Christian Brueffer

2022

Clinical associations of ESR2 (estrogen receptor beta) expression across thousands of primary breast tumors

Dalal, H., Dahlgren, M., Gladchuk, S., Brueffer, C., Gruvberger-Saal, S. K. & Saal, L. H., 2022, In: Scientific Reports. 12, p. 1-12 4696.

Research output: Contribution to journal › Article › peer-review

Open Access

Molecular and Serologic Diagnostic Technologies for SARS-CoV-2

Rando, H. M., Brueffer, C., Lordan, R., Dattoli, A. A., Manheim, D., Meyer, J. G., Mundo, A. I., Perrin, D., Mai, D., Wellhausen, N., COVID-19 Review Consortium, Gitter, A. & Greene, C. S., 2022 Apr 26, arXiv.org, (arXiv.org).

Research output: Working paper/Preprint › Preprint (in preprint archive)

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

Olson, N. D., Wagner, J., McDaniel, J., Stephens, S. H., Westreich, S. T., Prasanna, A. G., Johanson, E., Boja, E., Maier, E. J., Serang, O., Jáspez, D., Lorenzo-Salazar, J. M., Muñoz-Barrera, A., Rubio-Rodríguez, L. A., Flores, C., Kyriakidis, K., Malousi, A., Shafin, K., Pesout, T., Jain, M., & 53 othersPaten, B., Chang, P-C., Kolesnikov, A., Nattestad, M., Baid, G., Goel, S., Yang, H., Carroll, A., Eveleigh, R., Bourgey, M., Bourque, G., Li, G., MA, C., Tang, L., DU, Y., Zhang, S., Morata, J., Tonda, R., Parra, G., Trotta, J-R., Brueffer, C., Demirkaya-Budak, S., Kabakci-Zorlu, D., Turgut, D., Kalay, Ö., Budak, G., Narcı, K., Arslan, E., Brown, R., Johnson, I. J., Dolgoborodov, A., Semenyuk, V., Jain, A., Tetikol, H. S., Jain, V., Ruehle, M., Lajoie, B., Roddey, C., Catreux, S., Mehio, R., Ahsan, M. U., Liu, Q., Wang, K., Sahraeian, S. M. E., Fang, L. T., Mohiyuddin, M., Hung, C., Jain, C., Feng, H., Li, Z., Chen, L., Sedlazeck, F. J. & Zook, J. M., 2022 May 11, In: Cell Genomics. 2, 5, p. 1-12 100129.

Research output: Contribution to journal › Article › peer-review

Open Access

2021

Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment

Lordan, R., Rando, H. M., COVID-19 Review Consortium, Brueffer, C. & Greene, C. S., 2021 May 4, In: mSystems. 6, 3, 22 p., e00122-21.

Research output: Contribution to journal › Review article › peer-review

Open Access

Identification and development of therapeutics for COVID-19

Rando, H. M., Wellhausen, N., Ghosh, S., Lee, A. J., Dattoli, A. A., Hu, F., Byrd, J. B., Rafizadeh, D. N., Lordan, R., Qi, Y., Sun, Y., Brueffer, C., Field, J. M., Guebila, M. B., Jadavji, N. M., Skelly, A. N., Ramsundar, B., Wang, J., Goel, R. R., Park, Y., & 4 othersBoca, S. M., Gitter, A., Greene, C. S. & COVID-19 Review Consortium, 2021 Dec, In: mSystems. 6, 6, e00233-21.

Research output: Contribution to journal › Review article › peer-review

Open Access

Identification and Development of Therapeutics for COVID-19

Brueffer, C. & COVID-19 Review Consortium, 2021 Mar 3, (arXiv.org).

Research output: Working paper/Preprint › Preprint (in preprint archive)

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through analysis of Viral Genomics and Structure

Rando, H. M., MacLean, A. L., Lee, A. J., Ray, S., Bansal, V., Skelly, A. N., Sell, E., Dziak, J. J., Shinholster, L., McGowan, L. DA., Guebila, M. B., Wellhausen, N., Knyazev, S., Boca, S. M., Capone, S., Qi, Y., Park, Y., Sun, Y., Mai, D., Brueffer, C., & 12 othersByrd, J. B., Wang, J., Lordan, R., Velazquez, R., Szeto, G. L., Barton, J. P., Goel, R. R., Mangul, S., Lubiana, T., COVID-19 Review Consortium, Gitter, A. & Greene, C. S., 2021 Feb 1, arXiv.org.

