DTU Sundhedsteknologi
DTU Bioinformatik
Lars Rønn Olsen

Lars Rønn Olsen

Groupleader, Associate Professor

Department of Health Technology

Technical University of Denmark

Kemitorvet

Building 208, room 015

2800 Kgs. Lyngby

Ph.
Ph.
Fax +45 45 93 15 85
E-mail lronn@dtu.dk
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2019
 

Analysis of Mass Cytometry Data

Pedersen, Christina B. ; Olsen, Lars R.
part of: Mass Cytometry: Methods and Protocols, pages: 267-279, 2019, Springer

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/978-1-4939-9454-0_17

  PDF

BioReader: a text mining tool for performing classification of biomedical literature

Simon, Christian ; Davidsen, Kristian ; Hansen, Christina ; Seymour, Emily ; Barnkob, Mike Bogetofte ; Olsen, Lars Rønn
in: BMC Bioinformatics, vol: 19, issue: S13, pages: 165-170

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12859-019-2607-x

 

Computational Methods for Identification of T Cell Neoepitopes in Tumors

Jurtz, Vanessa Isabell ; Olsen, Lars Rønn
part of: Cancer Bioinformatics, pages: 157-172, 2019, Springer

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/978-1-4939-8868-6_9

 

Getting the Most from Your High-Dimensional Cytometry Data

Olsen, Lars R. ; Pedersen, Christina B. ; Leipold, Michael D. ; Maecker, Holden T.
in: Immunity, vol: 50, issue: 3, pages: 535-536

Type: Letter (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.immuni.2019.02.015

 

Publisher Correction: Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses

Napolitani, Giorgio ; Teng, Karen Wei Weng ; Gibani, Malick M. ; Kurupati, Prathiba ; Rei, Margarida ; Aulicino, Anna ; Preciado-Llanes, Lorena ; Wong, Michael Thomas ; Becht, Etienne ; Howson, Lauren ; de Haas, Paola ; Salio, Mariolina ; Blohmke, Christoph J. ; Olsen, Lars Rønn ; Pinto, David Miguel Susano ; Scifo, Laura ; Jones, Claire ; Dobinson, Hazel ; Campbell, Danielle ; Juel, Helene B. ; Thomaides-Brears, Helena ; Pickard, Derek ; Bumann, Dirk ; Baker, Stephen ; Dougan, Gordon ; Simmons, Alison ; Gordon, Melita A. ; Newell, Evan William ; Pollard, Andrew J. ; Cerundolo, Vincenzo
in: Nature Immunology

Type: Journal article

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41590-019-0357-6

 

The anatomy of single cell mass cytometry data

Olsen, Lars Rønn ; Leipold, Michael D. ; Pedersen, Christina B. ; Maecker, Holden Terry
in: Cytometry. Part A, vol: 95, issue: 2, pages: 156-172

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/cyto.a.23621

2018
 

Clonal analysis of Salmonella-specific effector T cells reveals serovar-specific and cross-reactive T cell responses

Napolitani, Giorgio ; Kurupati, Prathiba ; Teng, Karen Wei Weng ; Gibani, Malick M. ; Rei, Margarida ; Aulicino, Anna ; Preciado-Llanes, Lorena ; Wong, Michael Thomas ; Becht, Etienne ; Howson, Lauren ; de Haas, Paola ; Salio, Mariolina ; Blohmke, Christoph J. ; Olsen, Lars Rønn ; Pinto, David Miguel Susano ; Scifo, Laura ; Jones, Claire ; Dobinson, Hazel ; Campbell, Danielle ; Juel, Helene B. ; Thomaides-Brears, Helena ; Pickard, Derek ; Bumann, Dirk ; Baker, Stephen ; Dougan, Gordon ; Simmons, Alison ; Gordon, Melita A. ; Newell, Evan William ; Pollard, Andrew J. ; Cerundolo, Vincenzo
in: Nature Immunology, vol: 19, issue: 7, pages: 1-13

