Research output per year
Research output per year
- 49 results
Search results
-
2024
Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions
Mori, M., Zhang, Z., Banaei-Esfahani, A., Lalanne, J.-B., Okano, H., Collins, B. C., Schmidt, A., Schubert, O. T., Lee, D.-S., Li, G.-W., Aebersold, R., Hwa, T. & Ludwig, C., 01 Oct 2024, (Early online date) In: Molecular systems biology.Research output: Contribution to journal › Article › peer-review
Open AccessFile7 Downloads (Pure) -
Freeze-drying donor human milk allows compositional stability for 12 months at ambient temperatures
Cheema, S. K., Grimwade-Mann, M., Weaver, G., Collins, B., Shenker, N. & Cameron, S., Jan 2025, In: Journal of Food Composition and Analysis. 137, Part A, 9 p., 106936.Research output: Contribution to journal › Article › peer-review
Open AccessFile3 Downloads (Pure) -
Proteomic characterisation of heart failure reveals a unique molecular phenotype for hypertrophic cardiomyopathy
Tonry, C., Linden, K., Collier, P., Ledwidge, M., McDonald, K., Collins, B. C. & Watson, C. J., 01 Aug 2024, In: Biomedicines. 12, 8, 15 p., 1712.Research output: Contribution to journal › Article › peer-review
Open AccessFile20 Downloads (Pure) -
2023
A gas phase fractionation acquisition scheme integrating ion mobility for rapid diaPASEF library generation
Penny, J., Arefian, M., Schroeder, G. N., Bengoechea, J. A. & Collins, B. C., Apr 2023, In: Proteomics. 23, 7-8, 8 p., 2200038.Research output: Contribution to journal › Article › peer-review
Open AccessFile3 Citations (Scopus)97 Downloads (Pure) -
Rapid profiling of protein complex reorganization in perturbed systems
Bludau, I., Nicod, C., Martelli, C., Xue, P., Heusel, M., Fossati, A., Uliana, F., Frommelt, F., Aebersold, R. & Collins, B. C., 05 May 2023, In: Journal of Proteome Research. 22, 5, p. 1520-1536 17 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile6 Citations (Scopus)84 Downloads (Pure) -
2021
Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial
Čuklina, J., Lee, C. H., Williams, E. G., Sajic, T., Collins, B. C., Martínez, M. R., Sharma, V. S., Wendt, F., Goetze, S., Keele, G. R., Wollscheid, B., Aebersold, R. & Pedrioli, P. G. A., 25 Aug 2021, In: Molecular systems biology. 17, 8, 17 p., e10240.Research output: Contribution to journal › Article › peer-review
Open AccessFile61 Citations (Scopus)497 Downloads (Pure) -
Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance
Trauner, A., Banaei-Esfahani, A., Gygli, S. M., Warmer, P., Feldmann, J., Zampieri, M., Borrell, S., Collins, B. C., Beisel, C., Aebersold, R. & Gagneux, S., Sept 2021, In: Antimicrobial Agents and Chemotherapy. 65, 9, 18 p., e00504-21.Research output: Contribution to journal › Article › peer-review
Open AccessFile8 Citations (Scopus)75 Downloads (Pure) -
From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions
Mori, M., Zhang, Z., Banaei‐Esfahani, A., Lalanne, J., Okano, H., Collins, B. C., Schmidt, A., Schubert, O. T., Lee, D., Li, G., Aebersold, R., Hwa, T. & Ludwig, C., 01 May 2021, In: Molecular systems biology. 17, 5, e9536.Research output: Contribution to journal › Article › peer-review
Open AccessFile60 Citations (Scopus)179 Downloads (Pure) -
Multilayered regulation of autophagy by the Atg1 kinase orchestrates spatial and temporal control of autophagosome formation
Schreiber, A., Collins, B. C., Davis, C., Enchev, R. I., Sedra, A., D'Antuono, R., Aebersold, R. & Peter, M., 16 Dec 2021, In: Molecular Cell. 81, 24, p. 5066-5081.e10Research output: Contribution to journal › Article › peer-review
Open AccessFile16 Citations (Scopus)128 Downloads (Pure) -
Systematic detection of functional proteoform groups from bottom-up proteomic datasets