Research output: Working paper/Preprint › Preprint (in preprint archive)

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure

Rando, H. M., MacLean, A. L., Lee, A. J., Lordan, R., Ray, S., Bansal, V., Skelly, A. N., Sell, E., Dziak, J. J., Shinholster, L., D'Agostino McGowan, L., Ben Guebila, M., Wellhausen, N., Knyazev, S., Boca, S. M., Capone, S., Qi, Y., Park, Y., Mai, D., Sun, Y., & 14 othersBoerckel, J. D., Brueffer, C., Byrd, J. B., Kamil, J. P., Wang, J., Velazquez, R., Szeto, G. L., Barton, J. P., Goel, R. R., Mangul, S., Lubiana, T., Gitter, A., Greene, C. S. & COVID-19 Review Consortium, 2021 Oct 26, In: mSystems. 6, 5, 32 p., e0009521.

Research output: Contribution to journal › Review article › peer-review

Open Access

Preexisting Somatic Mutations of Estrogen Receptor Alpha (ESR1) in Early-Stage Primary Breast Cancer

Dahlgren, M., George, A., Brueffer, C., Gladchuk, S., Chen, Y., Vallon-Christersson, J., Hegardt, C., Häkkinen, J., Ryden, L., Malmberg, M., Larsson, C., Gruvberger, S., Ehinger, A., Loman, N., Borg, Å. & Saal, L., 2021 Apr 22, In: JNCI Cancer Spectrum. 5, 2, pkab028.

Research output: Contribution to journal › Article › peer-review

Open Access

RNA Sequencing for Molecular Diagnostics in Breast Cancer

Brueffer, C., 2021, Lund: Lund University, Faculty of Medicine. 110 p.

Research output: Thesis › Doctoral Thesis (compilation)

Open Access

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2020

Abstract CT074: Pre-existing ESR1 mutations in early-stage primary breast cancer predict failure of endocrine therapy and poor survival

Dahlgren, M., George, A., Brueffer, C., Gladchuk, S., Chen, Y., Vallon-Christersson, J., Hegardt, C., Häkkinen, J., Ryden, L., Malmberg, M., Larsson, C., Gruvberger, S., Ehinger, A., Loman, N., Borg, Å. & Saal, L., 2020 Aug, In: Cancer research. Supplement. 80, 16

Research output: Contribution to journal › Published meeting abstract

A crowdsourced set of curated structural variants for the human genome

Chapman, L. M., Spies, N., Pai, P., Lim, C. S., Carroll, A., Narzisi, G., Watson, C. M., Proukakis, C., Clarke, W. E., Nariai, N., Dawson, E., Jones, G., Blankenberg, D., Brueffer, C., Xiao, C., Kolora, S. R. R., Alexander, N., Wolujewicz, P., Ahmed, A. E., Smith, G., & 4 othersShehreen, S., Wenger, A. M., Salit, M. & Zook, J. M., 2020 Jun 19, In: PLoS Computational Biology. 16, 6, e1007933.

Research output: Contribution to journal › Article › peer-review

Open Access

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).

Brueffer, C., Gladchuk, S., Winter, C., Vallon-christersson, J., Hegardt, C., Häkkinen, J., George, A. M., Chen, Y., Ehinger, A., Larsson, C., Loman, N., Malmberg, M., Rydén, L., Borg, Å. & Saal, L. H., 2020 May 20, In: Journal of Clinical Oncology. 38, 15_suppl, p. 518-518

Research output: Contribution to journal › Published meeting abstract

Features of increased malignancy in eosinophilic clear cell renal cell carcinoma

Nilsson, H., Lindgren, D., Axelson, H., Brueffer, C., Saal, L., Lundgren, J. & Johansson, M., 2020 Dec, In: Journal of Pathology. 252, 4, p. 384-397 14 p.

