Genomics

  1. A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2

    1. Toni M. Delorey
    2. Carly G. K. Ziegler
    3. Graham Heimberg
    4. Rachelly Normand
    5. Yiming Yang
    6. Asa Segerstolpe
    7. Domenic Abbondanza
    8. Stephen J. Fleming
    9. Ayshwarya Subramanian
    10. Daniel T. Montoro
    11. Karthik A. Jagadeesh
    12. Kushal K. Dey
    13. Pritha Sen
    14. Michal Slyper
    15. Yered H. Pita-Juárez
    16. Devan Phillips
    17. Zohar Bloom-Ackerman
    18. Nick Barkas
    19. Andrea Ganna
    20. James Gomez
    21. Erica Normandin
    22. Pourya Naderi
    23. Yury V. Popov
    24. Siddharth S. Raju
    25. Sebastian Niezen
    26. Linus T.-Y. Tsai
    27. Katherine J. Siddle
    28. Malika Sud
    29. Victoria M. Tran
    30. Shamsudheen K. Vellarikkal
    31. Liat Amir-Zilberstein
    32. Deepak S. Atri
    33. Joseph Beechem
    34. Olga R. Brook
    35. Jonathan Chen
    36. Prajan Divakar
    37. Phylicia Dorceus
    38. Jesse M. Engreitz
    39. Adam Essene
    40. Donna M. Fitzgerald
    41. Robin Fropf
    42. Steven Gazal
    43. Joshua Gould
    44. John Grzyb
    45. Tyler Harvey
    46. Jonathan Hecht
    47. Tyler Hether
    48. Judit Jane-Valbuena
    49. Michael Leney-Greene
    50. Hui Ma
    51. Cristin McCabe
    52. Daniel E. McLoughlin
    53. Eric M. Miller
    54. Christoph Muus
    55. Mari Niemi
    56. Robert Padera
    57. Liuliu Pan
    58. Deepti Pant
    59. Carmel Pe’er
    60. Jenna Pfiffner-Borges
    61. Christopher J. Pinto
    62. Jacob Plaisted
    63. Jason Reeves
    64. Marty Ross
    65. Melissa Rudy
    66. Erroll H. Rueckert
    67. Michelle Siciliano
    68. Alexander Sturm
    69. Ellen Todres
    70. Avinash Waghray
    71. Sarah Warren
    72. Shuting Zhang
    73. Daniel R. Zollinger
    74. Lisa Cosimi
    75. Rajat M. Gupta
    76. Nir Hacohen
    77. Winston Hide
    78. Alkes L. Price
    79. Jayaraj Rajagopal
    80. Purushothama Rao Tata
    81. Stefan Riedel
    82. Gyongyi Szabo
    83. Timothy L. Tickle
    84. Deborah Hung
    85. Pardis C. Sabeti
    86. Richard Novak
    87. Robert Rogers
    88. Donald E. Ingber
    89. Z. Gordon Jiang
    90. Dejan Juric
    91. Mehrtash Babadi
    92. Samouil L. Farhi
    93. James R. Stone
    94. Ioannis S. Vlachos
    95. Isaac H. Solomon
    96. Orr Ashenberg
    97. Caroline B.M. Porter
    98. Bo Li
    99. Alex K. Shalek
    100. Alexandra-Chloé Villani
    101. Orit Rozenblatt-Rosen
    102. Aviv Regev

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  2. PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Reveals Important Insights into the Outbreak

    1. Arindam Maitra
    2. Sunil Raghav
    3. Ashwin Dalal
    4. Farhan Ali
    5. Vanessa Molin Paynter
    6. Dhiraj Paul
    7. Nidhan K Biswas
    8. Arup Ghosh
    9. Kunal Jani
    10. Sreedhar Chinnaswamy
    11. Sanghamitra Pati
    12. Arvind Sahu
    13. Debashis Mitra
    14. Manoj Kumar Bhat
    15. Satyajit Mayor
    16. Apurva Sarin
    17. The PAN-INDIA 1000 SARS-CoV-2 RNA Genome Sequencing Consortium
    18. Yogesh S. Sauche
    19. Aswin Sai Narain Seshasayee
    20. Dasaradhi Palakodeti
    21. Murali D. Bashyam
    22. Ajay Parida
    23. Saumitra Das

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  3. Metagenomic diagnosis and pathogenic network profile of SARS-CoV-2 in patients co-morbidly affected by type 2 diabetes

    1. Hassan M. Al-Emran
    2. M. Shaminur Rahman
    3. Md. Shazid Hasan
    4. A. S. M. Rubayet Ul Alam
    5. Ovinu Kibria Islam
    6. Ajwad Anwar
    7. Iqbal Kabir Jahid
    8. M. Anwar Hossain

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  4. Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania

    1. Ahmed M. Moustafa
    2. Colleen Bianco
    3. Lidiya Denu
    4. Azad Ahmed
    5. Brandy Neide
    6. John Everett
    7. Shantan Reddy
    8. Emilie Rabut
    9. Jasmine Deseignora
    10. Michael D. Feldman
    11. Kyle G. Rodino
    12. Frederic Bushman
    13. Rebecca M. Harris
    14. Josh Chang Mell
    15. Paul J. Planet

