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1. Full Text Response to comments on ‘Empirical comparison of web-based antimicrobial peptide prediction tools’
by Gabere, Musa Nur and Noble, William Stafford
Bioinformatics, ISSN 1367-4803, 08/2019, Volume 35, Issue 15, pp. 2695 - 2696
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2. Full Text Response to "Mass spectrometrists should search for all peptides, but assess only the ones they care about"
by Noble, William Stafford and Keich, Uri
Nature methods, ISSN 1548-7091, 06/2017, Volume 14, Issue 7, p. 644
Usage | Peptides | Mass spectrometry | Identification and classification | Proteomics
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3. Full Text Machine learning applications in genetics and genomics
by Libbrecht, Maxwell W and Noble, William Stafford
Nature Reviews Genetics, ISSN 1471-0056, 05/2015, Volume 16, Issue 6, pp. 321 - 332
The field of machine learning, which aims to develop computer algorithms that improve with experience, holds promise to enable computers to assist humans in... 
ELEMENTS | DATABASE | FAMILIES | GENETICS & HEREDITY | FRAMEWORK | CLASSIFICATION | NETWORKS | SELECTION | EXPRESSION | FUNCTION PREDICTION | DISCOVERY | Amino Acid Sequence | Animals | Genetics, Medical | Artificial Intelligence | Base Sequence | Computer Simulation | Genomics | Humans | Molecular Sequence Annotation | Models, Genetic | Discriminant Analysis | Technology application | Human genetics | Machine learning | Innovations | Computational biology
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4. Full Text Correction to “On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra”
by Keich, Uri and Noble, William Stafford
Journal of Proteome Research, ISSN 1535-3893, 12/2016, Volume 15, Issue 12, pp. 4770 - 4778
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5. Full Text Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing
by Bittremieux, Wout and Meysman, Pieter and Noble, William Stafford and Laukens, Kris
Journal of Proteome Research, ISSN 1535-3893, 10/2018, Volume 17, Issue 10, pp. 3463 - 3474
Open modification searching (OMS) is a powerful search strategy that identifies peptides carrying any type of modification by allowing a modified spectrum to... 
mass spectrometry | approximate nearest neighbors | post-translational modifications | proteomics | open modification searching | spectral library | PEPTIDE IDENTIFICATION | SHOTGUN PROTEOMICS | QUANTIFICATION | BIOCHEMICAL RESEARCH METHODS | MS/MS SPECTRA | POSTTRANSLATIONAL MODIFICATIONS | PROTEIN MODIFICATIONS | DATABASE SEARCH | DISCOVERY | TANDEM MASS-SPECTRA | SPECTROMETRY | Computational Biology - methods | Reproducibility of Results | Peptides - chemistry | Humans | Peptide Library | Search Engine - methods | Tandem Mass Spectrometry | Algorithms | Peptides - metabolism | Time Factors | Databases, Protein | HEK293 Cells | Protein Processing, Post-Translational | Software | Proteomics - methods
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6. Full Text Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate
by Keich, Uri and Tamura, Kaipo and Noble, William Stafford
Journal of Proteome Research, ISSN 1535-3893, 02/2019, Volume 18, Issue 2, pp. 585 - 593
Decoy database search with target-decoy competition (TDC) provides an intuitive, easy-to-implement method for estimating the false discovery rate (FDR)... 
mass spectrometry | false discovery rate | spectrum identification | P-VALUES | PROTEIN IDENTIFICATIONS | PEPTIDE IDENTIFICATION | STATISTICAL SIGNIFICANCE | BIOCHEMICAL RESEARCH METHODS | SPECTRA | MS/MS | PROTEOMICS | PROBABILITIES
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7. Full Text Detecting Modifications in Proteomics Experiments with Param-Medic
by May, DH and Tamura, K and Noble, WS
JOURNAL OF PROTEOME RESEARCH, ISSN 1535-3893, 04/2019, Volume 18, Issue 4, pp. 1902 - 1906
Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details... 
