Biomedical Statistics and Informatics

Research Output 2007 2019

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2014
25 Citations (Scopus)

Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E

Sun, Z. D., Wu, Y., Ordog, T., Baheti, S., Nie, J., Duan, X., Hojo, K., Kocher, J-P., Dyck, P. J. & Klein, C. J., Jul 7 2014, In : Epigenetics. 9, 8, p. 1184-1193 10 p.

Research output: Contribution to journal › Article

Hereditary Sensory and Autonomic Neuropathies
Methyltransferases
Mutation
DNA
Genetic Databases
48 Citations (Scopus)

Activation of TAK1 by MYD88 L265P drives malignant B-cell growth in non-Hodgkin lymphoma

Ansell, S. M., Hodge, L. S., Secreto, F. J., Manske, M., Braggio, E. D., Price-Troska, T., Ziesmer, S., Li, Y., Johnson, S. H., Hart, S., Kocher, J-P., Vasmatzis, G., Chanan Khan, A. A., Gertz, M., Fonseca, R., Dogan, A., Cerhan, J. R. & Novak, A. J., 2014, In : Blood Cancer Journal. 4, 2, 20144.

Research output: Contribution to journal › Article

Waldenstrom Macroglobulinemia
Non-Hodgkin's Lymphoma
B-Lymphocytes
Growth
TNF Receptor-Associated Factor 6
9 Citations (Scopus)

Antiemetic prescribing practices using a computerized physician order entry system

Kadakia, K. C., Leal, A. D., Seisler, D. K., Qin, R., Fee-Schroeder, K. C., Grendahl, D. C., Sorgatz, K. M. & Loprinzi, C. L., Jan 2014, In : Supportive Care in Cancer. 22, 1, p. 217-223 7 p.

Research output: Contribution to journal › Article

Medical Order Entry Systems
Antiemetics
Drug Therapy
Nausea
Vomiting
30 Citations (Scopus)

Application of whole exome sequencing in undiagnosed inherited polyneuropathies

Klein, C. J., Middha, S., Duan, X., Wu, Y., Litchy, W. J., Gu, W., Dyck, P. J. B., Gavrilova, R. M., Smith, D. I., Kocher, J-P. & Dyck, P. J., Mar 6 2014, (Accepted/In press) In : Journal of Neurology, Neurosurgery and Psychiatry.

Research output: Contribution to journal › Article

Exome
Polyneuropathies
Mutation
Genes
Genetic Association Studies
1 Citation (Scopus)

A use case study on late stent thrombosis for ontology-based temporal reasoning and analysis

Clark, K., Sharma, D., Qin, R., Chute, C. G. & Tao, C., Dec 11 2014, In : Journal of Biomedical Semantics. 5, 1, 49.

Research output: Contribution to journal › Article

Stents
Ontology
Thrombosis
Libraries
Equipment and Supplies
72 Citations (Scopus)

CAP-miRSeq: A comprehensive analysis pipeline for microRNA sequencing data

Sun, Z. D., Evans, J., Bhagwate, A., Middha, S., Bockol, M., Yan, H. D. & Kocher, J-P., Jun 3 2014, In : BMC Genomics. 15, 1, 423.

Research output: Contribution to journal › Article

MicroRNAs
Biomarkers
Computational Biology
Research
Research Personnel
25 Citations (Scopus)

Chemoimmunotherapy for relapsed/refractory and progressive 17p13-deleted chronic lymphocytic leukemia (CLL) combining pentostatin, alemtuzumab, and low-dose rituximab is effective and tolerable and limits loss of CD20 expression by circulating CLL cells

Zent, C. S., Taylor, R. P., Lindorfer, M. A., Beum, P. V., Laplant, B., Wu, W., Call, T. G., Bowen, D. A., Conte, M. J., Frederick, L. A., Link, B. K., Blackwell, S. E., Veeramani, S., Baig, N. A., Viswanatha, D. S., Weiner, G. J. & Witzig, T. E., 2014, In : American Journal of Hematology. 89, 7, p. 757-765 9 p.

