BIOINFORMATICS CORE

2021

• Bao R, Ng A, Sasaki M, Esai Selvan M, Katti A, Lee H, et al. Functional Common and Rare ERBB2 Germline Variants Cooperate in Familial and Sporadic Cancer Susceptibility. Cancer Prev Res (Phila). 2021 Jan 8. doi: 10.1158/1940-6207.CAPR-20-0094. Epub ahead of print. PMID: 33419763.

2020

• Luke JJ, Onderdonk BE, Bhave SR, Karrison T, Lemons JM, Chang P, et al. Improved Survival Associated with Local Tumor Response Following Multisite Radiotherapy and Pembrolizumab: Secondary Analysis of a Phase I Trial. Clin Cancer Res. 2020 Dec 15;26(24):6437-6444. doi: 10.1158/1078-0432.CCR-20-1790. Epub 2020 Oct 7. PMID: 33028595.

• Kahn JH, Goddi A, Sharma A, Heiman J, Carmona A, Li Y, et al. SMRT Regulates Metabolic Homeostasis and Adipose Tissue Macrophage Phenotypes in Tandem. Transcriptome clarifies mechanisms of lesion genesis versus progression. Endocrinology. 2020 Aug 8. doi: 10.1210/endocr/bqaa132.

• Bao R, Hernandez K, Huang L, Luke JJ. ACE2 and TMPRSS2 expression by clinical, HLA, immune, and microbial correlates across 34 human cancers and matched normal tissues: implications for SARS-CoV-2 COVID-19. J Immunother Cancer. 2020 Jul;8(2):e001020. doi: 10.1136/jitc-2020-001020. PMID: 32675312; PMCID: PMC7372174.

• Koskimäki J, Polster SP, Li Y, Romanos S, Srinath A, Zhang D, et al. Common transcriptome, plasma molecules, and imaging signatures in the aging brain and a Mendelian neurovascular disease, cerebral cavernous malformation. GeroScience. 2020 June 17. doi: 10.1007/s11357-020-00201-4.

• Sun KA, Li Y, Meliton AY, Woods PS, Kimmig LM, Cetin-Atalay R, et al. Endogenous itaconate is not required for particulate matter-induced NRF2 expression or inflammatory response. eLife. 2020 Apr 7. doi: 10.7554/eLife.54877.

• Meliton AY, Li Y, Sun K, Tian Y, Andrade J, Hamanaka RB, Mutlu GM. Developmental Exposure to PM Causes Feminization of Liver in Male Mice Later in Life. Am J Respir Crit Care Med. 2020;201:A4614.

2019

• Balagopal V, Hantel A, Kadri S, Steinhardt G, Zhen CJ, Kang W, et al. Measurable residual disease monitoring for patients with acute myeloid leukemia following hematopoietic cell transplantation using error corrected hybrid capture next generation sequencing. PLoS One. 2019 Oct 28;14(10):e0224097. doi: 10.1371/journal.pone.0224097. PMID: 31658273; PMCID: PMC6816574.

