Volume 11, 2022

Data Note

Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus

Youngik Yang and others

GigaScience, Volume 11, 2022, giab089, https://doi.org/10.1093/gigascience/giab089

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Review

Inferring microbiota functions from taxonomic genes: a review

Christophe Djemiel and others

GigaScience, Volume 11, 2022, giab090, https://doi.org/10.1093/gigascience/giab090

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Technical Note

Halvade somatic: Somatic variant calling with Apache Spark

Dries Decap and others

GigaScience, Volume 11, 2022, giab094, https://doi.org/10.1093/gigascience/giab094

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Research

Citation needed? Wikipedia bibliometrics during the first wave of the COVID-19 pandemic

Omer Benjakob and others

GigaScience, Volume 11, 2022, giab095, https://doi.org/10.1093/gigascience/giab095

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Data Note

Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map

Olli-Pekka Smolander and others

GigaScience, Volume 11, 2022, giab097, https://doi.org/10.1093/gigascience/giab097

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Research

Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle

Adrián López-García and others

GigaScience, Volume 11, 2022, giab088, https://doi.org/10.1093/gigascience/giab088

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Technical Note

ExTaxsI: an exploration tool of biodiversity molecular data

Giulia Agostinetto and others

GigaScience, Volume 11, 2022, giab092, https://doi.org/10.1093/gigascience/giab092

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Technical Note

DENTIST—using long reads for closing assembly gaps at high accuracy

Arne Ludwig and others

GigaScience, Volume 11, 2022, giab100, https://doi.org/10.1093/gigascience/giab100

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Research

Comparative analysis of common alignment tools for single-cell RNA sequencing

Ralf Schulze Brüning and others

GigaScience, Volume 11, 2022, giac001, https://doi.org/10.1093/gigascience/giac001

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Research

MBGC: Multiple Bacteria Genome Compressor

Szymon Grabowski and Tomasz M Kowalski

GigaScience, Volume 11, 2022, giab099, https://doi.org/10.1093/gigascience/giab099

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Research

LED color gradient as a new screening tool for rapid phenotyping of plant responses to light quality

Pierre Lejeune and others

GigaScience, Volume 11, 2022, giab101, https://doi.org/10.1093/gigascience/giab101

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Technical Note

Qiber3D—an open-source software package for the quantitative analysis of networks from 3D image stacks

Anna Jaeschke and others

GigaScience, Volume 11, 2022, giab091, https://doi.org/10.1093/gigascience/giab091

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Research

Interpretable network-guided epistasis detection

Diane Duroux and others

GigaScience, Volume 11, 2022, giab093, https://doi.org/10.1093/gigascience/giab093

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Data Note

An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome

Kimberly M Davenport and others

GigaScience, Volume 11, 2022, giab096, https://doi.org/10.1093/gigascience/giab096

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Research

A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles

Nazila Koochekian and others

GigaScience, Volume 11, 2022, giab098, https://doi.org/10.1093/gigascience/giab098

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Technical Note

NETMAGE: A human disease phenotype map generator for the network-based visualization of phenome-wide association study results

Vivek Sriram and others

GigaScience, Volume 11, 2022, giac002, https://doi.org/10.1093/gigascience/giac002

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Technical Note

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package

Emma J Griffiths and others

GigaScience, Volume 11, 2022, giac003, https://doi.org/10.1093/gigascience/giac003

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Research

Maternal plasma lipids are involved in the pathogenesis of preterm birth

Yile Chen and others

GigaScience, Volume 11, 2022, giac004, https://doi.org/10.1093/gigascience/giac004

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Technical Note

Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework

Matthias Fahrner and others

GigaScience, Volume 11, 2022, giac005, https://doi.org/10.1093/gigascience/giac005

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Data Note

Fully resolved assembly of Cryptosporidium parvum

Vipin K Menon and others

GigaScience, Volume 11, 2022, giac010, https://doi.org/10.1093/gigascience/giac010

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Research

Genome of the ramshorn snail Biomphalaria straminea—an obligate intermediate host of schistosomiasis

Wenyan Nong and others

GigaScience, Volume 11, 2022, giac012, https://doi.org/10.1093/gigascience/giac012

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Technical Note

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

Romain Feron and Robert M Waterhouse

GigaScience, Volume 11, 2022, giac006, https://doi.org/10.1093/gigascience/giac006

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Research

Genome size evolution in the diverse insect order Trichoptera

Jacqueline Heckenhauer and others

GigaScience, Volume 11, 2022, giac011, https://doi.org/10.1093/gigascience/giac011

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Research

A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum–infected red blood cell proteome

Ghizal Siddiqui and others

GigaScience, Volume 11, 2022, giac008, https://doi.org/10.1093/gigascience/giac008

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Data Note

The Nencki-Symfonia electroencephalography/event-related potential dataset: Multiple cognitive tasks and resting-state data collected in a sample of healthy adults

Patrycja Dzianok and others

GigaScience, Volume 11, 2022, giac015, https://doi.org/10.1093/gigascience/giac015

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Data Note

X-ray microtomography imaging of craniofacial hard tissues in selected reptile species with different types of dentition

Michaela Kavková and others

GigaScience, Volume 11, 2022, giac016, https://doi.org/10.1093/gigascience/giac016

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Research

How to remove or control confounds in predictive models, with applications to brain biomarkers

Darya Chyzhyk and others

GigaScience, Volume 11, 2022, giac014, https://doi.org/10.1093/gigascience/giac014

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Technical Note

Triku: a feature selection method based on nearest neighbors for single-cell data

Alex M Ascensión and others

GigaScience, Volume 11, 2022, giac017, https://doi.org/10.1093/gigascience/giac017

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Data Note

Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes

James P Bernot and others

GigaScience, Volume 11, 2022, giac021, https://doi.org/10.1093/gigascience/giac021

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Research

Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators

Débora Pires Paula and others

GigaScience, Volume 11, 2022, giac020, https://doi.org/10.1093/gigascience/giac020

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Data Note

KOREF_S1: phased, parental trio-binned Korean reference genome using long reads and Hi-C sequencing methods

Hui-su Kim and others

GigaScience, Volume 11, 2022, giac022, https://doi.org/10.1093/gigascience/giac022

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Research

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

Weihong Qi and others

GigaScience, Volume 11, 2022, giac028, https://doi.org/10.1093/gigascience/giac028

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Data Note

Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

Diana A Robledo-Ruiz and others

GigaScience, Volume 11, 2022, giac025, https://doi.org/10.1093/gigascience/giac025

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Data Note

Living in darkness: Exploring adaptation of Proteus anguinus in 3 dimensions by X-ray imaging

Markéta Tesařová and others

GigaScience, Volume 11, 2022, giac030, https://doi.org/10.1093/gigascience/giac030

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Data Note

GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes

Ravin Poudel and others

GigaScience, Volume 11, 2022, giac007, https://doi.org/10.1093/gigascience/giac007

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Data Note

A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

Marc Palmada-Flores and others

GigaScience, Volume 11, 2022, giac026, https://doi.org/10.1093/gigascience/giac026

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Research

A high-quality assembled genome and its comparative analysis decode the adaptive molecular mechanism of the number one Chinese cotton variety CRI-12

Xuke Lu and others

GigaScience, Volume 11, 2022, giac019, https://doi.org/10.1093/gigascience/giac019

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Review

The rise of genomics in snake venom research: recent advances and future perspectives

Wei-qiao Rao and others

GigaScience, Volume 11, 2022, giac024, https://doi.org/10.1093/gigascience/giac024

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Data Note

Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens)

Hangwei Liu and others

GigaScience, Volume 11, 2022, giac009, https://doi.org/10.1093/gigascience/giac009

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Research

A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl

Shaojuan Liu and others

GigaScience, Volume 11, 2022, giac018, https://doi.org/10.1093/gigascience/giac018