Bludau, I., Frank, M., Dörig, C., Cai, Y., Heusel, M., Rosenberger, G., Picotti, P., Collins, B. C., Röst, H. & Aebersold, R., 21 Jun 2021, In: Nature Communications. 12, 3810.Research output: Contribution to journal › Article › peer-review
Open AccessFile34 Citations (Scopus)89 Downloads (Pure) -
The Protein Landscape of Chronic Lymphocytic Leukemia (CLL)
Meier-Abt, F., Lu, J., Cannizzaro, E., Pohly, M. F., Kummer, S., Pfammatter, S., Kunz, L., Collins, B. C., Nadeu, F., Lee, K. S., Xue, P., Gwerder, M., Roiss, M., Hüllein, J., Scheinost, S., Dietrich, S., Campo, E., Huber, W., Aebersold, R. & Zenz, T., 29 Jun 2021, (Early online date) In: Blood.Research output: Contribution to journal › Article › peer-review
Open AccessFile23 Citations (Scopus)208 Downloads (Pure) -
2020
A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS
Heusel, M., Frank, M., Köhler, M., Amon, S., Frommelt, F., Rosenberger, G., Bludau, I., Aulakh, S., Linder, M. I., Liu, Y., Collins, B. C., Gstaiger, M., Kutay, U. & Aebersold, R., 05 Feb 2020, In: Cell systems. 10, 2, p. 133-155.e6 23 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile45 Citations (Scopus)78 Downloads (Pure) -
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes
Bludau, I., Heusel, M., Frank, M., Rosenberger, G., Hafen, R., Banaei-Esfahani, A., Drogen, A. V., Collins, B. C., Gstaiger, M. & Aebersold, R., 20 Jul 2020, (Early online date) In: Nature Protocols.Research output: Contribution to journal › Article › peer-review
Open AccessFile37 Citations (Scopus)374 Downloads (Pure) -
diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition
Meier, F., Brunner, A.-D., Frank, M., Ha, A., Bludau, I., Voytik, E., Kaspar-Schoenefeld, S., Lubeck, M., Raether, O., Bache, N., Aebersold, R., Collins, B. C., Röst, H. L. & Mann, M., 01 Dec 2020, In: Nature Methods. 17, p. 1229-1236Research output: Contribution to journal › Article › peer-review
Open AccessFile385 Citations (Scopus)1608 Downloads (Pure) -
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles
Rosenberger, G., Heusel, M., Bludau, I., Collins, B. C., Martelli, C., Williams, E. G., Xue, P., Liu, Y., Aebersold, R. & Califano, A., 16 Dec 2020, In: Cell systems. 11, 6, p. 589-607.e8Research output: Contribution to journal › Article › peer-review
Open AccessFile26 Citations (Scopus)80 Downloads (Pure) -
2019
Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins
Shao, W., Guo, T., Toussaint, N. C., Xue, P., Wagner, U., Li, L., Charmpi, K., Zhu, Y., Wu, J., Buljan, M., Sun, R., Rutishauser, D., Hermanns, T., Fankhauser, C. D., Poyet, C., Ljubicic, J., Rupp, N., Rüschoff, J. H., Zhong, Q. & Beyer, A. & 6 others, , 07 Jun 2019, In: Nature Communications. 10, 1Research output: Contribution to journal › Article › peer-review
Open AccessFile33 Citations (Scopus)217 Downloads (Pure) -
Complex‐centric proteome profiling by SEC ‐ SWATH ‐ MS
Heusel, M., Bludau, I., Rosenberger, G., Hafen, R., Frank, M., Banaei‐Esfahani, A., Drogen, A., Collins, B. C., Gstaiger, M. & Aebersold, R., 01 Jan 2019, In: Molecular systems biology.Research output: Contribution to journal › Article › peer-review
Open AccessFile94 Citations (Scopus)327 Downloads (Pure) -
Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness
Liu, Y., Chen, J., Sethi, A., Li, Q. K., Chen, L., Collins, B., Gillet, L. C. J., Wollscheid, B., Zhang, H. & Aebersold, R., 01 Jul 2019, In: Molecular and Cellular Proteomics. 13, 7, p. 1753-1768 16 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile102 Citations (Scopus)122 Downloads (Pure) -
2018
AP-SWATH Reveals Direct Involvement of VCP/p97 in Integrated Stress Response Signaling Through Facilitating CReP/PPP1R15B Degradation
Hülsmann, J., Kravic, B., Weith, M., Gstaiger, M., Aebersold, R., Collins, B. C. & Meyer, H., 01 Jul 2018, In: Molecular and Cellular Proteomics. p. 1295-1307 13 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile25 Citations (Scopus)306 Downloads (Pure) -