tandem mass tags | proteomics | QUANTIFICATION | BIOCHEMICAL RESEARCH METHODS | database search | IDENTIFICATION | CANCER | DATABASE | mass spectrometry | ITRAQ | PROTEINS | phosphorylation | isobaric labeling | REVEALS | TOOL
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8. Full Text Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units
by Bittremieux, W and Laukens, K and Noble, WS
JOURNAL OF PROTEOME RESEARCH, ISSN 1535-3893, 10/2019, Volume 18, Issue 10, pp. 3792 - 3799
Open modification searching (OMS) is a powerful search strategy to identify peptides with any type of modification. OMS works by using a very wide precursor... 
proteomics | PEPTIDE IDENTIFICATION | PROTEOME | BIOCHEMICAL RESEARCH METHODS | approximate nearest neighbor indexing | post-translational modification | feature hashing | DATABASE | spectral library | graphics processing unit | mass spectrometry | open modification searching | SPECTROMETRY
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9. Full Text Correction: On the Importance of Well-Calibrated Scores for Identifying Shotgun Proteomics Spectra (Journal of Proteome Research (2015) 14:2 (1147-1160) DOI: 10.1021/pr5010983)
Journal of Proteome Research, ISSN 1535-3893, 12/2016, Volume 15, Issue 12, pp. 4770 - 4778
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10. Full Text Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair
by Chen, Wei and McKenna, Aaron and Schreiber, Jacob and Haeussler, Maximilian and Yin, Yi and Agarwal, Vikram and Noble, William Stafford and Shendure, Jay
Nucleic Acids Research, ISSN 0305-1048, 09/2019, Volume 47, Issue 15, pp. 7989 - 8003
Abstract Non-homologous end-joining (NHEJ) plays an important role in double-strand break (DSB) repair of DNA. Recent studies have shown that the error... 
Genome Integrity, Repair and
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11. Full Text Mass spectrometrists should only search for peptides they care about
by Noble, William Stafford
Nature methods, ISSN 1548-7091, 7/2015, Volume 12, Issue 7, pp. 605 - 608
Analysis pipelines that assign peptides to shotgun proteomics spectra often discard identified spectra deemed irrelevant to the scientific hypothesis being... 
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12. Full Text Unsupervised embedding of single-cell Hi-C data
by Liu, Jie and Lin, Dejun and Yardımcı, Galip Gürkan and Noble, William Stafford
Bioinformatics, ISSN 1367-4803, 07/2018, Volume 34, Issue 13, pp. i96 - i104
Abstract Motivation Single-cell Hi-C (scHi-C) data promises to enable scientists to interrogate the 3D architecture of DNA in the nucleus of the cell, studying... 
ORGANIZATION | CHROMOSOME | RNA-SEQ | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | TRAJECTORIES | RESOLUTION | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | DYNAMICS | REORGANIZATION | GENOME | Ismb 2018–Intelligent Systems for Molecular Biology Proceedings
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13. Full Text PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition
by Durham, Timothy J and Libbrecht, Maxwell W and Howbert, J Jeffry and Bilmes, Jeff and Noble, William Stafford
Nature communications, 04/2018, Volume 9, Issue 1, p. 1402
The Encyclopedia of DNA Elements (ENCODE) and the Roadmap Epigenomics Project seek to characterize the epigenome in diverse cell types using assays that... 
Epigenomics - statistics & numerical data | Chromatin - metabolism | Datasets as Topic | Histones - genetics | Epigenesis, Genetic | Humans | Software | Histones - metabolism | Genome, Human | Cloud Computing - statistics & numerical data | Chromatin - chemistry
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14. Full Text Response to “Mass spectrometrists should search for all peptides, but assess only the ones they care about”
by Noble, William Stafford and Keich, Uri
Nature Methods, ISSN 1548-7091, 07/2017, Volume 14, Issue 7, pp. 644 - 644
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15. Full Text MCAST: scanning forcis-regulatory motif clusters
by Grant, Charles E and Johnson, James and Bailey, Timothy L and Noble, William Stafford
Bioinformatics, ISSN 1367-4803, 04/2016, Volume 32, Issue 8, pp. 1217 - 1219
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16. Full Text Correction to “Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics”
by Keich, Uri and Kertesz-Farkas, Attila and Noble, William Stafford
Journal of Proteome Research, ISSN 1535-3893, 12/2016, Volume 15, Issue 12, pp. 4779 - 4780
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17. Full Text Mass spectrometrists should search only for peptides they care about
by Noble, William Stafford
Nature Methods, ISSN 1548-7091, 06/2015, Volume 12, Issue 7, pp. 605 - 608
Analysis pipelines that assign peptides to shotgun proteomics mass spectra often discard identified spectra deemed irrelevant to the scientific hypothesis... 
