Research output per year
Research output per year
- 1 - 50 out of 59 results
Search results
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2022
Association between Antibiotic Exposure and Systemic Immune Parameters in Cancer Patients Receiving Checkpoint Inhibitor Therapy
von Itzstein, M. S., Gonugunta, A. S., Sheffield, T., Homsi, J., Dowell, J. E., Koh, A. Y., Raj, P., Fattah, F., Wang, Y., Basava, V. S., Khan, S., Park, J. Y., Popat, V., Saltarski, J. M., Gloria-Mccutchen, Y., Hsiehchen, D., Ostmeyer, J., Xie, Y., Li, Q., Wakeland, E. K., & 1 others, Mar 1 2022, In: Cancers. 14, 5, 1327.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
2021
Association between body mass index, dosing strategy, and efficacy of immune checkpoint inhibitors
Ahmed, M., Von Itzstein, M. S., Sheffield, T., Khan, S., Fattah, F., Park, J. Y., Popat, V., Saltarski, J. M., Gloria-Mccutchen, Y., Hsiehchen, D., Ostmeyer, J., Khan, S. A., Sultana, N., Xie, Y., Li, Q. Z., Wakeland, E. K. & Gerber, D. E., Jun 14 2021, In: Journal for ImmunoTherapy of Cancer. 9, 6, e002349.Research output: Contribution to journal › Article › peer-review
Open Access15 Scopus citations -
Reconstituting T cell receptor selection in-silico
Ostmeyer, J., Cowell, L., Greenberg, B. & Christley, S., Jul 2021, In: Genes and Immunity. 22, 3, p. 187-193 7 p.Research output: Contribution to journal › Article › peer-review
3 Scopus citations -
T Cell Receptor Repertoires Acquired via Routine Pap Testing May Help Refine Cervical Cancer and Precancer Risk Estimates
Christley, S., Ostmeyer, J., Quirk, L., Zhang, W., Sirak, B., Giuliano, A. R., Zhang, S., Monson, N., Tiro, J., Lucas, E. & Cowell, L. G., Apr 2 2021, In: Frontiers in immunology. 12, 624230.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
2020
Biophysicochemical motifs in T cell receptor sequences as a potential biomarker for highgrade serous ovarian carcinoma
Ostmeyer, J., Lucas, E., Christley, S., Lea, J., Monson, N., Tiro, J. & Cowell, L. G., 2020, In: PloS one. 15, 3, e0229569.Research output: Contribution to journal › Article › peer-review
Open Access13 Scopus citations -
2019
Biophysicochemical motifs in T-cell receptor sequences distinguish repertoires from tumor-infiltrating lymphocyte and adjacent healthy tissue
Ostmeyer, J., Christley, S., Toby, I. T. & Cowell, L. G., Apr 1 2019, In: Cancer research. 79, 7, p. 1671-1680 10 p.Research output: Contribution to journal › Article › peer-review
Open Access57 Scopus citations -
Machine learning on sequential data using a recurrent weighted average
Ostmeyer, J. & Cowell, L. G., Feb 28 2019, In: Neurocomputing. 331, p. 281-288 8 p.Research output: Contribution to journal › Article › peer-review
Open Access17 Scopus citations -
2018
iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories
Corrie, B. D., Marthandan, N., Zimonja, B., Jaglale, J., Zhou, Y., Barr, E., Knoetze, N., Breden, F. M. W., Christley, S., Scott, J. K., Cowell, L. G. & Breden, F., Jul 2018, In: Immunological Reviews. 284, 1, p. 24-41 18 p.Research output: Contribution to journal › Review article › peer-review
Open Access90 Scopus citations -
VDJServer: A cloud-based analysis portal and data commons for immune repertoire sequences and rearrangements
