Publications

Tommaso De Marchi, Chun-Fui Lai, Georgia M. Simmons, Isabella Goldsbrough, Alison Harrod, Thai Lam, Lakjaya Buluwela, Sven Kjellström, Christian Brueffer, Lao H. Saal, Johan Malmström, Simak Ali, Emma Niméus. Proteomic profiling reveals that ESR1 mutations enhance cyclin-dependent kinase signaling.
Scientific Reports, 2024. 14:6873

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Pei Meng, Hina Dalal, Yilun Chen, Christian Brueffer, Sergii Gladchuk, Miguel Alcaide, Anna Ehinger, Lao H. Saal. Digital PCR quantification of ultrahigh ERBB2 copy number identifies poor breast cancer survival after trastuzumab.
npj Breast Cancer, 2024. 10:14

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Arturas Dobilas, Yilun Chen, Christian Brueffer, Pia Leandersson, Lao H. Saal, Christer Borgfeldt. Preoperative ctDNA Levels are Associated with Poor Overall Survival in Patients with Ovarian Cancer.
Cancer Genomics & Proteomics, 2023. 20(6suppl):763-770

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Christoph Grimm, Valentina Paspalj, Magdalena Postl, Lao H. Saal, Christian Brueffer, Nuria Segui Gracia, Miguel Alcaide, Stephan Polterauer, Lucia Oton, Yilun Chen, Gerda Hofstetter, Leonhard Müllauer. 805P Tumor-informed ctDNA detection as a predictive marker for postoperative residual disease in epithelial ovarian cancer: A feasibility study.
Annals of Oncology, 2023. 34:S536, Supplement 2

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Magdalena Postl, Valentina Paspalj, Christian Brueffer, Nuria Segui Gracia, Miguel Alcaide, Lucia Oton, Yilun Chen, Lao H. Saal, Gerda Hofstetter, Leonhard Müllauer, Stephan Polterauer, Christoph Grimm. #898 Tumor-informed ctDNA detection as a marker for postoperative residual disease in epithelial ovarian cancer – results of a feasibility study.
International Journal of Gynecologic Cancer, 2023. 33:A38-A39

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Xiaotong Li, Lao H. Saal, Christian Brueffer, Yilun Chen, Johanna Asklin, Saman Alvi, Srinivas Venkatram, Jeremy A. Ross. Abstract 5710: Detection and monitoring of t(11;14) in liquid biopsies from patients with relapsed/refractory multiple myeloma treated with venetoclax-based regimens.
Cancer Research, 2023. 83:7_Supplement

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Arturas Dobilas, Pia Leandersson, Yilun Chen, Miguel Alcaide, Christian Brueffer, Lao H. Saal, Christer Borgfeldt. 2022-RA-627-ESGO: Preoperative circulating tumor DNA level is associated to poor overall survival in patients with ovarian cancer.
International Journal of Gynecologic Cancer, 2022. 32:A405

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Nathan D. Olson, Justin Wagner, Jennifer McDaniel, Sarah H. Stephens, Samuel T. Westreich, Anish G. Prasanna, Elaine Johanson, Emily Boja, Ezekiel J. Maier, Omar Serang, David Jáspez, José M. Lorenzo-Salazar, Adrián Muñoz Barrera, Luis A. Rubio-Rodríguez, Carlos Flores, Konstantinos Kyriakidis, Andigoni Malousi, Kishwar Shafin, Trevor Pesout, Miten Jain, Benedict Paten, Pi-Chuan Chang, Alexey Kolesnikov, Maria Nattestad, Gunjan Baid, Sidharth Goel, Howard Yang, Andrew Carroll, Robert Eveleigh, Mathieu Bourgey, Guillaume Bourque, Gen Li, ChouXian Ma, LinQi Tang, YuanPing Du, ShaoWei Zhang, Jordi Morata, Raúl Tonda, Genís Parra, Jean-Rémi Trotta, Christian Brueffer, Sinem Demirkaya-Budak, Duygu Kabakci-Zorlu, Deniz Turgut, Özem Kalay, Gungor Budak, Kübra Narcı, Elif Arslan, Richard Brown, Ivan J. Johnson, Alexey Dolgoborodov, Vladimir Semenyuk, Amit Jain, H. Serhat Tetikol, Varun Jain, Mike Ruehle, Bryan Lajoie, Cooper Roddey, Severine Catreux, Rami Mehio, Mian Umair Ahsan, Qian Liu, Kai Wang, Sayed Mohammad Ebrahim Sahraeian, Li Tai Fang, Marghoob Mohiyuddin, Calvin Hung, Chirag Jain, Hanying Feng, Zhipan Li, Luoqi Chen, Fritz J. Sedlazeck, Justin M. Zook. PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions.
Cell Genomics, 2022. 2(5): 100129

