Open-content preprint peer review

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Preprint Authors Area Date Reviews
BOLD5000: A public fMRI dataset of 5000 images N. Chang ... E. M. Aminoff Sep 2018 R1
Combining citizen science and deep learning to amplify expertise in neuroimaging A. Keshavan ... A. Rokem Jul 2018 R1
Rice Galaxy: an open resource for plant science V. M. J. Juanillas ... R. P. Mauleon Jun 2018 R1, R2, R3
Aequatus: An open-source homology browser A. S. Thanki ... R. P. Davey Jun 2018 R1, R2
Thought experiment: Decoding cognitive processes from the fMRI data of one individual M. Wegrzyn ... K. Labudda Jun 2018 R1
NAT/NCS2-hound: A webserver for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. A. Chaliotis ... G. Amoutzias May 2018 R1, R2
Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes L. K. Johnson ... C. T. Brown May 2018 R1, R2, R3
Genome analyses show strong selection on coloration, morphological and behavioral phenotypes in birds-of-paradise S. Prost ... M. Irestedt May 2018 R1, R2, R3
LAESI mass spectrometry imaging as a tool to differentiate the root metabolome of native and range-expanding plant species P. Kulkarni ... P. Garbeva May 2018 R1
Monitoring changes in the Gene Ontology and their impact on genomic data analysis M. Jacobson ... P. Pavlidis May 2018 R1, R2
Modeling brain dynamics in brain tumor patients using The Virtual Brain H. Aerts ... D. Marinazzo May 2018 R1
FMRIPrep: a robust preprocessing pipeline for functional MRI O. Esteban ... K. J. Gorgolewski Apr 2018 R1, R2
Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences C. Leimeister ... B. Morgenstern Apr 2018 R1, R2, R3, R4
Reproducible genomics analysis pipelines with GNU Guix R. Wurmus ... A. Akalin Apr 2018 R1, R2, R3
Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers J. A. Borghi, A. E. V. Gulick, Neuroscience Feb 2018 R1
Predicting functional networks from region connectivity profiles in task-based versus resting-state fMRI data J. R. Daparte ... D. Marinazzo Feb 2018 R1
Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of Arabidopsis originome J. Sequeira-Mendes ... C. Gutierrez Feb 2018 R1
Effect of head volume conduction on directed connectivity estimated between reconstructed EEG sources A. Anzolin ... D. Marinazzo Jan 2018 R1, R2
Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors T. Lukes ... G. M. Hagen Bioinformatics Jan 2018 R1
A nonparametric estimator of population structure unifying admixture models and principal components analysis I. Cabreros, J. D. Storey, Dec 2017 R1
A CRISPR screening approach for identifying novel autophagy-related factors and cytoplasm-to-lysosome trafficking routes C. J. Shoemaker ... V. Denic Dec 2017 R1
A short, robust brain activation control task optimised for pharmacological fMRI studies J. Harvey ... M. B. Wall Dec 2017 R1
Estimating heritability without environmental bias A. I. Young ... A. Kong Genetics Nov 2017 R1
Using experimental data as a voucher for study pre-registration M. Mazor ... R. Mukamel Pharmacology And Toxicology Nov 2017 R1
Data science for urban equity: Making gentrification an accessible topic for data scientists, policymakers, and the community B. Herman ... A. Tan Oct 2017 R1
Privacy and anonymity in public sharing of high-dimensional datasets: legal and ethical restrictions J. J. E. V. M. R. K. a. M. Lorist Sep 2017 R1
Porcupine: a visual pipeline tool for neuroimaging analysis T. v. Mourik ... D. Norris Neuroscience Sep 2017 R1
Artificial Intelligence and Data Science in the Automotive Industry. M. Hofmann, T. B. . F. Neukart, Ck Csai Sep 2017 R1
AFQ-Browser: Supporting reproducible human neuroscience research through browser-based visualization tools J. D. Yeatman ... A. Rokem Neuroscience Aug 2017 R1, R2
Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning H. Teng ... L. Coin Aug 2017 R1, R2
Data-driven Advice for Applying Machine Learning to Bioinformatics Problems. R. S. Olson, Z. M. . W. L. C. . A. V. . J. H. Moore Qbioqm Aug 2017 R1
Structural and functional MRI from a cross-sectional Southwest University Adult lifespan Dataset (SALD) D. W. K. Z. Q. C. W. Y. W. L. K. W. J. S. a. J. Qiu Aug 2017 R1
