- Home
- Publications
- Publication Search
- Publication Details
Title
Systematic benchmarking of omics computational tools
Authors
Keywords
-
Journal
Nature Communications
Volume 10, Issue 1, Pages -
Publisher
Springer Nature
Online
2019-03-28
DOI
10.1038/s41467-019-09406-4
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Repeat-aware evaluation of scaffolding tools
- (2018) Igor Mandric et al. BIOINFORMATICS
- Involving undergraduates in genomics research to narrow the education–research gap
- (2018) Serghei Mangul et al. NATURE BIOTECHNOLOGY
- Bias, robustness and scalability in single-cell differential expression analysis
- (2018) Charlotte Soneson et al. NATURE METHODS
- An empirical analysis of journal policy effectiveness for computational reproducibility
- (2018) Victoria Stodden et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- “Available upon request”: not good enough for microbiome data!
- (2018) Morgan G. I. Langille et al. Microbiome
- High-quality science requires high-quality open data infrastructure
- (2018) Susanna-Assunta Sansone et al. Scientific Data
- Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants
- (2017) Alexander Artyomenko et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
- (2017) Alexander Sczyrba et al. NATURE METHODS
- Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades
- (2016) Jonathan D. Wren BIOINFORMATICS
- 1,500 scientists lift the lid on reproducibility
- (2016) Monya Baker NATURE
- Standardized benchmarking in the quest for orthologs
- (2016) Adrian M Altenhoff et al. NATURE METHODS
- Simulation-based comprehensive benchmarking of RNA-seq aligners
- (2016) Giacomo Baruzzo et al. NATURE METHODS
- A comparison of tools for the simulation of genomic next-generation sequencing data
- (2016) Merly Escalona et al. NATURE REVIEWS GENETICS
- Computational genomics tools for dissecting tumour–immune cell interactions
- (2016) Hubert Hackl et al. NATURE REVIEWS GENETICS
- Crowdsourcing biomedical research: leveraging communities as innovation engines
- (2016) Julio Saez-Rodriguez et al. NATURE REVIEWS GENETICS
- An evaluation of the accuracy and speed of metagenome analysis tools
- (2016) Stinus Lindgreen et al. Scientific Reports
- Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
- (2015) Adam D Ewing et al. NATURE METHODS
- Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks: Fig. 1.
- (2015) Ge Tan et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Ten Simple Rules for a Community Computational Challenge
- (2015) Iddo Friedberg et al. PLoS Computational Biology
- Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
- (2015) Alexander Kanitz et al. GENOME BIOLOGY
- Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
- (2014) Justin M Zook et al. NATURE BIOTECHNOLOGY
- A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
- (2014) NATURE BIOTECHNOLOGY
- A community effort to assess and improve drug sensitivity prediction algorithms
- (2014) James C Costello et al. NATURE BIOTECHNOLOGY
- Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations
- (2014) Francesca Di Giallonardo et al. NUCLEIC ACIDS RESEARCH
- A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data
- (2014) Zong Hong Zhang et al. PLoS One
- Simple chained guide trees give high-quality protein multiple sequence alignments
- (2014) K. Boyce et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A comprehensive evaluation of assembly scaffolding tools
- (2014) Martin Hunt et al. GENOME BIOLOGY
- Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt
- (2014) Rachael P Huntley et al. GigaScience
- A Turing test for artificial expression data
- (2013) Robert Maier et al. BIOINFORMATICS
- Information-theoretic evaluation of predicted ontological annotations
- (2013) Wyatt T. Clark et al. BIOINFORMATICS
- Benchmarking short sequence mapping tools
- (2013) Ayat Hatem et al. BMC BIOINFORMATICS
- A survey of tools for variant analysis of next-generation genome sequencing data
- (2013) S. Pabinger et al. BRIEFINGS IN BIOINFORMATICS
- Seeking the Wisdom of Crowds Through Challenge-Based Competitions in Biomedical Research
- (2013) J C Costello et al. CLINICAL PHARMACOLOGY & THERAPEUTICS
- Critical assessment of automated flow cytometry data analysis techniques
- (2013) Nima Aghaeepour et al. NATURE METHODS
- Sequence assembly demystified
- (2013) Niranjan Nagarajan et al. NATURE REVIEWS GENETICS
- CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction
- (2013) Tomasz Puton et al. NUCLEIC ACIDS RESEARCH
- CAFA and the Open World of protein function predictions
- (2013) Christophe Dessimoz et al. TRENDS IN GENETICS
- Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
- (2013) Keith R Bradnam et al. GigaScience
- The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
- (2012) T. Derrien et al. GENOME RESEARCH
- A framework for human microbiome research
- (2012) NATURE
- Wisdom of crowds for robust gene network inference
- (2012) Daniel Marbach et al. NATURE METHODS
- A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae
- (2012) Intawat Nookaew et al. NUCLEIC ACIDS RESEARCH
- Estimation of alternative splicing isoform frequencies from RNA-Seq data
- (2011) Marius Nicolae et al. Algorithms for Molecular Biology
- Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling
- (2011) Paweł P. Łabaj et al. BIOINFORMATICS
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
- (2011) Bo Li et al. BMC BIOINFORMATICS
- Verification of systems biology research in the age of collaborative competition
- (2011) Pablo Meyer et al. NATURE BIOTECHNOLOGY
- A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives
- (2011) Julie D. Thompson et al. PLoS One
- Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
- (2010) M. R. Aniba et al. NUCLEIC ACIDS RESEARCH
- The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction
- (2009) Curtis Huttenhower et al. BIOINFORMATICS
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now