Research output: Contribution to journal › Article

Pentostatin
B-Cell Chronic Lymphocytic Leukemia
Therapeutics
alemtuzumab
Rituximab
22 Citations (Scopus)

Clinical proteome informatics workbench detects pathogenic mutations in hereditary amyloidoses

Dasari, S., Theis, J. D., Vrana, J. A., Zenka, R. M., Zimmermann, M. T., Kocher, J-P., Highsmith, W. E. J., Kurtin, P. J. & Dogan, A., May 2 2014, In : Journal of Proteome Research. 13, 5, p. 2352-2358 7 p.

Research output: Contribution to journal › Article

Familial Amyloidosis
Medical Informatics
Workflow
Proteome
Amyloid
17 Citations (Scopus)

Comprehensive assessment of genetic variants within TCF4 in Fuchs’ endothelial corneal dystrophy

Wieben, E. D., Aleff, R. A., Eckloff, B. W., Atkinson, E. J., Baheti, S., Middha, S., Brown, W. L., Patel, S. V., Kocher, J-P. & Baratz, K., 2014, In : Investigative Ophthalmology and Visual Science. 55, 9, p. 6101-6107 7 p.

Research output: Contribution to journal › Article

Fuchs' Endothelial Dystrophy
Transcription Factors
Trinucleotide Repeat Expansion
Corneal Dystrophy, Fuchs Endothelial, 4
Introns
82 Citations (Scopus)

CrossMap: A versatile tool for coordinate conversion between genome assemblies

Zhao, H., Sun, Z. D., Wang, J., Huang, H., Kocher, J-P. & Wang, L., Apr 1 2014, In : Bioinformatics. 30, 7, p. 1006-1007 2 p.

Research output: Contribution to journal › Article

Convert
Genome
Sequence Alignment
Genes
Gene transfer
39 Citations (Scopus)

Doxepin rinse versus placebo in the treatment of acute oral mucositis pain in patients receiving head and neck radiotherapy with or without chemotherapy: A phase III, randomized, double-blind trial (NCCTG-N09C6 [Alliance])

Leenstra, J. L., Miller, R. C., Qin, R., Martenson, J. A., Dornfeld, K. J., Bearden, J. D., Puri, D. R., Stella, P. J., Mazurczak, M. A., Klish, M. D., Novotny, P. J., Foote, R. L. & Loprinzi, C. L., May 20 2014, In : Journal of Clinical Oncology. 32, 15, p. 1571-1577 7 p.

Research output: Contribution to journal › Article

Doxepin
Stomatitis
Neck
Radiotherapy
Head
1 Citation (Scopus)

From days to hours: Reporting clinically actionable variants from whole genome sequencing

Middha, S., Baheti, S., Hart, S. & Kocher, J-P., Feb 5 2014, In : PLoS One. 9, 2, e86803.

Research output: Contribution to journal › Article

Workflow
Genes
Genome
Technology
genome
4 Citations (Scopus)

Genome-wide analysis of loss of heterozygosity in breast infiltrating ductal carcinoma distant normal tissue highlights arm specific enrichment and expansion across tumor stages

Ruan, X., Liu, H. D., Boardman, L. A. & Kocher, J-P., Apr 18 2014, In : PLoS One. 9, 4, e95783.

Research output: Contribution to journal › Article

Carcinoma, Ductal, Breast
Loss of Heterozygosity
breasts
carcinoma
Tumors
17 Citations (Scopus)

HiChIP: A high-throughput pipeline for integrative analysis of ChIP-Seq data

Yan, H. D., Evans, J., Kalmbach, M., Moore, R., Middha, S., Luban, S., Wang, L., Bhagwate, A., Li, Y., Sun, Z. D., Chen, X. & Kocher, J-P., Aug 15 2014, In : BMC Bioinformatics. 15, 1, 280.