Data‐independent acquisition‐based SWATH-MS for quantitative proteomics: a tutorial
Ludwig, C., Gillet, L., Rosenberger, G., Amon, S., Collins, B. C. & Aebersold, R., Aug 2018, In: Molecular systems biology. 14, 23 p., e8126.Research output: Contribution to journal › Article › peer-review
Open AccessFile695 Citations (Scopus)494 Downloads (Pure) -
Proteomics goes parallel
Collins, B. C. & Aebersold, R., Nov 2018, In: Nature Biotechnology. 36, 11Research output: Contribution to journal › Article › peer-review
Open AccessFile13 Citations (Scopus)274 Downloads (Pure) -
2017
Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival
Cortes, T., Schubert, O. T., Banaei‐Esfahani, A., Collins, B., Aebersold, R. & Young, D. B., 15 Aug 2017, In: Scientific Reports. 8208.Research output: Contribution to journal › Article › peer-review
Open AccessFile31 Citations (Scopus)154 Downloads (Pure) -
Elucidation of host–pathogen protein–protein interactions to uncover mechanisms of host cell rewiring
Nicod, C., Banaei‐Esfahani, A. & Collins, B., 01 Oct 2017, In: Current Opinion in Microbiology.Research output: Contribution to journal › Article › peer-review
Open AccessFile54 Citations (Scopus)142 Downloads (Pure) -
Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS
Rosenberger, G., Liu, Y., Röst, H. L., Ludwig, C., Buil, A., Bensimon, A., Soste, M., Spector, T. D., Dermitzakis, E. T., Collins, B. C., Malmström, L. & Aebersold, R., 12 Jun 2017, In: Nature Biotechnology. 35, 8, p. nbt.3908Research output: Contribution to journal › Article › peer-review
Open AccessFile96 Citations (Scopus)410 Downloads (Pure) -
In Vivo and in Vitro Proteome Analysis of Human Immunodeficiency Virus (HIV)-1-infected, Human CD4+ T Cells
Nemeth, J., Vongrad, V., Metzner, K. J., Strouvelle, V. P., Weber, R., Pedrioli, P., Aebersold, R., Günthard, H. F. & Collins, B. C., 31 Mar 2017, In: Molecular and Cellular Proteomics. 16, 4 suppl 1, p. S108-S123Research output: Contribution to journal › Article › peer-review
Open AccessFile17 Citations (Scopus)127 Downloads (Pure) -
Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Collins, B. C., Hunter, C. L., Liu, Y., Schilling, B., Rosenberger, G., Bader, S. L., Chan, D. W., Gibson, B. W., Gingras, A.-C., Held, J. M., Hirayama-Kurogi, M., Hou, G., Krisp, C., Larsen, B., Lin, L., Liu, S., Molloy, M. P., Moritz, R. L., Ohtsuki, S. & Schlapbach, R. & 5 others, , 21 Aug 2017, In: Nature Communications. 8, 1, 291.Research output: Contribution to journal › Article › peer-review
Open AccessFile390 Citations (Scopus)258 Downloads (Pure) -
Precise Temporal Profiling of Signaling Complexes in Primary Cells Using SWATH Mass Spectrometry
Caron, E., Roncagalli, R., Hase, T., Wolski, W. E., Choi, M., Menoita, M. G., Durand, S., García-Blesa, A., Fierro-Monti, I., Sajic, T., Heusel, M., Weiss, T., Malissen, M., Schlapbach, R., Collins, B. C., Ghosh, S., Kitano, H., Aebersold, R., Malissen, B. & Gstaiger, M., 28 Mar 2017, (Early online date) In: Cell Reports. 18, 13, p. 3219-3226 8 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile29 Citations (Scopus)137 Downloads (Pure) -
Quantitative proteomics: challenges and opportunities in basic and applied research
Schubert, O. T., Röst, H. L., Collins, B. C., Rosenberger, G. & Aebersold, R., 01 Jun 2017, In: Nature Protocols. 12, 7, p. 1289-1294 6 p.Research output: Contribution to journal › Article
Open AccessFile195 Citations (Scopus)1110 Downloads (Pure) -
Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses
Rosenberger, G., Bludau, I., Schmitt, U., Heusel, M., Hunter, C. L., Liu, Y., MacCoss, M. J., MacLean, B. X., Nesvizhskii, A., Pedrioli, P. G., Reiter, L., Rost, H. L., Tate, S., Ting, Y. S., Collins, B. & Aebersold, R., 21 Aug 2017, In: Nature Methods. 14, 2017, p. 921Research output: Contribution to journal › Article › peer-review
