Biomedical Informatics
Publications
Division Publications
Adams AK, Bolanos LC, Dexheimer PJ, Karns RA, Aronow BJ, Komurov K, Jegga AG, Casper KA, Patil YJ, Wilson KM, Starczynowski DT, Wells SI. Irak1 Is a Novel Dek Transcriptional Target and Is Essential for Head and Neck Cancer Cell Survival. Oncotarget . 2015; 6:43395-407.
Arya R, Gillespie CW, Cnaan A, Devarajan M, Clark P, Shinnar S, Vinks AA, Mizuno K, Glauser TA, Childhood Absence Epilepsy Study Group. Obesity and Overweight as Cae Comorbidities and Differential Drug Response Modifiers. Neurology . 2016; 86:1613-21.
Berry RL, Ozdemir DD, Aronow B, Lindstrom NO, Dudnakova T, Thornburn A, Perry P, Baldock R, Armit C, Joshi A, Jeanpierre C, Shan J, Vainio S, Baily J, Brownstein D, Davies J, Hastie ND, Hohenstein P. Deducing the Stage of Origin of Wilms' Tumours from a Developmental Series of Wt1-Mutant Mice. Dis Model Mech . 2015; 8:903-17.
Bian F, Gao F, Kartashov AV, Jegga AG, Barski A, Das SK. Polycomb Repressive Complex 1 Controls Uterine Decidualization. Sci Rep . 2016; 6:26061.
Cai WF, Liu GS, Lam CK, Florea S, Qian J, Zhao W, Pritchard T, Haghighi K, Lebeche D, Lu LJ, Deng J, Fan GC, Hajjar RJ, Kranias EG. Up-Regulation of Micro-Rna765 in Human Failing Hearts Is Associated with Post-Transcriptional Regulation of Protein Phosphatase Inhibitor-1 and Depressed Contractility. Eur J Heart Fail . 2015; 17:782-93.
Chen S, Brunskill EW, Potter SS, Dexheimer PJ, Salomonis N, Aronow BJ, Hong CI, Zhang T, Kopan R. Intrinsic Age-Dependent Changes and Cell-Cell Contacts Regulate Nephron Progenitor Lifespan. Dev Cell . 2015; 35:49-62.
Chen Y, Mazlack LJ, Minai AA, Lu LJ. Inferring Causal Networks Using Fuzzy Cognitive Maps and Evolutionary Algorithms with Application to Gene Regulatory Network Reconstruction. Appl Soft Comput . 2015; 37:667-79.
Cheung D, Ma J. Probing the Impact of Temperature on Molecular Events in a Developmental System. Sci Rep . 2015; 5:13124.
Cohen K, Glass B, Greiner H, Holland-Bouley K, Standridge S, Arya R, Faist R, Morita D, Mangano F, Connolly B. Methodological Issues in Predicting Pediatric Epilepsy Surgery Candidates through Natural Language Processing and Machine Learning. pmc/PMC4876984. Biomed Inform Insights . 2016; 8:11-8.
Connolly N, Anixt J, Manning P, Ping ILD, Marsolo KA, Bowers K. Maternal Metabolic Risk Factors for Autism Spectrum Disorder-an Analysis of Electronic Medical Records and Linked Birth Data. Autism Res . 2016; 9:829-37.
Cooke JP, Meng S, Wong WT, Sayed N, Ospino F, Lee J, Jha A, Dexheimer P, Aronow B. Response to Letter Regarding Article Transdifferentiation of Human Fibroblasts to Endothelial Cells: Role of Innate Immunity. Circulation . 2015; 132:e197.
Davis J, Salomonis N, Ghearing N, Lin SC, Kwong JQ, Mohan A, Swanson MS, Molkentin JD. Mbnl1-Mediated Regulation of Differentiation Rnas Promotes Myofibroblast Transformation and the Fibrotic Response. Nat Commun . 2015; 6:10084.
Fukuma K, Kawanaka H, Prasath S, Aronow BJ, Takase H. Feature Extraction and Disease Stage Classification for Glioma Histopathology Images. 2015 17th International Conference on E-Health Networking, Application & Services (Healthcom) . 2015:598-99.
Fulford L, Milewski D, Ustiyan V, Ravishankar N, Cai Y, Le T, Masineni S, Kasper S, Aronow B, Kalinichenko VV, Kalin TV. The Transcription Factor Foxf1 Promotes Prostate Cancer by Stimulating the Mitogen-Activated Protein Kinase Erk5. Sci Signal . 2016; 9:ra48.