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Halie M. Rando, Christian Brueffer, Ronan Lordan, Anna Ada Dattoli, David Manheim, Jesse G. Meyer, Ariel I. Mundo, Dimitri Perrin, David Mai, Nils Wellhausen, COVID-19 Review Consortium, Anthony Gitter, Casey S. Greene. Molecular and Serologic Diagnostic Technologies for SARS-CoV-2.
arXiv, 2022

DOI arXiv Preprint Project

Hina Dalal, Malin Dahlgren, Sergii Gladchuk, Christian Brueffer, Sofia K. Gruvberger-Saal, Lao H. Saal. Clinical associations of ESR2 (estrogen receptor beta; ERβ) expression across thousands of primary breast tumors.
Scientific Reports, 2022. 12:4696

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Halie M. Rando, Nils Wellhausen, Soumita Ghosh, Alexandra J. Lee, Anna Ada Dattoli, Fengling Hu, James Brian Byrd, Diane N. Rafizadeh, Ronan Lordan, Yanjun Qi, Yuchen Sun, Christian Brueffer, Jeffrey M. Field, Marouen Ben Guebila, Nafisa M. Jadavji, Ashwin N. Skelly, Bharath Ramsundar, Jinhui Wang, Rishi Raj Goel, YoSon Park, COVID-19 Review Consortium, Simina M. Boca, Anthony Gitter, Casey S. Greene. Identification and Development of Therapeutics for COVID-19.
mSystems, 2021. 6(6): e00233-21

DOI PDF arXiv Preprint Project

Halie M. Rando, Adam L. MacLean, Alexandra J. Lee, Ronan Lordan, Sandipan Ray, Vikas Bansal, Ashwin N. Skelly, Elizabeth Sell, John J. Dziak, Lamonica Shinholster, Lucy D'Agostino McGowan, Marouen Ben Guebila, Nils Wellhausen, Sergey Knyazev, Simina M. Boca, Stephen Capone, Yanjun Qi, YoSon Park, David Mai, Yuchen Sun, Joel Boerckel, Christian Brueffer, James Brian Byrd, Jeremy P. Kamil, Jinhui Wang, Ryan Velazquez, Gregory L. Szeto, John P. Barton, Rishi Raj Goel, Serghei Mangul, Tiago Lubiana, COVID-19 Review Consortium, Anthony Gitter, Casey S. Greene. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure.
mSystems, 2021. 6(5): e00095-21

DOI PDF arXiv Preprint Project

Ronan Lordan, Halie M. Rando, Vikas Bansal, John P. Barton, Simina M. Boca, Christian Brueffer, James Brian Byrd, Stephen Capone, Shikta Das, Anna Ada Dattoli, John J. Dziak, Jeffrey M. Field, Soumita Ghosh, Anthony Gitter, Rishi Raj Goel, Marouen Ben Guebila, Fengling Hu, Nafisa M. Jadavji, Sergey Knyazev, Likhitha Kolla, Alexandra J. Lee, Tiago Lubiana, Temitayo Lukan, Adam L. MacLean, David Mai, Serghei Mangul, David Manheim, Lucy D'Agostino McGowan, YoSon Park, Dimitri Perrin, Yanjun Qi, Diane N. Rafizadeh, Bharath Ramsundar, Sandipan Ray, Michael P. Robson, Elizabeth Sell, Lamonica Shinholster, Ashwin N. Skelly, Yuchen Sun, Gregory L. Szeto, Ryan Velazquez, Jinhui Wang, Nils Wellhausen, Casey S. Greene. Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment.
mSystems, 2021. 6(3): e00122-21

