Publications

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User-Computer Interface
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010;43(5):709-15.
United States
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011;18(4):498-505.
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Translational Medical Research
Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011;18(4):354-7.
Transforming Growth Factor beta2
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Transforming Growth Factor beta
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Spermatozoa
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011;12:467.
Software Validation
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011;18(4):498-505.
Software
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011;12:467.
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010;43(5):709-15.
Brinza D, Schultz M, Tesler G, Bafna V. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010;26(22):2856-62.
Smad3 Protein
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Signal Transduction
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Sequence Analysis, RNA
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011;27(8):1068-75.
Sequence Analysis, DNA
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011;18(3):401-13.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011;12 Suppl 1:S24.
Sensitivity and Specificity
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011;18(4):498-505.
RNA, Messenger
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011;27(8):1068-75.
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Receptors, Transforming Growth Factor beta
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Protein-Serine-Threonine Kinases
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Prostatic Neoplasms
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011;27(8):1068-75.
Polymorphism, Single Nucleotide
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011;18(3):401-13.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011;12 Suppl 1:S24.
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Brinza D, Schultz M, Tesler G, Bafna V. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010;26(22):2856-62.
Pilot Projects
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011;18(4):498-505.
Phenotype
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Open Reading Frames
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Oligonucleotide Array Sequence Analysis
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011;12:467.
Mucocutaneous Lymph Node Syndrome
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
MicroRNAs
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Medical Informatics Applications
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010;43(5):709-15.
Medical Informatics
Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011;18(4):354-7.
Management Audit
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011;18(4):498-505.
Male
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011;12:467.
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011;27(8):1068-75.
Lung Neoplasms
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Logistic Models
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011;18(4):498-505.
Linkage Disequilibrium
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Introns
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Interprofessional Relations
Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011;18(4):354-7.
Information Storage and Retrieval
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010;43(5):709-15.
Immunoglobulins, Intravenous
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Humans
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011;18(4):498-505.
Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011;18(4):354-7.
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011;12:467.
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011;27(8):1068-75.
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011;18(3):401-13.
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010;43(5):709-15.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011;12 Suppl 1:S24.
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Human Genome Project
Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011;18(4):354-7.
Haplotypes
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011;12 Suppl 1:S24.
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Great Britain
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Genomics
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011;18(3):401-13.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011;12 Suppl 1:S24.
Brinza D, Schultz M, Tesler G, Bafna V. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010;26(22):2856-62.
Genome-Wide Association Study
Brinza D, Schultz M, Tesler G, Bafna V. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010;26(22):2856-62.
Genome, Human
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011;18(3):401-13.
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011;12 Suppl 1:S24.
Genome
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011;12:467.
Genetic Predisposition to Disease
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Gene Fusion
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011;27(8):1068-75.
Gene Expression Regulation, Neoplastic
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Gene Expression Profiling
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011;12:467.
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011;27(8):1068-75.
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010;43(5):709-15.
Gene Expression
Brinza D, Schultz M, Tesler G, Bafna V. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010;26(22):2856-62.
Electronic Health Records
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011;18(4):498-505.
Databases, Genetic
Brinza D, Schultz M, Tesler G, Bafna V. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010;26(22):2856-62.
Data Compression
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011;18(3):401-13.
Coronary Vessels
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Conserved Sequence
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Computer Security
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011;18(4):498-505.
Computer Communication Networks
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010;43(5):709-15.
Computational Biology
Sarkar IN, Butte AJ, Lussier YA, Tarczy-Hornoch P, Ohno-Machado L. Translational bioinformatics: linking knowledge across biological and clinical realms. J Am Med Inform Assoc. 2011;18(4):354-7.
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010;43(5):709-15.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011;12 Suppl 1:S24.
Cohort Studies
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Cell Line
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011;27(8):1068-75.
Carcinoma, Non-Small-Cell Lung
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Bias (Epidemiology)
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Australia
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Artificial Intelligence
Boxwala AA, Kim J, Grillo JM, Ohno-Machado L. Using statistical and machine learning to help institutions detect suspicious access to electronic health records. J Am Med Inform Assoc. 2011;18(4):498-505.
Aorta
Shimizu C, Jain S, Davila S, Hibberd ML, Lin KO, Molkara D, Frazer JR, Sun S, Baker AL, Newburger JW. Transforming growth factor-beta signaling pathway in patients with Kawasaki disease. Circ Cardiovasc Genet. 2011;4(1):16-25.
Animals
Hinske LCG, Galante PAF, Kuo WP, Ohno-Machado L. A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics. 2010;11:533.
Lacson R, Pitzer E, Kim J, Galante P, Hinske C, Ohno-Machado L. DSGeo: software tools for cross-platform analysis of gene expression data in GEO. J Biomed Inform. 2010;43(5):709-15.
Algorithms
Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011;12:467.
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011;18(3):401-13.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011;12 Suppl 1:S24.