Publications
Peer Reviewed (148)
    2020
  1. Samuels DC, Below JE, Ness S, Hui Y, Leng S, Guo Y, Alternative Applications of Genotyping Array Data Using Multi-Variant Methods, Trends in Genetics, 2020
  2. 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 Acid Research Cancer, 2020
  3. 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
  4. 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
  5. Sheng Q, Yu H, Oyebamiji O, Wang J, Chen D, Ness S, Zhao YY, Guo Y, AnnoGen: Annotating Genomewide Pragmatic Features, Bioinformatics, 2020
  6. Long JL, Lee LP, Small EM, Hillyer C, Guo Y, Osley M, Regulation of UV damage repair in quiescent yeast cells, DNA Repair, 2020
  7. 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
  8. 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
  9. 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 
  10. 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

  11. 2019
  12. 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, PMC6443780
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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 
  18. 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, PMCID: PMC6435843
  19. Yu H, Samuels DC, Zhao YY, Guo Y, Architectures and accuracy of artificial neural network for disease classification from omics data, BMC Genomics, 2019, PMCID:6399893
  20. 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, IWBBIO 2019
  21. Guo Y, Hui Y, Chen DQ, Zhao YY, Machine Learning Distilled Metabolite Biomarkers for Early Stage Renal Injury, Metabolomics, 2019
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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, 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 
  28. 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
  29. 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 & Molecular Medicine, 2019
  30. 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
  31. 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
  32. Microbiome-metabolome reveals the contribution of gut-kidney axis on kidney disease, Chen YY, Chen D, Chen L, Liu J, Vaziri ND, Guo Y, Zhao YY, Journal of Translational Medicine, 2019
  33. 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
  34. 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

  35. 2018
  36. 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
  37. 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
  38. 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
  39. 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, PMCID: PMC6546549
  40. 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
  41. 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
  42. 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
  43. Zhao S, Li CI, Guo Y, Sheng Q, Shyr Y, RnaSeqSampleSize: Real data based sample size estimation for RNA sequencing, BMC Bioinformatics, 2018
  44. Wang M, Chen DD, 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
  45. Chen L, Su W, Che H, Chen DD, Wang M, Guo Y, Zhao YY, Proteomics for Biomarker Identification and Clinical Application in Kidney Disease, Advances in Clinical Chemistry, 2018, PMID: 29655463
  46. 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
  47. Wang M, Chen DD, 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
  48. 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, Journal of Precision Oncology 2018, PMID: 30079384

  49. 2017
  50. Estimating Relative Mitochondria Copy Number Using High Throughput Sequencing Data, Zhang P, Lehmann BD, Samuels DC, Zhao S, Zhao Y, Shyr Y, Guo Y, Genomics 2017, PMID: 28734953
  51. Wang J, Samuels DC, Shyr Y, Guo Y, StrandScript: evaluation of Illumina genotyping array design and strand correction, Bioinformatics, 2017, PMID: 28402386
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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 Genomic, 2017, PMID: 28061744
  58. 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
  59. Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y, Current research on noncoding Ribonucleic Acid (RNA), Genes, 2017, PMID: 29206165
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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, PMID: 28216417
  66. 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 Report, 2017, PMID: 29123238
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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 
  72. 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
  73. 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
  74. 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
  75. 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

  76. 2016
  77. Guo Y, Andersen W, Shu XO, Michailidou K, Bolla MK, Wang Q, Garcia-Closas M, Milne RL, Schmidt MK, Chang-Claude J, Dunning A, Bojesen SE,Ahsan H, Aittomäki K, Andrulis IL, Anton-Culver H, Arndt V, Beckmann MW, Beeghly-Fadiel 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, Le Marchand L, 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 JI, Perkins B, Peterlongo P, Phillips 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
  78. 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
  79. Guo Y, Zhang P, Sheng Q, Zhao S, Hackett TA, lncRNA expression in the auditory forebrain during postnatal development, Gene, 2016, PMID: 27544636
  80. Guo Y, Xiong Y, Sheng Q, Zhao S, Flynn CR, A microRNA expression-signature for human NAFLD progression, Journal of Gastroenterology, 2016, PMID: 26874844
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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
  86. 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
  87. 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 
  88. 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
  89. Rabacal W, Pabbisetty SK, Hoek K, Cendron D, Guo Y, Maseda D, Sebzda E, Transcription factor KLF2 regulates homeostatic NK cell proliferation and survival, PNAS, 2016, PMID: 27114551
  90. Strugill, E, Norris, S, Guo Y, Ohi R, Kinesin-5 inhibitor resistance is driven by kinesin-12, Journal of Cell Biology, 2016, PMID: 27091450
  91. 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
  92. McCann TS, Guo Y, McDonald H, Tansey W, Antagonistic roles for Asr1 and Ubp3 in subtelomeric gene silencing, PNAS, 2016, PMID: 26787877

  93. 2015
  94. 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
  95. 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
  96. 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
  97. 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
  98. 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, PMCID: PMC4518285
  99. 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
  100. 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 Cell Biology, 2015, PMID: 26100022
  101. 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
  102. 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, PMCID: PMC4333215
  103. 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, PMC4403723
  104. TCGA HNSCC work group, Comprehensive genomic characterization of head and neck squamous cell carcinomas, Nature, 2015, PMID: 25631445
  105. 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, UP, Hhex is required at multiple stages of adult hematopoietic stem and progenitor cell differentiation, Stem Cells, 2015, PMID: 25968920
  106. 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
  107. 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

  108. 2014
  109. Han L, Vickers KC, Samuels DC, Guo Y, Alternative Applications for Distinct RNA Sequencing Strategies, Briefings in Bioinformatics, 2014, PMID:25246237
  110. 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 
  111. F, Samuels, DC, Clark T, Guo, Y, High-Throughput Sequencing in Mitochondrial DNA Research Mitochondrion. Mitochondrion, 2014, PMID: 24859348
  112. 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
  113. 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
  114. 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 
  115. Guo Y, Zhao S, Lehmann B, Pietenpol J, Shyr Yu, Detection of internal exon deletion with exon Del, BMC Bioinformatics, 2014, PMID: 25322818
  116. 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, Int J Comput Biol Drug Des. 2014. PMID: 24878723
  117. 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
  118. Guo Y, Zhao S, Sheng Q, Shyr Y. MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality Control, Biomedical Research International, 2014, PMID: 24977143
  119. 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
  120. 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
  121. Ye F, Samuels DC, Guo Y, Detection of Mitochondrial Mutations in Cancer by Next Generation Sequencing, Next Generation Sequencing & Applications, 2014 
  122. 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
  123. Zhao S, Guo Y, Sheng Q, Shyr Y, Advanced Heat Map and Clustering Analysis Using Heatmap3, Biomed Research International, 2014, PMID: 25143956
  124. 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
  125. 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, PMCID: PMC3679924
  126. 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. Proc Natl Acad Sci U S A 2014, 111(43):15544-15549. PMID: 25313082, PMCID: PMC4217452
  127. 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, JNCI,2012 Aug 8;104(15):1182-97. PMID: 22829656, PMCID: PMC3611812
  128. 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 Mar 30;149(1):146-58. PMID: 22464327, PMCID: PMC3563328
  129. 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
  130. Goodings C, Tripathi R, Cleveland SM, Elliott N, Guo Y, Shyr Y, Dave, UP, Enforced expression of E47 has differential effects on Lmo2-induced T-cell leukemias, Leukemia Research, 2014, PMID: 25499232
  131. 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
  132. 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
  133. Cleveland SM, Goodings C, Tripathi RM, Elliott N, Thompson MA, Guo Y, Shyr Y, Dave, UP, LMO2 induces T-cell leukemia with epigenetic deregulation of CD4, Experimental Hematology, 2014, PMID: 24792354

  134. 2013
  135. 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
  136. 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, Biomedical Research International 2013, PMID: 24303503, PMCID: PMC3835197
  137. 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, PMCID PMC4108916
  138. Guo Y, Li C, Ye F, Shyr Y, Evaluation of Read Count Based RNAseq Analysis Methods, BMC Genomics. 2013, PMID: 24564449
  139. Guo Y, Sheng Q, Ye F, Clark T, Samuels DC, Three-Stage Quality Control Strategies for DNA Sequencing Data, Briefing in Bioinformatics, 2013, PMID: 24067931
  140. Guo Y, Li J, Li CI, Shyr Y, Evaluation of allele frequency estimation using pooled sequencing data simulation, ScientificWorldJournal 2013, 2013:895496. PMID: 23476151, PMCID: PMC3582166
  141. 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, PMCID: PMC3861317
  142. 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 Aug 8;32(32):3698-710.  PMID: 23027130
  143. Li CI, Su P, Guo, Y, Shyr Y, Sample size calculation for differential expression analysis of RNA-seq data under Poisson distribution, Int J Comput Biol Drug Des, 2013 6(4), 358-375, PMID: 24088268, PMCID: PMC3874726
  144. 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 Jul 1. PMID: 23812431, PMCID: PMC3897569
  145. 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, Mol Cell Biol, 2013 Dec;33(24):4824-33. PMID: 24100014, PMCID: PMC3889555
  146. 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, Br J Cancer, 2013 Jul 23; 109(2): 444–451. PMID: 23799842, PMCID: PMC3721393

  147. 2012
  148. 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, PMCID: PMC3535703
  149. 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
  150. 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 May 20;13:194. PMID: 22607156
  151. 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, 2012 May 15;744(2):154-60. PMID: 22387842
  152. Savani M, Guo Y, Carbone DP, Csiki I, Sonic hedgehog pathway expression in non-small cell lung cancer, Ther Adv Med Oncol, 2012 Sep; 4(5): 225-33. PMID: 22942905, PMCID: PMC3424496 

  153. 2008-2011
  154. 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 Rep, 2010 Nov;11(11):876-82. PMID: 20930849, PMCID: PMC2966956
  155. 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 Sep 13;5(9):e12702. PMID: 20856931, PMCID: PMC2938338
  156. Guo Y, Ye F, Tang J, Phylogenetic reconstruction with disk-covering and Bayesian approaches, BioInformatics and BioEngineering, BIBE
  157. Ye F, Guo Y, Lawson A, and Tang J, Improving tree search in phylogenetic reconstruction from genome rearrangement data. JEA 4525/2007:352-364, 2007

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