Preprints published

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Paper Authors Journal Date
HLA-C variants associated with amino acid substitutions in the peptide binding groove influence susceptibility to Kawasaki disease C. Shimizu ... H. Shike Human immunology May 2019
An efficient and robust laboratory workflow and tetrapod database for larger scale eDNA studies J. Axtner ... A. Wilting GigaScience Feb 2019
SciPipe - A workflow library for agile development of complex and dynamic bioinformatics pipelines S. Lampa ... O. Spjuth GigaScience Oct 2018
Genome-Wide Analyses Identify KIF5A as a Novel ALS Gene A. Nicolas ... J. E. Landers Neuron Aug 2018
New de novo assembly of the Atlantic bottlenose dolphin (Tursiops truncatus) improves genome completeness and provides haplotype phasing. K. A. Martinez-Viaud ... A. Zimin GigaScience Aug 2018
SMRT long-read sequencing and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica) G. Formenti ... N. Saino GigaScience Jul 2018
Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat L. Gardiner ... A. Hall GigaScience Jul 2018
Aequatus: An open-source homology browser A. S. Thanki ... R. P. Davey GigaScience Jun 2018
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 GigaScience May 2018
Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes L. K. Johnson ... C. T. Brown GigaScience May 2018
Genome analyses show strong selection on coloration, morphological and behavioral phenotypes in birds-of-paradise S. Prost ... M. Irestedt GigaScience May 2018
Monitoring changes in the Gene Ontology and their impact on genomic data analysis M. Jacobson ... P. Pavlidis GigaScience May 2018
Octapeptin C4 Induces Less Resistance and Novel Mutations in an Epidemic Carbapenemase-producing Klebsiella pneumoniae ST258 Clinical Isolate Compared to Polymyxins M. Pitt ... M. Cooper Journal of Antimicrobial Chemotherapy Apr 2018
FMRIPrep: a robust preprocessing pipeline for functional MRI O. Esteban ... K. J. Gorgolewski Nature methods Apr 2018
Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences C. Leimeister ... B. Morgenstern GigaScience Apr 2018
Reproducible genomics analysis pipelines with GNU Guix R. Wurmus ... A. Akalin GigaScience Apr 2018
Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data F. Alakwaa ... L. Garmire GigaScience Mar 2018
Clustering trees: a visualisation for evaluating clusterings at multiple resolutions L. Zappia, A. Oshlack, GigaScience Mar 2018
Non-antibiotic antimicrobial triclosan induces multiple antibiotic resistance through genetic mutation J. Lu ... J. Guo Environment international Feb 2018
A complete nanonpore-only assembly of an XDR Mycobacterium tuberculosis Beijing lineage strain identifies novel genetic variation in repetitive PE/PPE gene regions A. Bainomugisa ... L. Coin Microbial Genomics Feb 2018
Genomes of trombidid mites reveal novel predicted allergens and laterally-transferred genes associated with secondary metabolism X. Dong ... B. L. Makepeace GigaScience Feb 2018
Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors T. Lukes ... G. M. Hagen GigaScience Jan 2018
GtTR: Bayesian estimation of absolute tandem repeat copy number using sequence capture and high throughput sequencing D. Ganesamoorthy ... L. J. M. Coin BMC bioinformatics Jan 2018
AMBER: Assessment of Metagenome BinnERs F. Meyer ... A. C. McHardy GigaScience Dec 2017
YAMP: a framework enabling reproducibility in metagenomics research A. Visconti ... M. Falchi GigaScience Nov 2017
Clinker: visualising fusion genes detected in RNA-seq data B. M. Schmidt ... A. Oshlack GigaScience Nov 2017
Efficient and accurate detection of splice junctions from RNAseq with Portcullis D. Mapleson ... D. Swarbreck GigaScience Nov 2017
FAST-SG: An alignment-free algorithm for hybrid assembly A. D. Genova ... A. Maass GigaScience Oct 2017
Necklace: combining reference and assembled transcriptomes for RNA-Seq analysis N. M. Davidson, A. Oshlack, GigaScience Oct 2017
Real-time DNA barcoding in a remote rainforest using nanopore sequencing A. Pomerantz ... S. Prost GigaScience Sep 2017
Interactive Visual Analysis of Mass Cytometry Data by Hierarchical Stochastic Neighbor Embedding Reveals Rare Cell Types V. v. Unen ... B. P. F. Lelieveldt Nature communications Sep 2017
Parallel sequencing lives, or what makes large sequencing projects successful J. Quilez ... G. Filion GigaScience Aug 2017
npInv: accurate detection and genotyping of inversions mediated by non-allelic homologous recombination using long read sub-alignment H. Shao ... L. Coin BMC bioinformatics Aug 2017
Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning H. Teng ... L. Coin GigaScience Aug 2017
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 GigaScience Jul 2017
Abelson tyrosine-protein kinase 2 Regulates Myoblast Proliferation and Controls Muscle Fiber Length S. J. Burden, J. K. Lee, eLife Jul 2017
The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum A. V. Zimin ... S. L. Salzberg GigaScience Jul 2017
Draft genome of the Reindeer (Rangifer tarandus) Z. Li ... G. Li GigaScience Jun 2017
Combining semi-automated image analysis techniques with machine learning algorithms to accelerate large scale genetic studies J. A. Atkinson ... D. M. Wells GigaScience Jun 2017
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 GigaScience Jun 2017
PhenoSpD: an atlas of phenotypic correlations and a multiple testing correction for the human phenome J. Zheng ... T. Gaunt GigaScience Jun 2017
Indexcov: fast coverage quality control for whole-genome sequencing B. S. Pedersen ... A. R. Quinlan GigaScience Jun 2017
Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics and epigenetics data Q. H. Nguyen ... B. P. Dalrymple GigaScience Jun 2017
Re-evaluation of SNP heritability in complex human traits D. Speed ... D. Balding Nature genetics May 2017