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Research

Benchmarking missing-values approaches for predictive models on health databases

Alexandre Perez-Lebel and others

GigaScience, Volume 11, 2022, giac013, https://doi.org/10.1093/gigascience/giac013

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Research

Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants

Leila Fattel and others

GigaScience, Volume 11, 2022, giac023, https://doi.org/10.1093/gigascience/giac023

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Research

Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

Jean-Marc Aury and others

GigaScience, Volume 11, 2022, giac034, https://doi.org/10.1093/gigascience/giac034

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Research

Lessons learned about the biology and genomics of Diaphorina citri infection with “Candidatus Liberibacter asiaticus” by integrating new and archived organ-specific transcriptome data

Marina Mann and others

GigaScience, Volume 11, 2022, giac035, https://doi.org/10.1093/gigascience/giac035

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Research

Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions

D Steinke and others

GigaScience, Volume 11, 2022, giac040, https://doi.org/10.1093/gigascience/giac040

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Data Note

A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae

Ziwei Wang and others

GigaScience, Volume 11, 2022, giac027, https://doi.org/10.1093/gigascience/giac027

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Data Note

Monash DaCRA fPET-fMRI: A dataset for comparison of radiotracer administration for high temporal resolution functional FDG-PET

Sharna D Jamadar and others

GigaScience, Volume 11, 2022, giac031, https://doi.org/10.1093/gigascience/giac031

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Technical Note

scMAPA: Identification of cell-type–specific alternative polyadenylation in complex tissues

Yulong Bai and others

GigaScience, Volume 11, 2022, giac033, https://doi.org/10.1093/gigascience/giac033

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Commentary

A decade of GigaScience: 10 years of the evolving genomic and biomedical standards landscape

Lynn M Schriml

GigaScience, Volume 11, 2022, giac047, https://doi.org/10.1093/gigascience/giac047

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Technical Note

Generation and application of pseudo–long reads for metagenome assembly

Mikang Sim and others

GigaScience, Volume 11, 2022, giac044, https://doi.org/10.1093/gigascience/giac044

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Technical Note

HaploMaker: An improved algorithm for rapid haplotype assembly of genomic sequences

Mario Fruzangohar and others

GigaScience, Volume 11, 2022, giac038, https://doi.org/10.1093/gigascience/giac038

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Research

NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer

Mohamed Amgad and others

GigaScience, Volume 11, 2022, giac037, https://doi.org/10.1093/gigascience/giac037

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Review

The state of Medusozoa genomics: current evidence and future challenges

Mylena D Santander and others

GigaScience, Volume 11, 2022, giac036, https://doi.org/10.1093/gigascience/giac036

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Technical Note

Fast and accurate estimation of multidimensional site frequency spectra from low-coverage high-throughput sequencing data

Alex Mas-Sandoval and others

GigaScience, Volume 11, 2022, giac032, https://doi.org/10.1093/gigascience/giac032

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Research

AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data

Simone Marini and others

GigaScience, Volume 11, 2022, giac029, https://doi.org/10.1093/gigascience/giac029

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Data Note

The assembled and annotated genome of the masked palm civet (Paguma larvata)

Ping Liu and others

GigaScience, Volume 11, 2022, giac041, https://doi.org/10.1093/gigascience/giac041

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Review

Modern venomics—Current insights, novel methods, and future perspectives in biological and applied animal venom research

Bjoern M von Reumont and others

GigaScience, Volume 11, 2022, giac048, https://doi.org/10.1093/gigascience/giac048

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Research

Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification

Chakravarthi Kanduri and others

GigaScience, Volume 11, 2022, giac046, https://doi.org/10.1093/gigascience/giac046

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Data Note

Chromosome‐level genome assembly of the black widow spider Latrodectus elegans illuminates composition and evolution of venom and silk proteins