• Koskimäki J, Zhang D, Li Y, Saadat L, Moore T, Lightle R, et al. Transcriptome clarifies mechanisms of lesion genesis versus progression in models of Ccm3 cerebral cavernous malformations. Acta Neuropathologica Communications. 2019 Aug 19. doi: 10.1186/s40478-019-0789-0.
• Tonsing-Carter E, Hernandez KM, Kim CR, Harkless RV, Oh A, Bowie KR, et al. Glucocorticoid receptor modulation decreases ER-positive breast cancer cell proliferation and suppresses wild-type and mutant ER chromatin association. Breast Cancer Res. 2019 Jul 24. doi: 10.1186/s13058-019-1164-6.
• Gao GF, Parker JS, Reynolds SM, Silva TC, Wang LB, Zhou W, et al. Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data. Cell Syst. 2019 Jul 24. doi: 10.1016/j.cels.2019.06.006.
• Cook LCC, Chatterjee N, Li Y, Andrade J, Federle MJ, Eichenbaum Z. Transcriptomic Analysis of Streptococcus pyogenes Colonizing the Vaginal Mucosa Identifies hupY, an MtsR-Regulated Adhesin Involved in Heme Utilization. MBio. 2019 Jun 25. doi: 10.1128/mBio.00848-19.
• Bao R, Onishi KG, Tolla E, Ebling FJP, Lewis JE, Anderson RL, et al. Genome sequencing and transcriptome analyses of the Siberian hamster hypothalamus identify mechanisms for seasonal energy balance. P Natl Acad Sci USA. 2019 Jun 12. doi: 10.1073/pnas.1902896116 
• Brooks JM, Menezes AN, Ibraham M, Archer L, Lal N, Bagnall CJ, et al. Development and Validation of a Combined Hypoxia and Immune Prognostic Classifier for Head and Neck Cancer. Clin Cancer Res. 2019 Jun 10. doi: 10.1158/1078-0432.CCR-18-3314
• Eckert MA, Coscia F, Chryplewicz A, Chang JW, Hernandez KM, Pan S, et al. Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts. Nature. 2019 01 May. doi: 10.1038/s41586-019-1173-8. 
• Domowicz MS, Chan WC, Claudio-Vázquez P, Henry JG, Ware CB, Andrade J, et al. Global Brain Transcriptome Analysis of a Tpp1 Neuronal Ceroid Lipofuscinoses Mouse Model. ASN Neuro. 2019 April 19. doi: 10.1177/1759091419843393 
• Du X, Wei C, Parviz Hejazi Pastor D, Rao ER, Li Y, Grasselli G, et al. α1ACT Is Essential for Survival and Early Cerebellar Programming in a Critical Neonatal Window. Neuron. 2019 Mar 25. doi: 10.1016/j.neuron.2019.02.036 
• Lee J, Yesilkanal AE, Wynne JP, Frankenberger C, Liu J, Elbaz M, et al. Effective breast cancer combination therapy targeting BACH1 and mitochondrial metabolism. Nature. 2019 Mar 6. doi: 10.1038/s41586-019-1005-x 
• Godfrey J, Tumuluru S, Bao R, Leukam M, Venkataraman G, Phillip J, et al. PD-L1 gene alterations identify a subset of diffuse large B-cell lymphoma harboring a T cell-inflamed phenotype. Blood. 2019 Mar. doi: 10.1182/blood-2018-10-879015 
• Johnson DB, Bao R, Ancell KK, Daniels AB, Wallace D, Sosman JA, Luke JJ. Response to Anti–PD-1 in Uveal Melanoma Without High-Volume Liver Metastasis. J Natl Compr Canc Netw. 2019 Feb. doi: 10.6004/jnccn.2018.7070 
• Pekow J, Hernandez K, Meckel K, Deng Z, Haider HI, Khalil A, et al. IBD-associated colon cancers differ in DNA methylation and gene expression profiles compared to sporadic colon cancers. J Crohns Colitis. 2019 Feb 11. doi: 10.1093/ecco-jcc/jjz014 
• Koskimäki J, Girard R, Li Y, Saadat L, Zeineddine HA, Lightle R, et al. Comprehensive transcriptome analysis of cerebral cavernous malformation across multiple species and genotypes.  JCI Insight. 2019 Feb 7. doi: 10.1172/jci.insight.126167 
• Veneris JT, Huang L, Churpek JE, Conzen SD, Fleming GF. Glucocorticoid receptor expression is associated with inferior overall survival independent of BRCA mutation status in ovarian cancer. Int J Gynecol Cancer. 2019 Jan 25. doi: 10.1136/ijgc-2018-000101. 
• Feehley T, Plunkett CH, Bao R, Hong SMC, Culleen E, Belda-Ferre P, et al. Healthy infants harbor intestinal bacteria that protect against food allergy. Nature Medicine. 2019 Jan 14. doi: 10.1038/s41591-018-0324-z 
• Luke JJ, Bao R, Sweis RF, Spranger S, Gajewski TF. WNT/β-catenin pathway activation correlates with immune exclusion across human cancers. Clin Cancer Res. 2019 Jan 11. doi: 10.1158/1078-0432.CCR-18-1942 
• Baeten JT, Waarts MR, Pruitt MM, Chan WC, Andrade J, de Jong JLO. The side population enriches for leukemia propagating cell activity and Wnt pathway expression in zebrafish acute lymphoblastic leukemia. Haematologica. 2019 Jan 10. doi: 10.3324/haematol.2018.206417. [Epub ahead of print] 

