Research graph
References from Proteotranscriptomics – A facilitator in omics research. Local targets link to admitted publications; unresolved targets remain external evidence.
10.12688/f1000research.12850.2
10.12688/f1000research.12850.2 · External reference
10.1038/260500a0
10.1038/260500a0 · External reference
10.1126/science.274.5287.546
10.1126/science.274.5287.546 · External reference
Genome sequence of the nematode C. elegans: a platform for investigating biology
10.1126/science.282.5396.2012 · 1998 · External reference
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
2000 · External reference
10.1073/pnas.1720115115
10.1073/pnas.1720115115 · External reference
The Earth BioGenome Project 2020: Starting the clock
10.1073/pnas.2115635118 · 2022 · External reference
Next-generation genome annotation: We still struggle to get it right
10.1186/s13059-019-1715-2 · 2019 · External reference
10.1073/pnas.2109019118
10.1073/pnas.2109019118 · External reference
Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies
10.1371/journal.pone.0021400 · 2011 · External reference
10.1038/s41586-021-03451-0
10.1038/s41586-021-03451-0 · External reference
GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
10.1186/s12864-020-6568-2 · 2020 · External reference
10.1093/bioinformatics/btv351
10.1093/bioinformatics/btv351 · External reference
Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank
10.1186/s13059-020-02023-1 · 2020 · External reference
10.1093/nar/gkaa1100
10.1093/nar/gkaa1100 · External reference
10.1038/nrg2484
10.1038/nrg2484 · External reference
Overview of Next Generation Sequencing Technologies
10.1002/cpmb.59 · 2018 · External reference
De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers
10.1093/gigascience/giz039 · 2019 · External reference
De novo assembly and analysis of RNA-seq data
10.1038/nmeth.1517 · 2010 · External reference
10.1038/nbt.1883
10.1038/nbt.1883 · External reference
10.1038/nprot.2013.084
10.1038/nprot.2013.084 · External reference
10.1093/bioinformatics/bts094
10.1093/bioinformatics/bts094 · External reference
10.1093/bioinformatics/btt219
10.1093/bioinformatics/btt219 · External reference
10.1093/bioinformatics/btu077
10.1093/bioinformatics/btu077 · External reference
An Information-Optimal de Novo RNA-Seq Assembler
2016 · External reference
Bridger: A new framework for de novo transcriptome assembly using RNA-seq data
10.1186/s13059-015-0596-2 · 2015 · External reference
BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data
10.1371/journal.pcbi.1004772 · 2016 · External reference
10.1089/cmb.2012.0021
10.1089/cmb.2012.0021 · External reference
10.1371/journal.pone.0086039
10.1371/journal.pone.0086039 · External reference
10.1101/gr.113779.110
10.1101/gr.113779.110 · External reference
De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis
10.1186/1471-2164-12-581 · 2011 · External reference
10.1371/journal.pone.0225073
10.1371/journal.pone.0225073 · External reference
10.1111/j.1755-0998.2012.03148.x
10.1111/j.1755-0998.2012.03148.x · External reference
Genomics and the origin of species
10.1038/nrg3644 · 2014 · External reference
10.1371/journal.pone.0185020
10.1371/journal.pone.0185020 · External reference
10.1111/1755-0998.13156
10.1111/1755-0998.13156 · External reference
Methodologies for Transcript Profiling Using Long-Read Technologies
10.3389/fgene.2020.00606 · 2020 · External reference
10.1371/journal.pcbi.1009730
10.1371/journal.pcbi.1009730 · External reference
rnaQUAST: a quality assessment tool for de novo transcriptome assemblies
10.1093/bioinformatics/btw218 · 2016 · External reference
10.1101/gr.196469.115
10.1101/gr.196469.115 · External reference
Evaluation of de novo transcriptome assemblies from RNA-Seq data
2014 · External reference
10.1093/molbev/msx319
10.1093/molbev/msx319 · External reference
Most non-canonical proteins uniquely populate the proteome or immunopeptidome
10.1016/j.celrep.2021.108815 · 2021 · External reference
10.1016/j.celrep.2019.11.026
10.1016/j.celrep.2019.11.026 · External reference
10.1371/journal.pcbi.1008287
10.1371/journal.pcbi.1008287 · External reference
10.1093/nar/gks1193
10.1093/nar/gks1193 · External reference
Collaboration on behalf of the INSD. The Sequence Read Archive
10.1093/nar/gkq1019 · 2011 · External reference
10.1093/nar/gky1106
10.1093/nar/gky1106 · External reference
Nextflow enables reproducible computational workflows
