Publications

Complete list of Peer Reviewed Publications († equal contribution)

    2024
  1. Yan F, Jiang L, Chen DQ, Ceccarelli M, Guo Y, Reinventing Gene Expression Connectivity Through Regulatory and Spatial Structural Empowerment via Principal Node Aggregation Graph Neural Network, Nucleic Acids Research, 2024, PMID: 38884259, PMC:
  2. Anyona S, Chen Q, Guo Y, Raballah E, Hurwitz I, Onyango C, Seidenberg P, Schneider K, Lambert C, McMahon B, Ouma C, Perkins D, Entire expressed peripheral blood transcriptome in pediatric severe malarial anemia, Nature Communications, 2024, PMID: 10371159, PMC:PMC37503086
  3. Gai X, Feng Y, Flores T, Kang H, Yu H, Leslie KK, Zhu Y, Doherty JA, Guo Y, Belinsky SA, Cook LS, Leng S, Early menopause and hormone therapy as determinants for lung health outcomes: a secondary analysis using the PLCO trial, Thorax, 2024, PMID: 38871464, PMC:
  4. Lantz BJ, Moriwki M, Oyebamiji OM, Guo Y, Bosc LG, Chronic hypoxia disrupts T regulatory cell phenotype contributing to the emergence of exTreg-TH17 cells, Frontiers in Physiology, 2024, PMID: 38347920, PMC:PMC10859758
  5. Xin R, Jiang L, Yu H, Yan F, Tang J, Guo Y, Comprehensive Cross Cancer Analyses Reveal Mutational Signature Cancer Specificity, Quantitative Biology, 2024, PMID: , PMC:

    6. 2023
  6. Bai J, Zhou D, Guo Y, Characterizing Racial Disparity in Cancers by Predicting Candidate Biomarker, 2023 IEEE International Conference on Bioinformatics and Biomedicine, 2023, PMID: , PMC:
  7. Miao H, Wang YN, Yu XY, Zou L, Guo Y, Su W, Liu F, Cao G, Zhao YY, Lactobacillus species ameliorate membranous nephropathy through inhibiting aryl hydrocarbon receptor pathway via tryptophan-produced indole metabolites, British Journal of Pharmacology, 2023, PMID: 37594378, PMC:
  8. Gong X, Huang Y, Duong J, Leng S, Zhan FB, Guo Y, Lin Y, Luo L, Industrial air pollution and low birth weight in New Mexico, USA, Journal of Environmental Management, 2023, PMID: 37857221, PMC:PMC10829484
  9. Yan F, Jiang L, Ye F, Ping J, Bowley T, Ness S, Marchetti D, Tang J, Guo Y, Deep Neural Network Based Tissue Deconvolution of circulating tumor cell RNA , Journal of Translational Medicine, 2023, PMID: 37925448, PMC:PMC10625696
  10. Wang YN, Miao H, Yu XY, Guo Y, Su W, Liu F, Cao G, Zhao YY, Oxidative stress and inflammation are mediated via aryl hydrocarbon receptor signalling in idiopathic membranous nephropathy, Free Radical Biology & Medicine, 2023, PMID: 37451370, PMC:
  11. van der Heijden YF, Maruri F, Blackman A, Morrison R, Guo Y, Sterling TR, Mycobacterium tuberculosis gene expression associated with fluoroquinolone resistance and efflux pump inhibition, The Journal of Infectious Diseases, 2023, PMID: 37079382, PMC:PMC10428193
  12. Yu H†, Jiang L†, Li CI, Ness S, Piccirillo S, Guo Y, Somatic mutation effects diffused over miRNA dysregulation , Bioinformatics, 2023, PMID: 37624931, PMC:PMC10474951
  13. Brayer KJ, Kang H, El-Naggar AK, Andreasen S, Homøe P, Kiss K, Mikkelsen L, Heegaard S, Pelaez D, Moeyersoms A, Tse DT, Guo Y, Lee DY, Ness SA, Development and Validation of a Gene Signature Classifier for Poor Survival in Salivary Gland Adenoid Cystic Carcinoma, Cancers, 2023, PMID: 36900183, PMC:PMC10000625
  14. Speer RM, Nandi SP, Cooper KL, Zhou X, Yu H, Guo Y, Hudson LG, Alexandrov LB, Liu KJ, Arsenic is a potent co-mutagen of ultraviolet light, Communication Biology, 2023, PMID: 36865271, PMC:PMC9980120
  15. Zhang T, Yu H, Jiang L, Bai Y, Liu X, Guo Y, Comprehensive Pan-Cancer Mutation Density Patterns in Enhancer RNA, International Journal of Molecular Sciences, 2023, PMID: 38203707, PMC:PMC10778997
  16. Bai J, Ma K, Xia S, Geng R, Shen C, Jiang L, Gong X, Yu H, Leng S, Guo Y, Pan-cancer mutational signature surveys correlated mutational signature with geospatial environmental exposures and viral infections, Computational and Structural Biotechnology Journal, 2023, PMID: 38022689, PMC:PMC10652135
  17. Zhang T, Yu H, Bai Y, Guo Y, Mutation Density Analyses on Long Noncoding RNA Reveal Comparable Patterns to Protein-Coding RNA and Prognostic Value , Computational and Structural Biotechnology Journal, 2023, PMID: 37860228, PMC:PMC10582829
  18. Jiang M, Hu CJ, Rowe CL, Kang H, Gong X, Dagucon CP, Wang J, Lin Y, Sood A, Guo Y, Zhu Y, Alexis NE, Gilliland FD, Belinsky SA, Xu X, Leng S, Application of artificial intelligence in quantifying lung deposition dose of black carbon in people with exposure to ambient combustion particles, Journal of Exposure Science & Environmental Epidemiology, 2023, PMID: 37848612, PMC:
  19. Thiel KW, Newtson AM, Devor EJ, Zhang Y, Malmrose PK, Bi J, Losh HA, Davies S, Smith L, Padilla J, Leiva SM, Grueter CE, Breheny P, Hagan CR, Pufall MA, Gertz J, Guo Y, Leslie KK, Global expression analysis of endometrial cancer cells in response to progesterone identifies new therapeutic targets, The Journal of Steroid Biochemistry and Molecular Biology, 2023, PMID: 37716459, PMC:
  20. Speer RM, Yu H, Zhou X, Nandi S, Alexandrov L, Guo Y, Hudson LG, Liu, K, Arsenic and UVR co-exposure results in unique gene expression profile identifying key co-carcinogenic mechanisms, Toxicology and Applied Pharmacology, 2023, PMID: 38036231, PMC:PMC10883297
  21. Jiang L, Yu H, Guo Y, Modeling the relationship between gene expression and mutational signature, Quantitative Biology, 2023, PMID: 37032811, PMC:PMC10078980 (Cover Story)

    22. 2022
  22. Zhao S, Jiang L, Yu H, Guo Y, GTQC: Automated Genotyping Array Quality Control and Report, Journal of Genomics, 2022, PMID: 35300047, PMC:PMC8922302
  23. Bowley TY, Lagutina RV, Francis C, Sivakumar S, Selwyn RG, Taylor E, Guo Y, Fahy BN, Tawfik B, Marchetti D, The RPL/RPS gene signature of melanoma CTCs associates with brain metastasis, Cancer Research Communications, 2022, PMID: 36407834, PMC:PMC9668078
  24. Chen DQ, Guo Y, Li X, Zhang GQ, Li P, Small molecules as modulators of regulated cell death against ischemia/reperfusion injury, Medicinal Research Reviews, 2022, PMID: 35730121, PMC:NA
  25. Samuels DC, Yu H, Guo Y, Is it time to reassess variant annotation?, Trends in Genetics, 2022, PMID: 35232614, PMC:NA
  26. Yu H, Ness S, Li CI, Bai Y, Mao P, Guo Y, Surveying mutation density patterns around specific genomic features, Genome Research, 2022, PMID: 36100435, PMC:PMC9712630
  27. Jiang L, Yu H, Tang J, Guo Y, CoMutDB: The Landscape of Somatic Mutation Co-occurrence in Cancers, Bioinformatics, 2022, PMID: 36355452, PMC:PMC9805589
  28. Chen DQ, Chen L, Guo Y, Wu XQ, Zhao TT, Zhao HL, Zhang HJ, Yan MH, Zhang GQ, Li P, Poricoic acid A suppresses renal fibroblast activation and interstitial fibrosis in UUO rats via upregulating Sirt3 and promoting β-catenin K49 deacetylation, Acta Pharmacologica Sinica, 2022, PMID: 36470978, PMC:PMC10104829
  29. Cao G, Miao H, Wang Y, Chen DQ, Wu XQ, Chen L, Guo Y, Zou L, Vaziri ND, Li P, Zhao YY, Intrarenal 1-methoxypyrene, an aryl hydrocarbon receptor agonist, mediates progressive tubulointerstitial fibrosis in mice, Acta Pharmacologica Sinica, 2022, PMID: 35577910, PMC:PMC9622813
  30. Jiang L, Yu H, Ness S, Mao P, Guo F, Tang J, Guo Y, Comprehensive Analysis of Co-Mutations Identifies Cooperating Mechanisms of Tumorigenesis, Cancers, 2022, PMID: 35053577, PMC:PMC8774165
  31. Feng Y, Chen DQ, Tang J, Zhao YY, Guo Y, Serum Metabolites Associated with Blood Pressure in Chronic Kidney Disease Patients, Metabolites, 2022, PMID: 35448468, PMC:PMC9027690
  32. Jiang L, Tang J, Guo F, Guo Y, Prediction of Major Histocompatibility Complex Binding with Bilateral and Variable Long Short Term Memory Networks, Biology, 2022, PMID: 35741369, PMC:PMC9220200
  33. Guo Y, van der Heijden YF, Maruri F, Jiang L, Morrison R, Sterling T, RNA editing in Mycobacterium tuberculosis, Microbiological Research, 2022, PMID: 36067705, PMC:NA
  34. Pu J, Yu H, Guo Y, A Novel Strategy to Identify Prognosis-Relevant Gene Sets in Cancers, Genes, 2022, PMID: 35627247, PMC:PMC9141699
  35. Dai Y, Yu H, Yan Q, Li B, Liu A, Liu W, Jiang X, Yejin K, Guo Y†, Zhao Z†, Drug-Target Network Study Reveals the Core Target-protein Interactions of Various COVID-19 Treatments, Genes, 2022, PMID: 35885993, PMC:PMC9316565
  36. Dehority W, Morley VJ, Domman DB, Daly SM, Triplett KD, Disch K, Varjabedian R, Yousey A, Mortaji P, Hill D, Oyebamiji O, Guo Y, Schwalm K, Hall PR, Dinwiddie D, Femling J, Genomic characterization of Staphylococcus aureus isolates causing osteoarticular infections in otherwise healthy children, PLOS ONE, 2022, PMID: 36037235, PMC:PMC9423648
  37. Xi E, Bai J, Zhang K, Yu H, Guo Y, Genomic variants disrupt miRNA-mRNA regulation, Chemistry and Biodiversity, 2022, PMID: 35985010, PMC:NA

    38. 2021
  38. Hu HH, Zhang DD, Wang YN, Wu XQ, Liu JL, Guo Y, Miao H, Zhao YY, The dysregulation of eicosanoids and bile acids correlates with impaired kidney function and renal fibrosis in chronic tubulointerstitial nephropathy, Metabolites, 2021, PMID: 33672315, PMC:PMC7926759
  39. Wang YN, Wu X, Zhang DD, Hu HH, Liu JL, Vaziri ND, Guo Y, Zhao YY, Miao H, Polyporus umbellatus protects against renal fibrosis through regulating intrarenal fatty acyl metabolites based on lipidomics, Frontiers in Pharmacology, 2021, PMID: 33679418, PMC:PMC7934088
  40. Sheng Q, Yu H, Duan M, Ness S, He J, Kang H, Jiang L, Wyrick J, Mao P†, Guo Y†, A streamlined solution for quality control[ processing[ and elucidating cyclobutane pyrimidine dimer sequencing data, Nature Protocols, 2021, PMID: 33731963, PMC:PMC8555867
  41. Guo Y, Yu H, Song H, He J, Oyebamiji O, Kang H, Ping J, Ness S, Shyr Y, Ye F, MetaGSCA: a tool for meta-analysis of gene set differential coexpression, PLOS Computational Biology, 2021, PMID: 33945541, PMC:PMC8121311
  42. Yu H, Guo Y, Chen J, Chen X, Jia P, Zhao Z, Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods, Genes, 2021, PMID: 33946654, PMC:PMC8146818
  43. Jiang L†, Guo Y†, Yu H, Hoff K, Ding X, Zhou W, Edwards J, Detecting SARS-CoV-2 and its variant strains with a full genome tiling array, Briefings in Bioinformatics, 2021, PMID: 34097003, PMC:PMC8344516
  44. Jiang L, Yu H, Jiawei Li, Tang J, Guo Y†, Guo F†, Predicting MHC Class I Binder: Existing Approaches and a Novel Recurrent Neural Network Solution, Briefings in Bioinformatics, 2021, PMID: 34131696, PMC:PMC8574977
  45. Ritter EK, Buehler DP, Asher S, Deal KK, Zhao S, Guo Y, Southard-smith ME, 5-HT3 signaling alters development of sacral neural crest derivatives that innervate the lower urinary tract, International Journal of Molecular Sciences, 2021, PMID: 34202161, PMC:PMC8269166
  46. Kan Y, Jiang L, Tang J, Guo Y†, Guo F†, A systematic view of computational methods for identifying driver genes based on somatic mutation data, Briefings in Functional Genomics, 2021, PMID: 34312663, PMC:NA
  47. Wu YM†, Guo Y†, Yu H, Guo T, RNA editing affects cis-regulatory elements and predicts adverse cancer survival, Cancer Medicine, 2021, PMID: 34319007, PMC:PMC8419749
  48. Wang D, Lin M, Utz B, Bosompem A, Guo Y, Daneshbod Y, Alford CE, Nettles SA, Scher J, Gagne E, O'Neill M, Barrow L, Wojciechowska N, Keegan J, Mosse CA, Lederer JA, Kim AS, miR-378-3p knockdown recpitulates many of the features of myelodysplastic syndromes, American Journal of Pathology, 2021, PMID: 34364880, PMC:PMC8579243
  49. Merkley SD, Goodfellow SM, Guo Y, Wilton ZER, Byrum JR, Schwalm KC, Dinwiddie DL, Gullapalli RR, Deretic V, Hernandez AJ, Bradfute SB, In JG, Castillo EF, Non-autophagy role of Atg5 and NBR1 in unconventional secretion of IL-12 prevents gut dysbiosis and inflammation, Journal of Crohn's and Colitis, 2021, PMID: 34374750, PMC:PMC8864635
  50. Simons P, Guo Y, Bondu V, Tigert SL, Harkins M, Goodfellow S, Tompkins C, Chabot-Richards D, Yang XO, Bosc LG, Bradfute S, Lawrence D, Buranda T, Longitudinal Assessment of Cytokine Expression and Plas-minogen Activation in Hantavirus Cardiopulmonary Syndrome Reveals Immune Regulatory dysfunction in Endstage Disease, Viruses, 2021, PMID: 34452463, PMC:PMC8402847
  51. Goodfellows S, Nofchissey R, Schwalm K, Cook J, Dunnum J, Guo Y, Ye C, Mertz G, Chandran K, Harkins M, Domman D, Dinwiddie D, Bradfute S, Tracing transmission of Sin Nombre virus and discovery of infection in multiple rodent species, Journal of Virology, 2021, PMID: 34549977, PMC:PMC8577387
  52. Wang J, Ness S, Brown R, Yu H, Oyebamiji O, Jiang L, Sheng Q, Samuels DC, Zhao YY, Tang J, Guo Y, EditPredict: prediction of RNA editable site with convolutional neural network, Genomics, 2021, PMID: 34562567, PMC:PMC8671215
  53. Jiang L, Guo F, Tang J, Yu H, Ness S, Duan M, Mao P, Zhao YY†, Guo Y†, SBSA: An Online Service for Somatic Binding Sequence Annotation, Nucleic Acids Research, 2021, PMID: 34606615, PMC:PMC8500130
  54. Miao H, Wu XQ, Wang YN, Chen DQ, Zhang DD, Chen L, Vaziri ND, Zhuang S, Guo Y, Su W, Ma SX, Zhang HQ, SHang YQ, Yu XY, Zhao YL, Mao JR, Gao M, Zhang JH, Zhao J, Zhang Y, Zhang L, Zhao YY, 1-Hydroxypyrene mediates renal fibrosis through aryl hydrocarbon receptor signalling pathway, British Journal of Pharmacology, 2021, PMID: 34625952, PMC:NA
  55. Chen DQ, Shen MJ, Wang H, Li Y, Tang AL, Li S, Xiong MC, Guo Y, Zhang GQ, Sirt3 Maintains Microvascular Endothelial Adherens Junction Integrity to Alleviate Sepsis-Induced Lung Inflammation by Modulating the Interaction of VE-Cadherin and Β-Catenin, Oxidative Medicine and Cellular Longevity, 2021, PMID: 34630854, PMC:PMC8500765
  56. Pauken C, Kenney SR, Brayer KJ, Guo Y, Brown-Glaberman UA, Marchetti D, Heterogeneity of Circulating Tumor Cell Neoplastic Subpopulations Outlined by Single-Cell Transcriptomics, Cancers, 2021, PMID: 34638368, PMC:PMC8508335
  57. Kan Y, Jiang L, Guo Y, Tang J, Guo F, Two-stage-vote ensemble framework based on integration of mutation data and gene interaction network for uncovering driver genes, Briefings in Bioinformatics, 2021, PMID: 34791034, PMC:NA
  58. Yu H, Wang L, Chen D, Li J, Guo Y, Conditional transcriptional relationships may serve as cancer prognostic markers, BMC Medical Genomics, 2021, PMID: 34856998, PMC:PMC8638091

    59. 2020
  59. Sudhan DR, Guerrero-Zotano A, Won H, Ericsson PG, Servetto A,, Rosario MH, Ye D, Lee KM, Formisano L, Guo Y, Liu Q, Kinch LN, Brewer MR, Dugger T, Koch J, Wick MJ, Cutler RE, Jr., Lalani AS, Bryce R, Auerbach A, Hanker AB, Arteaga CL, Hyperactivation of TORC1 drives resistance to the pan-HER tyrosine kinase inhibitor neratinib in HER2-mutant cancers, Cancer Cell, 2020, PMID: 31978326, PMC:PMC7301608
  60. Chen DQ, Cao G, Zhao H, Chen L, Yang T, Wang M, Vaziri ND, Guo Y, Zhao YY, Combined melatonin and poricoic acid A inhibits renal fibrosis through modulating the interaction of Smad3 and β-catenin pathway in AKI-to-CKD continuum, Therapeutic Advances in Chronic Disease, 2020, PMID: 31452866, PMC:PMC6696851
  61. Ormseth M, Solu JF, Sheng Q, Ye F, Song H, Wu Q, Guo Y, Oeser AM, Allen RM, Vickers KC, Stein CM, The Endogenous Plasma Small RNAome of Rheumatoid Arthritis, ACR Open Rheumatology, 2020, PMID: 31913579, PMC:PMC7011423
  62. Sheng Q, Yu H, Oyebamiji O, Wang J, Chen D, Ness S, Zhao YY, Guo Y, AnnoGen: Annotating Genomewide Pragmatic Features, Bioinformatics, 2020, PMID: 31930398, PMC:PMC7203733
  63. Miao H, Cao G, Xu XQ, Chen YY, Chen DQ, Chen L, Vaziri ND, Feng YL, Su W, Goa Yi, Zhuang S, Yu XY, Zhang L, Guo Y, Zhao YY, Identification of endogenous 1-aminopyrene as a novel mediator of progressive chronic kidney disease via aryl hydrocarbon receptor activation, British Journal of Pharmacology, 2020, PMID: 32219844, PMC:PMC7348091
  64. Maruri F, Guo Y, Blackman A, van der Heijden YF, Rebeiro PF, Sterling TR, Resistance-conferring mutations on whole-genome sequencing of fluoroquinolone-resistant and –susceptible M. tuberculosis isolates: a proposed threshold for identifying resistance, Clinical Infectious Diseases, 2020, PMID: 32348473, PMC:PMC8315129
  65. Long JL, Lee LP, Small EM, Hillyer C, Guo Y, Osley M, Regulation of UV damage repair in quiescent yeast cells, DNA Repair, 2020, PMID: 32403026, PMC:PMC7891302
  66. Yu H, Zhao S, Ness S, Kang H, Sheng Q, Samuels DC, Oyebamiji O, Zhao YY, Guo Y, Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats, PLOS Computational Biology, 2020, PMID: 32511223, PMC:PMC7302867
  67. Samuels DC, Below JE, Ness S, Yu H, Leng S, Guo Y, Alternative Applications of Genotyping Array Data Using Multi-Variant Methods, Trends in Genetics, 2020, PMID: 32773169, PMC:PMC7572808
  68. Yu H, Chen DQ, Oyebamiji O, Zhao YY, Guo Y, Expression correlation attenuates within the between key signaling pathways in chronic kidney disease, BMC Medical Genomics, 2020, PMID: 32957963, PMC:PMC7504859
  69. Sheak JR, Jones DT, Lantz BJ, Maston LD, Vigil D, Resta TC, Resta MM, Howard TA, Kanagy NL, Guo Y, Jankowska-Gan E, Sullivan JA, Braun RK, Brulingham WJ, Gonzalez-Bosc LV, NFATc3 Regulation of Collagen V Expression Contributes to Cellular Immunity to Collagen Type V and Hypoxic Pulmonary Hypertension, American Journal of Physiology-Lung Cellular and Molecular Physiology, 2020, PMID: 32997513, PMC:PMC7792682
  70. Jiang L, Duan M, Guo F, Tang J, Oyebamiji O, Yu H, Ness S, Zhao YY, Mao P, Guo Y, SMDB: Pivotal Somatic Sequence Alterations Reprogramming Regulatory Cascades, Nucleic Acids Research Cancer, 2020, PMID: 33094288, PMC:PMC7556404
  71. Hua M, Wu XQ, Zhang DD, Wang YN, Guo Y, Li P, Xiong Q, Zhao YY, Deciphering the cellular mechanisms underlying fibrosis-associated diseases and therapeutic avenue, Pharmacological Research, 2020, PMID: 33248198, PMC:NA
  72. Jiang L, Guo F, Tang J, Leng S, Ness S, Ye F, Kang H, Samuels DC, Guo Y, Global Autozygosity is Associated with Cancer Risk, Mutational Signature and Prognosis, Cancers, 2020, PMID: 33291726, PMC:PMC7761949
  73. Blackman A, Morrison R, Maruri F, Van der Heriden Y, Nochowicz C, Guo Y, Scholz M, Rustad, T, Sherman D, Sterling T, Re-evaluation of a novel resistance mutation in eccC5 of the ESX-5 secretion system in ofloxacin-resistant Mycobacterium tuberculosis, Journal of Antimicrobial Chemotherapy, 2020, PMID: 33367727, PMC:PMC7879138
  74. Zhang D†, Guo Y†, Xie N, Prognostic Value and Co-expression Patterns of Metabolic Pathways in Cancers, BMC Genomics, 2020, PMID: 33372594, PMC:PMC7771089