The ANTs Longitudinal Cortical Thickness Pipeline N. J. Tustison ... M. A. Yassa Neuroscience Jul 2017 R1
Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola K. Grigorev ... T. K. Oleksyk Jul 2017 R1, R2
The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum A. V. Zimin ... S. L. Salzberg Jul 2017 R1, R2, R3, R4
Draft genome of the Reindeer (Rangifer tarandus) Z. Li ... G. Li Jun 2017 R1, R2
Unexpected Early Proteomic Changes in Alzheimer's Disease Model Mice Synaptosomes K. Ball ... M. Stowell Neuroscience Jun 2017 R1, R2
Beyond Consensus: Embracing Heterogeneity in Neuroimaging Meta-Analysis G. H. Ngo ... B. T. T. Yeo Neuroscience Jun 2017 R1
A new multi-genomic approach for the study of biogeochemical cycles at global scale: the molecular reconstruction of the sulfur cycle V. D. Anda ... V. Souza Bioinformatics Jun 2017 R1, R2, R3
PhenoSpD: an atlas of phenotypic correlations and a multiple testing correction for the human phenome J. Zheng ... T. Gaunt Jun 2017 R1, R2, R3
Indexcov: fast coverage quality control for whole-genome sequencing B. S. Pedersen ... A. R. Quinlan Genomics Jun 2017 R1
Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics and epigenetics data Q. H. Nguyen ... B. P. Dalrymple Genomics Jun 2017 R1, R2
Advances in studying brain morphology: The benefits of open-access data C. R. Madan Jun 2017 R1
Re-evaluation of SNP heritability in complex human traits D. Speed ... D. Balding Genetics May 2017 R1, R2
A standalone software platform for the interactive management and pre-processing of ATAC-seq samples Z. Ahmed, D. Ucar, Apr 2017 R1
The GridCAT: A toolbox for automated analysis of human grid cell codes in fMRI M. Stangl, J. Shine, T. Wolbers Neuroscience Feb 2017 R1
FAST Adaptive Smoothing and Thresholding for Improved Activation Detection in Low-Signal fMRI I. Almodóvar-Rivera, R. Maitra Feb 2017 R1
Documenting and Evaluating Data Science Contributions in Academic Promotion in Departments of Statistics and Biostatistics L. A. Waller, Jan 2017 R1
A unified encyclopedia of human functional DNA elements through fully automated annotation of 164 human cell types M. W. Libbrecht ... W. S. Noble Genomics Dec 2016 R1
Discovering event structure in continuous narrative perception and memory C. Baldassano ... K. A. Norman Neuroscience Oct 2016 R1
BIDS Apps: Improving ease of use, accessibility and reproducibility of neuroimaging data analysis methods K. J. Gorgolewski ... R. Poldrack Neuroinformatics Oct 2016 R1
Neural Encoding and Decoding with Deep Learning for Dynamic Natural Vision H. Wen ... Z. Liu Aug 2016 R1
The Future of Data Analysis in the Neurosciences D. Bzdok, B. T. Yeo Neuroscience Aug 2016 R1
GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome B. Simovski ... G. K. Sandve Genomics Aug 2016 R1, R2, R3, R4
sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors W. Chen ... L. Coin Bioinformatics Jul 2016 R1, R2
The queenslandensis and the type form of the dengue fever mosquito (Aedes aegypti L.) are genomically indistinguishable G. Rašić ... A. A. Hoffmann Genomics Jul 2016 R1, R2, R3
Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing M. D. Cao ... L. Coin Bioinformatics May 2016 R1, R2, R3
Teaching Data Science. R. J. Brunner, E. J. Kim Statot Apr 2016 R1
Bidirectional transcription marks accessible chromatin and is not specific to enhancers R. S. Young ... M. S. Taylor Genomics Apr 2016 R1
A Case for Data Commons: Towards Data Science as a Service. R. L. Grossman, M. M. . A. H. . M. P. . W. Wells Cscy Apr 2016 R1
An explicit-solvent conformation search method using open software K. Gaalswyk, C. Rowley Biophysics Apr 2016 R1
Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing M. D. Cao ... L. Coin Bioinformatics Apr 2016 R1
Clusterflock: A Flocking Algorithm for Isolating Congruent Phylogenomic Datasets A. Narechania ... P. J. Planet Bioinformatics Mar 2016 R1, R2, R3, R4
NanoSim: nanopore sequence read simulator based on statistical characterization C. Yang ... I. Birol Mar 2016 R1, R2, R3
Whole-genome characterization in pedigreed non-human primates using Genotyping-By-Sequencing and imputation. B. N. Bimber ... A. Vinson Genomics Mar 2016 R1