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41590-018-0133-z

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Comparison of CyTOF assays across sites: Results of a six-center pilot study

Leipold, Michael D. ; Obermoser, Gerlinde ; Fenwick, Craig ; Kleinstuber, Katja ; Rashidi, Narges ; McNevin, John P. ; Nau, Allison N. ; Wagar, Lisa E. ; Rozot, Virginie ; Davis, Mark M. ; DeRosa, Stephen ; Pantaleo, Giuseppe ; Scriba, Thomas J. ; Walker, Bruce D. ; Olsen, Lars R. ; Maecker, Holden T.
in: Journal of Immunological Methods, vol: 453, pages: 37-43

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.jim.2017.11.008

 

Molecular profiling of short-term and long-term surviving patients identifies CD34 mRNA level as prognostic for glioblastoma survival

Michaelsen, Signe Regner ; Urup, Thomas ; Olsen, Lars Rønn ; Broholm, Helle ; Lassen, Ulrik ; Poulsen, Hans Skovgaard
in: Journal of Neuro-Oncology, vol: 137, issue: 3, pages: 533-542

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/s11060-017-2739-7

 

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

Keskin, Derin B. ; Anandappa, Annabelle J. ; Sun, Jing ; Tirosh, Itay ; Mathewson, Nathan D. ; Li, Shuqiang ; Oliveira, Giacomo ; Giobbie-Hurder, Anita ; Felt, Kristen ; Gjini, Evisa ; Shukla, Sachet A. ; Hu, Zhuting ; Li, Letitia ; Le, Phuong M. ; Allesøe, Rosa Lundbye ; Richman, Alyssa R. ; Kowalczyk, Monika S ; Abdelrahman, Sara ; Geduldig, Jack E. ; Charbonneau, Sarah ; Pelton, Kristine ; Iorgulescu, J. Bryan ; Elagina, Liudmila ; Zhang, Wandi ; Olive, Oriol ; McCluskey, Christine ; Olsen, Lars Rønn ; Stevens, Jonathan ; Lane, William J. ; Salazar, Andres M. ; Daley, Heather ; Wen, Patrick Y. ; Chiocca, E. Antonio ; Harden, Maegan ; Lennon, Niall J. ; Gabriel, Stacey ; Getz, Gad ; Lander, Eric S. ; Regev, Aviv ; Ritz, Jerome ; Neuberg, Donna ; Rodig, Scott J. ; Ligon, Keith L. ; Suvà, Mario L. ; Wucherpfennig, Kai W. ; Hacohen, Nir ; Fritsch, Edward F. ; Livak, Kenneth J ; Ott, Patrick A ; Wu, Catherine J ; Reardon, David A.
in: Nature, vol: 565, pages: 234-239

Type: Letter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41586-018-0792-9

  PDF

Using microarray-based subtyping methods for breast cancer in the era of high-throughput RNA sequencing

Pedersen, Christina Bligaard ; Nielsen, Finn Cilius ; Rossing, Maria ; Olsen, Lars Rønn
in: Molecular Oncology, vol: 12, issue: 12, pages: 2136-2146

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1002/1878-0261.12389

2017
 

PATH-01. Identification of Prognastic Variables Based on Molecular Profiling of Long-Term and Short-Term Surviving Gglioblastoma Patients

Michaelsen, Signe Regner ; Urup, Thomas ; Olsen, Lars Rønn ; Gillberg, Linn ; Broholm, Helle ; Grunnet, Kirsten ; Grønbæk, Kirsten ; Hamerlik, Petra ; Lassen, Ulrik ; Poulsen, Hans Skovgaard
in: Neuro-Oncology, vol: 19, issue: suppl_6, pages: vi170-vi170
Presented at:
22nd Annual Scientific Meeting and Education Day of the Society for Neuro-Oncology

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1093/neuonc/nox168.692

 

