Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma
Published in Cancer Cell, 2021
Publications
PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results
Published in Molecular & Cellular Proteomics, 2020
Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer
Published in Cell, 2020
Regulation of ALT-associated homology-directed repair by polyADP-ribosylation
Published in Nature Structural & Molecular Biology, 2020
Philosopher: a versatile toolkit for shotgun proteomics data analysis
Published in Nature Methods, 2020
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma
Published in Cell, 2020
Quantitative Proteomic Landscape of Metaplastic Breast Carcinoma Pathological Subtypes and Their Relationship to Triple-Negative Tumors
Published in Nature Communications, 2020
Crystal-C: A Computational Tool for Refinement of Open Search Results
Published in Journal of Proteome Research, 2020
Deep Proteomics Using Two Dimensional Data Independent Acquisition Mass Spectrometry
Published in Analytical Chemistry, 2020
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
Published in Cell, 2019
Unveiling the Partners of the DRBD2-mRNP Complex, an RBP in Trypanosoma Cruzi and Ortholog to the Yeast SR-protein Gbp2
Published in BMC Microbiology, 2019
Recommendations for the Packaging and Containerizing of Bioinformatics Software
Published in F1000Research, 2018
The Ewing Sarcoma Secretome and Its Response to Activation of Wnt/beta-catenin Signaling
Published in Molecular & Cellular Proteomics, 2018
BioContainers: An Open-Source and Community-Driven Framework for Software Standardization
Published in Bioinformatics, 2017
A Multi-Protease, Multi-Dissociation, Bottom-Up-To-Top-Down Proteomic View of the Loxosceles Intermedia Venom
Published in Scientific Data, 2017
MSFragger: Ultrafast and Comprehensive Peptide Identification in Mass Spectrometry-Based Proteomics
Published in Nature Methods, 2017
Discovering and Linking Public ‘Omics’ Datasets using the Omics Discovery Index
Published in Nature Biotechnology, 2017
Quantitative Proteomic Analysis of the Saccharomyces Cerevisiae Industrial Strains CAT-1 and PE-2
Published in Journal of Proteomics, 2017
Ten Simple Rules for Taking Advantage of Git and GitHub
Published in PloS Computational Biology, 2016
Venomous Extract Protein Profile of Brazilian Tarantula Grammostola Iheringi: Searching for Potential Biotechnological Applications
Published in Journal of Proteomics, 2016
Integrated Analysis of Shotgun Proteomic Data With PatternLab for Proteomics 4.0
Published in Nature Protocols, 2016
Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results
Published in Current Protocols in Bioinformatics, 2015
Reevaluating the Trypanosoma Cruzi Proteomic Map: The Shotgun Description of Bloodstream Trypomastigotes
Published in Journal of Proteomics, 2015
PepExplorer: A Similarity-Driven Tool for Analyzing De Novo Sequencing Results
Published in Molecular & Cellular Proteomics, 2014
On Best Practices in the Development of Bioinformatics Software
Published in Frontiers in Genetics, 2014
Bio::DB::NextProt: A Perl Module for neXtProt Database Information Retrieval
Published in PeerJ, 2014
Proteome Analysis of Formalin-Fixed Paraffin-Embedded Tissues from a Primary Gastric Melanoma and its Meningeal Metastasis: A Case Report
Published in Current Topics in Medicinal Chemistry, 2014
Pinpointing differentially expressed domains in complex protein mixtures with the cloud service of PatternLab for Proteomics
Published in Journal of Proteomics, 2013
Effectively addressing complex proteomic search spaces with peptide spectrum matching
Published in Bioinformatics, 2013