Ghent University Academic Bibliography

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Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer CLEAN

Jonatan Linus Gabre (UGent) , Peter Merseburger (UGent) , Arne Claeys (UGent) , Joachim Siaw (UGent) , Sarah-Lee Bekaert (UGent) , Franki Speleman (UGent) , Bengt Hallberg, Ruth H Palmer and Jimmy Van den Eynden (UGent)

(2024) NAR CANCER. 6(1).
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ALK signaling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition

Marcus Borenäs, Ganesh Umapathy, Dan E. Lind, Wei-Yun Lai, Jikui Guan, Joel Johansson, Eva Jennische, Alexander Schmidt, Yeshwant Kurhe, Jonatan Linus Gabre (UGent) , et al.

(2024) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 121(1).
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Effects of hyperthermia on cisplatin tissue penetration and gene expression in peritoneal metastases : results from a randomized trial in ovarian cancer

Jesse Demuytere (UGent) , Charlotte Carlier, Tom Van Helden (UGent) , Joke Belza (UGent) , Frank Vanhaecke (UGent) , Feifan Xie, An Vermeulen (UGent) , Joseph Weerts, Jürgen Thomale, Hannelore Denys (UGent) , et al.

(2024) BRITISH JOURNAL OF SURGERY. 111(4).
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MHC class II genotypes are independent predictors of anti-PD1 immunotherapy response in melanoma

Arne Claeys (UGent) and Jimmy Van den Eynden (UGent)

(2024) Communications Medicine. 4(1).
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- Miscellaneous
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A systematic analysis of immune escape signals in the primary and metastatic tumor genome

Jimmy Van den Eynden (UGent)

(2023) NATURE GENETICS. 55. p.728-729
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ALK fusion NSCLC oncogenes promote survival and inhibit NK cell responses via SERPINB4 expression

Tzu-Po Chuang, Wei-Yun Lai, Jonatan Linus Gabre (UGent) , Dan E. Lind, Ganesh Umapathy, Abdulmalik A. Bokhari, Bengt Bergman, Linnea Kristenson, Fredrik B. Thorén, Anh Le, et al.

(2023) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 120(8).
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Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data

Arne Claeys (UGent) , Peter Merseburger (UGent) , Jasper Staut (UGent) , Kathleen Marchal (UGent) and Jimmy Van den Eynden (UGent)

(2023) BMC GENOMICS. 24.
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Quantification of neoantigen-mediated immunoediting in cancer evolution : letter

Arne Claeys (UGent) and Jimmy Van den Eynden (UGent)

(2023) CANCER RESEARCH. 83(6). p.971-972
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Novel human-derived EML4-ALK fusion cell lines identify ribonucleotide reductase RRM2 as a target of activated ALK in NSCLC

A.A. Bokhari, W-Y. Lai, A.T. Le, J.L. Gabre, T-P. Chuang, S. Fransson, B. Bergman, A. Djos, N. Chen, T. Martinsson, et al.

(2022) LUNG CANCER. 171. p.103-114
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- Miscellaneous
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Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data

Arne Claeys (UGent) , Jasper Staut (UGent) , Peter Merseburger (UGent) , Kathleen Marchal (UGent) and Jimmy Van den Eynden (UGent)

(2022)
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A clinically annotated post-mortem approach to study multi-organ somatic mutational clonality in normal tissues

Tom Luijts (UGent) , Kerryn Elliott, Joachim Siaw (UGent) , Joris Van de Velde (UGent) , Elien Beyls (UGent) , Arne Claeys (UGent) , Tim Lammens (UGent) , Erik Larsson, Wouter Willaert (UGent) , Anne Vral (UGent) , et al.

(2022) SCIENTIFIC REPORTS. 12.
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Low immunogenicity of common cancer hot spot mutations resulting in false immunogenic selection signals

Arne Claeys (UGent) , Tom Luijts (UGent) , Kathleen Marchal (UGent) and Jimmy Van den Eynden (UGent)

(2021) PLOS Genetics. 17(2).
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- Miscellaneous
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Pharmacologic RNA splicing modulation : a novel mechanism to enhance neoantigen-directed anti-tumor immunity and immunotherapy response

Kerryn Elliott, Jonas Nilsson and Jimmy Van den Eynden (UGent)