Open AccessFile154 Citations (Scopus)437 Downloads (Pure) -
Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis
Banaei‐Esfahani, A., Nicod, C., Aebersold, R. & Collins, B., 13 Oct 2017, In: Current Opinion in Microbiology.Research output: Contribution to journal › Article › peer-review
Open AccessFile26 Citations (Scopus)157 Downloads (Pure) -
2016
Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis
Großeholz, R., Koh, C.-C., Veith, N., Fiedler, T., Strauss, M., Olivier, B., Collins, B. C., Schubert, O. T., Bergmann, F., Kreikemeyer, B., Aebersold, R. & Kummer, U., 08 Sept 2016, In: npj Systems Biology and Applications. 2Research output: Contribution to journal › Article › peer-review
Open AccessFile24 Citations (Scopus)179 Downloads (Pure) -
TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
Röst, H. L., Liu, Y., D'Agostino, G., Zanella, M., Navarro, P., Rosenberger, G., Collins, B. C., Gillet, L., Testa, G., Malmström, L. & Aebersold, R., 01 Aug 2016, In: Nature Methods. 13, 9, p. 777-783 7 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile131 Citations (Scopus)308 Downloads (Pure) -
2015
Absolute Proteome Composition and Dynamics during Dormancy and Resuscitation of Mycobacterium tuberculosis
Schubert, O. T., Ludwig, C., Kogadeeva, M., Zimmermann, M., Rosenberger, G., Gengenbacher, M., Gillet, L. C., Collins, B. C., Röst, H. L., Kaufmann, S. H. E., Sauer, U. & Aebersold, R., 08 Jul 2015, In: Cell Host & Microbe. 18, 1, p. 96-108 13 p.Research output: Contribution to journal › Article › peer-review
Open Access163 Citations (Scopus) -
Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation
Marcon, E., Jain, H., Bhattacharya, A., Guo, H., Phanse, S., Pu, S., Byram, G., Collins, B. C., Dowdell, E., Fenner, M., Guo, X., Hutchinson, A., Kennedy, J. J., Krastins, B., Larsen, B., Lin, Z.-Y., Lopez, M. F., Loppnau, P., Miersch, S. & Nguyen, T. & 24 others, , 29 Jun 2015, In: Nature Methods. 12, 8, p. 725-731 7 p.Research output: Contribution to journal › Article › peer-review
88 Citations (Scopus) -
Building high-quality assay libraries for targeted analysis of SWATH MS data
Schubert, O. T., Gillet, L. C., Collins, B. C., Navarro, P., Rosenberger, G., Wolski, W. E., Lam, H., Amodei, D., Mallick, P., MacLean, B. & Aebersold, R., 12 Feb 2015, In: Nature Protocols. 10, 3, p. 426-441 16 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile247 Citations (Scopus)841 Downloads (Pure) -
Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry
Parker, S. J., Rost, H., Rosenberger, G., Collins, B. C., Malmström, L., Amodei, D., Venkatraman, V., Raedschelders, K., Eyk, J. E. V. & Aebersold, R., 01 Oct 2015, In: Molecular and Cellular Proteomics. 14, 10, p. 2800-2813 14 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile65 Citations (Scopus)100 Downloads (Pure) -
mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry
Teo, G., Kim, S., Tsou, C.-C., Collins, B., Gingras, A.-C., Nesvizhskii, A. I. & Choi, H., 03 Nov 2015, In: Journal of proteomics. 129, p. 108-120 13 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile115 Citations (Scopus)321 Downloads (Pure) -
Quantitative variability of 342 plasma proteins in a human twin population
Liu, Y., Buil, A., Collins, B. C., Gillet, L. C., Blum, L. C., Cheng, L.-Y., Vitek, O., Mouritsen, J., Lachance, G., Spector, T. D., Dermitzakis, E. T. & Aebersold, R., 04 Feb 2015, In: Molecular systems biology. 11, 2, 19 p., 786.Research output: Contribution to journal › Article › peer-review
Open AccessFile261 Citations (Scopus)98 Downloads (Pure) -
Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps
Guo, T., Kouvonen, P., Koh, C. C., Gillet, L. C., Wolski, W. E., Röst, H. L., Rosenberger, G., Collins, B. C., Blum, L. C., Gillessen, S., Joerger, M., Jochum, W. & Aebersold, R., 02 Mar 2015, In: Nature Medicine. 21, 4, p. 407-415 9 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile304 Citations (Scopus)755 Downloads (Pure) -
2014
A repository of assays to quantify 10,000 human proteins by SWATH-MS
Rosenberger, G., Koh, C. C., Guo, T., Röst, H. L., Kouvonen, P., Collins, B. C., Heusel, M., Liu, Y., Caron, E., Vichalkovski, A., Faini, M., Schubert, O. T., Faridi, P., Ebhardt, H. A., Matondo, M., Lam, H., Bader, S. L., Campbell, D. S., Deutsch, E. W. & Moritz, R. L. & 2 others, , 16 Sept 2014, In: Scientific Data. 1, 15 p., 140031.Research output: Contribution to journal › Article › peer-review
Open AccessFile318 Citations (Scopus)100 Downloads (Pure) -
2013
Mass spectrometric protein maps for biomarker discovery and clinical research
Liu, Y., Hüttenhain, R., Collins, B. & Aebersold, R., 09 Jan 2013, In: Expert Review of Molecular Diagnostics. 13, 8, p. 811-825 15 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile104 Citations (Scopus)97 Downloads (Pure) -
Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system
Collins, B. C., Gillet, L. C., Rosenberger, G., Röst, H. L., Vichalkovski, A., Gstaiger, M. & Aebersold, R., Dec 2013, In: Nature Methods. 10, 12, p. 1246-1253 8 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile262 Citations (Scopus)479 Downloads (Pure) -
2012
Development of a Pharmaceutical Hepatotoxicity Biomarker Panel Using a Discovery to Targeted Proteomics Approach
Collins, B. C., Miller, C. A., Sposny, A., Hewitt, P., Wells, M., Gallagher, W. M. & Pennington, S. R., 01 Aug 2012, In: Molecular and Cellular Proteomics. 11, 8, p. 394-410 17 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile29 Citations (Scopus)108 Downloads (Pure) -
Focus on Cancer Proteomics 12'13
Collins, B. C. & Gallagher, W. M., 17 Jul 2012, In: Proteomics. 12, 13, p. 2065-2066 2 p.Research output: Contribution to journal › Article
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Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate
Ebhardt, H. A., Sabidó, E., Hüttenhain, R., Collins, B. & Aebersold, R., 2012, In: Proteomics. 12, 8, p. 1185-1193 9 p.Research output: Contribution to journal › Article › peer-review
36 Citations (Scopus) -
2011
Sequence Tagging Reveals Unexpected Modifications in Toxicoproteomics
Dasari, S., Chambers, M. C., Codreanu, S. G., Liebler, D. C., Collins, B. C., Pennington, S. R., Gallagher, W. M. & Tabb, D. L., 07 Jan 2011, In: Chemical research in toxicology. 24, 2, p. 204-216 13 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile25 Citations (Scopus)166 Downloads (Pure) -
Serum Proteomic Profiling Reveals That Pretreatment Complement Protein Levels are Predictive of Esophageal Cancer Patient Response to Neoadjuvant Chemoradiation
Maher, S. G., McDowell, D. T., Collins, B. C., Muldoon, C. M., Gallagher, W. M. & Reynolds, J. V., 2011, In: Annals of Surgery. 254, 5, p. 809-817 9 p.Research output: Contribution to journal › Article › peer-review
45 Citations (Scopus) -
2010
Use of SELDI MS to discover and identify potential biomarkers of toxicity in InnoMed PredTox: A multi-site, multi-compound study
Collins, B. C., Sposny, A., McCarthy, D., Brandenburg, A., Woodbury, R., Pennington, S. R., Gautier, J.-C., Hewitt, P. & Gallagher, W. M., 15 Apr 2010, In: Proteomics. 10, 8, p. 1592-1608 17 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile13 Citations (Scopus)237 Downloads (Pure) -
2007
Use of proteomics for the discovery of early markers of drug toxicity
Collins, B. C., Clarke, A., Kitteringham, N. R., Gallagher, W. M. & Pennington, S. R., 19 Oct 2007, In: Expert Opinion on Drug Metabolism and Toxicology. 3, 5, p. 689-704 16 p.Research output: Contribution to journal › Article › peer-review
20 Citations (Scopus)