DOI PDF arXiv Preprint Project

Malin Dahlgren, Anthony M. George, Christian Brueffer, Sergii Gladchuk, Yilun Chen, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Lisa Rydén, Martin Malmberg, Christer Larsson, Sofia K. Gruvberger-Saal, Anna Ehinger, Niklas Loman, Åke Borg, Lao H. Saal. Preexisting Somatic Mutations of Estrogen Receptor Alpha (ESR1) in Early-Stage Primary Breast Cancer.
JNCI Cancer Spectrum, 2021. 5(2): pkab028

DOI PDF Dataset Press Release

Christian Brueffer. RNA Sequencing for Molecular Diagnostics in Breast Cancer.
Lund University, Faculty of Medicine Doctoral Dissertation Series. 2021:2

PDF Code PhD Project LUCRIS Project

Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony M. George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal. The mutational landscape of the SCAN-B real-world primary breast cancer transcriptome.
EMBO Molecular Medicine, 2020. 12(10):e12118

DOI PDF bioRxiv Preprint Code Dataset Press Release PhD Project

Helén Nilsson, David Lindgren, Håkan Axelson, Christian Brueffer, Lao H. Saal, Jaana Lundgren, Martin Johansson. Features of increased malignancy in eosinophilic clear cell renal cell carcinoma.
The Journal of Pathology, 2020. 252(4):384–397

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Malin Dahlgren, Anthony M. George, Christian Brueffer, Sergii Gladchuk, Yilun Chen, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Lisa Rydén, Martin Malmberg, Christer Larsson, Sofia K. Gruvberger-Saal, Anna Ehinger, Niklas Loman, Åke Borg, Lao H. Saal. Abstract CT074: Pre-existing ESR1 mutations in early-stage primary breast cancer predict failure of endocrine therapy and poor survival.
Cancer Research, 2020. 80:16_Supplement

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Lesley M. Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M. Watson, Christos Proukakis, Wayne E. Clarke, Naoki Nariai, Eric Dawson, Garan Jones, Daniel Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M. Wenger, Marc Salit, Justin M. Zook. A crowdsourced set of curated structural variants for the human genome.
PLoS Computational Biology, 2020. 16(6):e1007933

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Christian Brueffer, Sergii Gladchuk, Christof Winter, Johan Vallon-Christersson, Cecilia Hegardt, Jari Häkkinen, Anthony M George, Yilun Chen, Anna Ehinger, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Åke Borg, Lao H. Saal. Defining the mutational landscape of 3,217 primary breast cancer transcriptomes through large-scale RNA-seq within the Sweden Cancerome Analysis Network: Breast Project (SCAN-B; NCT03430492).
Journal of Clinical Oncology, 2020. 38:15_suppl

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Yoshiko Nanki, Anthony M. George, Yilun Chen, Christian Brueffer, Akira Hirasawa, Tatsuyuki Chiyoda, Tomoko Akahane, Daisuke Aoki, Lao H. Saal. Plasma circulating tumor DNA as a genomic biomarker for ovarian cancer.
European Journal of Human Genetics, 2019. 27:1670-1671

Daniel Förnvik, Kristina E. Aaltonen, Yilun Chen, Anthony M. George, Christian Brueffer, Robert Rigo, Niklas Loman, Lao H. Saal, Lisa Rydén. Detection of circulating tumor cells and circulating tumor DNA before and after mammographic breast compression in a cohort of breast cancer patients scheduled for neoadjuvant treatment.
Breast Cancer Research and Treatment, 2019. 177(2):447–445

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Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S. Pedersen, Youri Hoogstrate, Devon Ryan, Anthony Bretaudeau, Gildas Le Corguillé, Christian Brueffer, et al. Bioconda: sustainable and comprehensive software distribution for the life sciences.
Nature Methods, 2018. 15(7):475–476

