Genomics

  1. Nanopore ReCappable sequencing maps SARS-CoV-2 5′ capping sites and provides new insights into the structure of sgRNAs

    1. Camilla Ugolini
    2. Logan Mulroney
    3. Adrien Leger
    4. Matteo Castelli
    5. Elena Criscuolo
    6. Maia Kavanagh Williamson
    7. Andrew D Davidson
    8. Abdulaziz Almuqrin
    9. Roberto Giambruno
    10. Miten Jain
    11. Gianmaria Frigè
    12. Hugh Olsen
    13. George Tzertzinis
    14. Ira Schildkraut
    15. Madalee G Wulf
    16. Ivan R Corrêa
    17. Laurence Ettwiller
    18. Nicola Clementi
    19. Massimo Clementi
    20. Nicasio Mancini
    21. Ewan Birney
    22. Mark Akeson
    23. Francesco Nicassio
    24. David A Matthews
    25. Tommaso Leonardi

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  2. Chromatin topology defines estradiol-primed progesterone receptor and PAX2 binding in endometrial cancer cells

    1. Alejandro La Greca
    2. Nicolás Bellora
    3. François Le Dily
    4. Rodrigo Jara
    5. Ana Silvina Nacht
    6. Javier Quilez Oliete
    7. José Luis Villanueva
    8. Enrique Vidal
    9. Gabriela Merino
    10. Cristóbal Fresno
    11. Inti Tarifa Reischle
    12. Griselda Vallejo
    13. Guillermo Vicent
    14. Elmer Fernández
    15. Miguel Beato
    16. Patricia Saragüeta

    • Curated by eLife

      Evaluation Summary:

      All three reviewers are in agreement that the study is of potential interest in the field of ER/PR signaling and endometrial cancer and that it contains significant amount of genomic data. However, functional data linking PAX2 to the PR/ER pathway are lacking, and the study is limited to a single model cell line and thus has a relatively narrow scope. There is also a concern that ChIP-seq data appear to be from a single, unreplicated experiment.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 agreed to share their name with the authors.)

    Reviewed by eLife

    5 evaluationsAppears in 1 listLatest version Latest activity

  3. Unique structure and positive selection promote the rapid divergence of Drosophila Y chromosomes

    1. Ching-Ho Chang
    2. Lauren E Gregory
    3. Kathleen E Gordon
    4. Colin D Meiklejohn
    5. Amanda M Larracuente

    Reviewed by Review Commons

    4 evaluationsAppears in 1 listLatest version Latest activity

  4. Adaptive trends of sequence compositional complexity over pandemic time in the SARS-CoV-2 coronavirus

    1. José L. Oliver
    2. Pedro Bernaola-Galván
    3. Francisco Perfectti
    4. Cristina Gómez-Martín
    5. Silvia Castiglione
    6. Pasquale Raia
    7. Miguel Verdú
    8. Andrés Moya

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  5. Whole-Genome Sequencing of Vero E6 (VERO C1008) and Comparative Analysis of Four Vero Cell Sublines

    1. Kazuhiro Konishi
    2. Toshiyuki Yamaji
    3. Chisato Sakuma
    4. Fumio Kasai
    5. Toshinori Endo
    6. Arihiro Kohara
    7. Kentaro Hanada
    8. Naoki Osada

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  6. A multi-tissue study of immune gene expression profiling highlights the key role of the nasal epithelium in COVID-19 severity

    1. Alberto Gómez-Carballa
    2. Irene Rivero-Calle
    3. Jacobo Pardo-Seco
    4. José Gómez-Rial
    5. Carmen Rivero-Velasco
    6. Nuria Rodríguez-Núñez
    7. Gema Barbeito-Castiñeiras
    8. Hugo Pérez-Freixo
    9. Miriam Cebey-López
    10. Ruth Barral-Arca
    11. Carmen Rodriguez-Tenreiro
    12. Ana Dacosta-Urbieta
    13. Xabier Bello
    14. Sara Pischedda
    15. María José Currás-Tuala
    16. Sandra Viz-Lasheras
    17. Federico Martinón-Torres
    18. Antonio Salas
    19. Aguilera Guirao Antonio
    20. Álvarez Escudero Julián
    21. Antela López Antonio
    22. Barbeito Castiñeiras Gema
    23. Bello Paderne Xabier
    24. Ben García Miriam
    25. Carral García María Victoria
    26. Cebey López Miriam
    27. Coira Nieto Amparo
    28. Conde Pájaro Mónica
    29. Costa Alcalde José Javier
    30. Currás Tuala María José
    31. Dacosta Urbieta Ana Isabel
    32. Díaz Esteban Blanca
    33. Domínguez Santalla María Jesús
    34. Fernández Pérez Cristina
    35. Fernández Villaverde Juan
    36. Galbán Rodríguez Cristóbal
    37. García Allut José Luis
    38. García Vicente Luisa
    39. Giráldez Vázquez Elena
    40. Gómez Carballa Alberto
    41. Gómez Rial José
    42. González Barcala Francisco Javier
    43. Guerra Liñares Beatriz
    44. Leboráns Iglesias Pilar
    45. Lence Massa Beatriz
    46. López Franco Montserrat
    47. López Lago Ana
    48. Martinón-Torres Federico
    49. Antonio Salas
    50. Navarro De la Cruz Daniel
    51. Núñez Masid Eloína
    52. Ortolá Devesa Juan Bautista
    53. Pardo Seco Jacobo
    54. Pazo Núñez María
    55. Pérez del Molino Bernal Marisa
    56. Pérez Freixo Hugo
    57. Piñeiro Rodríguez Lidia
    58. Pischedda Sara
    59. Portela Romero Manuel
    60. Pose Reino Antonio
    61. Prada Hervella Gloria María
    62. Queiro Verdes Teresa
    63. Redondo Collazo Lorenzo
    64. Regueiro Casuso Patricia
    65. Rey García Susana
    66. Rey Vázquez Sara
    67. Riveiro Blanco Vanessa
    68. Rivero Calle Irene
    69. Rivero Velasco Carmen
    70. Rodríguez Núñez Nuria
    71. Rodríguez-Tenreiro Sánchez Carmen
    72. Saborido Paz Eva
    73. Sadiki Orayyou José Miguel
    74. Saito Villanueva Carla
    75. Serén Fernández Sonia
    76. Souto Sanmartín Pablo
    77. Taboada Muñiz Manuel
    78. Trastoy Pena Rocío
    79. Treviño Castellano Mercedes
    80. Valdés Cuadrado Luis
    81. Varela García Pablo
    82. Vilas Iglesias María Soledad
    83. Viz Lasheras Sandra
    84. Ferreiro-Iglesias Rocio
    85. Bastón-Rey iria
    86. Calviño-Suárez Cristina

