Publications

Featured Publications

Cardiac Complications After SARS-CoV-2 Infection and mRNA COVID-19 Vaccination - PCORnet, United States, January 2021-January 2022.

Block JP, Boehmer TK, Forrest CB, Carton TW, Lee GM, Ajani UA, Christakis DA, Cowell LG, Draper C, Ghildayal N, Harris AM, Kappelman MD, Ko JY, Mayer KH, Nagavedu K, Oster ME, Paranjape A, Puro J, Ritchey MD, Shay DK, Thacker D, Gundlapalli AV, 2022 Apr MMWR Morb Mortal Wkly Rep 14 71 517-523

TCRMatch: Predicting T-Cell Receptor Specificity Based on Sequence Similarity to Previously Characterized Receptors.

Chronister WD, Crinklaw A, Mahajan S, Vita R, Kosaloglu-Yalçin Z, Yan Z, Greenbaum JA, Jessen LE, Nielsen M, Christley S, Cowell LG, Sette A, Peters B, 2021 Front Immunol 12 640725

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 AR, Zhang S, Monson N, Tiro J, Lucas E, Cowell LG, 2021 Front Immunol 12 624230

The Diagnostic, Prognostic, and Therapeutic Potential of Adaptive Immune Receptor Repertoire Profiling in Cancer.

Cowell LG, 2020 02 Cancer Res 4 80 643-654

Biophysicochemical motifs in T cell receptor sequences as a potential biomarker for high-grade serous ovarian carcinoma.

Ostmeyer J, Lucas E, Christley S, Lea J, Monson N, Tiro J, Cowell LG, 2020 PLoS One 3 15 e0229569

Biophysicochemical motifs in T cell receptor sequences distinguish repertoires from tumor-infiltrating lymphocytes and adjacent healthy tissue.

Ostmeyer J, Christley S, Toby IT, Cowell LG 2019 Jan Cancer Res.

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements.

Christley S, Scarborough W, Salinas E, Rounds WH, Toby IT, Fonner JM, Levin MK, Kim M, Mock SA, Jordan C, Ostmeyer J, Buntzman A, Rubelt F, Davila ML, Monson NL, Scheuermann RH, Cowell LG 2018 Front Immunol 9 976

Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis.

Ostmeyer J, Christley S, Rounds WH, Toby I, Greenberg BM, Monson NL, Cowell LG 2017 Sep BMC Bioinformatics 1 18 401

Individual heritable differences result in unique cell lymphocyte receptor repertoires of naive and antigen-experienced cells.

Rubelt F, Bolen CR, McGuire HM, Heiden JA, Gadala-Maria D, Levin M, M Euskirchen G, Mamedov MR, Swan GE, Dekker CL, Cowell LG, Kleinstein SH, Davis MM 2016 Nat Commun 7 11112

RAG Represents a Widespread Threat to the Lymphocyte Genome.

Teng G, Maman Y, Resch W, Kim M, Yamane A, Qian J, Kieffer-Kwon KR, Mandal M, Ji Y, Meffre E, Clark MR, Cowell LG, Casellas R, Schatz DG 2015 Aug Cell 4 162 751-65

Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus.

Johnson NV, Ahn SH, Deshmukh H, Levin MK, Nelson CL, Scott WK, Allen A, Fowler VG, Cowell LG 2012 Jun G3 (Bethesda) 6 2 693-700

Conserved cryptic recombination signals in Vkappa gene segments are cleaved in small pre-B cells.

Lieberman AE, Kuraoka M, Davila M, Kelsoe G, Cowell LG 2009 BMC Immunol. 10 37

An improved ontological representation of dendritic cells as a paradigm for all cell types.

Masci AM, Arighi CN, Diehl AD, Lieberman AE, Mungall C, Scheuermann RH, Smith B, Cowell LG 2009 BMC Bioinformatics 10 70

Prospective estimation of recombination signal efficiency and identification of functional cryptic signals in the genome by statistical modeling.

