Sequence-to-sequence translation from mass spectra to peptides with a transformer model
Yilmaz, Melih, Fondrie, William E, Bittremieux, Wout, Melendez, Carlo F, Nelson, Rowan, Ananth, Varun, Oh, Sewoong, Noble, William Stafford
Published in Nature communications (30.07.2024)
Published in Nature communications (30.07.2024)
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Journal Article
Identification of the ESKAPE pathogens by mass spectrometric analysis of microbial membrane glycolipids
Leung, Lisa M, Fondrie, William E, Doi, Yohei, Johnson, J Kristie, Strickland, Dudley K, Ernst, Robert K, Goodlett, David R
Published in Scientific reports (25.07.2017)
Published in Scientific reports (25.07.2017)
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Journal Article
Redefining the Breast Cancer Exosome Proteome by Tandem Mass Tag Quantitative Proteomics and Multivariate Cluster Analysis
Clark, David J, Fondrie, William E, Liao, Zhongping, Hanson, Phyllis I, Fulton, Amy, Mao, Li, Yang, Austin J
Published in Analytical chemistry (Washington) (20.10.2015)
Published in Analytical chemistry (Washington) (20.10.2015)
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LRP1 (Low-Density Lipoprotein Receptor–Related Protein 1) Regulates Smooth Muscle Contractility by Modulating Ca2+ Signaling and Expression of Cytoskeleton-Related Proteins
Au, Dianaly T, Ying, Zhekang, Hernández-Ochoa, Erick O, Fondrie, William E, Hampton, Brian, Migliorini, Mary, Galisteo, Rebeca, Schneider, Martin F, Daugherty, Alan, Rateri, Debra L, Strickland, Dudley K, Muratoglu, Selen C
Published in Arteriosclerosis, thrombosis, and vascular biology (01.11.2018)
Published in Arteriosclerosis, thrombosis, and vascular biology (01.11.2018)
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Assessment of the Therapeutic Potential of Persimmon Leaf Extract on Prediabetic Subjects
Khan, Mohd M, Tran, Bao Quoc, Jang, Yoon-Jin, Park, Soo-Hyun, Fondrie, William E, Chowdhury, Khadiza, Yoon, Sung Hwan, Goodlett, David R, Chae, Soo-Wan, Chae, Han-Jung, Seo, Seung-Young, Goo, Young Ah
Published in Molecules and cells (01.07.2017)
Published in Molecules and cells (01.07.2017)
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Journal Article
Evaluating Proteomics Imputation Methods with Improved Criteria
Harris, Lincoln, Fondrie, William E., Oh, Sewoong, Noble, William S.
Published in Journal of proteome research (03.11.2023)
Published in Journal of proteome research (03.11.2023)
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Journal Article
Semisupervised Machine Learning for Sensitive Open Modification Spectral Library Searching
Arab, Issar, Fondrie, William E., Laukens, Kris, Bittremieux, Wout
Published in Journal of proteome research (03.02.2023)
Published in Journal of proteome research (03.02.2023)
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Journal Article
ppx: Programmatic Access to Proteomics Data Repositories
Fondrie, William E, Bittremieux, Wout, Noble, William S
Published in Journal of proteome research (03.09.2021)
Published in Journal of proteome research (03.09.2021)
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Journal Article
Target‐decoy false discovery rate estimation using Crema
Lin, Andy, See, Donavan, Fondrie, William E., Keich, Uri, Noble, William Stafford
Published in Proteomics (Weinheim) (01.04.2024)
Published in Proteomics (Weinheim) (01.04.2024)
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Journal Article
Accounting for Digestion Enzyme Bias in Casanovo
Melendez, Carlo, Sanders, Justin, Yilmaz, Melih, Bittremieux, Wout, Fondrie, William E, Oh, Sewoong, Noble, William Stafford
Published in Journal of proteome research (30.08.2024)
Published in Journal of proteome research (30.08.2024)
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Journal Article
nf-encyclopedia: A Cloud-Ready Pipeline for Chromatogram Library Data-Independent Acquisition Proteomics Workflows
Allen, Carolyn, Meinl, Rico, Paez, J. Sebastian, Searle, Brian C., Just, Seth, Pino, Lindsay K., Fondrie, William E.
Published in Journal of proteome research (04.08.2023)
Published in Journal of proteome research (04.08.2023)
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Journal Article
Rapid Microbial Identification and Antibiotic Resistance Detection by Mass Spectrometric Analysis of Membrane Lipids
Liang, Tao, Leung, Lisa M, Opene, Belita, Fondrie, William E, Lee, Young In, Chandler, Courtney E, Yoon, Sung Hwan, Doi, Yohei, Ernst, Robert K, Goodlett, David R
Published in Analytical chemistry (Washington) (15.01.2019)
Published in Analytical chemistry (Washington) (15.01.2019)
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Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments
Mudge, Miranda C., Nunn, Brook L., Firth, Erin, Ewert, Marcela, Hales, Kianna, Fondrie, William E., Noble, William S., Toner, Jonathan, Light, Bonnie, Junge, Karen A.
Published in Environmental microbiology (01.07.2021)
Published in Environmental microbiology (01.07.2021)
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Journal Article
Building Spectral Libraries from Narrow-Window Data-Independent Acquisition Mass Spectrometry Data
Heil, Lilian R., Fondrie, William E., McGann, Christopher D., Federation, Alexander J., Noble, William S., MacCoss, Michael J., Keich, Uri
Published in Journal of proteome research (03.06.2022)
Published in Journal of proteome research (03.06.2022)
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Journal Article
The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data
Kertesz-Farkas, Attila, Nii Adoquaye Acquaye, Frank Lawrence, Bhimani, Kishankumar, Eng, Jimmy K., Fondrie, William E., Grant, Charles, Hoopmann, Michael R., Lin, Andy, Lu, Yang Y., Moritz, Robert L., MacCoss, Michael J., Noble, William Stafford
Published in Journal of proteome research (03.02.2023)
Published in Journal of proteome research (03.02.2023)
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Journal Article
Assessment of the Therapeutic Potential of Persimmon Leaf Extract on Prediabetic Subjects
Khan, Mohd M, Tran, Bao Quoc, Jang, Yoon-Jin, Park, Soo-Hyun, Fondrie, William E, Chowdhury, Khadiza, Yoon, Sung Hwan, Goodlett, David R, Chae, Soo-Wan, Chae, Han-Jung, Seo, Seung-Young, Goo, Young Ah
Published in Molecules and cells (2017)
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Published in Molecules and cells (2017)
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