Zhongkai Wang and others

GigaScience, Volume 11, 2022, giac049, https://doi.org/10.1093/gigascience/giac049

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Review

Data standardization of plant–pollinator interactions

José A Salim and others

GigaScience, Volume 11, 2022, giac043, https://doi.org/10.1093/gigascience/giac043

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Research

Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers

Xiaofeng Dong and others

GigaScience, Volume 11, 2022, giac045, https://doi.org/10.1093/gigascience/giac045

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Data Note

Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus

R Alan Harris and others

GigaScience, Volume 11, 2022, giac039, https://doi.org/10.1093/gigascience/giac039

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Commentary

A Decade of GigaScience: GigaDB and the Open Data Movement

Chris Armit and others

GigaScience, Volume 11, 2022, giac053, https://doi.org/10.1093/gigascience/giac053

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Commentary

A decade of GigaScience: A perspective on conservation genetics

Stephen J O'Brien

GigaScience, Volume 11, 2022, giac055, https://doi.org/10.1093/gigascience/giac055

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Commentary

A Decade of GigaScience: The Challenges of Gigapixel Pathology Images

Geert Litjens and others

GigaScience, Volume 11, 2022, giac056, https://doi.org/10.1093/gigascience/giac056

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Commentary

A decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature?

Anita Bandrowski

GigaScience, Volume 11, 2022, giac058, https://doi.org/10.1093/gigascience/giac058

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Commentary

A decade of GigaScience: the importance of community organizations for open and FAIR efforts in neuroinformatics

Maryann E Martone

GigaScience, Volume 11, 2022, giac060, https://doi.org/10.1093/gigascience/giac060

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Research

A chromosome-level genome assembly of Artocarpus nanchuanensis (Moraceae), an extremely endangered fruit tree

Jiaoyu He and others

GigaScience, Volume 11, 2022, giac042, https://doi.org/10.1093/gigascience/giac042

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Data Note

Genomes and demographic histories of the endangered Bretschneidera sinensis (Akaniaceae)

Han Zhang and others

GigaScience, Volume 11, 2022, giac050, https://doi.org/10.1093/gigascience/giac050

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Data Note

A novel ground truth multispectral image dataset with weight, anthocyanins, and Brix index measures of grape berries tested for its utility in machine learning pipelines

Pedro J Navarro and others

GigaScience, Volume 11, 2022, giac052, https://doi.org/10.1093/gigascience/giac052

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Research

ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks

Connah G M Johnson and others

GigaScience, Volume 11, 2022, giac051, https://doi.org/10.1093/gigascience/giac051

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Research

Agricultural plant cataloging and establishment of a data framework from UAV-based crop images by computer vision

Maurice Günder and others

GigaScience, Volume 11, 2022, giac054, https://doi.org/10.1093/gigascience/giac054

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Editorial

A Decade of GigaScience: Milestones in Open Science

Scott C Edmunds and others

GigaScience, Volume 11, 2022, giac067, https://doi.org/10.1093/gigascience/giac067

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Research

The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

Xiang Li and others

GigaScience, Volume 11, 2022, giac057, https://doi.org/10.1093/gigascience/giac057

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Research

A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability

Qingyun Wang and others

GigaScience, Volume 11, 2022, giac059, https://doi.org/10.1093/gigascience/giac059

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Commentary

A Decade of GigaScience: Women in Science: Past, Present, and Future

Lijun Liu and others

GigaScience, Volume 11, 2022, giac069, https://doi.org/10.1093/gigascience/giac069

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Technical Note

Loop detection using Hi-C data with HiCExplorer

Joachim Wolff and others

GigaScience, Volume 11, 2022, giac061, https://doi.org/10.1093/gigascience/giac061

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Data Note

Chromosome-level genome assembly of Plazaster borealis sheds light on the morphogenesis of multiarmed starfish and its regenerative capacity

Yujung Lee and others

GigaScience, Volume 11, 2022, giac063, https://doi.org/10.1093/gigascience/giac063