2018

• Huang L, David O, Cabay RJ, Valyi-Nagy K, Macias V, Zhong R, et al. Molecular Classification of Lymph Node Metastases Subtypes Predict for Survival in Head and Neck Cancer. Clin Cancer Res. 2018 Dec 20. doi: 10.1158/1078-0432.CCR-18-1884 
• Kline DE, MacNabb BW, Chen X, Chan WC, Fosco D, Kline J. CD8α+ Dendritic Cells Dictate Leukemia-Specific CD8+ T Cell Fates. J Immunol. 2018 Dec 15. doi: 10.4049/jimmunol.1801184
• Labadie BW, Bao R, Luke JJ. Reimagining IDO pathway inhibition in cancer immunotherapy via downstream focus on the tryptophan-kynurenine-aryl hydrocarbon axis. Clin Cancer Res. 2018 Oct 30. doi: 10.1158/1078-0432.CCR-18-2882 
• Andrade J, Cox SM, Volchenboum SL. Large-Scale Data Sharing Initiatives in Genomic Oncology. Advances in Molecular Pathology. 2018 Nov. doi: 10.1016/j.yamp.2018.06.009 
• Lee J, Zhang LL, Wu W, Guo H, Li Y, Sukhanova M, et al. Activation of MYC, a bona fide client of HSP90, contributes to intrinsic ibrutinib resistance in mantle cell lymphoma. Blood Adv. 2018 Aug 28. doi: 10.1182/bloodadvances.2018016048 
• Sokol EA, Engelmann R, Kang W, Pinto N, Starkey A, Lai H, et al. Computer‐assisted Curie scoring for metaiodobenzylguanidine (MIBG) scans in patients with neuroblastoma. Pediatr Blood Cancer. 2018 Sep 10. doi: 10.1002/pbc.27417 
• Trujillo JA, Sweis RF, Bao R, Luke JJ. T Cell–Inflamed versus Non-T Cell–Inflamed Tumors: A Conceptual Framework for Cancer Immunotherapy Drug Development and Combination Therapy Selection. Cancer Immunol Res. 2018 Sep. doi: 10.1158/2326-6066.CIR-18-0277 
• Barbeira AN, Dickinson SP, Bonazzola R, Zheng J, Wheeler HE, Torres JM, et al. Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. Nat Commun. 2018 May 8. doi: 10.1038/s41467-018-03621-1 
• Bhanvadia RR, VanOpstall C, Brechka H, Barashi NS, Gillard M, McAuley EM, et al. MEIS1 and MEIS2 Expression and Prostate Cancer Progression: A Role For HOXB13 Binding Partners in Metastatic Disease. Clin Cancer Res. 2018 May 1. doi: 10.1158/1078-0432.CCR-17-3673. [Epub ahead of print] 
• Friedrich M, Bao R, Dia S, Issa HA, Alhussein D. Comparative evidence of an exceptional impact of gene duplication on the developmental evolution of Drosophila and the higher Diptera. Front Ecol Evol. 2018 May. doi: 10.3389/fevo.2018.00063 
• Publication Highlight: Pitroda SP, Khodarev NN, Huang L, Uppal A, Wightman SC, Ganai S, et al. Integrated molecular subtyping defines a curable oligometastatic state in colorectal liver metastasis. Nature Communications. 2018 May 4. doi: 10.1038/s41467-018-04278-6 
• Publication Highlight: Kang W, Kadri S, Puranik R, Wurst MN, Patil SA, Mujacic I, et al. System for Informatics in the Molecular Pathology Laboratory (SIMPL): An Open-Source End-to-End Solution for Next-Generation Sequencing Clinical Data Management. J Mol Diagn. 2018 Apr 24. doi: 10.1016/j.jmoldx.2018.03.008 
• Xie T, Bloom L, Padmanaban M, Bertacchi B, Kang W, MacCracken E, et al. Long-term effect of low frequency stimulation of STN on dysphagia, freezing of gait and other motor symptoms in PD. J Neurol Neurosurg Psychiatry. 2018 Apr 13. doi: 10.1136/jnnp-2018-318060. [Epub ahead of print] 
• Publication Highlight: Han J, Perez JT, Chen C, Li Y, Benitez A, Kandasamy M, et al. Genome-wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication. Cell Rep. 2018 Apr 10. doi: 10.1016/j.celrep.2018.03.045 
• Publication Highlight: Matson V, Fessler J, Bao R, Chongsuwat T, Zha Y, Alegre M, et al. The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science. 2018 Jan 5. doi: 10.1126/science.aao3290