Hawrylycz M, Miller JA, Menon V, Feng D, Dolbeare T, Guillozet-Bongaarts AL, Jegga AG, Aronow BJ, Lee CK, Bernard A, Glasser MF, Dierker DL, Menche J, Szafer A, Collman F, Grange P, Berman KA, Mihalas S, Yao Z, Stewart L, et al. Canonical Genetic Signatures of the Adult Human Brain. Nat Neurosci . 2015; 18:1832-44.
Heink A, Davidson WS, Swertfeger DK, Lu LJ, Shah AS. A Comparison of Methods to Enhance Protein Detection of Lipoproteins by Mass Spectrometry. J Proteome Res . 2015; 14:2943-50.
Herr TM, Bielinski SJ, Bottinger E, Brautbar A, Brilliant M, Chute CG, Cobb BL, Denny JC, Hakonarson H, Hartzler AL, Hripcsak G, Kannry J, Kohane IS, Kullo IJ, Lin S, Manzi S, Marsolo K, Overby CL, Pathak J, Peissig P, et al. Practical Considerations in Genomic Decision Support: The Emerge Experience. J Pathol Inform . 2015; 6:50.
Hoffman L, DeWire M, Ryall S, Buczkowicz P, Leach J, Miles L, Ramani A, Brudno M, Kumar S, Drissi R. Spatial Genomic Heterogeneity in Diffuse Intrinsic Pontine and Midline High-Grade Glioma: Implications for Diagnostic Biopsy and Targeted Therapeutics. Acta Neuropathol Commun . 2016; 4:1.
Hutton JS, Horowitz-Kraus T, Mendelsohn AL, DeWitt T, Holland SK, C-Mind Authorship Consortium. Home Reading Environment and Brain Activation in Preschool Children Listening to Stories. Pediatrics . 2015; 136:466-78.
Jin X, Khatwani C, Niu N, Wagner M, Savolainen J. Pragmatic Software Reuse in Bioinformatics: How Can Social Network Information Help? In: G Kapitsaki, E DeAlmeida, eds. Software Reuse: Bridging with Social-Awareness . Switzerland: Springer; 2016:247-64.
Kamath-Rayne BD, Du Y, Hughes M, Wagner EA, Muglia LJ, DeFranco EA, Whitsett JA, Salomonis N, Xu Y. Systems Biology Evaluation of Cell-Free Amniotic Fluid Transcriptome of Term and Preterm Infants to Detect Fetal Maturity. BMC Med Genomics . 2015; 8:67.
Kouril M. Leveraging Fpga Clusters for Sat Computations. Adv Parallel Computing . 2016; 27:525-32.
Li H, Gordon SM, Zhu X, Deng J, Swertfeger DK, Davidson WS, Lu LJ. Network-Based Analysis on Orthogonal Separation of Human Plasma Uncovers Distinct High Density Lipoprotein Complexes. J Proteome Res . 2015; 14:3082-94.
Li MH, Abrudan JL, Dulik MC, Sasson A, Brunton J, Jayaraman V, Dugan N, Haley D, Rajagopalan R, Biswas S, Sarmady M, DeChene ET, Deardorff MA, Wilkens A, Noon SE, Scarano MI, Santani AB, White PS, Pennington J, Conlin LK, et al. Utility and Limitations of Exome Sequencing as a Genetic Diagnostic Tool for Conditions Associated with Pediatric Sudden Cardiac Arrest/Sudden Cardiac Death. Hum Genomics . 2015; 9:15.
Li Q, Kirkendall ES, Hall ES, Ni Y, Lingren T, Kaiser M, Lingren N, Zhai H, Solti I, Melton K. Automated Detection of Medication Administration Errors in Neonatal Intensive Care. J Biomed Inform . 2015; 57:124-33.
Liu J, Ma J. Modulation of Temporal Dynamics of Gene Transcription by Activator Potency in the Drosophila Embryo. Development . 2015; 142:3781-90.
Lu Y, Lu Y, Deng J, Peng H, Lu H, Lu LJ. A Novel Essential Domain Perspective for Exploring Gene Essentiality. Bioinformatics . 2015; 31:2921-9.
Ma J, He F, Xie G, Deng WM. Maternal Ap Determinants in the Drosophila Oocyte and Embryo. Wiley Interdiscip Rev Dev Biol . 2016; 5:562-81.
Marsolo K, Margolis PA, Forrest CB, Colletti RB, Hutton JJ. A Digital Architecture for a Network-Based Learning Health System: Integrating Chronic Care Management, Quality Improvement, and Research. EGEMS (Wash DC) . 2015; 3:1168.
