List of works - Kristen Naegle

ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models

scientific article published on 17 October 2019

ASPEN: Analyzing and reconstructing protein divergence using sequence subsampling

scientific article published in August 2017

Accounting for noise when clustering biological data

scientific article

An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells

scientific article

Avoiding common pitfalls when clustering biological data

scientific article

Criteria for biological reproducibility: what does "n" mean?

scientific article published on 07 April 2015

Design Considerations for a 10GHz CMOS Transmit-Receive Switch

scholarly article

Different Epidermal Growth Factor Receptor (EGFR) Agonists Produce Unique Signatures for the Recruitment of Downstream Signaling Proteins

scientific article published on 19 January 2016

Ensemble clustering of phosphoproteomic data identifies differences in protein interactions and cell-cell junction integrity of HER2-overexpressing cells

scientific article

High-Resolution Identification of Specificity Determining Positions in the LacI Protein Family Using Ensembles of Sub-Sampled Alignments.

scientific article

Injury-Induced HDAC5 Nuclear Export Is Essential for Axon Regeneration

scientific article published on 23 April 2015

Injury-induced HDAC5 nuclear export is essential for axon regeneration.

scientific article

MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets

scientific article

New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data

scientific article published on 15 June 2020

PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies

scientific article

Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants

scientific article

ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

scientific article published on 09 March 2020

ProteomeScout: a repository and analysis resource for post-translational modifications and proteins.

scientific article

Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations

scientific article

Ten simple rules for effective presentation slides

scientific article published on 02 December 2021

Using ProteomeScout: A Resource of Post-Translational Modifications, Their Experiments, and the Proteins That They Annotate

scientific article

List of works by Kristen Naegle

ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models

ASPEN: Analyzing and reconstructing protein divergence using sequence subsampling

Accounting for noise when clustering biological data

An integrated comparative phosphoproteomic and bioinformatic approach reveals a novel class of MPM-2 motifs upregulated in EGFRvIII-expressing glioblastoma cells

Avoiding common pitfalls when clustering biological data

Criteria for biological reproducibility: what does "n" mean?

Design Considerations for a 10GHz CMOS Transmit-Receive Switch

Different Epidermal Growth Factor Receptor (EGFR) Agonists Produce Unique Signatures for the Recruitment of Downstream Signaling Proteins

Ensemble clustering of phosphoproteomic data identifies differences in protein interactions and cell-cell junction integrity of HER2-overexpressing cells

High-Resolution Identification of Specificity Determining Positions in the LacI Protein Family Using Ensembles of Sub-Sampled Alignments.

Injury-Induced HDAC5 Nuclear Export Is Essential for Axon Regeneration

Injury-induced HDAC5 nuclear export is essential for axon regeneration.

MCAM: multiple clustering analysis methodology for deriving hypotheses and insights from high-throughput proteomic datasets

New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data

PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies

Phosphoproteomics of collagen receptor networks reveals SHP-2 phosphorylation downstream of wild-type DDR2 and its lung cancer mutants

ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis

ProteomeScout: a repository and analysis resource for post-translational modifications and proteins.

Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations

Ten simple rules for effective presentation slides

Using ProteomeScout: A Resource of Post-Translational Modifications, Their Experiments, and the Proteins That They Annotate