2017

• Shah S, Wood K, Labadie B, Won B, Brisson R, Karrison T, et al. Clinical and molecular features of innate and acquired resistance to anti-PD-1/PD-L1 therapy in lung cancer. Oncotarget. 2017 Dec 15. doi:10.18632/oncotarget.23315 
• Vougiouklakis T, Bao R, Nakamura Y, Saloura V. Protein methyltransferases and demethylases dictate CD8+ T-cell exclusion in squamous cell carcinoma of the head and neck. Oncotarget. 2017 Nov 22. doi: 10.18632/oncotarget.22627 
• Gray JA, MacKillop J, Weafer J, Hernandez KM, Gao J, Palmer AA, et al. Genetic analysis of impulsive personality traits: Examination of a priori candidates and genome-wide variation. Psych Res. 2017 Oct. doi: 10.1016/j.psychres.2017.10.047 
• Samant SA, Kanwal A, Pillai VB, Bao R, Gupta MP. The histone deacetylase SIRT6 blocks myostatin expression and development of muscle atrophy. Sci Rep. 2017 Sep 19. doi:10.1038/s41598-017-10838-5 
• Girard R, Zeineddine HA, Fam MD, Mayampurath A, Cao Y, Shi C, et al. Plasma Biomarkers of Inflammation Reflect Seizures and Hemorrhagic Activity of Cerebral Cavernous Malformations. Transl Stroke Res. 2017 Aug 17. doi: 10.1007/s12975-017-0561-3. [Epub ahead of print] 
• 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. 
• Gozal D, Gileles-Hillel A, Cortese R, Li Y, Almendros I, Qiao Z, et al. Visceral white adipose tissue after chronic intermittent and sustained hypoxia in mice. Am J Respir Cell Mol Biol. 2017 Apr. doi: 10.1165/rcmb.2016-0243OC. 
• 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 
• Publication Highlight: 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. [Epub ahead of print] 

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: 10.1261/rna.052829.115. [Epub ahead of print] 
• 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 cerceral 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

2023

2022

• Xie T, Liao C, Lee D, Yu H, Padmanaban M, Kang W, et al. Disparities in diagnosis, treatment and survival between Black and White Parkinson patients. Parkinsonism Relat Disord. 2021 Apr 21;87:7-12. doi: 10.1016/j.parkreldis.2021.04.013

2020

• Gupta S, Hayek SS, Wang W, Chan L, Mathews KS, Melamed ML, et al. Factors Associated With Death in Critically Ill Patients With Coronavirus Disease 2019 in the US. JAMA Intern Med. 2020 Jul 15;e203596. doi: 10.1001/jamainternmed.2020.3596.

2018

• Pitroda SP, Khodarev NN, Huang L, Uppal A, Wightman SC, Ganai S, et al. Integrated molecular subtyping defines a curable oligometastatic state in colorectal liver metastasis. Nat Commun 9,1793 (2018). doi: 10.1038/s41467-018-04278-6 