Cowell LG, Davila M, Yang K, Kepler TB, Kelsoe G 2003 Jan J. Exp. Med. 2 197 207-20

Identification and utilization of arbitrary correlations in models of recombination signal sequences.

Cowell LG, Davila M, Kepler TB, Kelsoe G 2002 Genome Biol. 12 3 RESEARCH0072

The distribution of variation in regulatory gene segments, as present in MHC class II promoters.

Cowell LG, Kepler TB, Janitz M, Lauster R, Mitchison NA 1998 Feb Genome Res. 2 8 124-34

Prevalence of Select New Symptoms and Conditions Among Persons Aged Younger Than 20 Years and 20 Years or Older at 31 to 150 Days After Testing Positive or Negative for SARS-CoV-2.

Hernandez-Romieu AC, Carton TW, Saydah S, Azziz-Baumgartner E, Boehmer TK, Garret NY, Bailey LC, Cowell LG, Draper C, Mayer KH, Nagavedu K, Puro JE, Rasmussen SA, Trick WE, Wanga V, Chevinsky JR, Jackson BR, Goodman AB, Cope JR, Gundlapalli AV, Block JP, 2022 02 JAMA Netw Open 2 5 e2147053

Data Sharing and Reuse: A Method by the AIRR Community.

Corrie BD, Christley S, Busse CE, Cowell LG, Neller KCM, Rubelt F, Schwab N, 2022 Methods Mol Biol 2453 447-476

Immune Repertoire Analysis on High-Performance Computing Using VDJServer V1: A Method by the AIRR Community.

Christley S, Stervbo U, Cowell LG, 2022 Methods Mol Biol 2453 439-446

Burden of Renal Cysts Imaging: A Survey of Patients among the Greater Plains Collaborative.

Kalot MA, Dahm P, Cowell LG, Noureddine L, Mustafa RA, 2021 Sep Urol Int 1-7

Blood-based biomarkers of human papillomavirus-associated cancers: A systematic review and meta-analysis.

Balachandra S, Kusin SB, Lee R, Blackwell JM, Tiro JA, Cowell LG, Chiang CM, Wu SY, Varma S, Rivera EL, Mayo HG, Ding L, Sumer BD, Lea JS, Bagrodia A, Farkas LM, Wang R, Fakhry C, Dahlstrom KR, Sturgis EM, Day AT, 2021 Mar Cancer 6 127 850-864

Effect of the Affordable Care Act on diabetes care at major health centers: newly detected diabetes and diabetes medication management.

Furmanchuk A, Liu M, Song X, Waitman LR, Meurer JR, Osinski K, Stoddard A, Chrischilles E, McClay JC, Cowell LG, Tachinardi U, Embi PJ, Mosa ASM, Mandhadi V, Shah RC, Garcia D, Angulo F, Patino A, Trick WE, Markossian TW, Rasmussen-Torvik LJ, Kho AN, Black BS, 2021 Jun BMJ Open Diabetes Res Care 1 9

Effect of the Affordable Care Act on diabetes care at major health centers: newly detected diabetes and diabetes medication management.

The Infectious Disease Ontology in the age of COVID-19.

Babcock S, Beverley J, Cowell LG, Smith B, 2021 07 J Biomed Semantics 1 12 13

The ADC API: A Web API for the Programmatic Query of the AIRR Data Commons.

Christley S, Aguiar A, Blanck G, Breden F, Bukhari SAC, Busse CE, Jaglale J, Harikrishnan SL, Laserson U, Peters B, Rocha A, Schramm CA, Taylor S, Vander Heiden JA, Zimonja B, Watson CT, Corrie B, Cowell LG, 2020 Front Big Data 3 22

iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories.

Corrie BD, Marthandan N, Zimonja B, Jaglale J, Zhou Y, Barr E, Knoetze N, Breden FMW, Christley S, Scott JK, Cowell LG, Breden F 2018 Jul Immunol. Rev. 1 284 24-41

VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data.

Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG 2017 Oct BMC Bioinformatics 1 18 448

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data.

