Publications

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2022
 

A literature study and public survey on mass cytometry dataset release and reuse

Leipold, Michael D. ; Olsen, Lars Rønn
in: Cytometry Part A, vol: 101, issue: 2, pages: 109-113

Type: Editorial (Peer reviewed)

Status: Published     |    Year: 2022     |    DOI: https://doi.org/10.1002/cyto.a.24512

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cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies

Pedersen, Christina Bligaard ; Dam, Søren Helweg ; Barnkob, Mike Bogetofte ; Leipold, Michael D. ; Purroy, Noelia ; Rassenti, Laura Z. ; Kipps, Thomas J. ; Nguyen, Jennifer ; Lederer, James Arthur ; Gohil, Satyen Harish ; Wu, Catherine J. ; Olsen, Lars Rønn
in: Nature Communications, vol: 13

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2022     |    DOI: https://doi.org/10.1038/s41467-022-29383-5

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High CD34 surface expression in BCP-ALL predicts poor induction therapy response and is associated with altered expression of genes related to cell migration and adhesion

Modvig, Signe ; Wernersson, Rasmus ; Øbro, Nina Friesgaard ; Olsen, Lars Rønn ; Christensen, Claus ; Rosthøj, Susanne ; Degn, Matilda ; Jürgensen, Gitte Wullf ; Madsen, Hans O. ; Albertsen, Birgitte Klug ; Wehner, Peder Skov ; Rosthøj, Steen ; Lilljebjörn, Henrik ; Fioretos, Thoas ; Schmiegelow, Kjeld ; Marquart, Hanne Vibeke
in: Molecular Oncology, vol: 16, issue: 10, pages: 2015-2030

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2022     |    DOI: https://doi.org/10.1002/1878-0261.13207

2021
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A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data

Gabrielaite, Migle ; Torp, Mathias Husted ; Rasmussen, Malthe Sebro ; Andreu-Sánchez, Sergio ; Vieira, Filipe Garrett ; Pedersen, Christina Bligaard ; Kinalis, Savvas ; Madsen, Majbritt Busk ; Kodama, Miyako ; Demircan, Gül Sude ; Simonyan, Arman ; Yde, Christina Westmose ; Olsen, Lars Rønn ; Marvig, Rasmus L. ; Østrup, Olga ; Rossing, Maria ; Nielsen, Finn Cilius ; Winther, Ole ; Bagger, Frederik Otzen
in: Cancers, vol: 13, issue: 24

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.3390/cancers13246283

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Automated download and clean-up of family specific databases for kmer-based virus identification

Allesøe, Rosa Lundbye ; Lemvigh, Camilla Koldbæk ; Phan, My V T ; Clausen, Philip Thomas Lanken Conradsen ; Florensa, Alfred Ferrer ; Koopmans, Marion P G ; Lund, Ole ; Cotten, Matthew
in: Bioinformatics, vol: 37, issue: 5, pages: 705–710

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.1093/bioinformatics/btaa857

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Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation

Crump, Nicholas T. ; Hadjinicolaou, Andreas V. ; Xia, Meng ; Walsby-Tickle, John ; Gileadi, Uzi ; Chen, Ji Li ; Setshedi, Mashiko ; Olsen, Lars R. ; Lau, I. Jun ; Godfrey, Laura ; Quek, Lynn ; Yu, Zhanru ; Ballabio, Erica ; Barnkob, Mike B. ; Napolitani, Giorgio ; Salio, Mariolina ; Koohy, Hashem ; Kessler, Benedikt M. ; Taylor, Stephen ; Vyas, Paresh ; McCullagh, James S.O. ; Milne, Thomas A. ; Cerundolo, Vincenzo
in: Cell Reports, vol: 35, issue: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.1016/j.celrep.2021.109101

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Clinical implications of intrinsic molecular subtypes of breast cancer for sentinel node status

Rossing, Maria ; Pedersen, Christina Bligaard ; Tvedskov, Tove ; Vejborg, Ilse ; Talman, Maj Lis ; Olsen, Lars Rønn ; Kroman, Niels ; Nielsen, Finn Cilius ; Jensen, Maj Britt ; Ejlertsen, Bent
in: Scientific Reports, vol: 11, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.1038/s41598-021-81538-4

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Inverted CD8 T-Cell Exhaustion and Co-Stimulation Marker Balance Differentiate Aviremic HIV-2-Infected From Seronegative Individuals

Scharf, Lydia ; Pedersen, Christina B. ; Johansson, Emil ; Lindman, Jacob ; Olsen, Lars R ; Buggert, Marcus ; Wilhelmson, Sten ; Månsson, Fredrik ; Esbjörnsson, Joakim ; Biague, Antonio ; Medstrand, Patrik ; Norrgren, Hans ; Karlsson, Annika C. ; Jansson, Marianne
in: Frontiers in Immunology, vol: 12

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.3389/fimmu.2021.744530

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Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma

Hu, Zhuting ; Leet, Donna E. ; Allesøe, Rosa L. ; Oliveira, Giacomo ; Li, Shuqiang ; Luoma, Adrienne M. ; Liu, Jinyan ; Forman, Juliet ; Huang, Teddy ; Iorgulescu, J. Bryan ; Holden, Rebecca ; Sarkizova, Siranush ; Gohil, Satyen H. ; Redd, Robert A. ; Sun, Jing ; Elagina, Liudmila ; Giobbie-Hurder, Anita ; Zhang, Wandi ; Peter, Lauren ; Ciantra, Zoe ; Rodig, Scott ; Olive, Oriol ; Shetty, Keerthi ; Pyrdol, Jason ; Uduman, Mohamed ; Lee, Patrick C. ; Bachireddy, Pavan ; Buchbinder, Elizabeth I. ; Yoon, Charles H. ; Neuberg, Donna ; Pentelute, Bradley L. ; Hacohen, Nir ; Livak, Kenneth J. ; Shukla, Sachet A. ; Olsen, Lars Rønn ; Barouch, Dan H. ; Wucherpfennig, Kai W. ; Fritsch, Edward F. ; Keskin, Derin B. ; Wu, Catherine J. ; Ott, Patrick A.
in: Nature Medicine, vol: 27, issue: 3, pages: 515-525

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.1038/s41591-020-01206-4

 

Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy

Kretzmer, Helene ; Biran, Anat ; Purroy, Noelia ; Lemvigh, Camilla K. ; Clement, Kendell ; Gruber, Michaela ; Gu, Hongcang ; Rassenti, Laura ; Mohammad, Arman W. ; Lesnick, Connie ; Slager, Susan L. ; Braggio, Esteban ; Shanafelt, Tait D. ; Kay, Neil E. ; Fernandes, Stacey M. ; Brown, Jennifer R. ; Wang, Lili ; Li, Shuqiang ; Livak, Kenneth J. ; Neuberg, Donna S. ; Klages, Sven ; Timmermann, Bernd ; Kipps, Thomas J. ; Campo, Elias ; Gnirke, Andreas ; Wu, Catherine J. ; Meissner, Alexander
in: Cancer Discovery, vol: 2, issue: 1, pages: 54-69

Type: Comment/debate (Peer reviewed)

Status: Published     |    Year: 2021     |    DOI: https://doi.org/10.1158/2643-3230.BCD-19-0058