Research output: Contribution to journal › Article › peer-review

precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions

Olson, N. D., Wagner, J., McDaniel, J., Stephens, S. H., Westreich, S. T., Prasanna, A. G., Johanson, E., Maier, E. J., Boja, E., Serang, O., Jáspez, D., Lorenzo-Salazar, J. M., Muñoz-Barrera, A., Rubio-Rodríguez, L. A., Flores, C., Kyriakidis, K., Malousi, A., Shafin, K., Pesout, T., Jain, M., & 53 othersPaten, B., Chang, P-C., Kolesnikov, A., Nattestad, M., Baid, G., Goel, S., Yang, H., Carroll, A., Eveleigh, R., Bourgey, M., Bourque, G., Li, G., MA, C., Tang, L., DU, Y., Zhang, S., Morata, J., Tonda, R., Parra, G., Trotta, J-R., Brueffer, C., Demirkaya-Budak, S., Kabakci-Zorlu, D., Turgut, D., Kalay, Ö., Budak, G., Narcı, K., Arslan, E., Brown, R., Johnson, I. J., Dolgoborodov, A., Semenyuk, V., Jain, A., Tetikol, H. S., Jain, V., Ruehle, M., Lajoie, B., Roddey, C., Catreux, S., Mehio, R., Ahsan, M. U., Liu, Q., Wang, K., Sahraeian, S. M. E., Fang, L. T., Mohiyuddin, M., Hung, C., Jain, C., Feng, H., Li, Z., Chen, L., Sedlazeck, F. J. & Zook, J. M., 2020 Nov 15, bioRxiv.

Research output: Working paper/Preprint › Preprint (in preprint archive)

The Mutational Landscape of the SCAN-B Real-World Primary Breast Cancer Transcriptome

Brueffer, C., Gladchuk, S., Winter, C., Vallon-Christersson, J., Hegardt, C., Häkkinen, J., George, A., Chen, Y., Ehinger, A., Larsson, C., Loman, N., Malmberg, M., Ryden, L., Borg, Å. & Saal, L., 2020 Jan 31, bioRxiv.

Research output: Working paper/Preprint › Preprint (in preprint archive)

The mutational landscape of the SCAN‐B real‐world primary breast cancer transcriptome

Brueffer, C., Gladchuk, S., Winter, C., Vallon-Christersson, J., Hegardt, C., Häkkinen, J., George, A., Chen, Y., Ehinger, A., Larsson, C., Loman, N., Malmberg, M., Ryden, L., Borg, Å. & Saal, L., 2020 Sep 14, In: EMBO Molecular Medicine. 12, 10, e12118.

Research output: Contribution to journal › Article › peer-review

Open Access

2019

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

Förnvik, D., Aaltonen, K., Chen, Y., George, A., Brueffer, C., Rigo, R., Loman, N., Saal, L. & Rydén, L., 2019, In: Breast Cancer Research and Treatment. 177, 2, p. 447-455

Research output: Contribution to journal › Article › peer-review

Open Access

SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome

Chapman, L. M., Spies, N., Pai, P., Lim, C. S., Carroll, A., Narzisi, G., Watson, C. M., Proukakis, C., Clarke, W. E., Nariai, N., Dawson, E., Jones, G., Blankenberg, D., Brueffer, C., Xiao, C., Kolora, S. R. R., Alexander, N., Wolujewicz, P., Ahmed, A. E., Smith, G., & 4 othersShehreen, S., Wenger, A. M., Salit, M. & Zook, J. M., 2019 Mar 26, bioRxiv, 35 p.

Research output: Working paper/Preprint › Preprint (in preprint archive)

2018

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

Loman, N., Chen, Y., Aaltonen, K., Brueffer, C., George, A., Zander, L., Vallon-Christersson, J., Häkkinen, J., Förnvik, D., Rigo, R., Ehinger, A., Malmberg, M., Larsson, C., Hegardt, C., Borg, Å., Rydén, L. & Saal, L., 2018 Feb, In: Cancer research. Supplement. 78, 4

Research output: Contribution to journal › Published meeting abstract › peer-review

Open Access

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

Brueffer, C., Vallon-Christersson, J., Grabau, D., Ehinger, A., Häkkinen, J., Hegardt, C., Malina, J., Chen, Y., Bendahl, P-O., Manjer, J., Malmberg, M., Larsson, C., Loman, N., Rydén, L., Borg, Å. & Saal, L., 2018 Feb, In: Cancer research. Supplement. 78, 4

Research output: Contribution to journal › Published meeting abstract › peer-review

Open Access

Bioconda: sustainable and comprehensive software distribution for the life sciences

Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., Bioconda Team & Brueffer, C., 2018 Jul 2, In: Nature Methods. 15, 7, p. 475-476 2 p.