2017

• Wiest K, Farnan J, Byrne E, Matern L, Cappaert M, Hirsch K, et al. Use of Simulation to Assess Incoming Interns’ Recognition of Opportunities to Choose Wisely. J Hosp Med. 2017 Jul; 12(7):493-497. PMID: 28699935 
• Lyons PG, Snyder A, Sokol S, Edelson DP, Mokhlesi B, Churpek MM. Association Between Opioid and Benzodiazepine Use and Clinical Deterioration in Ward Patients. J Hosp Med. 2017 Jun; 12(6):428-434. PMID: 28574532 
• Alverdy JC, Hyman N, Gilbert J, Luo JN, Krezalek M. Preparing the Bowel for Surgery: Learning from the Past and Planning for the Future. J Am Coll Surg. 2017 May 19. PMID: 28529136 
• Edelson DP, Churpek MM. Annals for Hospitalists Inpatient Notes – Predicting Codes-A Future With Fewer In-Hospital Cardiac Arrests. Ann Intern Med. 2017 May 16; 166(10):HO2-HO3. PMID: 28505657 
• Tabit CE, Coplan MJ, Spencer KT, Alcain CF, Spiegel T, Vohra AS, et al. Cardiology Consultation in the Emergency Department Reduces Re-hospitalizations for Low-Socioeconomic Patients with Acute Decompensated Heart Failure. Am J Med. 2017 Apr 27. PMID: 28457798 
• Churpek MM, Snyder A, Han X, Sokol S, Pettit N, Howell MD, et al. Quick Sepsis-related Organ Failure Assessment, Systemic Inflammatory Response Syndrome, and Early Warning Scores for Detecting Clinical Deterioration in Infected Patients outside the Intensive Care Unit. Am J Respir Crit Care Med. 2017 Apr 01; 195(7):906-911. PMID: 27649072 
• Padula WV, Gibbons RD, Pronovost PJ, Hedeker D, Mishra MK, Makic MB, et al. Using clinical data to predict high-cost performance coding issues associated with pressure ulcers: a multilevel cohort model. J Am Med Inform Assoc. 2017 Apr 01; 24(e1):e95-e102. PMID: 27539199 
• Krezalek MA, Yeh A, Alverdy JC, Morowitz M. Influence of nutrition therapy on the intestinal microbiome. Curr Opin Clin Nutr Metab Care. 2017 Mar; 20(2):131-137. PMID: 27997410 
• Sokol E, Huang E, Pytel P, Cohn SL, Pinto N. Rebound thymic hyperplasia following high dose chemotherapy and stem cell transplant in three neuroblastoma patients. Pediatr Blood Cancer. 2017 Mar; 64(3). PMID: 27663277 
• Grossman MN, Anderson SL, Worku A, Marsack W, Desai N, Tuvilleja A, et al. Awakenings? Patient and Hospital Staff Perceptions of Nighttime Disruptions and Their Effect on Patient Sleep. J Clin Sleep Med. 2017 Feb 15; 13(2):301-306. PMID: 27923432 
• Applebaum MA, Vaksman Z, Lee SM, Hungate EA, Henderson TO, London WB, et al. Neuroblastoma survivors are at increased risk for second malignancies: A report from the International Neuroblastoma Risk Group Project. Eur J Cancer. 2017 Feb; 72:177-185. PMID: 28033528 
• Siva S, Rubin DT, Gulotta G, Wroblewski K, Pekow J. Zinc Deficiency is Associated with Poor Clinical Outcomes in Patients with Inflammatory Bowel Disease. Inflamm Bowel Dis. 2017 Jan; 23(1):152-157. PMID: 27930412 

2016

• Churpek MM, Edelson DP. Moving Beyond Single-Parameter Early Warning Scores for Rapid Response System Activation. Crit Care Med. 2016 Dec; 44(12):2283-2285. PMID: 27858814 
• 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 Sep; 65:1-10. PMID: 27434878 

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

2023

• Kaskovich, S., Wyatt K. D., Oliwa, T., Graglia, L., Furner, B., Lee, J., Mayampurath, A., & Volchenboum, S. (2023). Automated Matching of Patients to Clinical Trials: A Patient-Centric Natural Language Processing Approach for Pediatric Leukemia. JCO Clinical Cancer Informatics, 7(2023), e2300009. doi: 10.1200/CCI.23.00009

2021

• Ridgway JP, Uvin A, Schmitt J, Oliwa T, Almirol E, Devlin S, Schneider J. Natural Language Processing of Clinical Notes to Identify Mental Illness and Substance Use Among People Living with HIV: Retrospective Cohort Study. JMIR Med Inform 2021;9(3):e23456. doi: 10.2196/23456