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Research

Chromosome-level assembly and annotation of the blue catfish Ictalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies

Haolong Wang and others

GigaScience, Volume 11, 2022, giac070, https://doi.org/10.1093/gigascience/giac070

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Data Note

A chromosome-level genome of the booklouse, Liposcelis brunnea, provides insight into louse evolution and environmental stress adaptation

Shiqian Feng and others

GigaScience, Volume 11, 2022, giac062, https://doi.org/10.1093/gigascience/giac062

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Technical Note

Spacemake: processing and analysis of large-scale spatial transcriptomics data

Tamas Ryszard Sztanka-Toth and others

GigaScience, Volume 11, 2022, giac064, https://doi.org/10.1093/gigascience/giac064

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Review

Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods

Paula Arribas and others

GigaScience, Volume 11, 2022, giac065, https://doi.org/10.1093/gigascience/giac065

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Technical Note

Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake

Luke R Thompson and others

GigaScience, Volume 11, 2022, giac066, https://doi.org/10.1093/gigascience/giac066

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Technical Note

Meta-Prism 2.0: Enabling algorithm and web server for ultra-fast, memory-efficient, and accurate analysis among millions of microbial community samples

Kai Kang and others

GigaScience, Volume 11, 2022, giac073, https://doi.org/10.1093/gigascience/giac073

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Research

SurvBenchmark: comprehensive benchmarking study of survival analysis methods using both omics data and clinical data

Yunwei Zhang and others

GigaScience, Volume 11, 2022, giac071, https://doi.org/10.1093/gigascience/giac071

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Research

Antibiotic resistance genes are differentially mobilized according to resistance mechanism

Tue Kjærgaard Nielsen and others

GigaScience, Volume 11, 2022, giac072, https://doi.org/10.1093/gigascience/giac072

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Research

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Hollis A Dahn and others

GigaScience, Volume 11, 2022, giac068, https://doi.org/10.1093/gigascience/giac068

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Technical Note

Stardust: improving spatial transcriptomics data analysis through space-aware modularity optimization-based clustering

Simone Avesani and others

GigaScience, Volume 11, 2022, giac075, https://doi.org/10.1093/gigascience/giac075

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Review

Evolution of complex genome architecture in gymnosperms

Tao Wan and others

GigaScience, Volume 11, 2022, giac078, https://doi.org/10.1093/gigascience/giac078

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Technical Note

DeePVP: Identification and classification of phage virion proteins using deep learning

Zhencheng Fang and others

GigaScience, Volume 11, 2022, giac076, https://doi.org/10.1093/gigascience/giac076

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Research

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications

Maaly Nassar and others

GigaScience, Volume 11, 2022, giac077, https://doi.org/10.1093/gigascience/giac077

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Research

The complexity landscape of viral genomes

Jorge Miguel Silva and others

GigaScience, Volume 11, 2022, giac079, https://doi.org/10.1093/gigascience/giac079

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Research

Quantifying research interests in 7,521 mammalian species with h-index: a case study

Jessica Tam and others

GigaScience, Volume 11, 2022, giac074, https://doi.org/10.1093/gigascience/giac074

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Research

Association mapping across a multitude of traits collected in diverse environments in maize

Ravi V Mural and others

GigaScience, Volume 11, 2022, giac080, https://doi.org/10.1093/gigascience/giac080

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Research

A curated human cellular microRNAome based on 196 primary cell types

Arun H Patil and others

GigaScience, Volume 11, 2022, giac083, https://doi.org/10.1093/gigascience/giac083

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Research

Statistical quantification of confounding bias in machine learning models

Tamas Spisak

GigaScience, Volume 11, 2022, giac082, https://doi.org/10.1093/gigascience/giac082

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Research

Comparative maternal protein profiling of mouse biparental and uniparental embryos

Fumei Chen and others

GigaScience, Volume 11, 2022, giac084, https://doi.org/10.1093/gigascience/giac084