Multifactorial Chromosomal Variants Regulate Polymyxin Resistance In Extensively Drug-Resistant Klebsiella pneumoniae M. Pitt ... L. J. M. Coin Microbial Genomics May 2017
Simulating The Dynamics Of Targeted Capture Sequencing With CapSim M. D. Cao, D. Ganesamoorthy, L. Coin Bioinformatics May 2017
Nanopore Long-Read RNAseq Reveals Widespread Transcriptional Variation Among the Surface Receptors of Individual B cells A. Byrne ... C. Vollmers Nature communications Apr 2017
Bio-Docklets: Virtualization Containers for Single-Step Execution of NGS Pipelines. B. Kim ... K. Krampis GigaScience Mar 2017
16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model R. Luo ... S. Salzberg GigaScience Mar 2017
A recurrence based approach for validating structural variation using long-read sequencing technology. X. Zhao ... R. E. Mills GigaScience Feb 2017
Reverse-engineering human olfactory perception from chemical features of odor molecules A. Keller ... P. Meyer Science Feb 2017
A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation P. R. Sternes ... A. R. Borneman GigaScience Jan 2017
fastBMA: Scalable Network Inference and Transitive Reduction L. Hung ... K. Y. Yeung GigaScience Jan 2017
High precision registration between zebrafish brain atlases using symmetric diffeomorphic normalization G. D. Marquart ... H. A. Burgess GigaScience Oct 2016
DNA damage is a major cause of sequencing errors, directly confounding variant identification. L. Chen ... L. M. Ettwiller Science Aug 2016
GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome B. Simovski ... G. K. Sandve GigaScience Aug 2016
sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors W. Chen ... L. Coin Nucleic acids research Jul 2016
The queenslandensis and the type form of the dengue fever mosquito (Aedes aegypti L.) are genomically indistinguishable G. Rašić ... A. A. Hoffmann PLoS neglected tropical diseases Jul 2016
iCAVE: an open source tool for immersive 3D visualization of complex biomolecular interaction networks V. Liluashvili ... Z. H. Gümüş GigaScience Jun 2016
Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing M. D. Cao ... L. Coin Nature communications May 2016
An explicit-solvent conformation search method using open software K. Gaalswyk, C. Rowley PeerJ Apr 2016
Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing M. D. Cao ... L. Coin GigaScience Apr 2016
Clusterflock: A Flocking Algorithm for Isolating Congruent Phylogenomic Datasets A. Narechania ... P. J. Planet GigaScience Mar 2016
NanoSim: nanopore sequence read simulator based on statistical characterization C. Yang ... I. Birol GigaScience Mar 2016
Kronos: a workflow assembler for genome analytics and informatics M. J. Taghiyar ... S. Shah GigaScience Feb 2016
sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors W. Chen ... L. Coin Nucleic acids research Feb 2016
Real time selective sequencing using nanopore technology. M. Loose, S. Malla, M. Stout Nature methods Feb 2016
INC-Seq: Accurate single molecule reads using nanopore sequencing C. Li ... N. Nagarajan GigaScience Jan 2016
AGOUTI: improving genome assembly and annotation using transcriptome data S. V. Zhang ... M. W. Hahn GigaScience Nov 2015
A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data J. Risse ... M. Watson GigaScience Aug 2015
Determination of Nonlinear Genetic Architecture using Compressed Sensing C. M. Ho, S. D. H. Hsu, GigaScience Jul 2015
Tools and techniques for computational reproducibility S. R. Piccolo ... M. B. Frampton GigaScience Jul 2015
The seasonal reproduction number of dengue fever: impacts of climate on transmission S. Polwiang, PeerJ Jul 2015
Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing M. D. Cao ... L. Coin GigaScience May 2015
LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads R. L. Warren ... I. Birol GigaScience Mar 2015
Swabs to genomes: a comprehensive workflow M. I. Dunitz ... D. A. Coil PeerJ Jan 2015
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 GigaScience Jan 2015
Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols P. A. Combs, M. B. Eisen, PeerJ Jan 2015
NxRepair: Error correction in de novo sequence assembly using Nextera mate pairs R. R. Murphy ... O. B. Schulz-Trieglaff PeerJ Dec 2014
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 PeerJ Dec 2014
Reducing workplace burnout: The relative benefits of cardiovascular and resistance exercise R. J. Bretland, E. B. Thorsteinsson, PeerJ Dec 2014
Subject-specific body segment parameter estimation using 3D photogrammetry with multiple cameras K. E. Peyer ... W. I. Sellers PeerJ Nov 2014
Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: Analysis with multiple merger coalescent models E. Árnason, K. Halldórsdóttir, PeerJ Oct 2014
A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer A. Quinlan ... N. Loman GigaScience Sep 2014
Endothelial cell-initiated extravasation of cancer cells visualized in zebrafish PeerJ Sep 2014
Application of compressed sensing to genome wide association studies and genomic selection S. Vattikuti ... C. C. Chow GigaScience May 2014
Temporal variability predicts the magnitude of between-group attentional blink differences in developmental dyslexia: a meta-analysis N. A. Badcock, J. C. Kidd, PeerJ Mar 2014
A data repository and analysis framework for spontaneous neural activity recordings in developing retina S. Eglen ... E. Sernagor GigaScience Nov 2013
Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication C. Nossa ... N. H. Putnam GigaScience Sep 2013
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species K. R. Bradnam ... I. F. Korf GigaScience Jun 2013
YHap: software for probabilistic assignment of Y haplogroups from population re-sequencing data F. Zhang ... L. Coin BMC bioinformatics May 2013