Matrka MC, Hennigan RF, Kappes F, DeLay ML, Lambert PF, Aronow BJ, Wells SI. Dek over-Expression Promotes Mitotic Defects and Micronucleus Formation. Cell Cycle . 2015; 14:3939-53.
Meyer SE, Qin T, Muench DE, Masuda K, Venkatasubramanian M, Orr E, Suarez L, Gore SD, Delwel R, Paietta E, Tallman MS, Fernandez H, Melnick A, Le Beau MM, Kogan S, Salomonis N, Figueroa ME, Grimes HL. Dnmt3a Haploinsufficiency Transforms Flt3itd Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia. Cancer Discov . 2016; 6:501-15.
Miethke AG, Zhang W, Simmons J, Taylor AE, Shi T, Shanmukhappa SK, Karns R, White S, Jegga AG, Lages CS, Nkinin S, Keller BT, Setchell KD. Pharmacological Inhibition of Apical Sodium-Dependent Bile Acid Transporter Changes Bile Composition and Blocks Progression of Sclerosing Cholangitis in Multidrug Resistance 2 Knockout Mice. Hepatology . 2016; 63:512-23.
Mo H, Thompson WK, Rasmussen LV, Pacheco JA, Jiang G, Kiefer R, Zhu Q, Xu J, Montague E, Carrell DS, Lingren T, Mentch FD, Ni Y, Wehbe FH, Peissig PL, Tromp G, Larson EB, Chute CG, Pathak J, Denny JC, et al. Desiderata for Computable Representations of Electronic Health Records-Driven Phenotype Algorithms. J Am Med Inform Assoc . 2015; 22:1220-30.
Morgan A, Mooney S, Aronow B, Brenner S. Precision Medicine: Data and Discovery for Improved Health and Therapy. Pac Symp Biocomput . 2016; 21:243-48.
Mrug M, Zhou J, Yang C, Aronow BJ, Cui X, Schoeb TR, Siegal GP, Yoder BK, Guay-Woodford LM. Genetic and Informatic Analyses Implicate Kif12 as a Candidate Gene within the Mpkd2 Locus That Modulates Renal Cystic Disease Severity in the Cys1cpk Mouse. PLoS One . 2015; 10:e0135678.
Namjou B, Marsolo K, Lingren T, Ritchie MD, Verma SS, Cobb BL, Perry C, Kitchner TE, Brilliant MH, Peissig PL, Borthwick KM, Williams MS, Grafton J, Jarvik GP, Holm IA, Harley JB. A Gwas Study on Liver Function Test Using Emerge Network Participants. PLoS One . 2015; 10:e0138677.
Nayak RC, Trump LR, Aronow BJ, Myers K, Mehta P, Kalfa T, Wellendorf AM, Valencia CA, Paddison PJ, Horwitz MS, Grimes HL, Lutzko C, Cancelas JA. Pathogenesis of Elane-Mutant Severe Neutropenia Revealed by Induced Pluripotent Stem Cells. J Clin Invest . 2015; 125:3103-16.
Pestian JP, Grupp-Phelan J, Bretonnel Cohen K, Meyers G, Richey LA, Matykiewicz P, Sorter MT. A Controlled Trial Using Natural Language Processing to Examine the Language of Suicidal Adolescents in the Emergency Department. Suicide Life Threat Behav . 2016; 46:154-9.
Pfluger PT, Kabra DG, Aichler M, Schriever SC, Pfuhlmann K, Garcia VC, Lehti M, Weber J, Kutschke M, Rozman J, Elrod JW, Hevener AL, Feuchtinger A, Hrabe de Angelis M, Walch A, Rollmann SM, Aronow BJ, Muller TD, Perez-Tilve D, Jastroch M, et al. Calcineurin Links Mitochondrial Elongation with Energy Metabolism. Cell Metab . 2015; 22:838-50.
Pogacar R, Plant E, Rosulek LF, Kouril M. Sounds Good: Phonetic Sound Patterns in Top Brand Names. Mark Lett . 2015; 26:549-63.
Prasath VBS, Fukuma K, Aronow BJ, Kawanaka H. Cell Nuclei Segmentation in Glioma Histopathology Images with Color Decomposition Based Active Contours. Proceedings (IEEE Int Conf Bioinformatics Biomed) . 2015:1734-36.