    75. 2019
  75. Ping J, Oyebamiji O, Yu H, Ness S, Cien J, Ye F, Kang H, Samuels DC, Ivanov S, Chen DQ, Zhao YY, Guo Y, MutEx: a multi-faceted gateway for exploring integrative pan-cancer genomic data, Briefings in Bioinformatics, 2019, PMID: 31588509, PMC:PMC7373173
  76. Feng YL, Chen H, Chen L, Vaziri ND, Gao M, Zhang JH, Zhang Y, Ma SX, Shang YQ, Su W, Mao JR, Yu XY, Zhang L, Guo Y, Zhao YY, Activated NF-κB/Nrf2 and Wnt/β-catenin pathways are associated with lipid metabolism in CKD patients with microalbuminuria and macroalbuminuria, BBA - Molecular Basis of Disease, 2019, PMID: 31102786, PMC:NA
  77. Chen Z, Li Z, Soutto M, Wang W, Piazuelo MB, Zhu S, Guo Y, Maturana MJ, Gorvalan AJ, Chen X, Xu Z, El-Rifai WM, Integrated analysis of mouse and human gastric neoplasm identifies conserved miRNA networks in gastric carcinogenesis, Gastroenterology, 2019, PMID: 30502323, PMC:PMC6409191
  78. Chen YY, Chen D, Chen L, Liu J, Vaziri ND, Guo Y, Zhao YY, Microbiome-metabolome reveals the contribution of gut-kidney axis on kidney disease, Journal of Translational Medicine, 2019, PMID: 30602367, PMC:PMC6317198
  79. Fleming JT, Brignola E, Chen L, Guo Y, Zhao S, Wang Q, Li B, Correa H, Ermilov AN, Dlugosz AA, Chiang C, Insight into the etiology of undifferentiated soft tissue sarcomas from a novel mouse model, Molecular Cancer Research, 2019, PMID: 30683671, PMC:PMC6497566
  80. Blum AE, Venkitachalam S, Ravillah D, Chelluboyina AK, Kieber-Emmons AM, Ravi L, Kresak A, Chandar AK, Markowitz SD, Canto MI, Wang JS, Shaheen NJ, Guo Y, Shyr Y, Willis JE, Chak A, Varadan V, Guda K, Systems Biology Analyses Reveal Hyperactivation of Transforming Growth Factor beta and JNK Signaling pathways in Esophageal Cancer, Gastroenterology, 2019, PMID: 30768984, PMC:PMC6701681
  81. Yu H, Samuels DC, Zhao YY, Guo Y, Architectures and accuracy of artificial neural network for disease classification from omics data, BMC Genomics, 2019, PMID: 30832569, PMC:PMC6399893
  82. Formisano L, Lu Y, Jansen VM, Bauer JA, Hanker AB, Guerrero-Zotano AL, Guo Y, Ericsson PG, Lee, KM, Nixon MJ, Schwarz LJ, Sanders ME, Sudhan D, Dugger TC, Cruz MR, Behdad A, Cristofanillli M, Bardia A, O’Shaughnessy J, Nagy RJ Lanman RB, Solovieff N, Miller M, Su F, Shyr Y, Mayer IA, Balko JM, Arteaga CL, Aberrant FGFR pathway signaling mediates resistance to CDK4/6 inhibitors in ER+ breast cancer, Nature Communications, 2019, PMID: 30914635, PMC:PMC6435685
  83. Chen L, Chen DQ, Liu JR, Zhang J, Vaziri ND, Zhuang S, Chen H, Feng YL, Guo Y, Zhao YY, Unilateral ureteral obstruction causes gut microbial dysbiosis and metabolome disorders contributing to interstitial fibrosis, Experimental and Molecular Medicine, 2019, PMID: 30918245, PMC:PMC6437207
  84. Chen D, Cao G, Su W, Chen H, Argyopoulos CP, Yu H, Su W, Chen L, Samuels DC, XZhuang S, Bayliss GP, Zhao S, Yu XY, Vaziri ND, Wang M, Liu D, Mao JR, Ma SX, Zhao J, Zhang Y, Shang YQ, Kang H, Ye F, Chen XH, Li XR, Zhang L, Meng M, Guo Y†, Zhao YY†, Identification of serum metabolites associating with chronic kidney disease progression and anti fibrotic effect of 5-methoxytryptophan, Nature Communications, 2019, PMID: 30931940, PMC:PMC6443780
  85. Chigaev M, Yu H, Samuels DC, Sheng Q, Oyebamiji O, Ness S, Yue W, Zhao YY, Guo Y, Genomic positional dissection of RNA Editomes in tumor and normal samples, Frontiers in Genetics, 2019, PMID: 30949194, PMC:PMC6435843
  86. Ormseth MJ, Solus JF, Sheng Q, Ye F, Wu Q, Guo Y, Oeser AM, Allen RM, Vickers KC, Stein M, Development and Validation of a microRNA Panel to Differentiate between Patients with Rheumatoid Arthritis and Control Subjects, The Journal of Rheumatology, 2019, PMID: 31092710, PMC:PMC6856415
  87. Feng YL, Chen DQ, Vaziri ND, Guo Y, Zhao YY, Small molecule inhibitors of epithelial-mesenchymal transition for the treatment of cancer and fibrosis, Medicinal Research Reviews, 2019, PMID: 31131921, PMC:NA
  88. Feng YL, Cao G, Chen DQ, Vaziri ND, Chen L, Zhang J, Wang M, Guo Y Zhao YY, Microbiome-metabolomics reveals gut microbiota associated with glycine-conjugated metabolites and polyamine metabolism in chronic kidney disease, Cellular and Molecular Life Sciences, 2019, PMID: 31147751, PMC:NA
  89. Dosoky N, Chen Z, Guo Y, Flynn CR, Davies SS, Two-week administration of engineered Escherichia coli establishes persistent resistance to diet induced obesity even without antibiotic pretreatment, Applied Environmental Microbiology, 2019, PMID: 31203417, PMC:PMC7066869
  90. Yang T, Chen YY, Liu JR, Zhao H, Vaziri ND, Guo Y, Zhao YY, Natural products against renin-angiotensin system for antifibrosis therapy, European Journal of Medicinal Chemistry, 2019, PMID: 31279295, PMC:NA
  91. Cunningham I, Hamele-Bena, Guo Y, Papp A, Yang J, Hinck L, Brantley-Sieders D, Shyr Y, R Fisher R, Extramedullary Leukemia Behaving as Solid Cancer: Clinical, Histologic, and Genetic Clues to Chemoresistance in Organ Sites, Hematology, 2019, PMID: 31353508, PMC:NA
  92. Zhao H, Chen L, Yang T, Feng YL, Vaziri ND, Liu BL, Liu QQ, Guo Y, Zhao YY, Aryl hydrocarbon receptor activation mediates kidney disease and renal cell carcinoma, Journal of Translational Medicine, 2019, PMID: 31488157, PMC:PMC6727512
  93. Ye B, Shi J, Kang H, Oyebamiji O, Hill D, Yu H, Ness S, Ye F, Ping J, He J, Edwards J, Zhao YY, Guo Y, Advancing Pan-cancer Gene Expression Survival Analysis by Inclusion of Non-coding RNA, RNA Biology, 2019, PMID: 31607216, PMC:PMC7567505
  94. Guo Y, Yu H, Chen DQ, Zhao YY, Machine Learning Distilled Metabolite Biomarkers for Early Stage Renal Injury, Metabolomics, 2019, PMID: 31807893, PMC:NA
  95. Feng B, Zhao YY, Wang J, Yu H, Potu S, Wang J, Tang J, Guo Y, The Application of Machine Learning Algorithms to Diagnose CKD Stages and Identify Critical Metabolites Features, Bioinformatics and Biomedical Engineering Proceedings of the 7th International Work-Conference, 2019, PMID: NA, PMC:NA

    96. 2018
  96. Guo Y, Wang J, Sheng Q, Zhao S, Zhao YY, Lehmann, BD, The Landscape of small non-coding RNAs in Triple-Negative Breast Cancer, Genes, 2018, PMID: 29320459, PMC:PMC5793181
  97. Ma D, Tu C, Sheng Q, Yang Y, Kan Z, Guo Y, Shyr Y, Scott IC, Lou X, Dynamics of Zebrafish Heart Regeneration Using an HPLC-ESI-MS/MS Approach, Journal of Proteome Research, 2018, PMID: 29369637, PMC:NA
  98. Wang M, Chen DQ, Chen L, Zhao H, Liu D, Zhang ZH, Vaziri N, Guo Y, Cao G, Zhao YY, Novel RAS inhibitors poricoic acid ZG and poricoic acid ZH attenuate renal fibrosis via Wnt/β-catenin pathway and targeted phosphorylation smad3 signaling, Journal of Agricultural and Food Chemistry, 2018, PMID: 29383936, PMC:NA
  99. Chen L, Su W, Che H, Chen DQ, Wang M, Guo Y, Zhao YY, Proteomics for Biomarker Identification and Clinical Application in Kidney Disease, Advances in Clinical Chemistry, 2018, PMID: 29655463, PMC:NA
  100. Wang M, Chen DQ, Cao G, Zhao H, Liu D, Vaziri N, Guo Y, Zhao YY, Novel inhibitors of the cellular RAS components, Poricoic acids, target Smad3 phosphorylation and Wnt/β-catenin pathway against renal fibrosis, British Journal of Pharmacology, 2018, PMID: 29679507, PMC:PMC6003649
  101. Zhao S, Li CI, Guo Y, Sheng Q, Shyr Y, RnaSeqSampleSize: Real data based sample size estimation for RNA sequencing, BMC Bioinformatics, 2018, PMID: 29843589, PMC:PMC5975570
  102. Guo M, Yue W, Samuels DC, Yu H, He J, Zhao YY, Guo Y, Quality and concordance of genotyping array data of 12,064 samples, Genomics, 2018, PMID: 29902512, PMC:PMC6546549
  103. Greenplate A, Wang K, Tripathi R, Palma N, Ali S, Stephens P, Miller V, Shyr Y, Guo Y, Reddy N, Kozhaya L, Unutmaz D, Chen X, Irish J, Dave U, Genomic profiling of T cell neoplasms reveals frequent JAK1 and JAK3 mutations with clonal evasion from targeted therapies, npj Precision Oncology, 2018, PMID: 30079384, PMC:PMC6072266
  104. Guo Y, Yu H, Yue W, Samuels DC, Ness S, Zhao YY, Single-nucleotide variants in human RNA: RNA editing and beyond, Briefings in Functional Genomics, 2018, PMID: 30312373, PMC:PMC7962770
  105. Laroumanie F, Korneva A, Bersi MR, Alexander M, Xiao L, Zhong X, Beusecum J, Chen Y, Saleh MA, McMaster W, Gavulic KA, Dale B, Zhao S, Guo Y, Shyr Y, Perrien DS, Cox N, Curci J, Humphrey J, Madhur MS, LNK Deficiency Promotes Acute Aortic Dissection and Rupture, JCI Insight, 2018, PMID: 30333305, PMC:PMC6237478
  106. Albaugh VL, Banan B, Antoun J, Xiong Y, Guo Y, Ping J, Alikhan M, Clements, Abumrad NN, Flynn CR, Role of Bile Acids and GLP-1 in Mediating the Metabolic Improvements of Bariatric Surgery, Gastroenterology, 2018, PMID: 30445014, PMC:PMC6409186
  107. Bing F, Hoskings W, Zhang Y, Meng Z, Tang J†, Guo Y†, Bi-stream CNN Down Syndrome screening model based on genotyping array, BMC Medical Genomics, 2018, PMID: 30453947, PMC:PMC6245487
  108. Sheng Q, Samuels DC, Yu H, Yue W, Ness S, Zhao YY, Guo Y, Cancer-specific expression quantitative loci are affected by expression dysregulation, Briefings in Bioinformatics, 2018, PMID: 30475999, PMC:NA
  109. Samuels DC, Kallianpur AR, Guo Y, Barnholtz-Sloan JS, Gittleman H, Brown T, Ellis R, Letendre S, Hulgan T, Peripheral blood mtDNA content estimated from genome-wide genotype data is associated with neurocognitive impairment in persons with chronic HIV infection, Journal of Acquired Immune Deficiency Syndrome, 2018, PMID: 30531306, PMC:PMC6391216