Christley, S., Scarborough, W., Salinas, E., Rounds, W. H., Toby, I. T., Fonner, J. M., Levin, M. K., Kim, M., Mock, S. A., Jordan, C., Ostmeyer, J., Buntzman, A., Rubelt, F., Davila, M. L., Monson, N. L., Scheuermann, R. H. & Cowell, L. G., May 8 2018, In: Frontiers in immunology. 9, MAY, 976.Research output: Contribution to journal › Article › peer-review
Open Access44 Scopus citations -
2017
Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data
The AIRR Community, Nov 16 2017, In: Nature immunology. 18, 12, p. 1274-1278 5 p.Research output: Contribution to journal › Comment/debate › peer-review
Open Access113 Scopus citations -
Cell type discovery and representation in the era of high-content single cell phenotyping
Bakken, T., Cowell, L., Aevermann, B. D., Novotny, M., Hodge, R., Miller, J. A., Lee, A., Chang, I., McCorrison, J., Pulendran, B., Qian, Y., Schork, N. J., Lasken, R. S., Lein, E. S. & Scheuermann, R. H., Dec 21 2017, In: BMC Bioinformatics. 18, 559.Research output: Contribution to journal › Article › peer-review
Open Access36 Scopus citations -
Peripheral VH4+ plasmablasts demonstrate autoreactive B cell expansion toward brain antigens in early multiple sclerosis patients
Rivas, J. R., Ireland, S. J., Chkheidze, R., Rounds, W. H., Lim, J., Johnson, J., Ramirez, D. M. O., Ligocki, A. J., Chen, D., Guzman, A. A., Woodhall, M., Wilson, P. C., Meffre, E., White, C., Greenberg, B. M., Waters, P., Cowell, L. G., Stowe, A. M. & Monson, N. L., Jan 1 2017, In: Acta Neuropathologica. 133, 1, p. 43-60 18 p.Research output: Contribution to journal › Article › peer-review
Open Access25 Scopus citations -
Reproducibility and reuse of adaptive immune receptor repertoire data
Breden, F., Luning Prak, E. T., Peters, B., Rubelt, F., Schramm, C. A., Busse, C. E., Vander Heiden, J. A., Christley, S., Bukhari, S. A. C., Thorogood, A., Matsen, F. A., Wine, Y., Laserson, U., Klatzmann, D., Douek, D. C., Lefranc, M. P., Collins, A. M., Bubela, T., Kleinstein, S. H., Watson, C. T., & 3 others, Nov 1 2017, In: Frontiers in immunology. 8, NOV, 1418.Research output: Contribution to journal › Article › peer-review
Open Access66 Scopus citations -
Statistical classifiers for diagnosing disease from immune repertoires: A case study using multiple sclerosis
Ostmeyer, J., Christley, S., Rounds, W. H., Toby, I., Greenberg, B. M., Monson, N. L. & Cowell, L. G., Sep 7 2017, In: BMC Bioinformatics. 18, 1, 401.Research output: Contribution to journal › Article › peer-review
Open Access47 Scopus citations -
VDJPipe: A pipelined tool for pre-processing immune repertoire sequencing data
Christley, S., Levin, M. K., Toby, I. T., Fonner, J. M., Monson, N. L., Rounds, W. H., Rubelt, F., Scarborough, W., Scheuermann, R. H. & Cowell, L. G., Oct 11 2017, In: BMC Bioinformatics. 18, 1, 448.Research output: Contribution to journal › Article › peer-review
Open Access12 Scopus citations -
2016
Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells
Rubelt, F., Bolen, C. R., McGuire, H. M., Heiden, J. A. V., Gadala-Maria, D., Levin, M., Euskirchen, G. M., Mamedov, M. R., Swan, G. E., Dekker, C. L., Cowell, L. G., Kleinstein, S. H. & Davis, M. M., Mar 23 2016, In: Nature communications. 7, 11112.Research output: Contribution to journal › Article › peer-review
Open Access86 Scopus citations -
iWAS – A novel approach to analyzing Next Generation Sequence data for immunology
Vincent, B., Buntzman, A., Hopson, B., McEwen, C., Cowell, L., Akoglu, A., Zhang, H. & Frelinger, J., Jan 2016, In: Cellular Immunology. 299, p. 6-13 8 p.Research output: Contribution to journal › Article › peer-review