Research output: Contribution to journal › Article

Chromatin Immunoprecipitation
Chromatin
High Throughput
Pipelines
Throughput
44 Citations (Scopus)

IM-TORNADO: A tool for comparison of 16S reads from paired-end libraries

Jeraldo, P., Kalari, K. R., Chen, X., Bhavsar, J., Mangalam, A., White, B., Nelson, H., Kocher, J-P. & Chia, N. D., Dec 15 2014, In : PLoS One. 9, 12, e114804.

Research output: Contribution to journal › Article

Ribosomal DNA
Libraries
Pipelines
RNA
Taxonomies
153 Citations (Scopus)

Integrated Genomic Characterization Reveals Novel, Therapeutically Relevant Drug Targets in FGFR and EGFR Pathways in Sporadic Intrahepatic Cholangiocarcinoma

Borad, M. J., Champion, M. D., Egan, J. B., Liang, W. S., Fonseca, R., Bryce, A. H., McCullough, A. E., Barrett, M., Hunt, K., Patel, M. D., Young, S. W., Collins, J. M., Silva, A. C., Condjella, R. M., Block, M. S., Mc Williams, R. R., Lazaridis, K. N., Klee, E. W., Bible, K. C., Harris, P. & 29 others, Oliver, G. R., Bhavsar, J. D., Nair, A. A., Middha, S., Asmann, Y., Kocher, J-P., Schahl, K., Kipp, B. R., Barr Fritcher, E. G., Baker, A., Aldrich, J., Kurdoglu, A., Izatt, T., Christoforides, A., Cherni, I., Nasser, S., Reiman, R., Phillips, L., McDonald, J., Adkins, J., Mastrian, S. D., Placek, P., Watanabe, A. T., LoBello, J., Han, H., Von Hoff, D., Craig, D. W., Stewart, A. K. & Carpten, J. D., Feb 2014, In : PLoS Genetics. 10, 2, e1004135.

Research output: Contribution to journal › Article

Cholangiocarcinoma
tumor
genomics
drug
inhibitor
10 Citations (Scopus)

Long-term outcomes and role of chemotherapy in adults with newly diagnosed medulloblastoma

Call, J. A., Naik, M., Rodriguez, F. J., Giannini, C., Wu, W., Buckner, J. C., Parney, I. F. & Laack, N. N., Feb 2014, In : American Journal of Clinical Oncology: Cancer Clinical Trials. 37, 1, p. 1-7 7 p.

Research output: Contribution to journal › Article

Medulloblastoma
Disease-Free Survival
Drug Therapy
Survival
Histology
35 Citations (Scopus)

MACE: model based analysis of ChIP-exo

Wang, L., Chen, J., Wang, C., Uusküla-Reimand, L., Chen, K., Medina-Rivera, A., Young, E. J., Zimmermann, M. T., Yan, H. D., Sun, Z. D., Zhang, Y., Wu, S. T., Huang, H., Wilson, M. D., Kocher, J-P. & Li, W., Nov 10 2014, In : Nucleic Acids Research. 42, 20, p. e156

Research output: Contribution to journal › Article

Transcription Factors
Binding Sites
Nucleotides
Exonucleases
Workflow
91 Citations (Scopus)

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

Kalari, K. R., Nair, A. A., Bhavsar, J. D., O'Brien, D. R., Davila, J. I., Bockol, M. A., Nie, J., Tang, X., Baheti, S., Doughty, J. B., Middha, S., Sicotte, H., Thompson, E. A., Asmann, Y. & Kocher, J-P., Jun 27 2014, In : BMC Bioinformatics. 15, 1, 224.

Research output: Contribution to journal › Article

RNA Sequence Analysis
Workflow
RNA
Sequencing
Work Flow
17 Citations (Scopus)

Murine leukemia virus uses NXF1 for nuclear export of spliced and unspliced viral transcripts

Sakuma, T., Davila, J. I., Malcolm, J. A., Kocher, J-P., Tonne, J. M. & Ikeda, Y. H., 2014, In : Journal of Virology. 88, 8, p. 4069-4082 14 p.