PROTEIN | IDENTIFICATIONS | BIOCHEMICAL RESEARCH METHODS | STATISTICAL-MODEL | PROBABILITIES | Plasmodium - chemistry | Proteomics - methods | Humans | Mass Spectrometry | Peptides - analysis | Scientific imaging | Peptides | Analysis | Proteomics
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18. Full Text Joint Precursor Elution Profile Inference via Regression for Peptide Detection in Data-Independent Acquisition Mass Spectra
by Hu, Alex and Lu, Yang Young and Bilmes, Jeff and Noble, William Stafford
Journal of Proteome Research, ISSN 1535-3893, 01/2019, Volume 18, Issue 1, pp. 86 - 94
In data independent acquisition (DIA) mass spectrometry, precursor scans are interleaved with wide-window fragmentation scans, resulting in complex... 
precursor inference | interference | data-dependent acquisition | regression | data-independent acquisition | DECONVOLUTION | PROTEOME | BIOCHEMICAL RESEARCH METHODS | SELECTION | SOFTWARE | TOOLS
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19. Full Text Calibration Using a Single-Point External Reference Material Harmonizes Quantitative Mass Spectrometry Proteomics Data between Platforms and Laboratories
by Pino, Lindsay K and Searle, Brian C and Huang, Eric L and Noble, William Stafford and Hoofnagle, Andrew N and MacCoss, Michael J
Analytical Chemistry, ISSN 0003-2700, 11/2018, Volume 90, Issue 21, pp. 13112 - 13117
Mass spectrometry (MS) measurements are not inherently calibrated. Researchers use various calibration methods to assign meaning to arbitrary signal... 
CHEMISTRY, ANALYTICAL | ASSAYS | PROTEIN | WATERS | QUANTIFICATION | THYROGLOBULIN
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20. Full Text Combining High-Resolution and Exact Calibration To Boost Statistical Power: A Well-Calibrated Score Function for High-Resolution MS2 Data
by Lin, Andy and Howbert, J. Jeffry and Noble, William Stafford
Journal of Proteome Research, ISSN 1535-3893, 11/2018, Volume 17, Issue 11, pp. 3644 - 3656
To achieve accurate assignment of peptide sequences to observed fragmentation spectra, a shotgun proteomics database search tool must make good use of the very... 
high-resolution MS2 | database search | statistical calibration | PEPTIDE IDENTIFICATION | STRATEGY | BIOCHEMICAL RESEARCH METHODS | SEARCH TOOL | MS/MS | ACCURACY | TANDEM MASS-SPECTRA | CONFIDENCE | SPECTROMETRY | PROTEOMICS | Humans | Escherichia coli Proteins - classification | Proteolysis | Databases, Protein | Protozoan Proteins - chemistry | Aquatic Organisms - chemistry | Proteomics - methods | Tandem Mass Spectrometry - methods | Plasmodium falciparum - chemistry | Tandem Mass Spectrometry - statistics & numerical data | Amino Acid Sequence | Datasets as Topic | Peptides - chemistry | Benchmarking | Complex Mixtures - chemistry | Peptide Mapping - methods | Peptide Mapping - statistics & numerical data | Calibration | Escherichia coli Proteins - isolation & purification | Peptides - isolation & purification | Algorithms | Protozoan Proteins - isolation & purification | Peptides - classification | Software | Escherichia coli Proteins - chemistry | Adrenal Glands - chemistry | Protozoan Proteins - classification
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