Rubelt F, Busse CE, Bukhari SAC, Bürckert JP, Mariotti-Ferrandiz E, Cowell LG, Watson CT, Marthandan N, Faison WJ, Hershberg U, Laserson U, Corrie BD, Davis MM, Peters B, Lefranc MP, Scott JK, Breden F, Luning Prak ET, Kleinstein SH 2017 Nov Nat. Immunol. 12 18 1274-1278

Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data.

Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB 2017 Front Immunol 8 1418

Peripheral VH4+ plasmablasts demonstrate autoreactive B cell expansion toward brain antigens in early multiple sclerosis patients.

Rivas JR, Ireland SJ, Chkheidze R, Rounds WH, Lim J, Johnson J, Ramirez DM, Ligocki AJ, Chen D, Guzman AA, Woodhall M, Wilson PC, Meffre E, White C, Greenberg BM, Waters P, Cowell LG, Stowe AM, Monson NL 2016 Oct Acta Neuropathol.

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements.

Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG 2016 Oct BMC Bioinformatics Suppl 13 17 333

MSPrecise: A molecular diagnostic test for multiple sclerosis using next generation sequencing.

Rounds WH, Salinas EA, Wilks TB, Levin MK, Ligocki AJ, Ionete C, Pardo CA, Vernino S, Greenberg BM, Bigwood DW, Eastman EM, Cowell LG, Monson NL 2015 Jul Gene

owlcpp: a C++ library for working with OWL ontologies.

Levin MK, Cowell LG 2015 J Biomed Semantics 6 35

A genome-wide association study of variants associated with acquisition of Staphylococcus aureus bacteremia in a healthcare setting.

Nelson CL, Pelak K, Podgoreanu MV, Ahn SH, Scott WK, Allen AS, Cowell LG, Rude TH, Zhang Y, Tong A, Ruffin F, Sharma-Kuinkel BK, Fowler VG 2014 BMC Infect. Dis. 1 14 83

The antibody genetics of multiple sclerosis: comparing next-generation sequencing to sanger sequencing.

Rounds WH, Ligocki AJ, Levin MK, Greenberg BM, Bigwood DW, Eastman EM, Cowell LG, Monson NL 2014 Front Neurol 5 166

CD19-Targeted T Cells Rapidly Induce Molecular Remissions in Adults with Chemotherapy-Refractory Acute Lymphoblastic Leukemia.

Brentjens RJ, Davila ML, Riviere I, Park J, Wang X, Cowell LG, Bartido S, Stefanski J, Taylor C, Olszewska M, Borquez-Ojeda O, Qu J, Wasielewska T, He Q, Bernal Y, Rijo IV, Hedvat C, Kobos R, Curran K, Steinherz P, Jurcic J, Rosenblat T, Maslak P, Frattini M, Sadelain M 2013 Mar Sci Transl Med 177 5 177ra38

Ontology for vector surveillance and management.

Lozano-Fuentes S, Bandyopadhyay A, Cowell LG, Goldfain A, Eisen L 2013 Jan J. Med. Entomol. 1 50 1-14

Expansion of CD27(high) plasmablasts in transverse myelitis patients that utilize VH4 and JH6 genes and undergo extensive somatic hypermutation.

Ligocki AJ, Rounds WH, Cameron EM, Harp CT, Frohman EM, Courtney AM, Vernino S, Cowell LG, Greenberg B, Monson NL 2013 Apr Genes Immun.

Design and evaluation of a bacterial clinical infectious diseases ontology.

Gordon CL, Pouch S, Cowell LG, Boland MR, Platt HL, Goldfain A, Weng C 2013 AMIA Annu Symp Proc 2013 502-11

Towards an ontological representation of resistance: the case of MRSA.

Goldfain A, Smith B, Cowell LG 2011 Feb J Biomed Inform 1 44 35-41

Hematopoietic cell types: prototype for a revised cell ontology.

Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ 2011 Feb J Biomed Inform 1 44 75-9

Logical development of the cell ontology.

Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD 2011 BMC Bioinformatics 12 6

Memory B cells from a subset of treatment-naive relapsing-remitting multiple sclerosis patients elicit CD4(+) T-cell proliferation and IFN-? production in response to myelin basic protein and myelin oligodendrocyte glycoprotein.