Rational design and whole-genome predictions of single guide RNAs for efficient CRISPR/Cas9-mediated genome editing in Ciona S. Gandhi, L. Christiaen, A. Stolfi Developmental Biology Feb 2016 R1, R2, R3
Kronos: a workflow assembler for genome analytics and informatics M. J. Taghiyar ... S. Shah Bioinformatics Feb 2016 R1
Contents of Consciousness Investigated as Integrated Information in Direct Human Brain Recordings A. M. Haun ... N. Tsuchiya Neuroscience Feb 2016 R1
sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors W. Chen ... L. Coin Bioinformatics Feb 2016 R1, R2
INC-Seq: Accurate single molecule reads using nanopore sequencing C. Li ... N. Nagarajan Genomics Jan 2016 R1, R2
Methylation Analysis Reveals Fundamental Differences Between Ethnicity and Genetic Ancestry J. M. Galanter ... N. Zaitlen Genetics Jan 2016 R1
Disease variants alter transcription factor levels and methylation of their binding sites M. J. Bonder ... B. T. Heijmans Genomics Dec 2015 R1
AGOUTI: improving genome assembly and annotation using transcriptome data S. V. Zhang ... M. W. Hahn Bioinformatics Nov 2015 R1, R2, R3
Generic decoding of seen and imagined objects using hierarchical visual features T. Horikawa, Y. Kamitani, Oct 2015 R1
A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data J. Risse ... M. Watson Genomics Aug 2015 R1, R2, R3
Determination of Nonlinear Genetic Architecture using Compressed Sensing C. M. Ho, S. D. H. Hsu, Jul 2015 R1, R2
Tools and techniques for computational reproducibility S. R. Piccolo ... M. B. Frampton Bioinformatics Jul 2015 R1, R2
The seasonal reproduction number of dengue fever: impacts of climate on transmission S. Polwiang, Jul 2015 R1, R2
Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing M. D. Cao ... L. Coin Bioinformatics May 2015 R1, R2, R3
Improving the Power of Structural Variation Detection by Augmenting the Reference J. Schroeder ... P. Medvedev Bioinformatics May 2015 R1
LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads R. L. Warren ... I. Birol Bioinformatics Mar 2015 R1
Swabs to genomes: a comprehensive workflow M. I. Dunitz ... D. A. Coil Jan 2015 R1, R2
RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing V. Gupta ... A. Loraine Jan 2015 R1
Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols P. A. Combs, M. B. Eisen, Jan 2015 R1, R2
NxRepair: Error correction in de novo sequence assembly using Nextera mate pairs R. R. Murphy ... O. B. Schulz-Trieglaff Bioinformatics Dec 2014 R1, R2, R3
An assessment of fracture resistance of three composite resin core build-up materials on three prefabricated non-metallic posts, cemented in endodontically treated teeth: An in vitro study L. Kumar ... P. Pujari Dec 2014 R1
Reducing workplace burnout: The relative benefits of cardiovascular and resistance exercise R. J. Bretland, E. B. Thorsteinsson, Dec 2014 R1
Subject-specific body segment parameter estimation using 3D photogrammetry with multiple cameras K. E. Peyer ... W. I. Sellers Nov 2014 R1
Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: Analysis with multiple merger coalescent models E. Árnason, K. Halldórsdóttir, Oct 2014 R1
A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer A. Quinlan ... N. Loman Genomics Sep 2014 R1, R2, R3
Endothelial cell-initiated extravasation of cancer cells visualized in zebrafish Sep 2014 R1, R2
Efficient Bayesian mixed model analysis increases association power in large cohorts P. Loh ... A. L. Price Genetics Aug 2014 R1
Application of compressed sensing to genome wide association studies and genomic selection S. Vattikuti ... C. C. Chow May 2014 R1
Temporal variability predicts the magnitude of between-group attentional blink differences in developmental dyslexia: a meta-analysis N. A. Badcock, J. C. Kidd, Mar 2014 R1
A data repository and analysis framework for spontaneous neural activity recordings in developing retina S. Eglen ... E. Sernagor Nov 2013 R1, R2
Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication C. Nossa ... N. H. Putnam Sep 2013 R1, R2
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species K. R. Bradnam ... I. F. Korf Jun 2013 R1, R2
Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM H. Li, Bioinformatics May 2013 R1