Below is a selection of publications made possible in part by the CRI’s research resources and expertise.
Bioinformatics Core | Clinical Research Data Warehouse | Other CRI Work

Have you used CRI resources in a publication not listed below? Let us know!

BIOINFORMATICS CORE

2017

  • Kadri S, Lee J, Fitzpatrick C, Galanina N, Sukhanova M, Venkataraman G, et al. Clonal evolution underlying leukemia progression and Richter transformation in patients with ibrutinib-relapsed CLL. Blood Advances. 2017 May 9. doi: 10.1182/bloodadvances.2016003632. 
  • Saloura V, Fatima A, Zewde M, Kiyotani K, Brisson RJ, Park JH, et al. Characterization of the tumor T-cell receptor repertoire and immune microenvironment in patients with locoregionally advanced squamous cell carcinoma of the head and neck. Clin Cancer Res. 2017 April 25. doi: 10.1158/1078-0432.CCR-17-0103. 
  • Kach J, Long TM, Selman P, Tonsing-Carter EY, Bacalao MA, Lastra RR, et al. Selective glucocorticoid receptor modulators (SGRMs) delay castrate-resistant prostate cancer growth. Mol Cancer Ther. 2017 Apr 20. doi: 10.1158/1535-7163.MCT-16-0923. [Epub ahead of print] 
  • Wang LJ, Chan WC, Chou MC, Chou WJ, Lee MJ, Lee SY, et al. Polymorphisms of STS gene and SULT2A1 gene and neurosteroid levels in Han Chinese boys with attention-deficit/hyperactivity disorder: an exploratory investigation. Sci Rep. 2017 Apr 3. doi: 10.1038/srep45595. 
  • Pitroda S, Bao R, Andrade J, Weichselbaum RR, Connell PP. Low Recombination Proficiency Score (RPS) predicts heightened sensitivity to DNA-damaging chemotherapy in breast cancer. Clin Cancer Res. 2017 Mar 24. doi: 10.1158/1078-0432.CCR-16-2845 
  • Cortese R, Gileles-Hillel A, Khalyfa A, Almendros I, Akbarpour M, Khalyfa AA, et al. Aorta macrophage inflammatory and epigenetic changes in a murine model of obstructive sleep apnea: Potential role of CD36. Sci. Rep. 2017 Feb 27. doi: 10.1038/srep43648 
  • Li Y, Andrade J. DEApp: an interactive web interface for differential expression analysis of next generation sequence data. Source Code for Biology and Medicine. 2017 Feb 3. doi: 10.1186/s13029-017-0063-4 
  • Deb DK, Bao R, Li YC. Critical role of the cAMP-PKA pathway in hyperglycemia-induced epigenetic activation of fibrogenic program in the kidney. FASEB J. 2017 Feb 1. doi: 10.1096/fj.201601116R. [Epub ahead of print] 
  • Khalyfa A, Cortese R, Qiao Z, Ye H, Bao R, Andrade J, et al. Late gestational intermittent hypoxia induces metabolic and epigenetic changes in male adult offspring mice. J Physiology. 2017 Jan 15. doi: 10.1113/JP273570. [Epub ahead of print] 