TANTIGEN: a comprehensive database of tumor T cell antigens

Olsen, Lars Rønn ; Tongchusak, Songsak ; Lin, Honghuang ; Reinherz, Ellis L. ; Brusic, Vladimir ; Zhang, Guang Lan
in: Cancer Immunology Immunotherapy, vol: 66, pages: 731-735

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1007/s00262-017-1978-y

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Transcriptional changes induced by bevacizumab combination therapy in responding and non-responding recurrent glioblastoma patients

Urup, Thomas ; Staunstrup, Line Maersk ; Michaelsen, Signe Regner ; Vitting-Seerup, Kristoffer ; Bennedbaek, Marc ; Toft, Anders ; Olsen, Lars Rønn ; Jønson, Lars ; Issazadeh-Navikas, Shohreh ; Broholm, Helle ; Hamerlik, Petra ; Poulsen, Hans Skovgaard ; Lassen, Ulrik
in: B M C Cancer, vol: 17

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1186/s12885-017-3251-3

2016
 

A comprehensive profile of recurrent glioblastoma

Campos, B. ; Olsen, Lars Rønn ; Urup, T. ; Poulsen, H. S.
in: Oncogene, vol: 35, pages: 5819-5825

Type: Review (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1038/onc.2016.85

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Angiotensinogen and HLA class II predict bevacizumab response in recurrent glioblastoma patients

Urup, Thomas ; Michaelsen, Signe Regner ; Olsen, Lars Rønn ; Toft, Anders ; Christensen, Ib Jarle ; Grunnet, Kirsten ; Winther, Ole ; Broholm, Helle ; Kosteljanetz, Michael ; Issazadeh-Navikas, Shohreh ; Poulsen, Hans Skovgaard ; Lassen, Ulrik
in: Molecular Oncology, vol: 10, issue: 8, pages: 1160-1168

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.molonc.2016.05.005

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Nutritional Stress Induced by Tryptophan-Degrading Enzymes Results in ATF4-Dependent Reprogramming of the Amino Acid Transporter Profile in Tumor Cells

Timosenko, Elina ; Ghadbane, Hemza ; Silk, Jonathan D ; Shepherd, Dawn ; Gileadi, Uzi ; Howson, Lauren J. ; Laynes, Robert ; Zhao, Qi ; Strausberg, Robert L. ; Olsen, Lars Rønn ; Taylor, Stephen ; Buffa, Francesca M. ; Boyd, Richard ; Cerundolo, Vincenzo
in: Cancer Research, vol: 76, issue: 21, pages: 6193-6204

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1158/0008-5472.CAN-15-3502

2015
  PDF

A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

Olsen, Lars Rønn ; Simon, Christian ; Kudahl, Ulrich J. ; Bagger, Frederik Otzen ; Winther, Ole ; Reinherz, Ellis L. ; Zhang, Guang L. ; Brusic, Vladimir
in: BMC Medical Genomics, vol: 8, issue: Suppl. 4, pages: 566
Presented at:
Joint 26th Genome Informatics Workshop and 14th International Conference on Bioinformatics: Medical Genomics

Type: Conference article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1186/1755-8794-8-S4-S1

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FluKB: A Knowledge-Based System for Influenza Vaccine Target Discovery and Analysis of the Immunological Properties of Influenza Viruses

Simon, Christian ; Kudahl, Ulrich Johan ; Sun, Jing ; Olsen, Lars Rønn ; Zhang, Guang Lan ; Reinherz, Ellis L. ; Brusic, Vladimir
in: Journal of Immunology Research

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1155/2015/380975

 

MTR-18 Predictive Biomarkers Of Bevacizumab Response In Recurrent Glioblastoma Patients