Research output: Contribution to journal › Article

Murine leukemia virus
Murine Leukemia Viruses
Cell Nucleus Active Transport
Gammaretrovirus
messenger RNA
24 Citations (Scopus)

Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network

Zhang, Y., Tao, C., Jiang, G. D., Nair, A. A., Su, J., Chute, C. G. & Liu, H. D., Aug 6 2014, In : Journal of Biomedical Semantics. 5, 1, 33.

Research output: Contribution to journal › Article

Gene Regulatory Networks
Semantics
MEDLINE
Genes
Pharmaceutical Preparations
40 Citations (Scopus)

North Central Cancer Treatment Group/Alliance trial N08CA - The use of glutathione for prevention of paclitaxel/carboplatin-induced peripheral neuropathy: A phase 3 randomized, double-blind, placebo-controlled study

Leal, A. D., Qin, R., Atherton, P. J., Haluska, P., Behrens, R. J., Tiber, C. H., Watanaboonyakhet, P., Weiss, M., Adams, P. T., Dockter, T. J. & Loprinzi, C. L., Jun 15 2014, In : Cancer. 120, 12, p. 1890-1897 8 p.

Research output: Contribution to journal › Article

Carboplatin
Peripheral Nervous System Diseases
Paclitaxel
Glutathione
Placebos
23 Citations (Scopus)

PatternCNV: A versatile tool for detecting copy number changes from exome sequencing data

Wang, C., Evans, J. M., Bhagwate, A. V., Prodduturi, N., Sarangi, V., Middha, M., Sicotte, H., Vedell, P. T., Hart, S., Oliver, G. R., Kocher, J-P., Maurer, M. J., Novak, A. J., Slager, S. L., Cerhan, J. R. & Asmann, Y., 2014, In : Bioinformatics. 30, 18, p. 2678-2680 3 p.

Research output: Contribution to journal › Article

Exome
Sequencing
Exons
Software
Chromosomes
115 Citations (Scopus)

Phase III randomized, placebo-controlled, double-blind study of intravenous calcium and magnesium to prevent oxaliplatin-induced sensory neurotoxicity (N08CB/Alliance)

Loprinzi, C. L., Qin, R., Dakhil, S. R., Fehrenbacher, L., Flynn, K. A., Atherton, P., Seisler, D., Qamar, R., Lewis, G. C. & Grothey, A. F., Apr 1 2014, In : Journal of Clinical Oncology. 32, 10, p. 997-1005 9 p.

Research output: Contribution to journal › Article

oxaliplatin
Double-Blind Method
Magnesium
Placebos
Calcium

Prioritizing disease-related genes and pathways by integrating patient-specific iPSC-derived RNA-seq and whole genome sequencing in hypoplastic left heart syndrome

Li, X., Martinez-Fernandez, A., Theis, J., Kocher, J-P., Terzic, A., Olson, T. M. & Nelson, T. J., Sep 29 2014, In : BMC Bioinformatics. 15, 10, P7.

Research output: Contribution to journal › Article

Genes
RNA
1 Citation (Scopus)

PVAAS: Identify variants associated with aberrant splicing from RNA-seq

Wang, L., Nie, J. J. & Kocher, J-P., Sep 25 2014, In : Bioinformatics. 31, 10, p. 1668-1670 3 p.

Research output: Contribution to journal › Article

RNA Splicing
RNA
Nucleotides
RNA Sequence Analysis
Alternative Splicing

Reply to C.D. Atkins and A. Avan et al

Loprinzi, C. L., Qin, R. & Grothey, A. F., Oct 10 2014, In : Journal of Clinical Oncology. 32, 29, p. 3342-3343 2 p.