2016

  • Spranger S, Luke JJ, Bao R, Zha Y, Hernandez KM, Gakewski AP, et al. Density of immunogenic antigens does not explain the presence or absence of the T-cell-inflamed tumor microenvironment in melanoma. P Natl Acad Sci USA. 2016 Nov 11. 10.1113/JP273570. [Epub ahead of print] 
  • Applebaum MA, Jha AR, Kao C, Hernandez KM, DeWane G, Salwen HR, et al. Integrative genomics reveals hypoxia inducible genes that are associated with a poor prognosis in neuroblastoma patients. Oncotarget. 2016 Oct 17. doi:10.18632/oncotarget.12713 
  • Eckert MA, Pan S, Hernandez KM, Loth RM, Andrade J, Volchenboum S, et al. Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube. Cancer Discov. 2016 Oct 7. doi:10.1158/2159-8290.CD-16-0607 
  • Shah S, Ward JE, Bao R, Hall CR, Brockstein BE, Luke JJ. Clinical response of a patient to anti-PD-1 immunotherapy and the immune landscape of testicular germ cell tumors. Cancer Immunol Res. 2016 Sep 16. doi:10.1158/2326-6066.CIR-16-0087. [Epub ahead of print] 
  • Khalyfa A, Zhang C, Khalyfa AA, Foster GE, Beaudin AE, Andrade J, et al. Effect on Intermittent Hypoxia on Plasma Exosomal Micro RNA Signature and Endothelial Function in Healthy Adults. Sleep. 2016 Sep 9.  pii: sp-00145-16. [Epub ahead of print] 
  • Almendros I, Khalyfa A, Trzepizur W, Gileles-Hillel A, Huang L, Akbarpour M, et al. Tumor Cell Malignant Properties Are Enhanced by Circulating Exosomes in Sleep Apnea. Chest. 2016 Aug 25. doi:10.1016/j.chest.2016.08.1438. [Epub ahead of print] 
  • Khalyfa A, Almendros I, Gileles-Hillel A, Akbarpour M, Trzepizur W, Mokhlesl Babak, et al. Circulating exosomes potentiate tumor malignant properties in a mouse model of chronic sleep fragmentation. Oncotarget. 2016 Jul 13.
  • Gunasekharan VK, Li Y, Andrade J, Laimins LA. Post-Transcriptional Regulation of KLF4 by High-Risk Human Papillomaviruses Is Necessary for the Differentiation-Dependent Viral Life Cycle. PLoS Pathogens. 2016 Jul 7. doi:10.1371/journal.ppat.1005747 
  • McConnell SC, Hernandez KM, Wcisel DJ, Kettleborough RN, Stemple DL, Yoder JA, et al. Alternative halotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution. P Natl Acad Sci USA. 2016 Jun 23. doi:10.1073/pnas.1607602113 
  • Kuo HC, Hsieh KS, Ming-Huey Guo M, Weng KP, Ger LP, Chan WC, et al. Next-generation sequencing identifies micro-RNA-based biomarker panel for Kawasaki disease. J Allergy Clin Immunol. 2016 Jun 18. doi:10.1016/j.jaci.2016.04.050. [Epub ahead of print] 
  • Publication Highlight: The 1001 Genomes Consortium. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell. 2016 Jun 9. doi:10.1016/j.cell.2016.05.063 
  • Sweis R, Spranger S, Bao R, Paner GP, Stadler WM, Steinberg G, et al. Molecular Drivers of the Non-T Cell-Inflamed Tumor Microenvironment in Urothelial Bladder Cancer. Cancer Immunol Res. 2016 May 17. doi: 10.1158/2326-6066.CIR-15-0274 [Epub ahead of print] 
  • Kuo H, Li S, Guo M, Huang Y, Yu H, Huang F, et al. Genome-Wide Association Study Identifies Novel Susceptibility Genes Associated with Coronary Artery Aneurysm Formation in Kawasaki Disease. PLoS One. 2016 May 12. doi:10.1371/journal.pone.0154943 
  • Khalyfa A, Kheirandish-Gozal L, Khalyfa AA, Philby MF, Alonso-Alvarez ML, Mohammadi M, et al. Circulating Plasma Extracellular Microvesicle miRNA Cargo and Endothelial Dysfunction in OSA Children. Am J Respir Crit Care Med. 2016 May 10. doi:10.1164/rccm.201602-0323OC [Epub ahead of print] 
  • Khalyfa A, Khalyfa AA, Akbarpour M, Connes P, Romana M, Lapping-Carr G, et al. Extracellular microvesicle microRNAs in children with sickle cell anaemia with divergent clinical phenotypes. Brit J Haematol. 2016 May 10. doi: 10.1111/bjh.14104. [Epub ahead of print] 
  • West DC, Pan D, Tonsing-Carter EY, Hernandez KM, Pierce CF, Styke SC, et al. GR and ER co-activation alters the expression of differentiation genes and associates with improved ER+ breast cancer outcome. Mol Cancer Res. 2016 May 2. doi: 10.1158/1541-7786.MCR-15-0433. [Epub ahead of print] 
  • Des Marais DL, Razzaque S, Hernandez KM, Garvin DF, Juenger TE. Quantitative trait loci associated with natural diversity in water-use efficiency and response to soil drying in Brachypodium distachyon. Plant Sci. 2016 Mar 24. doi: 10.1016/j.plantsci.2016.03.010. [Epub ahead of print] 
  • Ranoa DR, Parekh AD, Pitroda SP, Huang X, Darga T, Wong AC, et al. Cancer therapies activate RIG-I-like receptor pathway through endogenous non-coding RNAs. Oncotarget. 2016 Mar 28. doi: 10.18632/oncotarget.8420
  • Cortese R, Zhang C, Bao R, Andrade J, Khalyfa A, Mokhlesi B, et al. DNA methylation profiling of blood monocytes in obesity hypoventilation syndrome patients: Effect of positive airway pressure treatment. Chest. 2016 Feb 25. doi: 10.1016/j.chest.2016.02.648