Open Access7 Scopus citations -
VDJML: A file format with tools for capturing the results of inferring immune receptor rearrangements
Toby, I. T., Levin, M. K., Salinas, E. A., Christley, S., Bhattacharya, S., Breden, F., Buntzman, A., Corrie, B., Fonner, J., Gupta, N. T., Hershberg, U., Marthandan, N., Rosenfeld, A., Rounds, W., Rubelt, F., Scarborough, W., Scott, J. K., Uduman, M., Vander Heiden, J. A., Scheuermann, R. H., & 3 others, Oct 6 2016, In: BMC Bioinformatics. 17, 333.Research output: Contribution to journal › Article › peer-review
Open Access10 Scopus citations -
2015
MSPrecise: A molecular diagnostic test for multiple sclerosis using next generation sequencing
Rounds, W. H., Salinas, E. A., Wilks, T. B., Levin, M. K., Ligocki, A. J., Ionete, C., Pardo, C. A., Vernino, S., Greenberg, B. M., Bigwood, D. W., Eastman, E. M., Cowell, L. G. & Monson, N. L., Nov 10 2015, In: Gene. 572, 2, p. 191-197 7 p.Research output: Contribution to journal › Article › peer-review
Open Access16 Scopus citations -
Owlcpp: A C++ library for working with OWL ontologies
Levin, M. K. & Cowell, L. G., Sep 16 2015, In: Journal of Biomedical Semantics. 6, 1, 35.Research output: Contribution to journal › Article › peer-review
4 Scopus citations -
RAG Represents a Widespread Threat to the Lymphocyte Genome
Teng, G., Maman, Y., Resch, W., Kim, M., Yamane, A., Qian, J., Kieffer-Kwon, K. R., Mandal, M., Ji, Y., Meffre, E., Clark, M. R., Cowell, L. G., Casellas, R. & Schatz, D. G., Aug 17 2015, In: Cell. 162, 4, p. 751-765 15 p.Research output: Contribution to journal › Article › peer-review
Open Access84 Scopus citations -
2014
A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting
Nelson, C. L., Pelak, K., Podgoreanu, M. V., Ahn, S. H., Scott, W. K., Allen, A. S., Cowell, L. G., Rude, T. H., Zhang, Y., Tong, A., Ruffin, F., Sharma-Kuinkel, B. K. & Fowler, V. G., Feb 13 2014, In: BMC Infectious Diseases. 14, 1, 83.Research output: Contribution to journal › Article › peer-review
32 Scopus citations -
Ontological representation of CDC active bacterial core surveillance case reports
Goldfain, A., Smith, B. & Cowell, L. G., 2014, CEUR Workshop Proceedings. CEUR-WS, Vol. 1327. p. 74-77 4 p.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
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The antibody genetics of multiple sclerosis: Comparing next-generation sequencing to Sanger sequencing
Rounds, W. H., Ligocki, A. J., Levin, M. K., Greenberg, B. M., Bigwood, D. W., Eastman, E. M., Cowell, L. G. & Monson, N. L., 2014, In: Frontiers in Neurology. 5 AUG, Article 166.Research output: Contribution to journal › Article › peer-review
9 Scopus citations -
2013
CD19-targeted T cells rapidly induce molecular remissions in adults with chemotherapy-refractory acute lymphoblastic leukemia
Brentjens, R. J., Davila, M. L., Riviere, I., Park, J., Wang, X., Cowell, L. G., Bartido, S., Stefanski, J., Taylor, C., Olszewska, M., Borquez-Ojeda, O., Qu, J., Wasielewska, T., He, Q., Bernal, Y., Rijo, I. V., Hedvat, C., Kobos, R., Curran, K., Steinherz, P., & 5 others, Mar 20 2013, In: Science translational medicine. 5, 177, 177ra38.Research output: Contribution to journal › Article › peer-review
Open Access1648 Scopus citations -
Design and evaluation of a bacterial clinical infectious diseases ontology.