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Review

The Pioneer Advantage: Filling the blank spots on the map of genome diversity in Europe

Taras K Oleksyk and others

GigaScience, Volume 11, 2022, giac081, https://doi.org/10.1093/gigascience/giac081

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Data Note

Identification of candidate sex‐specific genomic regions in male and female Asian arowana genomes

Xidong Mu and others

GigaScience, Volume 11, 2022, giac085, https://doi.org/10.1093/gigascience/giac085

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Technical Note

d-StructMAn: Containerized structural annotation on the scale from genetic variants to whole proteomes

Alexander Gress and others

GigaScience, Volume 11, 2022, giac086, https://doi.org/10.1093/gigascience/giac086

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Technical Note

SYNPRED: prediction of drug combination effects in cancer using different synergy metrics and ensemble learning

António J Preto and others

GigaScience, Volume 11, 2022, giac087, https://doi.org/10.1093/gigascience/giac087

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Research

Discovery of druggable cancer-specific pathways with application in acute myeloid leukemia

Quang Thinh Trac and others

GigaScience, Volume 11, 2022, giac091, https://doi.org/10.1093/gigascience/giac091

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Research

Clonality, inbreeding, and hybridization in two extremotolerant black yeasts

Cene Gostinčar and others

GigaScience, Volume 11, 2022, giac095, https://doi.org/10.1093/gigascience/giac095

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Technical Note

Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies

Miguel A Naranjo-Ortiz and others

GigaScience, Volume 11, 2022, giac088, https://doi.org/10.1093/gigascience/giac088

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Data Note

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

F Gözde Çilingir and others

GigaScience, Volume 11, 2022, giac090, https://doi.org/10.1093/gigascience/giac090

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A virtual library for behavioral performance in standard conditions—rodent spontaneous activity in an open field during repeated testing and after treatment with drugs or brain lesions

Henry Szechtman and others

GigaScience, Volume 11, 2022, giac092, https://doi.org/10.1093/gigascience/giac092

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Technical Note

CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis

Pavel S Novichkov and others

GigaScience, Volume 11, 2022, giac089, https://doi.org/10.1093/gigascience/giac089

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High temporal resolution Nanopore sequencing dataset of SARS-CoV-2 and host cell RNAs

Dóra Tombácz and others

GigaScience, Volume 11, 2022, giac094, https://doi.org/10.1093/gigascience/giac094

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Research

Disease classification for whole-blood DNA methylation: Meta-analysis, missing values imputation, and XAI

Alena Kalyakulina and others

GigaScience, Volume 11, 2022, giac097, https://doi.org/10.1093/gigascience/giac097

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Technical Note

BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data

Carol Moraga and others

GigaScience, Volume 11, 2022, giac093, https://doi.org/10.1093/gigascience/giac093

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Data Note

A dataset of ant colonies’ motion trajectories in indoor and outdoor scenes to study clustering behavior

Meihong Wu and others

GigaScience, Volume 11, 2022, giac096, https://doi.org/10.1093/gigascience/giac096

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Research

Best genome sequencing strategies for annotation of complex immune gene families in wildlife

Emma Peel and others

GigaScience, Volume 11, 2022, giac100, https://doi.org/10.1093/gigascience/giac100

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Commentary

The Global Atlas of Bamboo and Rattan (GABR) Phase II: new resources for sustainable development

Hansheng Zhao and others

GigaScience, Volume 11, 2022, giac113, https://doi.org/10.1093/gigascience/giac113

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Data Note

The Capparis spinosa var. herbacea genome provides the first genomic instrument for a diversity and evolution study of the Capparaceae family

Lei Wang and others

GigaScience, Volume 11, 2022, giac106, https://doi.org/10.1093/gigascience/giac106

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Technical Note

Alignstein: Optimal transport for improved LC-MS retention time alignment

Grzegorz Skoraczyński and others

GigaScience, Volume 11, 2022, giac101, https://doi.org/10.1093/gigascience/giac101