2015

  • Qin D, Huang L, Wlodaver A, Andrade J, Staley J. Sequencing of lariat termini in S. cerevisiae reveals 5′ splice site, branch points, and novel splicing events. RNA. 2015 Dec 8. doi: 
  • Luke JJ, Spranger S, Bao R, Andrade J, Gajewski TF. The genetic landscape of the T cell non-inflamed tumor microenvironment in human solid tumors. J Immunother Cancer. 2015 Nov 4;3(Suppl 2):97. doi: 10.1186/2051-1426-3-S2-P97
  • Zha Y, Spranger S, Hernandez KM, Li Y, Bao R, Alexieff P, et al. Density of immunogenic antigens does not explain presence or absence of the T cell-inflamed tumor microenvironment in metastatic melanoma. J Immunother Cancer. 2015 Nov 4;3(Suppl 2):425.
    doi: 10.1186/2051-1426-3-S2-P425 
  • Singh P, Brock CO, Volden PA, Hernandez K, Skor M, Kocherginsky M, et al. Glucocorticoid receptor ChIP-sequencing of subcutaneous fat reveals modulation of inflammatory pathways. Obesity. 2015 Nov;23(11):2286-93. doi: 10.1002/oby.21251
  • Sasaki MM, Skol AD, Hungate EA, Bao R, Huang L, Kahn SA, et al. Whole-exome Sequence Analysis Implicates Rare II17REL Variants in Familial and Sporadic Inflammatory Bowel Disease. Inflamm Bowel Dis. 2015 Oct 16. [Epub ahead of print] 
  • Kadri S, Zhen CJ, Wurst MN, Long BC, Jiang Z, Wang YL, et al. Amplicon Indel Hunter: A Novel Bioinformatics Tool to Detect Large Somatic Insertion/Deletion Mutations in Amplicon-Based Next-Generation Sequencing Data. J Mol Diagn. 2015 Aug 28. doi: 10.1016/j.jmoldx.2015.06.005. [Epub ahead of print] 
  • Hernandez KM. Understanding the genetic architecture of complex traits using the function-valued approach. New Phytol. 2015 Oct;208(1):1-3. doi: 10.1111/nph.13607. Epub 2015 Aug 26. 
  • Zhong R, Bao R, Faber PW, Bindokas VP, Bechill J, Lingem M, et al. Notch1 activation or loss promotes HPV-induced oral tumorigenesis. Cancer Res. 2015 Aug 20. doi: 10.1158/0008-5472.CAN-15-0199. [Epub ahead of print] 
  • Publication Highlight: Bao R, Hernandez K, Huang L, Kang W, Bartom E, Onel K, et al. ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification. PLoS One. 2015 Aug 13;10(8):e0135800. doi:10.1371/journal.pone.0135800. eCollection 2015. 
  • Sasaki MM, Skol AD, Bao R, Rhodes LV, Chambers R, Vokes EE, et al. Integrated Genomic Analysis Suggests MLL3 is a Novel Candidate Susceptibility Gene for Familial Nasopharyngeal Carcinoma. Cancer Epidem Biomar. 2015 Aug;24(8):1222-8. doi: 10.1158/1055-9965.EPI-15-0275. Epub 2015 May 26.
  • Ernst LM, Rand CM, Bao R, Andrade J, Linn RL, Minturn L, et al. Stillbirth: Genome-wide Copy Number Variation Profiling in Archived Placental Umbilical Cord Samples with Pathologic and Clinical Correlation. Placenta. 2015 Aug;36(8):783-9. doi: 10.1016/j.placenta.2015.04.010. Epub 2015 May 15.
  • Publication Highlight: Spranger S, Bao R, Gajewski T. Melanoma-intrinsic β-catenin signalling prevents anti-tumour immunity. Nature. 2015 Jul 9;523(7559):231-5. doi: 10.1038/nature14404. Epub 2015 May 11.
  • Volchenboum SL, Andrade J, Huang L, Barkauskas DA, Krailo M, Womer R, et al. Gene expression profiling of Ewing sarcoma tumours reveals the prognostic importance of tumour–stromal interactions: a report from the Children’s Oncology Group. J Pathol: Clin Res. 2015 Apr;1(2):83-94. doi: 10.1002/cjp2.9. 
  • Cortese R, Khalyfa A, Bao R, Andrade J, Gozal D. Epigenomic profiling in visceral white adipose tissue of offspring of mice exposed to late gestational sleep fragmentation. Int J Obesity. 2015 Jul;39(7):1135-42. doi: 10.1038/ijo.2015.38. Epub 2015 Mar 24. 
  • Uppal A, Wightman SC, Mallon S, Oshima G, Pitroda SP, Zhang Q, et al. 14q32-encoded microRNAs mediate an oligometastatic phenotype. Oncotarget. 2015 Feb 28;6(6):3540-52.
  • Vragovic K, Sela A, Friedlander-Shani L, Fridman Y, Hacham Y, Holland N, et al. Translatome analyses capture of opposing tissue-specific brassinosteroid signals orchestrating root meristem differentiation. P Natl Acad Sci USA. 2015 Jan 20;112(3):923-8. doi: 10.1073/pnas.1417947112. Epub 2015 Jan 5. 