Harp CT, Ireland S, Davis LS, Remington G, Cassidy B, Cravens PD, Stuve O, Lovett-Racke AE, Eagar TN, Greenberg BM, Racke MK, Cowell LG, Karandikar NJ, Frohman EM, Monson NL 2010 Oct Eur. J. Immunol. 10 40 2942-56

Two genes on A/J chromosome 18 are associated with susceptibility to Staphylococcus aureus infection by combined microarray and QTL analyses.

Ahn SH, Deshmukh H, Johnson N, Cowell LG, Rude TH, Scott WK, Nelson CL, Zaas AK, Marchuk DA, Keum S, Lamlertthon S, Sharma-Kuinkel BK, Sempowski GD, Fowler VG 2010 PLoS Pathog. 9 6 e1001088

Multiple, conserved cryptic recombination signals in VH gene segments: detection of cleavage products only in pro B cells.

Davila M, Liu F, Cowell LG, Lieberman AE, Heikamp E, Patel A, Kelsoe G 2007 Dec J. Exp. Med. 13 204 3195-208

V(D)J recombinase-mediated processing of coding junctions at cryptic recombination signal sequences in peripheral T cells during human development.

Murray JM, O'Neill JP, Messier T, Rivers J, Walker VE, McGonagle B, Trombley L, Cowell LG, Kelsoe G, McBlane F, Finette BA 2006 Oct J. Immunol. 8 177 5393-404

Reassignment of the murine 3'TRDD1 recombination signal sequence.

Touvrey C, Cowell LG, Lieberman AE, Marche PN, Jouvin-Marche E, Candéias SM 2006 Nov Immunogenetics 11 58 895-903

The recombination difference between mouse kappa and lambda segments is mediated by a pair-wise regulation mechanism.

Larijani M, Chen S, Cunningham LA, Volpe JM, Cowell LG, Lewis SM, Wu GE 2006 Mar Mol. Immunol. 7 43 870-81

SoDA: implementation of a 3D alignment algorithm for inference of antigen receptor recombinations.

Volpe JM, Cowell LG, Kepler TB 2006 Feb Bioinformatics 4 22 438-44

Neonate-primed CD8+ memory cells rival adult-primed memory cells in antigen-driven expansion and anti-viral protection.

Fadel SA, Cowell LG, Cao S, Ozaki DA, Kepler TB, Steeber DA, Sarzotti M 2006 Feb Int. Immunol. 2 18 249-57

Computational tools for understanding sequence variability in recombination signals.

Cowell LG, Davila M, Ramsden D, Kelsoe G 2004 Aug Immunol. Rev. 200 57-69

A functional analysis of the spacer of V(D)J recombination signal sequences.

Lee AI, Fugmann SD, Cowell LG, Ptaszek LM, Kelsoe G, Schatz DG 2003 Oct PLoS Biol. 1 1 E1

The "dispensable" portion of RAG2 is necessary for efficient V-to-DJ rearrangement during B and T cell development.

Liang HE, Hsu LY, Cado D, Cowell LG, Kelsoe G, Schlissel MS 2002 Nov Immunity 5 17 639-51

The targeting of somatic hypermutation closely resembles that of meiotic mutation.

Oprea M, Cowell LG, Kepler TB 2001 Jan J. Immunol. 2 166 892-9

The nucleotide-replacement spectrum under somatic hypermutation exhibits microsequence dependence that is strand-symmetric and distinct from that under germline mutation.

Cowell LG, Kepler TB 2000 Feb J. Immunol. 4 164 1971-6

Enhanced evolvability in immunoglobulin V genes under somatic hypermutation.

Cowell LG, Kim HJ, Humaljoki T, Berek C, Kepler TB 1999 Jul J. Mol. Evol. 1 49 23-6

Density-dependent prenatal androgen exposure as an endogenous mechanism for the generation of cycles in small mammal populations

Cowell LG, Crowder LB, Kepler TB 1998 Jan J. Theor. Biol. 1 190 93-106