    110. 2017
  110. Ma Y, Wang L, Neitzel L, Loganathan S, Tang N, Emily C, Guo Y, Knapp S, Beauchamp R, Lee E, Wang J, The MAPK Pathway Regulates Intrinsic Resistance to BET Inhibitors in Colorectal Cancer, Clinical Cancer Research, 2017, PMID: 27678457, PMC:NA
  111. Guo Y, Vickers K, Xiong Y, Zhao S, Sheng Q, Zhang P, Zhou W, Flynn CR, Comprehensive Evaluation of Extracellular Small RNA Isolation Methods from Serum in High Throughput Sequencing, BMC Genomics, 2017, PMID: 28061744, PMC:PMC5219650
  112. Oelsner KT, Guo Y, To SB, Non AL, Barkin S, Maternal BMI as a predictor of methylation of obesity-related genes in saliva samples from preschool-age Hispanic children at-risk for obesity, BMC Genomics, 2017, PMID: 28068899, PMC:PMC5223358
  113. Guo Y, Strickland SA, Li S, Mohan S, Bosompem A, Zhao S, Sheng Q, Kim AS, MicroRNAs and tRNA-derived fragments predict the transformation of myelodysplastic syndromes to acute myeloid leukemia, Leukemia and Lymphoma, 2017, PMID: 28084850, PMC:PMC5505168
  114. Peng D†, Guo Y†, Chen H, Zhao S, El-Rifai W, Integrated molecular analysis reveals complex interactions between genomic and epigenomic alterations in esophageal adenocarcinomas, Scientific Reports, 2017, PMID: 28102292, PMC:PMC5244375
  115. Guo Y, Dai Y, Yu H, Zhao S, Samuels DC, Shyr Y, Improvements and Impacts of GRCh38 Human Reference on High Throughput Sequencing Data Analysis, Genomics, 2017, PMID: 28131802, PMC:NA
  116. Panaccione A, Guo Y, Yarbrough W, Ivanov S, Expression Profiling Of Clinical Specimens Supports The Existence Of Neural Progenitor-Like Stem Cells In Basal Breast Cancers, Clinical Breast Cancer, 2017, PMID: 28216417, PMC:PMC5482752
  117. Zhang P, Lehmann BD, Shyr Y, Guo Y, The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies, International Journal of Genomics, 2017, PMID: 28246590, PMC:PMC5299160
  118. Su P, Mau YL, Guo Y, Li CI, Liu Q, Boice J, Shyr Y, Bivariate Poisson models with varying offsets: An application to the paired mitochondrial DNA dataset, Statistical Applications in Genetics and Molecular Biology, 2017, PMID: 28248637, PMC:NA
  119. Panaccione A, Zhang Yi, Mi Y, Mitani Y, Guo Y, Prasad M, McDonald H, El-Naggar AK, Yarbrough W, Ivanov S, Chromosomal Abnormalities and Molecular Landscape of Metastasizing Mucinous Salivary Adenocarcinoma, Oral Oncology, 2017, PMID: 28249646, PMC:PMC5335866
  120. Zhao S, Jing W, Samuels DC, Sheng Q, Shyr Y, Guo Y, Strategies for Processing and Quality Control of Illumina Genotyping Arrays, Briefings in Bioinformatics, 2017, PMID: 28334151, PMC:PMC6171493
  121. Jovanovic B, Sheng Q, Seitz RS, Lawrence KD, Morris SW, Thomas LR, Hout DR, Schweitzer BL, Guo Y, Pietenpol JA, Lehmann BD, Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue, BMC Cancer, 2017, PMID: 28376728, PMC:PMC5379658
  122. Wang J, Samuels DC, Shyr Y, Guo Y, StrandScript: evaluation of Illumina genotyping array design and strand correction, Bioinformatics, 2017, PMID: 28402386, PMC:NA
  123. Spurlock CF, Shaginurova G, Tossberg JT, Hester JD, Chapman N, Guo Y, Crooke PS, Profiles of long noncoding RNAs in human naïve and memory T cells, Journal of Immunology, 2017, PMID: 28600289, PMC:PMC5508595
  124. LI CI, Zhao Y, Samuels DC, Guo Y, Power and Sample Size Calculations for High Throughput Sequencing Based Experiments, Briefings in Bioinformatics, 2017, PMID: 28605403, PMC:PMC6291796
  125. Durbin MD, Cadar AG, Williams CH, Guo Y, Bichell DP, Su Y, Hong, CC, Hypoplastic Left Heart Syndrome Sequencing Reveals a Novel NOTCH1 Mutation in a Family with Single Ventricle Defects, Pediatric Cardiology, 2017, PMID: 28608148, PMC:PMC5577922
  126. Zhang P, Lehmann BD, Samuels DC, Zhao S, Zhao Y, Shyr Y, Guo Y, Estimating Relative Mitochondria Copy Number Using High Throughput Sequencing Data, Genomics, 2017, PMID: 28734953, PMC:NA
  127. Idrees K, Padmanabhan C, Liu E, Guo Y, Gonzalez RS, Dahlman K, Berlin J, Shi C, Frequent BRAF Mutations Suggest a Novel Oncogenic Driver in High-Grade Colonic Neuroendocrine Carcinoma, Journal of Surgical Oncology, 2017, PMID: 28940307, PMC:NA
  128. Zhao S, Samuels DC, Zhao Y, Guo Y, Tri-allelic Heteroplasmies[ DNA-RNA Differences and Their Polynucleotide Tract Associations in the Mitochondrial Genome, Genomics, 2017, PMID: 28970049, PMC:NA
  129. Guo Y, Zhao S, Sheng Q, Samuels DC, Shyr Y, The Discrepancy among Single Nucleotide Variants Detected by DNA and RNA High Throughput Sequencing Data, BMC Genomics, 2017, PMID: 28984205, PMC:PMC5629567
  130. Richmond BW, Guo Y, Yu C, Kendall PL, Mason WR, Cogan JD, Loyd JE, GWAS of 58 individuals with fibrosing mediastinitis reveals possible underlying genetic susceptibility, Am J Respir Crit Care Medicine, 2017, PMID: 29043856, PMC:PMC6019928
  131. Bing F, Lin Y, Zhao L, Guo Y, Friedman B, Xia R, Hu F, Liu C, Tang J, Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data, Scientific Reports, 2017, PMID: 29123238, PMC:PMC5680185
  132. Ma Y, Cheng Z, Liu J, Torre-Healy L, Lathia JD, Nkano I, Guo Y, Thompson RC, Freeman ML, Wang J, Inhibition of farnesyltransferase potentiates NOTCH-targeted therapy against glioblastoma stem cells, Stem Cell Reports, 2017, PMID: 29198824, PMC:PMC5785731
  133. Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y, Current research on noncoding Ribonucleic Acid (RNA), Genes, 2017, PMID: 29206165, PMC:PMC5748684
  134. Raskin L, Guo Y, Du L, Clendenning M, Rosty C, Colon Cancer Family Registry (CCFR), Lindor NM, Gruber SB, Buchanan DD, Targeted sequencing of established and candidate colorectal cancer genes in the Colon Cancer Family Registry Cohort, Oncotarget, 2017, PMID: 29212164, PMC:PMC5706810
  135. Absi TS, Galindo CL, Gumina RJ, Atkinson J, Guo Y, Thomasek K, Sawyer DB, Byrne JG, Kaiser CA, Shah AS, Su YR, Petracek M, Altered ADAMTS5 Expression and Versican Proteolysis: a possible molecular mechanism in Barlow’s Disease, The Annals of Thoracic Surgery, 2017, PMID: 29248417 , PMC:NA