2014

  • Xie T, Vigil J, MacCracken E, Gasparaitis A, Young J, Kang W, et al. Low-frequency stimulation of STN-DBS reduces aspiration and freezing of gait in patients with PD. Neurology. 2015 Jan 27;84(4):415-20. doi: 10.1212/WNL.0000000000001184. Epub 2014 Dec 24.
  • Regnier SM, Kirkley AG, Ye H, El-Hashani E, Zhang X, Neel BA, et al. Dietary Exposure to the Endocrine Disruptor Tolylfluanid Promotes Global Metabolic Dysfunction in Male Mice. Endocrinology. 2015 Mar;156(3):896-910. doi: 10.1210/en.2014-1668. Epub 2014 Dec 23.
  • Malcom JW, Hernandez KM, Likos R, Wayne T, Leibold MA, Juenger TE. Extensive cross-environment fitness variation lies along few axes of genetic variation in the model alga, Chlamydomonas reinhardtii. New Phytol. 2015 Jan;205(2):841-51. doi: 10.1111/nph.13063. Epub 2014 Sep 29. 
  • Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, et al. The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. New Phytol. 2015 Jan;205(1):402-14. doi: 10.1111/nph.13027. Epub 2014 Sep 23.
  • Chen C, Zhang C, Cheng L, Reilly JL, Bishop JR, Sweeney JA, et al. Correlation between DNA methylation and gene expression in the brains of patients with bipolar disorder and schizophrenia. Bipolar Disord. 2014 Dec;16(8):790-9. doi: 10.1111/bdi.12255. Epub 2014 Sep 22.
  • Bao R, Huang L, Andrade J, Tan W, Kibbe WA, Jiang H, et al. Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. Cancer Informatics. 2014 Sep 21;13(Suppl 2):67-82. doi: 10.4137/CIN.S13779. eCollection 2014. 
  • Chen B, Moore TV, Li Z, Sperling AI, Zhang C, Andrade J, et al. Gata5 Deficiency Causes Airway Constrictor Hyperresponsiveness in Mice. Am J Resp Cell Mol. 2014 Apr;50(4):787-95. doi: 10.1165/rcmb.2013-0294OC. 
  • Fahrenbach J, Andrade J, McNally EM. The CO-Regulation Database (CORD): a tool to identify coordinately expressed genes. PLoS One. 2014 Mar 5;9(3):e90408. doi: 10.1371/journal.pone.0090408. eCollection 2014. 
  • Widau RC, Parekh A, Ranck MC, Golden DW, Kumar KA, Sood RF, et al. The RIG-I like receptor LGP2 protects tumor cells from ionizing radiation. P Natl Acad Sci. 2014 Jan 28;111(4):E484-91. doi: 10.1073/pnas.1323253111. Epub 2014 Jan 13. 