10.1038/nbt.3820 · 2017 · External reference
10.1093/bioinformatics/bts480
10.1093/bioinformatics/bts480 · External reference
Bpipe: a tool for running and managing bioinformatics pipelines
10.1093/bioinformatics/bts167 · 2012 · External reference
Unresolved reference
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Unresolved reference
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Unresolved reference
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Rcorrector: efficient and accurate error correction for Illumina {RNA}-seq reads
10.1186/s13742-015-0089-y · 2015 · External reference
QuorUM: An Error Corrector for Illumina Reads
10.1371/journal.pone.0130821 · 2015 · External reference
10.14806/ej.17.1.200
10.14806/ej.17.1.200 · External reference
10.1093/bioinformatics/bts635
10.1093/bioinformatics/bts635 · External reference
10.1038/nmeth.1923
10.1038/nmeth.1923 · External reference
10.1093/bioinformatics/btp324
10.1093/bioinformatics/btp324 · External reference
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
10.1038/s41587-019-0201-4 · 2019 · External reference
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
2013 · External reference
FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences
10.1093/nar/gkg610 · 2003 · External reference
10.1093/nar/29.12.2607
10.1093/nar/29.12.2607 · External reference
10.1038/nbt.1511
10.1038/nbt.1511 · External reference
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics
10.1038/nmeth.4256 · 2017 · External reference
MS-GF+ makes progress towards a universal database search tool for proteomics
2014 · External reference
10.1016/j.celrep.2016.12.063
10.1016/j.celrep.2016.12.063 · External reference
10.1093/nar/gkn176
10.1093/nar/gkn176 · External reference
annot8r: GO, EC and KEGG annotation of EST datasets
10.1186/1471-2105-9-180 · 2008 · External reference
10.1093/bioinformatics/btv106
10.1093/bioinformatics/btv106 · External reference
10.1186/1471-2105-10-421
10.1186/1471-2105-10-421 · External reference
Fast and sensitive protein alignment using DIAMOND
2014 · External reference
Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line
2020 · External reference
High-quality genome assembly of the silkworm
10.1016/j.ibmb.2019.02.002 · 2019 · External reference
Assembling the Community-Scale Discoverable Human Proteome
2018 · External reference
10.1021/pr101060v
10.1021/pr101060v · External reference
10.1093/bib/bbz163
10.1093/bib/bbz163 · External reference
10.1074/mcp.tir119.001906
10.1074/mcp.tir119.001906 · External reference
10.1021/acs.jproteome.2c00023
10.1021/acs.jproteome.2c00023 · External reference
10.15252/msb.20178126
10.15252/msb.20178126 · External reference
Data-Independent Acquisition Mass Spectrometry-Based Proteomics and Software Tools: A Glimpse in 2020
10.1002/pmic.201900276 · 2020 · External reference
BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes
10.1038/s41592-018-0003-5 · 2018 · External reference
The separation sciences, the front end to proteomics: An historical perspective
10.1002/bmc.4995 · 2021 · External reference
10.15252/msb.20188503
10.15252/msb.20188503 · External reference
A time-resolved proteotranscriptomics atlas of the human placenta reveals pan-cancer immunomodulators
2020 · External reference
ProteomeGenerator: A Framework for Comprehensive Proteomics Based on de Novo Transcriptome Assembly and High-Accuracy Peptide Mass Spectral Matching
10.1021/acs.jproteome.8b00295 · 2018 · External reference
10.1371/journal.pone.0194518
10.1371/journal.pone.0194518 · External reference
Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation
10.1074/mcp.m114.047126 · 2016 · External reference
10.1016/j.yjmcc.2020.10.005
10.1016/j.yjmcc.2020.10.005 · External reference
10.1101/gr.201368.115
10.1101/gr.201368.115 · External reference
A Bioinformatics Approach for Integrated Transcriptomic and Proteomic Comparative Analyses of Model and Non-sequenced Anopheline Vectors of Human Malaria Parasites
10.1074/mcp.m112.019596 · 2013 · External reference
10.1038/nmeth.2227
10.1038/nmeth.2227 · External reference
Integration of deep transcriptome and proteome analyses reveals the components of alkaloid metabolism in opium poppy cell cultures
10.1186/1471-2229-10-252 · 2010 · External reference
Integrated Metabolome and Transcriptome Analysis Uncovers the Role of Anthocyanin Metabolism in Michelia maudiae. Int
2019 · External reference
