Publications

Major Publications ( equal contribution)

  1. Sheng Q, Hui Y, 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
  2. 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
  3. 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 
  4. 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
  5. Guo Y, Andersen W, Shu XO, Michailidou K, Bolla MK, Wang Q, et al. 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
  6. 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
  7. McCann TS, Guo Y, McDonald H, Tansey W, Antagonistic roles for Asr1 and Ubp3 in subtelomeric gene silencing, PNAS, 2016, PMID: 26787877
  8. 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
  9. 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
  10. 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
  11. TCGA HNSCC work group, Comprehensive genomic characterization of head and neck squamous cell carcinomas, Nature, 2015, PMID: 25631445
  12. 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
  13. 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
  14. 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
  15. 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 
  16. 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
  17. 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

Complete list of Peer Reviewed Publications ( equal contribution)

    2021
  1. Sheng Q, Hui Y, 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
  2. 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
  3. 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
  4. 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
  5. Yu H, Wang L, Chen D, Li J, Guo Y, Conditional transcriptional relationships may serve as cancer prognostic markers, BMC Medical Genomics, 2021
  6. Wu YM, Guo Y, Hui Y, Guo T, RNA editing affects cis-regulatory elements and predicts adverse cancer survival, Cancer Medicine, 2021
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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

  14. 2020
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. Sheng Q, Yu H, Oyebamiji O, Wang J, Chen D, Ness S, Zhao YY, Guo Y, AnnoGen: Annotating Genomewide Pragmatic Features, Bioinformatics, 2020
  21. Zhang D, Guo Y, Xie N, Prognostic Value and Co-expression Patterns of Metabolic Pathways in Cancers, BMC Genomics, 2020
  22. Long JL, Lee LP, Small EM, Hillyer C, Guo Y, Osley M, Regulation of UV damage repair in quiescent yeast cells, DNA Repair, 2020
  23. 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
  24. 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
  25. 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 
  26. 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
  27. 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
  28. 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
  29. 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

  30. 2019
  31. 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
  32. 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
  33. 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 
  34. 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
  35. 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
  36. 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
  37. Guo Y, Hui Y, Chen DQ, Zhao YY, Machine Learning Distilled Metabolite Biomarkers for Early Stage Renal Injury, Metabolomics, 2019
  38. 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
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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 
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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

  51. 2018
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. Zhao S, Li CI, Guo Y, Sheng Q, Shyr Y, RnaSeqSampleSize: Real data based sample size estimation for RNA sequencing, BMC Bioinformatics, 2018
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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

  66. 2017
  67. 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
  68. Wang J, Samuels DC, Shyr Y, Guo Y, StrandScript: evaluation of Illumina genotyping array design and strand correction, Bioinformatics, 2017, PMID: 28402386
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y, Current research on noncoding Ribonucleic Acid (RNA), Genes, 2017, PMID: 29206165
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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
  86. 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
  87. 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
  88. 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 
  89. 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
  90. 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
  91. 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
  92. 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

  93. 2016
  94. Guo Y, Andersen W, Shu XO, Michailidou K, Bolla MK, Wang Q, et al. 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
  95. 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
  96. Guo Y, Zhang P, Sheng Q, Zhao S, Hackett TA, lncRNA expression in the auditory forebrain during postnatal development, Gene, 2016, PMID: 27544636
  97. Guo Y, Xiong Y, Sheng Q, Zhao S, Flynn CR, A microRNA expression-signature for human NAFLD progression, Journal of Gastroenterology, 2016, PMID: 26874844
  98. 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
  99. 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
  100. 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
  101. 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
  102. 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
  103. 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
  104. 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 
  105. 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
  106. 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
  107. Strugill, E, Norris, S, Guo Y, Ohi R, Kinesin-5 inhibitor resistance is driven by kinesin-12, Journal of Cell Biology, 2016, PMID: 27091450
  108. 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
  109. McCann TS, Guo Y, McDonald H, Tansey W, Antagonistic roles for Asr1 and Ubp3 in subtelomeric gene silencing, PNAS, 2016, PMID: 26787877

  110. 2015
  111. 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
  112. 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
  113. 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
  114. 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
  115. 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
  116. 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
  117. 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
  118. 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
  119. 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
  120. 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
  121. TCGA HNSCC work group, Comprehensive genomic characterization of head and neck squamous cell carcinomas, Nature, 2015, PMID: 25631445
  122. 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
  123. 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
  124. 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

  125. 2014
  126. Han L, Vickers KC, Samuels DC, Guo Y, Alternative Applications for Distinct RNA Sequencing Strategies, Briefings in Bioinformatics, 2014, PMID:25246237
  127. 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 
  128. 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
  129. Ye F, Samuels, DC, Clark T, Guo, Y, High-Throughput Sequencing in Mitochondrial DNA Research Mitochondrion. Mitochondrion, 2014, PMID: 24859348
  130. 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
  131. 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
  132. 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 
  133. Guo Y, Zhao S, Lehmann B, Pietenpol J, Shyr Yu, Detection of internal exon deletion with exon Del, BMC Bioinformatics, 2014, PMID: 25322818
  134. 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
  135. 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
  136. 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
  137. 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
  138. 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
  139. Ye F, Samuels DC, Guo Y, Detection of Mitochondrial Mutations in Cancer by Next Generation Sequencing, Next Generation Sequencing & Applications, 2014 
  140. 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
  141. Zhao S, Guo Y, Sheng Q, Shyr Y, Advanced Heat Map and Clustering Analysis Using Heatmap3, Biomed Research International, 2014, PMID: 25143956
  142. 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
  143. 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
  144. 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
  145. 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
  146. 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
  147. 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
  148. 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
  149. 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
  150. 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
  151. 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

  152. 2013
  153. 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
  154. 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
  155. 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
  156. 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
  157. Guo Y, Li C, Ye F, Shyr Y, Evaluation of Read Count Based RNAseq Analysis Methods, BMC Genomics. 2013, PMID: 24564449
  158. 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
  159. 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
  160. 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
  161. 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
  162. 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
  163. 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
  164. 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
  165. 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

  166. 2012
  167. 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
  168. 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
  169. 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
  170. 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
  171. 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 

  172. 2008-2011
  173. 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
  174. 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
  175. Guo Y, Ye F, Tang J, Phylogenetic reconstruction with disk-covering and Bayesian approaches, BioInformatics and BioEngineering, BIBE
  176. 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
  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