(2021) SIGNAL TRANSDUCTION AND TARGETED THERAPY. 6(1).
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Network-based analysis to identify drivers of metastatic prostate cancer using GoNetic

Louise de Schaetzen van Brienen (UGent) , Giles Miclotte (UGent) , Maarten Larmuseau (UGent) , Jimmy Van den Eynden (UGent) and Kathleen Marchal (UGent)

(2021) CANCERS. 13(21).
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ATR inhibition enables complete tumour regression in ALK-driven NB mouse models

Joanna Szydzik, Dan E. Lind, Badrul Arefin, Yeshwant Kurhe, Ganesh Umapathy, Joachim Tetteh Siaw, Arne Claeys (UGent) , Jonatan Linus Gabre (UGent) , Jimmy Van den Eynden (UGent) , Bengt Hallberg, et al.

(2021) NATURE COMMUNICATIONS. 12(1).
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Loss of RET promotes mesenchymal identity in neuroblastoma cells

Joachim T. Siaw, Jonatan Linus Gabre (UGent) , Ezgi Uçkun, Marc Vigny, Wancun Zhang, Jimmy Van den Eynden (UGent) , Bengt Hallberg, Ruth H. Palmer and Jikui Guan

(2021) CANCERS. 13(8).
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ALK ligand ALKAL2 potentiates MYCN‐driven neuroblastoma in the absence of ALK mutation

Marcus Borenäs, Ganesh Umapathy, Wei‐Yun Lai, Dan E Lind, Barbara Witek, Jikui Guan, Patricia Mendoza‐Garcia, Tafheem Masudi, Arne Claeys (UGent) , Tzu‐Po Chuang, et al.

(2021) EMBO JOURNAL. 40(3).
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11q deletion or ALK activity curbs DLG2 expression to maintain an undifferentiated state in neuroblastoma

Joachim Tetteh Siaw, Niloufar Javanmardi, Jimmy Van den Eynden (UGent) , Dan Emil Lind, Susanne Fransson, Angela Martinez-Monleon, Anna Djos, Rose-Marie Sjöberg, Malin Östensson, Helena Carén, et al.

(2020) CELL REPORTS. 32(12).
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- A2
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Separating positional noise from neutral alignment in multicomponent statistical shape models

Emmanuel Audenaert (UGent) , Jimmy Van den Eynden (UGent) , DF de Almeida, G Steenackers, D Vandermeulen and P Claes

(2020) BONE REPORTS. 12.
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Lack of detectable neoantigen depletion signals in the untreated cancer genome

Jimmy Van den Eynden (UGent) , Alejandro Jiménez-Sánchez, Martin L Miller and Erik Larsson

(2019) NATURE GENETICS. 51(12). p.1741-1748

Academic Bibliography

Preclinical exploration of the DNA damage response pathway using the interactive neuroblastoma cell line explorer CLEAN

ALK signaling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition

Effects of hyperthermia on cisplatin tissue penetration and gene expression in peritoneal metastases : results from a randomized trial in ovarian cancer

MHC class II genotypes are independent predictors of anti-PD1 immunotherapy response in melanoma

A systematic analysis of immune escape signals in the primary and metastatic tumor genome

ALK fusion NSCLC oncogenes promote survival and inhibit NK cell responses via SERPINB4 expression

Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data

Quantification of neoantigen-mediated immunoediting in cancer evolution : letter

Novel human-derived EML4-ALK fusion cell lines identify ribonucleotide reductase RRM2 as a target of activated ALK in NSCLC

Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data

A clinically annotated post-mortem approach to study multi-organ somatic mutational clonality in normal tissues

Low immunogenicity of common cancer hot spot mutations resulting in false immunogenic selection signals

Pharmacologic RNA splicing modulation : a novel mechanism to enhance neoantigen-directed anti-tumor immunity and immunotherapy response

Network-based analysis to identify drivers of metastatic prostate cancer using GoNetic

ATR inhibition enables complete tumour regression in ALK-driven NB mouse models

Loss of RET promotes mesenchymal identity in neuroblastoma cells

ALK ligand ALKAL2 potentiates MYCN‐driven neuroblastoma in the absence of ALK mutation

11q deletion or ALK activity curbs DLG2 expression to maintain an undifferentiated state in neuroblastoma

Separating positional noise from neutral alignment in multicomponent statistical shape models

Lack of detectable neoantigen depletion signals in the untreated cancer genome

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