Genomics

  1. CellCover Defines Marker Gene Panels Capturing Developmental Progression in Neocortical Neural Stem Cell Identity

    1. Lanlan Ji
    2. An Wang
    3. Shreyash Sonthalia
    4. Seungmae Seo
    5. Daniel Q Naiman
    6. Laurent Younes
    7. Carlo Colantuoni
    8. Donald Geman

    • Curated by eLife

      eLife Assessment

      This study offers a valuable methodological advance by introducing a gene panel selection approach that captures combinatorial specificity to define cell identity. The findings address key limitations of current single-gene marker methods. The evidence is compelling, but would be strengthened by further validation of rare cell states and unexpected marker categories.

    Reviewed by eLife

    2 evaluationsAppears in 1 listLatest version Latest activity

  2. The genetic control of rapid genome content divergence in Arabidopsis thaliana

    1. Christopher J Fiscus
    2. Daniel Koenig

    • Curated by eLife

      eLife Assessment

      This important study systematically investigates repeat expansion in the plant Arabidopsis thaliana using a new k-mer-based method, expanding on smaller studies to more comprehensively identify cis- and trans-acting loci associated with repeat dynamics. The approach is methodologically sound and broadly applicable to large-scale short-read datasets for assessing copy number variation and genomic repeat content. While convincing in its scope and novelty, the findings would be further strengthened with exploratory analyses of datasets from other species with more or fewer repeats in their genomes.

    Reviewed by eLife

    3 evaluationsAppears in 1 listLatest version Latest activity

  3. Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases

    1. Raehoon Jeong
    2. Martha L Bulyk

    • Curated by eLife

      eLife Assessment

      This paper addresses a significant question regarding the low overlap between genetic discoveries for human complex diseases and those for gene expression by emphasizing the contribution of cell-type-specific chromatin accessibility QTLs. The analyses supporting the main claims are convincing, and the key conclusions are valuable and of interest to readers in the fields of human genetics and functional genomics.

    Reviewed by eLife

    7 evaluationsAppears in 1 listLatest version Latest activity

  4. PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking

    1. Engy Nasr
    2. Anna Henger
    3. Björn Grüning
    4. Paul Zierep
    5. Bérénice Batut

    Reviewed by GigaScience

    2 evaluationsAppears in 1 listLatest version Latest activity

  5. A high-quality reference genome for the Ural Owl ( Strix uralensis ) enables investigations of cell cultures as a genomic resource for endangered species

    1. Ioannis Chrysostomakis
    2. Annika Mozer
    3. Camilla Bruno Di-Nizo
    4. Dominik Fischer
    5. Nafiseh Sargheini
    6. Laura von der Mark
    7. Bruno Huettel
    8. Jonas J. Astrin
    9. Till Töpfer
    10. Astrid Böhne

    Reviewed by GigaScience

    2 evaluationsAppears in 1 listLatest version Latest activity

  6. First chromosome-level genome assembly of the colonial tunicate Botryllus schlosseri

    1. Olivier De Thier
    2. Mohammed M.Tawfeeq
    3. Roland Faure
    4. Marie Lebel
    5. Philippe Dru
    6. Simon Blanchoud
    7. Alexandre Alié
    8. Federico D. Brown
    9. Jean-François Flot
    10. Stefano Tiozzo

    Reviewed by GigaScience

    3 evaluationsAppears in 1 listLatest version Latest activity

  7. Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

    1. Larissa S. Arantes
    2. Tom Brown
    3. Diego De Panis
    4. Scott D. Whiting
    5. Erin L. LaCasella
    6. Gabriella A. Carvajal
    7. Adam Kennedy
    8. Deana Edmunds
    9. Blair P. Bentley
    10. Jennifer Balacco
    11. Conor Whelan
    12. Nivesh Jain
    13. Tatiana Tilley
    14. Brian O’Toole
    15. Patrick Traore
    16. Erich D. Jarvis
    17. Oliver Berry
    18. Peter H. Dutton
    19. Lisa M. Komoroske
    20. Camila J. Mazzoni

    Reviewed by GigaScience

    3 evaluationsAppears in 1 listLatest version Latest activity

  8. CNSistent integration and feature extraction from somatic copy number profiles

    1. Adam Streck
    2. Roland F. Schwarz

    Reviewed by GigaScience

    3 evaluationsAppears in 1 listLatest version Latest activity

  9. The Open Pediatric Cancer Project

    1. Zhuangzhuang Geng
    2. Eric Wafula
    3. Ryan J Corbett
    4. Yuanchao Zhang
    5. Run Jin
    6. Krutika S Gaonkar
    7. Sangeeta Shukla
    8. Komal S Rathi
    9. Dave Hill
    10. Aditya Lahiri
    11. Daniel P Miller
    12. Alex Sickler
    13. Kelsey Keith
    14. Christopher Blackden
    15. Antonia Chroni
    16. Miguel A Brown
    17. Adam A Kraya
    18. Kaylyn L Clark
    19. Brian R Rood
    20. Adam C Resnick
    21. Nicholas Van Kuren
    22. John M Maris
    23. Alvin Farrel
    24. Mateusz P Koptyra
    25. Gerri R Trooskin
    26. Noel Coleman
    27. Yuankun Zhu
    28. Stephanie Stefankiewicz
    29. Zied Abdullaev
    30. Asif T Chinwalla
    31. Mariarita Santi
    32. Ammar S Naqvi
    33. Jennifer L Mason
    34. Carl J Koschmann
    35. Xiaoyan Huang
    36. Sharon J Diskin
    37. Kenneth Aldape
    38. Bailey K Farrow
    39. Weiping Ma
    40. Bo Zhang
    41. Brian M Ennis
    42. Sarah Tasian
    43. Saksham Phul
    44. Matthew R Lueder
    45. Chuwei Zhong
    46. Joseph M Dybas
    47. Pei Wang
    48. Deanne Taylor
    49. Jo Lynne Rokita

    Reviewed by GigaScience

    2 evaluationsAppears in 1 listLatest version Latest activity

  10. A comprehensive water buffalo pangenome reveals extensive structural variation linked to population specific signatures of selection

    1. Fazeela Arshad
    2. Siddharth Jayaraman
    3. Andrea Talenti
    4. Rachel Owen
    5. Muhammad Mohsin
    6. Shahid Mansoor
    7. Muhammad Asif
    8. James Prendergast

    Reviewed by GigaScience

    4 evaluationsAppears in 1 listLatest version Latest activity
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