549 Works

Peer review of "circlncRNAnet: An integrated web-based resource for mapping functional networks of long or circular forms of non-coding RNAs"

Wilfried Haerty
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Filling reference gaps via assembling DNA barcodes using high-throughput sequencing – moving toward barcoding the world"

Akifumi Tanabe
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Supporting data for "drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes"

Hsin-Hung Lin & Yu-Chieh Liao
Virus discovery using high-throughput next-generation sequencing (NGS) has become more commonplace. However, although analysis of deep NGS data allows us to identity potential pathogens, the entire analytical procedure requires competency in the bioinformatics domain, which includes implementing proper software packages and preparing prerequisite databases. Simple and user-friendly bioinformatics pipelines are urgently required to obtain complete viral genome sequences from metagenomic data. Here we present a pipeline, drVM (detect and reconstruct known viral genomes from metagenomes),...

Peer review of "drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes"

Simon Roux
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization"

Benjamin Marie
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

High quality chimpanzee reference genome (Pan_tro_30) from hybrid assembly approach

Lukas FK Kuderna, Chad Tomlinson, LaDeana W Hillier, Annabel Tran, Ian Fiddes, Joel Armstrong, Hafid Laayouni, David Gordon, John Huddleston, Raquel Garcia Perez, Inna Povolotskaya, Aitor Serres Armero, Jessica Gomez Garrido, Daniel Ho, Paolo Ribeca, Tyler Alioto, Richard E Green, Benedict Paten, Arcadi Navarro, Jaume Betranpetit, Javier Herrero, Evan E Eichler, Andrew J Sharp, Lars Feuk, Wesley C Warren … & Tomas Marques-Bonet
The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high quality reference genome assembly. The current iteration of the chimpanzee reference genome assembly (Pan_tro_2.1.4) is highly fragmented, with more than 183,000 contigs and incorporating over 159,000 gaps, with a genome wide contig N50 of 51 Kbp. In this work we produce an extensive and diverse array of sequencing datasets to rapidly assemble...

Peer review of "Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome"

Sujai Kumar
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Bayes Forest: a data-intensive generator of morphological tree clones"

Jean-Francois Cote
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Full Genome Survey and Dynamics of Gene Expression in the Greater Amberjack Seriola dumerili"

Benjamin Reading
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Supporting data for "Filling reference gaps via assembling DNA barcodes using high-throughput sequencing - moving toward barcoding the world"

Zhou Chengran, Yang Chentao, Liu Shanlin & Zhou Xin
Over the past decade, biodiversity scientists have dedicated tremendous efforts in constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2,000, further dramatic reduction on barcoding costs is unlikely because the Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also refrained High-Throughput-Sequencing (HTS)...

Peer review of "Genome sequence of the small brown planthopper Laodelphax striatellus"

Spencer Johnston
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Software for "Sim3C: simulation of Hi-C and Meta3C proximity ligation sequencing technologies"

Darling E Aaron & DeMaere Z Matthew
Chromosome conformation capture (3C) and HiC DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols.
We describe a computational simulator that, given reference genome sequences and some basic parameters, will simulate HiC sequencing on those sequences. The simulator models...

Peer review of "The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum "

Hikmet Budak
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Comparative performance of the BGISEQ-500 versus Illumina HiSeq2501 sequencing platforms for palaeogenomic sequencing"

Tatiana Tatarinova
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Supporting data for "An expanded mammal mitogenome dataset from Southeast Asia"

Faezah Mohd Salleh, Jazmin Ramos-Madrigal, Fernando Penaloza, Shanlin Liu, Mikkel-Holger S Sinding, Riddhi P Patel, Renata Martins, Dorina Lenz, Jorns Fickel, Christian Roos, Mohd Shahir Shamsir, Mohammad Shahfiz Azman, Burton K Lim, Stephen J Rossiter, Andreas Wilting & M.Thomas P Gilbert
Southeast (SE) Asia is one of the most biodiverse regions in the world and it holds approximately 20% of all mammal species. Despite this, the majority of SE Asia’s genetic diversity is still poorly characterised. The growing interest in using environmental DNA (eDNA) to assess and monitor SE Asian species, in particular threatened mammals - has created the urgent need to expand the available reference database of mitochondrial barcode and complete mitogenome sequences. We have...

Peer review of "Plant phenomics: an overview of image acquisition technologies and image data analysis algorithms"

Wanneng Yang
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "PSSMHCpan: a novel PSSM based software for predicting class I peptide-HLA binding affinity"

Sinu Paul
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Taxonomic structure and functional association of foxtail millet root microbiome"

Jason Wallace
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of " The genome sequence of the wisent (Bison bonasus) "

Derek Bickhart
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "De Novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads"

Lex Nederbragt
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Taxonomic structure and functional association of foxtail millet root microbiome"

Alison Berry
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Proteomic landscape of the primary somatosensory cortex upon sensory deprivation"

Alex Bayes
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Improving amphibian genomic resources: a multi-tissue reference transcriptome of an iconic invader"

Masanori Taira
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 4D"

Min Zheng
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Peer review of "Genomic data for 78 chickens from 14 populations"

Andrew Mason
This is the open peer reviewers comments and recommendations regarding the submitted GigaScience article and/or dataset.

Registration Year

  • 2017
    549

Resource Types

  • Text
    432
  • Dataset
    117