    136. 2016
  136. McCann TS, Guo Y, McDonald H, Tansey W, Antagonistic roles for Asr1 and Ubp3 in subtelomeric gene silencing, Proceedings of the National Acadmey of Sciences, 2016, PMID: 26787877, PMC:PMC4747757
  137. Guo Y, Xiong Y, Sheng Q, Zhao S, Flynn C, A microRNA expression-signature for human NAFLD progression, Journal of Gastroenterology, 2016, PMID: 26874844, PMC:PMC4983265
  138. Zhang P, Samuels DC, Wang J, Zhao S, Shyr Y, Guo Y, Mitochondria Single Nucleotide Variation across Six Blood Cell Types, Mitochondrion, 2016, PMID: 26956645, PMC:PMC5755964
  139. Sheng Q, Zhao S, Li C, Shyr Y, Guo Y, Practicability of Detecting Somatic Point Mutation from RNA High Throughput Sequencing Data, Genomics, 2016, PMID: 27046520, PMC:PMC5663213
  140. Panaccione A, Chang MT, Carbone BE, Guo Y, Moskaluk CA, Virk RK, Chirboga L, Prasad ML, Judson B, Mehra S, Yarbrough WG, Ivanov SV, NOTCH1 and SOX10 are Essential for Proliferation and Radiation Resistance of Cancer Stem-like Cells in Adenoid Cystic Carcinoma, Clinical Cancer Research, 2016, PMID: 27084744, PMC:PMC4834904
  141. Strugill, E, Norris, S, Guo Y, Ohi R, Kinesin-5 inhibitor resistance is driven by kinesin-12, Journal of Cell Biology, 2016, PMID: 27091450, PMC:PMC5084272
  142. Rabacal W, Pabbisetty SK, Hoek K, Cendron D, Guo Y, Maseda D, Sebzda E, Transcription factor KLF2 regulates homeostatic NK cell proliferation and survival, Proceedings of the National Acadmey of Sciences, 2016, PMID: 27114551, PMC:PMC4868471
  143. Eilertson B, Maruri F, Balckman A, Guo Y, Herrera M, van der Heijden Y, Shyr Y, Sterling T, A Novel Resistance Mutation in eccC5 of the ESX-5 Secretion System Confers Ofloxacin Resistance in Mycobacterium Tuberculosis, Journal of Antimicrobial Chemotherapy, 2016, PMID: 27261264, PMC:PMC4992850
  144. Blum A, Venkitachalam S, Guo Y, Kieber-Emmons AM, Ravi L, Chandar AK, Iyer PG, Canto MI, Wang JS, Shaheen NJ, Barnholtz-Sloan JS, Markowitz SD, Willis JE, Shyr Y, Chak A, Varadan V, Guda K, RNA Sequencing Identifies Transcriptionally Viable Gene Fusions in Esophageal Adenocarcinomas, Cancer Research, 2016, PMID: 27503924, PMC:PMC5050127
  145. Guo Y, Zhang P, Sheng Q, Zhao S, Hackett TA, lncRNA expression in the auditory forebrain during postnatal development, Gene, 2016, PMID: 27544636, PMC:PMC5034298
  146. Guo Y, Andersen W, Shu XO, Michailidou K, Bolla MK, Wang Q, Carcia-Closas M, Milne RL, Schmidt MK, Chang-Claude J, Dunning A, Bojesen SE, Ahsan H, Aittomaki K, Andrulis IL, Anton-Culver H, Arndt V, Beckmann MW, Fadiel-Beeghly A, Benitez J, Bogdanova NV, Bonanni B, Børresen-Dale AL, Brand J, Brauch H, Brenner H, Brüning T, Burwinkel B, Casey G, Chenevix-Trench G, Couch FJ, Cox A, Cross SS, Czene K, Devilee P, Dörk T, Dumont M, Fasching PA, Figueroa J, Flesch-Janys, D, Fletcher O, Flyger H, Fostira F, Gammon M, Giles GG, Guénel P, Haiman CA, Hamann U, Hooning MJ, Hopper JL, Jakubowska A, Jasmine F, Jenkins M, John EM, Johnson N, Jones ME, kabisch M, Kibriya M, Knight JA, Koppert LB, Kosma VM, Kristensen V, Marchand LL, Lee E, Li J, Lindblom A, Luben R, Lubinski J, Malone KE, Mannermaa A, Margolin S, Marme F, McLean C, Meijers-Heijboer H, Meindl A, Neuhausen SL, Nevanlinna H, Neven P, Olson JE, Perez JIA, Perkins B, Peterlongo, P, Philips KA, Pylkäs K, Rudolph A, Santella R, Sawyer EJ, Schmutzler RK, Seynaeve C, Shah M, Shrubsole MJ, Southey MC, Swerdlow AJ, Toland AE, Tomlinson I, Torres D, Truong T, Ursin G, Van Der Luijt RB, Verhoef S, Whittemore AS, Winqvist R, Zhao H, Zhao S, Hall P, Simard J, Kraft P, Pharoah P, Hunter D, Easton DF, Zheng W, Body Mass Index Genetic Scores and Breast Cancer Risk: Mendelian Randomization Analyses of Data from 145[000 women of European Descent, PLOS Medicine, 2016, PMID: 27551723, PMC:PMC4995025
  147. Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capro JA, Shyr Y, Zheng W, Guo Y, Heterozygosity Ratio[ a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk, Genetics, 2016, PMID: 27585849, PMC:PMC5105867
  148. Zhang P, Samuels DC, Zhao S, Wang J, Shyr Y, Guo Y, Practicability of Mitochondrial Heteroplasmy Detection through an Illumina Genotyping Array, Mitochondrion, 2016, PMID: 27628068, PMC:NA
  149. Sheng Q, Vickers K, Zhao S, Wang J, Samuels DC, Koues O, Shyr Y, Guo Y, Multi-Perspective Quality Control of Illumina RNA Sequencing Data Analysis, Briefings in Functional Genomics, 2016, PMID: 27687708, PMC:PMC5860075
  150. Guo Y, Wu J, Zhao S, Ye F, Su Y, Clark T, Sheng Q, Lehmann B, Shu X, Cai Q, RNA sequencing of Formalin-Fixed[ Paraffin-Embedded Specimens for Gene Expression Quantification and Data Mining, International Journal of Genomics, 2016, PMID: 27774452, PMC:PMC5059559
  151. Herington J, Guo Y, Reese J, Paria B, Gene profiling the window of implantation: microarray analyses from human and rodent models, Journal of Reproductive Health and Medicine, 2016, PMID: 28239559, PMC:PMC5321051
  152. Loganathan, S, Tang N, Fleming J, Ma Y, Guo Y, Borinstein S, Chiang C, Wang J, BET bromodomain inhibitors suppress EWS-FLI1-dependent transcription and the IGF1 autocrine mechanism in Ewing sarcoma, Oncotarget, 2016, PMID: 27259270 , PMC:PMC5190040

    153. 2015
  153. Vickers KC, Roteta, LA, Dilks H, Han L, Guo Y, Mining diverse small RNA species in the deep transcriptome, Trends in Biochemical Sciences, 2015, PMID: 25435401, PMC:PMC4362530
  154. Spurlock CF, Tossberg, JT, Guo Y, Sriram S, Crooke SP, Aune TM, Expression and functions of long noncoding RNAs during human T helper cell differentiation, Nature Communications, 2015, PMID: 25621826, PMC:PMC4333215
  155. TCGA HNSCC work group, Comprehensive genomic characterization of head and neck squamous cell carcinomas, Nature, 2015, PMID: 25631445, PMC:PMC4311405
  156. Spurlock CF, Tossberg, JT, Guo, Y, Sriram S, Crooke PS, Aune TM, Defective structural RNA processing in relapsing-remitting multiple sclerosis, Genome Biology, 2015, PMID: 25885816, PMC:PMC4403723
  157. Carroll C, Hunley T, Guo Y, Cortez D, A Novel Splice Site Mutation in SMARCAL1 Results in Aberrant Exon Definition in a Child with Schimke Immunoosseous Dysplasia, American Journal of Medical Genetics, 2015, PMID: 25943327, PMC:PMC4743909
  158. Goodings C, Smith E, Mathia E, Elliott, N, Cleveland S, Tripathi R, Layer J, Chen X, Guo Y, Shyr Yu, Hamid R, Du Y, Dave U, Hhex is required at multiple stages of adult hematopoietic stem and progenitor cell differentiation, Stem Cells, 2015, PMID: 25968920, PMC:PMC4641572
  159. Di Salvo TG, Guo Y, Su YR, Clark T, Brittain E, Absi T, Maltais S, Hemnes A, Right ventricular long noncoding RNA expression in human heart failure, Pulmonary Circulation, 2015, PMID: 25992278, PMC:PMC4405709
  160. Kavanaugh G, Zhao R, Guo Y, Mohni KN, Glick G, Lacy ME, Hutson MS, Ascano M, Cortez D, Enhancer of Rudimentary Homolog affects the replication stress response through regulation of RNA processing, Molecular and Cellular Biology, 2015, PMID: 26100022, PMC:PMC4525316
  161. Flynn CR, Albaugh VL, Cai S, Cheung-Flynn J, Williams PE, Brucker RM, Bordenstein SR, Guo Y, Wasserman DH, Abumrad NN, Bile Diversion to the Distal Small Intestine has comparable metabolic benefits to bariatric surgery, Nature Communications, 2015, PMID: 26197299, PMC:PMC4518285
  162. Zhang P, Samuels DC, Lehmann B, Stricker T, Pietenpol J, Shyr Y, Guo Y, Mitochondria Sequence Mapping Strategies and Practicability of Mitochondria Variant Detection from Exome and RNA sequencing Data, Briefings in Bioinformatics, 2015, PMID: 26249222, PMC:PMC5974936
  163. Hackett TA, Guo Y, Clause A, Hackett NJ, Garbett K, Zhang P, Poley Daniel, Mirnics K, Transcriptional maturation of the mouse auditory forebrain, BMC Genomics, 2015, PMID: 26271746, PMC:PMC4536593
  164. Pickup M, Hover L, Guo Y, Gorska A, Chytil A, Novitskiy S, Moses H, Owens P, Deletion of the BMP receptor BMPR1a impairs mammary tumor formation and metastasis, Oncotarget, 2015, PMID: 26274893, PMC:PMC4673207
  165. Guo Y, Bosompem A, Sheng Q, Mohan S, Erdogan B, Ye F, Vickers KC, Sheng Q, Zhao S, Li CI, Su PF, Jagasia M, Strickland SA, Griffith E, Kim A, Transfer RNA Detection by Small RNA Deep Sequencing and Disease Association with Myelodysplastic Syndromes, BMC Genomics, 2015, PMID: 26400237, PMC:PMC4581457
  166. Guo Y, Zhao S, Sheng Q, Guo M, Stricker T, Lehmann B, Pietenpol J, Samuels DC, Shyr Yu, RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA library, BioMed Research International, 2015, PMID: 26543871, PMC:PMC4620295
  167. Hoek K, Samir P, Niu X, Howard LM, Prasad N, Galassie A, Liu Q, Allos TM, Guo Y, Shyr Y, Levy SE, Joyce S, Edwards KM, Link AJ, A Cell-based Systems Biology Assessment of Human Blood to Monitor Immune Responses Following Influenza Vaccination, PLOS ONE, 2015, PMID: 26706537, PMC:PMC4691531

