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List of works by David Fenyo

A Complex Systems Approach to Causal Discovery in Psychiatry

scientific article

A First Step towards a Clinical Decision Support System for Post-traumatic Stress Disorders

scientific article published on January 2016

A Gene Selection Method Based on Outliers for Breast Cancer Subtype Classification

scientific article published on 03 December 2021

A Method for Quantifying Molecular Interactions Using Stochastic Modelling and Super-Resolution Microscopy.

scientific article published in November 2017

A Strategy for Rapid, High-Confidence Protein Identification ⬇️

scientific article published on October 1, 1997

A Systems Biology Approach Identifies FUT8 as a Driver of Melanoma Metastasis

scientific article published in June 2017

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.

scientific article

A model of random mass-matching and its use for automated significance testing in mass spectrometric proteome analysis

scientific article published in March 2002

A proteomics approach to the study of absorption, distribution, metabolism, excretion, and toxicity.

scientific article

A robust pipeline for rapid production of versatile nanobody repertoires

scientific article

A software tool for the analysis of mass spectrometric disulfide mapping experiments

scientific article published on 01 December 1997

Adaptive Multiview Nonnegative Matrix Factorization Algorithm for Integration of Multimodal Biomedical Data.

scientific article

Adenosine A2A receptor null chondrocyte transcriptome resembles that of human osteoarthritic chondrocytes

scientific article published on 11 May 2021

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer.

scientific article

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis

scientific article published on August 2005

Atypical and classical memory B cells produce Plasmodium falciparum neutralizing antibodies.

scientific article published on 14 January 2013

BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells

scientific article published on 10 February 2020

Baseline Serum Autoantibody Signatures Predict Recurrence and Toxicity in Melanoma Patients Receiving Adjuvant Immune Checkpoint Blockade

scientific article published in 2022

Breast Cancer Prognostics Using Multi-Omics Data

scientific article

Breast tumors educate the proteome of stromal tissue in an individualized but coordinated manner.

scientific article

Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication

scientific article published on 10 February 2020

Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium.

scientific article

Clinical Decision Support Tool and Rapid Point-of-Care Platform for Determining Disease Severity in Patients with COVID-19

scientific article published on 22 April 2020

Comparative proteomic analysis of the ATP-sensitive K+ channel complex in different tissue types

scientific article published on 03 January 2013

Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function

scientific article published on 30 October 2019

Computer experiments on molecular ejection from an amorphous solid: Comparison to an analytic continuum mechanical model.

scientific article

Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts.

scientific article published on 25 April 2017

Crystallization of Proliferating Cell Nuclear Antigen (PCNA) from Saccharomyces cerevisiae

scientific article published on 01 August 1994

Cyclin F-Mediated Degradation of SLBP Limits H2A.X Accumulation and Apoptosis upon Genotoxic Stress in G2

scientific article published on 24 September 2016

Detection and correction of interference in SRM analysis

scientific article published on 23 May 2013

Detection of artifacts and peptide modifications in liquid chromatography/mass spectrometry data using two-dimensional signal intensity map data visualization.

scientific article

Determinants for Escherichia coli RNA polymerase assembly within the beta subunit.

scientific article published in August 1997

Determining the overall merit of protein identification data sets: rho-diagrams and rho-scores

scientific article

Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics

scientific article published on 22 March 2021

Dissection of affinity captured LINE-1 macromolecular complexes.

scientific article published on 8 January 2018

Distinct Features of Human Myeloid Cell Cytokine Response Profiles Identify Neutrophil Activation by Cytokines as a Prognostic Feature during Tuberculosis and Cancer

scientific article published on 29 April 2020

Efficient identification of phosphorylation by mass spectrometric phosphopeptide fingerprinting

scientific article published on 6 March 2008

Endothelium-Independent Primitive Myxoid Vascularization Creates Invertebrate-Like Channels to Maintain Blood Supply in Optic Gliomas.

scientific article

Erratum: Nanoscale visualization of functional adhesion/excitability nodes at the intercalated disc

scientific article published on 22 February 2016

Evaluation of the variation in sample preparation for comparative proteomics using stable isotope labeling by amino acids in cell culture

scientific article published on March 2009

Extracting Pathway-level Signatures from Proteogenomic Data in Breast Cancer Using Independent Component Analysis

scientific article published on 18 June 2019

Finding protein sequences using PROWL.

scientific article published in October 2004

Fluorescence ImmunoPrecipitation (FLIP): a Novel Assay for High-Throughput IP.

scientific article published on 15 August 2016

Formation of fullerenes in MeV-ion sputtering from organic solids

article

Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei

scientific article published on 15 April 2009

GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome.

scientific article published on 9 March 2010

GenomeVIP: a cloud platform for genomic variant discovery and interpretation.

scientific article

High-Capacity Ion Trap Coupled to a Time-of-Flight Mass Spectrometer for Comprehensive Linked Scans with no Scanning Losses

scientific article

Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells

scientific article published on 10 February 2020

Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer

scientific article published on 17 January 2017

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

scientific article published on 28 June 2016

Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines.

scientific article

Integration and Analysis of CPTAC Proteomics Data in the Context of Cancer Genomics in the cBioPortal

scientific article published on 15 July 2019

Integrative omics analyses broaden treatment targets in human cancer

scientific article published on 27 July 2018

Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.