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Research

Selection signatures in goats reveal a novel deletion mutant underlying cashmere yield and diameter

Hu Han and others

GigaScience, Volume 11, 2022, giac107, https://doi.org/10.1093/gigascience/giac107

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Commentary

Publishing data to support the fight against human vector-borne diseases

Scott C Edmunds and others

GigaScience, Volume 11, 2022, giac114, https://doi.org/10.1093/gigascience/giac114

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Data Note

High-quality genome assembles from key Hawaiian coral species

Timothy G Stephens and others

GigaScience, Volume 11, 2022, giac098, https://doi.org/10.1093/gigascience/giac098

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Technical Note

Accurate gene consensus at low nanopore coverage

Rocío Espada and others

GigaScience, Volume 11, 2022, giac102, https://doi.org/10.1093/gigascience/giac102

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Data Note

The whole-genome assembly of an endangered Salicaceae species: Chosenia arbutifolia (Pall.) A. Skv

Xudong He and others

GigaScience, Volume 11, 2022, giac109, https://doi.org/10.1093/gigascience/giac109

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An in vitro whole-cell electrophysiology dataset of human cortical neurons

Derek Howard and others

GigaScience, Volume 11, 2022, giac108, https://doi.org/10.1093/gigascience/giac108

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Research

Defining the characteristics of interferon-alpha–stimulated human genes: insight from expression data and machine learning

Haiting Chai and others

GigaScience, Volume 11, 2022, giac103, https://doi.org/10.1093/gigascience/giac103

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Technical Note

learnMSA: learning and aligning large protein families

Felix Becker and Mario Stanke

GigaScience, Volume 11, 2022, giac104, https://doi.org/10.1093/gigascience/giac104

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Research

Making Common Fund data more findable: catalyzing a data ecosystem

Amanda L Charbonneau and others

GigaScience, Volume 11, 2022, giac105, https://doi.org/10.1093/gigascience/giac105

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Technical Note

What the Phage: a scalable workflow for the identification and analysis of phage sequences

Mike Marquet and others

GigaScience, Volume 11, 2022, giac110, https://doi.org/10.1093/gigascience/giac110

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Research

Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads

Yan Zhang and others

GigaScience, Volume 11, 2022, giac116, https://doi.org/10.1093/gigascience/giac116

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Technical Note

Utilizing an artificial intelligence system to build the digital structural proteome of reef-building corals

Yunchi Zhu and others

GigaScience, Volume 11, 2022, giac117, https://doi.org/10.1093/gigascience/giac117

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Technical Note

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

Mihaly Varadi and others

GigaScience, Volume 11, 2022, giac118, https://doi.org/10.1093/gigascience/giac118

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Research

High-throughput proteomics and in vitro functional characterization of the 26 medically most important elapids and vipers from sub-Saharan Africa

Giang Thi Tuyet Nguyen and others

GigaScience, Volume 11, 2022, giac121, https://doi.org/10.1093/gigascience/giac121

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Research

annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing

Carlos Farkas and others

GigaScience, Volume 11, 2022, giac099, https://doi.org/10.1093/gigascience/giac099

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Research

Open-source benchmarking of IBD segment detection methods for biobank-scale cohorts

Kecong Tang and others

GigaScience, Volume 11, 2022, giac111, https://doi.org/10.1093/gigascience/giac111

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Commentary

The opportunities of research parasitism: A case study using the Barcode of Life Data System (BOLD)

Jack Pilgrim

GigaScience, Volume 11, 2022, giac123, https://doi.org/10.1093/gigascience/giac123

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Data Note

A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization

Hongbo Wang and others

GigaScience, Volume 11, 2022, giac120, https://doi.org/10.1093/gigascience/giac120

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Correction Notice

Correction to: The state of Medusozoa genomics: current evidence and future challenges

GigaScience, Volume 11, 2022, giac115, https://doi.org/10.1093/gigascience/giac115

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