    168. 2014
  168. Ye F, Samuels DC, Guo Y, Detection of Mitochondrial Mutations in Cancer by Next Generation Sequencing, Next Generation Sequencing & Applications, 2014, PMID: NA, PMC:NA
  169. Guo Y, Li C, Cai Q, Shyr Y, Very Low level Heteroplasmy mtDNA Variations Are Inherited in Humans, Journal of Genetics and Genomics, 2014, PMID: 24377867, PMC:PMC4149221
  170. Weeke P, Mosley JD, Hanna D, Shaffer C, Delaney JT, Wells QS, Van Driest S, Karnes JH, Ingram C, Guo Y, Shyr Y, Norris K, Kannankeril P, Ramirez AH, Smith J, Mardis ER, Nickerson D, George AL Jr, Roden DM, Exome Sequencing Implicates an Increased Burden of Rare Potassium Channel Variants in the Risk of Drug-Induced Long QT Interval Syndrome, Journal of the American College of Cardiology, 2014, PMID: 24561134, PMC:PMC4018823
  171. Cleveland SM, Goodings C, Tripathi RM, Elliott N, Thompson MA, Guo Y, Shyr Y, Dave U, LMO2 induces T-cell leukemia with epigenetic deregulation of CD4, Experimental Hematology, 2014, PMID: 24792354, PMC:PMC4241760
  172. Zhang B, Jia WH, Matsuda K, Kweon SS, Matsuo K, Xiang YB, Shin A, Jee SH, Kim DH, Cai Q, Long J, Shi J, Wen W, Yang G, Zhang Y, Li C, Li B, Guo Y, Ren Z, Ji BT, Pan ZZ, Takahashi A, Shin MH, Matsuda F, Gao YT, Oh JH, Kim S, Ahn YO, Chan A, Chang-Claude J, Slattery M, Gruber S, Schumacher F, Stenzel S, Casey G, Kim HR, Jeong JY, Park JW, Li HL, Hosono S, Cho SH, Kubo M, Shu XO, Zeng YX, Zheng W, Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk, Nature Genetics, 2014, PMID: 24836286, PMC:PMC3679924
  173. Ye F, Samuels, DC, Clark T, Guo, Y, High-Throughput Sequencing in Mitochondrial DNA Research Mitochondrion, Mitochondrion, 2014, PMID: 24859348, PMC:PMC4149223
  174. Guo Y, Bosompem A, Zhong, X, Clark T, Shyr Y, Kim A, A comparison of MicroRNA Sequencing Reproducibility and Noise Reduction Using mirVana and TRIzol Isolation Methods, International Journal of Computational Biology and Drug Design, 2014, PMID: 24878723, PMC:PMC5798231
  175. Guo Y, Miyagi M, Zeng R, Sheng Q, O18Quant: A Semi-automatic Strategy for Quantitative Analysis of High-Resolution 16O/18O Labeled Data, BioMed Research International, 2014, PMID: 24901003, PMC:PMC4037588
  176. Guo Y, Zhao S, Sheng Q, Shyr Y, MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality Control, BioMed Research International, 2014, PMID: 24977143, PMC:PMC4058234
  177. Zhao S†, Guo Y†, Sheng Q, Shyr , Advanced Heat Map and Clustering Analysis Using Heatmap3, BioMed Research International, 2014, PMID: 25143956, PMC:PMC4124803
  178. Han L, Vickers KC, Samuels DC, Guo Y, Alternative Applications for Distinct RNA Sequencing Strategies, Briefings in Bioinformatics, 2014, PMID: 25246237, PMC:PMC4542857
  179. Guo Y, Su P, Li C, Zhao S, Ye F, Flynn CR, Shyr Yu, Statistical Strategies for microRNAseq Batch Effect Reduction, Translational Cancer Research, 2014, PMID: 25258704, PMC:PMC4171948
  180. Wang J, Raskin L, Samuels DC, Shyr Y, Guo Y, Genome Measures used for Quality Control are Dependent on Gene Function and Ancestry, Bioinformatics, 2014, PMID: 25297068, PMC:PMC4308666
  181. Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar, Meyerson M, Park PJ, Chin Lynda, Seidman JG, Hammerman PS, Kucherlapati R, the Cancer Genome Atlas Network, Characterization of HPV and host genome interactions in primary head and neck cancers, Proceedings of the National Acadmey of Sciences, 2014, PMID: 25313082, PMC:PMC4217452
  182. Guo Y, Zhao S, Lehmann B, Pietenpol J, Shyr Yu, Detection of internal exon deletion with exon Del, BMC Bioinformatics, 2014, PMID: 25322818, PMC:PMC4288651
  183. Guo Y, Zhao S, Li C, Sheng Q, Shyr Y, RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq experiment, Cancer Informatics, 2014, PMID: 25374457, PMC:PMC4213196
  184. Sheng Q, Li R, Dai J, Li Q, Su Z, Guo Y, Li C, Shyr Y, Zeng R, Removing isobaric-related ions significantly improves the peptide/protein identification sensitivity of high resolution tandem mass spectrometry data, Molecular & Cellular Proteomics, 2014, PMID: 25435543, PMC:PMC4350035
  185. Goodings C, Tripathi R, Cleveland SM, Elliott N, Guo Y, Shyr Y, Dave U, Enforced expression of E47 has differential effects on Lmo2-induced T-cell leukemias, Leukemia Research, 2014, PMID: 25499232, PMC:PMC4277943
  186. Saraswati S, Guo Y, Atkinson J, Young P, Prolonged hypoxia induces MCT4 expression in MSCs resulting in a secretome that is deleterious to cardiovascular repair, Stem Cells, 2014, PMID: 25537659, PMC:PMC4376598
  187. Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann, B, Pietenpol J, Samuels DC, Shyr Yu, Multi-Perspective Quality Control of Illumina Exome Sequencing Data Using QC3, Genomics, 2014, PMID: 24703969 , PMC:PMC5755963
  188. Guo Y, Jing, H, Zhao S, Wu H, Sheng Q, Zhong X, Samuels DC, Shyr Y, Long J, Illumina human exome genotyping array clustering and quality control, Nature Protocols, 2014, PMID: 25321409 , PMC:PMC4441213