scientific article

Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels

scientific article

L1EM: a tool for accurate locus specific LINE-1 RNA quantification

scientific article published on 01 February 2020

LINE-1 protein localization and functional dynamics during the cell cycle.

scientific article published on 8 January 2018

Large Scale Identification of Variant Proteins in Glioma Stem Cells.

scientific article published on 18 December 2017

Location, structure, and function of the target of a transcriptional activator protein.

scientific article

Low escape-rate genome safeguards with minimal molecular perturbation of Saccharomyces cerevisiae

scientific article

MALDI sample preparation: the ultra thin layer method

scientific article

Macrophage-derived netrin-1 promotes abdominal aortic aneurysm formation by activating MMP3 in vascular smooth muscle cells

scientific article published in Nature Communications

Mass spectrometric protein identification using the global proteome machine.

scientific article

Methods, Tools and Current Perspectives in Proteogenomics

scientific article published on 29 April 2017

Modeling experimental design for proteomics.

scientific article published on January 2010

Modeling mass spectrometry-based protein analysis

scientific article published on January 2011

Molecular-dynamics study of electronic sputtering of large organic molecules.

scientific article

Monitoring genome-wide replication fork directionality by Okazaki fragment sequencing in mammalian cells

scientific article published on 13 January 2021

Much ado about zero

scientific article published on 22 October 2015

Neuropeptidomics strategies for specific and sensitive identification of endogenous peptides

scientific article published on 30 March 2007

Next Generation Sequencing Data and Proteogenomics.

scientific article

OpenSlice: Quantitative data sharing from HyperPeaks to global ion chromatograms (GICs).

scientific article

Optimizing selection of large animals for antibody production by screening immune response to standard vaccines

scientific article published on 9 January 2016

Organization and dynamics of the nonhomologous end-joining machinery during DNA double-strand break repair

scientific article published on 4 May 2015

PGx: Putting Peptides to BED

scientific article published on 7 December 2015

Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study

scientific article published on 8 December 2014

Phosphotyrosine signaling networks in epidermal growth factor receptor overexpressing squamous carcinoma cells

scientific article

Physical and biological characterization of a growth-inhibitory activity purified from the neuroepithelioma cell line A673

scientific article published on January 1995

Probity: a protein identification algorithm with accurate assignment of the statistical significance of the results

scientific article published in January 2004

Protein Identification in Complex Mixtures

scientific article published on 01 March 2005

Protein identification using mass spectrometric information.

scientific article

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

scientific article published on 28 March 2017

Proteogenomics from a bioinformatics angle: A growing field.

scientific article published on 15 December 2015

Quantitative Mass Spectrometry to Interrogate Proteomic Heterogeneity in Metastatic Lung Adenocarcinoma and Validate a Novel Somatic Mutation CDK12-G879V

scientific article published on 07 January 2019

Rapid sensitive analysis of cysteine rich peptide venom components.

scientific article

Rapid, optimized interactomic screening

scientific article published on 4 May 2015

Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability

scientific article published on 13 June 2019

Reproducibility of LC-MS-based protein identification

scientific article published on 21 March 2006

Selenocysteine: Wherefore Art Thou?

scientific article published on 18 December 2015

Separable roles for Mycobacterium tuberculosis ESX-3 effectors in iron acquisition and virulence.

scientific article

Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding

scientific article

Single Molecule Localization Microscopy of DNA Damage Response Pathways in Cancer

scientific article published on 25 July 2016

Spatiotemporal dynamics of homologous recombination repair at single collapsed replication forks

scientific article published in Nature Communications

Sputtering by fast ions based on a sum of impulses.

scientific article

Strategy for identifying dendritic cell-processed CD4+ T cell epitopes from the HIV gag p24 protein.

scientific article

Structural and Functional Characterization of A Nav1.5-Mitochondrial Couplon

scientific article published on 21 December 2020

Structural and functional properties of region II-plus of the malaria circumsporozoite protein

scientific article published on July 1994

Super-resolution fluorescence microscopy of the cardiac connexome reveals plakophilin-2 inside the connexin43 plaque

scientific article

Super-resolution imaging reveals that loss of the C-terminus of connexin43 limits microtubule plus-end capture and NaV1.5 localization at the intercalated disc.

scientific article

Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond.

scientific article

The GPMDB REST interface

scientific article

The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes

scientific article published on 09 December 2019

The Statistical Significance of Protein Identification Results as a Function of the Number of Protein Sequences Searched

scientific article published on 01 September 2004

The ULK1-FBXW5-SEC23B nexus controls autophagy

scientific article published on 31 December 2018

Transcription shapes DNA replication initiation and termination in human cells

scientific article published on 31 December 2018

Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome

scientific article published on 08 March 2019

Trends and developments in bioinformatics in 2010: prospects and perspectives.

scientific article published on January 2011

Use of DNA ladders for reproducible protein fractionation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) for quantitative proteomics

scientific article published on 12 January 2008

Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome.

scientific article

Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays

scientific article published on January 2016

Validation of endogenous peptide identifications using a database of tandem mass spectra

scientific article published on 13 June 2008

g2pDB: A Database Mapping Protein Post-Translational Modifications to Genomic Coordinates.

scientific article

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