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  7. Novel insights from a multiomics dissection of the Hayflick limit

    1. Michelle Chan
    2. Han Yuan
    3. Ilya Soifer
    4. Tobias M Maile
    5. Rebecca Y Wang
    6. Andrea Ireland
    7. Jonathon J O'Brien
    8. Jérôme Goudeau
    9. Leanne JG Chan
    10. Twaritha Vijay
    11. Adam Freund
    12. Cynthia Kenyon
    13. Bryson D Bennett
    14. Fiona E McAllister
    15. David R Kelley
    16. Margaret Roy
    17. Robert L Cohen
    18. Arthur D Levinson
    19. David Botstein
    20. David G Hendrickson

    • Curated by eLife

      Evaluation Summary:

      This manuscript presents a well-done integrative analysis of data from many genome-wide technologies for the study of replicative senescence, contrasting the data to non-senescence and acute senescence controls. The time-course study design and the combinatorial analyses have revealed many interesting features of senescence that were previously unknown. Data mining by scientists in the future promises to unlock other aspects of senescence biology and hence this study serves as a great resource to the community. This paper and resource will be invaluable not only for researchers specifically studying the molecular biology of cell senescence but should also be more broadly relevant for researchers studying aging, inflamm-aging, cancer, regeneration, and other fields where senescence plays a role.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

    Reviewed by eLife

    5 evaluationsAppears in 1 listLatest version Latest activity

  8. A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO gene wmk

    1. Jessamyn I Perlmutter
    2. Jane E Meyers
    3. Seth R Bordenstein

    • Curated by eLife

      Evaluation Summary:

      This study aims to find the genetic mechanisms underlying sex-ratio distortion through male-killing in Drosophila melanogaster flies infected with the endosymbiont Wolbachia. The endosymbiont carries the prophage WO, which is in the center of interested in this study. The key result of this study is that a synonymous mutation in a prophage gene can explain the differences between sex-ratio distorting and not distorting symbionts.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

    Reviewed by eLife

    4 evaluationsAppears in 1 listLatest version Latest activity

  9. Mitochondrial genome sequencing of marine leukaemias reveals cancer contagion between clam species in the Seas of Southern Europe

    1. Daniel Garcia-Souto
    2. Alicia L Bruzos
    3. Seila Diaz
    4. Sara Rocha
    5. Ana Pequeño-Valtierra
    6. Camila F Roman-Lewis
    7. Juana Alonso
    8. Rosana Rodriguez
    9. Damian Costas
    10. Jorge Rodriguez-Castro
    11. Antonio Villanueva
    12. Luis Silva
    13. Jose Maria Valencia
    14. Giovanni Annona
    15. Andrea Tarallo
    16. Fernando Ricardo
    17. Ana Bratoš Cetinić
    18. David Posada
    19. Juan Jose Pasantes
    20. Jose MC Tubio

    • Curated by eLife

      Evaluation Summary:

      This paper is of broad interest to biologists and oncologists who study tumour evolution. The study provides new insights into the propagation of a transmissible cancer in clams. Remarkably, based on the analysis of mitochondrial DNA, the transmissible cancer seems to have jumped species. The findings reported have implications to understand the conditions that allow this cancer to spread across huge regions, threatening certain clam species.

      (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1, Reviewer #2 and Reviewer #3 agreed to share their name with the authors.)

    Reviewed by eLife

    5 evaluationsAppears in 1 listLatest version Latest activity

  10. Intensive single-cell analysis reveals immune-cell diversity among healthy individuals

    1. Yukie Kashima
    2. Keiya Kaneko
    3. Patrick Reteng
    4. Nina Yoshitake
    5. Lucky Ronald Runtuwene
    6. Satoi Nagasawa
    7. Masaya Onishi
    8. Masahide Seki
    9. Ayako Suzuki
    10. Sumio Sugano
    11. Mamiko Sakata-Yanagimoto
    12. Yumiko Imai
    13. Kaori Nakayama-Hosoya
    14. Ai Kawana-Tachikawa
    15. Taketoshi Mizutani
    16. Yutaka Suzuki

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity
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