    189. 2013
  189. Ivanov SV, Panaccione A, Brown B, Guo Y, Moskaluk CA, Wick MJ, Brown JL, Ivanova AV, Issaeva N, El-Naggar AK, Yarbrough WG, TrkC signaling is activated in adenoid cystic carcinoma and requires NT-3 to stimulate invasive behavior, Oncogene, 2013, PMID: 23027130, PMC:NA
  190. Guo Y, Li J, Li CI, Shyr Y, Samuels DC, MitoSeek: extracting mitochondria information and performing high throughput mitochondria sequencing analysis, Bioinformatics, 2013, PMID: 23471301, PMC:PMC4492415
  191. Guo Y, Li J, Li CI, Shyr Y, Evaluation of allele frequency estimation using pooled sequencing data simulation, The Scientific World Journal, 2013, PMID: 23476151, PMC:PMC3582166
  192. Ivanov S, Panaccione A, Nonaka D, Prasad M, Boyd K, Brown B, Guo Y, Sewell A, Yarbrough W, Diagnostic SOX10 Gene Signatures in Salivary Adenoid Cystic and Breast Basal-like Carcinomas, British Journal of Cancer, 2013, PMID: 23799842, PMC:PMC3721393
  193. Lu X, An H, Jin R, Zou M, Guo Y, Su P-F, Liu D, Shyr Y, Yarbrough WG, PPM1A is a RelA phosphatase with tumor suppressor-like activity, OncoGene, 2013, PMID: 23812431, PMC:PMC3897569
  194. Samuels D, Han L, Li J, Sheng Q, Clark T, Yu Shyr, Guo Y, Finding the Lost Treasures in exome sequencing data, Trends in Genetics, 2013, PMID: 23972387, PMC:PMC3926691
  195. Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y, Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data, PLOS ONE, 2013, PMID: 23977046, PMC:PMC3748065
  196. Guo Y, Sheng Q, Ye F, Clark T, Samuels DC, Three-Stage Quality Control Strategies for DNA Sequencing Data, Briefings in Bioinformatics, 2013, PMID: 24067931, PMC:PMC4492405
  197. Guo Y, Cai Q, Li C, Li J, Courtney R, Li CI, Zheng W, Long J, An evaluation of allele frequency estimation accuracy using pooled sequencing data, International Journal of Computational Biology and Drug Design, 2013, PMID: 24088264, PMC:PMC4108916
  198. Li CI, Su P, Guo, Y, Shyr Y, Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution, International Journal of Computational Biology and Drug Design, 2013, PMID: 24088268, PMC:PMC3874726
  199. Yan L, Womack B, Wotton D, Guo Y, Shyr Y, Dave U, Li C, Hiebert S, Brandt S, and Hamid R, Tgif1 regulates the quiescence and self-renewal of hematopoietic stem cells, Molecular and Cellular Biology, 2013, PMID: 24100014, PMC:PMC3889555
  200. Guo Y, Sheng Q, Li J, Lehmann B, Bauer J, Pietenpol J, Shyr Y, Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control, BioMed Research International, 2013, PMID: 24303503, PMC:PMC3835197
  201. Mosley JD, Van Driest SL, Larkin EK, Weeke PE, Witte JS, Wells QS, Karnes JH, Guo Y, Bastarache L, Olson LM, McCarty CA, Pacheco JA, Jarvik GP, Larson EB, Crosslin DR, Kullo IJ, Tromp G, Kuivaniemi H, Carey DJ, Ritchie MD, Denny JC, Roden DM, Mechanistic Phenotypes: An Aggregative Phenotyping Strategy to Identify Disease Mechanisms Using GWAS Data, PLOS ONE, 2013, PMID: 24349080, PMC:PMC3861317
  202. Guo Y, Li C, Ye F, Shyr Y, Evaluation of Read Count Based RNAseq Analysis Methods, BMC Genomics, 2013, PMID: 24564449, PMC:PMC4092879

    203. 2012
  203. Guo Y, Cai Q, Samuels DC, Ye F, Long J, Li CI, Winther JF, Tawn EJ, Stovall M, Lähteenmäki P, Malila N,Levy S, Shaffer C, Shyr Y, Shu XO, Boice JD Jr., The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation, Mutation Research-Genetic Toxicology and Environmental Mutagenesis, 2012, PMID: 22387842, PMC:PMC3354959
  204. Powell AE, Wang Y, Li Y, Poulin EJ, Means AL, Washington MK, Higginbotham JN, Juchheim A, Prasad N,Levy SE, Guo Y, Shyr Y, Aronow BJ, Haigis KM, Franklin JL, Coffey RJ, The pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor, Cell, 2012, PMID: 22464327, PMC:PMC3563328
  205. Guo Y, Long J, Cai Q, He J, Zheng W, Li C, Exome sequencing generates high quality data in non-target regions, BMC Genomics, 2012, PMID: 22607156, PMC:PMC3416685
  206. Zhuang G, Song W, Amato K, Hwang Y, Lee K, Boothby M, Ye F, Guo Y, Shyr Y, Lin L, Carbone D, Brantley-Sieders D, Chen J, Effects of Cancer-Associated EPHA3 Mutations on Lung Cancer, Journal of the National Cancer Institute, 2012, PMID: 22829656, PMC:PMC3611812
  207. Savani M, Guo Y, Carbone DP, Csiki , Sonic hedgehog pathway expression in non-small cell lung cancer, Therapeutic Advances in Medical Oncology, 2012, PMID: 22942905, PMC:PMC3424496
  208. Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y, The effect of strand bias in Illumina short-read sequencing data, BMC Genomics, 2012, PMID: 23176052, PMC:PMC3532123
  209. Liu Q†, Guo Y†, Jiang L, Long J, Zhang B, Shyr Y, Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data, BMC Genomics, 2012, PMID: 23281772, PMC:PMC3535703

    210. 2007-2011
  210. Hatakeyama H, Cheng H, Wirth P, Counsell A, Marcrom S, Wood C, Pohlmann P, Gilbert J, Murphy B, Yarbrough W, Wheeler D, Harari P, Guo Y, Shyr Y, Slebos R, Chung CH, Regulation of heparin-binding EGF-like growth factor by miR-212 and acquired cetuximab-resistance in head and neck squamous cell carcinoma, PLOS ONE, 2010, PMID: 20856931, PMC:PMC2938338
  211. Yu DS, Zhao R, Hsu EL, Cayer J, Ye F, Guo Y, Shyr Y, Cortez D, Cyclin-dependent kinase 9-cyclin K functions in the replication stress response, EMBO Reports, 2010, PMID: 20930849, PMC:PMC2966956
  212. Guo Y, Ye F, Tang J, Phylogenetic reconstruction with disk-covering and Bayesian approaches, 8th IEEE International Conference on Bioinformatics and BioEngineering, 2008, PMID: NA, PMC:NA
  213. Ye F, Guo Y, Lawson A, and Tang J, Improving tree search in phylogenetic reconstruction from genome rearrangement data, International Workshop on Experimental and Efficient Algorithms, 2007, PMID: NA, PMC:NA

Book Chapters

  1. Guo Y, Ye F, Bjoring M, AACR 2014 Education Book, chapter name: Lost Treasures in Sequence Data, 2014 AACR.
  2. Guo Y, Zhao S, Bjoring M, Han L, Big Data Analytics in Bioinformatics and Healthcare, Chapter Name: Data Mining of High Throughput Sequencing, IGI-Global. 2014

Editorials

  1. Han L, Zheng S, Lu ZX, Su, Z, Guo Y, Advances in Computational Genomics, Biomed Research International, 2014
  2. Guo Y, Sheng Q, Advances in Computational Biology and Genomics, International Journal of Computational Biology and Drug Design, 2015 
  3. Guo Y, Leng H, Sheng Q, Recent Advances in High Throughput Sequencing Analysis, International Journal of Genomics, 2017
  4. Zhao Z, Liu Z, Chen K, Guo Y, Allen GI, Zhang J, Zheng W, Ruan J, The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics, BMC Genomics, 2017
  5. Wang K, Liu X, Guo Y, Wu Z, Zhi D, Ruan J, Zhao Z, The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: system biology on diverse data types, BMC System Biology, 2018
  6. Wu Z, Yan J, Wang K, Liu X, Guo Y, Yue F, Zhi D, Ruan J, Li J, Zhao Z, The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: Genomics with bigger data and wider applications, BMC Genomics, 2018
  7. Mathé E, Zhang C, Wang K, Ning X, Guo Y, Zhao Z. The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics. BMC Genomics. 2020
  8. Zhang C, Mathé E, Ning X, Zhao Z, Wang K, Li L, Guo Y, The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): computational methods and applications in medical genomics, BMC Medical Genomics, 2020
  9. Guo Y, Ning X, Mathé E, Wang K, Li L, Zhang C, Zhao Z, Innovating Computational Biology and Intelligent Medicine: ICIBM 2019 Special Issue, Genes, 2020
  10. Guo Y, Shen L, Shi X, Wang K, Dai Y, Zhao Z, Accelerating bioinformatics research with International Conference on Intelligent Biology and Medicine, BMC Bioinformatics, 2020
  11. Chen DQ, Guo Y, Guo ZY, Tang YP, New insights into renal fibrosis and therapeutic effects of natural products volume II, Frontiers in Pharmacology, 2022
  12. Chen DQ, Guo Y, Li P, New insights into the novel metabolic biomarker and therapeutic target of chronic kidney disease, Integrative Medicine in Nephrology and Andrology, 2024