Combination of Proteogenomics with PeptideDe NovoSequencing Identifies New Genes and Hidden Posttranscriptional Modifications

FairBase: a comprehensive database of fungal A-to-I RNA editing

(2019) Jinding Liu et al.   Database-The Journal of Biological Databases and Curation

STRIPAK, a highly conserved signaling complex, controls multiple eukaryotic cellular and developmental processes and is linked with human diseases

(2019) Ulrich Kück et al.   BIOLOGICAL CHEMISTRY

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

(2018) Yafeng Zhu et al.   Nature Communications

Correction to: Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity

(2018) Paula Moolhuijzen et al.   BMC GENOMICS

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome

(2018) Roman Mylonas et al.   MOLECULAR & CELLULAR PROTEOMICS

Adenosine to inosine mRNA editing in fungi and how it may relate to fungal pathogenesis

(2018) Ines Teichert   PLoS Pathogens

The transcription factor PRO44 and the histone chaperone ASF1 regulate distinct aspects of multicellular development in the filamentous fungus Sordaria macrospora

(2018) David Immanuel Schumacher et al.   BMC GENETICS

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets

(2018) Zhe Ren et al.   MOLECULAR & CELLULAR PROTEOMICS

In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins

(2018) Vaishnavi Ravikumar et al.   Scientific Reports

RNA Editing During Sexual Development Occurs in Distantly Related Filamentous Ascomycetes

(2017) Ines Teichert et al.   Genome Biology and Evolution

Combining De Novo Peptide Sequencing Algorithms, A Synergistic Approach to Boost Both Identifications and Confidence in Bottom-up Proteomics

(2017) Bernhard Blank-Landeshammer et al.   JOURNAL OF PROTEOME RESEARCH

Annotation of the Domestic Pig Genome by Quantitative Proteogenomics

(2017) Harald Marx et al.   JOURNAL OF PROTEOME RESEARCH

Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity

(2017) Xiaojing Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

(2017) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

A-to-I RNA editing is developmentally regulated and generally adaptive for sexual reproduction inNeurospora crassa

(2017) Huiquan Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteogenomic Re-Annotation of Coccidioides posadasii Strain Silveira

(2017) Natalie M. Mitchell et al.   PROTEOMICS

Alternative Splicing May Not Be the Key to Proteome Complexity

(2017) Michael L. Tress et al.   TRENDS IN BIOCHEMICAL SCIENCES

Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients

(2016) Jason B. Noon et al.   BMC EVOLUTIONARY BIOLOGY

The composition and function of the striatin-interacting phosphatases and kinases (STRIPAK) complex in fungi

(2016) Ulrich Kück et al.   FUNGAL GENETICS AND BIOLOGY

Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

(2016) T.S. Keshava Prasad et al.   GENOME RESEARCH

Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes

(2016) Huiquan Liu et al.   GENOME RESEARCH

Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics

(2016) Alison McAfee et al.   JOURNAL OF PROTEOME RESEARCH

Transcription factor PRO1 targets genes encoding conserved components of fungal developmental signaling pathways

(2016) Eva Katharina Steffens et al.   MOLECULAR MICROBIOLOGY

Proteogenomics ofCandida tropicalis—An Opportunistic Pathogen with Importance for Global Health

(2016) Keshava K. Datta et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Novor: Real-Time Peptide de Novo Sequencing Software

(2015) Bin Ma   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data

(2015) Xiaojing Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis

(2015) Hajk-Georg Drost et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution: Dynamics of De Novo Gene Emergence

(2014) Rafik Neme et al.   CURRENT BIOLOGY

Mannosylglycerate: structural analysis of biosynthesis and evolutionary history

(2014) Nuno Borges et al.   EXTREMOPHILES

New Insights Into the Roles of NADPH Oxidases in Sexual Development and Ascospore Germination in Sordaria macrospora

(2014) D. E. Dirschnabel et al.   GENETICS

Non-model organisms, a species endangered by proteogenomics

(2014) Jean Armengaud et al.   Journal of Proteomics

PepExplorer: A Similarity-driven Tool for Analyzingde NovoSequencing Results

(2014) Felipe V. Leprevost et al.   MOLECULAR & CELLULAR PROTEOMICS

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

(2014) B. A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Fungal Alternative Splicing is Associated with Multicellular Complexity and Virulence: A Genome-Wide Multi-Species Study

(2013) K. Grutzmann et al.   DNA RESEARCH

An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes inZea mays

(2013) Natalie E. Castellana et al.   MOLECULAR & CELLULAR PROTEOMICS

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

(2013) Stefanie Traeger et al.   PLoS Genetics

Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development

(2012) Ines Teichert et al.   BMC GENOMICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra

(2012) Hao Chi et al.   JOURNAL OF PROTEOME RESEARCH

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Whole-Genome Sequencing of Sordaria macrospora Mutants Identifies Developmental Genes

(2012) Minou Nowrousian et al.   G3-Genes Genomes Genetics

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

PEAKS DB:De NovoSequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

(2011) Jing Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Quality control of nano-LC-MS systems using stable isotope-coded peptides

(2011) Julia Maria Burkhart et al.   PROTEOMICS

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

(2011) Marc Vaudel et al.   PROTEOMICS

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

De novo Assembly of a 40 Mb Eukaryotic Genome from Short Sequence Reads: Sordaria macrospora, a Model Organism for Fungal Morphogenesis

(2010) Minou Nowrousian et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS