GigaByte

Latest preprint reviews

1. Closely related, yet phenotypically different - Genome assemblies of two sister species of widow spiders: Latrodectus hasselti and L. katipo, Theridiidae

   This article has 8 authors:

   1. Vladislav Ivanov
   2. Kardelen Özgün Uludağ
   3. Jutta M. Schneider
   4. Yannis Schöneberg
   5. Susan Kennedy
   6. Alexander Ben Hamadou
   7. Cor J. Vink
   8. Henrik Krehenwinkel

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     The paper presents high-quality reference genome assemblies for two closely related widow spider species, the Australian redback (Latrodectus hasselti) and the New Zealand endemic katipō (L. katipo), providing an important genomic resource for studies of venom evolution, adaptation, and conservation biology. Rather than simply reporting assembly statistics, the authors compare the genomic architecture of the two species, showing that both genomes are highly complete (BUSCO scores >94%) and share similar repeat content, while differing in overall genome size, scaffold continuity, and predicted gene numbers. The chromosome-level assembly achieved for L. katipo enables more detailed comparative analyses than previously possible, whereas the more fragmented L. hasselti assembly still captures a highly complete gene repertoire. Ortholog analyses reveal substantial conservation between the species but also indicate lineage-specific differences, with evidence suggesting either gene duplication in L. hasselti or gene loss in L. katipo, providing insight into their divergent evolutionary histories despite their close relationship and contrasting ecological distributions. Beyond generating sequence data, the study establishes foundational genomic resources that will facilitate future investigations into venom gene evolution, population genomics, species divergence, and the conservation of these ecologically and medically significant spiders.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

2. AI in practice: a multilingual survey of 2025 BioHackathon participants

   This article has 9 authors:

   1. Nattawet Sriwichai
   2. Lucas Feriau
   3. Pumipat Tongyoo
   4. Yukiko Noda
   5. Hikaru Gyoji
   6. Pitiporn Noisagul
   7. Susumu Goto
   8. David Steinberg
   9. Chatarin Wangsanuwat

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This Data Release presents a multilingual dataset collected from a survey of participants and community members at the 2025 DBCLS BioHackathon, with the goal of understanding how AIis being used in bioinformatics and related scientific fields. The survey, available in English, Japanese, and Thai, gathered responses from 105 participants about AI usage frequency, applications, challenges, institutional support, satisfaction, concerns, and demographic information. The released dataset includes anonymized raw responses, a cleaned English-language version for quantitative analysis, the original questionnaire, a data dictionary, and a translation lookup table to support reproducible research. To protect participant privacy, the authors carefully removed personally identifiable information. This openly available resource provides researchers with valuable data for studying AI adoption, evaluating policy and institutional support, and developing methods for analyzing survey data related to AI use in scientific research. Overall, this work contributes a well-documented, reusable dataset that can help inform future research on the evolving role of artificial intelligence in genomics, bioinformatics, software development, and the broader scientific community.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

3. Transcriptomic profile of embryoid bodies under hypoxia at single cell level

   This article has 5 authors:

   1. Bárbara Acosta-Iborra
   2. Yosra Berrouayel
   3. Laura Puente-Santamaría
   4. Luis del Peso
   5. Benilde Jiménez

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This is a Data Release paper describing a mouse embryoid body single-cell RNA-seq dataset generated to study how oxygen availability shapes early cell differentiation. Acosta-Iborra et al. differentiated R1 mouse embryonic stem cells into embryoid bodies for 8 or 10 days, exposing them to hypoxia or normoxia for the final 16 or 48 hours of differentiation, then profiled thousands of cells per condition using droplet-based scRNA-seq from 10X. This yielding eight raw/filtered HDF5 count matrices across the four conditions. This was validated with flow cytometry, immunofluorescence, and EdU assays, confirming that hypoxia increased endothelial marker expression and vascular network complexity while inducing cell cycle arrest. This pattern mirrored transcriptionally, with hypoxic samples showing markedly higher proportions of cells in G0/G1 phase and elevated hypoxia gene-signature scores. QC analysis (and peer review in GigaByte) confirmed high data quality across samples, and conservative low-resolution clustering revealed a largely homogeneous progenitor population with a smaller, more differentiated subset. While there are limitations (mature endothelial cells were too sparse to robustly test the original hypothesis) the authors present this as an open, well-validated resource for comparative studies of hypoxia responses, benchmarking single-cell computational tools, and investigating early lineage specification and oxygen signaling more broadly.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

4. The genome of the reef-building coral Porites harrisoni from the southern Persian/Arabian Gulf

   This article has 7 authors:

   1. Anna Fiesinger
   2. Abdoallah Sharaf
   3. Rachel Alderdice
   4. Gabriela Perna
   5. Hannah Manns
   6. John A. Burt
   7. Christian R. Voolstra

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This data paper is a genome note presenting the assembly of Porites harrisoni, a stony coral species endemic to the thermally extreme southern Persian Gulf. Using ONT PromethION long nanopore reads the final genome size encompassed 626.7 Mb across 1,883 contigs, achieving a BUSCO completeness of 86.3%. This revealed significant repeat content, comprising 59.23% of the nuclear genome and highlighting a diploid structure with predominant homozygosity. A total of 27,823 protein-coding genes were annotated from this assembly, facilitating discussions on thermal resilience under climate change. The research underscores the genomic framework supporting adaptive capacities in corals, with implications for evolutionary biology and conservation science, especially in context to ongoing ocean warming.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

5. Inference of admixture in dogs from whole genome sequences

   This article has 6 authors:

   1. Gregory Kislik
   2. Garrett Moore
   3. Liudmilla Rubbi
   4. Veninka Nikki Supara
   5. Grace Chen
   6. Matteo Pellegrini

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     In this new methodological work researchers investigate the genetic structure and admixture patterns among dog breeds through a comprehensive analysis using whole genome sequencing data. A reference population was established comprising 349 individuals across 65 breeds, from which breed-informative single nucleotide polymorphisms (SNPs) were derived. Using the SCOPE algorithm previously employed in many global ancestry studies to estimate admixture proportions effectively, this demonstrated strong accuracy even at low sequencing depths (<1x). After peer review suggested changes to data processing the work was suitably solid to make some interesting findings using this approach. Results indicate that specific breeds, such as Catahoula Leopard Dogs and Greek Tracers, present unique challenges in admixture inference due to their genetic proximity to other breeds. With challenges in estimating Pit Bull Terrier ancestry/admixture, suggesting that there could be several genotypes associated with the Pit Bull Terrier breed . The methods provide a robust framework for future assessments of canine genetic diversity and health implications in canid populations. And processed reference population data is also available in the Github repository for reuse.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

6. EMImR: a Shiny application for identifying transcriptomic and epigenomic changes

   This article has 5 authors:

   1. Hiba Ben Aribi
   2. Careen Naitore
   3. Farah Ayadi
   4. Souheila Guerbouj
   5. Olaitan I. Awe

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     Coded and written up as part of the African Society for Bioinformatics and Computational Biology (ASBCB) Omicscodeathons, EMImR is a novel Shiny application for transcriptomic and epigenomic change identification and correlation wrapped up using a combination of Bioconductor and CRAN packages. Case studies are on publicly available GEO data corresponding to sequencing data of human blood cell samples of multiple sclerosis patients to demonstrate how the tool works. And a documentation and videos are provided. Peer review and the study highlighting the usefulness of the developed tool for analyzing transcriptomic and epigenomic data.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

7. Aedes mosquito distribution across urban and peri-urban areas of Kinshasa city, Democratic Republic of Congo

   This article has 15 authors:

   1. Victoire Nsabatien
   2. Josue Zanga
   3. Nono Mvuama
   4. Arsene Bokulu
   5. Hyacinthe Lukoki
   6. Glodie Diza
   7. Dorcas Kantin
   8. Leon Mbashi
   9. Christelle Bosulu
   10. Narcisse Basosila
   11. Erick Bukaka
   12. Fiacre Agossa
   13. Jonas Nagahuedi
   14. Jean-Claude Palata
   15. Emery Metelo

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     In the Democratic Republic of Congo (DRC) Aedes mosquitoes are principal vectors of the arboviruses that cause yellow fever, chikungunya and dengue in the human population. However systematic surveillance data on these species remains limited, hindering for entomological and modelling research and control strategies. This paper is one of a series of Data Release papers in GigaByte supported by TDR and the WHO describing datasets hosted in GBIF to tackle these data gaps in vectors of human disease data. To address this data deficiency this paper presents a geo-referenced dataset of 6,577 entomological occurrence records collected in 2024 throughout urban and peri-urban areas of Kinshasa in the Democratic Republic of Congo. The data collected using Larval dipping, Human landing catches, Prokopack aspirator, and BG-Sentinel traps. Data auditing and peer review found the data well validated, but requested some additional fields and methodological details. This work and the extremely useful data provided representing an important step towards building a pan-African resource for Aedes mosquito data collection.

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

8. Whole genome sequencing and assembly of the house sparrow, Passer domesticus

   This article has 13 authors:

   1. Vikas Kumar
   2. Gopesh Sharma
   3. Sankalp Sharma
   4. Samvrutha Prasad
   5. Shailesh Desai
   6. Toral Vaishnani
   7. Dalia Vishnudasan
   8. Gopinathan Maheswaran
   9. Kaomud Tyagi
   10. Inderjeet Tyagi
   11. Polavarapu B Kavi Kishor
   12. Gyaneshwer Chaubey
   13. Prashanth Suravajhala

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This paper presents present the genome sequencing of the house sparrow (Passer domesticus) carrying out genome assembly and annotation using in silico approaches with tools that could be a valuable resource for understanding passerine evolution, biology, ethnology, geography, and demography. The final genome assembly was generated using short read sequencing and a computational workflow that included Shovill, SPAdes, MaSuRCA, and BUSCO benchmarking. Producing a 922 MB reference genome with 24,152 genes. The first draft was significantly smaller than this but peer review provided suggestions on how to improve the assembly quality. And after a few attempts and assembly with a reasonable size and BUSCO score was achieved. This openly available data potentially serving as a valuable resource for checking adaptation, divergence, and speciation of birds.

     This evaluation refers to version 2 of the preprint

   Reviewed by GigaByte

9. Chevreul: an R bioconductor package for exploratory analysis of full-length single cell sequencing

   This article has 3 authors:

   1. Kevin Stachelek
   2. Bhavana Bhat
   3. David Cobrinik

   This article has been curated by 1 group:

   • Curated by GigaByte

     Editors Assessment:

     This paper presents Chevreul, a new open-source R Bioconductor (meta-)package for processing and integration of scRNA-seq data from cDNA end-counting, full-length short-read or long-read protocols. Alongside a R Shiny app for easy visualization, formatting, and analysis for exploratory analyses of scRNA-seq data processed in the SingleCellExperiment Bioconductor or Seurat formats. The name of the tool is inspired by the colour theorist Michel-Eugène Chevreul and the optical illusion of the same name. To demonstrate the use of Chevreul, the authors provide a sample analysis, which helps to demonstrate how users can visualize a wide range of parameters, enabling transparent and reproducible scRNA-seq analyses. Peer review also pushing the author to provide extensive guidance materials to assist with use. Being implemented in R, the R package and integrated Shiny application are freely available under an open-source MIT license in Bioconductor and their GitHub page here: https://github.com/cobriniklab/chevreul

     This evaluation refers to version 1 of the preprint

   Reviewed by GigaByte

10. Chromosome-level genome assembly of the lemon sole, Microstomus kitt (Pleuronectiformes: Pleuronectidae)

    This article has 15 authors:

    1. Marcel Nebenführ
    2. David Prochotta
    3. Maria A. Nilsson
    4. Menno J. de Jong
    5. Tunca D. Yazici
    6. Fabienne Langefeld
    7. Malambo Muloongo
    8. Helena Woköck
    9. Jakob Jilg
    10. Sina C. Bender
    11. Marvin M. Zangl
    12. Juan-Manuel Ortega Guatame
    13. Kimberley Williams
    14. Moritz Sonnewald
    15. Axel Janke

    This article has been curated by 1 group:

    • Curated by GigaByte

      Editors Assessment:

      This Data Release paper presents the first genome assembly of the lemon sole (Microstomus kitt), a commercially important flatfish found in European coastal waters. It is also interesting that this work was carried out in a University course setting involving the students. The resulting chromosome-level genome was assembled using long-read PacBio HiFi sequencing and the Hi-C technique. The 628 Mbp reference (which is consistent with other Pleuronectidae fish species) is assembled into 24 chromosome-length scaffolds with high completeness, achieving a scaffold N50 of 27.2 Mbp. Peer review and data curation made the author clarify a few points and share all of the data and results in an open and well curated manner. The annotated genome of the lemon sole, with its high continuity, should therefore provide important reference data for future population genetic analyses and conservation strategies of this organism.

      This evaluation refers to version 1 of the preprint

    Reviewed by GigaByte