Research output: Contribution to journal › Article

Organoplatinum Compounds
Antineoplastic Combined Chemotherapy Protocols
Peripheral Nervous System Diseases
Colonic Neoplasms
Magnesium
13 Citations (Scopus)

RVboost: RNA-seq variants prioritization using a boosting method

Wang, C., Davila, J. I., Baheti, S., Bhagwate, A. V., Wang, X., Kocher, J-P., Slager, S. L., Feldman, A. L., Novak, A. J., Cerhan, J. R., Thompson, E. A. & Asmann, Y., 2014, In : Bioinformatics. 30, 23, p. 3414-3416 3 p.

Research output: Contribution to journal › Article

Prioritization
Boosting
RNA
Sequencing
Preparation
42 Citations (Scopus)

Sequencing of charcot-marie-tooth disease genes in a toxic polyneuropathy

Beutler, A. S., Kulkarni, A. A., Kanwar, R., Klein, C. J., Therneau, T. M., Qin, R., Banck, M. S., Boora, G. K., Ruddy, K. J., Wu, Y., Smalley, R. L., Cunningham, J. M., Le-Lindqwister, N. A., Beyerlein, P., Schroth, G. P., Windebank, A. J., Züchner, S. & Loprinzi, C. L., Nov 1 2014, In : Annals of Neurology. 76, 5, p. 727-737 11 p.

Research output: Contribution to journal › Article

Charcot-Marie-Tooth Disease
Polyneuropathies
Poisons
Peripheral Nervous System Diseases
Genes
28 Citations (Scopus)

The Biological Reference Repository (BioR): A rapid and flexible system for genomics annotation

Kocher, J-P., Quest, D. J., Duffy, P., Meiners, M. A., Moore, R. M., Rider, D., Hossain, A., Hart, S. & Dinu, V., Jul 1 2014, In : Bioinformatics. 30, 13, p. 1920-1922 3 p.

Research output: Contribution to journal › Article

UNIX
Genomics
Repository
Annotation
Pipelines
19 Citations (Scopus)

The eSNV-detect: A computational system to identify expressed single nucleotide variants from transcriptome sequencing data

Tang, X., Baheti, S., Shameer, K., Thompson, K. J., Wills, Q., Niu, N., Holcomb, I. N., Boutet, S. C., Ramakrishnan, R., Kachergus, J. M., Kocher, J-P., Weinshilboum, R. M., Wang, L. M., Thompson, E. A. & Kalari, K. R., Dec 16 2014, In : Nucleic Acids Research. 42, 22, e172.

Research output: Contribution to journal › Article

Transcriptome
Nucleotides
RNA
Breast Neoplasms
Exome
26 Citations (Scopus)

Transcriptional atlas of cardiogenesis maps congenital heart disease interactome

Li, X., Martinez-Fernandez, A., Hartjes, K. A., Kocher, J-P., Olson, T. M., Terzic, A. & Nelson, T. J., Jul 1 2014, In : Physiological Genomics. 46, 13, p. 482-495 14 p.

Research output: Contribution to journal › Article

Atlases
Heart Diseases
Epithelial-Mesenchymal Transition
Spatio-Temporal Analysis
Gene Expression Profiling
34 Citations (Scopus)

Understanding protein-nanoparticle interaction: A new gateway to disease therapeutics

Giri, K., Shameer, K., Zimmermann, M. T., Saha, S., Chakraborty, P. K., Sharma, A., Arvizo, R. R., Madden, B. J., Mc Cormick, D. J., Kocher, J-P., Bhattacharya, R. & Mukherjee, P., Jun 18 2014, In : Bioconjugate Chemistry. 25, 6, p. 1078-1090 13 p.

Research output: Contribution to journal › Article

Nanoparticles
Proteins
Ovarian Neoplasms
Therapeutics
Proteomics
2013
8 Citations (Scopus)

Addition of granulocyte macrophage colony stimulating factor does not improve response to early treatment of high-risk chronic lymphocytic leukemia with alemtuzumab and rituximab

Zent, C. S., Wu, W., Bowen, D. A., Hanson, C. A., Pettinger, A. M., Shanafelt, T. D., Kay, N. E., Leis, J. F. & Call, T. G., Mar 2013, In : Leukemia and Lymphoma. 54, 3, p. 476-482 7 p.