2013

  • Jiang ZF, Xia F, Johnson KW, Brown CD, Bartom E, Tuteja JH, et al. Comparison of the genome sequences of “Candidatus Portiera aleyrodidarum” primary endosymbionts of the whitefly Bemisiatabaci B and Q biotypes. Appl Environ Microbiol. 2013 Mar;79(5):1757-9. doi: 10.1128/AEM.02976-12. Epub 2013 Jan 11.

2012

  • McNerney ME, Brown CD, Wang X, Bartom ET, Karmakar S, Bandlamudi C, et al. CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia. Blood. 2013 Feb 7;121(6):975-83. doi: 10.1182/blood-2012-04-426965. Epub 2012 Dec 3.
  • Jiang ZF, Xia F, Johnson KW, Bartom E, Tuteja JH, Stevens R, et al. Genome sequences of the primary endosymbiont Candidatus Portiera aleyrodidarum in the whitefly Bemisia tabaci B and Q biotypes. J Bacteriol. 2012 Dec;194(23):6678-9. doi: 10.1128/JB.01841-12. 

CLINICAL RESEARCH DATA WAREHOUSE

2015

  • Kinnucan J, Tomal J, Rubin DT. U.S. Patients with Ulcerative Colitis Do Not Have a Decreased Risk of Diverticulosis. Inflamm Bowel Dis. 2015 Sep;21(9):2154-7. doi: 10.1097/MIB.0000000000000467 
  • Churpek MM, Yuen TC, Winslow C, Hall J, Edelson DP. Differences in Vital Signs Between Elderly and Nonelderly Patients Prior to Ward Cardiac Arrest. Crit Care Med. 2015 Apr;43(4):816-22. doi: 10.1097/CCM.0000000000000818