2020-21 Collaboration with STOP-COVID Investigators

• Al-Samkari H, Gupta S, Leaf RK, Wang W, Rosovsky RP, Brenner SK, et al. Thrombosis, Bleeding, and the Observational Effect of Early Therapeutic Anticoagulation on Survival in Critically Ill Patients With COVID-19. Ann Intern Med. 2021 Jan 26. doi: 10.7326/M20-6739. Epub ahead of print. PMID: 33493012.
• Gupta S, Hayek SS, Wang W, et al. Factors Associated With Death in Critically Ill Patients With Coronavirus Disease 2019 in the US. JAMA Intern Med. 2020;180(11):1436–1446. doi:10.1001/jamainternmed.2020.3596
• Leaf, R.K., Al‐Samkari, H., Brenner, S.K., Gupta, S. and Leaf, D.E. (2020), ABO phenotype and death in critically ill patients with COVID‐19. Br J Haematol, 190: e204-e208. https://doi.org/10.1111/bjh.16984
• Molnar, MZ, Bhalla, A, Azhar, A, et al; for the STOP-COVID Investigators. Outcomes of critically ill solid organ transplant patients with COVID‐19 in the United States. Am J Transplant. 2020; 20: 3061– 3071. https://doi.org/10.1111/ajt.16280
• Flythe JE, Assimon MM, Tugman MJ, et al. Characteristics and Outcomes of Individuals With Pre-existing Kidney Disease and COVID-19 Admitted to Intensive Care Units in the United States [published online ahead of print, 2020 Sep 19]. Am J Kidney Dis. 2020;S0272-6386(20)30999-9. doi:10.1053/j.ajkd.2020.09.003
• Hayek Salim S, Brenner Samantha K, Azam Tariq U, Shadid Husam R, Anderson Elizabeth, Berlin Hanna et al. In-hospital cardiac arrest in critically ill patients with covid-19: multicenter cohort study. BMJ 2020; 371 :m3513
• Easter SR, Gupta S, Brenner SK, Leaf DE. Outcomes of Critically Ill Pregnant Women with COVID-19 in the United States. Am J Respir Crit Care Med. 2020 Oct 7. doi: 10.1164/rccm.202006-2182LE. Epub ahead of print. PMID: 33026829.
• Gupta S, Coca SG, Chan L, Melamed ML, Brenner SK, Hayek SS, et al; STOP-COVID Investigators. AKI Treated with Renal Replacement Therapy in Critically Ill Patients with COVID-19. J Am Soc Nephrol. 2020 Oct 16:ASN.2020060897. doi: 10.1681/ASN.2020060897. Epub ahead of print. PMID: 33067383. 
• Gupta S, Wang W, Hayek SS, et al. Association Between Early Treatment With Tocilizumab and Mortality Among Critically Ill Patients With COVID-19. JAMA Intern Med. Published online October 20, 2020. doi:10.1001/jamainternmed.2020.6252

2020

• Oliwa T, Furner B, Schmitt J, Schneider J, Ridgway JP. Development of a predictive model for retention in HIV care using natural language processing of clinical notes. J Am Med Inform Assoc. 2020 Nov 5. doi: 10.1093/jamia/ocaa220.

2019

• Oliwa T, Maron SB, Chase LM, Lomnicki S, Catenacci DVT, Furner B, et al. Obtaining Knowledge in Pathology Reports Through a Natural Language Processing Approach With Classification, Named-Entity Recognition, and Relation-Extraction Heuristics. JCO Clin Cancer Inform. 2019 Aug 3. doi: 10.1200/CCI.19.00008.
• Borden BA, Lee SM, Danahey K, Galecki P, Patrick-Miller L, Siegler M, et al. Patient-provider communications about pharmacogenomic results increase patient recall of medication changes. Pharmacogenomics J. 2019 Feb 11. doi: 10.1038/s41397-019-0076-2. [Epub ahead of print] 
• Borden BA, Galecki P, Wellmann R, Danahey K, Lee SM, Patrick-Miller L. Assessment of provider-perceived barriers to clinical use of pharmacogenomics during participation in an institutional implementation study. Pharmacogenet Genomics. 2019 Feb. doi: 10.1097/FPC.0000000000000362. [Epub ahead of print] 