Research output: Contribution to journal › Article

B-Cell Chronic Lymphocytic Leukemia
Granulocyte-Macrophage Colony-Stimulating Factor
Cytomegalovirus
Therapeutics
Viremia
48 Citations (Scopus)

A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis

Reese, S. E., Archer, K. J., Therneau, T. M., Atkinson, E. J., Vachon, C. M., De Andrade, M., Kocher, J-P. & Eckel-Passow, J. E., Nov 15 2013, In : Bioinformatics. 29, 22, p. 2877-2883 7 p.

Research output: Contribution to journal › Article

Passive Cutaneous Anaphylaxis
Principal Component Analysis
Principal component analysis
High Throughput
Batch

A phase II flexible screening design allowing for interim analysis and comparison with historical control

Wu, W., Bot, B., Hu, Y., Geyer, S. M. & Sargent, D. J., Jul 2013, In : Contemporary Clinical Trials. 35, 2, p. 128-137 10 p.

Research output: Contribution to journal › Article

Sample Size
Therapeutics
45 Citations (Scopus)

A phase II safety and efficacy study of the vascular endothelial growth factor receptor tyrosine kinase inhibitor pazopanib in patients with metastatic urothelial cancer

Pili, R., Qin, R., Flynn, P. J., Picus, J., Millward, M., Ho, W. M., Pitot, H. C., Tan, W., Miles, K. M., Erlichman, C. & Vaishampayan, U., Dec 2013, In : Clinical Genitourinary Cancer. 11, 4, p. 477-483 7 p.

Research output: Contribution to journal › Article

Vascular Endothelial Growth Factor Receptor
Protein-Tyrosine Kinases
Safety
Neoplasms
Carcinoma
35 Citations (Scopus)

A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data

Tao, C., Jiang, G. D., Oniki, T. A., Freimuth, R., Zhu, Q., Sharma, D., Pathak, J., Huff, S. M. & Chute, C. G., 2013, In : Journal of the American Medical Informatics Association. 20, 3, p. 554-562 9 p.

Research output: Contribution to journal › Article

Electronic Health Records
Semantics
Terminology
Language
24 Citations (Scopus)

A sequence-based variation map of zebrafish

Patowary, A., Purkanti, R., Singh, M., Chauhan, R., Singh, A. R., Swarnkar, M., Singh, N., Pandey, V., Torroja, C., Clark, M. D., Kocher, J-P., Clark, K. J., Stemple, D. L., Klee, E. W., Ekker, S. C., Scaria, V. & Sivasubbu, S., Mar 1 2013, In : Zebrafish. 10, 1, p. 15-20 6 p.

Research output: Contribution to journal › Article

Zebrafish
Danio rerio
Genome
genome
Nucleotides
72 Citations (Scopus)

Assessing patient-reported peripheral neuropathy: The reliability and validity of the European Organization for Research and Treatment of Cancer QLQ-CIPN20 Questionnaire

Smith, E. M. L., Barton, D. L., Qin, R., Steen, P. D., Aaronson, N. K. & Loprinzi, C. L., Dec 2013, In : Quality of Life Research. 22, 10, p. 2787-2799 13 p.

Research output: Contribution to journal › Article

Peripheral Nervous System Diseases
Reproducibility of Results
Drug Therapy
Research
Neoplasms
84 Citations (Scopus)

Calculating sample size estimates for RNA sequencing data

Hart, S., Therneau, T. M., Zhang, Y., Poland, G. A. & Kocher, J-P., Dec 1 2013, In : Journal of Computational Biology. 20, 12, p. 970-978 9 p.

Research output: Contribution to journal › Article

RNA Sequence Analysis
RNA
Sample Size
Sequencing
Gene Expression
1 Citation (Scopus)

Combining infobuttons and semantic web rules for identifying patterns and delivering highly-personalized education materials.