Gordon, C. L., Pouch, S., Cowell, L. G., Boland, M. R., Platt, H. L., Goldfain, A. & Weng, C., 2013, In: AMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium. 2013, p. 502-511 10 p.Research output: Contribution to journal › Article › peer-review
10 Scopus citations -
Expansion of CD27high plasmablasts in transverse myelitis patients that utilize VH4 and JH6 genes and undergo extensive somatic hypermutation
Ligocki, A. J., Rounds, W. H., Cameron, E. M., Harp, C. T., Frohman, E., Courtney, A. M., Vernino, S., Cowell, L. G., Greenberg, B. & Monson, N. L., Jul 2013, In: Genes and Immunity. 14, 5, p. 291-301 11 p.Research output: Contribution to journal › Article › peer-review
Open Access11 Scopus citations -
Ontology for vector surveillance and management
Lozano-Fuentes, S., Bandyopadhyay, A., Cowell, L. G., Goldfain, A. & Eisen, L., Jan 2013, In: Journal of Medical Entomology. 50, 1, p. 1-14 14 p.Research output: Contribution to journal › Review article › peer-review
8 Scopus citations -
2012
Constructing a lattice of Infectious Disease Ontologies from a Staphylococcus aureus isolate repository
Goldfain, A., Smith, B. & Cowell, L. G., 2012, CEUR Workshop Proceedings. Vol. 897.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
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Haplotype association mapping identifies a candidate gene region in mice infected with staphylococcus aureus
Johnson, N. V., Ahn, S. H., Deshmukh, H., Levin, M. K., Nelson, C. L., Scott, W. K., Allen, A., Fowler, V. G. & Cowell, L. G., Jun 2012, In: G3: Genes, Genomes, Genetics. 2, 6, p. 693-700 8 p.Research output: Contribution to journal › Article › peer-review
12 Scopus citations -
2011
Bridging multiple ontologies: Representation of the liver immune response
Masci, A. M., Roach, J., De Bono, B., Grenon, P. & Cowell, L., 2011, CEUR Workshop Proceedings. Vol. 833. p. 393-398 6 p.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
1 Scopus citations -
Connecting ontologies for the representation of biological pathways
Masci, A. M., Levin, M., Ruttenberg, A. & Cowell, L. G., 2011, CEUR Workshop Proceedings. Vol. 833. p. 387-392 6 p.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
3 Scopus citations -
Hematopoietic cell types: Prototype for a revised cell ontology
Diehl, A. D., Augustine, A. D., Blake, J. A., Cowell, L. G., Gold, E. S., Gondré-Lewis, T. A., Masci, A. M., Meehan, T. F., Morel, P. A., Nijnik, A., Peters, B., Pulendran, B., Scheuermann, R. H., Yao, Q. A., Zand, M. S. & Mungall, C. J., Feb 2011, In: Journal of Biomedical Informatics. 44, 1, p. 75-79 5 p.Research output: Contribution to journal › Article › peer-review
30 Scopus citations -
Logical Development of the Cell Ontology
Meehan, T. F., Masci, A. M., Abdulla, A., Cowell, L. G., Blake, J. A., Mungall, C. J. & Diehl, A. D., Jan 5 2011, In: BMC Bioinformatics. 12, 6.Research output: Contribution to journal › Article › peer-review
119 Scopus citations -
Owl-cpp, a C++ library for working with OWL ontologies
Levin, M. K., Ruttenberg, A., Masci, A. M. & Cowell, L. G., 2011, CEUR Workshop Proceedings. Vol. 833. p. 255-257 3 p.Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
3 Scopus citations -
Towards an ontological representation of resistance: The case of MRSA
Goldfain, A., Smith, B. & Cowell, L. G., Feb 2011, In: Journal of Biomedical Informatics. 44, 1, p. 35-41 7 p.Research output: Contribution to journal › Article › peer-review
13 Scopus citations -
2010
Dispositions and the infectious disease ontology
Goldfain, A., Smith, B. & Cowell, L. G., 2010, Formal Ontology in Information Systems. IOS Press, p. 400-413 14 p. (Frontiers in Artificial Intelligence and Applications; vol. 209).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
31 Scopus citations -
Infectious disease ontology
Cowell, L. G. & Smith, B., 2010, Infectious Disease Informatics. Springer New York, p. 373-395 23 p.Research output: Chapter in Book/Report/Conference proceeding › Chapter
Open Access85 Scopus citations -
Memory B cells from a subset of treatment-naïve relapsing-remitting multiple sclerosis patients elicit CD4+ T-cell proliferation and IFN-γ production in response to myelin basic protein and myelin oligodendrocyte glycoprotein