2014

  • Li L, Zhan X, Wang N, Pinto JM, Ge X, Wang C, et al. Does Airway Surgery Lower Serum Lipid Levels in Obstructive Sleep Apnea Patients? A Retrospective Case Review. Med Sci Monitor. 2014 Dec 13;20:2651-7. doi: 10.12659/MSM.892230. 
  • Hong S, Le-Rademacher J, Artz A, McCarthy PL, Logan BR, Pasquini MC. Comparison of non-myeloablative conditioning regimens for lymphoproliferative disorders. Bone Marrow Transpl. 2015 Mar;50(3):367-74. doi: 10.1038/bmt.2014.269. Epub 2014 Dec 1. 
  • Bailey KA, Savic D, Zielinski M, Park SY, Wang LJ, Witkowski P, et al. Evidence of non-pancreatic beta cell-dependent roles of Tcf7l2 in the regulation of glucose metabolism in mice. Hum Mol Genet. 2015 Mar 15;24(6):1646-54. doi: 10.1093/hmg/ddu577. Epub 2014 Nov 14.
  • Kern DW, Wroblewski KE, Schumm LP, Pinto JM, Chen RC, McClintock MK. Olfactory function in Wave 2 of the National Social Life, Health, and Aging Project. J Gerontol B-Psychol. 2014 Nov;69 Suppl 2:S134-43. doi: 10.1093/geronb/gbu093. 
  • Pinto JM, Wroblewski KE, Kern DW, Schumm LP, McClintock MK. Olfactory dysfunction predicts 5-year mortality in older adults. PLoS One. 2014 Oct 1;9(10):e107541. doi: 10.1371/journal.pone.0107541. eCollection 2014. 
  • Blair DR, Wang K, Nestorov S, Evans JA, Rzhetsky A. Quantifying the impact and extent of undocumented biomedical synonymy. PLoS Comput Biol. 2014 Sep 25;10(9):e1003799. doi: 10.1371/journal.pcbi.1003799. eCollection 2014.
  • Yao L, Pinto JM, Yi X, Li L, Peng P, Wei Y. Gray matter volume reduction of olfactory cortices in patients with idiopathic olfactory loss. Chem Senses. 2014 Nov;39(9):755-60. doi: 10.1093/chemse/bju047. Epub 2014 Sep 18.
  • Churpek MM, Yuen TC, Winslow C, Robicsek AA, Meltzer DO, Gibbons RD, et al. Multicenter Development and Validation of a Risk Stratification Tool for Ward Patients. Am J Respir Crit Care Med. 2014 Sep 15;190(6):649-55. doi: 10.1164/rccm.201406-1022OC. 
  • Town JA, Churpek MM, Yuen TC, Huber MT, Kress JP, Edelson DP. Relationship Between ICU Bed Availability, ICU Readmission, and Cardiac Arrest in the General Wards. Crit Care Med. 2014 Sep;42(9):2037-41. doi: 10.1097/CCM.0000000000000401.
  • Lang GD, Konda VJ, Siddiqui UD, Koons A, Waxman I. A Single-Center Experience of Endoscopic Submucosal Dissection Performed in a Western Setting. Digest Dis Sci. 2015 Feb;60(2):531-6. doi: 10.1007/s10620-014-3260-x. Epub 2014 Aug 5.
  • Naclerio RM, Pinto JM, Baroody FM. Drowning in applications for residency training: a program’s perspective and simple solutions. J Otolaryngol – Head N. 2014 Aug;140(8):695-6. doi: 10.1001/jamaoto.2014.1127. 
  • Choi CH, Poroyko V, Watanabe S, Jiang D, Lane J, deTineo M, et al. Seasonal allergic rhinitis affects sinonasal microbiota. Am J Rhinol Allergy. 2014 Jul-Aug;28(4):281-6. doi: 10.2500/ajra.2014.28.4050. 
  • Liu CC, Tseng YT, Li W, Wu CY, Mayzus I, Rzhetsky A, et al. DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W137-46. doi: 10.1093/nar/gku412. Epub 2014 Jun 3. doi: 10.1093/nar/gku412. 
  • Feng Y, Stram DO, Rhie SK, Millikan RC, Ambrosone CB, John EM, et al. A Comprehensive Examination of Breast Cancer Risk Loci in African American Women. Hum Mol Genet. 2014 Oct 15;23(20):5518-26. doi: 10.1093/hmg/ddu252. Epub 2014 May 22.
  • Sofia MA, Rubin DT, Hou N, Pekow J. Clinical presentation and disease course of inflammatory bowel disease differs by race in a large tertiary care hospital. Digest Dis Sci. 2014 Sep;59(9):2228-35. doi: 10.1007/s10620-014-3160-0. Epub 2014 Apr 22.
  • Watanabe S, Pinto JM, Bashir ME, De Tineo M, Suzaki H, Baroody FM, et al. Effect of prednisone on nasal symptoms and peripheral blood T-cell function in chronic rhinosinusitis. Int Forum Allergy Rhinol. 2014 Aug;4(8):609-16. doi: 10.1002/alr.21336. Epub 2014 Apr 21. 
  • Konda C, Haba Ruiz MG, Koons A, Hart J, Xiao SY, Siddiqui UD, et al. Complete Endoscopic Mucosal Resection is Effective and Durable Treatment for Barrett’s-associated Neoplasia. Clin Gastroenterol Hepatol. 2014 Dec;12(12):2002-10.e1-2. doi: 10.1016/j.cgh.2014.04.010. Epub 2014 Apr 13.
  • Churpek MM, Yuen TC, Park SY, Gibbons R, Edelson DP. Using electronic health record data to develop and validate a prediction model for adverse outcomes in the wards. Crit Care Med. 2014 Apr;42(4):841-8. doi: 10.1097/CCM.0000000000000038. 
  • Rzhetsky A, Bagley SC, Wang K, Lyttle CS, Cook EH Jr, Altman RB, et al. Environmental and state-level regulatory factors affect the incidence of autism and intellectual disability. PLoS Comput Biol. 2014 Mar 13;10(3):e1003518. doi: 10.1371/journal.pcbi.1003518. eCollection 2014. 
  • Li H, Giger ML, Sun C, Ponsukcharoen U, Huo D, Lan L, et al. Pilot study demonstrating potential association between breast cancer image-based risk phenotypes and genomic biomarkers. Med Phys. 2014 Mar;41(3):031917. doi: 10.1118/1.4865811. 
  • Nelson R, Liao C, Fichera A, Rubin DT, Pekow J. Rescue therapy with cyclosporine or infliximab is not associated with an increased risk for postoperative complications in patients hospitalized for severe steroid-refractory ulcerative colitis. Inflamm Bowel Dis. 2014 Jan;20(1):14-20. doi: 10.1097/01.MIB.0000437497.07181.05. 