    Reviewed by ScreenIT

    1 evaluationAppears in 1 listLatest version Latest activity

  5. Glucocorticoid receptor activation induces gene-specific transcriptional memory and universally reversible changes in chromatin accessibility

    1. Melissa Bothe
    2. René Buschow
    3. Sebastiaan H. Meijsing

    Reviewed by Review Commons

    4 evaluationsAppears in 1 listLatest version Latest activity

  6. The costs of competition: high social status males experience accelerated epigenetic aging in wild baboons

    1. Jordan A. Anderson
    2. Rachel A. Johnston
    3. Amanda J. Lea
    4. Fernando A. Campos
    5. Tawni N. Voyles
    6. Mercy Y. Akinyi
    7. Susan C. Alberts
    8. Elizabeth A. Archie
    9. Jenny Tung

    • Curated by eLife

      Evaluation Summary:

      In this paper, the authors collect epigenomic data from a well-studied wild baboon community, which they use to construct an epigenetic clock, a method of measuring "biological age" that is increasingly used as a tool in human aging research. The authors find that deviations between biological and chronological age can in part be explained by social phenomena. In particular, for male baboons, maintaining social dominance may play an important role in accelerating the dimension of aging indexed by this measure. This is a foundational study for social-biological-health research.

      (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 and Reviewer #2 agreed to share their names with the authors.)

    Reviewed by eLife

    3 evaluationsAppears in 3 listsLatest version Latest activity

  7. Jumping back and forth: anthropozoonotic and zoonotic transmission of SARS-CoV-2 on mink farms

    1. Bas B. Oude Munnink
    2. Reina S. Sikkema
    3. David F. Nieuwenhuijse
    4. Robert Jan Molenaar
    5. Emmanuelle Munger
    6. Richard Molenkamp
    7. Arco van der Spek
    8. Paulin Tolsma
    9. Ariene Rietveld
    10. Miranda Brouwer
    11. Noortje Bouwmeester-Vincken
    12. Frank Harders
    13. Renate Hakze-van der Honing
    14. Marjolein C.A. Wegdam-Blans
    15. Ruth J. Bouwstra
    16. Corine GeurtsvanKessel
    17. Annemiek A. van der Eijk
    18. Francisca C. Velkers
    19. Lidwien A.M. Smit
    20. Arjan Stegeman
    21. Wim H.M. van der Poel
    22. Marion P.G. Koopmans

    Reviewed by ScreenIT, NCRC

    3 evaluationsAppears in 3 listsLatest version Latest activity

  8. Evolution of cytokine production capacity in ancient and modern European populations

    1. Jorge Domínguez-Andrés
    2. Yunus Kuijpers
    3. Olivier B Bakker
    4. Martin Jaeger
    5. Cheng-Jian Xu
    6. Jos WM Van der Meer
    7. Mattias Jakobsson
    8. Jaume Bertranpetit
    9. Leo AB Joosten
    10. Yang Li
    11. Mihai G Netea

    • Curated by eLife

      Evaluation Summary:

      Dominguez-Andrés et al. collect a large amount of immune-related trait association data from a cohort made up of 534 individuals of Western European ancestry. The goal was to track the evolutionary trajectories of cytokine production capacity over time in a number of patients with different exposure to infectious organisms, infectious disease, autoimmune and inflammatory diseases, using the 500 Functional Genomics cohort of the Human Functional Genomics Project. From this analysis it was hypothesized that the Neolithic transition was characterized by strong changes in the adaptive response to pathogens in human biology. Overall, the manuscript is interesting but could be improved by significant enhancements to statistical methodology.

      (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

    4 evaluationsAppears in 1 listLatest version Latest activity

  9. Improving oligo-conjugated antibody signal in multimodal single-cell analysis

    1. Terkild Brink Buus
    2. Alberto Herrera
    3. Ellie Ivanova
    4. Eleni Mimitou
    5. Anthony Cheng
    6. Ramin Sedaghat Herati
    7. Thales Papagiannakopoulos
    8. Peter Smibert
    9. Niels Ødum
    10. Sergei B. Koralov

    Reviewed by eLife

    3 evaluationsAppears in 1 listLatest version Latest activity

  10. In vitro evolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells

    1. Juan Carlos Jado
    2. Michelle Dow
    3. Krypton Carolino
    4. Adam Klie
    5. Gregory J. Fonseca
    6. Trey Ideker
    7. Hannah Carter
    8. Elizabeth A. Winzeler

    • Curated by eLife

      Summary: The authors examined the genomic basis of resistance evolution in human chronic myelogenous leukemia (CML) near-haploid cell lines to 5 separate chemotherapeutic agents.

      Using either whole genome or whole exome analysis, they found numerous instances of single nucleotide polymorphisms and copy number variants, including amplifications and deletions, among lines. They then used subsequent knockdown or knockout experiments to confirm that these variants, in fact, lead to increased resistance in these lines.

      The work is interesting, timely, and has potential clinical implications. For example, the resistance alleles identified here could be closely examined in future studies in order to develop treatment strategies. However, the experimental design has certain limitations, advances in understanding chemotherapy resistance mechanisms is currently modest, and the presentation of results can be improved. We feel overall that these could be addressed, but that they will require significant extra experimental work.

    Reviewed by eLife

    4 evaluationsAppears in 1 listLatest version Latest activity
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