Urup, Thomas ; Michaelsen, Signe Regner ; Olsen, Lars Rønn ; Toft, Anders ; Christensen, Ib Jarle ; Grunnet, Kirsten ; Broholm, Helle ; Kosteljanetz, Michael ; Poulsen, Hans Skovgaard ; Lassen, Ulrik
in: Neuro-Oncology, vol: 17, issue: suppl. 5, pages: v128-v128
Presented at:
The 20th Annual Scientific Meeting of the Society for Neuro-Oncology

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1093/neuonc/nov219.18

 

Software-Supported USER Cloning Strategies for Site-Directed Mutagenesis and DNA Assembly

Genee, Hans Jasper ; Bonde, Mads Tvillinggaard ; Bagger, Frederik Otzen ; Jespersen, Jakob Berg ; Sommer, Morten O. A. ; Wernersson, Rasmus ; Olsen, Lars Rønn
in: A C S Synthetic Biology, vol: 4, issue: 3, pages: 342-349

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1021/sb500194z

2014
 

Bioinformatics for cancer immunotherapy target discovery.

Olsen, Lars Rønn ; Campos, Benito ; Barnkob, Mike Stein ; Winther, Ole ; Brusic, Vladimir ; Andersen, Mads Hald
in: Cancer Immunology, Immunotherapy, vol: 63, issue: 12, pages: 1235-1249

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1007/s00262-014-1627-7

  PDF

Characterizing the human hematopoietic CDome

Barnkob, Mike Stein ; Simon, Christian ; Olsen, Lars Rønn
in: Frontiers in Genetics, vol: 5

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.3389/fgene.2014.00331

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Tumor antigens as proteogenomic biomarkers in invasive ductal carcinomas

Olsen, Lars Rønn ; Campos, Benito ; Winther, Ole ; Sgroi, Dennis C. ; Karger, Barry L. ; Brusic, Vladimir
in: BMC Medical Genomics, vol: 7, issue: Suppl. 3

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2014     |    DOI: https://doi.org/10.1186/1755-8794-7-S3-S2

2013
 

BlockLogo: Visualization of peptide and sequence motif conservation

Olsen, Lars Rønn ; Kudahl, Ulrich Johan ; Simon, Christian ; Sun, Jing ; Schönbach, Christian ; Reinherz, Ellis L. ; Zhang, Guang Lan ; Brusic, Vladimir
in: Journal of Immunological Methods, vol: 400-401, pages: 37-44

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1016/j.jim.2013.08.014

  PDF

Literature classification for semi-automated updating of biological knowledgebases

Olsen, Lars Rønn ; Kudahl, Ulrich Johan ; Winther, Ole ; Brusic, Vladimir
in: B M C Genomics, vol: 14, issue: Suppl. 5

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2013     |    DOI: https://doi.org/10.1186/1471-2164-14-S5-S14

2011
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Conservation analysis of dengue virust-cell epitope-based vaccine candidates using peptide block entropy

Olsen, Lars Rønn ; Zhang, Guang Lan ; Keskin, Derin B. ; Reinherz, Ellis L. ; Brusic, Vladimir
in: Frontiers in Immunology, vol: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2011     |    DOI: https://doi.org/10.3389/fimmu.2011.00069

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FLAVIdB: A data mining system for knowledge discovery in flaviviruses with direct applications in immunology and vaccinology

Olsen, Lars Rønn ; Zhang, Guang Lan ; Reinherz, Ellis L. ; Brusic, Vladimir
in: Immunome Research, vol: 7, issue: 3

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2011

  PDF

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design

Olsen, Lars Rønn ; Hansen, Niels Bjørn ; Bonde, Mads ; Genee, Hans Jasper ; Holm, Dorte Marie Koefoed ; Carlsen, Simon ; Hansen, Bjarne Gram ; Patil, Kiran Raosaheb ; Mortensen, Uffe Hasbro ; Wernersson, Rasmus
in: Nucleic Acids Research, vol: 39, issue: Suppl. 2, pages: W61-W67

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2011     |    DOI: https://doi.org/10.1093/nar/gkr394