2013

  • He BZ, Ludwig MZ, Dickerson DA, Barse L, Arun B, Vilhjalmsson BJ, et al. Effect of genetic variation in a Drosophila model of diabetes-associated misfolded human proinsulin. Genetics. 2014 Feb;196(2):557-67. doi: 10.1534/genetics.113.157800. Epub 2013 Nov 26.
  • Patel RM, Pinto JM. Olfaction: anatomy, physiology, and disease. Clin Anat. 2014 Jan;27(1):54-60. doi: 10.1002/ca.22338. Epub 22 Nov 2013. 
  • Yamaguchi K, Schacht D, Newstead GM, Bradbury AR, Verp MS, Olopade OI. Breast Cancer Detected on an Incident (Second or Subsequent) Round of Screening MRI: MRI Features of False-Negative Cases. Am J Roentgenol. 2013 Nov;201(5):1155-63. doi: 10.2214/AJR.12.9707.
  • Valentini A, Lubinski J, Byrski T, Ghadirian P, Moller P, Lynch HT, et al. The impact of pregnancy on breast cancer survival in women who carry a BRCA1 or BRCA2 mutation. Breast Cancer Res Treat. 2013 Nov;142(1):177-85. doi: 10.1007/s10549-013-2729-1. Epub 2013 Oct 18.
  • Harrell JC, Pfefferle AD, Zalles N, Prat A, Fan C, Khramtsov A, et al. Endothelial-like properties of claudin-low breast cancer cells promote tumor vascular permeability and metastasis. Clin Exp Metastasis. 2014 Jan;31(1):33-45. doi: 10.1007/s10585-013-9607-4. Epub 2013 Aug 22.
  • Bhatta SS, Hou N, Moton ZN, Polite BN, Fleming GF, Olopade OI, et al. Factors associated with compliance to adjuvant hormone therapy in Black and White women with breast cancer. SpringerPlus. 2013 Jul 30;2:356. doi: 10.1186/2193-1801-2-356. eCollection 2013.
  • Wang Y, Hong S, Li M, Zhang J, Bi Y, He Y, et al. Noggin resistance contributes to the potent osteogenic capability of BMP9 in mesenchymal stem cells. J Orthop Res. 2013 Nov;31(11):1796-803. doi: 10.1002/jor.22427. Epub 2013 Jul 16.
  • Wang PY, Huo D, Sun C, Olopade OI. The use of allelic imbalance to ascertain cis-regulation for human UGT2B7 in vivo. Eur J Clin Pharmacol. 2013 Sep;69(9):1733-5. doi: 10.1007/s00228-013-1538-0. Epub 2013 Jun 6.
  • Pinto JM, Schumm LP, Wroblewski KE, Kern DW, McClintock MK. Racial disparities in olfactory loss among older adults in the United States. J Gerontol A-Biol. 2014 Mar;69(3):323-9. doi: 10.1093/gerona/glt063. Epub 2013 May 20. 
  • Ha M, Hong S, Li WH. Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context. Bioinformatics (Oxford, England). 2013 May 1;29(9):1199-205. doi: 10.1093/bioinformatics/btt126. Epub 2013 Mar 19.
  • Yoder J, Yuen TC, Churpek MM, Arora VM, Edelson DP. A Prospective Study of Nighttime Vital Sign Frequency and Risk of Clinical Deterioration. JAMA Internal Medicine. 2013 Sep 9;173(16):1554-5. doi: 10.1001/jamainternmed.2013.7791.

