| Paper |
Authors |
Journal |
Date |
Reviews |
| 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 |
R1, R2 |
| 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 |
R1, R2, R3 |
| Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes |
L. K. Johnson ... C. T. Brown |
GigaScience |
May 2018 |
R1, R2, R3, R4 |
| Genome analyses show strong selection on coloration, morphological and behavioral phenotypes in birds-of-paradise |
S. Prost ... M. Irestedt |
GigaScience |
May 2018 |
R1, R2, R3 |
| Monitoring changes in the Gene Ontology and their impact on genomic data analysis |
M. Jacobson ... P. Pavlidis |
GigaScience |
May 2018 |
R1, R2 |
| FMRIPrep: a robust preprocessing pipeline for functional MRI |
O. Esteban ... K. J. Gorgolewski |
Nature methods |
Apr 2018 |
R1, R2, R3 |
| Prot-SpaM: Fast alignment-free phylogeny reconstruction based on whole-proteome sequences |
C. Leimeister ... B. Morgenstern |
GigaScience |
Apr 2018 |
R1, R2, R3, R4 |
| Reproducible genomics analysis pipelines with GNU Guix |
R. Wurmus ... A. Akalin |
GigaScience |
Apr 2018 |
R1, R2, R3 |
| Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics data |
F. Alakwaa ... L. Garmire |
GigaScience |
Mar 2018 |
R1 |
| 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 |
R1 |
| 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 |
|
| Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning |
H. Teng ... L. Coin |
GigaScience |
Aug 2017 |
R1, R2 |
| 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 |
|
| 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 |
R1, R2 |
| 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 |
R1, R2, R3, R4 |
| Draft genome of the Reindeer (Rangifer tarandus) |
Z. Li ... G. Li |
GigaScience |
Jun 2017 |
R1, R2 |
| 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 |
R1, R2, R3 |
| PhenoSpD: an atlas of phenotypic correlations and a multiple testing correction for the human phenome |
J. Zheng ... T. Gaunt |
GigaScience |
Jun 2017 |
R1, R2, R3, R4 |
| Indexcov: fast coverage quality control for whole-genome sequencing |
B. S. Pedersen ... A. R. Quinlan |
GigaScience |
Jun 2017 |
R1 |
| Mammalian genomic regulatory regions predicted by utilizing human genomics, transcriptomics and epigenetics data |
Q. H. Nguyen ... B. P. Dalrymple |
GigaScience |
Jun 2017 |
R1, R2 |
| Re-evaluation of SNP heritability in complex human traits |
D. Speed ... D. Balding |
Nature genetics |
May 2017 |
R1, R2, R3 |
| Multifactorial Chromosomal Variants Regulate Polymyxin Resistance In Extensively Drug-Resistant Klebsiella pneumoniae |
M. Pitt ... L. J. M. Coin |
Microbial Genomics |
May 2017 |
R1 |
| 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 |
R1 |
| 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 |
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 |
Nucleic acids research |
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 |
PLoS neglected tropical diseases |
Jul 2016 |
R1, R2, R3 |
| 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 |
R1, R2, R3 |
| An explicit-solvent conformation search method using open software |
K. Gaalswyk, C. Rowley |
PeerJ |
Apr 2016 |
R1 |
| Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing |
M. D. Cao ... L. Coin |
GigaScience |
Apr 2016 |
R1 |
| Clusterflock: A Flocking Algorithm for Isolating Congruent Phylogenomic Datasets |
A. Narechania ... P. J. Planet |
GigaScience |
Mar 2016 |
R1, R2, R3, R4 |
| NanoSim: nanopore sequence read simulator based on statistical characterization |
C. Yang ... I. Birol |
GigaScience |
Mar 2016 |
R1, R2, R3, R4 |
| Kronos: a workflow assembler for genome analytics and informatics |
M. J. Taghiyar ... S. Shah |
GigaScience |
Feb 2016 |
R1 |
| 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 |
R1, R2 |
| Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing |
M. D. Cao ... L. Coin |
GigaScience |
Dec 2015 |
R1, R2, R3, R4, R5, R6 |
| AGOUTI: improving genome assembly and annotation using transcriptome data |
S. V. Zhang ... M. W. Hahn |
GigaScience |
Nov 2015 |
R1, R2, R3 |
| A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data |
J. Risse ... M. Watson |
GigaScience |
Aug 2015 |
R1, R2, R3 |
| Determination of Nonlinear Genetic Architecture using Compressed Sensing |
C. M. Ho, S. D. H. Hsu, |
GigaScience |
Jul 2015 |
R1, R2 |
| Tools and techniques for computational reproducibility |
S. R. Piccolo ... M. B. Frampton |
GigaScience |
Jul 2015 |
R1, R2 |
| The seasonal reproduction number of dengue fever: impacts of climate on transmission |
S. Polwiang, |
PeerJ |
Jul 2015 |
R1, R2 |
| Real-time strain typing and analysis of antibiotic resistance potential using Nanopore MinION sequencing |
M. D. Cao ... L. Coin |
GigaScience |
May 2015 |
R1, R2, R3, R4, R5 |
| LINKS: Scaffolding genome assemblies with kilobase-long nanopore reads |
R. L. Warren ... I. Birol |
GigaScience |
Mar 2015 |
R1 |
| Swabs to genomes: a comprehensive workflow |
M. I. Dunitz ... D. A. Coil |
PeerJ |
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 |
GigaScience |
Jan 2015 |
R1 |
| Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols |
P. A. Combs, M. B. Eisen, |
PeerJ |
Jan 2015 |
R1, R2 |
| NxRepair: Error correction in de novo sequence assembly using Nextera mate pairs |
R. R. Murphy ... O. B. Schulz-Trieglaff |
PeerJ |
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 |
PeerJ |
Dec 2014 |
R1 |
| Reducing workplace burnout: The relative benefits of cardiovascular and resistance exercise |
R. J. Bretland, E. B. Thorsteinsson, |
PeerJ |
Dec 2014 |
R1 |
| Subject-specific body segment parameter estimation using 3D photogrammetry with multiple cameras |
K. E. Peyer ... W. I. Sellers |
PeerJ |
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, |
PeerJ |
Oct 2014 |
R1 |
| A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer |
A. Quinlan ... N. Loman |
GigaScience |
Sep 2014 |
R1, R2, R3 |
| Endothelial cell-initiated extravasation of cancer cells visualized in zebrafish |
|
PeerJ |
Sep 2014 |
R1, R2 |
| Application of compressed sensing to genome wide association studies and genomic selection |
S. Vattikuti ... C. C. Chow |
GigaScience |
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, |
PeerJ |
Mar 2014 |
R1 |
| A data repository and analysis framework for spontaneous neural activity recordings in developing retina |
S. Eglen ... E. Sernagor |
GigaScience |
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 |
GigaScience |
Sep 2013 |
R1, R2 |
| Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species |
K. R. Bradnam ... I. F. Korf |
GigaScience |
Jun 2013 |
R1, R2 |
| YHap: software for probabilistic assignment of Y haplogroups from population re-sequencing data |
F. Zhang ... L. Coin |
BMC bioinformatics |
May 2013 |
|