, Yu YP, Luo JH. Oncogenic activity of amplified miniature chromosome maintenance 8 in human malignancies. Oncogene. 2017 Jun 22;36(25):3629-3639. doi: 10.1038/onc.2017.123. Epub 2017 May 8. PMID: 28481876; PMCID: PMC5481462. [Role: fusion transcript analysis and statistical support.]

  83. Chen ZH, Yu YP, Zuo ZH, Nelson JB, Michalopoulos GK, Monga S, Liu S, Tseng G, Luo JH. Targeting genomic rearrangements in tumor cells through Cas9-mediated insertion of a suicide gene. Nat Biotechnol. 2017 Jun;35(6):543-550. doi: 10.1038/nbt.3843. Epub 2017 May 1. PMID: 28459452; PMCID: PMC5462845. [Role: statistical analysis]

  84. Becker T, Lee WP, Leone J, Zhu Q, Zhang C, Liu S, Sargent J, Shanker K, Mil-Homens A, Cerveira E, Ryan M, Cha J, Navarro FCP, Galeev T, Gerstein M, Mills RE, Shin DG, Lee C, Malhotra A. FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods. Genome Biol. 2018 Mar 20;19(1):38. doi: 10.1186/s13059-018-1404-6. PMID: 29559002; PMCID: PMC5859555. [Role: Model development and application]

  85. Tsagianni A, Mars WM, Bhushan B, Bowen WC, Orr A, Stoops J, Paranjpe S, Tseng GC, Liu S, Michalopoulos GK. Combined Systemic Disruption of MET and Epidermal Growth Factor Receptor Signaling Causes Liver Failure in Normal Mice. Am J Pathol. 2018 Oct;188(10):2223-2235. doi: 10.1016/j.ajpath.2018.06.009. Epub 2018 Jul 20. PMID: 30031724; PMCID: PMC6168971. [Role: statistical analysis.]

  86. Ma T, Huo Z, Kuo A, Zhu L, Fang Z, Zeng X, Lin CW, Liu S, Wang L, Liu P, Rahman T, Chang LC, Kim S, Li J, Park Y, Song C, Oesterreich S, Sibille E, Tseng GC. MetaOmics: analysis pipeline and browser-based software suite for transcriptomic meta-analysis. Bioinformatics. 2019 May 1;35(9):1597-1599. doi: 10.1093/bioinformatics/bty825. PMID: 30304367; PMCID: PMC6499246. [Role: coding for Meta-QC pipeline.]

  87. Adebayo Michael AO, Ko S, Tao J, Moghe A, Yang H, Xu M, Russell JO, Pradhan-Sundd T, Liu S, Singh S, Poddar M, Monga JS, Liu P, Oertel M, Ranganathan S, Singhi A, Rebouissou S, Zucman-Rossi J, Ribback S, Calvisi D, Qvartskhava N, Görg B, Häussinger D, Chen X, Monga SP. Inhibiting Glutamine-Dependent mTORC1 Activation Ameliorates Liver Cancers Driven by β-Catenin Mutations. Cell Metab. 2019 May 7;29(5):1135-1150.e6. doi: 10.1016/j.cmet.2019.01.002. Epub 2019 Jan 31. PMID: 30713111; PMCID: PMC6506359. [Role: statistical analysis]

  88. Yu YP, Tsung A, Liu S, Nalesnick M, Geller D, Michalopoulos G, Luo JH. Detection of fusion transcripts in the serum samples of patients with hepatocellular carcinoma. Oncotarget. 2019 May 21;10(36):3352-3360. PMID: 31164957; PMCID: PMC6534357. [Role: statistical analysis.]

  89. Fu H, Liu S, Bastacky SI, Wang X, Tian XJ, Zhou D. Diabetic kidney diseases revisited: A new perspective for a new era. Mol Metab. 2019 Dec;30:250-263. doi: 10.1016/j.molmet.2019.10.005. Epub 2019 Oct 17. PMID: 31767176; PMCID: PMC6838932. [Role: statistical analysis]

Last Modified: 02/2025