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Injury-Induced HDAC5 Nuclear Export Is Essential for Axon Regeneration

Cell, 2013-11, Vol.155 (4), p.894-908

2013

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Ten simple rules for effective presentation slides

PLoS computational biology, 2021-12, Vol.17 (12), p.e1009554-e1009554

Naegle, Kristen M

2021

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Avoiding common pitfalls when clustering biological data

Science signaling, 2016-06, Vol.9 (432), p.re6

2016

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KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions

PLoS computational biology, 2021-02, Vol.17 (2), p.e1008681-e1008681

2021

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KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data

Nature communications, 2022-07, Vol.13 (1), p.4283-4283, Article 4283

2022

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

PloS one, 2016-09, Vol.11 (9), p.e0162579-e0162579

2016

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

PLoS computational biology, 2020-03, Vol.16 (3), p.e1007741-e1007741

2020

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

eLife, 2019-10, Vol.8

2019

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

Biochemical journal, 2013-09, Vol.454 (3), p.501-513

2013

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Injury-Induced HDAC5 Nuclear Export Is Essential for Axon Regeneration

Cell, 2015-04, Vol.161 (3), p.691-691

2015

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

The Journal of biological chemistry, 2016-03, Vol.291 (11), p.5528-5540

2016

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

PloS one, 2015-12, Vol.10 (12), p.e0144692-e0144692

2015

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

The Journal of biological chemistry, 2020-08, Vol.295 (32), p.11346-11363

2020

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

PLoS computational biology, 2011-07, Vol.7 (7), p.e1002119-e1002119

2011

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Proteome-Level Analysis Indicates Global Mechanisms for Post-Translational Regulation of RRM Domains

Journal of molecular biology, 2018-01, Vol.430 (1), p.41-44

2018

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Defining phenotypic and functional heterogeneity of glioblastoma stem cells by mass cytometry

JCI insight, 2021-02, Vol.6 (4)

2021

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Logic-based mechanistic machine learning on high-content images reveals how drugs differentially regulate cardiac fibroblasts

Proceedings of the National Academy of Sciences - PNAS, 2024-01, Vol.121 (5), p.e2303513121

2024

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Predicting Patient Response to the Antiarrhythmic Mexiletine Based on Genetic Variation: Personalized Medicine for Long QT Syndrome

Circulation research, 2019-02, Vol.124 (4), p.539-552

2019

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

Nucleic acids research, 2015-01, Vol.43 (Database issue), p.D521-D530

2015

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A path to translation: How 3D patient tumor avatars enable next generation precision oncology

Cancer cell, 2022-12, Vol.40 (12), p.1448-1453

2022

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Using deep learning to decipher the impact of telomerase promoter mutations on the dynamic metastatic morpholome

PLoS computational biology, 2024-07, Vol.20 (7), p.e1012271

2024

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

Molecular bioSystems, 2009-01, Vol.5 (1), p.59-67

2009

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Accounting for noise when clustering biological data

Briefings in bioinformatics, 2013-07, Vol.14 (4), p.423-436

2013

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

Current Protocols in Bioinformatics, 2017-09, Vol.59 (1), p.13.32.1-13.32.27

2017

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PTMScout, a Web Resource for Analysis of High Throughput Post-translational Proteomics Studies

Molecular & cellular proteomics, 2010-11, Vol.9 (11), p.2558-2570

2010

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Injury-Induced HDAC5 Nuclear Export Is Essential for Axon Regeneration

Ten simple rules for effective presentation slides

Avoiding common pitfalls when clustering biological data

KinPred: A unified and sustainable approach for harnessing proteome-level human kinase-substrate predictions

KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data

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

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

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

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

Injury-Induced HDAC5 Nuclear Export Is Essential for Axon Regeneration

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

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

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

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

Proteome-Level Analysis Indicates Global Mechanisms for Post-Translational Regulation of RRM Domains

Defining phenotypic and functional heterogeneity of glioblastoma stem cells by mass cytometry

Logic-based mechanistic machine learning on high-content images reveals how drugs differentially regulate cardiac fibroblasts

Predicting Patient Response to the Antiarrhythmic Mexiletine Based on Genetic Variation: Personalized Medicine for Long QT Syndrome

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

A path to translation: How 3D patient tumor avatars enable next generation precision oncology

Using deep learning to decipher the impact of telomerase promoter mutations on the dynamic metastatic morpholome

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

Accounting for noise when clustering biological data

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

PTMScout, a Web Resource for Analysis of High Throughput Post-translational Proteomics Studies

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