DOI bioRxiv Preprint Project Code

Christian Brueffer, Johan Vallon-Christersson, Dorthe Grabau, Anna Ehinger, Jari Häkkinen, Cecilia Hegardt, Janne Malina, Yilun Chen, Pär-Ola Bendahl, Jonas Manjer, Martin Malmberg, Christer Larsson, Niklas Loman, Lisa Rydén, Åke Borg, Lao H. Saal. Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network–Breast Initiative.
JCO Precision Oncology, 2018. 2:1–18

DOI PDF Dataset PhD Project

Christian Brueffer, Johan Vallon-Christersson, Dorthe Grabau, Anna Ehinger, Jari Häkkinen, Cecilia Hegardt, Janne Malina, Yilun Chen, Pär-Ola Bendahl, Jonas Manjer, Martin Malmberg, Christer Larsson, Niklas Loman, Lisa Rydén, Åke Borg, Lao H. Saal. Abstract P4-09-03: On the development and clinical value of RNA-sequencing-based classifiers for prediction of the five conventional breast cancer biomarkers: A report from the population-based multicenter SCAN-B study.
Cancer Research, 2018. 78:4_Supplement P4-09-03

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Niklas Loman, Yilun Chen, Kristina Aaltonen, Christian Brueffer, Anthony M. George, Lina Zander, Johan Vallon-Christersson, Jari Häkkinen, Daniel Förnvik, Robert Rigo, Anna Ehinger, Martin Malmberg, Christer Larsson, Cecilia Hegardt, Åke Borg, Lisa Rydén, Lao H. Saal. Abstract P2-02-09: Breast cancer subtype distribution and circulating tumor DNA in response to neoadjuvant chemotherapy: Experiences from a preoperative cohort within SCAN-B.
Cancer Research, 2018. 78:4_Supplement P2-02-09

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Christian Brueffer, Lao H. Saal. TopHat-Recondition: A post-processor for TopHat unmapped reads.
BMC Bioinformatics, 2016. 17(1):199

DOI PDF bioRxiv Preprint Code PhD Project

Man-Hung Eric Tang, Malin Dahlgren, Christian Brueffer, Tamara Tjitrowirjo, Christof Winter, Yilun Chen, Eleonor Olsson, Kun Wang, Therese Törngren, Martin Sjöström, Dorthe Grabau, Pär-Ola Bendahl, Lisa Rydén, Emma Niméus, Lao H. Saal, Åke Borg, Sofia K. Gruvberger-Saal. Remarkable similarities of chromosomal rearrangements between primary human breast cancers and matched distant metastases as revealed by whole-genome sequencing.
Oncotarget, 2015. 6(35):37169–37184

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Sara Alkner, Man-Hung Eric Tang, Christian Brueffer, Malin Dahlgren, Yilun Chen, Eleonor Olsson, Christof Winter, Sara Baker, Anna Ehinger, Lisa Rydén, Lao H. Saal, Mårten Fernö, Sofia K. Gruvberger-Saal. Contralateral breast cancer can represent a metastatic spread of the first primary tumor: determination of clonal relationship between contralateral breast cancers using next-generation whole genome sequencing.
Breast Cancer Research, 2015. 17:102

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Man-Hung Eric Tang, Malin Dahlgren, Christian Brueffer, Christof Winter, Yilun Chen, Eleonor Olsson, Martin Sjöström, Pär-Ola Bendahl, Emma Niméus-Malmström, Lao H. Saal, Åke Borg, Sofia K. Gruvberger-Saal. Abstract 4805: Whole genome sequencing of primary breast cancers and matched distant metastases.
Cancer Research, 2015. 75:15_Supplement 4805

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Lao H. Saal, Johan Vallon-Christersson, Jari Häkkinen, Cecilia Hegardt, Dorthe Grabau, Christof Winter, Christian Brueffer, Man-Hung Eric Tang, Christel Reuterswärd, Ralph Schulz, Anna Karlsson, Anna Ehinger, Janne Malina, Jonas Manjer, Martin Malmberg, Christer Larsson, Lisa Rydén, Niklas Loman, Åke Borg. The Sweden Cancerome Analysis Network-Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine.
Genome Medicine, 2015. 7(1):20

DOI PDF Dataset PhD Project

Christian Brueffer. FreeBSD Security Event Auditing.
BSD Magazine issue 4/2009

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