Hulse, N. C., Long, J. & Tao, C., 2013, In : AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium. 2013, p. 638-647 10 p.

Research output: Contribution to journal › Article

Electronic Health Records
Semantics
Point-of-Care Systems
Education
Information Storage and Retrieval
25 Citations (Scopus)

Comprehensive temporal information detection from clinical text: Medical events, time, and TLINK identification

Sohn, S., Wagholikar, K. B., Li, D., Jonnalagadda, S. R., Tao, C., Elayavilli, R. K. & Liu, H. D., 2013, In : Journal of the American Medical Informatics Association. 20, 5, p. 836-842 7 p.

Research output: Contribution to journal › Article

Natural Language Processing
Information Management
Information Systems
Language
Machine Learning
476 Citations (Scopus)

CPAT: Coding-potential assessment tool using an alignment-free logistic regression model

Wang, L., Park, H. J., Dasari, S., Wang, S., Kocher, J-P. & Li, W., Apr 2013, In : Nucleic Acids Research. 41, 6

Research output: Contribution to journal › Article

Software
Logistic Models
Transcriptome
Sensitivity and Specificity
Codon
16 Citations (Scopus)

Dose-finding designs using a novel quasi-continuous endpoint for multiple toxicities

Ezzalfani, M., Zohar, S., Qin, R., Mandrekar, S. J. & Deley, M. C. L., Jul 20 2013, In : Statistics in Medicine. 32, 16, p. 2728-2746 19 p.

Research output: Contribution to journal › Article

Dose Finding
Toxicity
Continual Reassessment Method
Dose
Weights and Measures
13 Citations (Scopus)

Efficacy of protracted temozolomide dosing is limited in MGMT unmethylated GBM xenograft models

Cen, L., Carlson, B. L., Pokorny, J. L., Mladek, A. C., Grogan, P. T., Schroeder, M. A., Decker, P. A., Anderson, S. K., Giannini, C., Wu, W., Ballman, K. V., Kitange, G. J. & Sarkaria, J. N., Jun 2013, In : Neuro-Oncology. 15, 6, p. 735-746 12 p.

Research output: Contribution to journal › Article

temozolomide
Methyltransferases
Glioblastoma
Heterografts
Placebos
85 Citations (Scopus)

Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding

Myers, K. S., Yan, H. D., Ong, I. M., Chung, D., Liang, K., Tran, F., Keleş, S., Landick, R. & Kiley, P. J., Jun 2013, In : PLoS Genetics. 9, 6, e1003565.

Research output: Contribution to journal › Article

Transcription Factors
transcription factors
genome
Genome
Escherichia coli
6 Citations (Scopus)

Harmonization and semantic annotation of data dictionaries from the Pharmacogenomics Research Network: A case study

Zhu, Q., Freimuth, R., Lian, Z., Bauer, S., Pathak, J., Tao, C., Durski, M. J. & Chute, C. G., Apr 2013, In : Journal of Biomedical Informatics. 46, 2, p. 286-293 8 p.

Research output: Contribution to journal › Article

Pharmacogenetics
Semantics
Research
Data Curation
Data integration
12 Citations (Scopus)

Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol.

Sun, Z., Asmann, Y., Nair, A., Zhang, Y., Wang, L., Kalari, K. R., Bhagwate, A. V., Baker, T. R., Carr, J. M., Kocher, J-P., Perez, E. A. & Thompson, E. A., 2013, In : PLoS One. 8, 8, e71745.

Research output: Contribution to journal › Article

Libraries
Long Noncoding RNA
RNA
Genes
Untranslated RNA
15 Citations (Scopus)

Network-based analysis of vaccine-related associations reveals consistent knowledge with the vaccine ontology

Zhang, Y., Tao, C., He, Y., Kanjamala, P. & Liu, H. D., Nov 11 2013, In : Journal of Biomedical Semantics. 4, 1, 33.

Research output: Contribution to journal › Article

Vaccines
Ontology
Semantics
Genes
MEDLINE