Ren S, Hinzman AA, Kang EL, Szczesniak RD, Lu LJ. Computational and Statistical Analysis of Metabolomics Data. Metabolomics . 2015; 11:1492-513.
Shinnar S, Cnaan A, Hu F, Clark P, Dlugos D, Hirtz DG, Masur D, Mizrahi EM, Moshe SL, Glauser TA, Childhood Absence Epilepsy Study Group. Long-Term Outcomes of Generalized Tonic-Clonic Seizures in a Childhood Absence Epilepsy Trial. Neurology . 2015; 85:1108-14.
Sigdel T, Bestard O, Salomonis N, Hsieh S, Torras J, Naesens M, Tran T, Roedder S, Sarwal M. Intragraft Antiviral-Specific Gene Expression as a Distinctive Transcriptional Signature for Studies in Polyomavirus-Associated Nephropathy. Transplantation . 2016.
Soreq L, Salomonis N, Israel Z, Bergman H, Soreq H. Analyzing Alternative Splicing Data of Splice Junction Arrays from Parkinson Patients' Leukocytes before and after Deep Brain Stimulation as Compared with Control Donors. Genom Data . 2015; 5:340-3.
Sumegi J, Nestheide S, Aronow B, Fletcher D, Keddache M, Villanueva J, Zhang K, Filipovich AH. Microrna Activation Signature in Patients with Hemophagocytic Lymphohistiocytosis and Reversibility with Disease-Specific Therapy. J Allergy Clin Immunol . 2016; 137:309-12.
Tan L, Holland SK, Deshpande AK, Chen Y, Choo DI, Lu LJ. A Semi-Supervised Support Vector Machine Model for Predicting the Language Outcomes Following Cochlear Implantation Based on Pre-Implant Brain Fmri Imaging. Brain Behav . 2015; 5:e00391.
Toledo CM, Ding Y, Hoellerbauer P, Davis RJ, Basom R, Girard EJ, Lee E, Corrin P, Hart T, Bolouri H, Davison J, Zhang Q, Hardcastle J, Aronow BJ, Plaisier CL, Baliga NS, Moffat J, Lin Q, Li XN, Nam DH, et al. Genome-Wide Crispr-Cas9 Screens Reveal Loss of Redundancy between Pkmyt1 and Wee1 in Glioblastoma Stem-Like Cells. Cell Rep . 2015; 13:2425-39.
Topol A, English JA, Flaherty E, Rajarajan P, Hartley BJ, Gupta S, Desland F, Zhu S, Goff T, Friedman L, Rapoport J, Felsenfeld D, Cagney G, Mackay-Sim A, Savas JN, Aronow B, Fang G, Zhang B, Cotter D, Brennand KJ. Increased Abundance of Translation Machinery in Stem Cell-Derived Neural Progenitor Cells from Four Schizophrenia Patients. Transl Psychiatry . 2015; 5:e662.
Unruh D, Srinivasan R, Benson T, Haigh S, Coyle D, Batra N, Keil R, Sturm R, Blanco V, Palascak M, Franco RS, Tong W, Chatterjee T, Hui DY, Davidson WS, Aronow BJ, Kalfa T, Manka D, Peairs A, Blomkalns A, et al. Red Blood Cell Dysfunction Induced by High-Fat Diet: Potential Implications for Obesity-Related Atherosclerosis. Circulation . 2015; 132:1898-908.
Venek V, Scherer S, Morency LP, Rizzo A, Pestian J. Adolescent Suicidal Risk Assessment in Clinician-Patient Interaction: A Study of Verbal and Acoustic Behaviors. IEEE Trans Affect Comput . 2016; PP.
Vitalone MJ, Sigdel TK, Salomonis N, Sarwal RD, Hsieh SC, Sarwal MM. Transcriptional Perturbations in Graft Rejection. Transplantation . 2015; 99:1882-93.
Watson J, Kinstler A, Vidonish WP, 3rd, Wagner M, Lin L, Davis KG, Kotowski SE, Daraiseh NM. Impact of Noise on Nurses in Pediatric Intensive Care Units. Am J Crit Care . 2015; 24:377-84.
Wu H, Manu, Jiao R, Ma J. Temporal and Spatial Dynamics of Scaling-Specific Features of a Gene Regulatory Network in Drosophila. Nat Commun . 2015; 6:10031.
Xu J, Liu H, Lan Y, Aronow BJ, Kalinichenko VV, Jiang R. A Shh-Foxf-Fgf18-Shh Molecular Circuit Regulating Palate Development. PLoS Genet . 2016; 12:e1005769.