2012

  • Ganai S, Prachand VN, Posner MC, Alverdy JC, Choi E, Hussain M, et al. Predictors of unsuccessful laparoscopic resection of gastric submucosal neoplasms. J Gastrointest Surg. 2013 Feb;17(2):244-55; discussion 255-6. doi: 10.1007/s11605-012-2095-z. Epub 2012 Dec 8.
  • Wheeler HE, Gamazon ER, Wing C, Njiaju UO, Njoku C, Baldwin RM, et al. Integration of cell line and clinical trial genome-wide analyses supports a polygenic architecture of Paclitaxel-induced sensory peripheral neuropathy. Clin Cancer Res. 2013 Jan 15;19(2):491-9. doi: 10.1158/1078-0432.CCR-12-2618. Epub 2012 Nov 30.
  • Ifat Keydar I, Ben-Asher E, Feldmesser E, Nativ N, Oshimoto A, Restrepo D, et al. General olfactory sensitivity: candidate genes and their genomic variations. Hum Mutat. 2013 Jan;34(1):32-41. doi: 10.1002/humu.22212. Epub 2012 Oct 11.
  • Savic D, Park SY, Bailey KA, Bell GI, Nobrega MA. In vitro scan for enhancers at the TCF7L2 locus. Diabetologia. 2013 Jan;56(1):121-5. doi: 10.1007/s00125-012-2730-y. Epub 2012 Sep 26.
  • Churpek MM, Yuen TC, Edelson DP. Predicting clinical deterioration in the hospital: The impact of outcome selection. Resuscitation. 2013 May;84(5):564-8. doi: 10.1016/j.resuscitation.2012.09.024. Epub 2012 Sep 25.
  • Njiaju UO, Gamazon ER, Gorsic LK, Delaney SM, Wheeler HE, Im HK, et al. Whole-genome studies identify solute carrier transporters in cellular susceptibility to paclitaxel. Pharmacogenet Genom. 2012 Jul;22(7):498-507. doi: 10.1097/FPC.0b013e328352f436.

OTHER CRI WORK

2016

  • Volchenboum SL, Mayampurath A, Göksu-Gürsoy G, Edelson DP, Howell MD, Churpek MM. Research Letter: Association Between In-Hospital Critical Illness Events and Outcomes in Patients on the Same Ward. JAMA. 2016 Dec 27. doi: 10.1001/jama.2016.15505 
  • McKillip RP, Borden BA, Galecki P, Ham SA, Patrick-Miller L, Hall JP, et al. Patient perceptions of care as influenced by a large institutional pharmacogenomic implementation program. Clin Pharmacol Ther. 2016 Dec 16. doi: 10.1002/cpt.586 [Epub ahead of print] 
  • Lyon SM, Mayampurath A, Rogers MR, Wolfgeher DJ, Fisher SM, Volchenboum SL, et al. A method for whole protein isolation from human cranial bone. Anal Biochem. 2016 Sep 24. doi: 10.1016/j.ab.2016.09.021 [Epub ahead of print] 
  • Morgenstern DA, London WB, Stephens D, Volchenboum SL, Simon T, Nakagawara A, et al. Prognostic significance of pattern and burden of metastatic disease in patients with stage 4 neuroblastoma: A study from the International Neuroblastoma Risk Group Database. Eur J Cancer. 2016 Jul 17. doi: 10.1016/j.ejca.2016.06.005 [Epub ahead of print] 
  • Hussain S, Kenigsberg BB, Danahey K, Lee YM, Galecki PM, Ratain MJ, et al. Disease-drug database for pharmacogenomic-based prescribing. Clin Pharmacol Ther. 2016 Jun 8. doi: 10.1002/cpt.364 [Epub ahead of print] 
  • Thompson D, Vo KT, London WB, Fischer M, Ambros PF, Nakagawara A, et al. Identification of patient subgroups with markedly disparate rates of MYCN amplification in neuroblastoma: A report from the International Neuroblastoma Risk Group project. Cancer. 2016 Mar 15. doi: 10.1002/cncr.29848. 
  • O’Donnell PH, Danahey K, Ratain MJ. The Outlier in All of Us: Why Implementing Pharmacogenomics Could Matter for Everyone. Clin Pharmacol Ther. 2016 Feb 15. doi: 10.1002/cpt.333 [Epub ahead of print] 

2015

  • Pinto NR, Applebaum MA, Volchenboum SL, Matthay KK, London WB, Ambros PF, et al. Advances in Risk Classification and Treatment Strategies for Neuroblastoma. J Clin Oncol. 2015 Aug 24. doi: 10.1200/JCO.2014.59.4648 [Epub ahead of print] 
  • Kaufman AL, Spitz J, Jacobs M, Sorrentino M, Yuen S, Danahey K, et al. Evidence for Clinical Implementation of Pharmacogenomics in Cardiac Drugs. Mayo Clin Proc. 2015 Jun;90(6):716-29. doi: 10.1016/j.mayocp.2015.03.016
  • Pinto N, Volchenboum SL, Skol AD, Rhodes L, Doan A, Fein-Levy C, et al. Establishing a translational genomics infrastructure in pediatric cancer: the GREAT KIDS experience. Pers Med. 2015:12(3):221-9. doi: 10.2217/pme.14.90.