Harp, C. T., Ireland, S., Davis, L. S., Remington, G., Cassidy, B., Cravens, P. D., Stuve, O., Lovett-Racke, A. E., Eagar, T. N., Greenberg, B., Racke, M. K., Cowell, L. G., Karandikar, N. J., Frohman, E. & Monson, N. L., Oct 2010, In: European Journal of Immunology. 40, 10, p. 2942-2956 15 p.Research output: Contribution to journal › Article › peer-review
97 Scopus citations -
Two genes on A/J chromosome 18 are associated with susceptibility to Staphylococcus aureus infection by combined microarray and QTL analyses
Ahn, S. H., Deshmukh, H., Johnson, N., Cowell, L. G., Rude, T. H., Scott, W. K., Nelson, C. L., Zaas, A. K., Marchuk, D. A., Keum, S., Lamlertthon, S., Sharma-Kuinkel, B. K., Sempowski, G. D. & Fowler, V. G., Sep 2010, In: PLoS pathogens. 6, 9, e01088.Research output: Contribution to journal › Article › peer-review
60 Scopus citations -
2009
An improved ontological representation of dendritic cells as a paradigm for all cell types
Masci, A. M., Arighi, C. N., Diehl, A. D., Lieberman, A. E., Mungall, C., Scheuermann, R. H., Smith, B. & Cowell, L. G., Feb 25 2009, In: BMC Bioinformatics. 10, 70.Research output: Contribution to journal › Article › peer-review
31 Scopus citations -
2007
Multiple, conserved cryptic recombination signals in VH gene segments: Detection of cleavage products only in pro-B cells
Davila, M., Liu, F., Cowell, L. G., Lieberman, A. E., Heikamp, E., Patel, A. & Kelsoe, G., Dec 24 2007, In: Journal of Experimental Medicine. 204, 13, p. 3195-3208 14 p.Research output: Contribution to journal › Article › peer-review
28 Scopus citations -
2006
Neonate-primed CD8+ memory cells rival adult-primed memory cells in antigen-driven expansion and anti-viral protection
Fadel, S. A., Cowell, L. G., Cao, S., Ozaki, D. A., Kepler, T. B., Steeber, D. A. & Sarzotti, M., Feb 2006, In: International Immunology. 18, 2, p. 249-257 9 p.Research output: Contribution to journal › Article › peer-review
19 Scopus citations -
Reassignment of the murine 3′TRDD1 recombination signal sequence
Touvrey, C., Cowell, L. G., Lieberman, A. E., Marche, P. N., Jouvin-Marche, E. & Candéias, S. M., Nov 2006, In: Immunogenetics. 58, 11, p. 895-903 9 p.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
SoDA: Implementation of a 3D alignment algorithm for inference of antigen receptor recombinations
Volpe, J. M., Cowell, L. G. & Kepler, T. B., Feb 15 2006, In: Bioinformatics. 22, 4, p. 438-444 7 p.Research output: Contribution to journal › Article › peer-review
103 Scopus citations -
The recombination difference between mouse κ and λ segments is mediated by a pair-wise regulation mechanism
Larijani, M., Chen, S., Cunningham, L. A., Volpe, J. M., Cowell, L. G., Lewis, S. M. & Wu, G. E., Mar 2006, In: Molecular Immunology. 43, 7, p. 870-881 12 p.Research output: Contribution to journal › Article › peer-review
7 Scopus citations -
V(D)J recombinase-mediated processing of coding junctions at cryptic recombination signal sequences in peripheral T cells during human development
Murray, J. M., O'Neill, J. P., Messier, T., Rivers, J., Walker, V. E., McGonagle, B., Trombley, L., Cowell, L. G., Kelsoe, G., McBlane, F. & Finette, B. A., Oct 15 2006, In: Journal of Immunology. 177, 8, p. 5393-5404 12 p.Research output: Contribution to journal › Article › peer-review
Open Access13 Scopus citations -
2004
Computational tools for understanding sequence variability in recombination signals
Cowell, L. G., Davila, M., Ramsden, D. & Kelsoe, G., Aug 2004, In: Immunological Reviews. 200, p. 57-69 13 p.Research output: Contribution to journal › Review article › peer-review
21 Scopus citations -
2003
A functional analysis of the spacer of V(D)J recombination signal sequences
Lee, A. I., Fugmann, S. D., Cowell, L. G., Ptaszek, L. M., Kelsoe, G. & Schatz, D. G., 2003, In: PLoS biology. 1, 1Research output: Contribution to journal › Article › peer-review
62 Scopus citations -
Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling
Cowell, L. G., Davila, M., Yang, K., Kepler, T. B. & Kelsoe, G., Jan 20 2003, In: Journal of Experimental Medicine. 197, 2, p. 207-220 14 p.Research output: Contribution to journal › Article › peer-review
52 Scopus citations