Research Output per year
Research Output 2007 2019
- 100 - 150 out of 254 results
- Publication Year, Title (descending)
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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, , Feb 2014, In : PLoS Genetics. 10, 2, e1004135.Research output: Contribution to journal › Article
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
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. e156Research output: Contribution to journal › Article
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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, 6Research output: Contribution to journal › Article
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
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
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
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
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
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