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Bioinformatics, ISSN 1367-4803, 08/2019, Volume 35, Issue 15, pp. 2695 - 2696
Journal Article
Nature methods, ISSN 1548-7091, 06/2017, Volume 14, Issue 7, p. 644
Journal Article
Nature Reviews Genetics, ISSN 1471-0056, 05/2015, Volume 16, Issue 6, pp. 321 - 332
Journal Article
Journal of Proteome Research, ISSN 1535-3893, 12/2016, Volume 15, Issue 12, pp. 4770 - 4778
Journal Article
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
Journal Article
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
Journal Article
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
Journal Article
Journal of Proteome Research, ISSN 1535-3893, 12/2016, Volume 15, Issue 12, pp. 4770 - 4778
Journal Article
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
Journal Article
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... 
Journal Article
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
Journal Article
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
Journal Article
Nature Methods, ISSN 1548-7091, 07/2017, Volume 14, Issue 7, pp. 644 - 644
Journal Article
Bioinformatics, ISSN 1367-4803, 04/2016, Volume 32, Issue 8, pp. 1217 - 1219
Journal Article
Journal of Proteome Research, ISSN 1535-3893, 12/2016, Volume 15, Issue 12, pp. 4779 - 4780
Journal Article
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
Journal Article
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
Journal Article
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
Journal Article
Journal Article
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