Research output: Contribution to journal › Letter › peer-review

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

Brueffer, C., Vallon-Christersson, J., Grabau, D., Ehinger, A., Häkkinen, J., Hegardt, C., Malina, J., Chen, Y., Bendahl, P-O., Manjer, J., Malmberg, M., Larsson, C., Loman, N., Rydén, L., Borg, Å. & Saal, L. H., 2018 Mar 9, In: JCO Precision Oncology. 2, p. 1-18

Research output: Contribution to journal › Article › peer-review

Open Access

2017

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Grüning, B., Dale, R., Sjödin, A., Chapman, B., Rowe, J., Tomkins-Tinch, C., Valieris, R., Caprez, A., Batut, B., Haudgaard, M., Cokelaer, T., Beauchamp, K., Pedersen, B., Hoogstrate, Y., Bretaudeau, A., Ryan, D., Le Corguillé, G., Yusuf, D., Luna-Valero, S., Kirchner, R., & 138 othersBrinda, K., Wollmann, T., Raden, M., van Heeringen, S., Soranzo, N., Pantano, L., Charlop-Powers, Z., Unneberg, P., De Smet, M., Martin, M., Von Kuster, G., Antao, T., Miladi, M., Thornton, K., Brueffer, C., van der Beek, M., Maticzka, D., Blank, C., Will, S., Gravouil, K., Wolff, J., Holtgrewe, M., Fallmann, J., Piro, V., Shlyakhter, I., Yousif, A., Mabon, P., Zhang, X-O., Shen, W., Cabral, J., Thomas, C., Enns, E., Brown, J., Boekel, J., de Hollander, M., Kelleher, J., Turaga, N., de Ruiter, J., Bouvier, D., Gladman, S., Choudhary, S., Harding, N., Eggenhofer, F., Kratz, A., Fang, Z., Kleinkauf, R., Timm, H., Cock, P., Seiler, E., Brislawn, C., Nguyen, H., Bakken Stovner, E., Ewels, P., Chambers, M., Johnson, J., Hägglund, E., Ye, S., Valls Guimera, R., Pruesse, E., Dunn, A., Parsons, L., Patro, R., Koppstein, D., Grassi, E., Wohlers, I., Reynolds, A., Cornwell, M., Stoler, N., Blankenberg, D., He, G., Bargull, M., Junge, A., Farouni, R., Freeberg, M., Singh, S., Bogema, D., Cumbo, F., Wang, L-B., Larson, D., Workentine, M., Kumar Devisetty, U., Laurent, S., Roger, P., Garnier, X., Agren, R., Khan, A., Eppley, J., Li, W., Stöcker, B. K., Rausch, T., Taylor, J., Wright, P., Taranto, A., Chicco, D., Sennblad, B., Baaijens, J., Gopez, M., Abdennur, N., Milne, I., Preussner, J., Pinello, L., Srivastava, A., Chande, A., Kensche, P. R., Pirola, Y., Knudsen, M., de Bruijn, I., Blin, K., Gonnella, G., Enache, O., Rai, V., Waters, N., Hiltemann, S., Bendall, M., Stahl, C., Miles, A., Boursin, Y., Perez-Riverol, Y., Schmeier, S., Clarke, E., Arvai, K., Jung, M., Di Domenico, T., Seiler, J., Rasche, E., Kornobis, E., Beisser, D., Rahmann, S., Mikheyev, A., Tran, C., Capellades, J., Schröder, C., Salatino, A. E., Dirmeier, S., Webster, T., Moskalenko, O., Stephen, G. & Köster, J., 2017 Oct 21, bioRxiv, 13 p.

Research output: Working paper/Preprint › Preprint (in preprint archive)

Biopython Project Update 2017

Singh, S., Brueffer, C., Cock, P. & The Biopython Contributors, 2017 Jul 26.

Research output: Contribution to conference › Other

Open Access

2016

Biopython Project Update 2016

Brueffer, C., Antao, T., Cock, P., Talevich, E., de Hoon, M., Arindrarto, W., Pritchard, L., Sharma, A., Rasche, E., Rosenfeld, A., Skennerton, C., Galardini, M. & Piotrowski, M., 2016 Jul 15.

Research output: Contribution to conference › Other

Open Access