2018

• Lee YM, Danahey K, Knoebel RW, Ratain MJ, Meltzer DO, O’Donnell PH. Analysis of comprehensive pharmacogenomic profiling to impact in-hospital prescribing. Pharmacogenet Genomics. 2018 Dec 6. doi: 10.1097/FPC.0000000000000346. [Epub ahead of print] 
• Borden BA, Galecki P, Wellmann R, Danahey K, Lee SM, Patrick-Miller L, et al. Assessment of provider-perceived barriers to clinical use of pharmacogenomics during participation in an institutional implementation study. Pharmacogenet Genomics. 2018 Dec 6. doi: 10.1097/FPC.0000000000000362. [Epub ahead of print] 
• Patil SA, Mujacic I, Ritterhouse LL, Segal JP, Kadri S. insiM: in silico Mutator software for bioinformatics pipeline validation of clinical next-generation sequencing (NGS) assays. J Mol Diagn. 2018 Sep 29. doi: 10.1016/j.jmoldx.2018.08.001 
• Sokol EA, Engelmann R, Kang W, Pinto N, Starkey A, Lai H, et al. Computer‐assisted Curie scoring for metaiodobenzylguanidine (MIBG) scans in patients with neuroblastoma. Pediatr Blood Cancer. 2018 Sep 10. doi: 10.1002/pbc.27417 
• Wellmann R, Borden BA, Danahey K, Nanda R, Polite BN, Stadler WM, et al. Analyzing the clinical actionability of germline pharmacogenomic findings in oncology. Cancer. 2018 Jul 15;124(14):3052-3065. doi: 10.1002/cncr.31382. Epub 2018 May 9. 
• Cox SM, Lane A, Volchenboum SL. Use of Wearable, Mobile, and Sensor Technology in Cancer Clinical Trials. JCO Clin Cancer Inform. 2018 Jun 29. doi: 10.1200/CCI.17.00147 
• Mayampurath A, Volchenboum SL, Sanchez-Pinto LN. Using photoplethysmography data to estimate heart rate variability and its association with organ dysfunction in pediatric oncology patients. NPJ Digital Medicine. 2018 Jul 25. doi:10.1038/s41746-018-0038-0 

2017

• O’Donnell PH, Wadhwa N, Danahey K, Borden BA, Lee SM, Hall JP, et al. Pharmacogenomics-Based Point-of-Care Clinical Decision Support Significantly Alters Drug Prescribing. Clin Pharmacol Ther. 2017 Nov. doi: 10.1002/cpt.709 
• Danahey K, Borden BA, Furner B, Yukman P, Hussain S, Saner D, et al. Simplifying the Use of Pharmacogenomics in Clinical Practice: Building the Genomic Prescribing System. J Biomed Inform. 2017 Sep 28. doi: 10.1016/j.jbi.2017.09.012 
• 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. 2017 Jul;102(1):106-114. doi: 10.1002/cpt.586. Epub 2017 Apr 4. 
• Krezalek MA, Mayampurath A, Johnson JA, Milner R, Skelly CL, Babrowski T. Gender differences in carotid artery restenosis rates following surgical intervention. J Vasc Surg. 2017 Jun. doi: 10.1016/j.jvs.2017.03.165 
• Collier ZJ, Gottlieb LJ, Alverdy JC. Stochasticity among antibiotic-resistance profiles of common burn-related pathogens over a six-year period. Surg Infect. 2017 Apr. doi: 10.1089/sur.2016.191 
• Leung EKY, Agolini E, Pei X, Melis R, McMillin GA, Friedman PN, et al. Validation of an Extensive CYP2D6 Assay Panel Based on Invader and TaqMan Copy Number Assays. J Appl Lab Med. 2017 Mar; DOI: 10.1373/jalm.2016.021923. 

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] 
• Padhye L, Mayampurath A, Fenny N, Wolf R, Ciaccio C. Cross-sensitization patterns among common food allergens are similar between black and white patients. Annals of Allergy, Asthma & Immunology. 2016 Nov. doi: 10.1016/j.anai.2016.09.301 
• 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. 

2014

• O’Donnell PH, Danahey K, Jacobs M, Wadhwa NR, Yuen S, Bush A, et al. Adoption of a clinical pharmacogenomics implementation program during outpatient care–initial results of the University of Chicago “1,200 Patients Project”. Am J Med Genet C Semin Med Genet. 2014 Mar;166C(1):68-75. doi: 10.1002/ajmg.c.31385. Epub 2014 Mar 10. 

2012

• O’Donnell PH, Bush A, Spitz J, Danahey K, Saner D, Das S, et al. The 1200 patients project: creating a new medical model system for clinical implementation of pharmacogenomics. Clin Pharmacol Ther. 2012 Oct;92(4):446-9. doi: 10.1038/clpt.2012.117. Epub 2012 Aug 29. Review.